[maven-release-plugin] prepare release dspace-5.3

it is now false

.gitignore

@@ -1,15 +1,10 @@
 ## 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
@@ -26,19 +21,11 @@ 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

@@ -5,23 +5,24 @@ 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-  # Remove outdated settings.xml from Travis builds.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
+  # Install latest Node.js 0.10.x & print version info
-  - rm ~/.m2/settings.xml
+  - nvm install 0.10
+  - node --version
+  # Install Bower
+  - npm install -g bower
+  # Install Grunt & print version info
+  - npm install -g grunt && npm install -g grunt-cli
+  - grunt --version
+  # Print ruby version info (should be installed)
+  - ruby -v
+  # Install Sass & print version info
+  - gem install sass
+  - sass -v
+  # Install Compass & print version info
+  - gem install compass
+  - compass version
 
 # Skip install stage, as we'll do it below
 install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
@@ -31,14 +32,15 @@ install: "echo 'Skipping install stage, dependencies will be downloaded during b
 # 2. Assemble DSpace
 script:
   # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
+  #    (This explicitly skips building the 'dspace' assembly module, since we only want to do that ONCE.)
   #        license:check => Validate all source code license headers
   #        -Dmaven.test.skip=false => Enable DSpace Unit Tests
-  #        -DskipITs=false         => Enable DSpace Integration Tests
+  #        -P !dspace => SKIP full DSpace assembly (will do below)
-  #        -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 -P !dspace -B -V"
-  - "mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+  # 2. [Assemble DSpace] Ensure assembly process works (from [src]/dspace/), including Mirage 2
-  # 2. [Assemble DSpace] Ensure overlay & assembly process works (from [src]/dspace/)
+  #        -Dmirage2.on=true => Build Mirage2
+  #        -Dmirage2.deps.included=false => Don't include Mirage2 build dependencies (We installed them in before_install)
   #        -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"
+  - "cd dspace && mvn package -Dmirage2.on=true -Dmirage2.deps.included=false -P !assembly -B -V"

LICENSE

@@ -1,7 +1,7 @@
 DSpace source code license:
 
 
-Copyright (c) 2002-2016, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2015, 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

@@ -1,19 +1,19 @@
 
-DSpace uses third-party libraries which may be distributed under different
+DSpace uses third-party libraries which may be distributed under different 
 licenses. We have listed all of these third party libraries and their licenses
 below. This file can be regenerated at any time by simply running:
-
+    
     mvn clean verify -Dthird.party.licenses=true
 
-You must agree to the terms of these licenses, in addition to the DSpace
+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.
 
 PLEASE NOTE: Some dependencies may be listed under multiple licenses if they
-are dual-licensed. This is especially true of anything listed as
+are dual-licensed. This is especially true of anything listed as 
-"GNU General Public Library" below, as DSpace actually does NOT allow for any
+"GNU General Public Library" below, as DSpace actually does NOT allow for any 
 dependencies that are solely released under GPL terms. For more info see:
 https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 ---------------------------------------------------
@@ -21,69 +21,68 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
     Apache Software License, Version 2.0:
 
         * Ant-Contrib Tasks (ant-contrib:ant-contrib:1.0b3 - http://ant-contrib.sourceforge.net)
-        * Code Generation Library (cglib:cglib:2.2.2 - http://cglib.sourceforge.net/)
+        * Code Generation Library (cglib:cglib:3.1 - http://cglib.sourceforge.net/)
-        * AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.10.50 - https://aws.amazon.com/sdkforjava)
-        * AWS Java SDK for AWS KMS (com.amazonaws:aws-java-sdk-kms:1.10.50 - https://aws.amazon.com/sdkforjava)
-        * AWS Java SDK for Amazon S3 (com.amazonaws:aws-java-sdk-s3:1.10.50 - https://aws.amazon.com/sdkforjava)
         * HPPC Collections (com.carrotsearch:hppc:0.5.2 - http://labs.carrotsearch.com/hppc.html/hppc)
         * metadata-extractor (com.drewnoakes:metadata-extractor:2.6.2 - http://code.google.com/p/metadata-extractor/)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.5.4 - http://github.com/FasterXML/jackson)
+        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.3.0 - http://wiki.fasterxml.com/JacksonHome)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.7.0 - http://github.com/FasterXML/jackson)
+        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.1.3 - http://wiki.fasterxml.com/JacksonHome)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.5.4 - https://github.com/FasterXML/jackson)
+        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
-        * 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:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.5.4 - http://github.com/FasterXML/jackson)
+        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.19.0 - http://code.google.com/p/google-api-java-client/google-api-client/)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.7.0 - http://github.com/FasterXML/jackson)
+        * Google Analytics API v3-rev103-1.19.0 (com.google.apis:google-api-services-analytics:v3-rev103-1.19.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-analytics)
-        * Jackson-JAXRS-base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-base)
+        * FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.0 - http://findbugs.sourceforge.net/)
-        * Jackson-JAXRS-JSON (com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-json-provider)
+        * Gson (com.google.code.gson:gson:2.2.1 - http://code.google.com/p/google-gson/)
-        * Jackson-module-JAXB-annotations (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.5.4 - http://wiki.fasterxml.com/JacksonJAXBAnnotations)
+        * Guava: Google Core Libraries for Java (com.google.guava:guava:13.0 - http://code.google.com/p/guava-libraries/guava)
-        * 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 (com.google.guava:guava:18.0 - http://code.google.com/p/guava-libraries/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)
+        * Guava: Google Core Libraries for Java (com.google.guava:guava-jdk5:13.0 - 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)
+        * Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.19.0 - http://code.google.com/p/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)
+        * Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.19.0 - http://code.google.com/p/google-http-java-client/google-http-client-jackson2/)
-        * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.21.0 - https://github.com/google/google-oauth-java-client/google-oauth-client)
+        * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client/)
+        * Java 6 (and higher) extensions to the Google OAuth Client Library for Java. (com.google.oauth-client:google-oauth-client-java6:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client-java6/)
+        * Jetty extensions to the Google OAuth Client Library for Java. (com.google.oauth-client:google-oauth-client-jetty:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client-jetty/)
         * ConcurrentLinkedHashMap (com.googlecode.concurrentlinkedhashmap:concurrentlinkedhashmap-lru:1.2 - http://code.google.com/p/concurrentlinkedhashmap)
+        * FORESITE :: Object Reuse and Exchange library (com.googlecode.foresite-toolkit:foresite:0.9 - http://www.openarchives.org/ore)
         * 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)
+        * XOAI : OAI-PMH Java Toolkit (com.lyncode:xoai:3.2.9 - http://www.lyncode.com)
         * 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/)
+        * Commons BeanUtils (commons-beanutils:commons-beanutils:1.8.3 - http://commons.apache.org/beanutils/)
-        * Apache Commons CLI (commons-cli:commons-cli:1.3.1 - http://commons.apache.org/proper/commons-cli/)
+        * Commons CLI (commons-cli:commons-cli:1.2 - http://commons.apache.org/cli/)
-        * Apache Commons Codec (commons-codec:commons-codec:1.10 - http://commons.apache.org/proper/commons-codec/)
+        * Apache Commons Codec (commons-codec:commons-codec:1.9 - http://commons.apache.org/proper/commons-codec/)
-        * Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
+        * Collections (commons-collections:commons-collections:3.2 - http://jakarta.apache.org/commons/collections/)
-        * Apache Commons Configuration (commons-configuration:commons-configuration:1.10 - http://commons.apache.org/configuration/)
+        * Commons Configuration (commons-configuration:commons-configuration:1.6 - http://commons.apache.org/${pom.artifactId.substring(8)}/)
-        * Commons Digester (commons-digester:commons-digester:1.8.1 - http://commons.apache.org/digester/)
+        * Commons Configuration (commons-configuration:commons-configuration:1.8 - http://commons.apache.org/configuration/)
-        * Apache Commons FileUpload (commons-fileupload:commons-fileupload:1.3.1 - http://commons.apache.org/proper/commons-fileupload/)
+        * Commons DBCP (commons-dbcp:commons-dbcp:1.4 - http://commons.apache.org/dbcp/)
+        * Digester (commons-digester:commons-digester:1.8 - http://jakarta.apache.org/commons/digester/)
+        * Commons FileUpload (commons-fileupload:commons-fileupload:1.2.1 - http://commons.apache.org/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 IO (commons-io:commons-io:2.3 - 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/)
+        * Commons Logging (commons-logging:commons-logging:1.1.1 - http://commons.apache.org/logging)
-        * Apache Commons Validator (commons-validator:commons-validator:1.5.0 - http://commons.apache.org/proper/commons-validator/)
+        * Commons Pool (commons-pool:commons-pool:1.4 - http://commons.apache.org/pool/)
+        * Commons Validator (commons-validator:commons-validator:1.4.0 - http://commons.apache.org/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/)
+        * Joda-Time (joda-time:joda-time:2.3 - http://www.joda.org/joda-time/)
+        * Apache Log4j (log4j:log4j:1.2.16 - http://logging.apache.org/log4j/1.2/)
         * 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:1.7.2 - http://ehcache.sf.net/ehcache-core)
-        * Ehcache Core (net.sf.ehcache:ehcache-core:2.4.3 - http://ehcache.org)
+        * opencsv (net.sf.opencsv:opencsv:2.0 - http://opencsv.sf.net)
         * 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 Client (org.apache.abdera:abdera-client:1.1.1 - http://abdera.apache.org/abdera-client)
-        * Abdera Core (org.apache.abdera:abdera-core:1.1.3 - http://abdera.apache.org/abdera-core)
+        * Abdera Core (org.apache.abdera:abdera-core:1.1.1 - http://abdera.apache.org/abdera-core)
-        * I18N Libraries (org.apache.abdera:abdera-i18n:1.1.3 - http://abdera.apache.org)
+        * I18N Libraries (org.apache.abdera:abdera-i18n:1.1.1 - http://abdera.apache.org)
-        * Abdera Parser (org.apache.abdera:abdera-parser:1.1.3 - http://abdera.apache.org/abdera-parser)
+        * Abdera Parser (org.apache.abdera:abdera-parser:1.1.1 - 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/)
@@ -112,133 +111,123 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * 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/)
+        * Commons Lang (org.apache.commons:commons-lang3:3.1 - http://commons.apache.org/lang/)
-        * 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)
+        * Activation (org.apache.geronimo.specs:geronimo-activation_1.0.2_spec:1.1 - http://geronimo.apache.org/geronimo-activation_1.0.2_spec)
-        * 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)
+        * Activation 1.1 (org.apache.geronimo.specs:geronimo-activation_1.1_spec:1.0.2 - http://geronimo.apache.org/specs/geronimo-activation_1.1_spec)
+        * JavaMail 1.4 (org.apache.geronimo.specs:geronimo-javamail_1.4_spec:1.6 - http://geronimo.apache.org/maven/specs/geronimo-javamail_1.4_spec/1.6)
+        * Streaming API for XML (STAX API 1.0) (org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:1.0 - http://geronimo.apache.org/specs/geronimo-stax-api_1.0_spec)
         * 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 (org.apache.httpcomponents:httpclient:4.3.5 - 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 HttpCore (org.apache.httpcomponents:httpcore:4.3.2 - 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 - Libraries POM (org.apache.jena:apache-jena-libs:2.12.0 - 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 - ARQ (SPARQL 1.1 Query Engine) (org.apache.jena:jena-arq:2.12.0 - 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 - Core (org.apache.jena:jena-core:2.12.0 - 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 - IRI (org.apache.jena:jena-iri:1.1.0 - 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/)
+        * Apache Jena - TDB (Native Triple Store) (org.apache.jena:jena-tdb:1.1.0 - 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-icu)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-kuromoji)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-morfologik)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-phonetic)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-smartcn)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-stempel)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-codecs)
-        * 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:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-expressions)
-        * 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:1.8.7 - http://pdfbox.apache.org/)
-        * Apache FontBox (org.apache.pdfbox:fontbox:2.0.2 - http://pdfbox.apache.org/)
+        * Apache JempBox (org.apache.pdfbox:jempbox:1.8.7 - http://www.apache.org/pdfbox-parent/jempbox/)
-        * Apache JempBox (org.apache.pdfbox:jempbox:1.8.4 - http://www.apache.org/pdfbox-parent/jempbox/)
+        * Apache PDFBox (org.apache.pdfbox:pdfbox:1.8.7 - http://www.apache.org/pdfbox-parent/pdfbox/)
-        * Apache PDFBox (org.apache.pdfbox:pdfbox:2.0.2 - http://www.apache.org/pdfbox-parent/pdfbox/)
+        * Apache POI (org.apache.poi:poi:3.6 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi:3.13 - http://poi.apache.org/)
+        * Apache POI (org.apache.poi:poi-ooxml:3.6 - 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-ooxml-schemas:3.6 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-scratchpad:3.13 - http://poi.apache.org/)
+        * Apache POI (org.apache.poi:poi-scratchpad:3.6 - http://poi.apache.org/)
-        * Apache Solr Search Server (org.apache.solr:solr:4.10.4 - http://lucene.apache.org/solr-parent/solr)
+        * Apache Solr Search Server (org.apache.solr:solr:4.10.2 - 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 Analysis Extras (org.apache.solr:solr-analysis-extras:4.10.2 - 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 Content Extraction Library (org.apache.solr:solr-cell:4.10.2 - 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 Core (org.apache.solr:solr-core:4.10.2 - 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 Solr Solrj (org.apache.solr:solr-solrj:4.10.2 - 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 API (org.apache.ws.commons.axiom:axiom-api:1.2.10 - http://ws.apache.org/axiom/axiom-api/)
-        * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.14 - http://ws.apache.org/axiom/)
+        * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.10 - http://ws.apache.org/axiom/axiom-impl/)
+        * XmlBeans (org.apache.xmlbeans:xmlbeans:2.3.0 - http://xmlbeans.apache.org)
         * 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)
+        * Evo Inflector (org.atteo:evo-inflector:1.0.1 - 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)
+        * Jackson (org.codehaus.jackson:jackson-core-asl:1.9.2 - http://jackson.codehaus.org)
+        * JAX-RS provider for JSON content type (org.codehaus.jackson:jackson-jaxrs:1.9.2 - 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)
+        * Data Mapper for Jackson (org.codehaus.jackson:jackson-mapper-asl:1.9.2 - http://jackson.codehaus.org)
+        * Xml Compatibility extensions for Jackson (org.codehaus.jackson:jackson-xc:1.9.2 - http://jackson.codehaus.org)
+        * Jettison (org.codehaus.jettison:jettison:1.1 - no url defined)
         * 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)
+        * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
+        * elasticsearch (org.elasticsearch:elasticsearch:1.4.0 - http://nexus.sonatype.org/oss-repository-hosting.html/elasticsearch)
+        * flyway-core (org.flywaydb:flyway-core:3.0 - http://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/)
+        * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
+        * Jetty Server (org.mortbay.jetty:jetty:6.1.14 - http://jetty.mortbay.org/project/modules/jetty)
         * 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 Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.14 - http://jetty.mortbay.org/project/jetty-servlet-tester)
+        * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.14 - http://jetty.mortbay.org/project/jetty-util)
         * 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)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
-        * org.restlet.ext.servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - no url defined)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
         * rome-modules (org.rometools:rome-modules:1.0 - http://www.rometools.org)
-        * Spring AOP (org.springframework:spring-aop:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * spring-aop (org.springframework:spring-aop:3.1.1.RELEASE - no url defined)
         * 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-asm (org.springframework:spring-asm:3.1.1.RELEASE - no url defined)
+        * spring-beans (org.springframework:spring-beans:3.1.1.RELEASE - no url defined)
         * 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:3.1.1.RELEASE - no url defined)
         * 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-context-support (org.springframework:spring-context-support:3.1.1.RELEASE - no url defined)
-        * Spring Core (org.springframework:spring-core:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
+        * spring-core (org.springframework:spring-core:3.1.1.RELEASE - no url defined)
         * 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 (org.springframework:spring-expression:3.1.1.RELEASE - no url defined)
         * 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:3.1.1.RELEASE - no url defined)
-        * Spring JDBC (org.springframework:spring-jdbc:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * Spring Framework: Mock (org.springframework:spring-mock:2.0.8 - http://www.springframework.org)
-        * 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-tx (org.springframework:spring-tx:3.1.1.RELEASE - no url defined)
-        * Spring Transaction (org.springframework:spring-tx:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
+        * spring-web (org.springframework:spring-web:3.1.1.RELEASE - no url defined)
-        * 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-webmvc (org.springframework:spring-webmvc:3.1.1.RELEASE - no url defined)
         * 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/)
@@ -249,159 +238,148 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * oai4j (se.kb:oai4j:0.6b1 - http://oai4j-client.sourceforge.net/)
         * StAX API (stax:stax-api:1.0.1 - http://stax.codehaus.org/)
         * standard (taglibs:standard:1.1.2 - no url defined)
-        * Xalan Java Serializer (xalan:serializer:2.7.2 - http://xml.apache.org/xalan-j/)
+        * xalan (xalan:xalan:2.7.0 - no url defined)
-        * Xalan Java (xalan:xalan:2.7.2 - http://xml.apache.org/xalan-j/)
+        * Xerces2 Java Parser (xerces:xercesImpl:2.8.1 - http://xerces.apache.org/xerces2-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 External Components XML APIs (xml-apis:xml-apis:1.0.b2 - http://xml.apache.org/commons/#external)
+        * xml-apis (xml-apis:xml-apis:1.3.02 - http://xml.apache.org/commons/#external)
+        * xmlParserAPIs (xml-apis:xmlParserAPIs:2.0.2 - no url defined)
         * XML Commons Resolver Component (xml-resolver:xml-resolver:1.2 - http://xml.apache.org/commons/components/resolver/)
 
