[maven-release-plugin] prepare release dspace-3.2

DS 1527 Fix memory leak in Caching service

.gitignore

@@ -1,22 +1,16 @@
 ## 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/
@@ -26,19 +20,8 @@ dist/
 nbdist/
 nbactions.xml
 nb-configuration.xml
+META-INF/
 
 ## Ignore all *.properties file in root folder, EXCEPT build.properties (the default)
-## KEPT FOR BACKWARDS COMPATIBILITY WITH 5.x (build.properties is now replaced with local.cfg)
 /*.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

.travis.yml

@@ -1,44 +0,0 @@
-language: java
-sudo: false
-
-env: 
-  # Give Maven 1GB of memory to work with
-  - MAVEN_OPTS=-Xmx1024M
-
-jdk:
-  # DS-3384 Oracle JDK 8 has DocLint enabled by default.
-  # Let's use this to catch any newly introduced DocLint issues.
-  - oraclejdk8
-
-## Should we run into any problems with oraclejdk8 on Travis, we may try the following workaround.
-## https://docs.travis-ci.com/user/languages/java#Testing-Against-Multiple-JDKs
-## https://github.com/travis-ci/travis-ci/issues/3259#issuecomment-130860338
-#addons:
-#  apt:
-#    packages:
-#      - oracle-java8-installer
-
-# Install prerequisites for building Mirage2 more rapidly
-before_install:
-  # Remove outdated settings.xml from Travis builds. Workaround for https://github.com/travis-ci/travis-ci/issues/4629
-  - rm ~/.m2/settings.xml
-
-# Skip install stage, as we'll do it below
-install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
-
-# Two stage Build and Test
-# 1. Install & Unit Test APIs
-# 2. Assemble DSpace
-script:
-  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
-  #        license:check => Validate all source code license headers
-  #        -Dmaven.test.skip=false => Enable DSpace Unit Tests
-  #        -DskipITs=false         => Enable DSpace Integration Tests
-  #        -P !assembly            => Skip normal assembly (as it can be memory intensive)
-  #        -B => Maven batch/non-interactive mode (recommended for CI)
-  #        -V => Display Maven version info before build
-  #        -Dsurefire.rerunFailingTestsCount=2 => try again for flakey tests, and keep track of/report on number of retries
-  - "mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
-  # 2. [Assemble DSpace] Ensure overlay & assembly process works (from [src]/dspace/)
-  #        -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
-  - "cd dspace && mvn package -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"

LICENSE

@@ -1,7 +1,7 @@
 DSpace source code license:
 
 
-Copyright (c) 2002-2016, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2012, DuraSpace.  All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are

LICENSES_THIRD_PARTY

@@ -1,424 +1,144 @@
-
 DSpace uses third-party libraries which may be distributed under different 
-licenses. We have listed all of these third party libraries and their licenses
+licenses. We have attempted to list all of these third party libraries and 
-below. This file can be regenerated at any time by simply running:
+their licenses below (however the most up-to-date information can be found
-
+via Maven, see NOTE #2 at bottom of this page). 
-    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.
+Third party Java libraries listed by License type
+[Format: Name (Maven Project) - URL]
+--------------------------------------------------
 
-PLEASE NOTE: Some dependencies may be listed under multiple licenses if they
+Apache Software License, Version 2.0 (http://opensource.org/licenses/apache2.0)
-are dual-licensed. This is especially true of anything listed as
+  * Ant-Contrib Tasks (ant-contrib:*) - http://ant-contrib.sourceforge.net/
-"GNU General Public Library" below, as DSpace actually does NOT allow for any
+  * Apache Abdera (org.apache.abdera::*) - http://projects.apache.org/projects/abdera.html
-dependencies that are solely released under GPL terms. For more info see:
+  * Apache Ant (org.apache.ant:*) - http://ant.apache.org/
-https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
+  * Apache Axis (axis:*) - http://axis.apache.org/axis/
----------------------------------------------------
+  * Apache Cocoon (org.apache.cocoon:*) - http://cocoon.apache.org/2.2/license.html
+  * Apache Commons BeanUtils (commons-beanutils:*) - http://commons.apache.org/beanutils/
+  * 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 Configuration (commons-configuration:*) - http://commons.apache.org/configuration/license.html
+  * Apache Commons DBCP (commons-dbcp:*) - http://commons.apache.org/dbcp/license.html
+  * Apache Commons Digester (commons-digester:*) - http://commons.apache.org/digester/
+  * 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 Geronimo (org.apache.geronimo.specs:*) - http://geronimo.apache.org/
+  * Apache HTTPComponents (org.apache.httpcomponents:*) - http://hc.apache.org/
+  * Apache Jakarta ORO (oro:*) - http://svn.apache.org/repos/asf/jakarta/oro/trunk/LICENSE
+  * Apache Jakarta Regexp (jakarta-regexp:*) - http://jakarta.apache.org/regexp/
+  * Apache JaxMe (jaxme:jaxme-api) - http://ws.apache.org/old/jaxme-old/license.html
+  * Apache Jena (com.hp.hpl.jena:*) - http://jena.apache.org/
+  * 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
+  * Apache XMLBeans (org.apache.xmlbeans:*) - http://xmlbeans.apache.org/
+  * Apache ZooKeeper (org.apache.zookeeper:*) - http://zookeeper.apache.org/
+  * Databene ContiPerf (org.databene:contiperf) - http://databene.org/contiperf
+  * Ehcache (net.sf.ehcache:*) - http://ehcache.org/about/license
+  * ElasticSearch (org.elasticsearch:*) - http://www.elasticsearch.org/
+  * flexjson (net.sf.flexjson:*) - http://sourceforge.net/projects/flexjson/
+  * Google GSON (com.google.code.gson:*) - http://code.google.com/p/google-gson/
+  * Google Guava (com.google.guava:*) - http://code.google.com/p/guava-libraries/
+  * Jetty (org.mortbay.jetty:*) - http://jetty.codehaus.org/jetty/license.html
+  * Lyncode XOAI (com.lyncode:xoai) - http://www.lyncode.com/
+  * OpenCSV (net.sf.opencsv:*) - http://opencsv.sourceforge.net/
+  * 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
+  * Woodstox (org.codehaus.woodstox:*) - http://woodstox.codehaus.org/Download
 
-    Apache Software License, Version 2.0:
+BSD License (http://www.opensource.org/licenses/BSD-3-Clause)
+  * Biblio Transformation Engine (gr.ekt:biblio-transformation-engine) - http://code.google.com/p/biblio-transformation-engine/
+  * DNSJava (org.dspace.dnsjava:dnsjava)- http://www.xbill.org/dnsjava/dnsjava-current/README
+  * dom4j (dom4j:*, maven:dom4j) - http://dom4j.sourceforge.net/dom4j-1.6.1/license.html
+  * Foresite Toolkit (com.googlecode.foresite-toolkit:*) - http://code.google.com/p/foresite-toolkit/
+  * Java BibTeX Parser (org.jbibtex:*) - https://code.google.com/p/java-bibtex/
+  * Jaxen (jaxen:*) -  http://jaxen.codehaus.org/license.html
+  * JLine (jline:*) - http://jline.sourceforge.net/
+  * JUnitPerf (junitperf:*) - http://www.clarkware.com/software/JUnitPerf.html#license
+  * MSV (msv:*) - http://msv.java.net/
+  * StAX (Streaming API for XML) (stax:*) - http://stax.codehaus.org/
+  * XMLUnit (xmlunit:*) - http://xmlunit.sourceforge.net/
+  * YUI (com.yahoo.platform.yui:*) - http://yuilibrary.com/license/
   
-        * Ant-Contrib Tasks (ant-contrib:ant-contrib:1.0b3 - http://ant-contrib.sourceforge.net)
+Common Development and Distribution License (CDDL) v1.0 (http://www.opensource.org/licenses/CDDL-1.0)
-        * Code Generation Library (cglib:cglib:2.2.2 - http://cglib.sourceforge.net/)
+  * JavaBeans Activation Framework (javax.activation:*) - http://www.opensource.org/licenses/CDDL-1.0  
-        * AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.10.50 - https://aws.amazon.com/sdkforjava)
+  * Java Mail (javax.mail:*) - http://www.opensource.org/licenses/CDDL-1.0
-        * AWS Java SDK for AWS KMS (com.amazonaws:aws-java-sdk-kms:1.10.50 - https://aws.amazon.com/sdkforjava)
+  * JAX-RPC (javax.xml:jaxrpc-api) - http://java.net/projects/jax-rpc/
-        * AWS Java SDK for Amazon S3 (com.amazonaws:aws-java-sdk-s3:1.10.50 - https://aws.amazon.com/sdkforjava)
+  * JAXB (com.sun.xml.bind:jaxb-impl) - http://jaxb.java.net/
-        * 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/)
   
-    BSD License:
+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/
   
-        * AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
+Lesser GPL (http://www.opensource.org/licenses/LGPL-2.1)
-        * ASM Core (asm:asm:3.3.1 - http://asm.objectweb.org/asm/)
+  * JExcelAPI (net.sourceforge.jexcelapi:*) - http://sourceforge.net/projects/jexcelapi/
-        * XMP Library for Java (com.adobe.xmp:xmpcore:5.1.2 - http://www.adobe.com/devnet/xmp.html)
+  * MaxMind GeoIP (org.dspace.dependencies:dspace-geoip) - http://geoip.cvs.sourceforge.net/viewvc/geoip/java/LICENSE
-        * coverity-escapers (com.coverity.security:coverity-escapers:1.1.1 - http://coverity.com/security)
+  * Text-mining (org.dspace.dependencies:dspace-tm-extractors) - http://code.google.com/p/text-mining/
-        * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.1 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
+  * XOM (xom:*) - http://www.xom.nu/
-        * 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/)
 
-    Common Development and Distribution License (CDDL):
+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
   
-        * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
+Mozilla Public License (http://www.opensource.org/licenses/MPL-2.0)
-        * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
+  * H2 database (com.h2database:*) - http://www.h2database.com/html/license.html
-        * 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/)
   
-    Eclipse Public License:
+Other Open Source Licenses:
+  * AOP Alliance (aopalliance:*) - Public Domain: http://aopalliance.sourceforge.net/
+  * 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/
+  * Pull-parser / XPP3 (pull-parser:*, xpp3:*) - Indiana University Extreme! Lab Software License (BSD-based): http://www.extreme.indiana.edu/xgws/xsoap/xpp/download/PullParser2/LICENSE.txt
   
-        * JUnit (junit:junit:4.11 - http://junit.org)
+----
-        * AspectJ runtime (org.aspectj:aspectjrt:1.6.11 - http://www.aspectj.org)
+NOTE #1: Some individual web application files in DSpace (e.g. Javascript 
-        * JPA 2.0 API (org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final - http://hibernate.org)
+libraries, CSS Frameworks) may have their own open source license. In that 
-        * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
+scenario, we place a copy of the full text of the license alongside the 
-        * Jetty Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-servlet-tester)
+licensed files. You can locate these additional licenses in our codebase 
-        * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
+by searching for files with a ".LICENSE" file extension.
 
-    GNU General Public License, Version 2 with the Classpath Exception:
+For example, on Linux you can use the 'find' command from the source directory:
 
-        * 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)
+find . -type f -name "*.LICENSE"
+----
 
-    GNU Lesser General Public License (LGPL):
+----
+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):
 
-        * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
+mvn project-info-reports:dependencies
-        * 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)
 
-    ICU License:
+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).
 
-        * ICU4J (com.ibm.icu:icu4j:56.1 - http://icu-project.org/)
+Additionally, you may wish to run:
 
-    JDOM License (Apache-style license):
+mvn project-info-reports:dependency-convergence
 
-        * jdom (jdom:jdom:1.0 - no url defined)
+This generates a summary report at 
+"[dspace]/target/site/dependency-convergence.html" which lists all dependencies
+of all DSpace projects (though it does not list license information)
 
-    MIT License:
+For more information see the maven-project-info-reports-plugin:
-
+http://maven.apache.org/plugins/maven-project-info-reports-plugin/
-        * 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)

README

@@ -0,0 +1,54 @@
+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.

README.md

@@ -1,85 +0,0 @@
-
-# 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/

build.properties

@@ -0,0 +1,151 @@
+# 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.
+#
+# IMPORTANT: Do not remove or comment out settings in build.properties
+# When you edit the "build.properties" file (or a custom *.properties file),
+# take care not to remove or comment out any settings. Doing so, may cause
+# your final "dspace.cfg" file to be misconfigured with regards to that
+# particular setting.  Instead, if you wish to remove/disable a particular
+# setting, just clear out its value.  For example, if you don't want to be
+# notified of new user registrations, ensure the "mail.registration.notify"
+# setting has no value, e.g. "mail.registration.notify="
+#
+
+##########################
+# SERVER CONFIGURATION #
+##########################
+
+# DSpace installation directory. This is the location where you want
+# to install DSpace. NOTE: this value will be copied over to the
+# "dspace.dir" setting in the final "dspace.cfg" file. It can be
+# modified later on in your "dspace.cfg", if needed.
+dspace.install.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 =

checkstyle-suppressions.xml

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

checkstyle.xml

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

dspace-api/pom.xml

@@ -1,5 +1,4 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.dspace</groupId>
     <artifactId>dspace-api</artifactId>
@@ -13,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.0-SNAPSHOT</version>
+        <version>3.2</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -26,24 +25,6 @@
        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>
@@ -72,93 +53,16 @@
                     </execution>
                 </executions>
             </plugin>
-            <!-- Verify OS license headers for all source code files -->
-            <plugin>
-                <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>
-                        <phase>validate</phase>
-                        <goals>
-                            <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>
+                <version>2.3</version>
+                <executions>
+                    <execution>
+                        <id>setupTestEnvironment</id>
+                        <phase>generate-test-resources</phase>
+                        <goals>
+                            <goal>unpack</goal>
+                        </goals>
                         <configuration>
                             <outputDirectory>${project.build.directory}/testing</outputDirectory>
                             <artifactItems>
@@ -171,117 +75,104 @@
                                 </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 needed by the FileWeaver & Surefire plugins (see below)
+                    This is necessary so that the FileWeaver & Surefire plugins can
-                         to initialize the Unit Test environment's dspace.cfg file.
+                    use it to initialize the Unit Test Framework'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>groovy-maven-plugin</artifactId>
+                <artifactId>gmaven-plugin</artifactId>
-                        <version>2.0</version>
+                <version>1.4</version>
                 <executions>
                     <execution>
                         <id>setproperty</id>
-                                <phase>generate-test-resources
+                        <phase>generate-test-resources</phase>
-                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
                         <goals>
                             <goal>execute</goal>
                         </goals>
                         <configuration>
                             <source>
-                                        project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
+                            pom.properties['agnostic.build.dir']=project.build.directory.replace('\\','/');
                             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.install.dir>${agnostic.build.dir}/testing/dspace</dspace.install.dir>
+                            </properties>
+                        </output>
+                    </outputs>
+                </configuration>
+                <executions>
+                    <execution>
+                        <id>edit-dspace-cfg</id>
+                        <phase>process-test-resources</phase>
+                        <goals>
+                            <goal>weave</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <!--
+                The ant plugin below ensures that the dspace "woven" configuration file ends up in the dspace directory
+                The dspace service manager needs this "woven" configuration file when it starts
+            -->
+            <plugin>
+              <artifactId>maven-antrun-plugin</artifactId>
+              <executions>
+                <execution>
+                  <phase>process-test-resources</phase>
+                  <configuration>
+                    <tasks>
+                        <copy file="${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>
-                                <!-- Specify the dspace.dir to use for test environment -->
+                        <dspace.dir>${agnostic.build.dir}/testing/dspace</dspace.dir>
-                                <!-- This system property is loaded by AbstractDSpaceTest to initialize the test environment -->
+                        <dspace.dir.static>${basedir}/src/test/data/dspaceFolder</dspace.dir.static>
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
+                        <dspace.configuration>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</dspace.configuration>
-                                <!-- Turn off any DSpace logging -->
+                        <db.schema.path>${agnostic.build.dir}/testing/dspace/etc/h2/database_schema.sql</db.schema.path>
-                                <dspace.log.init.disable>true</dspace.log.init.disable>
-                            </systemPropertyVariables>
-                        </configuration>
-                    </plugin>
-
-
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>xml-maven-plugin</artifactId>
-                        <version>1.0.1</version>
-                        <executions>
-                            <execution>
-                                <id>validate-ALL-xml-and-xsl</id>
-                                <phase>process-test-resources</phase>
-                                <goals>
-                                    <goal>validate</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                        <configuration>
-                            <validationSets>
-                                <!-- validate ALL XML and XSL config files in the testing folder -->
-                                <validationSet>
-                                    <dir>${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>
@@ -289,39 +180,7 @@
         </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>
@@ -339,19 +198,12 @@
             <artifactId>dspace-tm-extractors</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.jena</groupId>
+            <groupId>org.apache.lucene</groupId>
-            <artifactId>apache-jena-libs</artifactId>
+            <artifactId>lucene-core</artifactId>
-            <type>pom</type>
+        </dependency>
-            <exclusions>
+        <dependency>
-                <exclusion>
+            <groupId>org.apache.lucene</groupId>
-                    <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>lucene-analyzers</artifactId>
-                    <artifactId>jackson-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -366,18 +218,19 @@
             <artifactId>commons-collections</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.commons</groupId>
+            <groupId>commons-dbcp</groupId>
-            <artifactId>commons-collections4</artifactId>
+            <artifactId>commons-dbcp</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>
@@ -387,12 +240,8 @@
             <artifactId>commons-lang</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.commons</groupId>
+            <groupId>commons-pool</groupId>
-            <artifactId>commons-pool2</artifactId>
+            <artifactId>commons-pool</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-validator</groupId>
-            <artifactId>commons-validator</artifactId>
         </dependency>
         <dependency>
             <groupId>javax.mail</groupId>
@@ -414,7 +263,7 @@
             </exclusions>
         </dependency>
         <dependency>
-            <groupId>org.jdom</groupId>
+            <groupId>jdom</groupId>
             <artifactId>jdom</artifactId>
         </dependency>
         <dependency>
@@ -433,6 +282,10 @@
            <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>
@@ -450,7 +303,11 @@
             <artifactId>poi-scratchpad</artifactId>
         </dependency>
         <dependency>
-            <groupId>rome</groupId>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi-ooxml</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>net.java.dev.rome</groupId>
             <artifactId>rome</artifactId>
         </dependency>
         <dependency>
@@ -464,16 +321,10 @@
         <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>xml-apis</artifactId>
+            <artifactId>xmlParserAPIs</artifactId>
         </dependency>
         <dependency>
             <groupId>javax.activation</groupId>
@@ -491,19 +342,14 @@
             <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.hamcrest</groupId>
+            <groupId>org.dspace.dependencies.jmockit</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>dspace-jmockit</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -512,57 +358,34 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.mockito</groupId>
+            <groupId>org.databene</groupId>
-            <artifactId>mockito-core</artifactId>
+            <artifactId>contiperf</artifactId>
             <scope>test</scope>
         </dependency>
-
         <dependency>
             <groupId>org.rometools</groupId>
             <artifactId>rome-modules</artifactId>
             <version>1.0</version>
         </dependency>
         <dependency>
-            <groupId>gr.ekt.bte</groupId>
+            <groupId>gr.ekt</groupId>
-            <artifactId>bte-core</artifactId>
+            <artifactId>biblio-transformation-engine</artifactId>
-            <version>0.9.3.5</version>
+            <version>0.82</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
-            <groupId>gr.ekt.bte</groupId>
+            <groupId>net.sf.opencsv</groupId>
-            <artifactId>bte-io</artifactId>
+            <artifactId>opencsv</artifactId>
-            <version>0.9.3.5</version>
+            <version>2.3</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.apache.httpcomponents</groupId>
+            <groupId>org.jbibtex</groupId>
-            <artifactId>httpcore</artifactId>
+            <artifactId>jbibtex</artifactId>
-        </dependency>
+            <version>1.0.0</version>
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpclient</artifactId>
         </dependency>
         <dependency>
             <groupId>org.apache.solr</groupId>
             <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
+            <version>${lucene.version}</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -574,30 +397,30 @@
                 </exclusion>
             </exclusions>
         </dependency>
-
         <dependency>
             <groupId>commons-configuration</groupId>
             <artifactId>commons-configuration</artifactId>
+            <version>1.8</version>
         </dependency>
         <dependency>
-            <groupId>com.maxmind.geoip2</groupId>
+            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>geoip2</artifactId>
+            <artifactId>dspace-geoip</artifactId>
-            <version>2.11.0</version>
+            <version>1.2.3</version>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
             <artifactId>ant</artifactId>
         </dependency>
         <dependency>
-            <groupId>dnsjava</groupId>
+            <groupId>org.dspace.dnsjava</groupId>
             <artifactId>dnsjava</artifactId>
-            <version>2.1.7</version>
+            <version>2.0.6</version>
         </dependency>
 
         <dependency>
-            <groupId>org.apache.lucene</groupId>
+            <groupId>org.elasticsearch</groupId>
-            <artifactId>lucene-core</artifactId>
+            <artifactId>elasticsearch</artifactId>
-            <version>4.10.4</version>
+            <version>0.18.6</version>
         </dependency>
 
         <dependency>
@@ -610,130 +433,15 @@
         <dependency>
             <groupId>com.google.code.gson</groupId>
             <artifactId>gson</artifactId>
+            <version>2.2.1</version>
             <scope>compile</scope>
         </dependency>
 
         <dependency>
-            <groupId>com.google.guava</groupId>
+            <groupId>postgresql</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>

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

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

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

@@ -9,23 +9,18 @@ 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.factory.HandleServiceFactory;
+import org.dspace.handle.HandleManager;
-import org.dspace.handle.service.HandleService;
+import org.dspace.storage.rdbms.DatabaseManager;
 
 /**
  * A command-line tool for setting/removing community/sub-community
@@ -35,21 +30,10 @@ import org.dspace.handle.service.HandleService;
  * @version $Revision$
  */
 
-public class CommunityFiliator {
+public class CommunityFiliator
-
+{
-    protected CommunityService communityService;
+    public static void main(String[] argv) throws Exception
-    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();
 
@@ -70,7 +54,8 @@ public class CommunityFiliator {
         String parentID = null;
         String childID = null;
 
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("CommunityFiliator\n", options);
             System.out
@@ -81,37 +66,45 @@ public class CommunityFiliator {
             System.exit(0);
         }
 
-        if (line.hasOption('s')) {
+        if (line.hasOption('s'))
+        {
             command = "set";
         }
 
-        if (line.hasOption('r')) {
+        if (line.hasOption('r'))
+        {
             command = "remove";
         }
 
-        if (line.hasOption('p')) { // parent
+        if (line.hasOption('p')) // parent
+        {
             parentID = line.getOptionValue('p');
         }
 
-        if (line.hasOption('c')) { // child
+        if (line.hasOption('c')) // child
+        {
             childID = line.getOptionValue('c');
         }
 
         // now validate
         // must have a command set
-        if (command == null) {
+        if (command == null)
+        {
             System.out
                     .println("Error - must run with either set or remove (run with -h flag for details)");
             System.exit(1);
         }
 
-        if ("set".equals(command) || "remove".equals(command)) {
+        if ("set".equals(command) || "remove".equals(command))
-            if (parentID == null) {
+        {
+            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);
             }
@@ -120,58 +113,63 @@ public class CommunityFiliator {
         CommunityFiliator filiator = new CommunityFiliator();
         Context c = new Context();
 
-        // we are superuser!
+        // ve are superuser!
-        c.turnOffAuthorisationSystem();
+        c.setIgnoreAuthorization(true);
 
-        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 = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities()
+        Community childDad = child.getParentCommunity();
-                                                                                             .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);
@@ -179,10 +177,12 @@ public class CommunityFiliator {
 
         // second test - circularity: parent's parents can't include proposed
         // child
-        List<Community> parentDads = parent.getParentCommunities();
+        Community[] parentDads = parent.getAllParents();
 
-        for (int i = 0; i < parentDads.size(); i++) {
+        for (int i = 0; i < parentDads.length; i++)
-            if (parentDads.get(i).getID().equals(child.getID())) {
+        {
+            if (parentDads[i].getID() == 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
-        communityService.addSubcommunity(c, parent, child);
+        parent.addSubcommunity(child);
 
         // complete the pending transaction
         c.complete();
@@ -198,29 +198,25 @@ 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
-        List<Community> parentKids = parent.getSubcommunities();
+        Community[] parentKids = parent.getSubcommunities();
         boolean isChild = false;
 
-        for (int i = 0; i < parentKids.size(); i++) {
+        for (int i = 0; i < parentKids.length; i++)
-            if (parentKids.get(i).getID().equals(child.getID())) {
+        {
+            if (parentKids[i].getID() == child.getID())
+            {
                 isChild = true;
 
                 break;
             }
         }
 
-        if (!isChild) {
+        if (!isChild)
+        {
             System.out
                     .println("Error, child community not a child of parent community");
             System.exit(1);
@@ -228,10 +224,9 @@ public class CommunityFiliator {
 
         // OK remove the mappings - but leave the community, which will become
         // top-level
-        child.getParentCommunities().remove(parent);
+        DatabaseManager.updateQuery(c,
-        parent.getSubcommunities().remove(child);
+                "DELETE FROM community2community WHERE parent_comm_id= ? "+
-        communityService.update(c, child);
+                "AND child_comm_id= ? ", parent.getID(), child.getID());
-        communityService.update(c, parent);
 
         // complete the pending transaction
         c.complete();
@@ -240,30 +235,27 @@ public class CommunityFiliator {
                 + "'");
     }
 
-    /**
+    private Community resolveCommunity(Context c, String communityID)
-     * Find a community by ID
+            throws SQLException
-     *
+    {
-     * @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) handleService.resolveToObject(c,
+            community = (Community) HandleManager.resolveToObject(c,
                     communityID);
 