     BSD License:
 
-        * AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
+        * ASM Core (asm:asm:3.1 - http://asm.objectweb.org/asm/)
-        * ASM Core (asm:asm:3.3.1 - http://asm.objectweb.org/asm/)
         * XMP Library for Java (com.adobe.xmp:xmpcore:5.1.2 - http://www.adobe.com/devnet/xmp.html)
         * coverity-escapers (com.coverity.security:coverity-escapers:1.1.1 - http://coverity.com/security)
-        * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.1 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
+        * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.0 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
         * Protocol Buffer Java API (com.google.protobuf:protobuf-java:2.5.0 - http://code.google.com/p/protobuf)
         * Jena IRI (com.hp.hpl.jena:iri:0.8 - http://jena.sf.net/iri)
         * Jena (com.hp.hpl.jena:jena:2.6.4 - http://www.openjena.org/)
         * yui compressor (com.yahoo.platform.yui:yuicompressor:2.3.6 - http://developer.yahoo.com/yui/compressor/)
-        * dnsjava (dnsjava:dnsjava:2.1.7 - http://www.dnsjava.org)
+        * dnsjava (dnsjava:dnsjava:2.1.1 - 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/)
+        * jaxen (jaxen:jaxen:1.1 - 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)
+        * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
-        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
+        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:5.3-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 I18N :: Language Packs (org.dspace:dspace-api-lang:5.0.4 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-api-lang)
-        * DSpace JSP-UI (org.dspace:dspace-jspui:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
+        * DSpace JSP-UI (org.dspace:dspace-jspui:5.3-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 OAI-PMH (org.dspace:dspace-oai:5.3-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 RDF (org.dspace:dspace-rdf:5.3-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 REST :: API and Implementation (org.dspace:dspace-rest:5.3-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)
+        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:5.3-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)
+        * Apache Solr Webapp (org.dspace:dspace-solr:5.3-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 (org.dspace:dspace-sword:5.3-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 SWORD v2 (org.dspace:dspace-swordv2:5.3-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) (org.dspace:dspace-xmlui:5.3-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)
+        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:5.0.5 - http://nexus.sonatype.org/oss-repository-hosting.html/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)
+        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:5.3-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
         * Hamcrest All (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
-        * Hamcrest Core (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
+        * Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
         * JBibTeX (org.jbibtex:jbibtex:1.0.10 - http://www.jbibtex.org)
         * ASM Core (org.ow2.asm:asm:4.1 - http://asm.objectweb.org/asm/)
+        * ASM Core (org.ow2.asm:asm:4.2 - http://asm.objectweb.org/asm/)
         * ASM Analysis (org.ow2.asm:asm-analysis:4.1 - http://asm.objectweb.org/asm-analysis/)
         * ASM Commons (org.ow2.asm:asm-commons:4.1 - http://asm.objectweb.org/asm-commons/)
         * ASM Tree (org.ow2.asm:asm-tree:4.1 - http://asm.objectweb.org/asm-tree/)
         * ASM Util (org.ow2.asm:asm-util:4.1 - http://asm.objectweb.org/asm-util/)
+        * PostgreSQL JDBC Driver (postgresql:postgresql:9.1-901-1.jdbc4 - http://jdbc.postgresql.org)
         * 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):
 
+        * jersey-core (com.sun.jersey:jersey-core:1.17.1 - https://jersey.java.net/jersey-core/)
+        * jersey-json (com.sun.jersey:jersey-json:1.17.1 - https://jersey.java.net/jersey-json/)
+        * jersey-server (com.sun.jersey:jersey-server:1.17.1 - https://jersey.java.net/jersey-server/)
+        * jersey-servlet (com.sun.jersey:jersey-servlet:1.17.1 - https://jersey.java.net/jersey-servlet/)
+        * jersey-spring (com.sun.jersey.contribs:jersey-spring:1.8 - http://maven.apache.org)
+        * JAXB RI (com.sun.xml.bind:jaxb-impl:2.2.3-1 - http://jaxb.java.net/)
         * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
-        * JavaBeans(TM) Activation Framework (javax.activation:activation:1.1.1 - http://java.sun.com/javase/technologies/desktop/javabeans/jaf/index.jsp)
+        * JavaBeans Activation Framework (JAF) (javax.activation:activation:1.1 - http://java.sun.com/products/javabeans/jaf/index.jsp)
-        * javax.annotation API (javax.annotation:javax.annotation-api:1.2 - http://jcp.org/en/jsr/detail?id=250)
+        * JavaMail API (javax.mail:mail:1.4 - https://glassfish.dev.java.net/javaee5/mail/)
-        * 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)
+        * jstl (javax.servlet:jstl:1.1.2 - no url defined)
         * servlet-api (javax.servlet:servlet-api:2.5 - no url defined)
-        * javax.ws.rs-api (javax.ws.rs:javax.ws.rs-api:2.0.1 - http://jax-rs-spec.java.net)
+        * JAXB API bundle for GlassFish V3 (javax.xml.bind:jaxb-api:2.2.2 - https://jaxb.dev.java.net/)
-        * Class Model for Hk2 (org.glassfish.hk2:class-model:2.4.0-b31 - https://hk2.java.net/class-model)
+        * Streaming API for XML (javax.xml.stream:stax-api:1.0-2 - no url defined)
-        * 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)
+        * Servlet Specification 2.5 API (org.mortbay.jetty:servlet-api-2.5:6.1.14 - http://jetty.mortbay.org/project/modules/servlet-api-2.5)
-        * HK2 module of HK2 itself (org.glassfish.hk2:hk2:2.4.0-b31 - https://hk2.java.net/hk2)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
-        * HK2 API module (org.glassfish.hk2:hk2-api:2.4.0-b31 - https://hk2.java.net/hk2-api)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
-        * 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:
 
         * JUnit (junit:junit:4.11 - http://junit.org)
         * AspectJ runtime (org.aspectj:aspectjrt:1.6.11 - http://www.aspectj.org)
-        * JPA 2.0 API (org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final - http://hibernate.org)
+        * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
         * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
-        * Jetty Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-servlet-tester)
         * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
 
-    GNU General Public License, Version 2 with the Classpath Exception:
+    GNU General Public Library:
 
-        * 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)
+        * Streaming API for XML (javax.xml.stream:stax-api:1.0-2 - no url defined)
 
     GNU Lesser General Public License (LGPL):
 
-        * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
+        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.3.0 - http://wiki.fasterxml.com/JacksonHome)
-        * MaxMind GeoIP Legacy API (com.maxmind.geoip:geoip-api:1.3.0 - https://github.com/maxmind/geoip-api-java)
+        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
+        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
+        * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.0 - http://findbugs.sourceforge.net/)
+        * MaxMind GeoIP API (com.maxmind.geoip:geoip-api:1.2.11 - https://github.com/maxmind/geoip-api-java)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
+        * JAX-RS provider for JSON content type (org.codehaus.jackson:jackson-jaxrs:1.9.2 - http://jackson.codehaus.org)
+        * Xml Compatibility extensions for Jackson (org.codehaus.jackson:jackson-xc:1.9.2 - http://jackson.codehaus.org)
+        * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
         * 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/)
+        * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
-        * JBoss Logging 3 (org.jboss.logging:jboss-logging:3.1.0.GA - http://www.jboss.org)
         * org.jdesktop - Swing Worker (org.jdesktop:swing-worker:1.1 - no url defined)
+        * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
+        * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
         * xom (xom:xom:1.1 - http://www.xom.nu)
-        * XOM (xom:xom:1.2.5 - http://xom.nu)
 
     ICU License:
 
-        * ICU4J (com.ibm.icu:icu4j:56.1 - http://icu-project.org/)
+        * ICU4J (com.ibm.icu:icu4j:51.1 - http://icu-project.org/)
 
-    JDOM License (Apache-style license):
+    JDOM License:
 
         * jdom (jdom:jdom:1.0 - no url defined)
 
     MIT License:
 
-        * Bouncy Castle CMS and S/MIME API (org.bouncycastle:bcmail-jdk15:1.46 - http://www.bouncycastle.org/java.html)
+        * Bouncy Castle CMS and S/MIME API (org.bouncycastle:bcmail-jdk15:1.44 - http://www.bouncycastle.org/java.html)
-        * Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15:1.46 - http://www.bouncycastle.org/java.html)
+        * Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15:1.44 - http://www.bouncycastle.org/java.html)
-        * Main (org.jmockit:jmockit:1.21 - http://www.jmockit.org)
+        * Main (org.jmockit:jmockit:1.10 - 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)
+        * Mockito (org.mockito:mockito-all:1.9.5 - http://www.mockito.org)
-        * JCL 1.1.1 implemented over SLF4J (org.slf4j:jcl-over-slf4j:1.7.14 - http://www.slf4j.org)
+        * Mockito (org.mockito:mockito-core:1.9.5 - http://www.mockito.org)
-        * JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:1.7.14 - http://www.slf4j.org)
+        * Objenesis (org.objenesis:objenesis:1.0 - http://objenesis.googlecode.com/svn/docs/index.html)
-        * SLF4J API Module (org.slf4j:slf4j-api:1.7.14 - http://www.slf4j.org)
+        * JCL 1.1.1 implemented over SLF4J (org.slf4j:jcl-over-slf4j:1.6.1 - http://www.slf4j.org)
-        * SLF4J LOG4J-12 Binding (org.slf4j:slf4j-log4j12:1.7.14 - http://www.slf4j.org)
+        * JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:1.6.1 - http://www.slf4j.org)
+        * SLF4J API Module (org.slf4j:slf4j-api:1.6.1 - http://www.slf4j.org)
+        * SLF4J JDK14 Binding (org.slf4j:slf4j-jdk14:1.6.1 - http://www.slf4j.org)
+        * SLF4J LOG4J-12 Binding (org.slf4j:slf4j-log4j12:1.6.1 - 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)
+        * H2 Database Engine (com.h2database:h2:1.4.180 - http://www.h2database.com)
-        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
+        * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
         * Rhino (rhino:js:1.6R7 - http://www.mozilla.org/rhino/)
 
     Public Domain:
@@ -410,15 +388,3 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * 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 @@
+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/
+ - http://sourceforge.net/projects/dspace/files/DSpace%20Stable/
+     (select a version and read DSpace-Manual.pdf)
+
+Installation instructions are to be found in that documentation.
+
+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.
+
+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) 2002-2015, 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 +1,171 @@
+# 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
+
+# The user interface you will be using for DSpace. Common usage is either xmlui or jspui
+dspace.ui = xmlui
+
+# Full link your end users will use to access DSpace. In most cases, this will be the baseurl followed by
+# the context path to the UI you are using.
+#
+# Alternatively, you can use a url redirect or deploy the web application under the servlet container root.
+# In this case, make sure to remove the /${dspace.ui} from the dspace.url property.
+dspace.url = ${dspace.baseUrl}/${dspace.ui}
+
+# 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 #
+##########################
+
+# 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 that is used for DSpace.
+# ORACLE USAGE NOTE: In Oracle, schema is equivalent to "username". This means
+# specifying a "db.schema" is often unnecessary (i.e. you can leave it blank),
+# UNLESS your Oracle DB Account (in db.username) has access to multiple schemas.
+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 =
+
+#####################
+# LOGLEVEL SETTINGS #
+#####################
+loglevel.other = INFO
+# loglevel.other: Log level for other third-party tools/APIs used by DSpace
+# Possible values (from most to least info): DEBUG, INFO, WARN, ERROR, FATAL
+loglevel.dspace = INFO
+# loglevel.dspace: Log level for all DSpace-specific code (org.dspace.*)
+# Possible values (from most to least info): DEBUG, INFO, WARN, ERROR, FATAL

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>5.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -90,7 +89,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>build-helper-maven-plugin</artifactId>
-                <version>1.9.1</version>
+                <version>1.9</version>
                 <executions>
                     <execution>
                         <phase>validate</phase>
@@ -104,7 +103,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>buildnumber-maven-plugin</artifactId>
-                <version>1.4</version>
+                <version>1.3</version>
                 <executions>
                     <execution>
                         <phase>validate</phase>
@@ -114,7 +113,6 @@
                     </execution>
                 </executions>
             </plugin>
-
         </plugins>
     </build>
 
@@ -138,7 +136,6 @@
                 </plugins>
             </build>
         </profile>
-
         <!-- If Unit Testing is enabled, then setup the Unit Test Environment.
              See also the 'skiptests' profile in Parent POM. -->
         <profile>
@@ -159,18 +156,6 @@
                     <plugin>
                         <artifactId>maven-dependency-plugin</artifactId>
                         <version>2.8</version>
-                        <configuration>
-                            <outputDirectory>${project.build.directory}/testing</outputDirectory>
-                            <artifactItems>
-                                <artifactItem>
-                                    <groupId>org.dspace</groupId>
-                                    <artifactId>dspace-parent</artifactId>
-                                    <version>${project.version}</version>
-                                    <type>zip</type>
-                                    <classifier>testEnvironment</classifier>
-                                </artifactItem>
-                            </artifactItems>
-                        </configuration>
                         <executions>
                             <execution>
                                 <id>setupTestEnvironment</id>
@@ -178,13 +163,18 @@
                                 <goals>
                                     <goal>unpack</goal>
                                 </goals>
-                            </execution>
+                                <configuration>
-                            <execution>
+                                    <outputDirectory>${project.build.directory}/testing</outputDirectory>
-                                <id>setupIntegrationTestEnvironment</id>
+                                    <artifactItems>
-                                <phase>pre-integration-test</phase>
+                                        <artifactItem>
-                                <goals>
+                                            <groupId>org.dspace</groupId>
-                                    <goal>unpack</goal>
+                                            <artifactId>dspace-parent</artifactId>
-                                </goals>
+                                            <version>${project.version}</version>
+                                            <type>zip</type>
+                                            <classifier>testEnvironment</classifier>
+                                        </artifactItem>
+                                    </artifactItems>
+                                </configuration>
                             </execution>
                         </executions>
                     </plugin>
@@ -206,81 +196,86 @@
                         <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, '/');
+                                    project.properties['agnostic.build.dir']=project.build.directory.replace(File.separator,'/');
-                                        println("Initializing Maven property 'agnostic.build.dir' to: " + project.properties['agnostic.build.dir']);
+                                    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 environment.
+                         It weaves two files, the default 'dspace.cfg' and 'dspace.cfg.more',
+                         both of which are included in the testEnvironment.zip. -->
+                    <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>
 
-                    <!-- Run Unit Testing! This plugin just kicks off the tests (when enabled). -->
+                    <!-- The ant plugin below ensures that the final "woven" dspace.cfg
+                         ends up in the /target/testing/dspace/ directory. This becomes
+                         our final dspace.cfg for the Unit Testing environment. 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>
+                                    <target>
+                                        <copy file="${agnostic.build.dir}/testing/dspace.cfg.woven" tofile="${agnostic.build.dir}/testing/dspace/config/dspace.cfg" />
+                                    </target>
+                                </configuration>
+                                <goals>
+                                    <goal>run</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+
+                    <!-- Run Unit/Integration 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 -->
+                                <!-- Specify the dspace.cfg file to use for test environment -->
-                                <!-- This system property is loaded by AbstractDSpaceTest to initialize the test environment -->
+                                <dspace.configuration>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</dspace.configuration>
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
-                                <!-- Turn off any DSpace logging -->
-                                <dspace.log.init.disable>true</dspace.log.init.disable>
-                            </systemPropertyVariables>
-                        </configuration>
-                    </plugin>
-
-
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>xml-maven-plugin</artifactId>
-                        <version>1.0.1</version>
-                        <executions>
-                            <execution>
-                                <id>validate-ALL-xml-and-xsl</id>
-                                <phase>process-test-resources</phase>
-                                <goals>
-                                    <goal>validate</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                        <configuration>
-                            <validationSets>
-                                <!-- validate ALL XML and XSL config files in the testing folder -->
-                                <validationSet>
-                                    <dir>${agnostic.build.dir}/testing</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xconf</include>
-                                    </includes>
-                                </validationSet>
-                                <!-- validate ALL XML and XSL files throughout the project -->
-                                <validationSet>
-                                    <dir>${root.basedir}</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xmap</include>
-                                    </includes>
-                                </validationSet>
-                            </validationSets>
-                        </configuration>
-                    </plugin>
-
-
-                    <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
-                    <plugin>
-                        <artifactId>maven-failsafe-plugin</artifactId>
-                        <configuration>
-                            <systemPropertyVariables>
-                                <!-- Specify the dspace.dir to use for test environment -->
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
                             </systemPropertyVariables>
@@ -292,36 +287,8 @@
         </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>
 
+    <dependencies>
         <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>handle</artifactId>
@@ -338,20 +305,22 @@
             <groupId>org.dspace.dependencies</groupId>
             <artifactId>dspace-tm-extractors</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-common</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-queryparser</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
             <type>pom</type>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>commons-cli</groupId>
@@ -366,12 +335,8 @@
             <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>
@@ -387,8 +352,8 @@
             <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>
@@ -414,7 +379,7 @@
             </exclusions>
         </dependency>
         <dependency>
-            <groupId>org.jdom</groupId>
+            <groupId>jdom</groupId>
             <artifactId>jdom</artifactId>
         </dependency>
         <dependency>
@@ -430,8 +395,12 @@
             <artifactId>pdfbox</artifactId>
         </dependency>
         <dependency>
-            <groupId>org.apache.pdfbox</groupId>
+           <groupId>org.apache.pdfbox</groupId>
-            <artifactId>fontbox</artifactId>
+           <artifactId>fontbox</artifactId>
+        </dependency>
+        <dependency>
+           <groupId>org.apache.pdfbox</groupId>
+           <artifactId>jempbox</artifactId>
         </dependency>
         <dependency>
             <groupId>org.bouncycastle</groupId>
@@ -449,6 +418,10 @@
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-scratchpad</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.poi</groupId>
+            <artifactId>poi-ooxml</artifactId>
+        </dependency>
         <dependency>
             <groupId>rome</groupId>
             <artifactId>rome</artifactId>
@@ -464,16 +437,10 @@
         <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>
@@ -512,11 +479,10 @@
             <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>
@@ -526,30 +492,11 @@
             <groupId>gr.ekt.bte</groupId>
             <artifactId>bte-core</artifactId>
             <version>0.9.3.5</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>gr.ekt.bte</groupId>
             <artifactId>bte-io</artifactId>
             <version>0.9.3.5</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.apache.commons</groupId>
-                    <artifactId>commons-lang3</artifactId>
-                </exclusion>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
@@ -578,11 +525,12 @@
         <dependency>
             <groupId>commons-configuration</groupId>
             <artifactId>commons-configuration</artifactId>
+            <version>1.8</version>
         </dependency>
         <dependency>
-            <groupId>com.maxmind.geoip2</groupId>
+            <groupId>com.maxmind.geoip</groupId>
-            <artifactId>geoip2</artifactId>
+            <artifactId>geoip-api</artifactId>
-            <version>2.11.0</version>
+            <version>1.2.11</version>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
@@ -591,13 +539,13 @@
         <dependency>
             <groupId>dnsjava</groupId>
             <artifactId>dnsjava</artifactId>
-            <version>2.1.7</version>
+            <version>2.1.1</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>1.4.0</version>
         </dependency>
 
         <dependency>
@@ -616,15 +564,15 @@
         <dependency>
             <groupId>com.google.guava</groupId>
             <artifactId>guava</artifactId>
-            <version>19.0</version>
+            <version>18.0</version>
         </dependency>
 
 
         <dependency>
-            <groupId>org.postgresql</groupId>
+            <groupId>postgresql</groupId>
             <artifactId>postgresql</artifactId>
         </dependency>
-
+		
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
@@ -642,12 +590,12 @@
             <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>
+            <version>3.0</version>
         </dependency>
 
         <!-- Google Analytics -->
@@ -655,21 +603,13 @@
             <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>
+            <artifactId>google-oauth-client-jetty</artifactId>
         </dependency>
         <!-- FindBugs -->
         <dependency>
@@ -683,6 +623,7 @@
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
+            <version>2.3</version>
         </dependency>
         <dependency>
             <groupId>javax.inject</groupId>
@@ -690,50 +631,6 @@
             <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

@@ -19,145 +19,147 @@ 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.
+   * Map all generated attribute names to field names with lowercase and underscores.
-     */
+   */
-    public static final String LOWERNAMES = "lowernames";
+  public static final String LOWERNAMES = "lowernames";
 
-    /**
+  /**
-     * if true, ignore TikaException (give up to extract text but index meta data)
+   * if true, ignore TikaException (give up to extract text but index meta data)
-     */
+   */
-    public static final String IGNORE_TIKA_EXCEPTION = "ignoreTikaException";
+  public static final String IGNORE_TIKA_EXCEPTION = "ignoreTikaException";
 
 
-    /**
+  /**
-     * The param prefix for mapping Tika metadata to Solr fields.
+   * The param prefix for mapping Tika metadata to Solr fields.
-     * <p>
+   * <p/>
-     * To map a field, add a name like:
+   * To map a field, add a name like:
-     * <pre>fmap.title=solr.title</pre>
+   * <pre>fmap.title=solr.title</pre>
-     *
+   *
-     * In this example, the tika "title" metadata value will be added to a Solr field named "solr.title"
+   * 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.";
+   *
+   */
+  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.
+   * The boost value for the name of the field.  The boost can be specified by a name mapping.
-     * <p>
+   * <p/>
-     * For example
+   * For example
-     * <pre>
+   * <pre>
-     * map.title=solr.title
+   * map.title=solr.title
-     * boost.solr.title=2.5
+   * boost.solr.title=2.5
-     * </pre>
+   * </pre>
-     * will boost the solr.title field for this document by 2.5
+   * will boost the solr.title field for this document by 2.5
-     */
+   *
-    public static final String BOOST_PREFIX = "boost.";
+   */
+  public static final String BOOST_PREFIX = "boost.";
 
-    /**
+  /**
-     * Pass in literal values to be added to the document, as in
+   * Pass in literal values to be added to the document, as in
-     * <pre>
+   * <pre>
-     *  literal.myField=Foo
+   *  literal.myField=Foo 
-     * </pre>
+   * </pre>
-     */
+   *
-    public static final String LITERALS_PREFIX = "literal.";
+   */
+  public static final String LITERALS_PREFIX = "literal.";
 
 
-    /**
+  /**
-     * Restrict the extracted parts of a document to be indexed
+   * Restrict the extracted parts of a document to be indexed
-     * by passing in an XPath expression.  All content that satisfies the XPath expr.
+   *  by passing in an XPath expression.  All content that satisfies the XPath expr.
-     * will be passed to the {@link org.apache.solr.handler.extraction.SolrContentHandler}.
+   * will be passed to the {@link SolrContentHandler}.
-     * <p>
+   * <p/>
-     * See Tika's docs for what the extracted document looks like.
+   * See Tika's docs for what the extracted document looks like.
-     *
+   * <p/>
-     * @see #CAPTURE_ELEMENTS
+   * @see #CAPTURE_ELEMENTS
-     */
+   */
-    public static final String XPATH_EXPRESSION = "xpath";
+  public static final String XPATH_EXPRESSION = "xpath";
 
 
-    /**
+  /**
-     * Only extract and return the content, do not index it.
+   * Only extract and return the content, do not index it.
-     */
+   */
-    public static final String EXTRACT_ONLY = "extractOnly";
+  public static final String EXTRACT_ONLY = "extractOnly";
 