             // ensure it's a community
             if ((community == null)
-                || (community.getType() != Constants.COMMUNITY)) {
+                    || (community.getType() != Constants.COMMUNITY))
+            {
                 community = null;
             }
-        } else {
+        }
-            community = communityService.find(c, UUID.fromString(communityID));
+        else
+        {
+            community = Community.find(c, Integer.parseInt(communityID));
         }
 
         return community;

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

@@ -7,23 +7,21 @@
  */
 package org.dspace.administer;
 
-import java.io.Console;
+import java.io.BufferedReader;
-import java.util.Arrays;
+import java.io.InputStreamReader;
 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
@@ -41,26 +39,24 @@ import org.dspace.eperson.service.GroupService;
  * 
  * @author Robert Tansley
  * @author Richard Jones
+ * 
  * @version $Revision$
  */
-public final class CreateAdministrator {
+public final class CreateAdministrator
-    /**
+{
-     * DSpace Context object
+	/** DSpace Context object */
-     */
+	private Context context;
-    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 the command line arguments given
+     * @param argv
-     * @throws Exception if error
+     *            command-line arguments
      */
     public static void main(String[] argv)
-        throws Exception {
+    	throws Exception
+    {
     	CommandLineParser parser = new PosixParser();
     	Options options = new Options();
     	
@@ -75,11 +71,14 @@ public final class CreateAdministrator {
     	CommandLine line = parser.parse(options, argv);
     	
     	if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
-            line.hasOption("c") && line.hasOption("p")) {
+    			line.hasOption("c") && line.hasOption("p"))
+    	{
     		ca.createAdministrator(line.getOptionValue("e"),
     				line.getOptionValue("f"), line.getOptionValue("l"),
     				line.getOptionValue("c"), line.getOptionValue("p"));
-        } else {
+    	}
+    	else
+    	{
     		ca.negotiateAdministratorDetails();
     	}
     }
@@ -87,24 +86,25 @@ public final class CreateAdministrator {
     /** 
      * constructor, which just creates and object with a ready context
      * 
-     * @throws Exception if error
+     * @throws Exception
      */
-    protected CreateAdministrator()
+    private CreateAdministrator()
-        throws Exception {
+    	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 if error
+     * @throws Exception
      */
-    protected void negotiateAdministratorDetails()
+    private void negotiateAdministratorDetails()
-        throws Exception {
+    	throws Exception
-        Console console = System.console();
+    {
+    	// For easier reading of typing
+    	BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
     	
     	System.out.println("Creating an initial administrator account");
     	
@@ -113,90 +113,102 @@ public final class CreateAdministrator {
     	String email = null;
     	String firstName = null;
     	String lastName = null;
-        char[] password1 = null;
+    	String password1 = null;
-        char[] password2 = null;
+    	String password2 = null;
     	String language = I18nUtil.DEFAULTLOCALE.getLanguage();
     	
-        while (!dataOK) {
+    	while (!dataOK)
+    	{
     		System.out.print("E-mail address: ");
     		System.out.flush();
     		
-            email = console.readLine();
+    		email = input.readLine();
-            if (!StringUtils.isBlank(email)) {
+            if (email != null)
+            {
                 email = email.trim();
-            } else {
-                System.out.println("Please provide an email address.");
-                continue;
             }
     		
     		System.out.print("First name: ");
     		System.out.flush();
     		
-            firstName = console.readLine();
+    		firstName = input.readLine();
 
-            if (firstName != null) {
+            if (firstName != null)
+            {
                 firstName = firstName.trim();
             }
     		
     		System.out.print("Last name: ");
     		System.out.flush();
     		
-            lastName = console.readLine();
+    		lastName = input.readLine();
 
-            if (lastName != null) {
+            if (lastName != null)
+            {
                 lastName = lastName.trim();
             }
    		
-            if (ConfigurationManager.getProperty("webui.supported.locales") != null) {
+            if (ConfigurationManager.getProperty("webui.supported.locales") != null)
-                System.out.println("Select one of the following languages: " + ConfigurationManager
+            {
-                    .getProperty("webui.supported.locales"));
+                System.out.println("Select one of the following languages: " + ConfigurationManager.getProperty("webui.supported.locales"));
                 System.out.print("Language: ");
                 System.out.flush();
             
-                language = console.readLine();
+    		    language = input.readLine();
 
-                if (language != null) {
+                if (language != null)
+                {
                     language = language.trim();
                     language = I18nUtil.getSupportedLocale(new Locale(language)).getLanguage();
                 }
             }
             
-            System.out.println("Password will not display on screen.");
+    		System.out.println("WARNING: Password will appear on-screen.");
     		System.out.print("Password: ");
     		System.out.flush();
     		
-            password1 = console.readPassword();
+    		password1 = input.readLine();
+
+            if (password1 != null)
+            {
+                password1 = password1.trim();
+            }
     		
     		System.out.print("Again to confirm: ");
     		System.out.flush();
     		
-            password2 = console.readPassword();
+    		password2 = input.readLine();
 
-            //TODO real password validation
+            if (password2 != null)
-            if (password1.length > 1 && Arrays.equals(password1, password2)) {
+            {
+                password2 = password2.trim();
+            }
+    		
+    		if (!StringUtils.isEmpty(password1) && StringUtils.equals(password1, password2))
+    		{
     			// password OK
     			System.out.print("Is the above data correct? (y or n): ");
     			System.out.flush();
     			
-                String s = console.readLine();
+    			String s = input.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, String.valueOf(password1));
+    	createAdministrator(email, firstName, lastName, language, password1);
-
-        //Cleaning arrays that held password
-        Arrays.fill(password1, ' ');
-        Arrays.fill(password2, ' ');
     }
     
     /**
@@ -206,45 +218,48 @@ public final class CreateAdministrator {
      * @param email	the email for the user
      * @param first	user's first name
      * @param last	user's last name
-     * @param language preferred language
+     * @param ps	desired password
-     * @param pw       desired password
+     * 
-     * @throws Exception if error
+     * @throws Exception
      */
-    protected void createAdministrator(String email, String first, String last,
+    private void createAdministrator(String email, String first, String last,
     		String language, String pw)
-        throws Exception {
+    	throws Exception
+    {
     	// Of course we aren't an administrator yet so we need to
     	// circumvent authorisation
-        context.turnOffAuthorisationSystem();
+    	context.setIgnoreAuthorization(true);
     	
     	// Find administrator group
-        Group admins = groupService.findByName(context, Group.ADMIN);
+    	Group admins = Group.find(context, 1);
     	
-        if (admins == null) {
+    	if (admins == null)
+    	{
     		throw new IllegalStateException("Error, no admin group (group 1) found");
     	}
     	
     	// Create the administrator e-person
-        EPerson eperson = ePersonService.findByEmail(context, email);
+        EPerson eperson = EPerson.findByEmail(context,email);
         
         // check if the email belongs to a registered user,
         // if not create a new user with this email
-        if (eperson == null) {
+        if (eperson == null)
-            eperson = ePersonService.create(context);
+        {
+            eperson = EPerson.create(context);
             eperson.setEmail(email);
             eperson.setCanLogIn(true);
             eperson.setRequireCertificate(false);
             eperson.setSelfRegistered(false);
         }
     	
-        eperson.setLastName(context, last);
+    	eperson.setLastName(last);
-        eperson.setFirstName(context, first);
+    	eperson.setFirstName(first);
-        eperson.setLanguage(context, language);
+    	eperson.setLanguage(language);
-        ePersonService.setPassword(eperson, pw);
+    	eperson.setPassword(pw);
-        ePersonService.update(context, eperson);
+    	eperson.update();
     	
-        groupService.addMember(context, admins, eperson);
+    	admins.addMember(eperson);
-        groupService.update(context, admins);
+    	admins.update();
     	
     	context.complete();
     	

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

@@ -0,0 +1,287 @@
+/**
+ * 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);
+    }
+}

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

@@ -12,7 +12,6 @@ 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;
@@ -25,9 +24,6 @@ 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;
 
@@ -39,37 +35,27 @@ 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();
 
     /**
-     * Default constructor
+     * @param args
+     * @throws ParseException 
+     * @throws SAXException 
+     * @throws IOException 
+     * @throws SQLException 
+     * @throws RegistryExportException 
      */
-    private MetadataExporter() { }
+    public static void main(String[] args) throws ParseException, SQLException, IOException, SAXException, RegistryExportException
-
+    {
-    /**
-     * @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();
@@ -80,35 +66,29 @@ 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.turnOffAuthorisationSystem();
+        context.setIgnoreAuthorization(true);
 
         OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
         xmlFormat.setLineWidth(120);
@@ -122,25 +102,30 @@ public class MetadataExporter {
         // Save the schema definition(s)
         saveSchema(context, xmlSerializer, schema);
 
-        List<MetadataField> mdFields = null;
+        MetadataField[] mdFields = null;
 
         // If a single schema has been specified
-        if (schema != null && !"".equals(schema)) {
+        if (schema != null && !"".equals(schema))
+        {
             // Get the id of that schema
-            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
+            MetadataSchema mdSchema = MetadataSchema.find(context, schema);
-            if (mdSchema == null) {
+            if (mdSchema == null)
+            {
                 throw new RegistryExportException("no schema to export");
             }
             
             // Get the metadata fields only for the specified schema
-            mdFields = metadataFieldService.findAllInSchema(context, mdSchema);
+            mdFields = MetadataField.findAllInSchema(context, mdSchema.getSchemaID());
-        } else {
+        }
+        else
+        {
             // Get the metadata fields for all the schemas
-            mdFields = metadataFieldService.findAll(context);
+            mdFields = MetadataField.findAll(context);
         }
         
         // Output the metadata fields
-        for (MetadataField mdField : mdFields) {
+        for (MetadataField mdField : mdFields)
+        {
             saveType(context, xmlSerializer, mdField);
         }
         
@@ -153,26 +138,29 @@ public class MetadataExporter {
     
     /**
      * Serialize the schema registry. If the parameter 'schema' is null or empty, save all schemas
-     *
+     * @param context
-     * @param context       DSpace Context
+     * @param xmlSerializer
-     * @param xmlSerializer XML serializer
+     * @param schema
-     * @param schema        schema (may be null to save all)
+     * @throws SQLException
-     * @throws SQLException            if database error
+     * @throws SAXException
-     * @throws SAXException            if XML error
+     * @throws RegistryExportException
-     * @throws RegistryExportException if export error
      */
-    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema)
+    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema) throws SQLException, SAXException, RegistryExportException
-        throws SQLException, SAXException, RegistryExportException {
+    {
-        if (schema != null && !"".equals(schema)) {
+        if (schema != null && !"".equals(schema))
+        {
             // Find a single named schema
-            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
+            MetadataSchema mdSchema = MetadataSchema.find(context, schema);
             
             saveSchema(xmlSerializer, mdSchema);
-        } else {
+        }
+        else
+        {
             // Find all schemas
-            List<MetadataSchema> mdSchemas = metadataSchemaService.findAll(context);
+            MetadataSchema[] mdSchemas = MetadataSchema.findAll(context);
             
-            for (MetadataSchema mdSchema : mdSchemas) {
+            for (MetadataSchema mdSchema : mdSchemas)
+            {
                 saveSchema(xmlSerializer, mdSchema);
             }
         }
@@ -181,27 +169,30 @@ public class MetadataExporter {
     /**
      * Serialize a single schema (namespace) registry entry
      * 
-     * @param xmlSerializer XML serializer
+     * @param xmlSerializer
-     * @param mdSchema      DSpace metadata schema
+     * @param mdSchema
-     * @throws SAXException            if XML error
+     * @throws SAXException
-     * @throws RegistryExportException if export error
+     * @throws RegistryExportException
      */
-    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema)
+    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema) throws SAXException, RegistryExportException
-        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;
         }
@@ -225,18 +216,19 @@ public class MetadataExporter {
     /**
      * Serialize a single metadata field registry entry to xml
      * 
-     * @param context       DSpace context
+     * @param context
-     * @param xmlSerializer xml serializer
+     * @param xmlSerializer
-     * @param mdField       DSpace metadata field
+     * @param mdField
-     * @throws SAXException            if XML error
+     * @throws SAXException
-     * @throws RegistryExportException if export error
+     * @throws RegistryExportException
-     * @throws SQLException            if database error
+     * @throws SQLException
-     * @throws IOException             if IO error
+     * @throws IOException 
      */
-    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField)
+    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField) throws SAXException, RegistryExportException, SQLException, IOException
-        throws SAXException, RegistryExportException, SQLException, IOException {
+    {
         // If we haven't been given a field, it's an error
-        if (mdField == null) {
+        if (mdField == null)
+        {
             throw new RegistryExportException("no field to export");
         }
         
@@ -247,7 +239,8 @@ public class MetadataExporter {
         String scopeNote = mdField.getScopeNote();
 
         // We must have a schema and element
-        if (schemaName == null || element == null) {
+        if (schemaName == null || element == null)
+        {
             throw new RegistryExportException("incomplete field information");
         }
 
@@ -265,50 +258,53 @@ 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
      */
-    private static String getSchemaName(Context context, MetadataField mdField)
+    static Map<Integer, String> schemaMap = new HashMap<Integer, String>();
-        throws SQLException, RegistryExportException {
+    private static String getSchemaName(Context context, MetadataField mdField) throws SQLException, RegistryExportException
+    {
         // Get name from cache
-        String name = schemaMap.get(mdField.getMetadataSchema().getID());
+        String name = schemaMap.get(Integer.valueOf(mdField.getSchemaID()));
 
-        if (name == null) {
+        if (name == null)
+        {
             // Name not retrieved before, so get the schema now
-            MetadataSchema mdSchema = metadataSchemaService.find(context, mdField.getMetadataSchema().getID());
+            MetadataSchema mdSchema = MetadataSchema.find(context, mdField.getSchemaID());
-            if (mdSchema != null) {
+            if (mdSchema != null)
+            {
                 name = mdSchema.getName();
-                schemaMap.put(mdSchema.getID(), name);
+                schemaMap.put(Integer.valueOf(mdSchema.getSchemaID()), name);
-            } else {
+            }
+            else
+            {
                 // Can't find the schema
                 throw new RegistryExportException("Can't get schema name for field");
             }
@@ -319,7 +315,8 @@ public class MetadataExporter {
     /**
      * Print the usage message to stdout
      */
-    public static void usage() {
+    public static void usage()
+    {
         String usage = "Use this class with the following options:\n" +
                         " -f <xml output file> : specify the output file for the schemas\n" +
                         " -s <schema> : name of the schema to export\n";

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

@@ -9,6 +9,7 @@ package org.dspace.administer;
 
 import java.io.IOException;
 import java.sql.SQLException;
+
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
@@ -17,20 +18,19 @@ 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;
 
 /**
@@ -42,7 +42,6 @@ import org.xml.sax.SAXException;
  * 
  * The format of the XML file is as follows:
  * 
- * {@code
  * <dspace-dc-types>
  *   <dc-type>
  *     <schema>icadmin</schema>
@@ -54,42 +53,17 @@ 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
@@ -100,9 +74,12 @@ public class MetadataImporter {
         CommandLine line = parser.parse(options, args);
         
         String file = null;
-        if (line.hasOption('f')) {
+        if (line.hasOption('f'))
+        {
             file = line.getOptionValue('f');
-        } else {
+        }
+        else
+        {
             usage();
             System.exit(0);
         }
@@ -115,25 +92,14 @@ 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 = new Context();
+        Context context = new Context();
-            context.turnOffAuthorisationSystem();
+        context.setIgnoreAuthorization(true);
         
         // read the XML
         Document document = RegistryImporter.loadXML(file);
@@ -142,7 +108,8 @@ public class MetadataImporter {
         NodeList schemaNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-schema");
         
         // Add each one as a new format to the registry
-            for (int i = 0; i < schemaNodes.getLength(); i++) {
+        for (int i = 0; i < schemaNodes.getLength(); i++)
+        {
             Node n = schemaNodes.item(i);
             loadSchema(context, n, forceUpdate);
         }
@@ -151,73 +118,81 @@ 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 context
-     * @param node    the node in the DOM tree
+     *            DSpace context object
-     * @throws SQLException               if database error
+     * @param node
-     * @throws IOException                if IO error
+     *            the node in the DOM tree
-     * @throws TransformerException       if transformer error
+     * @throws NonUniqueMetadataException
-     * @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");
         }
 
-        // check to see if the schema already exists
+        System.out.print("Registering Schema: " + name + " - " + namespace + " ... ");
-        MetadataSchema s = metadataSchemaService.find(context, name);
         
-        if (s == null) {
+        // check to see if the schema already exists
+        MetadataSchema s = MetadataSchema.find(context, name);
+        
+        if (s == null)
+        {
             // Schema does not exist - create
-            log.info("Registering Schema " + name + " (" + namespace + ")");
+            MetadataSchema schema = new MetadataSchema(namespace, name);
-            metadataSchemaService.create(context, name, namespace);
+            schema.create(context);
-        } else {
+            System.out.println("created");
+        }
+        else
+        {
             // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace)) {
+            if (s.getNamespace().equals(namespace))
-                // This schema already exists with this namespace, skipping it
+            {
+                System.out.println("already exists, skipping to type import");
                 return;
             }
             
             // It's a different namespace - have we been told to update?
-            if (updateExisting) {
+            if (updateExisting)
+            {
                 // Update the existing schema namespace and continue to type import
-                log.info("Updating Schema " + name + ": New namespace " + namespace);
                 s.setNamespace(namespace);
-                metadataSchemaService.update(context, s);
+                s.update(context);
-            } else {
+                System.out.println("namespace updated (" + name + " = " + namespace + ")");
-                throw new RegistryImportException(
+            }
-                    "Schema " + name + " already registered with different namespace " + namespace + ". Rerun with " +
+            else
-                        "'update' option enabled if you wish to update this schema.");
+            {
+                // 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");
             }
         }
         
@@ -228,18 +203,16 @@ 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 context
-     * @param node    the node in the DOM tree
+     *            DSpace context object
-     * @throws SQLException               if database error
+     * @param node
-     * @throws IOException                if IO error
+     *            the node in the DOM tree
-     * @throws TransformerException       if transformer error
+     * @throws NonUniqueMetadataException
-     * @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");
@@ -247,38 +220,42 @@ 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 = metadataSchemaService.find(context, schema);
+        MetadataSchema schemaObj = MetadataSchema.find(context, schema);
         
-        if (schemaObj == null) {
+        if (schemaObj == null)
-            throw new RegistryImportException("Schema '" + schema + "' is not registered and does not exist.");
+        {
+            throw new RegistryImportException("Schema '" + schema + "' is not registered");
         }
         
-        MetadataField mf = metadataFieldService.findByElement(context, schemaObj, element, qualifier);
+        MetadataField mf = MetadataField.findByElement(context, schemaObj.getSchemaID(), element, qualifier);
-        if (mf != null) {
+        if (mf != null)
-            // Metadata field already exists, skipping it
+        {
+            System.out.println("already exists, skipping");
             return;
         }
         
-        // Actually create this metadata field as it doesn't yet exist
+        MetadataField field = new MetadataField();
-        String fieldName = schema + "." + element + "." + qualifier;
+        field.setSchemaID(schemaObj.getSchemaID());
-        if (qualifier == null) {
+        field.setElement(element);
-            fieldName = schema + "." + element;
+        field.setQualifier(qualifier);
-        }
+        field.setScopeNote(scopeNote);
-        log.info("Registering metadata field " + fieldName);
+        field.create(context);
-        MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
+        System.out.println("created");
-        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";

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

@@ -12,39 +12,44 @@ 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 exception message
+     * @param message
      */
-    public RegistryExportException(String message) {
+    public RegistryExportException(String message)
+    {
         super(message);
     }
     
     /**
      * create an exception with an inner exception and a message
      * 
-     * @param message exception message
+     * @param   message
-     * @param e       reference to Throwable
+     * @param   e
      */
-    public RegistryExportException(String message, Throwable e) {
+    public RegistryExportException(String message, Throwable e)
+    {
         super(message, e);
     }
     
     /**
      * create an exception with an inner exception
      * 
-     * @param e reference to Throwable
+     * @param   e
      */
-    public RegistryExportException(Throwable e) {
+    public RegistryExportException(Throwable e)
+    {
         super(e);
     }
     

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

@@ -12,39 +12,44 @@ 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 error message
+     * @param message
      */
-    public RegistryImportException(String message) {
+    public RegistryImportException(String message)
+    {
         super(message);
     }
     
     /**
      * create an exception with an inner exception and a message
      * 
-     * @param message error message
+     * @param	message
-     * @param e       throwable
+     * @param	e
      */
-    public RegistryImportException(String message, Throwable e) {
+    public RegistryImportException(String message, Throwable e)
+    {
     	super(message, e);
     }
     
     /**
      * create an exception with an inner exception
      * 
-     * @param e throwable
+     * @param	e
      */
-    public RegistryImportException(Throwable e) {
+    public RegistryImportException(Throwable e)
+    {
     	super(e);
     }
     

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

@@ -9,15 +9,18 @@ package org.dspace.administer;
 
 import java.io.File;
 import java.io.IOException;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
 import org.apache.xpath.XPathAPI;
+
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
+
 import org.xml.sax.SAXException;
 
 /**
@@ -28,24 +31,19 @@ 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();
 
@@ -66,17 +64,21 @@ public class RegistryImporter {
      * </P>
      * Why this isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
+     * @param parentElement
-     * @param childName     the name of the element you want the CDATA from
+     *            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;
         }
@@ -84,7 +86,8 @@ public class RegistryImporter {
         // Get the #text
         Node dataNode = childNode.getFirstChild();
 
-        if (dataNode == null) {
+        if (dataNode == null)
+        {
             return null;
         }
 
@@ -109,19 +112,23 @@ public class RegistryImporter {
      * </P>
      * Why this also isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
+     * @param parentElement
-     * @param childName     the name of the element you want the CDATA from
+     *            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();
 

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

@@ -10,8 +10,7 @@ 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;
@@ -21,8 +20,9 @@ import org.apache.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.BitstreamFormat;
-import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.MetadataField;
-import org.dspace.content.service.BitstreamFormatService;
+import org.dspace.content.MetadataSchema;
+import org.dspace.content.NonUniqueMetadataException;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.w3c.dom.Document;
@@ -43,86 +43,88 @@ import org.xml.sax.SAXException;
  * @author Robert Tansley
  * @version $Revision$
  */
-public class RegistryLoader {
+public class RegistryLoader
-    /**
+{
-     * log4j category
+    /** 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 the command line arguments given
+     * @param argv
-     * @throws Exception if error
+     *            command-line arguments
      */
-    public static void main(String[] argv) throws Exception {
+    public static void main(String[] argv) throws Exception
+    {
         String usage = "Usage: " + RegistryLoader.class.getName()
-            + " (-bitstream | -metadata) registry-file.xml";
+                + " (-bitstream | -dc) registry-file.xml";
 
         Context context = null;
 
-        try {
+        try
+        {
             context = new Context();
 
             // Can't update registries anonymously, so we need to turn off
             // authorisation
-            context.turnOffAuthorisationSystem();
+            context.setIgnoreAuthorization(true);
 
             // Work out what we're loading
-            if (argv[0].equalsIgnoreCase("-bitstream")) {
+            if (argv[0].equalsIgnoreCase("-bitstream"))
+            {
                 RegistryLoader.loadBitstreamFormats(context, argv[1]);
-            } else if (argv[0].equalsIgnoreCase("-metadata")) {
+            }
-                // Call MetadataImporter, as it handles Metadata schema updates
+            else if (argv[0].equalsIgnoreCase("-dc"))
-                MetadataImporter.loadRegistry(argv[1], true);
+            {
-            } else {
+                loadDublinCoreTypes(context, argv[1]);
+            }
+            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);
 
-            System.err.println("Error: \n - " + e.getMessage());
+            if (context != null)
-            System.exit(1);
+            {
-        } finally {
-            // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
                 context.abort();
             }
+
+            System.err.println("Error: \n - " + e.getMessage());
+            System.exit(1);
         }
     }
 
     /**
      * Load Bitstream Format metadata
      * 
-     * @param context  DSpace context object
+     * @param context
-     * @param filename the filename of the XML file to load
+     *            DSpace context object
-     * @throws SQLException                 if database error
+     * @param filename
-     * @throws IOException                  if IO error
+     *            the filename of the XML file to load
-     * @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
@@ -130,7 +132,8 @@ public class RegistryLoader {
                 "dspace-bitstream-types/bitstream-type");
 
         // Add each one as a new format to the registry
-        for (int i = 0; i < typeNodes.getLength(); i++) {
+        for (int i = 0; i < typeNodes.getLength(); i++)
+        {
             Node n = typeNodes.item(i);
             loadFormat(context, n);
         }
@@ -143,16 +146,15 @@ 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 context
-     * @param node    the node in the DOM tree
+     *            DSpace context object
-     * @throws SQLException         if database error
+     * @param node
-     * @throws IOException          if IO error
+     *            the node in the DOM tree
-     * @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");
@@ -166,32 +168,124 @@ 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 = bitstreamFormatService.create(context);
+        BitstreamFormat format = BitstreamFormat.create(context);
 
         // Fill it out with the values
         format.setMIMEType(mimeType);
-            bitstreamFormatService.setShortDescription(context, format, shortDesc);
+        format.setShortDescription(shortDesc);
         format.setDescription(desc);
         format.setSupportLevel(supportLevel);
         format.setInternal(internal);
-            ArrayList<String> extensionList = new ArrayList<>();
+        format.setExtensions(extensions);
-            extensionList.addAll(Arrays.asList(extensions));
-            format.setExtensions(extensionList);
 
         // Write to database
-            bitstreamFormatService.update(context, format);
+        format.update();
     }
+
+    /**
+     * 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 =========================
@@ -199,14 +293,14 @@ 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();
 