-    /**
+  /**
-     * Content output format if extractOnly is true. Default is "xml", alternative is "text".
+   * Content output format if extractOnly is true. Default is "xml", alternative is "text".
-     */
+   */
-    public static final String EXTRACT_FORMAT = "extractFormat";
+  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
+   * Capture attributes separately according to the name of the element, instead of just adding them to the string buffer
-     * buffer
+   */
-     */
+  public static final String CAPTURE_ATTRIBUTES = "captureAttr";
-    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
+   * 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
-     * revert to pre-4.0 behaviour
+   */
-     */
+  public static final String LITERALS_OVERRIDE = "literalsOverride";
-    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)
+   * 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
-     * separately from the default.  This is different
+   * then the case of passing in an XPath expression.
-     * then the case of passing in an XPath expression.
+   * <p/>
-     * <p>
+   * The Capture field is based on the localName returned to the {@link SolrContentHandler}
-     * The Capture field is based on the localName returned to the
+   * by Tika, not to be confused by the mapped field.  The field name can then
-     * {@link org.apache.solr.handler.extraction.SolrContentHandler}
+   * be mapped into the index schema.
-     * by Tika, not to be confused by the mapped field.  The field name can then
+   * <p/>
-     * be mapped into the index schema.
+   * For instance, a Tika document may look like:
-     * <p>
+   * <pre>
-     * For instance, a Tika document may look like:
+   *  &lt;html&gt;
-     * <pre>
+   *    ...
-     *  &lt;html&gt;
+   *    &lt;body&gt;
-     *    ...
+   *      &lt;p&gt;some text here.  &lt;div&gt;more text&lt;/div&gt;&lt;/p&gt;
-     *    &lt;body&gt;
+   *      Some more text
-     *      &lt;p&gt;some text here.  &lt;div&gt;more text&lt;/div&gt;&lt;/p&gt;
+   *    &lt;/body&gt;
-     *      Some more text
+   * </pre>
-     *    &lt;/body&gt;
+   * By passing in the p tag, you could capture all P tags separately from the rest of the t
-     * </pre>
+   * Thus, in the example, the capture of the P tag would be: "some text here.  more text"
-     * 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";
-    public static final String CAPTURE_ELEMENTS = "capture";
 
-    /**
+  /**
-     * The type of the stream.  If not specified, Tika will use mime type detection.
+   * The type of the stream.  If not specified, Tika will use mime type detection.
-     */
+   */
-    public static final String STREAM_TYPE = "stream.type";
+  public static final String STREAM_TYPE = "stream.type";
 
 
-    /**
+  /**
-     * Optional.  The file name. If specified, Tika can take this into account while
+   * Optional.  The file name. If specified, Tika can take this into account while
-     * guessing the MIME type.
+   * guessing the MIME type.
-     */
+   */
-    public static final String RESOURCE_NAME = "resource.name";
+  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
+   * 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";
+  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
+   * 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
+   * to setup a dynamic field to automatically capture it
-     */
+   */
-    public static final String UNKNOWN_FIELD_PREFIX = "uprefix";
+  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
+   * Optional.  If specified and the name of a potential field cannot be determined, the default Field specified
-     * will be used instead.
+   * will be used instead.
-     */
+   */
-    public static final String DEFAULT_FIELD = "defaultField";
+  public static final String DEFAULT_FIELD = "defaultField";
 
-    /**
+  /**
-     * Optional. If specified, loads the file as a source for password lookups for Tika encrypted documents.
+   * Optional. If specified, loads the file as a source for password lookups for Tika encrypted documents.
-     * <p>
+   * <p>
-     * File format is Java properties format with one key=value per line.
+   * 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 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
+   * 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
+   * 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";
+  public static final String PASSWORD_MAP_FILE = "passwordsFile";
 }

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

@@ -9,47 +9,31 @@ 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
  * relationships. Takes community DB Id or handle arguments as inputs.
- *
+ * 
  * @author rrodgers
  * @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();
 
@@ -57,11 +41,11 @@ public class CommunityFiliator {
 
         options.addOption("s", "set", false, "set a parent/child relationship");
         options.addOption("r", "remove", false,
-                          "remove a parent/child relationship");
+                "remove a parent/child relationship");
         options.addOption("p", "parent", true,
-                          "parent community (handle or database ID)");
+                "parent community (handle or database ID)");
         options.addOption("c", "child", true,
-                          "child community (handle or databaseID)");
+                "child community (handle or databaseID)");
         options.addOption("h", "help", false, "help");
 
         CommandLine line = parser.parse(options, argv);
@@ -70,48 +54,57 @@ 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
-                .println("\nestablish a relationship: CommunityFiliator -s -p parentID -c childID");
+                    .println("\nestablish a relationship: CommunityFiliator -s -p parentID -c childID");
             System.out
-                .println("remove a relationship: CommunityFiliator -r -p parentID -c childID");
+                    .println("remove a relationship: CommunityFiliator -r -p parentID -c childID");
 
             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)");
+                    .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);
             }
@@ -120,150 +113,149 @@ 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);
+                        + parentID);
                 System.exit(1);
             }
 
-            if (child == null) {
+            if (child == null)
+            {
                 System.out.println("Error, child community cannot be found: "
-                                       + childID);
+                        + 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());
+                    + 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());
+                    + " already a child of: " + childDad.getID());
             System.exit(1);
         }
 
         // 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");
+                        .println("Error, circular parentage - child is parent of parent");
                 System.exit(1);
             }
         }
 
         // everthing's OK
-        communityService.addSubcommunity(c, parent, child);
+        parent.addSubcommunity(child);
 
         // complete the pending transaction
         c.complete();
         System.out.println("Filiation complete. Community: '" + parent.getID()
-                               + "' is parent of community: '" + child.getID() + "'");
+                + "' 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");
+                    .println("Error, child community not a child of parent community");
             System.exit(1);
         }
 
         // OK remove the mappings - but leave the community, which will become
         // top-level
-        child.getParentCommunities().remove(parent);
+        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();
         System.out.println("Defiliation complete. Community: '" + child.getID()
-                               + "' is no longer a child of community: '" + parent.getID()
+                + "' is no longer a child of community: '" + parent.getID()
-                               + "'");
+                + "'");
     }
 
-    /**
+    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);
+                    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

@@ -15,15 +15,13 @@ 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
@@ -33,221 +31,238 @@ import org.dspace.eperson.service.GroupService;
  * <P>
  * Alternatively, it can be used to take the email, first name, last name and
  * desired password as arguments thus:
- *
+ * 
  * CreateAdministrator -e [email] -f [first name] -l [last name] -p [password]
- *
+ * 
- * This is particularly convenient for automated deploy scripts that require an
+ * This is particularly convenient for automated deploy scripts that require an 
  * initial administrator, for example, before deployment can be completed
- *
+ * 
  * @author Robert Tansley
  * @author Richard Jones
+ * 
  * @version $Revision$
  */
-public final class CreateAdministrator {
+public final class CreateAdministrator
-    /**
+{
-     * DSpace Context object
+	/** DSpace Context object */
-     */
+	private final 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();
+    	CommandLineParser parser = new PosixParser();
-
+    	Options options = new Options();
-        CreateAdministrator ca = new CreateAdministrator();
+    	
-
+    	CreateAdministrator ca = new CreateAdministrator();
-        options.addOption("e", "email", true, "administrator email address");
+    	
-        options.addOption("f", "first", true, "administrator first name");
+    	options.addOption("e", "email", true, "administrator email address");
-        options.addOption("l", "last", true, "administrator last name");
+    	options.addOption("f", "first", true, "administrator first name");
-        options.addOption("c", "language", true, "administrator language");
+    	options.addOption("l", "last", true, "administrator last name");
-        options.addOption("p", "password", true, "administrator password");
+    	options.addOption("c", "language", true, "administrator language");
-
+    	options.addOption("p", "password", true, "administrator password");
-        CommandLine line = parser.parse(options, argv);
+    	
-
+    	CommandLine line = parser.parse(options, argv);
-        if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
+    	
-            line.hasOption("c") && line.hasOption("p")) {
+    	if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
-            ca.createAdministrator(line.getOptionValue("e"),
+    			line.hasOption("c") && line.hasOption("p"))
-                                   line.getOptionValue("f"), line.getOptionValue("l"),
+    	{
-                                   line.getOptionValue("c"), line.getOptionValue("p"));
+    		ca.createAdministrator(line.getOptionValue("e"),
-        } else {
+    				line.getOptionValue("f"), line.getOptionValue("l"),
-            ca.negotiateAdministratorDetails();
+    				line.getOptionValue("c"), line.getOptionValue("p"));
-        }
+    	}
+    	else
+    	{
+    		ca.negotiateAdministratorDetails();
+    	}
     }
-
+    
-    /**
+    /** 
      * 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();
+    	context = new Context();
-        ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
     }
-
+    
     /**
-     * Method which will negotiate with the user via the command line to
+     * 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();
-
+    	
-        System.out.println("Creating an initial administrator account");
+    	System.out.println("Creating an initial administrator account");
-
+    	
-        boolean dataOK = false;
+    	boolean dataOK = false;
-
+    	
-        String email = null;
+    	String email = null;
-        String firstName = null;
+    	String firstName = null;
-        String lastName = null;
+    	String lastName = null;
         char[] password1 = null;
         char[] password2 = null;
-        String language = I18nUtil.DEFAULTLOCALE.getLanguage();
+    	String language = I18nUtil.DEFAULTLOCALE.getLanguage();
-
+    	
-        while (!dataOK) {
+    	while (!dataOK)
-            System.out.print("E-mail address: ");
+    	{
-            System.out.flush();
+    		System.out.print("E-mail address: ");
-
+    		System.out.flush();
-            email = console.readLine();
+    		
-            if (!StringUtils.isBlank(email)) {
+    		email = console.readLine();
+            if (!StringUtils.isBlank(email))
+            {
                 email = email.trim();
-            } else {
+            }
+            else
+            {
                 System.out.println("Please provide an email address.");
                 continue;
             }
+    		
+    		System.out.print("First name: ");
+    		System.out.flush();
+    		
+    		firstName = console.readLine();
 
-            System.out.print("First name: ");
+            if (firstName != null)
-            System.out.flush();
+            {
-
-            firstName = console.readLine();
-
-            if (firstName != null) {
                 firstName = firstName.trim();
             }
+    		
+    		System.out.print("Last name: ");
+    		System.out.flush();
+    		
+    		lastName = console.readLine();
 
-            System.out.print("Last name: ");
+            if (lastName != null)
-            System.out.flush();
+            {
-
-            lastName = console.readLine();
-
-            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 = console.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.print("Password: ");
+    		System.out.flush();
 
-            System.out.println("Password will not display on screen.");
+    		password1 = console.readPassword();
-            System.out.print("Password: ");
+    		
-            System.out.flush();
+    		System.out.print("Again to confirm: ");
-
+    		System.out.flush();
-            password1 = console.readPassword();
+    		
-
+    		password2 = console.readPassword();
-            System.out.print("Again to confirm: ");
-            System.out.flush();
-
-            password2 = console.readPassword();
 
             //TODO real password validation
-            if (password1.length > 1 && Arrays.equals(password1, password2)) {
+            if (password1.length > 1 && Arrays.equals(password1, password2))
-                // password OK
+    		{
-                System.out.print("Is the above data correct? (y or n): ");
+    			// password OK
-                System.out.flush();
+    			System.out.print("Is the above data correct? (y or n): ");
+    			System.out.flush();
+    			
+    			String s = console.readLine();
 
-                String s = console.readLine();
+                if (s != null)
-
+                {
-                if (s != null) {
                     s = s.trim();
-                    if (s.toLowerCase().startsWith("y")) {
+                    if (s.toLowerCase().startsWith("y"))
+                    {
                         dataOK = true;
                     }
                 }
-            } else {
+    		}
-                System.out.println("Passwords don't match");
+    		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));
+    	
+    	// if we make it to here, we are ready to create an administrator
+    	createAdministrator(email, firstName, lastName, language, String.valueOf(password1));
 
         //Cleaning arrays that held password
         Arrays.fill(password1, ' ');
         Arrays.fill(password2, ' ');
     }
-
+    
     /**
      * Create the administrator with the given details.  If the user
      * already exists then they are simply upped to administrator status
-     *
+     * 
-     * @param email    the email for the user
+     * @param email	the email for the user
-     * @param first    user's first name
+     * @param first	user's first name
-     * @param last     user's last name
+     * @param last	user's last name
      * @param language preferred language
-     * @param pw       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)
+    		String language, String pw)
-        throws Exception {
+    	throws Exception
-        // Of course we aren't an administrator yet so we need to
+    {
-        // circumvent authorisation
+    	// Of course we aren't an administrator yet so we need to
-        context.turnOffAuthorisationSystem();
+    	// circumvent authorisation
-
+    	context.setIgnoreAuthorization(true);
-        // Find administrator group
+    	
-        Group admins = groupService.findByName(context, Group.ADMIN);
+    	// Find administrator group
-
+    	Group admins = Group.find(context, 1);
-        if (admins == null) {
+    	
-            throw new IllegalStateException("Error, no admin group (group 1) found");
+    	if (admins == null)
-        }
+    	{
-
+    		throw new IllegalStateException("Error, no admin group (group 1) found");
-        // Create the administrator e-person
+    	}
-        EPerson eperson = ePersonService.findByEmail(context, email);
+    	
-
+    	// Create the administrator e-person
+        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();
+    	context.complete();
-
+    	
-        System.out.println("Administrator account created");
+    	System.out.println("Administrator account created");
     }
 }

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;
 