@@ -225,17 +319,21 @@ public class RegistryLoader {
      * </P>
      * Why this isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
+     * @param parentElement
-     * @param childName     the name of the element you want the CDATA from
+     *            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;
         }
@@ -243,7 +341,8 @@ public class RegistryLoader {
         // Get the #text
         Node dataNode = childNode.getFirstChild();
 
-        if (dataNode == null) {
+        if (dataNode == null)
+        {
             return null;
         }
 
@@ -268,19 +367,23 @@ public class RegistryLoader {
      * </P>
      * Why this also isn't a core part of the XML API I do not know...
      * 
-     * @param parentElement the element, whose child element you want the CDATA from
+     * @param parentElement
-     * @param childName     the name of the element you want the CDATA from
+     *            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();
 

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

@@ -14,6 +14,7 @@ import java.io.IOException;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -27,12 +28,8 @@ 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.factory.EPersonServiceFactory;
+import org.dspace.eperson.EPerson;
-import org.dspace.eperson.service.EPersonService;
 import org.jdom.Element;
 import org.jdom.output.XMLOutputter;
 import org.w3c.dom.Document;
@@ -45,7 +42,7 @@ import org.xml.sax.SAXException;
  * an XML file.
  * 
  * The XML file structure needs to be:
- * {@code
+ * 
  * <import_structure>
  *     <community>
  *         <name>....</name>
@@ -55,56 +52,42 @@ 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 {
+public class StructBuilder
-    /**
+{
-     * the output xml document which will contain updated information about the
+    /** the output xml document which will contain updated information about the 
      * imported structure
      */
     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:
      * 
-     * {@code StructBuilder -f [xml source] -e [administrator email] -o [output file]}
+     * 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();
@@ -119,19 +102,23 @@ 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);
     	}
@@ -140,7 +127,7 @@ public class StructBuilder {
         Context context = new Context();
         
         // set the context
-        context.setCurrentUser(ePersonService.findByEmail(context, eperson));
+        context.setCurrentUser(EPerson.findByEmail(context, eperson));
  
         // load the XML
         Document document = loadXML(file);
@@ -172,16 +159,20 @@ 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);
         }
@@ -192,11 +183,10 @@ 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(
+        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");
-            "Communities will be created from the top level, and a map of communities to handles will be returned in " +
-                "the output file");
         return;
     }
     
@@ -205,10 +195,12 @@ public class StructBuilder {
      * fails it generates an error and ceases execution
      * 
      * @param	document	the XML document object
-     * @throws TransformerException if transformer error
+     * @throws TransformerException
+     * 
      */
     private static void validate(org.w3c.dom.Document document)
-        throws TransformerException {
+    	throws TransformerException
+    {
         StringBuffer err = new StringBuffer();
         boolean trip = false;
         
@@ -216,19 +208,22 @@ 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);
         }
@@ -241,19 +236,23 @@ 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");
@@ -263,7 +262,8 @@ 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;
 	        }
@@ -271,13 +271,15 @@ 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();
         }
         
@@ -290,18 +292,22 @@ 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");
@@ -309,7 +315,8 @@ public class StructBuilder {
 	        }
         }
         
-        if (trip) {
+        if (trip)
+        {
             errs = err.toString();
         }
         
@@ -319,11 +326,14 @@ public class StructBuilder {
     /**
      * Load in the XML from file.
      * 
-     * @param filename the filename to load from
+     * @param filename
+     *            the filename to load from
+     * 
      * @return the DOM representation of the XML file
      */
     private static org.w3c.dom.Document loadXML(String filename) 
-        throws IOException, ParserConfigurationException, SAXException {
+    	throws IOException, ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                 .newDocumentBuilder();
 
@@ -336,15 +346,19 @@ public class StructBuilder {
      * Return the String value of a Node
      * 
      * @param node the node from which we want to extract the string value
+     * 
      * @return the string value of the node
      */
-    public static String getStringValue(Node node) {
+    public static String getStringValue(Node node)
+    {
         String value = node.getNodeValue();
 
-        if (node.hasChildNodes()) {
+        if (node.hasChildNodes())
+        {
             Node first = node.getFirstChild();
 
-            if (first.getNodeType() == Node.TEXT_NODE) {
+            if (first.getNodeType() == Node.TEXT_NODE)
+            {
                 return first.getNodeValue().trim();
             }
         }
@@ -359,33 +373,41 @@ 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) {
+            if (parent != null)
-                community = communityService.create(parent, context);
+            {
-            } else {
+                community = parent.createSubcommunity();
-                community = communityService.create(null, context);
+            }
+            else
+            {
+                community = Community.create(null, context);
             }
             
             // default the short description to be an empty string
-            communityService.setMetadata(context, community, "short_description", " ");
+            community.setMetadata("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) {
+                if (nl.getLength() == 1)
-                    communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
+                {
+                    community.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
             
@@ -398,7 +420,7 @@ public class StructBuilder {
             // difficult
             // to isolate the community that already exists without hitting
             // the database directly.
-            communityService.update(context, community);
+            community.update();
             
             // build the element with the handle that identifies the new
             // community
@@ -411,30 +433,34 @@ public class StructBuilder {
             element.setAttribute("identifier", community.getHandle());
             
             Element nameElement = new Element("name");
-            nameElement.setText(communityService.getMetadata(community, "name"));
+            nameElement.setText(community.getMetadata("name"));
             element.addContent(nameElement);
             
-            if (communityService.getMetadata(community, "short_description") != null) {
+            if (community.getMetadata("short_description") != null)
+            {
                 Element descriptionElement = new Element("description");
-                descriptionElement.setText(communityService.getMetadata(community, "short_description"));
+                descriptionElement.setText(community.getMetadata("short_description"));
                 element.addContent(descriptionElement);
             }
             
-            if (communityService.getMetadata(community, "introductory_text") != null) {
+            if (community.getMetadata("introductory_text") != null)
+            {
                 Element introElement = new Element("intro");
-                introElement.setText(communityService.getMetadata(community, "introductory_text"));
+                introElement.setText(community.getMetadata("introductory_text"));
                 element.addContent(introElement);
             }
             
-            if (communityService.getMetadata(community, "copyright_text") != null) {
+            if (community.getMetadata("copyright_text") != null)
+            {
                 Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
+                copyrightElement.setText(community.getMetadata("copyright_text"));
                 element.addContent(copyrightElement);
             }
             
-            if (communityService.getMetadata(community, "side_bar_text") != null) {
+            if (community.getMetadata("side_bar_text") != null)
+            {
                 Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(communityService.getMetadata(community, "side_bar_text"));
+                sidebarElement.setText(community.getMetadata("side_bar_text"));
                 element.addContent(sidebarElement);
             }
             
@@ -447,10 +473,12 @@ public class StructBuilder {
             Element[] collectionElements = handleCollections(context, collections, community);
             
             int j;
-            for (j = 0; j < subCommunityElements.length; j++) {
+            for (j = 0; j < subCommunityElements.length; j++)
+            {
                 element.addContent(subCommunityElements[j]);
             }
-            for (j = 0; j < collectionElements.length; j++) {
+            for (j = 0; j < collectionElements.length; j++)
+            {
                 element.addContent(collectionElements[j]);
             }
             
@@ -466,70 +494,81 @@ 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 = collectionService.create(context, parent);
+            Collection collection = parent.createCollection();
             
             // default the short description to the empty string
-            collectionService.setMetadata(context, collection, "short_description", " ");
+            collection.setMetadata("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) {
+                if (nl.getLength() == 1)
-                    collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
+                {
+                    collection.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
             
-            collectionService.update(context, collection);
+            collection.update();
             
             element.setAttribute("identifier", collection.getHandle());
             
             Element nameElement = new Element("name");
-            nameElement.setText(collectionService.getMetadata(collection, "name"));
+            nameElement.setText(collection.getMetadata("name"));
             element.addContent(nameElement);
             
-            if (collectionService.getMetadata(collection, "short_description") != null) {
+            if (collection.getMetadata("short_description") != null)
+            {
                 Element descriptionElement = new Element("description");
-                descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
+                descriptionElement.setText(collection.getMetadata("short_description"));
                 element.addContent(descriptionElement);
             }
             
-            if (collectionService.getMetadata(collection, "introductory_text") != null) {
+            if (collection.getMetadata("introductory_text") != null)
+            {
                 Element introElement = new Element("intro");
-                introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
+                introElement.setText(collection.getMetadata("introductory_text"));
                 element.addContent(introElement);
             }
             
-            if (collectionService.getMetadata(collection, "copyright_text") != null) {
+            if (collection.getMetadata("copyright_text") != null)
+            {
                 Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
+                copyrightElement.setText(collection.getMetadata("copyright_text"));
                 element.addContent(copyrightElement);
             }
             
-            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
+            if (collection.getMetadata("side_bar_text") != null)
+            {
                 Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
+                sidebarElement.setText(collection.getMetadata("side_bar_text"));
                 element.addContent(sidebarElement);
             }
             
-            if (collectionService.getMetadata(collection, "license") != null) {
+            if (collection.getMetadata("license") != null)
+            {
                 Element sidebarElement = new Element("license");
-                sidebarElement.setText(collectionService.getMetadata(collection, "license"));
+                sidebarElement.setText(collection.getMetadata("license"));
                 element.addContent(sidebarElement);
             }
             
-            if (collectionService.getMetadata(collection, "provenance_description") != null) {
+            if (collection.getMetadata("provenance_description") != null)
+            {
                 Element sidebarElement = new Element("provenance");
-                sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
+                sidebarElement.setText(collection.getMetadata("provenance_description"));
                 element.addContent(sidebarElement);
             }
             

dspace-api/src/main/java/org/dspace/administer/Upgrade101To11.java

@@ -0,0 +1,97 @@
+/**
+ * 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);
+        }
+    }
+}

dspace-api/src/main/java/org/dspace/administer/Upgrade11To12.java

@@ -0,0 +1,198 @@
+/**
+ * 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();
+    }
+}

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

@@ -7,93 +7,68 @@
  */
 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 {
+public class BulkEditChange
-    /**
+{
-     * The item these changes relate to
+    /** The item these changes relate to */
-     */
     private Item item;
 
-    /**
+    /** The List of hashtables with the new elements */
-     * The List of hashtables with the new elements
+    private List<DCValue> adds;
-     */
-    private List<BulkEditMetadataValue> adds;
 
-    /**
+    /** The List of hashtables with the removed elements */
-     * The List of hashtables with the removed elements
+    private List<DCValue> removes;
-     */
-    private List<BulkEditMetadataValue> removes;
 
-    /**
+    /** The List of hashtables with the unchanged elements */
-     * The List of hashtables with the unchanged elements
+    private List<DCValue> constant;
-     */
-    private List<BulkEditMetadataValue> constant;
 
-    /**
+    /** The List of the complete set of new values (constant + adds) */
-     * The List of the complete set of new values (constant + adds)
+    private List<DCValue> complete;
-     */
-    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;
@@ -102,12 +77,12 @@ public class BulkEditChange {
         newOwningCollection = null;
 
         // Initialise the arrays
-        adds = new ArrayList<>();
+        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<>();
+        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<>();
+        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<>();
+        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<>();
+        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<>();
+        newMappedCollections = new ArrayList<Collection>();
     }
 
     /**
@@ -115,19 +90,20 @@ 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<>();
+        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<>();
+        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<>();
+        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<>();
+        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<>();
+        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<>();
+        newMappedCollections = new ArrayList<Collection>();
     }
 
     /**
@@ -135,7 +111,8 @@ public class BulkEditChange {
      *
      * @param i The item
      */
-    public void setItem(Item i) {
+    public void setItem(Item i)
+    {
         // Store the item
         item = i;
     }
@@ -145,7 +122,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to add
      */
-    public void registerAdd(BulkEditMetadataValue dcv) {
+    public void registerAdd(DCValue dcv)
+    {
         // Add the added value
         adds.add(dcv);
         complete.add(dcv);
@@ -157,7 +135,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to remove
      */
-    public void registerRemove(BulkEditMetadataValue dcv) {
+    public void registerRemove(DCValue dcv)
+    {
         // Add the removed value
         removes.add(dcv);
         empty = false;
@@ -168,7 +147,8 @@ public class BulkEditChange {
      *
      * @param dcv The value to keep unchanged
      */
-    public void registerConstant(BulkEditMetadataValue dcv) {
+    public void registerConstant(DCValue dcv)
+    {
         // Add the removed value
         constant.add(dcv);
         complete.add(dcv);
@@ -179,7 +159,8 @@ public class BulkEditChange {
      *
      * @param c The new mapped Collection
      */
-    public void registerNewMappedCollection(Collection c) {
+    public void registerNewMappedCollection(Collection c)
+    {
         // Add the new owning Collection
         newMappedCollections.add(c);
         empty = false;
@@ -190,22 +171,27 @@ public class BulkEditChange {
      *
      * @param c The old mapped Collection
      */
-    public void registerOldMappedCollection(Collection c) {
+    public void registerOldMappedCollection(Collection c)
+    {
         // Add the old owning Collection (if it isn't there already, or is an old collection)
         boolean found = false;
 
         if ((this.getOldOwningCollection() != null) &&
-            (this.getOldOwningCollection().getHandle().equals(c.getHandle()))) {
+            (this.getOldOwningCollection().getHandle().equals(c.getHandle())))
+        {
             found = true;
         }
 
-        for (Collection collection : oldMappedCollections) {
+        for (Collection collection : oldMappedCollections)
-            if (collection.getHandle().equals(c.getHandle())) {
+        {
+            if (collection.getHandle().equals(c.getHandle()))
+            {
                 found = true;
             }
         }
 
-        if (!found) {
+        if (!found)
+        {
             oldMappedCollections.add(c);
             empty = false;
         }
@@ -217,7 +203,8 @@ public class BulkEditChange {
      * @param oldC The old owning collection
      * @param newC The new owning collection
      */
-    public void changeOwningCollection(Collection oldC, Collection newC) {
+    public void changeOwningCollection(Collection oldC, Collection newC)
+    {
         // Store the old owning collection
         oldOwningCollection = oldC;
 
@@ -231,7 +218,8 @@ public class BulkEditChange {
      *
      * @param newC The new owning collection
      */
-    public void setOwningCollection(Collection newC) {
+    public void setOwningCollection(Collection newC)
+    {
         // Store the new owning collection
         newOwningCollection = newC;
         //empty = false;
@@ -242,7 +230,8 @@ public class BulkEditChange {
      *
      * @return The item
      */
-    public Item getItem() {
+    public Item getItem()
+    {
         // Return the item
         return item;
     }
@@ -252,7 +241,8 @@ public class BulkEditChange {
      *
      * @return the list of elements and their values that have been added.
      */
-    public List<BulkEditMetadataValue> getAdds() {
+    public List<DCValue> getAdds()
+    {
         // Return the array
         return adds;
     }
@@ -262,7 +252,8 @@ public class BulkEditChange {
      *
      * @return the list of elements and their values that have been removed.
      */
-    public List<BulkEditMetadataValue> getRemoves() {
+    public List<DCValue> getRemoves()
+    {
         // Return the array
         return removes;
     }
@@ -272,7 +263,8 @@ public class BulkEditChange {
      *
      * @return the list of unchanged values
      */
-    public List<BulkEditMetadataValue> getConstant() {
+    public List<DCValue> getConstant()
+    {
         // Return the array
         return constant;
     }
@@ -282,7 +274,8 @@ public class BulkEditChange {
      *
      * @return the list of all values
      */
-    public List<BulkEditMetadataValue> getComplete() {
+    public List<DCValue> getComplete()
+    {
         // Return the array
         return complete;
     }
@@ -292,7 +285,8 @@ public class BulkEditChange {
      *
      * @return the list of new mapped collections
      */
-    public List<Collection> getNewMappedCollections() {
+    public List<Collection> getNewMappedCollections()
+    {
         // Return the array
         return newMappedCollections;
     }
@@ -302,7 +296,8 @@ public class BulkEditChange {
      *
      * @return the list of old mapped collections
      */
-    public List<Collection> getOldMappedCollections() {
+    public List<Collection> getOldMappedCollections()
+    {
         // Return the array
         return oldMappedCollections;
     }
@@ -312,7 +307,8 @@ public class BulkEditChange {
      *
      * @return the old owning collection
      */
-    public Collection getOldOwningCollection() {
+    public Collection getOldOwningCollection()
+    {
         // Return the old owning collection
         return oldOwningCollection;
     }
@@ -322,7 +318,8 @@ public class BulkEditChange {
      *
      * @return the new owning collection
      */
-    public Collection getNewOwningCollection() {
+    public Collection getNewOwningCollection()
+    {
         // Return the new owning collection
         return newOwningCollection;
     }
@@ -332,7 +329,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a new item
      */
-    public boolean isNewItem() {
+    public boolean isNewItem()
+    {
         // Return the new item status
         return newItem;
     }
@@ -342,7 +340,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a deleted item
      */
-    public boolean isDeleted() {
+    public boolean isDeleted()
+    {
         // Return the new item status
         return deleted;
     }
@@ -361,7 +360,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a withdrawn item
      */
-    public boolean isWithdrawn() {
+    public boolean isWithdrawn()
+    {
         // Return the new item status
         return withdrawn;
     }
@@ -380,7 +380,8 @@ public class BulkEditChange {
      *
      * @return Whether or not this is for a reinstated item
      */
-    public boolean isReinstated() {
+    public boolean isReinstated()
+    {
         // Return the new item status
         return reinstated;
     }
@@ -399,7 +400,8 @@ public class BulkEditChange {
      *
      * @return Whether or not changes have been made
      */
-    public boolean hasChanges() {
+    public boolean hasChanges()
+    {
         return !empty;
     }
 }

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

@@ -1,83 +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.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;
-    }
-}

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

@@ -7,41 +7,15 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.BufferedReader;
+import org.dspace.content.*;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.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.core.ConfigurationManager;
-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;
+
+import java.util.*;
+import java.util.regex.Pattern;
+import java.util.regex.Matcher;
+import java.io.*;
 
 /**
  * Utility class to read and write CSV files
@@ -57,70 +31,41 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  *
  * @author Stuart Lewis
  */
-public class DSpaceCSV implements Serializable {
+public class DSpaceCSV implements Serializable
-    /**
+{
-     * The headings of the CSV file
+    /** The headings of the CSV file */
-     */
+    private List<String> headings;
-    protected List<String> headings;
 
-    /**
+    /** An array list of CSV lines */
-     * An array list of CSV lines
+    private List<DSpaceCSVLine> lines;
-     */
-    protected List<DSpaceCSVLine> lines;
 
-    /**
+    /** A counter of how many CSV lines this object holds */
-     * A counter of how many CSV lines this object holds
+    private int counter;
-     */
-    protected int counter;
 
-    /**
+    /** The value separator (defaults to double pipe '||') */
-     * The value separator (defaults to double pipe '||')
+    protected static String valueSeparator;
-     */
-    protected String valueSeparator;
 
-    /**
+    /** The value separator in an escaped form for using in regexs */
-     * The value separator in an escaped form for using in regexes
+    protected static String escapedValueSeparator;
-     */
-    protected String escapedValueSeparator;
 
-    /**
+    /** The field separator (defaults to comma) */
-     * The field separator (defaults to comma)
+    protected static String fieldSeparator;
-     */
-    protected String fieldSeparator;
 
-    /**
+    /** The field separator in an escaped form for using in regexs */
-     * The field separator in an escaped form for using in regexes
+    protected static String escapedFieldSeparator;
-     */
-    protected String escapedFieldSeparator;
 
-    /**
+    /** The authority separator (defaults to dobule colon '::') */
-     * The authority separator (defaults to double colon '::')
+    protected static String authoritySeparator;
-     */
-    protected String authoritySeparator;
 
-    /**
+    /** The authority separator in an escaped form for using in regexs */
-     * The authority separator in an escaped form for using in regexes
+    protected static String escapedAuthoritySeparator;
-     */
-    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 */
-     * Whether to export all metadata such as handles and provenance information
+    private boolean exportAll;
-     */
-    protected boolean exportAll;
 
-    /**
+    /** A list of metadata elements to ignore */
-     * A list of metadata elements to ignore
+    private Map<String, String> ignore;
-     */
-    protected Map<String, String> ignore;
 
 
     /**
@@ -128,7 +73,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @param exportAll Whether to export all metadata such as handles and provenance information
      */
-    public DSpaceCSV(boolean exportAll) {
+    public DSpaceCSV(boolean exportAll)
+    {
         // Initialise the class
         init();
 
@@ -141,45 +87,48 @@ public class DSpaceCSV implements Serializable {
      *
      * @param f The file to read from
      * @param c The DSpace Context
+     *
      * @throws Exception thrown if there is an error reading or processing the file
      */
-    public DSpaceCSV(File f, Context c) throws Exception {
+    public DSpaceCSV(File f, Context c) throws Exception
+    {
         // Initialise the class
         init();
 
         // Open the CSV file
         BufferedReader input = null;
-        try {
+        try
+        {
             input = new BufferedReader(new InputStreamReader(new FileInputStream(f),"UTF-8"));
 
             // Read the heading line
             String head = input.readLine();
             String[] headingElements = head.split(escapedFieldSeparator);
             int columnCounter = 0;
-            for (String element : headingElements) {
+            for (String element : headingElements)
+            {
                 columnCounter++;
 
                 // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
+                if ((element.startsWith("\"")) && (element.endsWith("\"")))
+                {
                     element = element.substring(1, element.length() - 1);
                 }
 
                 // Store the heading
-                if ("collection".equals(element)) {
+                if ("collection".equals(element))
+                {
                     // Store the heading
                     headings.add(element);
-                } else if ("action".equals(element)) { // Store the action
-                    // Store the 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());
                 }
-
+                // Store the action
+                else if ("action".equals(element))
+                {
+                    // Store the heading
+                    headings.add(element);
+                }
+                else if (!"id".equals(element))
+                {
                     // Verify that the heading is valid in the metadata registry
                     String[] clean = element.split("\\[");
                     String[] parts = clean[0].split("\\.");
@@ -198,7 +147,7 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Check that the scheme exists
-                    MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
+                    MetadataSchema foundSchema = MetadataSchema.find(c, metadataSchema);
                     if (foundSchema == null) {
                         throw new MetadataImportInvalidHeadingException(clean[0],
                                                                         MetadataImportInvalidHeadingException.SCHEMA,
@@ -206,8 +155,8 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Check that the metadata element exists in the schema
-                    MetadataField foundField = metadataFieldService
+                    int schemaID = foundSchema.getSchemaID();
-                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
+                    MetadataField foundField = MetadataField.findByElement(c, schemaID, metadataElement, metadataQualifier);
                     if (foundField == null) {
                         throw new MetadataImportInvalidHeadingException(clean[0],
                                                                         MetadataImportInvalidHeadingException.ELEMENT,
@@ -215,7 +164,7 @@ public class DSpaceCSV implements Serializable {
                     }
 
                     // Store the heading
-                    headings.add(authorityPrefix + element);
+                    headings.add(element);
                 }
             }
 
@@ -223,7 +172,8 @@ public class DSpaceCSV implements Serializable {
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while ((lineRead = input.readLine()) != null) {
+            while ((lineRead = input.readLine()) != null)
+            {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line
                     lineBuilder.append("\n").append(lineRead);
@@ -262,8 +212,11 @@ public class DSpaceCSV implements Serializable {
                     addItem(lineRead);
                 }
             }
-        } finally {
+        }
-            if (input != null) {
+        finally
+        {
+            if (input != null)
+            {
                 input.close();
             }
         }
@@ -272,7 +225,8 @@ public class DSpaceCSV implements Serializable {
     /**
      * Initialise this class with values from dspace.cfg
      */
-    protected void init() {
+    private void init()
+    {
         // Set the value separator
         setValueSeparator();
 
@@ -283,28 +237,28 @@ public class DSpaceCSV implements Serializable {
         setAuthoritySeparator();
 
         // Create the headings
-        headings = new ArrayList<>();
+        headings = new ArrayList<String>();
 
         // Create the blank list of items
-        lines = new ArrayList<>();
+        lines = new ArrayList<DSpaceCSVLine>();
 
         // Initialise the counter
         counter = 0;
 
         // Set the metadata fields to ignore
-        ignore = new HashMap<>();
+        ignore = new HashMap<String, String>();
-
+        String toIgnore = ConfigurationManager.getProperty("bulkedit", "ignore-on-export");
-        // Specify default values
+        if ((toIgnore == null) || ("".equals(toIgnore.trim())))
-        String[] defaultValues =
+        {
-            new String[] {
+            // Set a default value
-                "dc.date.accessioned, dc.date.available, dc.date.updated, dc.description.provenance"
+            toIgnore = "dc.date.accessioned, dc.date.available, " +
-            };
+                       "dc.date.updated, dc.description.provenance";
-        String[] toIgnoreArray =
+        }
-            DSpaceServicesFactory.getInstance()
+        String[] toIgnoreArray = toIgnore.split(",");
-                                 .getConfigurationService()
+        for (String toIgnoreString : toIgnoreArray)
-                                 .getArrayProperty("bulkedit.ignore-on-export", defaultValues);
+        {
-        for (String toIgnoreString : toIgnoreArray) {
+            if (!"".equals(toIgnoreString.trim()))
-            if (!"".equals(toIgnoreString.trim())) {
+            {
                 ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
             }
         }
@@ -332,13 +286,16 @@ public class DSpaceCSV implements Serializable {
      *
      * If not set, defaults to double pipe '||'
      */
-    private void setValueSeparator() {
+    private void setValueSeparator()
+    {
         // Get the value separator
-        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+        valueSeparator = ConfigurationManager.getProperty("bulkedit", "valueseparator");
-                                              .getProperty("bulkedit.valueseparator");
+        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim())))
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim()))) {
+        {
             valueSeparator = valueSeparator.trim();
-        } else {
+        }
+        else
+        {
             valueSeparator = "||";
         }
 