@@ -37,178 +33,173 @@ import org.xml.sax.SAXException;
  *
  * This class creates an xml document as passed in the arguments and
  * from the metadata schemas for the repository.
- *
+ * 
  * The form of the XML is as follows
- * {@code
+ * 
  * <metadata-schemas>
- * <schema>
+ *   <schema>
- * <name>dc</name>
+ *     <name>dc</name>
- * <namespace>http://dublincore.org/documents/dcmi-terms/</namespace>
+ *     <namespace>http://dublincore.org/documents/dcmi-terms/</namespace>
- * </schema>
+ *   </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();
-        options.addOption("f", "file", true, "output xml file for registry");
+        options.addOption("f", "file",   true, "output xml file for registry");
         options.addOption("s", "schema", true, "the name of the schema to export");
         CommandLine line = parser.parse(options, args);
-
+        
-        String file = null;
+        String file   = null;
         String schema = null;
 
-        if (line.hasOption('f')) {
+        if (line.hasOption('f'))
-            file = line.getOptionValue('f');
+        {
-        } else {
+            file   = line.getOptionValue('f');
+        }
+        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);
         xmlFormat.setIndent(4);
-
+        
         XMLSerializer xmlSerializer = new XMLSerializer(new BufferedWriter(new FileWriter(file)), xmlFormat);
         //        XMLSerializer xmlSerializer = new XMLSerializer(System.out, xmlFormat);
         xmlSerializer.startDocument();
         xmlSerializer.startElement("dspace-dc-types", null);
-
+        
         // 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 {
-            // Get the metadata fields for all the schemas
-            mdFields = metadataFieldService.findAll(context);
         }
-
+        else
+        {
+            // Get the metadata fields for all the schemas
+            mdFields = MetadataField.findAll(context);
+        }
+        
         // Output the metadata fields
-        for (MetadataField mdField : mdFields) {
+        for (MetadataField mdField : mdFields)
+        {
             saveType(context, xmlSerializer, mdField);
         }
-
+        
         xmlSerializer.endElement("dspace-dc-types");
         xmlSerializer.endDocument();
-
+        
         // abort the context, as we shouldn't have changed it!!
         context.abort();
     }
-
+    
     /**
      * 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);
             }
         }
     }
-
+    
     /**
      * 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 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;
         }
 
         // Output the parent tag
         xmlSerializer.startElement("dc-schema", null);
-
+        
         // Output the schema name
         xmlSerializer.startElement("name", null);
         xmlSerializer.characters(name.toCharArray(), 0, name.length());
@@ -221,25 +212,26 @@ public class MetadataExporter {
 
         xmlSerializer.endElement("dc-schema");
     }
-
+    
     /**
      * 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");
         }
-
+        
         // Get the data from the metadata field
         String schemaName = getSchemaName(context, mdField);
         String element = mdField.getElement();
@@ -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");
         }
 
@@ -265,64 +258,68 @@ 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");
             }
         }
         return name;
     }
-
+    
     /**
      * 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" +
+                        " -f <xml output file> : specify the output file for the schemas\n" +
-            " -s <schema> : name of the schema to export\n";
+                        " -s <schema> : name of the schema to export\n";
         System.out.println(usage);
     }
 }

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;
 
@@ -17,92 +18,73 @@ 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;
 
 /**
  * @author Richard Jones
  *
  * This class takes an xml document as passed in the arguments and
- * uses it to create metadata elements in the Metadata Registry if
+ * uses it to create metadata elements in the Metadata Registry if 
  * they do not already exist
- *
+ * 
  * The format of the XML file is as follows:
- *
+ * 
- * {@code
  * <dspace-dc-types>
- * <dc-type>
+ *   <dc-type>
- * <schema>icadmin</schema>
+ *     <schema>icadmin</schema>
- * <element>status</element>
+ *     <element>status</element>
- * <qualifier>dateset</qualifier>
+ *     <qualifier>dateset</qualifier>
- * <scope_note>the workflow status of an item</scope_note>
+ *     <scope_note>the workflow status of an item</scope_note>
- * </dc-type>
+ *   </dc-type>
- *
+ *   
- * [....]
+ *   [....]
- *
+ *   
  * </dspace-dc-types>
- * }
  */
-public class MetadataImporter {
+public class MetadataImporter
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+{
-                                                                                        .getMetadataSchemaService();
+    /** logging category */
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
-                                                                                      .getMetadataFieldService();
-
-    /**
-     * logging category
-     */
     private static final Logger log = LoggerFactory.getLogger(MetadataImporter.class);
 
-    /**
+	/**
-     * Default constructor
+	 * main method for reading user input from the command line
-     */
+	 */
-    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,
+    	throws ParseException, SQLException, IOException, TransformerException,
-        ParserConfigurationException, AuthorizeException, SAXException,
+    			ParserConfigurationException, AuthorizeException, SAXException,
-        NonUniqueMetadataException, RegistryImportException {
+    			NonUniqueMetadataException, RegistryImportException
+    {
         boolean forceUpdate = false;
-
+        
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
         Options options = new Options();
         options.addOption("f", "file", true, "source xml file for DC fields");
         options.addOption("u", "update", false, "update an existing schema");
         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);
         }
@@ -110,27 +92,20 @@ public class MetadataImporter {
         forceUpdate = line.hasOption('u');
         loadRegistry(file, forceUpdate);
     }
-
+    
     /**
      * Load the data from the specified file path into the database
-     *
+     * 
-     * @param file        the file path containing the source data
+     * @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,
+    	throws SQLException, IOException, TransformerException, ParserConfigurationException, 
-        AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException {
+    		AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException
+    {
         Context context = null;
 
-        try {
+        try
+        {
             // create a context
             context = new Context();
             context.turnOffAuthorisationSystem();
@@ -142,7 +117,8 @@ 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);
             }
@@ -151,95 +127,101 @@ 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
+        finally
-            if (context != null && context.isValid()) {
+        {
+           // 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
-        MetadataSchema s = metadataSchemaService.find(context, name);
+        MetadataSchema s = MetadataSchema.find(context, name);
-
+        
-        if (s == null) {
+        if (s == null)
+        {
             // Schema does not exist - create
             log.info("Registering Schema " + name + " (" + namespace + ")");
-            metadataSchemaService.create(context, name, namespace);
+            MetadataSchema schema = new MetadataSchema(namespace, name);
-        } else {
+            schema.create(context);
+        }
+        else
+        {
             // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace)) {
+            if (s.getNamespace().equals(namespace))
+            {
                 // This schema already exists with this namespace, skipping it
                 return;
             }
-
+            
             // It's a different namespace - have we been told to update?
-            if (updateExisting) {
+            if (updateExisting)
+            {
                 // Update the existing schema namespace and continue to type import
                 log.info("Updating Schema " + name + ": New namespace " + namespace);
                 s.setNamespace(namespace);
-                metadataSchemaService.update(context, s);
+                s.update(context);
-            } else {
+            }
-                throw new RegistryImportException(
+            else
-                    "Schema " + name + " already registered with different namespace " + namespace + ". Rerun with " +
+            {
-                        "'update' option enabled if you wish to update this schema.");
+                throw new RegistryImportException("Schema " + name + " already registered with different namespace " + namespace + ". Rerun with 'update' option enabled if you wish to update this schema.");
             }
         }
-
+        
     }
-
+    
     /**
      * Process a node in the metadata registry XML file. The node must
      * 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,
+            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");
@@ -247,41 +229,48 @@ 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;
         }
 
-
+        
         // 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.");
         }
-
+        
-        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
             return;
         }
-
+        
         // Actually create this metadata field as it doesn't yet exist
         String fieldName = schema + "." + element + "." + qualifier;
-        if (qualifier == null) {
+        if(qualifier==null)
             fieldName = schema + "." + element;
-        }
         log.info("Registering metadata field " + fieldName);
-        MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
+        MetadataField field = new MetadataField();
-        metadataFieldService.update(context, field);
+        field.setSchemaID(schemaObj.getSchemaID());
+        field.setElement(element);
+        field.setQualifier(qualifier);
+        field.setScopeNote(scopeNote);
+        field.create(context);
     }
-
+    
     /**
      * 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 " +
+        				" -f <xml source file> : specify which xml source file " +
-            "contains the DC fields to import.\n";
+        				"contains the DC fields to import.\n";
         System.out.println(usage);
     }
 }

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

@@ -12,40 +12,45 @@ 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

@@ -12,40 +12,45 @@ 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);
+    {
+    	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);
+    {
+    	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;
 
 /**
@@ -28,32 +31,27 @@ 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)
+    public static Document loadXML(String filename) 
-        throws IOException, ParserConfigurationException, SAXException {
+    	throws IOException, ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                                                        .newDocumentBuilder();
+                .newDocumentBuilder();
 
         Document document = builder.parse(new File(filename));
-
+        
         return document;
     }
-
+    
     /**
      * Get the CDATA of a particular element. For example, if the XML document
      * contains:
@@ -65,18 +63,22 @@ public class RegistryImporter {
      * return <code>application/pdf</code>.
      * </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;
         }
 
@@ -100,28 +103,32 @@ public class RegistryImporter {
      * <P>
      * <code>
      * &lt;foo&gt;
-     * &lt;bar&gt;val1&lt;/bar&gt;
+     *   &lt;bar&gt;val1&lt;/bar&gt;
-     * &lt;bar&gt;val2&lt;/bar&gt;
+     *   &lt;bar&gt;val2&lt;/bar&gt;
      * &lt;/foo&gt;
      * </code>
      * passing this the <code>foo</code> node and <code>bar</code> will
      * return <code>val1</code> and <code>val2</code>.
      * </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;
@@ -39,37 +39,30 @@ import org.xml.sax.SAXException;
  * <code>RegistryLoader -bitstream bitstream-formats.xml</code>
  * <P>
  * <code>RegistryLoader -dc dc-types.xml</code>
- *
+ * 
  * @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 | -metadata) registry-file.xml";
 
         Context context = null;
 
-        try {
+        try
+        {
             context = new Context();
 
             // Can't update registries anonymously, so we need to turn off
@@ -77,12 +70,17 @@ public class RegistryLoader {
             context.turnOffAuthorisationSystem();
 
             // Work out what we're loading
-            if (argv[0].equalsIgnoreCase("-bitstream")) {
+            if (argv[0].equalsIgnoreCase("-bitstream"))
+            {
                 RegistryLoader.loadBitstreamFormats(context, argv[1]);
-            } else if (argv[0].equalsIgnoreCase("-metadata")) {
+            }
+            else if (argv[0].equalsIgnoreCase("-metadata"))
+            {
                 // Call MetadataImporter, as it handles Metadata schema updates
                 MetadataImporter.loadRegistry(argv[1], true);
-            } else {
+            }
+            else
+            {
                 System.err.println(usage);
             }
 
@@ -90,69 +88,71 @@ public class RegistryLoader {
             context.complete();
 
             System.exit(0);
-        } catch (ArrayIndexOutOfBoundsException ae) {
+        }
+        catch (ArrayIndexOutOfBoundsException ae)
+        {
             System.err.println(usage);
 
             System.exit(1);
-        } catch (Exception e) {
+        }
+        catch (Exception e)
+        {
             log.fatal(LogManager.getHeader(context, "error_loading_registries",
-                                           ""), e);
+                    ""), e);
 
             System.err.println("Error: \n - " + e.getMessage());
             System.exit(1);
-        } finally {
+        }
+        finally
+        {
             // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
+            if(context!=null && context.isValid())
                 context.abort();
-            }
         }
     }
 
     /**
      * 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,
+            throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
+            SAXException, TransformerException, AuthorizeException
+    {
         Document document = loadXML(filename);
 
         // Get the nodes corresponding to formats
         NodeList typeNodes = XPathAPI.selectNodeList(document,
-                                                     "dspace-bitstream-types/bitstream-type");
+                "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);
         }
 
         log.info(LogManager.getHeader(context, "load_bitstream_formats",
-                                      "number_loaded=" + typeNodes.getLength()));
+                "number_loaded=" + typeNodes.getLength()));
     }
 
     /**
      * 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,
+            throws SQLException, IOException, TransformerException,
-        AuthorizeException {
+            AuthorizeException
+    {
         // Get the values
         String mimeType = getElementData(node, "mimetype");
         String shortDesc = getElementData(node, "short_description");
@@ -167,30 +167,30 @@ 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);
+        BitstreamFormat exists = BitstreamFormat.findByMIMEType(context, mimeType);
-
+        
         // If not found by mimeType, check by short description (since this must also be unique)
-        if (exists == null) {
+        if(exists==null)
-            exists = bitstreamFormatService.findByShortDescription(context, shortDesc);
+        {    
+            exists = BitstreamFormat.findByShortDescription(context, shortDesc);
         }
-
+            
         // If it doesn't exist, create it..otherwise skip it.
-        if (exists == null) {
+        if(exists==null)
+        {
             // Create the format object
-            BitstreamFormat format = bitstreamFormatService.create(context);
+            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();
         }
     }
 
@@ -198,17 +198,17 @@ 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();
+                .newDocumentBuilder();
 
         return builder.parse(new File(filename));
     }
@@ -224,18 +224,22 @@ public class RegistryLoader {
      * return <code>application/pdf</code>.
      * </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 +247,8 @@ public class RegistryLoader {
         // Get the #text
         Node dataNode = childNode.getFirstChild();
 
-        if (dataNode == null) {
+        if (dataNode == null)
+        {
             return null;
         }
 