@@ -358,22 +315,32 @@ public class DSpaceCSV implements Serializable {
      * Special values are 'tab', 'hash' and 'semicolon' which will
      * get substituted from the text to the value.
      */
-    private void setFieldSeparator() {
+    private void setFieldSeparator()
+    {
         // Get the value separator
-        fieldSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+        fieldSeparator = ConfigurationManager.getProperty("bulkedit", "fieldseparator");
-                                              .getProperty("bulkedit.fieldseparator");
+        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim())))
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim()))) {
+        {
             fieldSeparator = fieldSeparator.trim();
-            if ("tab".equals(fieldSeparator)) {
+            if ("tab".equals(fieldSeparator))
+            {
                 fieldSeparator = "\t";
-            } else if ("semicolon".equals(fieldSeparator)) {
+            }
+            else if ("semicolon".equals(fieldSeparator))
+            {
                 fieldSeparator = ";";
-            } else if ("hash".equals(fieldSeparator)) {
+            }
+            else if ("hash".equals(fieldSeparator))
+            {
                 fieldSeparator = "#";
-            } else {
+            }
+            else
+            {
                 fieldSeparator = fieldSeparator.trim();
             }
-        } else {
+        }
+        else
+        {
             fieldSeparator = ",";
         }
 
@@ -390,13 +357,16 @@ public class DSpaceCSV implements Serializable {
      *
      * If not set, defaults to double colon '::'
      */
-    private void setAuthoritySeparator() {
+    private void setAuthoritySeparator()
+    {
         // Get the value separator
-        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+        authoritySeparator = ConfigurationManager.getProperty("bulkedit", "authorityseparator");
-                                                  .getProperty("bulkedit.authorityseparator");
+        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim())))
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim()))) {
+        {
             authoritySeparator = authoritySeparator.trim();
-        } else {
+        }
+        else
+        {
             authoritySeparator = "::";
         }
 
@@ -410,15 +380,11 @@ public class DSpaceCSV implements Serializable {
      * Add a DSpace item to the CSV file
      *
      * @param i The DSpace item
+     *
      * @throws Exception if something goes wrong with adding the Item
      */
-    public final void addItem(Item i) throws Exception {
+    public final void addItem(Item i) throws Exception
-        // If the item does not have an "owningCollection" the the below "getHandle()" call will fail
+    {
-        // This should not happen but is here for safety.
-        if (i.getOwningCollection() == null) {
-            return;
-        }
-
         // Create the CSV line
         DSpaceCSVLine line = new DSpaceCSVLine(i.getID());
 
@@ -427,43 +393,48 @@ public class DSpaceCSV implements Serializable {
         line.add("collection", owningCollectionHandle);
 
         // Add in any mapped collections
-        List<Collection> collections = i.getCollections();
+        Collection[] collections = i.getCollections();
-        for (Collection c : collections) {
+        for (Collection c : collections)
+        {
             // Only add if it is not the owning collection
-            if (!c.getHandle().equals(owningCollectionHandle)) {
+            if (!c.getHandle().equals(owningCollectionHandle))
+            {
                 line.add("collection", c.getHandle());
             }
         }
 
         // Populate it
-        List<MetadataValue> md = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
+        DCValue md[] = i.getMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (MetadataValue value : md) {
+        for (DCValue value : md)
-            MetadataField metadataField = value.getMetadataField();
+        {
-            MetadataSchema metadataSchema = metadataField.getMetadataSchema();
             // Get the key (schema.element)
-            String key = metadataSchema.getName() + "." + metadataField.getElement();
+            String key = value.schema + "." + value.element;
 
             // Add the qualifier if there is one (schema.element.qualifier)
-            if (metadataField.getQualifier() != null) {
+            if (value.qualifier != null)
-                key = key + "." + metadataField.getQualifier();
+            {
+                key = key + "." + value.qualifier;
             }
 
             // Add the language if there is one (schema.element.qualifier[langauge])
             //if ((value.language != null) && (!"".equals(value.language)))
-            if (value.getLanguage() != null) {
+            if (value.language != null)
-                key = key + "[" + value.getLanguage() + "]";
+            {
+                key = key + "[" + value.language + "]";
             }
 
             // Store the item
-            if (exportAll || okToExport(metadataField)) {
+            if (exportAll || okToExport(value))
+            {
                 // Add authority and confidence if authority is not null
-                String mdValue = value.getValue();
+                String mdValue = value.value;
-                if (value.getAuthority() != null && !"".equals(value.getAuthority())) {
+                if (value.authority != null && !"".equals(value.authority))
-                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value
+                {
-                        .getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
+                    mdValue += authoritySeparator + value.authority + authoritySeparator + value.confidence;
                 }
                 line.add(key, mdValue);
-                if (!headings.contains(key)) {
+                if (!headings.contains(key))
+                {
                     headings.add(key);
                 }
             }
@@ -478,10 +449,12 @@ public class DSpaceCSV implements Serializable {
      * @param line The line of elements
      * @throws Exception Thrown if an error occurs when adding the item
      */
-    public final void addItem(String line) throws Exception {
+    public final void addItem(String line) throws Exception
-        // Check to see if the last character is a field separator, which hides the last empty column
+    {
+        // Check to see if the last character is a field separator, which hides the last empy 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 += " ";
@@ -489,17 +462,20 @@ public class DSpaceCSV implements Serializable {
 
         // Split up on field separator
         String[] parts = line.split(escapedFieldSeparator);
-        ArrayList<String> bits = new ArrayList<>();
+        ArrayList<String> bits = new ArrayList<String>();
         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);
@@ -514,8 +490,10 @@ public class DSpaceCSV implements Serializable {
 
         // Deal with quotes around the elements
         int i = 0;
-        for (String part : bits) {
+        for (String part : bits)
-            if ((part.startsWith("\"")) && (part.endsWith("\""))) {
+        {
+            if ((part.startsWith("\"")) && (part.endsWith("\"")))
+            {
                 part = part.substring(1, part.length() - 1);
                 bits.set(i, part);
             }
@@ -524,8 +502,10 @@ public class DSpaceCSV implements Serializable {
 
         // Remove embedded quotes
         i = 0;
-        for (String part : bits) {
+        for (String part : bits)
-            if (part.contains("\"\"")) {
+        {
+            if (part.contains("\"\""))
+            {
                 part = part.replaceAll("\"\"", "\"");
                 bits.set(i, part);
             }
@@ -537,12 +517,18 @@ public class DSpaceCSV implements Serializable {
         DSpaceCSVLine csvLine;
 
         // Is this an existing item, or a new item (where id = '+')
-        if ("+".equals(id)) {
+        if ("+".equals(id))
+        {
             csvLine = new DSpaceCSVLine();
-        } else {
+        }
-            try {
+        else
-                csvLine = new DSpaceCSVLine(UUID.fromString(id));
+        {
-            } catch (NumberFormatException nfe) {
+            try
+            {
+                csvLine = new DSpaceCSVLine(Integer.parseInt(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");
@@ -552,10 +538,13 @@ public class DSpaceCSV implements Serializable {
 
         // Add the rest of the parts
         i = 0;
-        for (String part : bits) {
+        for (String part : bits)
-            if (i > 0) {
+        {
+            if (i > 0)
+            {
                 // Is this a last empty item?
-                if ((last) && (i == headings.size())) {
+                if ((last) && (i == headings.size()))
+                {
                     part = "";
                 }
 
@@ -567,8 +556,10 @@ public class DSpaceCSV implements Serializable {
                 }
                 csvLine.add(headings.get(i - 1), null);
                 String[] elements = part.split(escapedValueSeparator);
-                for (String element : elements) {
+                for (String element : elements)
-                    if ((element != null) && (!"".equals(element))) {
+                {
+                    if ((element != null) && (!"".equals(element)))
+                    {
                         csvLine.add(headings.get(i - 1), element);
                     }
                 }
@@ -584,7 +575,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The lines
      */
-    public final List<DSpaceCSVLine> getCSVLines() {
+    public final List<DSpaceCSVLine> getCSVLines()
+    {
         // Return the lines
         return lines;
     }
@@ -594,20 +586,22 @@ public class DSpaceCSV implements Serializable {
      *
      * @return the array of CSV formatted Strings
      */
-    public final String[] getCSVLinesAsStringArray() {
+    public final String[] getCSVLinesAsStringArray()
+    {
         // Create the headings line
         String[] csvLines = new String[counter + 1];
         csvLines[0] = "id" + fieldSeparator + "collection";
-        List<String> headingsCopy = new ArrayList<>(headings);
+        Collections.sort(headings);
-        Collections.sort(headingsCopy);
+        for (String value : headings)
-        for (String value : headingsCopy) {
+        {
             csvLines[0] = csvLines[0] + fieldSeparator + value;
         }
 
         Iterator<DSpaceCSVLine> i = lines.iterator();
         int c = 1;
-        while (i.hasNext()) {
+        while (i.hasNext())
-            csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
+        {
+            csvLines[c++] = i.next().toCSV(headings);
         }
 
         return csvLines;
@@ -617,9 +611,11 @@ public class DSpaceCSV implements Serializable {
      * Save the CSV file to the given filename
      *
      * @param filename The filename to save the CSV file to
+     *
      * @throws IOException Thrown if an error occurs when writing the file
      */
-    public final void save(String filename) throws IOException {
+    public final void save(String filename) throws IOException
+    {
         // Save the file
         BufferedWriter out = new BufferedWriter(
                              new OutputStreamWriter(
@@ -637,14 +633,16 @@ public class DSpaceCSV implements Serializable {
      *
      * The list can be configured via the key ignore-on-export in bulkedit.cfg
      *
-     * @param md The Metadatum to examine
+     * @param md The DCValue to examine
      * @return Whether or not it is OK to export this element
      */
-    protected boolean okToExport(MetadataField md) {
+    private final boolean okToExport(DCValue md)
+    {
         // Now compare with the list to ignore
-        String key = md.getMetadataSchema().getName() + "." + md.getElement();
+        String key = md.schema + "." + md.element;
-        if (md.getQualifier() != null) {
+        if (md.qualifier != null)
-            key += "." + md.getQualifier();
+        {
+            key += "." + md.qualifier;
         }
         if (ignore.get(key) != null) {
             return false;
@@ -659,7 +657,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The headings
      */
-    public List<String> getHeadings() {
+    public List<String> getHeadings()
+    {
         return headings;
     }
 
@@ -668,22 +667,15 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The formatted String as a csv
      */
-    @Override
+    public final String toString()
-    public final String toString() {
+    {
         // Return the csv as one long string
-        StringBuilder csvLines = new StringBuilder();
+        StringBuffer csvLines = new StringBuffer();
         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;
-    }
 }

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

@@ -9,78 +9,44 @@ package org.dspace.app.bulkedit;
 
 import java.io.Serializable;
 import java.util.ArrayList;
-import java.util.Comparator;
+import java.util.HashMap;
 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 {
+public class DSpaceCSVLine implements Serializable
-    /**
+{
-     * The item id of the item represented by this line. -1 is for a new item
+    /** The item id of the item represented by this line. -1 is for a new item */
-     */
+    private int id;
-    private final UUID id;
 
-    /**
+    /** The elements in this line in a hashtable, keyed by the metadata type */
-     * The elements in this line in a hashtable, keyed by the metadata type
+    private Map<String, ArrayList> items;
-     */
-    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(UUID itemId) {
+    public DSpaceCSVLine(int itemId)
+    {
         // Store the ID + separator, and initialise the hashtable
         this.id = itemId;
-        items = new TreeMap<>(headerComparator);
+        items = new HashMap<String, ArrayList>();
-//        this.items = new HashMap<String, ArrayList>();
     }
 
     /**
      * Create a new CSV line for a new item
      */
-    public DSpaceCSVLine() {
+    public DSpaceCSVLine()
-        // Set the ID to be null, and initialise the hashtable
+    {
-        this.id = null;
+        // Set the ID to be -1, and initialise the hashtable
-        this.items = new TreeMap<>(headerComparator);
+        this.id = -1;
+        this.items = new HashMap<String, ArrayList>();
     }
 
     /**
@@ -88,7 +54,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return The item ID
      */
-    public UUID getID() {
+    public int getID()
+    {
         // Return the ID
         return id;
     }
@@ -99,14 +66,17 @@ public class DSpaceCSVLine implements Serializable {
      * @param key The metadata key (e.g. dc.contributor.author)
      * @param value The metadata value
      */
-    public void add(String key, String value) {
+    public void add(String key, String value)
+    {
         // Create the array list if we need to
-        if (items.get(key) == null) {
+        if (items.get(key) == null)
+        {
             items.put(key, new ArrayList<String>());
         }
 
         // Store the item if it is not null
-        if (value != null) {
+        if (value != null)
+        {
             items.get(key).add(value);
         }
     }
@@ -117,7 +87,8 @@ public class DSpaceCSVLine implements Serializable {
      * @param key The metadata key
      * @return All the elements that match
      */
-    public List<String> get(String key) {
+    public List<String> get(String key)
+    {
         // Return any relevant values
         return items.get(key);
     }
@@ -127,7 +98,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return The action (may be blank, 'withdraw', 'reinstate' or 'delete')
      */
-    public String getAction() {
+    public String getAction()
+    {
         if (items.containsKey("action")) {
             ArrayList actions = items.get("action");
             if (actions.size() > 0) {
@@ -142,7 +114,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return An enumeration of all the keys
      */
-    public Set<String> keys() {
+    public Set<String> keys()
+    {
         // Return the keys
         return items.keySet();
     }
@@ -151,23 +124,24 @@ 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, String fieldSeparator, String valueSeparator) {
+    protected String toCSV(List<String> headings)
+    {
         StringBuilder bits = new StringBuilder();
 
         // Add the id
-        bits.append("\"").append(id).append("\"").append(fieldSeparator);
+        bits.append("\"").append(id).append("\"").append(DSpaceCSV.fieldSeparator);
-        bits.append(valueToCSV(items.get("collection"), valueSeparator));
+        bits.append(valueToCSV(items.get("collection")));
 
         // Add the rest of the elements
-        for (String heading : headings) {
+        for (String heading : headings)
-            bits.append(fieldSeparator);
+        {
+            bits.append(DSpaceCSV.fieldSeparator);
             List<String> values = items.get(heading);
-            if (values != null && !"collection".equals(heading)) {
+            if (values != null && !"collection".equals(heading))
-                bits.append(valueToCSV(values, valueSeparator));
+            {
+                bits.append(valueToCSV(values));
             }
         }
 
@@ -178,26 +152,32 @@ 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, String valueSeparator) {
+    protected String valueToCSV(List<String> values)
+    {
         // 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) {
+            for (String value : values)
-                if (str.length() > 0) {
+            {
-                    str.append(valueSeparator);
+                if (str.length() > 0)
+                {
+                    str.append(DSpaceCSV.valueSeparator);
                 }
 
                 str.append(value);

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

@@ -7,51 +7,29 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.sql.SQLException;
+import org.apache.commons.cli.*;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
 
-import com.google.common.collect.Iterators;
+import org.dspace.content.*;
-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.factory.HandleServiceFactory;
+import org.dspace.handle.HandleManager;
+
+import java.util.ArrayList;
+import java.sql.SQLException;
+import java.util.List;
 
 /**
  * Metadata exporter to allow the batch export of metadata into a file
  *
  * @author Stuart Lewis
  */
-public class MetadataExport {
+public class MetadataExport
-    /**
+{
-     * The items to export
+    /** The items to export */
-     */
+    private ItemIterator toExport;
-    protected Iterator<Item> toExport;
 
-    protected ItemService itemService;
+    /** Whether to export all metadata, or just normally edited metadata */
-
+    private boolean exportAll;
-    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
@@ -60,13 +38,11 @@ public class MetadataExport {
      * @param toExport The ItemIterator of items to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll) {
+    public MetadataExport(Context c, ItemIterator toExport, boolean exportAll)
-        itemService = ContentServiceFactory.getInstance().getItemService();
+    {
-
         // Store the export settings
         this.toExport = toExport;
         this.exportAll = exportAll;
-        this.context = c;
     }
 
     /**
@@ -76,15 +52,16 @@ public class MetadataExport {
      * @param toExport The Community to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Community toExport, boolean exportAll) {
+    public MetadataExport(Context c, Community toExport, boolean exportAll)
-        itemService = ContentServiceFactory.getInstance().getItemService();
+    {
-
+        try
-        try {
+        {
             // Try to export the community
-            this.toExport = buildFromCommunity(c, toExport, 0);
+            this.toExport = new ItemIterator(c, buildFromCommunity(toExport, new ArrayList<Integer>(), 0));
             this.exportAll = exportAll;
-            this.context = c;
+        }
-        } catch (SQLException sqle) {
+        catch (SQLException sqle)
+        {
             // Something went wrong...
             System.err.println("Error running exporter:");
             sqle.printStackTrace(System.err);
@@ -95,47 +72,48 @@ 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 if database error
+     * @throws SQLException
      */
-    protected Iterator<Item> buildFromCommunity(Context context, Community community, int indent)
+    private List<Integer> buildFromCommunity(Community community, List<Integer> itemIDs, int indent)
-        throws SQLException {
+                                                                               throws SQLException
+    {
         // Add all the collections
-        List<Collection> collections = community.getCollections();
+        Collection[] collections = community.getCollections();
-        Iterator<Item> result = null;
+        for (Collection collection : collections)
-        for (Collection collection : collections) {
+        {
-            for (int i = 0; i < indent; i++) {
+            for (int i = 0; i < indent; i++)
+            {
                 System.out.print(" ");
             }
 
-            Iterator<Item> items = itemService.findByCollection(context, collection);
+            ItemIterator items = collection.getAllItems();
-            result = addItemsToResult(result, items);
+            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);
                 }
+            }
+        }
+
         // Add all the sub-communities
-        List<Community> communities = community.getSubcommunities();
+        Community[] communities = community.getSubcommunities();
-        for (Community subCommunity : communities) {
+        for (Community subCommunity : communities)
-            for (int i = 0; i < indent; i++) {
+        {
+            for (int i = 0; i < indent; i++)
+            {
                 System.out.print(" ");
             }
-            Iterator<Item> items = buildFromCommunity(context, subCommunity, indent + 1);
+            buildFromCommunity(subCommunity, itemIDs, indent + 1);
-            result = addItemsToResult(result, items);
         }
 
-        return result;
+        return itemIDs;
-    }
-
-    private Iterator<Item> addItemsToResult(Iterator<Item> result, Iterator<Item> items) {
-        if (result == null) {
-            result = items;
-        } else {
-            result = Iterators.concat(result, items);
-        }
-
-        return result;
     }
 
     /**
@@ -143,26 +121,22 @@ public class MetadataExport {
      *
      * @return the exported CSV lines
      */
-    public DSpaceCSV export() {
+    public DSpaceCSV export()
-        try {
+    {
-            Context.Mode originalMode = context.getCurrentMode();
+        try
-            context.setMode(Context.Mode.READ_ONLY);
+        {
-
             // Process each item
             DSpaceCSV csv = new DSpaceCSV(exportAll);
-            while (toExport.hasNext()) {
+            while (toExport.hasNext())
-                Item item = toExport.next();
+            {
-                csv.addItem(item);
+                csv.addItem(toExport.next());
-                context.uncacheEntity(item);
             }
 
-            context.setMode(originalMode);
             // Return the results
             return csv;
-        } catch (Exception e) {
+        }
-            // Something went wrong...
+        catch (Exception e)
-            System.err.println("Error exporting to CSV:");
+        {
-            e.printStackTrace();
             return null;
         }
     }
@@ -173,7 +147,8 @@ public class MetadataExport {
      * @param options The command line options the user gave
      * @param exitCode the system exit code to use
      */
-    private static void printHelp(Options options, int exitCode) {
+    private static void printHelp(Options options, int exitCode)
+    {
         // print the help message
         HelpFormatter myhelp = new HelpFormatter();
         myhelp.printHelp("MetadataExport\n", options);
@@ -186,9 +161,9 @@ 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();
 
@@ -196,70 +171,83 @@ 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,
+        options.addOption("a", "all", false, "include all metadata fields that are not normally changed (e.g. provenance)");
-                          "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.Mode.READ_ONLY);
+        Context c = new Context();
         c.turnOffAuthorisationSystem();
 
         // The things we'll export
-        Iterator<Item> toExport = null;
+        ItemIterator toExport = null;
         MetadataExport exporter = null;
 
         // Export everything?
         boolean exportAll = line.hasOption('a');
 
-        ContentServiceFactory contentServiceFactory = ContentServiceFactory.getInstance();
         // Check we have an item OK
-        ItemService itemService = contentServiceFactory.getItemService();
+        if (!line.hasOption('i'))
-        if (!line.hasOption('i')) {
+        {
             System.out.println("Exporting whole repository WARNING: May take some time!");
-            exporter = new MetadataExport(c, itemService.findAll(c), exportAll);
+            exporter = new MetadataExport(c, Item.findAll(c), exportAll);
-        } else {
+        }
+        else
+        {
             String handle = line.getOptionValue('i');
-            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, handle);
+            DSpaceObject dso = HandleManager.resolveToObject(c, handle);
-            if (dso == null) {
+            if (dso == null)
+            {
                 System.err.println("Item '" + handle + "' does not resolve to an item in your repository!");
                 printHelp(options, 1);
             }
 
-            if (dso.getType() == Constants.ITEM) {
+            if (dso.getType() == Constants.ITEM)
+            {
                 System.out.println("Exporting item '" + dso.getName() + "' (" + handle + ")");
-                List<Item> item = new ArrayList<>();
+                List<Integer> item = new ArrayList<Integer>();
-                item.add((Item) dso);
+                item.add(dso.getID());
-                exporter = new MetadataExport(c, item.iterator(), exportAll);
+                exporter = new MetadataExport(c, new ItemIterator(c, item), exportAll);
-            } else if (dso.getType() == Constants.COLLECTION) {
+            }
+            else if (dso.getType() == Constants.COLLECTION)
+            {
                 System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
                 Collection collection = (Collection)dso;
-                toExport = itemService.findByCollection(c, collection);
+                toExport = collection.getAllItems();
                 exporter = new MetadataExport(c, toExport, exportAll);
-            } else if (dso.getType() == Constants.COMMUNITY) {
+            }
+            else if (dso.getType() == Constants.COMMUNITY)
+            {
                 System.out.println("Exporting community '" + dso.getName() + "' (" + handle + ")");
                 exporter = new MetadataExport(c, (Community)dso, exportAll);
-            } else {
+            }
+            else
+            {
                 System.err.println("Error identifying '" + handle + "'");
                 System.exit(1);
             }

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

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

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

@@ -12,40 +12,27 @@ package org.dspace.app.bulkedit;
  *
  * @author Stuart Lewis
  */
-public class MetadataImportInvalidHeadingException extends Exception {
+public class MetadataImportInvalidHeadingException extends Exception
-    /**
+{
-     * The type of error (schema or element)
+    /** 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;
 
 
@@ -54,9 +41,9 @@ 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;
@@ -68,7 +55,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      *  @return the type of the exception
      */
-    public String getType() {
+    public String getType()
+    {
         return "" + type;
     }
 
@@ -77,7 +65,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      * @return the invalid heading
      */
-    public String getBadHeader() {
+    public String getBadHeader()
+    {
         return badHeading;
     }
 
@@ -86,7 +75,8 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      * @return the invalid column number
      */
-    public int getColumn() {
+    public int getColumn()
+    {
         return column;
     }
 
@@ -95,16 +85,20 @@ public class MetadataImportInvalidHeadingException extends Exception {
      *
      * @return The exception message
      */
-    @Override
+    public String getMessage()
-    public String getMessage() {
+    {
-        if (type == SCHEMA) {
+        if (type == SCHEMA)
-            return "Unknown metadata schema in column " + column + ": " + badHeading;
+        {
-        } else if (type == ELEMENT) {
+            return "Unknown metadata schema in row " + column + ": " + badHeading;
-            return "Unknown metadata element in column " + column + ": " + badHeading;
+        } else if (type == ELEMENT)
-        } else if (type == MISSING) {
+        {
-            return "Row with missing header: column " + column;
+            return "Unknown metadata element in row " + column + ": " + badHeading;
-        } else {
+        } else if (type == MISSING)
-            return "Bad metadata declaration in column" + column + ": " + badHeading;
+        {
+            return "Row with missing header: Row " + column;
+        } else
+        {
+            return "Bad metadata declaration in row " + column + ": " + badHeading;
         }
     }
 }

dspace-api/src/main/java/org/dspace/app/bulkedit/package-info.java

@@ -1,21 +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/
- */
-
-/**
- * <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;
-
-

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

@@ -8,12 +8,10 @@
 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;
@@ -25,43 +23,42 @@ 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.
+ * documentation for the main method.</p>
  * 
  * @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>
@@ -80,11 +77,9 @@ public final class ChecksumChecker {
      *            <dt>-p</dt>
      *            <dd>Don't prune results before running checker</dd>
      *            </dl>
-     *
-     * @param args the command line arguments given
-     * @throws SQLException if error
      */
-    public static void main(String[] args) throws SQLException {
+    public static void main(String[] args)
+    {
         // set up command line parser
         CommandLineParser parser = new PosixParser();
         CommandLine line = null;
@@ -108,37 +103,42 @@ 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(context, line.getOptionValue('p')) : ResultsPruner
+                        .getPruner(line.getOptionValue('p')) : ResultsPruner
-                        .getDefaultPruner(context);
+                        .getDefaultPruner();
-                } catch (FileNotFoundException e) {
+            }
+            catch (FileNotFoundException e)
+            {
                 LOG.error("File not found", e);
                 System.exit(1);
             }
@@ -153,55 +153,77 @@ public final class ChecksumChecker {
         
         // process should loop infinitely through
         // most_recent_checksum table
-            if (line.hasOption('l')) {
+        if (line.hasOption('l'))
-                dispatcher = new SimpleDispatcher(context, processStart, false);
+        {
-            } else if (line.hasOption('L')) {
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, false); 
-                dispatcher = new SimpleDispatcher(context, processStart, true);
+        }
-            } else if (line.hasOption('b')) {
+        else if (line.hasOption('L'))
+        {
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true);
+        }
+        else if (line.hasOption('b'))
+        {
             // check only specified bitstream(s)
             String[] ids = line.getOptionValues('b');
-                List<Bitstream> bitstreams = new ArrayList<>(ids.length);
+            List<Integer> idList = new ArrayList<Integer>(ids.length);
 
-                for (int i = 0; i < ids.length; i++) {
+            for (int i = 0; i < ids.length; i++)
-                    try {
+            {
-                        bitstreams.add(bitstreamService.find(context, UUID.fromString(ids[i])));
+                try
-                    } catch (NumberFormatException nfe) {
+                {
+                    idList.add(Integer.valueOf(ids[i]));
+                }
+                catch (NumberFormatException nfe)
+                {
                     System.err.println("The following argument: " + ids[i]
                             + " is not an integer");
                     System.exit(0);
                 }
             }
-                dispatcher = new IteratorDispatcher(bitstreams.iterator());
+            dispatcher = new ListDispatcher(idList);
-            } else if (line.hasOption('a')) {
+        }
-                dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
+
-            } else if (line.hasOption('d')) {
+        else if (line.hasOption('a'))
+        {
+            dispatcher = new HandleDispatcher(new BitstreamInfoDAO(), line.getOptionValue('a'));
+        }
+        else if (line.hasOption('d'))
+        {
             // run checker process for specified duration
-                try {
+            try
+            {
                 dispatcher = new LimitedDurationDispatcher(
-                        new SimpleDispatcher(context, processStart, true), new Date(
+                        new SimpleDispatcher(new BitstreamInfoDAO(), 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'));
+        else if (line.hasOption('c'))
+        {
+        	int count = Integer.valueOf(line.getOptionValue('c')).intValue();
             
         	// run checker process for specified number of bitstreams
             dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
-                    context, processStart, false), count);
+                    new BitstreamInfoDAO(), processStart, false), count);
-            } else {
+        }
+        else
+        {
             dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
-                    context, processStart, false), 1);
+                    new BitstreamInfoDAO(), processStart, false), 1);
         }
         
         ResultsLogger logger = new ResultsLogger(processStart);
-            CheckerCommand checker = new CheckerCommand(context);
+        CheckerCommand checker = new CheckerCommand();
         // verbose reporting
-            if (line.hasOption('v')) {
+        if (line.hasOption('v'))
+        {
             checker.setReportVerbose(true);
         }
 
@@ -209,13 +231,7 @@ public final class ChecksumChecker {
         checker.setDispatcher(dispatcher);
         checker.setCollector(logger);
         checker.process();
-            context.complete();
+        System.exit(0);
-            context = null;
-        } finally {
-            if (context != null) {
-                context.abort();
-            }
-        }
     }
 
     /**
@@ -223,19 +239,24 @@ public final class ChecksumChecker {
      * 
      * @param options that are available for the user
      */
-    private static void printHelp(Options options) {
+    private static void printHelp(Options options)
+    {
         HelpFormatter myhelp = new HelpFormatter();
 
         myhelp.printHelp("Checksum Checker\n", options);
-        System.out.println("\nSpecify a duration for checker process, using s(seconds),"
+        System.out
+                .println("\nSpecify a duration for checker process, using s(seconds),"
                         + "m(minutes), or h(hours): ChecksumChecker -d 30s"
                         + " OR ChecksumChecker -d 30m"
                         + " OR ChecksumChecker -d 2h");
-        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
+        System.out
+                .println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
         System.out.println("\nLoop once through all bitstreams: "
                 + "ChecksumChecker -l");
-        System.out.println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
+        System.out
-        System.out.println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
+                .println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
+        System.out
+                .println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
         System.out.println("\nReport all processing (verbose)(default reports only errors): ChecksumChecker -v");
         System.out.println("\nDefault (no arguments) is equivalent to '-c 1'");
         System.exit(0);

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

@@ -7,14 +7,16 @@
  */
 package org.dspace.app.configuration;
 
-import java.io.File;
-import java.net.MalformedURLException;
-
 import org.dspace.kernel.config.SpringLoader;
 import org.dspace.services.ConfigurationService;
 
+import java.io.File;
+import java.net.MalformedURLException;
+
 /**
- * @author Kevin Van de Velde (kevin at atmire dot com)
+ * User: kevin (kevin at atmire.com)
+ * Date: 3-aug-2011
+ * Time: 11:31:21
  */
 public class APISpringLoader implements SpringLoader {
 

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

@@ -9,9 +9,7 @@ package org.dspace.app.harvest;
 
 import java.io.IOException;
 import java.sql.SQLException;
-import java.util.Iterator;
 import java.util.List;
-import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
@@ -19,39 +17,30 @@ 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.factory.ContentServiceFactory;
+import org.dspace.content.ItemIterator;
-import org.dspace.content.service.CollectionService;
+import org.dspace.harvest.OAIHarvester;
-import org.dspace.content.service.ItemService;
+import org.dspace.harvest.OAIHarvester.HarvestingException;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.handle.HandleManager;
-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;
 	
-    private static final HarvestedCollectionService harvestedCollectionService =
+    public static void main(String[] argv) throws Exception
-        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();
 
@@ -67,19 +56,12 @@ public class Harvest {
         options.addOption("P", "purge", false, "purge all harvestable collections");
         
 
-        options.addOption("e", "eperson", true,
+        options.addOption("e", "eperson", true, "eperson");
-                          "eperson");
+        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
-        options.addOption("c", "collection", true,
+        options.addOption("t", "type", true, "type of harvesting (0 for none)");
-                          "harvesting collection (handle or id)");
+        options.addOption("a", "address", true, "address of the OAI-PMH server");
-        options.addOption("t", "type", true,
+        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
-                          "type of harvesting (0 for none)");
+        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("a", "address", true,
-                          "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true,
-                          "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true,
-                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
-                              "crosswalk in dspace.cfg");
 
         options.addOption("h", "help", false, "help");
 
@@ -93,21 +75,27 @@ public class Harvest {
         String metadataKey = null;
         int harvestType = 0;
         
-        if (line.hasOption('h')) {
+        if (line.hasOption('h'))
+        {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("Harvest\n", options);
-            System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
+            System.out
-            System.out.println(
+    				.println("\nPING OAI server: Harvest -g -s oai_source -i oai_set_id");
-                "RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a " +
+            System.out
-                    "oai_source -i oai_set_id -m metadata_format");
+					.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(
+            System.out
-                "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
+                    .println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
-                    "oai_set_id -m metadata_format");
+            System.out
-            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
+            		.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out.println("START harvest scheduler: Harvest -S");
+            System.out
-            System.out.println("RESET all harvest status: Harvest -R");
+    				.println("START harvest scheduler: Harvest -S");
-            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
+            System.out
-            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
+					.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);
@@ -163,17 +151,21 @@ public class Harvest {
 
         // Instantiate our class
         Harvest harvester = new Harvest();
-        harvester.context = new Context(Context.Mode.BATCH_EDIT);
+        harvester.context = new Context();
         
         
         // Check our options
-        if (command == null) {
+        if (command == null)
+        {
             System.out
                     .println("Error - no parameters specified (run with -h flag for details)");
             System.exit(1);
-        } else if ("run".equals(command)) {
+        }
         // Run a single harvest cycle on a collection using saved settings.
-            if (collection == null || eperson == null) {
+        else if ("run".equals(command))
+        {
+            if (collection == null || eperson == null)
+            {
                 System.out
                         .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -181,33 +173,41 @@ public class Harvest {
             }
             
             harvester.runHarvest(collection, eperson);
-        } else if ("start".equals(command)) {
+        }
         // start the harvest loop
+        else if ("start".equals(command))
+        {
         	startHarvester();
-        } else if ("reset".equals(command)) {
+        }
         // reset harvesting status
+        else if ("reset".equals(command))
+        {
         	resetHarvesting();
-        } else if ("purgeAll".equals(command)) {
+        }
         // purge all collections that are set up for harvesting (obviously for testing purposes only)
-            if (eperson == null) {
+        else if ("purgeAll".equals(command))
+        {
+        	if (eperson == null)
+            {
                 System.out
                         .println("Error - an eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
         	
-            List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
+        	List<Integer> cids = HarvestedCollection.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
+        	System.out.println("Purging the following collections (deleting items and resetting harvest status): " + cids.toString());
-                System.out.println(
+	    	for (Integer cid : cids) 
-                    "Purging the following collections (deleting items and resetting harvest status): " +
+	    	{
-                        harvestedCollection
+	    		harvester.purgeCollection(cid.toString(), eperson);
-                            .getCollection().getID().toString());
-                harvester.purgeCollection(harvestedCollection.getCollection().getID().toString(), eperson);
 	    	}
 	    	context.complete();
-        } else if ("purge".equals(command)) {
+        }
         // Delete all items in a collection. Useful for testing fresh harvests.
-            if (collection == null || eperson == null) {
+        else if ("purge".equals(command))
+        {
+            if (collection == null || eperson == null)
+            {
                 System.out
                         .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -218,34 +218,39 @@ public class Harvest {
             context.complete();
             
             //TODO: implement this... remove all items and remember to unset "last-harvested" settings
-        } else if ("config".equals(command)) {
+        }
         // Configure a collection with the three main settings 
-            if (collection == null) {
+        else if ("config".equals(command))
+        {
+            if (collection == null)
+            {
                 System.out.println("Error -  a target collection must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (oaiSource == null || oaiSetID == null) {
+            if (oaiSource == null || oaiSetID == null)
+            {
                 System.out.println("Error - both the OAI server address and OAI set id must be specified");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (metadataKey == null) {
+            if (metadataKey == null)
-                System.out
+            {
-                    .println("Error - a metadata key (commonly the prefix) must be specified for this collection");
+            	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);
         }
     }
     
@@ -260,30 +265,39 @@ public class Harvest {
     	
     	try {
 	    	// is the ID a handle?
-            if (collectionID != null) {
+	        if (collectionID != null)
-                if (collectionID.indexOf('/') != -1) {
+            {
+                if (collectionID.indexOf('/') != -1)
+                {
                     // string has a / so it must be a handle - try and resolve it
-                    dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, collectionID);
+                    dso = HandleManager.resolveToObject(context, collectionID);
 
                     // resolved, now make sure it's a collection
-                    if (dso == null || dso.getType() != Constants.COLLECTION) {
+                    if (dso == null || dso.getType() != Constants.COLLECTION)
+                    {
                         targetCollection = null;
-                    } else {
+                    }
+                    else
+                    {
                         targetCollection = (Collection) dso;
                     }
-                } else {
+                }
-                    // not a handle, try and treat it as an integer collection database ID
+                // not a handle, try and treat it as an integer collection
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer
+                // database ID
-                        .parseInt(collectionID) + "', " + "in context: " + context);
+                else
-                    targetCollection = collectionService.find(context, UUID.fromString(collectionID));
+                {
+                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer.parseInt(collectionID) + "', " + "in context: " + context);
+                    targetCollection = Collection.find(context, Integer.parseInt(collectionID));
                 }
             }
             // was the collection valid?
-            if (targetCollection == null) {
+            if (targetCollection == null)
+            {
                 System.out.println("Cannot resolve " + collectionID + " to collection");
                 System.exit(1);
             }
-        } catch (SQLException se) {
+    	}
+    	catch (SQLException se) {
     		se.printStackTrace();
     	}
     	
@@ -291,31 +305,33 @@ public class Harvest {
     }
     
     
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId,
+    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) {
-                                     String mdConfigId) {
     	System.out.println("Running: configure collection");
    	
     	Collection collection = resolveCollection(collectionID);
     	System.out.println(collection.getID());
     	    	
     	try {
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
         	if (hc == null) {
-                hc = harvestedCollectionService.create(context, collection);
+        		hc = HarvestedCollection.create(context, collection.getID());
         	}
     		
     		context.turnOffAuthorisationSystem();
     		hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
     		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-            harvestedCollectionService.update(context, hc);
+    		hc.update();
     		context.restoreAuthSystemState();
     		context.complete();
-        } catch (Exception e) {
+    	} 
+    	catch (Exception e) {
     		System.out.println("Changes could not be committed");
     		e.printStackTrace();
     		System.exit(1);
-        } finally {
+    	}
-            if (context != null) {
+    	finally {
+            if (context != null)
+            {
     		    context.restoreAuthSystemState();
             }
     	}
@@ -329,45 +345,47 @@ public class Harvest {
      * @param email
      */
     private void purgeCollection(String collectionID, String email) {
-        System.out.println(
+    	System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
-            "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
     	Collection collection = resolveCollection(collectionID);
    	
-        try {
+    	try 
-            EPerson eperson = ePersonService.findByEmail(context, email);
+    	{
+    		EPerson eperson = EPerson.findByEmail(context, email);
         	context.setCurrentUser(eperson);
     		context.turnOffAuthorisationSystem();
     		
-            ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    		ItemIterator it = collection.getAllItems();
-            Iterator<Item> it = itemService.findByCollection(context, collection);
+    		IndexBrowse ib = new IndexBrowse(context);
     		int i=0;
     		while (it.hasNext()) {
     			i++;
     			Item item = it.next();
     			System.out.println("Deleting: " + item.getHandle());
-                collectionService.removeItem(context, collection, item);
+    			ib.itemRemoved(item);
-                context.uncacheEntity(item);// Dispatch events every 50 items
+    			collection.removeItem(item);
+    			// commit every 50 items
     			if (i%50 == 0) {
-                    context.dispatchEvents();
+    				context.commit();
     				i=0;
     			}
     		}
     		
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
     		if (hc != null) {
-                hc.setLastHarvested(null);
+	    		hc.setHarvestResult(null,"");
-                hc.setHarvestMessage("");
 	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
 	    		hc.setHarvestStartTime(null);
-                harvestedCollectionService.update(context, hc);
+	    		hc.update();
     		}
     		context.restoreAuthSystemState();    		
-            context.dispatchEvents();
+    		context.commit();
-        } catch (Exception e) {
+    	} 
+    	catch (Exception e) {
     		System.out.println("Changes could not be committed");
     		e.printStackTrace();
     		System.exit(1);
-        } finally {
+    	}
+    	finally {
     		context.restoreAuthSystemState();
     	}
     }
@@ -383,10 +401,11 @@ public class Harvest {
     	OAIHarvester harvester = null;
     	try {
     		Collection collection = resolveCollection(collectionID);
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+        	HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
     		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);
@@ -398,87 +417,67 @@ public class Harvest {
     	    	
     	try {
     		// Harvest will not work for an anonymous user
-            EPerson eperson = ePersonService.findByEmail(context, email);
+        	EPerson eperson = EPerson.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
+     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the harvested_collections table 
-     * harvested_collections table
      */
     private static void resetHarvesting() {
     	System.out.print("Resetting harvest status flag on all collections... ");
     	
-        try {
+    	try 
-            List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
+    	{
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
+	    	List<Integer> cids = HarvestedCollection.findAll(context);
+	    	for (Integer cid : cids) 
+	    	{
+	    		HarvestedCollection hc = HarvestedCollection.find(context, cid);
 	    		//hc.setHarvestResult(null,"");
-                harvestedCollection.setHarvestStartTime(null);
+	    		hc.setHarvestStartTime(null);
-                harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
+	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-                harvestedCollectionService.update(context, harvestedCollection);
+	    		hc.update();
 	    	}
+	    	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() {
+    private static void startHarvester() 
-        try {
+    {
+	    try 
+	    {
 	    	System.out.print("Starting harvest loop... ");
-            HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
+	    	OAIHarvester.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);
-            }
-        }
-    }
 }

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

@@ -1,246 +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.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();
-    }
-}

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

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

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

@@ -1,27 +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.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);
-    }
-}

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

@@ -1,28 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.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;
-    }
-}

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

@@ -1,270 +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.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;
-
-}

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

@@ -1,106 +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.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;
-    }
-}

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

@@ -1,229 +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.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;
-    }
-}

dspace-api/src/main/java/org/dspace/app/itemimport/DataLoaderService.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.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;
+    }
+    
+}

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

@@ -1,431 +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.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);
-    }
-}

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

@@ -1,27 +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.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);
-    }
-}

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

@@ -1,28 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.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;
-    }
-}

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

@@ -1,253 +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.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);
-}

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

@@ -1,93 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.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;
-    }
-}

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

@@ -1,49 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.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;
-    }
-}

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

@@ -1,23 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.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;
-}

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

@@ -1,56 +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.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;
-    }
-}

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

@@ -1,64 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.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;
-    }
-}

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

@@ -16,25 +16,21 @@ 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> {
 	
-    protected Map<Class<? extends UpdateAction>, UpdateAction> registry
+	private 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);
 		}
@@ -43,9 +39,11 @@ public class ActionManager implements Iterable<UpdateAction> {
 	}
 	
 	/**
+	 * 
 	 * @return whether any actions have been registered with this manager
 	 */
-    public boolean hasActions() {
+	public boolean hasActions()
+	{
 		return !registry.isEmpty();
 	}
 	
@@ -55,24 +53,25 @@ public class ActionManager implements Iterable<UpdateAction> {
 	 * 
 	 * @return iterator for UpdateActions
 	 */
-    @Override
+	public Iterator<UpdateAction> iterator()
-    public Iterator<UpdateAction> iterator() {
+	{
-        return new Iterator<UpdateAction>() {
+		return new Iterator<UpdateAction>() 
+		{ 			
 			private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
 			
-            @Override
+			public boolean hasNext()
-            public boolean hasNext() {
+			{
 				return itr.hasNext();
 			}
 			
-            @Override
+			public UpdateAction next()
-            public UpdateAction next() {
+			{
 				return registry.get(itr.next());
 			}
 			
 			//not supported
-            @Override
+			public void remove()
-            public void remove() {
+			{
 				throw new UnsupportedOperationException();
 			}
 		};

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

@@ -17,59 +17,54 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.authorize.factory.AuthorizeServiceFactory;
+import org.dspace.authorize.AuthorizeManager;
-import org.dspace.authorize.service.AuthorizeService;
+import org.dspace.authorize.ResourcePolicy;
 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 {
 
-    protected AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
+	public AddBitstreamsAction()
-    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      DSpace Context
+	 *  @param context
-     * @param itarch       Item Archive
+	 *  @param itarch
-     * @param isTest       test flag
+	 *  @param isTest
-     * @param suppressUndo undo flag
+	 *  @param suppressUndo
-     * @throws IOException              if IO error
+	 *  @throws IllegalArgumentException
-     * @throws IllegalArgumentException if arg exception
+	 *  @throws ParseException
-     * @throws SQLException             if database error
+	 *  @throws IOException
-     * @throws AuthorizeException       if authorization error
+	 *  @throws AuthorizeException
-     * @throws ParseException           if parse error
+	 *  @throws SQLException
 	 */
-    @Override
 	public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws IllegalArgumentException,
-        ParseException, IOException, AuthorizeException, SQLException {
+            ParseException, IOException, AuthorizeException, SQLException 
+	{
 		Item item = itarch.getItem();
 		File dir = itarch.getDirectory();
 		
 		List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
 		
-        if (contents.isEmpty()) {
+		if (contents.isEmpty())
+		{
 			ItemUpdate.pr("Contents is empty - no bitstreams to add");
 			return;
 		}
@@ -78,59 +73,32 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 		
 		String[] files = dir.list(ItemUpdate.fileFilter);
 		List<String> fileList = new ArrayList<String>();
-        for (String filename : files) {
+		for (String filename : files)
+		{
 			fileList.add(filename);
 			ItemUpdate.pr("file: " + filename);
 		}
 		
-        for (ContentsEntry ce : contents) {
+		for (ContentsEntry ce : contents)
+		{
 			//validate match to existing file in archive
-            if (!fileList.contains(ce.filename)) {
+			if (!fileList.contains(ce.filename))
+			{
 				throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
 			}
 		}
-        int bitstream_bundles_updated = 0;
 						
 		//now okay to add
-        for (ContentsEntry ce : contents) {
+		for (ContentsEntry ce : contents)
-            String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
+		{        				
-            if (!targetBundleName.equals("")
+			addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
-                && !targetBundleName.equals("THUMBNAIL")
-                && !targetBundleName.equals("TEXT")) {
-                bitstream_bundles_updated++;
 		}
 	}
 		
-        if (alterProvenance && bitstream_bundles_updated > 0) {
+	private void addBitstream(Context context, ItemArchive itarch, Item item, File dir, 
-            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);
     	
@@ -140,29 +108,40 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
         Bitstream bs = null;
         String newBundleName = ce.bundlename;
 
-        if (ce.bundlename == null) { // should be required but default convention established
+        if (ce.bundlename == null)  // should be required but default convention established
-            if (ce.filename.equals("license.txt")) {
+        {
+            if (ce.filename.equals("license.txt"))
+            {
                 newBundleName = "LICENSE";
-            } else {
+            }
+            else  
+            {
                 newBundleName = "ORIGINAL";
             }
         }
         ItemUpdate.pr("  Bitstream " + ce.filename + " to be added to bundle: " + newBundleName);
         
-        if (!isTest) {
+        if (!isTest)
+        {
 	        // find the bundle
-            List<Bundle> bundles = itemService.getBundles(item, newBundleName);
+	        Bundle[] bundles = item.getBundles(newBundleName);
 	        Bundle targetBundle = null;
 	
-            if (bundles.size() < 1) {
+	        if (bundles.length < 1)
+	        {
 	            // not found, create a new one
-                targetBundle = bundleService.create(context, item, newBundleName);
+	            targetBundle = item.createBundle(newBundleName);
-            } else {
+	        }
+	        else
+	        {
 	    		//verify bundle + name are not duplicates
-                for (Bundle b : bundles) {
+	        	for (Bundle b : bundles)
-                    List<Bitstream> bitstreams = b.getBitstreams();
+	        	{
-                    for (Bitstream bsm : bitstreams) {
+	        		Bitstream[] bitstreams = b.getBitstreams();
-                        if (bsm.getName().equals(ce.filename)) {
+	        		for (Bitstream bsm : bitstreams)
+	        		{
+	        			if (bsm.getName().equals(ce.filename))
+	        			{
 	        				throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: " 
 	        						+ b.getName() + " + " + bsm.getName());
 	        			}
@@ -170,39 +149,55 @@ public class AddBitstreamsAction extends UpdateBitstreamsAction {
 	        	}
 
 	            // select first bundle
-                targetBundle = bundles.iterator().next();
+	            targetBundle = bundles[0];
 	        }
 	
-            bs = bitstreamService.create(context, targetBundle, bis);
+	        bs = targetBundle.createBitstream(bis);	
-            bs.setName(context, ce.filename);
+	        bs.setName(ce.filename);
 	
 	        // Identify the format
 	        // FIXME - guessing format guesses license.txt incorrectly as a text file format!
-            BitstreamFormat fmt = bitstreamFormatService.guessFormat(context, bs);
+	        BitstreamFormat fmt = FormatIdentifier.guessFormat(context, bs);
-            bitstreamService.setFormat(context, bs, fmt);
+	    	bs.setFormat(fmt);
 	    	
-            if (ce.description != null) {
+	        if (ce.description != null)
-                bs.setDescription(context, ce.description);
+	        {
+	        	bs.setDescription(ce.description);
 	        }
 	        	        
-            if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null)) {
+	        if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null))
-                Group group = groupService.findByName(context, ce.permissionsGroupName);
+	        {
+				Group group = Group.findByName(context, ce.permissionsGroupName);
 				
-                if (group != null) {
+				if (group != null)
-                    authorizeService.removeAllPolicies(context, bs);  // remove the default policy
+				{
-                    authorizeService.createResourcePolicy(context, bs, group, null, ce.permissionsActionId, null);
+			        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();
 				}
 	        }
 	        
-            //update after all changes are applied
+	        if (alterProvenance && !targetBundle.getName().equals("THUMBNAIL") 
-            bitstreamService.update(context, bs);
+	        		&& !targetBundle.getName().equals("TEXT"))
+	        {
+	        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
 	        	
-            if (!suppressUndo) {
+	        	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)
+	        {
 	        	itarch.addUndoDeleteContents(bs.getID());
 	        }
-            return targetBundle.getName();
         }
-        return "";
     }
 
 }

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

@@ -8,101 +8,104 @@
 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      DSpace Context
+	 *  @param context
-     * @param itarch       item archive
+	 *  @param itarch
-     * @param isTest       test flag
+	 *  @param isTest
-     * @param suppressUndo undo flag
+	 *  @param suppressUndo
-     * @throws AuthorizeException if authorization error
+	 *  @throws AuthorizeException
-     * @throws SQLException       if database error
+	 *  @throws SQLException
 	 */
-    @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 (DtoMetadata dtom : itarch.getMetadataFields())
-            for (String f : targetFields) {
+		{
-                if (dtom.matches(f, false)) {
+			for (String f : targetFields)
+			{
+				if (dtom.matches(f, false))
+				{
 					// match against metadata for this field/value in repository
 					// qualifier must be strictly matched, possibly null					
-                    List<MetadataValue> ardcv = null;
+					DCValue[] ardcv = null;
-                    ardcv = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+					ardcv = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
 					
 					boolean found = false;
-                    for (MetadataValue dcv : ardcv) {
+					for (DCValue dcv : ardcv)
-                        if (dcv.getValue().equals(dtom.value)) {
+					{
+						if (dcv.value.equals(dtom.value))
+						{
 							found = true;
 							break;
 						}
 					}
 					