@@ -259,28 +264,32 @@ public class RegistryLoader {
      * <P>
      * <code>
      * &lt;foo&gt;
-     * &lt;bar&gt;val1&lt;/bar&gt;
+     *   &lt;bar&gt;val1&lt;/bar&gt;
-     * &lt;bar&gt;val2&lt;/bar&gt;
+     *   &lt;bar&gt;val2&lt;/bar&gt;
      * &lt;/foo&gt;
      * </code>
      * passing this the <code>foo</code> node and <code>bar</code> will
      * return <code>val1</code> and <code>val2</code>.
      * </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;
@@ -43,119 +40,109 @@ import org.xml.sax.SAXException;
 /**
  * This class deals with importing community and collection structures from
  * an XML file.
- *
+ * 
  * The XML file structure needs to be:
- * {@code
+ * 
  * <import_structure>
- * <community>
+ *     <community>
- * <name>....</name>
+ *         <name>....</name>
- * <community>...</community>
+ *         <community>...</community>
- * <collection>
+ *         <collection>
- * <name>....</name>
+ *             <name>....</name>
- * </collection>
+ *         </collection>
- * </community>
+ *     </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)
+    public static void main(String[] argv) 
-        throws Exception {
+    	throws Exception
+    {
         CommandLineParser parser = new PosixParser();
 
-        Options options = new Options();
+    	Options options = new Options();
-
-        options.addOption("f", "file", true, "file");
-        options.addOption("e", "eperson", true, "eperson");
-        options.addOption("o", "output", true, "output");
-
-        CommandLine line = parser.parse(options, argv);
-
-        String file = null;
-        String eperson = null;
-        String output = null;
-
-        if (line.hasOption('f')) {
-            file = line.getOptionValue('f');
-        }
-
-        if (line.hasOption('e')) {
-            eperson = line.getOptionValue('e');
-        }
-
-        if (line.hasOption('o')) {
-            output = line.getOptionValue('o');
-        }
-
-        if (output == null || eperson == null || file == null) {
-            usage();
-            System.exit(0);
-        }
 
+    	options.addOption( "f", "file", true, "file");
+    	options.addOption( "e", "eperson", true, "eperson");
+    	options.addOption("o", "output", true, "output");
+    	
+    	CommandLine line = parser.parse( options, argv );
+    	
+    	String file = null;
+    	String eperson = null;
+    	String output = null;
+    	
+    	if (line.hasOption('f'))
+    	{
+    	    file = line.getOptionValue('f');
+    	}
+    	
+    	if (line.hasOption('e'))
+    	{
+    	    eperson = line.getOptionValue('e');
+    	}
+    	
+    	if (line.hasOption('o'))
+    	{
+    	    output = line.getOptionValue('o');
+    	}
+    	
+    	if (output == null || eperson == null || file == null)
+    	{
+    	    usage();
+    	    System.exit(0);
+    	}
+    	
         // create a context
         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);
-
+        
         // run the preliminary validation, to be sure that the the XML document
         // is properly structured
         validate(document);
-
+        
         // load the mappings into the member variable hashmaps
         communityMap.put("name", "name");
         communityMap.put("description", "short_description");
         communityMap.put("intro", "introductory_text");
         communityMap.put("copyright", "copyright_text");
         communityMap.put("sidebar", "side_bar_text");
-
+        
         collectionMap.put("name", "name");
         collectionMap.put("description", "short_description");
         collectionMap.put("intro", "introductory_text");
@@ -163,232 +150,267 @@ public class StructBuilder {
         collectionMap.put("sidebar", "side_bar_text");
         collectionMap.put("license", "license");
         collectionMap.put("provenance", "provenance_description");
-
+        
         // get the top level community list
         NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
-
+        
         // run the import starting with the top level communities
         Element[] elements = handleCommunities(context, first, null);
-
+        
         // 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);
         }
-
+        
         context.complete();
     }
-
+    
     /**
      * 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;
     }
-
+    
     /**
      * Validate the XML document.  This method does not return, but if validation
      * fails it generates an error and ceases execution
-     *
+     * 
-     * @param document the XML document object
+     * @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;
-
+        
         err.append("The following errors were encountered parsing the source XML\n");
         err.append("No changes have been made to the DSpace instance\n\n");
-
+        
         NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
-        if (first.getLength() == 0) {
+        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);
         }
     }
-
+    
     /**
      * Validate the communities section of the XML document.  This returns a string
      * containing any errors encountered, or null if there were no errors
-     *
+     * 
      * @param communities the NodeList of communities to validate
-     * @param level       the level in the XML document that we are at, for the purposes
+     * @param level the level in the XML document that we are at, for the purposes
-     *                    of error reporting
+     * 			of error reporting
+     * 
      * @return the errors that need to be generated by the calling method, or null if
-     * no errors.
+     * 			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");
+	        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);
+	            String pos = Integer.toString(i + 1);
-                err.append(" does not contain exactly one name field\n");
+	            err.append("-The level " + level + " community in position " + pos);
-                trip = true;
+	            err.append(" does not contain exactly one name field\n");
-            }
+	            trip = true;
-
+	        }
-            // validate sub communities
+	        
-            NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
+	        // validate sub communities
-            String comErrs = validateCommunities(subCommunities, level + 1);
+	        NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
-            if (comErrs != null) {
+	        String comErrs = validateCommunities(subCommunities, level + 1);
-                err.append(comErrs);
+	        if (comErrs != null)
-                trip = true;
+	        {
-            }
+	            err.append(comErrs);
-
+	            trip = true;
-            // validate collections
+	        }
-            NodeList collections = XPathAPI.selectNodeList(n, "collection");
+	        
-            String colErrs = validateCollections(collections, level + 1);
+	        // validate collections
-            if (colErrs != null) {
+	        NodeList collections = XPathAPI.selectNodeList(n, "collection");
-                err.append(colErrs);
+	        String colErrs = validateCollections(collections, level + 1);
-                trip = true;
+	        if (colErrs != null)
-            }
+	        {
+	            err.append(colErrs);
+	            trip = true;
+	        }
         }
-
+        
-        if (trip) {
+        if (trip)
+        {
             errs = err.toString();
         }
-
+        
         return errs;
     }
-
+    
     /**
      * validate the collection section of the XML document.  This generates a
      * string containing any errors encountered, or returns null if no errors
-     *
+     * 
      * @param collections a NodeList of collections to validate
-     * @param level       the level in the XML document for the purposes of error reporting
+     * @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");
+	        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);
+	            String pos = Integer.toString(i + 1);
-                err.append(" does not contain exactly one name field\n");
+	            err.append("-The level " + level + " collection in position " + pos);
-                trip = true;
+	            err.append(" does not contain exactly one name field\n");
-            }
+	            trip = true;
+	        }
         }
-
+        
-        if (trip) {
+        if (trip)
+        {
             errs = err.toString();
         }
-
+        
         return errs;
     }
-
+    
     /**
      * 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)
+    private static org.w3c.dom.Document loadXML(String filename) 
-        throws IOException, ParserConfigurationException, SAXException {
+    	throws IOException, ParserConfigurationException, SAXException
+    {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                                                        .newDocumentBuilder();
+                .newDocumentBuilder();
 
         org.w3c.dom.Document document = builder.parse(new File(filename));
-
+        
         return document;
     }
-
+    
     /**
      * 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();
             }
         }
 
         return value;
     }
-
+    
     /**
      * Take a node list of communities and build the structure from them, delegating
      * to the relevant methods in this class for sub-communities and collections
-     *
+     * 
-     * @param context     the context of the request
+     * @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
+     * @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)
+     * @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)));
                 }
             }
-
+            
             // FIXME: at the moment, if the community already exists by name
             // then this will throw a PSQLException on a duplicate key
             // violation
@@ -398,8 +420,8 @@ 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
             // along with all the information that we imported here
@@ -409,134 +431,151 @@ public class StructBuilder {
             // case
             // we want to move it or make it switchable later
             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);
             }
-
+            
             // handle sub communities
             NodeList subCommunities = XPathAPI.selectNodeList(tn, "community");
             Element[] subCommunityElements = handleCommunities(context, subCommunities, community);
-
+            
             // handle collections
             NodeList collections = XPathAPI.selectNodeList(tn, "collection");
             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]);
             }
-
+            
             elements[i] = element;
         }
-
+        
         return elements;
     }
-
+    
     /**
-     * Take a node list of collections and create the structure from them
+     *  Take a node list of collections and create the structure from them
-     *
+     * 
-     * @param context     the context of the request
+     * @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
+     * @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)
+     * 			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);
             }
-
+            
             elements[i] = element;
         }
-
+        
         return elements;
     }
-
+    
 }

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.Metadatum;
+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<Metadatum> adds;
-     */
-    private List<BulkEditMetadataValue> adds;
 
-    /**
+    /** The List of hashtables with the removed elements */
-     * The List of hashtables with the removed elements
+    private List<Metadatum> removes;
-     */
-    private List<BulkEditMetadataValue> removes;
 
-    /**
+    /** The List of hashtables with the unchanged elements */
-     * The List of hashtables with the unchanged elements
+    private List<Metadatum> 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<Metadatum> 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
+     * 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<Metadatum>();
-        removes = new ArrayList<>();
+        removes = new ArrayList<Metadatum>();
-        constant = new ArrayList<>();
+        constant = new ArrayList<Metadatum>();
-        complete = new ArrayList<>();
+        complete = new ArrayList<Metadatum>();
-        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<Metadatum>();
-        removes = new ArrayList<>();
+        removes = new ArrayList<Metadatum>();
-        constant = new ArrayList<>();
+        constant = new ArrayList<Metadatum>();
-        complete = new ArrayList<>();
+        complete = new ArrayList<Metadatum>();
-        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(Metadatum 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(Metadatum 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(Metadatum 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<Metadatum> 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<Metadatum> 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<Metadatum> 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<Metadatum> 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 +7,22 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.BufferedReader;
+import org.apache.commons.lang3.StringUtils;
-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.app.bulkedit.DSpaceCSVLine;
-import org.dspace.authority.service.AuthorityValueService;
+import org.dspace.app.bulkedit.MetadataImport;
+import org.dspace.app.bulkedit.MetadataImportInvalidHeadingException;
+import org.dspace.content.Collection;
+import org.dspace.content.*;
 import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.MetadataValue;
 import org.dspace.content.authority.Choices;
-import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.core.ConfigurationManager;
-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
@@ -52,75 +33,46 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  *
  * This class has been made serializable, as it is stored in a Session.
  * Is it wise to:
- * a) be putting this into a user's session?
+ *    a) be putting this into a user's session?
- * b) holding an entire CSV upload in memory?
+ *    b) holding an entire CSV upload in memory?
  *
  * @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 regexes */
-     * 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 regexes */
-     * The field separator in an escaped form for using in regexes
+    protected static String escapedFieldSeparator;
-     */
-    protected String escapedFieldSeparator;
 
-    /**
+    /** The authority separator (defaults to double 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 regexes */
-     * 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 +80,8 @@ 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();
 
@@ -141,39 +94,50 @@ 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"));
+        {
+            input = new BufferedReader(new InputStreamReader(new FileInputStream(f),"UTF-8"));
 
             // Read the heading line
             String head = input.readLine();
             String[] headingElements = head.split(escapedFieldSeparator);
             int columnCounter = 0;
-            for (String element : headingElements) {
+            for (String element : headingElements)
+            {
                 columnCounter++;
 
                 // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
+                if ((element.startsWith("\"")) && (element.endsWith("\"")))
+                {
                     element = element.substring(1, element.length() - 1);
                 }
 
                 // Store the heading
-                if ("collection".equals(element)) {
+                if ("collection".equals(element))
+                {
                     // Store the heading
                     headings.add(element);
-                } else if ("action".equals(element)) { // Store the action
+                }
+                // Store the action
+                else if ("action".equals(element))
+                {
                     // Store the heading
                     headings.add(element);
-                } else if (!"id".equals(element)) {
+                }
+                else if (!"id".equals(element))
+                {
                     String authorityPrefix = "";
-                    AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
+                    AuthorityValue authorityValueType = MetadataImport.getAuthorityValueType(element);
                     if (authorityValueType != null) {
                         String authorityType = authorityValueType.getAuthorityType();
                         authorityPrefix = element.substring(0, authorityType.length() + 1);
@@ -198,7 +162,7 @@ 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 +170,8 @@ 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,
@@ -223,7 +187,8 @@ public class DSpaceCSV implements Serializable {
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while ((lineRead = input.readLine()) != null) {
+            while (StringUtils.isNotBlank(lineRead = input.readLine()))
+            {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line
                     lineBuilder.append("\n").append(lineRead);
@@ -262,8 +227,11 @@ public class DSpaceCSV implements Serializable {
                     addItem(lineRead);
                 }
             }
-        } finally {
+        }
-            if (input != null) {
+        finally
+        {
+            if (input != null)
+            {
                 input.close();
             }
         }
@@ -272,7 +240,8 @@ 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 +252,28 @@ 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 +301,16 @@ 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 +330,32 @@ 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 = ",";
         }
 
@@ -383,20 +365,23 @@ public class DSpaceCSV implements Serializable {
         escapedFieldSeparator = match.replaceAll("\\\\$1");
     }
 
-    /**
+     /**
      * Set the authority separator for value with authority data.
      *
      * Is set in dspace.cfg as bulkedit.authorityseparator
      *
      * 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 = "::";
         }
 
@@ -410,9 +395,11 @@ 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) {
@@ -427,43 +414,48 @@ 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);
+        Metadatum md[] = i.getMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (MetadataValue value : md) {
+        for (Metadatum 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 != -1 ? value.confidence : Choices.CF_ACCEPTED);
                 }
                 line.add(key, mdValue);
-                if (!headings.contains(key)) {
+                if (!headings.contains(key))
+                {
                     headings.add(key);
                 }
             }
@@ -478,10 +470,12 @@ public class DSpaceCSV implements Serializable {
      * @param line The line of elements
      * @throws Exception Thrown if an error occurs when adding the item
      */
-    public final void addItem(String line) throws Exception {
+    public final void addItem(String line) throws Exception
+    {
         // Check to see if the last character is a field separator, which hides the last empty column
         boolean last = false;
-        if (line.endsWith(fieldSeparator)) {
+        if (line.endsWith(fieldSeparator))
+        {
             // Add a space to the end, then remove it later
             last = true;
             line += " ";
@@ -489,17 +483,20 @@ 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 +511,10 @@ 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 +523,10 @@ 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);
             }
@@ -537,25 +538,34 @@ 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");
+                                   "Item id must be numeric, or a '+' to add a new item");
-                throw (nfe);
+                throw(nfe);
             }
         }
 