-                    if (found) {
+					if (found)
+					{
 						ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname 
 								+ " for element " + f);						
-                    } else {
+					}
-                        if (isTest) {
+					else
+					{
+						if (isTest)
+						{
 							ItemUpdate.pr("Metadata to add: " + dtom.toString());
 							   //validity tests that would occur in actual processing
 	        	            // If we're just test the import, let's check that the actual metadata field exists.
-                            MetadataSchema foundSchema = metadataSchemaService.find(context, dtom.schema);
+	        	        	MetadataSchema foundSchema = MetadataSchema.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 " +
+	        	        			+ dtom.schema + "' was not found in the registry; found on item " + dirname);
-                                                  dirname);
+	        	        	}
-                            } else {
+	        	        	else
-                                MetadataField foundField = metadataFieldService
+	        	        	{
-                                    .findByElement(context, foundSchema, dtom.element, dtom.qualifier);
+		        	        	int schemaID = foundSchema.getSchemaID();
+		        	        	MetadataField foundField = MetadataField.findByElement(context, schemaID, 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 " +
+		        	        				+ dtom.qualifier + "' not found in registry; found on item " + dirname);
-                                                      dirname);
 		        	            }		
 	        				}						
-                        } else {
+						}
-                            itemService
+						else
-                                .addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language,
+						{
-                                             dtom.value);
+							item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, dtom.value);
 							ItemUpdate.pr("Metadata added: " + dtom.toString());
 	
-                            if (!suppressUndo) {
+							if (!suppressUndo)
+							{
 								//itarch.addUndoDtom(dtom);
 								//ItemUpdate.pr("Undo metadata: " + dtom);
 								
 								// add all as a replace record to be preceded by delete
-                                for (MetadataValue dcval : ardcv) {
+								for (DCValue dcval : ardcv)
-                                    MetadataField metadataField = dcval.getMetadataField();
+								{							
-                                    MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+									itarch.addUndoMetadataField(DtoMetadata.create(dcval.schema, dcval.element, 
-                                    itarch.addUndoMetadataField(
+											dcval.qualifier, dcval.language, dcval.value));
-                                        DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
-                                                           metadataField.getQualifier(), dcval.getLanguage(),
-                                                           dcval.getValue()));
 								}
 								
 							}

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

@@ -7,17 +7,17 @@
  */
 package org.dspace.app.itemupdate;
 
-import java.io.FileInputStream;
 import java.io.IOException;
-import java.io.InputStream;
 import java.util.Properties;
-
+import java.io.InputStream;
+import java.io.FileInputStream;
 import org.dspace.content.Bitstream;
 
 /**
  *   Filter interface to be used by ItemUpdate 
  *   to determine which bitstreams in an Item
  *   acceptable for removal.
+ *
  */
 public abstract class BitstreamFilter {
 
@@ -26,27 +26,33 @@ public abstract class BitstreamFilter {
 	/**
 	 *  The filter method 
 	 *  
-     * @param bitstream Bitstream
+	 * @param bitstream
 	 * @return whether the bitstream matches the criteria
-     * @throws BitstreamFilterException if filter error
+	 * @throws BitstreamFilterException
 	 */
 	public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;
 	
 	/**
+	 * 
 	 * @param filepath - The complete path for the properties file
-     * @throws IOException if IO error
+	 * @throws IOException
 	 */
 	public void initProperties(String filepath)
-        throws IOException {
+	throws IOException
+	{
 		props = new Properties();
 		
 		InputStream in = null;
 
-        try {
+        try
+        {
             in = new FileInputStream(filepath);
             props.load(in);
-        } finally {
+        }
-            if (in != null) {
+        finally
+        {
+            if (in != null)
+            {
                 in.close();
             }
         }

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

@@ -8,47 +8,56 @@
 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 Bitstream
+	 *    @param bitstream
+	 *    @throws BitstreamFilterException
 	 *    @return whether bitstream is in bundle
-     * @throws BitstreamFilterException if filter error
+	 *    
 	 */
-    @Override
 	public boolean accept(Bitstream bitstream) 
-        throws BitstreamFilterException {
+	throws BitstreamFilterException
-        if (bundleName == null) {
+	{
+		if (bundleName == null)
+		{
 			bundleName = props.getProperty("bundle");
-            if (bundleName == null) {
+			if (bundleName == null)
+			{
 				throw new BitstreamFilterException("Property 'bundle' not found.");
 			}			
 		}
 		
-        try {
+		try
-            List<Bundle> bundles = bitstream.getBundles();
+		{
-            for (Bundle b : bundles) {
+			Bundle[] bundles = bitstream.getBundles();
-                if (b.getName().equals(bundleName)) {
+			for (Bundle b : bundles)
+			{
+				if (b.getName().equals(bundleName))
+				{
 					return true;
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

@@ -7,20 +7,21 @@
  */
 package org.dspace.app.itemupdate;
 
-import java.util.regex.Matcher;
+import java.util.regex.*;
-import java.util.regex.Pattern;
 
 import org.dspace.content.Bitstream;
 
 /**
  * BitstreamFilter implementation to filter by filename pattern
+ *
  */
 public class BitstreamFilterByFilename extends BitstreamFilter {
 	
-    protected Pattern pattern;
+	private Pattern pattern;
-    protected String filenameRegex;
+	private String filenameRegex;
 	
-    public BitstreamFilterByFilename() {
+	public BitstreamFilterByFilename()
+	{
 		//empty
 	}
 
@@ -28,15 +29,15 @@ 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
 	 */
-    @Override
+	public boolean accept(Bitstream bitstream) throws BitstreamFilterException
-    public boolean accept(Bitstream bitstream) throws BitstreamFilterException {
+	{		
-        if (filenameRegex == null) {
+		if (filenameRegex == null)
+		{
 			filenameRegex = props.getProperty("filename");
-            if (filenameRegex == null) {
+			if (filenameRegex == null)
+			{
 				throw new BitstreamFilterException("BitstreamFilter property 'filename' not found.");
 			}
 			pattern = Pattern.compile(filenameRegex);

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

@@ -9,25 +9,20 @@ 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() {}
-    }
+	public BitstreamFilterException(String msg)
-
+	{
-    /**
-     * @param msg exception message
-     */
-    public BitstreamFilterException(String msg) {
 		super(msg);
 	}
-
+	public BitstreamFilterException(Exception e)
-    /**
+	{
-     * @param e exception
-     */
-    public BitstreamFilterException(Exception e) {
 		super(e);
 	}
 	

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

@@ -8,8 +8,7 @@
 package org.dspace.app.itemupdate;
 
 import java.text.ParseException;
-import java.util.regex.Matcher;
+import java.util.regex.*;
-import java.util.regex.Pattern;
 
 import org.dspace.core.Constants;
 
@@ -22,13 +21,14 @@ 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:";
@@ -41,11 +41,12 @@ public class ContentsEntry {
 	final int permissionsActionId;
 	final String description;
 	
-    protected ContentsEntry(String filename,
+	private ContentsEntry(String filename, 
 			             String bundlename,
 			             int permissionsActionId,
 			             String permissionsGroupName,
-                            String description) {
+			             String description)
+	{
 		this.filename = filename;
 		this.bundlename = bundlename;
 		this.permissionsActionId = permissionsActionId;
@@ -56,12 +57,13 @@ public class ContentsEntry {
 	/**
 	 *   Factory method parses a line from the Contents Entry file
 	 *   
-     * @param line line as string
+	 * @param line
 	 * @return the parsed ContentsEntry object 
-     * @throws ParseException if parse error
+	 * @throws ParseException
 	 */
 	public static ContentsEntry parse(String line)
-        throws ParseException {
+	throws ParseException
+	{
 		String[] ar = line.split("\t");
 		ItemUpdate.pr("ce line split: " + ar.length);
 		
@@ -71,33 +73,46 @@ public class ContentsEntry {
 		String groupName = null;
 		int actionId = -1;
 
-        if (ar.length > 1) {
+		if (ar.length > 1)
-            for (int i = 1; i < ar.length; i++) {
+		{
+			for (int i=1; i < ar.length; i++)
+			{
 				ItemUpdate.pr("ce " + i + " : " + ar[i]);
-                if (ar[i].startsWith(HDR_BUNDLE)) {
+				if (ar[i].startsWith(HDR_BUNDLE))
+				{
 					arp[1] = ar[i].substring(HDR_BUNDLE.length()).trim();
 					
-                } else if (ar[i].startsWith(HDR_PERMISSIONS)) {
+				}
+				else if (ar[i].startsWith(HDR_PERMISSIONS))
+				{
 					arp[2] = ar[i].substring(HDR_PERMISSIONS.length()).trim();
 					
 					// parse into actionId and group name
 					
 					Matcher m = permissionsPattern.matcher(arp[2]);
-                    if (m.matches()) {
+					if (m.matches())
+					{
 						String action = m.group(1); //
-                        if (action.equals("r")) {
+						if (action.equals("r"))
+						{
 							 actionId = Constants.READ;
-                        } else if (action.equals("w")) {
+						}
+						else if (action.equals("w"))
+						{
 							 actionId = Constants.WRITE;
 						}
 						
 						groupName = m.group(2).trim();
 					}
 					
-                } else if (ar[i].startsWith(HDR_DESCRIPTION)) {
+				}
+				else if (ar[i].startsWith(HDR_DESCRIPTION))
+				{
 					arp[3] = ar[i].substring(HDR_DESCRIPTION.length()).trim();
 					
-                } else {
+				}
+				else
+				{
 					throw new ParseException("Unknown text in contents file: " + ar[i], 0);				
 				}			
 			}
@@ -105,23 +120,30 @@ public class ContentsEntry {
 		return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
 	}
 	
-    public String toString() {
+	public String toString()
+	{
 		StringBuilder sb = new StringBuilder(filename);
-        if (bundlename != null) {
+		if (bundlename != null)
+		{
 			sb.append(HDR_BUNDLE).append(" ").append(bundlename);
 		}
 		
-        if (permissionsGroupName != null) {
+		if (permissionsGroupName != null)
+		{
 			sb.append(HDR_PERMISSIONS);
-            if (permissionsActionId == Constants.READ) {
+			if (permissionsActionId == Constants.READ)
+			{
 				sb.append(" -r ");
-            } else if (permissionsActionId == Constants.WRITE) {
+			}
+			else if (permissionsActionId == Constants.WRITE)
+			{
 				sb.append(" -w ");
 			}
 			sb.append(permissionsGroupName);
 		}
 		
-        if (description != null) {
+		if (description != null)
+		{
 			sb.append(HDR_DESCRIPTION).append(" ").append(description);
 		}		
 		

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

@@ -26,64 +26,84 @@ 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      DSpace Context
+	 *  @param context
-     * @param itarch       item archive
+	 *  @param itarch
-     * @param isTest       test flag
+	 *  @param isTest
-     * @param suppressUndo undo flag
+	 *  @param suppressUndo
-     * @throws IOException              if IO error
+	 *  @throws IllegalArgumentException
-     * @throws IllegalArgumentException if arg exception
+	 *  @throws ParseException
-     * @throws SQLException             if database error
+	 *  @throws IOException
-     * @throws AuthorizeException       if authorization error
+	 *  @throws AuthorizeException
-     * @throws ParseException           if parse error
+	 *  @throws SQLException
 	 */
-    @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<String> list = MetadataUtilities.readDeleteContentsFile(f);
+		else
-            if (list.isEmpty()) {
+		{
+			List<Integer> list = MetadataUtilities.readDeleteContentsFile(f);
+			if (list.isEmpty())
+			{
 				ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName() );
-            } else {
+			}
-                for (String id : list) {
+			else
-                    try {
+			{
-                        Bitstream bs = bitstreamService.findByIdOrLegacyId(context, id);
+				for (int id : list)
-                        if (bs == null) {
+				{
+					try
+					{
+			    		Bitstream bs = Bitstream.find(context, id);
+			    		if (bs == null)
+			    		{
 			    			ItemUpdate.pr("Bitstream not found by id: " + id);
-                        } else {
+			    		}
-                            List<Bundle> bundles = bs.getBundles();
+			    		else
-                            for (Bundle b : bundles) {
+			    		{
-                                if (isTest) {
+				    		Bundle[] bundles = bs.getBundles();
+				    		for (Bundle b : bundles)
+				    		{
+				    			if (isTest)
+				    			{
 					    			ItemUpdate.pr("Delete bitstream with id = " + id);
-                                } else {
+				    			}
-                                    bundleService.removeBitstream(context, b, bs);
+				    			else
+				    			{
+				    				b.removeBitstream(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
+				            	String append = "Bitstream " + bs.getName() + " deleted on " + DCDate.getCurrent() + "; ";
-                                    .getCurrent() + "; ";
+				            	Item item = bundles[0].getItems()[0];
-                                Item item = bundles.iterator().next().getItems().iterator().next();
 					    		ItemUpdate.pr("Append provenance with: " + append);
 					    		
-                                if (!isTest) {
+					    		if (!isTest)
-                                    MetadataUtilities.appendMetadata(context, item, dtom, false, append);
+					    		{
+					    			MetadataUtilities.appendMetadata(item, dtom, false, append);
 					    		}
 				            }
 			    		}	
-                    } catch (SQLException e) {
+					}
+					catch(SQLException e)
+					{
 						ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
 					}
 				}

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

@@ -28,67 +28,77 @@ 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 {
 
-    protected BitstreamFilter filter;
+	private BitstreamFilter filter;
 	
 	/**
 	 *   Set filter
 	 *   
-     * @param filter BitstreamFilter
+	 * @param filter
 	 */
-    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      DSpace Context
+	 *  @param context
-     * @param itarch       item archive
+	 *  @param itarch
-     * @param isTest       test flag
+	 *  @param isTest
-     * @param suppressUndo undo flag
+	 *  @param suppressUndo
-     * @throws IOException              if IO error
+	 *  @throws IllegalArgumentException
-     * @throws SQLException             if database error
+	 *  @throws ParseException
-     * @throws AuthorizeException       if authorization error
+	 *  @throws IOException
-     * @throws ParseException           if parse error
+	 *  @throws AuthorizeException
-     * @throws BitstreamFilterException if filter error
+	 *  @throws SQLException
 	 */
-    @Override
 	public void execute(Context context, ItemArchive itarch, boolean isTest,
             boolean suppressUndo) throws AuthorizeException,
-        BitstreamFilterException, IOException, ParseException, SQLException {
+            BitstreamFilterException, IOException, ParseException, SQLException 
+	{
 		
 		List<String> deleted = new ArrayList<String>();
 		
 		Item item = itarch.getItem();
-        List<Bundle> bundles = item.getBundles();
+		Bundle[] bundles = item.getBundles();
 		
-        for (Bundle b : bundles) {
+		for (Bundle b : bundles)    
-            List<Bitstream> bitstreams = b.getBitstreams();
+		{
+			Bitstream[] bitstreams = b.getBitstreams();
 			String bundleName = b.getName();
 			
-            for (Bitstream bs : bitstreams) {
+			for (Bitstream bs : bitstreams)
-                if (filter.accept(bs)) {
+			{		
-                    if (isTest) {
+			    if (filter.accept(bs))
+				{
+	    			if (isTest)
+	    			{
 		    			ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName() 
 		    					+ " with id = " + bs.getID());
-                    } else {
+	    			}
+	    			else
+	    			{	    					    				
 	    				//provenance is not maintained for derivative bitstreams
-                        if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT")) {
+	    				if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT"))
+	    				{
 	    					deleted.add(bs.getName());
 	    				}
-                        bundleService.removeBitstream(context, b, bs);
+	    				b.removeBitstream(bs); 
 		    			ItemUpdate.pr("Deleted " + bundleName + " bitstream " + bs.getName() 
 		    					+ " with id = " + bs.getID());		    			
 	    			}
@@ -96,11 +106,13 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
 			}			
 		}
 		
-        if (alterProvenance && !deleted.isEmpty()) {
+        if (alterProvenance && !deleted.isEmpty())
+        {     	
     		StringBuilder sb = new StringBuilder("  Bitstreams deleted on "); 	
     		sb.append(DCDate.getCurrent()).append(": ");
     		
-            for (String s : deleted) {
+    		for (String s : deleted)
+    		{
             	sb.append(s).append(", ");
     		}
     		        	
@@ -108,8 +120,9 @@ public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
         	
     		ItemUpdate.pr("Append provenance with: " + sb.toString());
     		
-            if (!isTest) {
+    		if (!isTest)
-                MetadataUtilities.appendMetadata(context, item, dtom, false, sb.toString());
+    		{
+    			MetadataUtilities.appendMetadata(item, dtom, false, sb.toString());
     		}
         }
 	}

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

@@ -7,58 +7,57 @@
  */
 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      DSpace Context
+	 *  @param context
-     * @param itarch       Item Archive
+	 *  @param itarch
-     * @param isTest       test flag
+	 *  @param isTest
-     * @param suppressUndo undo flag
+	 *  @param suppressUndo
-     * @throws SQLException       if database error
+	 *  @throws ParseException
-     * @throws AuthorizeException if authorization error
+	 *  @throws AuthorizeException
-     * @throws ParseException     if parse error
 	 */
-    @Override
 	public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException, ParseException, SQLException {
+            boolean suppressUndo) throws AuthorizeException, ParseException 
+	{
 		Item item = itarch.getItem();
-        for (String f : targetFields) {
+		for (String f : targetFields)
+		{
 			DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
-            List<MetadataValue> ardcv = itemService.getMetadataByMetadataString(item, f);
+			DCValue[] ardcv = item.getMetadata(f);
 
 			ItemUpdate.pr("Metadata to be deleted: ");
-            for (MetadataValue dcv : ardcv) {
+			for (DCValue dcv : ardcv)
+			{
 				ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
 			}
 
-            if (!isTest) {
+			if (!isTest)
-                if (!suppressUndo) {
+			{
-                    for (MetadataValue dcv : ardcv) {
+				if (!suppressUndo)
-                        MetadataField metadataField = dcv.getMetadataField();
+				{
-                        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+					for (DCValue dcv : ardcv)
-                        itarch.addUndoMetadataField(
+					{
-                            DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
+						itarch.addUndoMetadataField(DtoMetadata.create(dcv.schema, dcv.element, 
-                                               metadataField.getQualifier(), dcv.getLanguage(), dcv.getValue()));
+								dcv.qualifier, dcv.language, dcv.value));					
 					}
 				}
 				
-                itemService.clearMetadata(context, item, dummy.schema, dummy.element, dummy.qualifier, Item.ANY);
+				item.clearMetadata(dummy.schema, dummy.element, dummy.qualifier, Item.ANY);	
 			}
 		}
 	}

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

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

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

@@ -8,7 +8,6 @@
 package org.dspace.app.itemupdate;
 
 import java.text.ParseException;
-
 import org.dspace.content.Item;
 
 /**
@@ -17,19 +16,22 @@ import org.dspace.content.Item;
  *   
  *   Adds some utility methods
  *   
- * Really not at all general enough but supports Dublin Core and the compound form notation {@code <schema>
+ *   Really not at all general enough but supports Dublin Core and the compound form notation <schema>.<element>[.<qualifier>]
- * .<element>[.<qualifier>]}
  *   
  *   Does not support wildcard for qualifier
+ * 
+ *
  */
-class DtoMetadata {
+class DtoMetadata 
+{
 	final String schema;   
 	final String element;
 	final String qualifier;
 	final String language;
 	final String value;
 	
-    protected DtoMetadata(String schema, String element, String qualifier, String language, String value) {
+	private DtoMetadata(String schema, String element, String qualifier, String language, String value) 
+	{
 		this.schema = schema;
 		this.element = element;
 		this.qualifier = qualifier;
@@ -40,21 +42,23 @@ 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     value
+	 * @param 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 {
+	throws IllegalArgumentException
-        if ((qualifier != null) && (qualifier.equals(Item.ANY) || qualifier.equals(""))) {
+    {
+		if ((qualifier != null) &&  (qualifier.equals(Item.ANY) || qualifier.equals("")))
+		{
 			throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
 		}
 		return new DtoMetadata(schema, element, qualifier, language, value);
@@ -63,18 +67,19 @@ class DtoMetadata {
 	/**
 	 *   Factory method to create metadata object
 	 *   
+	 * 
 	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>]
 	 * @param language   null or empty
-     * @param value        value
+	 * @param 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];
 		}
 		
@@ -85,44 +90,56 @@ class DtoMetadata {
 	 *   Determine if this metadata field matches the specified type:
 	 *    schema.element or schema.element.qualifier
 	 *    
+	 * 
 	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>|.*]
 	 * @param wildcard       allow wildcards in compoundForm param
 	 * @return whether matches
 	 */
-    public boolean matches(String compoundForm, boolean wildcard) {
+	public boolean matches(String compoundForm, boolean wildcard)
+	{
 		String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
 		
-        if ((ar.length < 2) || (ar.length > 3)) {
+		if ((ar.length < 2) || (ar.length > 3))
+		{
 			return false;
 		}
 		
-        if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1])) {
+		if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1]))
+		{
 			return false;
 		}
 		
-        if (ar.length == 2) {
+		if (ar.length == 2)
-            if (this.qualifier != null) {
+		{
+			if (this.qualifier != null)
+			{
 				return false;
 			}
 		}
 		
-        if (ar.length == 3) {
+		if (ar.length == 3)	
-            if (this.qualifier == null) {
+		{
+			if (this.qualifier == null)
+			{
 				return false;
 			}
-            if (wildcard && ar[2].equals(Item.ANY)) {
+			if (wildcard && ar[2].equals(Item.ANY))
+			{
 				return true;
 			}
-            if (!this.qualifier.equals(ar[2])) {
+			if (!this.qualifier.equals(ar[2]))
+			{
 				return false;
 			}
 		}
 		return true;		
 	}
 	
-    public String toString() {
+	public String toString()
+	{
 		String s =  "\tSchema: " + schema + " Element: " + element;
-        if (qualifier != null) {
+		if (qualifier != null)
+		{
 			s+= " Qualifier: " + qualifier;
 		}
 		s+= " Language: " + ((language == null) ? "[null]" : language);
@@ -131,7 +148,8 @@ class DtoMetadata {
         return s;
 	}
 	
-    public String getValue() {
+	public String getValue()
+	{
 		return value;
 	}
 		

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

@@ -10,70 +10,64 @@ 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.FileWriter;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.io.PrintWriter;
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
-import java.util.UUID;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
+import javax.xml.transform.TransformerConfigurationException;
 
 import org.apache.log4j.Logger;
-import org.dspace.app.util.LocalSchemaFilenameFilter;
+import org.dspace.content.ItemIterator;
 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.factory.HandleServiceFactory;
+import org.dspace.handle.HandleManager;
-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";
 	
-    protected static DocumentBuilder builder = null;
+    private static DocumentBuilder builder = null;
-    protected Transformer transformer = null;
+    private static Transformer transformer = null;
    
-    protected List<DtoMetadata> dtomList = null;
+	private List<DtoMetadata> dtomList = null; 
-    protected List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
+	private List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
 	
-    protected List<UUID> undoAddContents = new ArrayList<>(); // for undo of add
+	private List<Integer> undoAddContents = new ArrayList<Integer>(); // for undo of add
 	
-    protected Item item;
+	private Item item;
-    protected File dir;  // directory name in source archive for this item
+	private File dir;  // directory name in source archive for this item
-    protected String dirname; //convenience
+	private String dirname; //convenience
-
-    protected HandleService handleService;
-    protected ItemService itemService;
 	
 //constructors
-    protected ItemArchive() {
+	private ItemArchive() 
-        handleService = HandleServiceFactory.getInstance().getHandleService();
+	{
-        itemService = ContentServiceFactory.getInstance().getItemService();
+		// nothing
 	}	
 	
-    /**
+/** factory method
-     * factory method
  * 
  * 	Minimal requirements for dublin_core.xml for this application
  *  is the presence of dc.identifier.uri
@@ -83,40 +77,40 @@ 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 {
+        finally
-            if (is != null) {
+        {
+            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);
 		}
 		
@@ -125,23 +119,21 @@ public class ItemArchive {
 		return itarch;
 	}
 		
-    protected static DocumentBuilder getDocumentBuilder()
+	private static DocumentBuilder getDocumentBuilder()
-        throws ParserConfigurationException {
+	throws ParserConfigurationException
-        if (builder == null) {
+	{
+		if (builder == null)
+		{
 		    builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
 		}
 		return builder;
 	}
 	
-    /**
+	private static Transformer getTransformer()
-     * Getter for Transformer
+	throws TransformerConfigurationException
-     *
+	{
-     * @return Transformer
+		if (transformer == null)
-     * @throws TransformerConfigurationException if config error
+		{
-     */
-    protected Transformer getTransformer()
-        throws TransformerConfigurationException {
-        if (transformer == null) {
 		    transformer = TransformerFactory.newInstance().newTransformer();
 		}
 		return transformer;
@@ -149,55 +141,55 @@ 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(UUID bitstreamId) {
+	public void addUndoDeleteContents(int bitstreamId)
+	{
 		this.undoAddContents.add(bitstreamId);
 	}
 	
@@ -208,14 +200,13 @@ 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"); 
     	}
     	
@@ -223,17 +214,21 @@ 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 = handleService.resolveToObject(context, handle);
+		DSpaceObject dso = HandleManager.resolveToObject(context, handle);  
-        if (dso instanceof Item) {
+		if (dso instanceof Item)
+		{
 			item =  (Item) dso;
-        } else {
+		}
+		else
+		{
 			ItemUpdate.pr("Warning: item not instantiated");
 			throw new IllegalArgumentException("Item " + handle + " not instantiated.");
 		}	
@@ -244,50 +239,53 @@ public class ItemArchive {
      * 	 Find and instantiate Item from the dublin_core.xml based
      *   on the specified itemField for the item identifier,
      *   
+     * 
      * @param context   - the DSpace context
      * @param itemField - the compound form of the metadata element <schema>.<element>.<qualifier>
-     * @throws SQLException if database error
+     * @throws SQLException
-     * @throws Exception    if error
+     * @throws Exception
      */
     private Item itemFromMetadataField(Context context, String itemField)
-        throws SQLException, AuthorizeException, Exception {
+    throws SQLException, AuthorizeException, Exception
+    {
     	DtoMetadata dtom = getMetadataField(itemField);
     	