         // 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 +577,10 @@ 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 +596,8 @@ 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 +607,23 @@ 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);
+        List<String> headingsCopy = new ArrayList<String>(headings);
         Collections.sort(headingsCopy);
-        for (String value : headingsCopy) {
+        for (String value : headingsCopy)
+        {
             csvLines[0] = csvLines[0] + fieldSeparator + value;
         }
 
         Iterator<DSpaceCSVLine> i = lines.iterator();
         int c = 1;
-        while (i.hasNext()) {
+        while (i.hasNext())
-            csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
+        {
+            csvLines[c++] = i.next().toCSV(headingsCopy);
         }
 
         return csvLines;
@@ -617,13 +633,15 @@ 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(
+                             new OutputStreamWriter(
-                new FileOutputStream(filename), "UTF-8"));
+                             new FileOutputStream(filename), "UTF-8"));
         for (String csvLine : getCSVLinesAsStringArray()) {
             out.write(csvLine + "\n");
         }
@@ -640,11 +658,13 @@ public class DSpaceCSV implements Serializable {
      * @param md The Metadatum to examine
      * @return Whether or not it is OK to export this element
      */
-    protected boolean okToExport(MetadataField md) {
+    private final boolean okToExport(Metadatum 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 +679,8 @@ public class DSpaceCSV implements Serializable {
      *
      * @return The headings
      */
-    public List<String> getHeadings() {
+    public List<String> getHeadings()
+    {
         return headings;
     }
 
@@ -668,22 +689,15 @@ 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

@@ -7,52 +7,38 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeMap;
-import java.util.UUID;
-
 import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.factory.AuthorityServiceFactory;
+
-import org.dspace.authority.service.AuthorityValueService;
+import java.io.Serializable;
+import java.util.*;
 
 /**
  * Utility class to store a line from a CSV file
  *
  * @author Stuart Lewis
  */
-public class DSpaceCSVLine implements Serializable {
+public class DSpaceCSVLine implements Serializable
-    /**
+{
-     * The item id of the item represented by this line. -1 is for a new item
-     */
-    private final UUID id;
 
-    /**
+    /** The item id of the item represented by this line. -1 is for a new item */
-     * The elements in this line in a hashtable, keyed by the metadata type
+    private int id;
-     */
-    private final Map<String, ArrayList> items;
 
-    protected transient final AuthorityValueService authorityValueService
+    /** The elements in this line in a hashtable, keyed by the metadata type */
-        = AuthorityServiceFactory.getInstance().getAuthorityValueService();
+    private Map<String, ArrayList> items;
 
-    /**
+    /** ensuring that the order-sensible columns of the csv are processed in the correct order */
-     * ensuring that the order-sensible columns of the csv are processed in the correct order
+    private final Comparator<? super String> headerComparator = new Comparator<String>() {
-     */
-    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 source1 = MetadataImport.getAuthorityValueType(md1);
-            AuthorityValue source2 = authorityValueService.getAuthorityValueType(md2);
+            AuthorityValue source2 = MetadataImport.getAuthorityValueType(md2);
 
             int compare;
             if (source1 == null && source2 != null) {
                 compare = -1;
-            } else if (source1 != null && source2 == null) {
+            }
+            else if (source1 != null && source2 == null) {
                 compare = 1;
             } else {
                 // the order of the rest does not matter
@@ -67,20 +53,23 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @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 TreeMap<String, ArrayList>(headerComparator);
 //        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 TreeMap<String, ArrayList>(headerComparator);
+//        this.items = new HashMap<String, ArrayList>();
     }
 
     /**
@@ -88,7 +77,8 @@ public class DSpaceCSVLine implements Serializable {
      *
      * @return The item ID
      */
-    public UUID getID() {
+    public int getID()
+    {
         // Return the ID
         return id;
     }
@@ -96,17 +86,20 @@ public class DSpaceCSVLine implements Serializable {
     /**
      * Add a new metadata value to this line
      *
-     * @param key   The metadata key (e.g. dc.contributor.author)
+     * @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 +110,8 @@ 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);
     }
@@ -127,11 +121,12 @@ 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) {
-                return ((String) actions.get(0)).trim();
+                return ((String)actions.get(0)).trim();
             }
         }
         return "";
@@ -142,7 +137,8 @@ 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();
     }
@@ -150,24 +146,25 @@ 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 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));
             }
         }
 
@@ -177,27 +174,33 @@ 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 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

@@ -7,84 +7,61 @@
  */
 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
      *
-     * @param c         The Context
+     * @param c The Context
-     * @param toExport  The ItemIterator of items to export
+     * @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;
     }
 
     /**
      * Method to export a community (and sub-communities and collections)
      *
-     * @param c         The Context
+     * @param c The Context
-     * @param toExport  The Community to export
+     * @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 indent    How many spaces to use when writing out the names of items added
+     * @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;
     }
 
     /**
@@ -143,23 +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) {
+        }
+        catch (Exception e)
+        {
             // Something went wrong...
             System.err.println("Error exporting to CSV:");
             e.printStackTrace();
@@ -170,10 +147,11 @@ public class MetadataExport {
     /**
      * Print the help message
      *
-     * @param options  The command line options the user gave
+     * @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);
@@ -183,12 +161,12 @@ public class MetadataExport {
     }
 
     /**
-     * main method to run the metadata exporter
+	 * main method to run the metadata exporter
-     *
+	 *
-     * @param argv the command line arguments given
+	 * @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 +174,83 @@ 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;
+                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);
+                exporter = new MetadataExport(c, (Community)dso, exportAll);
-            } else {
+            }
+            else
+            {
                 System.err.println("Error identifying '" + handle + "'");
                 System.exit(1);
             }
@@ -269,7 +260,7 @@ public class MetadataExport {
         DSpaceCSV csv = exporter.export();
 
         // Save the files to the file
-        csv.save(filename);
+        csv.save(filename);        
 
         // Finish off and tidy up
         c.restoreAuthSystemState();

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

@@ -12,23 +12,26 @@ 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);
+    {
+       super(message);
     }
 
     /**
      * Instantiate a new MetadataImportException
      *
-     * @param message   the error message
+     * @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);
+    {
+       super(message, exception);
     }
-}
+}

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

@@ -12,51 +12,38 @@ 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;
 
 
     /**
      * Instantiate a new MetadataImportInvalidHeadingException
      *
-     * @param message   the error message
+     * @param message the error message
-     * @param theType   the type of the error
+     * @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;
@@ -66,9 +53,10 @@ public class MetadataImportInvalidHeadingException extends Exception {
     /**
      * Get the type of the exception
      *
-     * @return the type of the 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

@@ -9,6 +9,7 @@
 /**
  * <p>The DSpace Batch Metadata Editor, which uses a CSV file to export/import
  * item metadata.</p>
+ * <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>

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

@@ -13,7 +13,6 @@ 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;
@@ -25,64 +24,61 @@ 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
+ * 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.
-     *
+     * 
-     * <dl>
+     * @param args
-     * <dt>-h</dt>
+     *            <dl>
-     * <dd>Print help on command line options</dd>
+     *            <dt>-h</dt>
-     * <dt>-l</dt>
+     *            <dd>Print help on command line options</dd>
-     * <dd>loop through bitstreams once</dd>
+     *            <dt>-l</dt>
-     * <dt>-L</dt>
+     *            <dd>loop through bitstreams once</dd>
-     * <dd>loop continuously through bitstreams</dd>
+     *            <dt>-L</dt>
-     * <dt>-d</dt>
+     *            <dd>loop continuously through bitstreams</dd>
-     * <dd>specify duration of process run</dd>
+     *            <dt>-d</dt>
-     * <dt>-b</dt>
+     *            <dd>specify duration of process run</dd>
-     * <dd>specify bitstream IDs</dd>
+     *            <dt>-b</dt>
-     * <dt>-a [handle_id]</dt>
+     *            <dd>specify bitstream IDs</dd>
-     * <dd>check anything by handle</dd>
+     *            <dt>-a [handle_id]</dt>
-     * <dt>-e</dt>
+     *            <dd>check anything by handle</dd>
-     * <dd>Report only errors in the logs</dd>
+     *            <dt>-e</dt>
-     * <dt>-p</dt>
+     *            <dd>Report only errors in the logs</dd>
-     * <dd>Don't prune results before running checker</dd>
+     *            <dt>-p</dt>
-     * </dl>
+     *            <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 {
         // set up command line parser
@@ -94,7 +90,7 @@ public final class ChecksumChecker {
 
         options.addOption("l", "looping", false, "Loop once through bitstreams");
         options.addOption("L", "continuous", false,
-                          "Loop continuously through bitstreams");
+                "Loop continuously through bitstreams");
         options.addOption("h", "help", false, "Help");
         options.addOption("d", "duration", true, "Checking duration");
         options.addOption("c", "count", true, "Check count");
@@ -102,140 +98,172 @@ public final class ChecksumChecker {
         options.addOption("v", "verbose", false, "Report all processing");
 
         OptionBuilder.withArgName("bitstream-ids").hasArgs().withDescription(
-            "Space separated list of bitstream ids");
+                "Space separated list of bitstream ids");
         Option useBitstreamIds = OptionBuilder.create('b');
 
         options.addOption(useBitstreamIds);
 
         options.addOption("p", "prune", false, "Prune configuration file");
-        options.addOption(OptionBuilder
+        options
-                              .withArgName("prune")
+                .addOption(OptionBuilder
-                              .hasOptionalArgs(1)
+                        .withArgName("prune")
-                              .withDescription(
+                        .hasOptionalArgs(1)
-                                  "Prune old results (optionally using specified properties file for configuration)")
+                        .withDescription(
-                              .create('p'));
+                                "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
-            // Prune stage
+        if (line.hasOption('p'))
-            if (line.hasOption('p')) {
+        {
-                ResultsPruner rp = null;
+            ResultsPruner rp = null;
-                try {
+            try
-                    rp = (line.getOptionValue('p') != null) ? ResultsPruner
+            {
-                        .getPruner(context, line.getOptionValue('p')) : ResultsPruner
+                rp = (line.getOptionValue('p') != null) ? ResultsPruner
-                        .getDefaultPruner(context);
+                        .getPruner(line.getOptionValue('p')) : ResultsPruner
-                } catch (FileNotFoundException e) {
+                        .getDefaultPruner();
-                    LOG.error("File not found", e);
-                    System.exit(1);
-                }
-                int count = rp.prune();
-                System.out.println("Pruned " + count
-                                       + " old results from the database.");
             }
+            catch (FileNotFoundException e)
+            {
+                LOG.error("File not found", e);
+                System.exit(1);
+            }
+            int count = rp.prune();
+            System.out.println("Pruned " + count
+                    + " old results from the database.");
+        }
 
-            Date processStart = Calendar.getInstance().getTime();
+        Date processStart = Calendar.getInstance().getTime();
 
-            BitstreamDispatcher dispatcher = null;
+        BitstreamDispatcher dispatcher = null;
+        
+        // process should loop infinitely through
+        // most_recent_checksum table
+        if (line.hasOption('l'))
+        {
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, false); 
+        }
+        else if (line.hasOption('L'))
+        {
+            dispatcher = new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true);
+        }
+        else if (line.hasOption('b'))
+        {
+            // check only specified bitstream(s)
+            String[] ids = line.getOptionValues('b');
+            List<Integer> idList = new ArrayList<Integer>(ids.length);
 
-            // process should loop infinitely through
+            for (int i = 0; i < ids.length; i++)
-            // most_recent_checksum table
+            {
-            if (line.hasOption('l')) {
+                try
-                dispatcher = new SimpleDispatcher(context, processStart, false);
+                {
-            } else if (line.hasOption('L')) {
+                    idList.add(Integer.valueOf(ids[i]));
-                dispatcher = new SimpleDispatcher(context, processStart, true);
-            } else if (line.hasOption('b')) {
-                // check only specified bitstream(s)
-                String[] ids = line.getOptionValues('b');
-                List<Bitstream> bitstreams = new ArrayList<>(ids.length);
-
-                for (int i = 0; i < ids.length; i++) {
-                    try {
-                        bitstreams.add(bitstreamService.find(context, UUID.fromString(ids[i])));
-                    } catch (NumberFormatException nfe) {
-                        System.err.println("The following argument: " + ids[i]
-                                               + " is not an integer");
-                        System.exit(0);
-                    }
                 }
-                dispatcher = new IteratorDispatcher(bitstreams.iterator());
+                catch (NumberFormatException nfe)
-            } else if (line.hasOption('a')) {
+                {
-                dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
+                    System.err.println("The following argument: " + ids[i]
-            } else if (line.hasOption('d')) {
+                            + " is not an integer");
-                // run checker process for specified duration
-                try {
-                    dispatcher = new LimitedDurationDispatcher(
-                        new SimpleDispatcher(context, processStart, true), new Date(
-                        System.currentTimeMillis()
-                            + Utils.parseDuration(line
-                                                      .getOptionValue('d'))));
-                } 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'));
-
-                // run checker process for specified number of bitstreams
-                dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
-                    context, processStart, false), count);
-            } else {
-                dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
-                    context, processStart, false), 1);
             }
+            dispatcher = new ListDispatcher(idList);
+        }
 