     	Item item = null;
     	
-        if (dtom == null) {
+    	if (dtom == null)
+    	{
     		throw new IllegalArgumentException("No field found for item identifier field: " + itemField);
     	}  
     	ItemUpdate.prv("Metadata field to match for item: " + dtom.toString());
 
     	this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
     	
-        Iterator<Item> itr = itemService
+	    ItemIterator itr = Item.findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
-            .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)
-     * Get DtoMetadata field
+    {
-     *
+    	for (DtoMetadata dtom : dtomList)
-     * @param compoundForm compound form
+    	{
-     * @return DtoMetadata field
+			if (dtom.matches(compoundForm, false))
-     */
+			{
-    private DtoMetadata getMetadataField(String compoundForm) {
-        for (DtoMetadata dtom : dtomList) {
-            if (dtom.matches(compoundForm, false)) {
 				return dtom;
 			}
     	}
@@ -297,44 +295,51 @@ 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 (UUID i : undoAddContents) {
+                    for (Integer i : undoAddContents)
+                    {
                         pw.println(i);
                     }
-                } finally {
+                }
+                finally
+                {
                     pw.close();
                 }
             }
-        } finally {
+        }
-            if (out != null) {
+        finally
+        {
+            if (out != null)
+            {
                 out.close();
             }
         }

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

@@ -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;
@@ -20,7 +20,6 @@ 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;
@@ -29,15 +28,12 @@ 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
@@ -62,7 +58,9 @@ import org.dspace.eperson.service.EPersonService;
  *      Some of this has been placed into the MetadataUtilities class
  *      for possible reuse elsewhere. 
  *   
+ * 
  * @author W. Hays based on a conceptual design by R. Rodgers
+ *
  */
 public class ItemUpdate {
 	
@@ -76,44 +74,45 @@ public class ItemUpdate {
 	
 	public static boolean verbose = false;
 	
-    protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
+	static
-    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+	{
-
-    static {
 		filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
-        filterAliases
+		filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
-            .put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
 		filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");		
 		filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");		
 	}
 	          	                
     // File listing filter to check for folders
-    static FilenameFilter directoryFilter = new FilenameFilter() {
+    static FilenameFilter directoryFilter = new FilenameFilter()
-        @Override
+    {
-        public boolean accept(File dir, String n) {
+        public boolean accept(File dir, String n)
+        {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return f.isDirectory();
         }
     };
  
     // File listing filter to check for files (not directories)
-    static FilenameFilter fileFilter = new FilenameFilter() {
+    static FilenameFilter fileFilter = new FilenameFilter()
-        @Override
+    {
-        public boolean accept(File dir, String n) {
+        public boolean accept(File dir, String n)
+        {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return (f.isFile());
         }
     };
 
     // instance variables
-    protected ActionManager actionMgr = new ActionManager();
+    private ActionManager actionMgr = new ActionManager(); 
-    protected List<String> undoActionList = new ArrayList<String>();
+    private List<String> undoActionList = new ArrayList<String>();  
-    protected String eperson;
+    private String eperson;
    
     /**
-     * @param argv the command line arguments given
+     * 
+     * @param argv
      */
-    public static void main(String[] argv) {
+    public static void main(String[] argv)
+    {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -124,23 +123,20 @@ public class ItemUpdate {
         options.addOption("s", "source", true, "root directory of source dspace archive ");
       
     //actions  on items     
-        options.addOption("a", "addmetadata", true,
+        options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'");
-                          "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,
+        Option delBitstreamOption = new Option("D", "deletebitstreams", true, "delete bitstreams as specified for each item");
-                                               "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,
+        options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
-                          "optional metadata field that containing item identifier; default is dc.identifier.uri");
         options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");  
         options.addOption("v", "verbose", false, "verbose logging");
       
@@ -158,10 +154,12 @@ public class ItemUpdate {
         Context context = null;
         ItemUpdate iu = new ItemUpdate();	
 
-        try {
+        try
+        {       
 	        CommandLine line = parser.parse(options, argv);
 	
-            if (line.hasOption('h')) {
+	        if (line.hasOption('h'))
+	        {
 	            HelpFormatter myhelp = new HelpFormatter();
 	            myhelp.printHelp("ItemUpdate", options);
 	            pr("");
@@ -175,79 +173,91 @@ public class ItemUpdate {
 	            System.exit(0);
 	        }
 	        
-            if (line.hasOption('v')) {
+	        if (line.hasOption('v'))
+	        {
 	        	verbose = true;
 	        }
 
  
-            if (line.hasOption('P')) {
+	        if (line.hasOption('P'))
+	        {
 	        	alterProvenance = false;
 	        	pr("Suppressing changes to Provenance field option");
 	        }
 
 	        iu.eperson = line.getOptionValue('e'); // db ID or email
 	        
-            if (!line.hasOption('s')) { // item specific changes from archive dir
+	        if (!line.hasOption('s')) // item specific changes from archive dir
+	        {
 	        	pr("Missing source archive option");
 	        	System.exit(1);
 	        }
 	        String sourcedir = line.getOptionValue('s');
 	        
-            if (line.hasOption('t')) { //test
+        	if (line.hasOption('t'))  //test
+        	{
         		isTest = true;
 	            pr("**Test Run** - not actually updating items.");
        		       	
 	        }
         	
-            if (line.hasOption('i')) {
+        	if (line.hasOption('i'))
+        	{
         		itemField = line.getOptionValue('i');      		
         	}
 
-            if (line.hasOption('d')) {
+	        if (line.hasOption('d'))
+	        {
 	        	String[] targetFields = line.getOptionValues('d'); 
 	        	
-                DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr
+	        	DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
-                    .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
+    			AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class); 
-                    .getUpdateAction(AddMetadataAction.class);
     			addMetadataAction.addTargetFields(targetFields);
         		
         		//undo is a delete followed by an add of a replace record for target fields
-                for (String field : targetFields) {
+	        	for (String field : targetFields)
+	        	{
 	        		iu.undoActionList.add(" -d " + field + " ");
 	        	}
     			
-                for (String field : targetFields) {
+	        	for (String field : targetFields)
+	        	{
 	        		iu.undoActionList.add(" -a " + field + " ");
 	        	}
     			
 	        	pr("Add metadata for fields: ");
-                for (String s : targetFields) {
+	        	for (String s : targetFields)
+	        	{
 	        		pr("    " + s);
 	        	}
         	}
     		
-            if (line.hasOption('D')) { // undo not supported
+	        if (line.hasOption('D'))  // undo not supported 
+	        {
 	        	pr("Delete bitstreams ");
 	        	
 	        	String[] filterNames = line.getOptionValues('D');
-                if ((filterNames != null) && (filterNames.length > 1)) {
+	        	if ((filterNames != null) && (filterNames.length > 1))
+	        	{
 	        		pr("Error: Only one filter can be a used at a time.");
 	        		System.exit(1);
 	        	}
@@ -255,127 +265,138 @@ public class ItemUpdate {
 	        	String filterName = line.getOptionValue('D');
 	        	pr("Filter argument: " + filterName);
 	        	
-                if (filterName == null) { // indicates using delete_contents files
+	        	if (filterName == null)  // indicates using delete_contents files
-                    DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr
+	        	{
-                        .getUpdateAction(DeleteBitstreamsAction.class);
+	        		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
+	        	    if (filterPropertiesName != null)  //not always required
-                        try {
+	        	    {
+	        	    	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: " +
+	        	    	catch(Exception e)
-                                   filterPropertiesName);
+	        	    	{
+		        	    	pr("Error:  Failure finding properties file for bitstream filter class: " + filterPropertiesName);
 		        	    	System.exit(1);
 	        	    	}
 	        	    }
 	        	    
 	        		DeleteBitstreamsByFilterAction delAction = 
-                        (DeleteBitstreamsByFilterAction) iu.actionMgr
+	        			(DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
-                            .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
+        		AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
-                    .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.Mode.BATCH_EDIT);
+	        context = new Context();  
 	        iu.setEPerson(context, iu.eperson);	
-            context.turnOffAuthorisationSystem();
+	        context.setIgnoreAuthorization(true);
 	        
 	    	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
-        } catch (Exception e) {
+	        context.setIgnoreAuthorization(false);
-            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);
         }
@@ -386,73 +407,91 @@ public class ItemUpdate {
         //Undo is suppressed to prevent undo of undo
         boolean suppressUndo = false;
         File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
-        if (fSuppressUndo.exists()) {
+        if (fSuppressUndo.exists())
+        {
         	suppressUndo = true;
         }
 
         File undoDir = null;  //sibling directory of source archive
         
-        if (!suppressUndo && !isTest) {
+    	if (!suppressUndo && !isTest) 
+    	{
     		undoDir = initUndoArchive(sourceDir);	
     	}
         
     	int itemCount = 0;
     	int successItemCount = 0;
     	
-        for (String dirname : dircontents) {
+        for (String dirname : dircontents)
+        {
         	itemCount++;
     		pr("");
     		pr("processing item " + dirname);
     		
-            try {
+    		try
+    		{
 	    		ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
 	    		
-                for (UpdateAction action : actionMgr) {
+	    		for (UpdateAction action : actionMgr)
+	    		{
 	    			pr("action: " + action.getClass().getName());
 	    			action.execute(context, itarch, isTest, suppressUndo);
-                    if (!isTest && !suppressUndo) {
+	    			if (!isTest && !suppressUndo)
+                    {
                         itarch.writeUndo(undoDir);
                     }
 	    		}
-                if (!isTest) {
+	    		if (!isTest)
+	    		{
     				Item item = itarch.getItem();
-                    itemService.update(context, item);  //need to update before commit
+    				item.update();  //need to update before commit
-                    context.uncacheEntity(item);
+    				context.commit();  
+	    			item.decache();
 	    		}
     			ItemUpdate.pr("Item " + dirname + " completed");
     			successItemCount++;
-            } catch (Exception e) {
+    		}
+    		catch(Exception e)
+    		{
     			pr("Exception processing item " + dirname + ": " + e.toString());
                 e.printStackTrace();
     		}
         }  
         
-        if (!suppressUndo && !isTest) {
+        if (!suppressUndo && !isTest)
+        {        	     	
         	StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
         	sb.append(" -e ").append(this.eperson);
         	sb.append(" -s ").append(undoDir);
         	
-            if (itemField != null) {
+        	if (itemField != null)
+        	{
         		sb.append(" -i ").append(itemField);
         	}
         	
-            if (!alterProvenance) {
+         	if (!alterProvenance)
+        	{
         		sb.append(" -P ");
         	}
-            if (isTest) {
+        	if (isTest)
+        	{
         		sb.append(" -t ");
         	}
         	
-            for (String actionOption : undoActionList) {
+        	for (String actionOption : undoActionList)
+        	{
         		sb.append(actionOption);
         	}   
         	
         	PrintWriter pw = null;
-            try {
+        	try
+        	{
                	File cmdFile = new File (undoDir.getParent(), undoDir.getName() + "_command.sh");
 	        	pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
 	        	pw.println(sb.toString());
-            } finally {
+        	}
+        	finally
+        	{
         		pw.close();
         	}
         }
@@ -464,42 +503,48 @@ 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 if file doesn't exist
+     * @throws FileNotFoundException
-     * @throws IOException           if IO error
+     * @throws IOException
      */
-    protected File initUndoArchive(File sourceDir)
+	private File initUndoArchive(File sourceDir)
-        throws FileNotFoundException, IOException {
+	throws FileNotFoundException, IOException
-        File parentDir = sourceDir.getCanonicalFile().getParentFile();
+	{				
-        if (parentDir == null) {
+		File parentDir = sourceDir.getAbsoluteFile().getParentFile(); 
-            throw new FileNotFoundException(
+		if (parentDir == null)
-                "Parent directory of archive directory not found; unable to write UndoArchive; no processing " +
+		{
-                    "performed");
+			throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");    			
 		}
 		
 		String sourceDirName = sourceDir.getName();
 		int seqNo = 1;
 		
 		File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
-        while (undoDir.exists()) {
+		while (undoDir.exists())
+		{
     		undoDir = new File(parentDir, "undo_" + sourceDirName+ "_" + ++seqNo); //increment
 		}
 		
 		// create root directory
-        if (!undoDir.mkdir()) {
+		if (!undoDir.mkdir())
-            pr("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
+		{
-            throw new IOException("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
+        	pr("ERROR creating  Undo Archive directory ");
+        	throw new IOException("ERROR creating  Undo Archive directory ");
 		}
 		
         //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;
         }
@@ -508,31 +553,29 @@ public class ItemUpdate {
 	
 	//private void write
 
-    /**
+    private void setEPerson(Context context, String eperson)
-     * Set EPerson doing import
+    throws Exception
-     *
+    {
-     * @param context DSpace Context
+        if (eperson == null)
-     * @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 = epersonService.findByEmail(context, eperson);
+            myEPerson = EPerson.findByEmail(context, eperson);
-        } else {
+        }
-            myEPerson = epersonService.find(context, UUID.fromString(eperson));
+        else
+        {
+            myEPerson = EPerson.find(context, Integer.parseInt(eperson));
         }
 
-        if (myEPerson == null) {
+        if (myEPerson == null)
+        {
             pr("Error, eperson cannot be found: " + eperson);
             throw new Exception("Invalid EPerson");
         }
@@ -544,20 +587,21 @@ public class ItemUpdate {
      *   poor man's logging
 	 *   As with ItemImport, API logging goes through log4j to the DSpace.log files
 	 *   whereas the batch logging goes to the console to be captured there.
-     *
+     * @param s
-     * @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) {
+    static void prv(String s)
-        if (verbose) {
+    {
+    	if (verbose) 
+    	{
         	System.out.println(s);
     	}
     }

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

@@ -11,13 +11,14 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 import java.io.OutputStream;
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.List;
+
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.Result;
@@ -30,15 +31,7 @@ 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;
@@ -46,6 +39,12 @@ 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
@@ -53,60 +52,67 @@ import org.xml.sax.SAXException;
  *      in context in ItemUpdate.
  *      
  *      The XML methods were based on those in ItemImport
+ * 
+ *
  */
 public class MetadataUtilities {
 	
-    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
     /**      
-     * Default constructor
+     * 
-     */
+     *  Working around Item API to delete a value-specific DCValue
-    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 context          DSpace Context
+     * 
-     * @param item             Item Object
+     * @param item
-     * @param dtom             metadata field
+     * @param dtom
-     * @param isLanguageStrict whether strict or not
+     * @param isLanguageStrict - 
+     * 
      * @return true if metadata field is found with matching value and was deleted
-     * @throws SQLException if database error
      */
-    public static boolean deleteMetadataByValue(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict)
+    public static boolean deleteMetadataByValue(Item item, DtoMetadata dtom, boolean isLanguageStrict)
-        throws SQLException {
+    {   	
-        List<MetadataValue> ar = null;
+    	DCValue[] ar = null;
     	
-        if (isLanguageStrict) {   // get all for given type
+    	if (isLanguageStrict)
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+    	{   // get all for given type
-        } else {
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+    	}
+    	else
+    	{
+    		ar = item.getMetadata(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 (MetadataValue dcv : ar) {
+    	for (DCValue dcv : ar)
-            if (dcv.getValue().equals(dtom.value)) {
+    	{
+    		if (dcv.value.equals(dtom.value))
+    		{
     			found = true;
-            } else {
+    		}
-                vals.add(dcv.getValue());
+    		else
+    		{
+    			vals.add(dcv.value);
     		}
     	}
     	
-        if (found) {  //remove all for given type  ??synchronize this block??
+    	if (found)  //remove all for given type  ??synchronize this block??
-            if (isLanguageStrict) {
+    	{   
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        	if (isLanguageStrict)
-            } else {
+        	{           		
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        	}
+        	else
+        	{
+        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
         	}
     	
-            itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
+    		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
     	}
 		return found;
     }
@@ -114,71 +120,83 @@ public class MetadataUtilities {
     /**
      *   Append text to value metadata field to item
      *   
-     * @param context          DSpace Context
+     * @param item
-     * @param item             DSpace Item
+     * @param dtom
-     * @param dtom             metadata field
+     * @param isLanguageStrict
-     * @param isLanguageStrict if strict
+     * @param textToAppend
-     * @param textToAppend     text to append
      * @throws IllegalArgumentException  - When target metadata field is not found
-     * @throws SQLException             if database error
      */
-    public static void appendMetadata(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict,
+    public static void appendMetadata(Item item, DtoMetadata dtom, boolean isLanguageStrict, 
     		String textToAppend)
-        throws IllegalArgumentException, SQLException {
+    throws IllegalArgumentException
-        List<MetadataValue> ar = null;
+    {   	
+    	DCValue[] ar = null;
     	
     	// get all values for given element/qualifier
-        if (isLanguageStrict) {  // get all for given element/qualifier
+    	if (isLanguageStrict)  // get all for given element/qualifier
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+    	{   
-        } else {
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+    	}
+    	else
+    	{
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
     	}
     	
-        if (ar.size() == 0) {
+    	if (ar.length == 0)
+    	{
     		throw new IllegalArgumentException("Metadata to append to not found");
     	}
     	
     	int idx = 0;  //index of field to change
-        if (ar.size() > 1) { //need to pick one, can't be sure it's the last one
+    	if (ar.length > 1)  //need to pick one, can't be sure it's the last one
+    	{
     		// TODO maybe get highest id ?
     	}
     	
     	//build new set minus the one to delete
     	List<String> vals = new ArrayList<String>();
-        for (int i = 0; i < ar.size(); i++) {
+    	for (int i=0; i < ar.length; i++) 
-            if (i == idx) {
+    	{
-                vals.add(ar.get(i).getValue() + textToAppend);
+    		if (i == idx)
-            } else {
+    		{
-                vals.add(ar.get(i).getValue());
+    			vals.add(ar[i].value + textToAppend);
+    		}
+    		else
+    		{
+    			vals.add(ar[i].value);
     		}
     	}
 
-        if (isLanguageStrict) {
+    	if (isLanguageStrict)
-            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+    	{           		
-        } else {
+    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+    	}
+    	else
+    	{
+    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
     	}
 	
-        itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
+		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
     }
  
     /**
      *  Modification of method from ItemImporter.loadDublinCore 
      *  as a Factory method
      * 
-     * @param docBuilder DocumentBuilder
+     * @param docBuilder  - 
      * @param is - InputStream of dublin_core.xml
      * @return list of DtoMetadata representing the metadata fields relating to an Item
-     * @throws SQLException                 if database error
+     * @throws SQLException
-     * @throws IOException                  if IO error
+     * @throws IOException
-     * @throws ParserConfigurationException if parser config error
+     * @throws ParserConfigurationException
-     * @throws SAXException                 if XML error
+     * @throws SAXException
-     * @throws TransformerException         if transformer error
+     * @throws TransformerException
-     * @throws AuthorizeException           if authorization error
+     * @throws AuthorizeException
      */
     public static List<DtoMetadata> loadDublinCore(DocumentBuilder docBuilder, InputStream is)
     throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
+           SAXException, TransformerException, AuthorizeException
+	{    	
 		Document document = docBuilder.parse(is);
 		
 		List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
@@ -188,43 +206,55 @@ public class MetadataUtilities {
 		String schema = null;
 		NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");		
 		Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
-        if (schemaAttr == null) {
+		if (schemaAttr == null)
+		{
 		    schema = MetadataSchema.DC_SCHEMA;
-        } else {
+		}
+		else
+		{
 		    schema = schemaAttr.getNodeValue();
 		}
 
 		// Get the nodes corresponding to formats
 		NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
 		
-        for (int i = 0; i < dcNodes.getLength(); i++) {
+		for (int i = 0; i < dcNodes.getLength(); i++)
+		{
 		    Node n = dcNodes.item(i);		    
 	        String value = getStringValue(n).trim(); 
 	        // compensate for empty value getting read as "null", which won't display
-            if (value == null) {
+	        if (value == null)
+	        {
 	            value = "";
 	        }
 	        String element = getAttributeValue(n, "element");
-            if (element != null) {
+	        if (element != null)
+	        {
 	        	element = element.trim();
 	        }
 	        String qualifier = getAttributeValue(n, "qualifier"); 
-            if (qualifier != null) {
+	        if (qualifier != null)
+	        {
 	        	qualifier = qualifier.trim();
 	        }
 	        String language = getAttributeValue(n, "language");
-            if (language != null) {
+	        if (language != null)
+	        {
 	        	language = language.trim();
 	        }
 
-            if ("none".equals(qualifier) || "".equals(qualifier)) {
+	        if ("none".equals(qualifier) || "".equals(qualifier))
+	        {
 	            qualifier = null;
 	        }
 	        
 	        // a goofy default, but consistent with DSpace treatment elsewhere  
-            if (language == null) {
+	        if (language == null)
+	        {
 	            language = "en";
-            } else if ("".equals(language)) {
+	        }
+	        else if ("".equals(language))
+	        {
 	            language = ConfigurationManager.getProperty("default.language");
 	        }
 	        
@@ -238,31 +268,39 @@ public class MetadataUtilities {
     /**
      *    Write dublin_core.xml 
      * 
-     * @param docBuilder DocumentBuilder
+     * @param docBuilder
-     * @param dtomList   List of metadata fields
+     * @param dtomList
      * @return xml document
-     * @throws ParserConfigurationException      if parser config error
+     * @throws ParserConfigurationException
-     * @throws TransformerConfigurationException if transformer config error
+     * @throws TransformerConfigurationException
-     * @throws TransformerException              if transformer error
+     * @throws TransformerException
      */
 	public static Document writeDublinCore(DocumentBuilder docBuilder, List<DtoMetadata> dtomList)
-        throws ParserConfigurationException, TransformerConfigurationException, TransformerException {
+	throws ParserConfigurationException, TransformerConfigurationException, TransformerException
+	{		
         Document doc = docBuilder.newDocument();
         Element root = doc.createElement("dublin_core");
         doc.appendChild(root);
     
-        for (DtoMetadata dtom : dtomList) {
+        for (DtoMetadata dtom : dtomList)
+        {
         	Element mel = doc.createElement("dcvalue");
         	mel.setAttribute("element", dtom.element);
-            if (dtom.qualifier == null) {
+        	if (dtom.qualifier == null)
+        	{
         		mel.setAttribute("qualifier", "none");
-            } else {
+        	}
+        	else
+        	{
         		mel.setAttribute("qualifier", dtom.qualifier);
         	}
  
-            if (StringUtils.isEmpty(dtom.language)) {
+        	if (StringUtils.isEmpty(dtom.language))
+        	{
         		mel.setAttribute("language", "en");
-            } else {
+        	}
+        	else
+        	{
         		mel.setAttribute("language", dtom.language);
         	}
         	mel.setTextContent(dtom.value);
@@ -274,37 +312,39 @@ public class MetadataUtilities {
 	
     /**
      *   write xml document to output stream
-     *
+     * @param doc
-     * @param doc         XML Document
+     * @param transformer
-     * @param transformer XML Transformer
+     * @param out
-     * @param out         OutputStream
+     * @throws IOException
-     * @throws IOException          if IO Error
+     * @throws TransformerException
-     * @throws TransformerException if Transformer error
      */
 	public static void writeDocument(Document doc, Transformer transformer, OutputStream out)
-        throws IOException, TransformerException {
+	throws IOException, TransformerException
+	{
         Source src = new DOMSource(doc); 
         Result dest = new StreamResult(out); 
         transformer.transform(src, dest); 
 	}
     
     
-    // XML utility methods
     
+    // XML utility methods
     /**
      * Lookup an attribute from a DOM node.
-     *
+     * @param n
-     * @param n    Node
+     * @param name
-     * @param name name
+     * @return
-     * @return attribute value
      */
-    private static String getAttributeValue(Node n, String name) {
+    private static String getAttributeValue(Node n, String name)
+    {
         NamedNodeMap nm = n.getAttributes();
 
-        for (int i = 0; i < nm.getLength(); i++) {
+        for (int i = 0; i < nm.getLength(); i++)
+        {
             Node node = nm.item(i);
 
-            if (name.equals(node.getNodeName())) {
+            if (name.equals(node.getNodeName()))
+            {
                 return node.getNodeValue();
             }
         }
@@ -314,17 +354,19 @@ public class MetadataUtilities {
     
     /**
      * Return the String value of a Node.
-     *
+     * @param node
-     * @param node node
+     * @return
-     * @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();
             }
         }
@@ -336,34 +378,39 @@ public class MetadataUtilities {
      * Rewrite of ItemImport's functionality
      * but just the parsing of the file, not the processing of its elements.
      *      
-     * @param f file
+     * @validate  flag to verify matching files in tree
-     * @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
     		}
     	}
@@ -372,33 +419,51 @@ public class MetadataUtilities {
     }
 
     /**
-     * @param f file
+     * 
-     * @return list of lines as strings
+     * @param f
-     * @throws FileNotFoundException if file doesn't exist
+     * @throws FileNotFoundException
-     * @throws IOException           if IO Error
+     * @throws IOException
      */
-    public static List<String> readDeleteContentsFile(File f)
+    public static List<Integer> readDeleteContentsFile(File f)
-        throws FileNotFoundException, IOException {
+    throws FileNotFoundException, IOException
-        List<String> list = new ArrayList<>();
+    {
+    	List<Integer> list = new ArrayList<Integer>();
     	
     	BufferedReader in = null;
     	
-        try {
+    	try
+    	{
 	    	in = new BufferedReader(new FileReader(f));
 	    	String line = null;
 	    	
-            while ((line = in.readLine()) != null) {
+	    	while ((line = in.readLine()) != null)
+	    	{
 	    		line = line.trim();
-                if ("".equals(line)) {
+	            if ("".equals(line))
+	            {
 	                continue;
 	            }
 	            
-                list.add(line);
+	            int n = 0;
+	            try
+	            {
+	            	n = Integer.parseInt(line);
+		    		list.add(n);	    		
 	            }
-        } finally {
+	            catch(NumberFormatException e)
-            try {
+	            {
+	            	ItemUpdate.pr("Error reading delete contents line:" + e.toString());
+	            }            	
+	    	}
+    	}
+    	finally
+    	{
+    		try
+    		{
     			in.close();
-            } catch (IOException e) {
+    		}
+    		catch(IOException e)
+    		{
     			//skip
     		}
     	}
@@ -407,55 +472,54 @@ public class MetadataUtilities {
     }
 
     /**
-     * Get display of Metadatum
+     *    Get display of DCValue    
 	 *
-     * @param dcv MetadataValue
+     * @param dcv
-     * @return string displaying elements of the Metadatum
+     * @return string displaying elements of the DCValue
      */
-    public static String getDCValueString(MetadataValue dcv) {
+    public static String getDCValueString(DCValue dcv)
-        MetadataField metadataField = dcv.getMetadataField();
+    {
-        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+    	return "schema: " + dcv.schema + "; element: " + dcv.element + "; qualifier: " + dcv.qualifier +
-        return "schema: " + metadataSchema.getName() + "; element: " + metadataField
+    	       "; language: " + dcv.language + "; value: " + dcv.value;
-            .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 {@code <schema>.<element>[.<qualifier>|.*]}
+	 *    Parses metadata field given in the form <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);
 		}
 		

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

@@ -8,7 +8,6 @@
 package org.dspace.app.itemupdate;
 
 import java.sql.SQLException;
-import java.util.List;
 
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
@@ -18,29 +17,36 @@ 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 class OriginalBitstreamFilter extends BitstreamFilterByBundleName 
-    public OriginalBitstreamFilter() {
+{	
+	public OriginalBitstreamFilter()
+	{
 		//empty
 	}
 	
 	/**
 	 *   Tests bitstreams for containment in an ORIGINAL bundle
 	 *  
-     * @param bitstream Bitstream
 	 *  @return true if the bitstream is in the ORIGINAL bundle
-     * @throws BitstreamFilterException if filter error
+	 *  
+	 *  @throws BitstreamFilterException
 	 */
-    @Override
 	public boolean accept(Bitstream bitstream) 
-        throws BitstreamFilterException {
+	throws BitstreamFilterException
-        try {
+	{		
-            List<Bundle> bundles = bitstream.getBundles();
+		try
-            for (Bundle bundle : bundles) {
+		{
-                if (bundle.getName().equals("ORIGINAL")) {
+			Bundle[] bundles = bitstream.getBundles();
+			for (Bundle b : bundles)
+			{
+				if (b.getName().equals("ORIGINAL"))
+				{
 					return true;
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

@@ -8,8 +8,6 @@
 package org.dspace.app.itemupdate;
 
 import java.sql.SQLException;
-import java.util.List;
-
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 
@@ -18,33 +16,41 @@ import org.dspace.content.Bundle;
  *      Also delete all derivative bitstreams, i.e.
  *      all bitstreams in the TEXT and THUMBNAIL bundles
  */
-public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter {
+public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter 
-    protected String[] bundlesToEmpty = {"ORIGINAL", "TEXT", "THUMBNAIL"};
+{
+	private String[] bundlesToEmpty = { "ORIGINAL", "TEXT", "THUMBNAIL" };	
 	
-    public OriginalWithDerivativesBitstreamFilter() {
+	public OriginalWithDerivativesBitstreamFilter()
+	{
 		//empty
 	}
 	
 	/**
 	 * 	Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
 	 * 
-     * @param bitstream Bitstream
+	 * @param bitstream
+	 * @throws BitstreamFilterException
 	 * @return true if bitstream is in specified bundles
-     * @throws BitstreamFilterException if error
 	 */
-    @Override
 	public boolean accept(Bitstream bitstream) 
-        throws BitstreamFilterException {
+	throws BitstreamFilterException
-        try {
+	{		
-            List<Bundle> bundles = bitstream.getBundles();
+		try
-            for (Bundle b : bundles) {
+		{
-                for (String bn : bundlesToEmpty) {
+			Bundle[] bundles = bitstream.getBundles();
-                    if (b.getName().equals(bn)) {
+			for (Bundle b : bundles)
+			{
+				for (String bn : bundlesToEmpty)
+				{
+					if (b.getName().equals(bn))
+					{
 						return true;
 					}
 				}
 			}		
-        } catch (SQLException e) {
+		}
+		catch(SQLException e)
+		{
 			throw new BitstreamFilterException(e);
 		}
 		return false;

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

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

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

@@ -7,25 +7,22 @@
  */
 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      DSpace context
+	 * @param context
-     * @param itarch       item archive
+	 * @param itarch
-     * @param isTest       test flag
+	 * @param isTest
-     * @param suppressUndo undo flag
+	 * @param suppressUndo
-     * @throws Exception if error
+	 * @throws Exception
 	 */
 	public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo) 
 	throws Exception;

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

@@ -7,36 +7,32 @@
  */
 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;
 	}
 

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

@@ -13,10 +13,12 @@ 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 ( {@code <schema>.<element>.<qualifier>} )
+ *   expressed as a string in the compound notation ( <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 {
 
@@ -34,10 +36,11 @@ public abstract class UpdateMetadataAction implements UpdateAction {
 	/**
 	 *   Set target fields
 	 *   
-     * @param targetFields Set of target fields to update
+	 * @param targetFields
 	 */
 	public void addTargetFields(Set<String> targetFields) {
-        for (String tf : targetFields) {
+		for (String tf : targetFields)
+		{
 			this.targetFields.add(tf);
 		}
 		
@@ -45,11 +48,11 @@ public abstract class UpdateMetadataAction implements UpdateAction {
 
 	/**
 	 *    Add array of target fields to update
-     *
+	 * @param targetFields
-     * @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);
 		}
 		
@@ -58,7 +61,7 @@ public abstract class UpdateMetadataAction implements UpdateAction {
 	/**
 	 *   Add single field to update
 	 * 
-     * @param targetField target field to update
+	 * @param targetField
 	 */
 	public void addTargetField(String targetField) {
 			this.targetFields.add(targetField);

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

@@ -1,104 +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.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;
-    }
-}

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

@@ -7,18 +7,15 @@
  */
 package org.dspace.app.launcher;
 
-import java.io.FileNotFoundException;
+import org.dspace.core.ConfigurationManager;
-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.
@@ -26,121 +23,89 @@ import org.jdom.input.SAXBuilder;
  * @author Stuart Lewis
  * @author Mark Diggory
  */
-public class ScriptLauncher {
+public class ScriptLauncher
-    /**
+{
-     * The service manager kernel
+    /** 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)
-        throws FileNotFoundException, IOException {
+    {
-        // Initialise the service manager kernel
+        // Check that there is at least one argument
-        try {
+        if (args.length < 1)
-            kernelImpl = DSpaceKernelInit.getKernel(null);
+        {
-            if (!kernelImpl.isRunning()) {
-                kernelImpl.start();
-            }
-        } catch (Exception e) {
-            // Failed to start so destroy it and log and throw an exception
-            try {
-                kernelImpl.destroy();
-            } catch (Exception e1) {
-                // Nothing to do
-            }
-            String message = "Failure during kernel init: " + e.getMessage();
-            System.err.println(message);
-            e.printStackTrace();
-            throw new IllegalStateException(message, e);
-        }
-
-        // 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);
+            display();
             System.exit(1);
         }
 
-        // Look up command in the configuration, and execute.
+        // Initialise the service manager kernel
-        int status;
+        try {
-        status = runOneCommand(commandConfigs, args);
+            kernelImpl = DSpaceKernelInit.getKernel(null);
-
+            if (!kernelImpl.isRunning())
-        // Destroy the service kernel if it is still alive
+            {
-        if (kernelImpl != null) {
+                kernelImpl.start(ConfigurationManager.getProperty("dspace.dir"));
+            }
+        } catch (Exception e)
+        {
+            // Failed to start so destroy it and log and throw an exception
+            try
+            {
                 kernelImpl.destroy();
-            kernelImpl = null;
+            }
+            catch (Exception e1)
+            {
+                // Nothing to do
+            }
+            String message = "Failure during filter init: " + e.getMessage();
+            System.err.println(message + ":" + e);
+            throw new IllegalStateException(message, e);
         }
 
-        System.exit(status);
+        // Parse the configuration file looking for the command entered
-    }
+        Document doc = getConfig();
-
-    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 = commandConfigs.getRootElement();
+        Element root = doc.getRootElement();
         List<Element> commands = root.getChildren("command");
-        Element command = null;
+        for (Element command : commands)
-        for (Element candidate : commands) {
+        {
-            if (request.equalsIgnoreCase(candidate.getChild("name").getValue())) {
+            if (request.equalsIgnoreCase(command.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 ("dsrun".equals(request))
-                if (args.length < 2) {
+                    {
+                        if (args.length < 2)
+                        {
                             System.err.println("Error in launcher.xml: Missing class name");
-                    return 1;
+                            System.exit(1);
                         }
                         className = args[1];
-            } else {
+                    }
+                    else {
                         className = step.getChild("class").getValue();
                     }
-            try {
+                    try
+                    {
                         target = Class.forName(className,
                                                true,
                                                Thread.currentThread().getContextClassLoader());
-            } catch (ClassNotFoundException e) {
+                    }
+                    catch (ClassNotFoundException e)
+                    {
                         System.err.println("Error in launcher.xml: Invalid class name: " + className);
-                return 1;
+                        System.exit(1);
                     }
 
                     // Strip the leading argument from the args, and add the arguments
@@ -149,20 +114,26 @@ public class ScriptLauncher {
                     Class[] argTypes = {useargs.getClass()};
                     boolean passargs = true;
                     if ((step.getAttribute("passuserargs") != null) &&
-                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue()))) {
+                        ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue())))
+                    {
                         passargs = false;
                     }
-            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs)) {
+                    if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs))
+                    {
                         useargs = new String[0];
-            } else {
+                    }
+                    else
+                    {
                         // The number of arguments to ignore
                         // If dsrun is the command, ignore the next, as it is the class name not an arg
                         int x = 1;
-                if ("dsrun".equals(request)) {
+                        if ("dsrun".equals(request))
+                        {
                             x = 2;
                         }
                         String[] argsnew = new String[useargs.length - x];
-                for (int i = x; i < useargs.length; i++) {
+                        for (int i = x; i < useargs.length; i++)
+                        {
                             argsnew[i - x] = useargs[i];
                         }
                         useargs = argsnew;
@@ -170,24 +141,25 @@ 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 requestService = kernelImpl.getServiceManager().getServiceByName(RequestService.class.getName(), RequestService.class);
-                RequestService.class.getName(), RequestService.class);
                     if (requestService == null) {
-                throw new IllegalStateException(
+                        throw new IllegalStateException("Could not get the DSpace RequestService to start the request transaction");
-                    "Could not get the DSpace RequestService to start the request transaction");
                     }
 
                     // Establish a request related to the current session
@@ -195,7 +167,8 @@ public class ScriptLauncher {
                     requestService.startRequest();
 
                     // Run the main() method
-            try {
+                    try
+                    {
                         Object[] arguments = {useargs};
 
                         // Useful for debugging, so left in the code...
@@ -211,20 +184,50 @@ 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();
-                return 1;
+                        System.exit(1);
                     }
+
+                }
+
+                // Destroy the service kernel
+                if (kernelImpl != null)
+                {
+                    kernelImpl.destroy();
+                    kernelImpl = null;
                 }
 
                 // Everything completed OK
-        return 0;
+                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);
     }
 
     /**
@@ -232,23 +235,22 @@ public class ScriptLauncher {
      *
      * @return The XML configuration file Document
      */
-    protected static Document getConfig() {
+    private static Document getConfig()
-        return getConfig(kernelImpl);
+    {
-    }
-
-    public static Document getConfig(DSpaceKernelImpl kernelImpl) {
         // Load the launcher configuration file
-        String config = kernelImpl.getConfigurationService().getProperty("dspace.dir") +
+        String config = ConfigurationManager.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;
@@ -256,24 +258,14 @@ public class ScriptLauncher {
 
     /**
      * Display the commands that the current launcher config file knows about
-     *
-     * @param commandConfigs configs as Document
      */
-    private static void display(Document commandConfigs) {
+    private static void display()
-        // List all command elements
+    {
-        List<Element> commands = commandConfigs.getRootElement().getChildren("command");
+        Document doc = getConfig();
-
+        List<Element> commands = doc.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 : sortedCommands.values()) {
+        for (Element command : commands)
+        {
             System.out.println(" - " + command.getChild("name").getValue() +
                                ": " + command.getChild("description").getValue());
         }

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

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

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

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

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

@@ -7,61 +7,64 @@
  */
 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 class BrandedPreviewJPEGFilter extends MediaFilter
-    @Override
+{
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".preview.jpg";
     }
 
     /**
      * @return String bundle name
+     *  
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "BRANDED_PREVIEW";
     }
 
     /**
      * @return String bitstreamformat
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "JPEG";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Generated Branded Preview";
     }
 
    
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     * 
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        throws Exception {
+    {
         // read in bitstream's image
         BufferedImage buf = ImageIO.read(source);
 
@@ -70,17 +73,89 @@ 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");
         
-        JPEGFilter jpegFilter = new JPEGFilter();
+        // now get the image dimensions
-        return jpegFilter
+        float xsize = (float) buf.getWidth(null);
-            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
+        float ysize = (float) buf.getHeight(null);
-                         brandFont);
+
+        // 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!
 	}
 }

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

@@ -1,99 +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.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;
-    }
-}

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

@@ -18,11 +18,13 @@ import org.dspace.core.Context;
  * from one format to another.  This interface should be implemented by any class
  * which defines a "filter" to be run by the MediaFilterManager.
  */
-public interface FormatFilter {
+public interface FormatFilter
+{
     /**
      * Get a filename for a newly created filtered bitstream
      * 
-     * @param sourceName name of source bitstream
+     * @param sourceName
+     *            name of source bitstream
      * @return filename generated by the filter - for example, document.pdf
      *         becomes document.pdf.txt
      */
@@ -42,21 +44,18 @@ public interface FormatFilter {
     public String getFormatString();
 
     /**
-     * @return string to describe the newly-generated Bitstream - how it was
+     * @return string to describe the newly-generated Bitstream's - how it was
      *         produced is a good idea
      */
     public String getDescription();
 
     /**
-     * Read the source stream and produce the filtered content.
+     * @param source
+     *            input stream
      * 
-     * @param item    Item
+     * @return result of filter's transformation, written out to a bitstream
-     * @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(Item item, InputStream source, boolean verbose)
+    public InputStream getDestinationStream(InputStream source)
             throws Exception;
 
     /**
@@ -67,15 +66,18 @@ 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 c
-     * @param source  source bitstream to be processed
+     *            context
-     * @param verbose verbose mode
+     * @param item
+     *            item containing bitstream to process
+     * @param source
+     *            source bitstream to be processed
+     * 
      * @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, boolean verbose)
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
             throws Exception;
         
     /**
@@ -86,11 +88,14 @@ 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 c
-     * @param generatedBitstream the bitstream which was generated by
+     *            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;

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
+{
 
-    @Override
+    public String getFilteredName(String oldFilename)
-    public String getFilteredName(String oldFilename) {
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *  
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "TEXT";
     }
 
     /**
      * @return String bitstreamformat
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "Text";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Extracted text";
     }
 
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     * 
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        throws Exception {
+    {
         // try and read the document - set to ignore character set directive,
         // assuming that the input stream is already set properly (I hope)
         HTMLEditorKit kit = new HTMLEditorKit();

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

@@ -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.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();
-            }
-        }
-    }
-
-
-}

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

@@ -1,43 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.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();
-            }
-        }
-    }
-
-}

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

@@ -1,202 +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.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
-    }
-
-}

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

@@ -7,113 +7,92 @@
  */
 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 class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
-    @Override
+{
-    public String getFilteredName(String oldFilename) {
+    public String getFilteredName(String oldFilename)
+    {
         return oldFilename + ".jpg";
     }
 
     /**
      * @return String bundle name
+     *  
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "THUMBNAIL";
     }
 
     /**
      * @return String bitstreamformat
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "JPEG";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Generated Thumbnail";
     }
 
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     * 
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        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 (verbose) {
+        if (MediaFilterManager.isVerbose)
+        {
             System.out.println("original size: " + xsize + "," + ysize);
         }
 
         // scale by x first if needed
-        if (xsize > xmax) {
+        if (xsize > xmax)
+        {
             // calculate scaling factor so that xsize * scale = new size (max)
             float scale_factor = xmax / xsize;
 
             // if verbose flag is set, print out extracted text
             // to STDOUT
-            if (verbose) {
+            if (MediaFilterManager.isVerbose)
+            {
                 System.out.println("x scale factor: " + scale_factor);
             }
 
@@ -124,13 +103,15 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
 
             // if verbose flag is set, print out extracted text
             // to STDOUT
-            if (verbose) {
+            if (MediaFilterManager.isVerbose)
-                System.out.println("size after fitting to maximum width: " + xsize + "," + ysize);
+            {
+                System.out.println("new size: " + xsize + "," + ysize);
             }
         }
 
         // scale by y if needed
-        if (ysize > ymax) {
+        if (ysize > ymax)
+        {
             float scale_factor = ymax / ysize;
 
             // now reduce x size
@@ -140,8 +121,9 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         }
 
         // if verbose flag is set, print details to STDOUT
-        if (verbose) {
+        if (MediaFilterManager.isVerbose)
-            System.out.println("size after fitting to maximum height: " + xsize + ", "
+        {
+            System.out.println("created thumbnail size: " + xsize + ", "
                     + ysize);
         }
 
@@ -149,34 +131,10 @@ 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();
 
@@ -189,127 +147,20 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
     }
 
 
-    @Override
+    public String[] getInputMIMETypes()
-    public String[] getInputMIMETypes() {
+    {
         return ImageIO.getReaderMIMETypes();
     }
 
-    @Override
+    public String[] getInputDescriptions()
-    public String[] getInputDescriptions() {
+    {
         return null;
     }
 
-    @Override
+    public String[] getInputExtensions()
-    public String[] getInputExtensions() {
+    {
         // Temporarily disabled as JDK 1.6 only
         // return ImageIO.getReaderFileSuffixes();
         return null;
     }
-
-    public BufferedImage getNormalizedInstance(BufferedImage buf) {
-        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;
-    }
 }

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

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

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

@@ -1,325 +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.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);
-    }
-}

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

@@ -0,0 +1,838 @@
+/**
+ * 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;
+        }
+    }
+    
+}

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

@@ -1,469 +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.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;
-    }
-}

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

@@ -1,94 +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.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;
-    }
-}

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

@@ -18,8 +18,7 @@ import java.io.Writer;
 
 import org.apache.log4j.Logger;
 import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.text.PDFTextStripper;
+import org.apache.pdfbox.util.PDFTextStripper;
-import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;
 
 /*
@@ -28,98 +27,118 @@ import org.dspace.core.ConfigurationManager;
  * instantiate filter - bitstream format doesn't exist
  *
  */
-public class PDFFilter extends MediaFilter {
+public class PDFFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(PDFFilter.class);
 
-    @Override
+    public String getFilteredName(String oldFilename)
-    public String getFilteredName(String oldFilename) {
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "TEXT";
     }
 
     /**
      * @return String bitstreamformat
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "Text";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Extracted text";
     }
 
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     *
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        throws Exception {
+    {
-        try {
+        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 {
+            finally
-                    if (pdfDoc != null) {
+            {
+                try
+                {
+                    if (pdfDoc != null)
+                    {
                         pdfDoc.close();
                     }
-                } catch (Exception e) {
+                }
+                catch(Exception e)
+                {
                    log.error("Error closing PDF file: " + e.getMessage(), e);
                 }
 
-                try {
+                try
+                {
                     writer.close();
-                } catch (Exception e) {
+                }
+                catch(Exception e)
+                {
                    log.error("Error closing temporary extract file: " + e.getMessage(), e);
                 }
             }
 
-            if (useTemporaryFile) {
+            if (useTemporaryFile)
+            {
                 return new FileInputStream(tempTextFile);
-            } else {
+            }
+            else
+            {
                 byte[] bytes = byteStream.toByteArray();
                 return new ByteArrayInputStream(bytes);
             }
-        } catch (OutOfMemoryError oome) {
+        }
+        catch (OutOfMemoryError oome)
+        {
             log.error("Error parsing PDF document " + oome.getMessage(), oome);
-            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
+            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false))
+            {
                 throw oome;
             }
         }

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

@@ -1,71 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import org.apache.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());
-    }
-}

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

@@ -10,31 +10,33 @@ package org.dspace.app.mediafilter;
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
 
-import org.apache.log4j.Logger;
-import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
-import org.apache.poi.hslf.extractor.PowerPointExtractor;
 import org.apache.poi.xslf.extractor.XSLFPowerPointExtractor;
-import org.dspace.content.Item;
+import org.apache.poi.hslf.extractor.PowerPointExtractor;
+import org.apache.poi.POITextExtractor;
+
+import org.apache.log4j.Logger;
 
 /*
  * TODO: Allow user to configure extraction of only text or only notes
  * 
  */
-public class PowerPointFilter extends MediaFilter {
+public class PowerPointFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(PowerPointFilter.class);
 
-    @Override
+    public String getFilteredName(String oldFilename)
-    public String getFilteredName(String oldFilename) {
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     * 
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "TEXT";
     }
 
@@ -43,31 +45,31 @@ public class PowerPointFilter extends MediaFilter {
      * 
      *         TODO: Check that this is correct
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "Text";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Extracted text";
     }
 
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     * 
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        throws Exception {
+    {
 
-        try {
+        try
+        {
 
             String extractedText = null;
             new ExtractorFactory();
@@ -78,22 +80,29 @@ public class PowerPointFilter extends MediaFilter {
             // require different classes and APIs for text extraction
 
             // If this is a PowerPoint XML file, extract accordingly
-            if (pptExtractor instanceof XSLFPowerPointExtractor) {
+            if (pptExtractor instanceof XSLFPowerPointExtractor)
+            {
 
                 // The true method arguments indicate that text from
                 // the slides and the notes is desired
                 extractedText = ((XSLFPowerPointExtractor) pptExtractor)
                         .getText(true, true);
-            } else if (pptExtractor instanceof PowerPointExtractor) { // Legacy PowerPoint files
+            }
+
+            // Legacy PowerPoint files
+            else if (pptExtractor instanceof PowerPointExtractor)
+            {
 
                 extractedText = ((PowerPointExtractor) pptExtractor).getText()
                         + " " + ((PowerPointExtractor) pptExtractor).getNotes();
 
             }
-            if (extractedText != null) {
+            if (extractedText != null)
+            {
                 // if verbose flag is set, print out extracted text
                 // to STDOUT
-                if (verbose) {
+                if (MediaFilterManager.isVerbose)
+                {
                     System.out.println(extractedText);
                 }
 
@@ -103,7 +112,9 @@ public class PowerPointFilter extends MediaFilter {
 
                 return bais;
             }
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             log.error("Error filtering bitstream: " + e.getMessage(), e);
             throw e;
         }

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

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

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

@@ -8,11 +8,11 @@
 package org.dspace.app.mediafilter;
 
 import java.io.ByteArrayInputStream;
-import java.io.IOException;
 import java.io.InputStream;
+import java.io.IOException;
 
 import org.apache.log4j.Logger;
-import org.dspace.content.Item;
+
 import org.textmining.extraction.TextExtractor;
 import org.textmining.extraction.word.WordTextExtractorFactory;
 
@@ -22,59 +22,62 @@ import org.textmining.extraction.word.WordTextExtractorFactory;
  * instantiate filter - bitstream format doesn't exist.
  *  
  */
-public class WordFilter extends MediaFilter {
+public class WordFilter extends MediaFilter
+{
 
     private static Logger log = Logger.getLogger(WordFilter.class);
 
-    @Override
+    public String getFilteredName(String oldFilename)
-    public String getFilteredName(String oldFilename) {
+    {
         return oldFilename + ".txt";
     }
 
     /**
      * @return String bundle name
+     *  
      */
-    @Override
+    public String getBundleName()
-    public String getBundleName() {
+    {
         return "TEXT";
     }
 
     /**
      * @return String bitstreamformat
      */
-    @Override
+    public String getFormatString()
-    public String getFormatString() {
+    {
         return "Text";
     }
 
     /**
      * @return String description
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return "Extracted text";
     }
 
     /**
-     * @param currentItem item
+     * @param source
-     * @param source      source input stream
+     *            source input stream
-     * @param verbose     verbose mode
+     * 
      * @return InputStream the resulting input stream
-     * @throws Exception if error
      */
-    @Override
+    public InputStream getDestinationStream(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+            throws Exception
-        throws Exception {
+    {
         // get input stream from bitstream
         // pass to filter, get string back
-        try {
+        try  
+        {
             WordTextExtractorFactory factory = new WordTextExtractorFactory();
             TextExtractor e = factory.textExtractor(source);
             String extractedText = e.getText();
 
             // if verbose flag is set, print out extracted text
             // to STDOUT
-            if (verbose) {
+            if (MediaFilterManager.isVerbose)
+            {
                 System.out.println(extractedText);
             }
 
@@ -83,7 +86,9 @@ public class WordFilter extends MediaFilter {
             ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
 
             return bais; // will this work? or will the byte array be out of scope?
-        } catch (IOException ioe) {
+        } 
+        catch (IOException ioe)
+        {
             System.out.println("Invalid Word Format");
             log.error("Error detected - Word File format not recognized: "
                     + ioe.getMessage(), ioe);