-            ResultsLogger logger = new ResultsLogger(processStart);
+        else if (line.hasOption('a'))
-            CheckerCommand checker = new CheckerCommand(context);
+        {
-            // verbose reporting
+            dispatcher = new HandleDispatcher(new BitstreamInfoDAO(), line.getOptionValue('a'));
-            if (line.hasOption('v')) {
+        }
-                checker.setReportVerbose(true);
+        else if (line.hasOption('d'))
+        {
+            // run checker process for specified duration
+            try
+            {
+                dispatcher = new LimitedDurationDispatcher(
+                        new SimpleDispatcher(new BitstreamInfoDAO(), processStart, true), new Date(
+                                System.currentTimeMillis()
+                                        + Utils.parseDuration(line
+                                                .getOptionValue('d'))));
             }
-
+            catch (Exception e)
-            checker.setProcessStartDate(processStart);
+            {
-            checker.setDispatcher(dispatcher);
+                LOG.fatal("Couldn't parse " + line.getOptionValue('d')
-            checker.setCollector(logger);
+                        + " as a duration: ", e);
-            checker.process();
+                System.exit(0);
-            context.complete();
-            context = null;
-        } finally {
-            if (context != null) {
-                context.abort();
             }
         }
+        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(
+                    new BitstreamInfoDAO(), processStart, false), count);
+        }
+        else
+        {
+            dispatcher = new LimitedCountDispatcher(new SimpleDispatcher(
+                    new BitstreamInfoDAO(), processStart, false), 1);
+        }
+        
+        ResultsLogger logger = new ResultsLogger(processStart);
+        CheckerCommand checker = new CheckerCommand();
+        // verbose reporting
+        if (line.hasOption('v'))
+        {
+            checker.setReportVerbose(true);
+        }
+
+        checker.setProcessStartDate(processStart);
+        checker.setDispatcher(dispatcher);
+        checker.setCollector(logger);
+        Context context = new Context();
+        try {
+            checker.process(context);
+        } finally {
+            context.commit();
+            context.complete();
+        }
+        System.exit(0);
     }
 
     /**
      * Print the help options for the user
-     *
+     * 
      * @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
-                               + "m(minutes), or h(hours): ChecksumChecker -d 30s"
+                .println("\nSpecify a duration for checker process, using s(seconds),"
-                               + " OR ChecksumChecker -d 30m"
+                        + "m(minutes), or h(hours): ChecksumChecker -d 30s"
-                               + " OR ChecksumChecker -d 2h");
+                        + " OR ChecksumChecker -d 30m"
-        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
+                        + " OR ChecksumChecker -d 2h");
+        System.out
+                .println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
         System.out.println("\nLoop once through all bitstreams: "
-                               + "ChecksumChecker -l");
+                + "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

@@ -7,12 +7,12 @@
  */
 package org.dspace.app.configuration;
 
-import java.io.File;
-import java.net.MalformedURLException;
-
 import org.dspace.kernel.config.SpringLoader;
 import org.dspace.services.ConfigurationService;
 
+import java.io.File;
+import java.net.MalformedURLException;
+
 /**
  * @author Kevin Van de Velde (kevin at atmire dot com)
  */
@@ -32,7 +32,7 @@ public class APISpringLoader implements SpringLoader {
 
 
         try {
-            return new String[] {new File(filePath.toString()).toURI().toURL().toString() + XML_SUFFIX};
+            return new String[]{new File(filePath.toString()).toURI().toURL().toString() + XML_SUFFIX};
         } catch (MalformedURLException e) {
             return new String[0];
         }

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.
+ *  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();
 
@@ -65,50 +54,49 @@ public class Harvest {
         options.addOption("S", "start", false, "start the harvest loop");
         options.addOption("R", "reset", false, "reset harvest status on all collections");
         options.addOption("P", "purge", false, "purge all harvestable collections");
+        
 
-
+        options.addOption("e", "eperson", true, "eperson");
-        options.addOption("e", "eperson", true,
+        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
-                          "eperson");
+        options.addOption("t", "type", true, "type of harvesting (0 for none)");
-        options.addOption("c", "collection", true,
+        options.addOption("a", "address", true, "address of the OAI-PMH server");
-                          "harvesting collection (handle or id)");
+        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
-        options.addOption("t", "type", true,
+        options.addOption("m", "metadata_format", true, "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
-                          "type of harvesting (0 for none)");
-        options.addOption("a", "address", true,
-                          "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true,
-                          "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true,
-                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
-                              "crosswalk in dspace.cfg");
 
         options.addOption("h", "help", false, "help");
 
         CommandLine line = parser.parse(options, argv);
 
-        String command = null;
+        String command = null; 
         String eperson = null;
         String collection = null;
         String oaiSource = null;
         String oaiSetID = null;
         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);
         }
@@ -138,7 +126,7 @@ public class Harvest {
             command = "purgeAll";
         }
 
-
+        
         if (line.hasOption('e')) {
             eperson = line.getOptionValue('e');
         }
@@ -148,7 +136,7 @@ public class Harvest {
         if (line.hasOption('t')) {
             harvestType = Integer.parseInt(line.getOptionValue('t'));
         } else {
-            harvestType = 0;
+        	harvestType = 0;
         }
         if (line.hasOption('a')) {
             oaiSource = line.getOptionValue('a');
@@ -159,87 +147,106 @@ public class Harvest {
         if (line.hasOption('m')) {
             metadataKey = line.getOptionValue('m');
         }
-
+        
 
         // 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)");
+                    .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.
+        // 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");
+                        .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-
+            
             harvester.runHarvest(collection, eperson);
-        } else if ("start".equals(command)) {
+        }
-            // start the harvest loop
+        // start the harvest loop
-            startHarvester();
+        else if ("start".equals(command))
-        } else if ("reset".equals(command)) {
+        {
-            // reset harvesting status
+        	startHarvester();
-            resetHarvesting();
+        }
-        } else if ("purgeAll".equals(command)) {
+        // reset harvesting status
-            // purge all collections that are set up for harvesting (obviously for testing purposes only)
+        else if ("reset".equals(command))
-            if (eperson == null) {
+        {
+        	resetHarvesting();
+        }
+        // purge all collections that are set up for harvesting (obviously for testing purposes only)
+        else if ("purgeAll".equals(command))
+        {
+        	if (eperson == null)
+            {
                 System.out
-                    .println("Error - an eperson must be provided");
+                        .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();
-            }
+        }
-            context.complete();
+        // Delete all items in a collection. Useful for testing fresh harvests.
-        } else if ("purge".equals(command)) {
+        else if ("purge".equals(command))
-            // Delete all items in a collection. Useful for testing fresh harvests.
+        {
-            if (collection == null || eperson == null) {
+            if (collection == null || eperson == null)
+            {
                 System.out
-                    .println("Error - a target collection and eperson must be provided");
+                        .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-
+            
             harvester.purgeCollection(collection, eperson);
             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
+        // 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);
+                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);
@@ -248,166 +255,183 @@ public class Harvest {
             pingResponder(oaiSource, oaiSetID, metadataKey);
         }
     }
-
+    
     /*
      * Resolve the ID into a collection and check to see if its harvesting options are set. If so, return
-     * the collection, if not, bail out.
+     * the collection, if not, bail out. 
      */
     private Collection resolveCollection(String collectionID) {
-
+    	
-        DSpaceObject dso;
+    	DSpaceObject dso;
-        Collection targetCollection = null;
+    	Collection targetCollection = null;
-
+    	
-        try {
+    	try {
-            // is the ID a handle?
+	    	// 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) {
+    	}
-            se.printStackTrace();
+    	catch (SQLException se) {
-        }
+    		se.printStackTrace();
-
+    	}
-        return targetCollection;
+    	
+    	return targetCollection;
     }
-
+    
-
+    
-    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");
-        System.out.println("Running: configure collection");
+   	
-
+    	Collection collection = resolveCollection(collectionID);
-        Collection collection = resolveCollection(collectionID);
+    	System.out.println(collection.getID());
-        System.out.println(collection.getID());
+    	    	
-
+    	try {
-        try {
+    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+        	if (hc == null) {
-            if (hc == null) {
+        		hc = HarvestedCollection.create(context, collection.getID());
-                hc = harvestedCollectionService.create(context, collection);
+        	}
+    		
+    		context.turnOffAuthorisationSystem();
+    		hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
+    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
+    		hc.update();
+    		context.restoreAuthSystemState();
+    		context.complete();
+    	} 
+    	catch (Exception e) {
+    		System.out.println("Changes could not be committed");
+    		e.printStackTrace();
+    		System.exit(1);
+    	}
+    	finally {
+            if (context != null)
+            {
+    		    context.restoreAuthSystemState();
             }
-
+    	}
-            context.turnOffAuthorisationSystem();
-            hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
-            hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-            harvestedCollectionService.update(context, hc);
-            context.restoreAuthSystemState();
-            context.complete();
-        } catch (Exception e) {
-            System.out.println("Changes could not be committed");
-            e.printStackTrace();
-            System.exit(1);
-        } finally {
-            if (context != null) {
-                context.restoreAuthSystemState();
-            }
-        }
     }
-
+    
-
+    
     /**
      * Purges a collection of all harvest-related data and settings. All items in the collection will be deleted.
-     *
+     * 
      * @param collectionID
      * @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);
-        Collection collection = resolveCollection(collectionID);
+   	
-
+    	try 
-        try {
+    	{
-            EPerson eperson = ePersonService.findByEmail(context, email);
+    		EPerson eperson = EPerson.findByEmail(context, email);
-            context.setCurrentUser(eperson);
+        	context.setCurrentUser(eperson);
-            context.turnOffAuthorisationSystem();
+    		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;
+    		int i=0;
-            while (it.hasNext()) {
+    		while (it.hasNext()) {
-                i++;
+    			i++;
-                Item item = it.next();
+    			Item item = it.next();
-                System.out.println("Deleting: " + item.getHandle());
+    			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);
-                if (i % 50 == 0) {
+    			// commit every 50 items
-                    context.dispatchEvents();
+    			if (i%50 == 0) {
-                    i = 0;
+    				context.commit();
-                }
+    				i=0;
-            }
+    			}
-
+    		}
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+    		
-            if (hc != null) {
+    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-                hc.setLastHarvested(null);
+    		if (hc != null) {
-                hc.setHarvestMessage("");
+	    		hc.setHarvestResult(null,"");
-                hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
+	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-                hc.setHarvestStartTime(null);
+	    		hc.setHarvestStartTime(null);
-                harvestedCollectionService.update(context, hc);
+	    		hc.update();
-            }
+    		}
-            context.restoreAuthSystemState();
+    		context.restoreAuthSystemState();    		
-            context.dispatchEvents();
+    		context.commit();
-        } catch (Exception e) {
+    	} 
-            System.out.println("Changes could not be committed");
+    	catch (Exception e) {
-            e.printStackTrace();
+    		System.out.println("Changes could not be committed");
-            System.exit(1);
+    		e.printStackTrace();
-        } finally {
+    		System.exit(1);
-            context.restoreAuthSystemState();
+    	}
-        }
+    	finally {
+    		context.restoreAuthSystemState();
+    	}
     }
-
+    
-
+    
     /**
-     * Run a single harvest cycle on the specified collection under the authorization of the supplied EPerson
+     * Run a single harvest cycle on the specified collection under the authorization of the supplied EPerson 
      */
     private void runHarvest(String collectionID, String email) {
-        System.out.println("Running: a harvest cycle on " + collectionID);
+    	System.out.println("Running: a harvest cycle on " + collectionID);
-
+    	
-        System.out.print("Initializing the harvester... ");
+    	System.out.print("Initializing the harvester... ");
-        OAIHarvester harvester = null;
+    	OAIHarvester harvester = null;
-        try {
+    	try {
-            Collection collection = resolveCollection(collectionID);
+    		Collection collection = resolveCollection(collectionID);
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
+        	HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-            harvester = new OAIHarvester(context, collection, hc);
+    		harvester = new OAIHarvester(context, collection, hc);
-            System.out.println("success. ");
+    		System.out.println("success. ");
-        } catch (HarvestingException hex) {
+    	}
-            System.out.print("failed. ");
+    	catch (HarvestingException hex) {
-            System.out.println(hex.getMessage());
+    		System.out.print("failed. ");
-            throw new IllegalStateException("Unable to harvest", hex);
+    		System.out.println(hex.getMessage());
-        } catch (SQLException se) {
+    		throw new IllegalStateException("Unable to harvest", hex);
+    	} catch (SQLException se) {
             System.out.print("failed. ");
             System.out.println(se.getMessage());
             throw new IllegalStateException("Unable to access database", se);
+		}
+    	    	
+    	try {
+    		// Harvest will not work for an anonymous user
+        	EPerson eperson = EPerson.findByEmail(context, email);
+        	System.out.println("Harvest started... ");
+        	context.setCurrentUser(eperson);
+    		harvester.runHarvest();
+    		context.complete();
+    	}
+        catch (SQLException e) {
+            throw new IllegalStateException("Failed to run harvester", e);
         }
-
+        catch (AuthorizeException e) {
-        try {
-            // Harvest will not work for an anonymous user
-            EPerson eperson = ePersonService.findByEmail(context, email);
-            System.out.println("Harvest started... ");
-            context.setCurrentUser(eperson);
-            harvester.runHarvest();
-            context.complete();
-        } catch (SQLException e) {
             throw new IllegalStateException("Failed to run harvester", e);
-        } catch (AuthorizeException e) {
+        }
-            throw new IllegalStateException("Failed to run harvester", e);
+        catch (IOException e) {
-        } catch (IOException e) {
             throw new IllegalStateException("Failed to run harvester", e);
         }
 
@@ -415,70 +439,78 @@ public class Harvest {
     }
 
     /**
-     * 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... ");
+    	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 server address of the responder's host.
-     * @param set            name of an item set.
+     * @param set name of an item set.
      * @param metadataFormat local prefix name, or null for "dc".
      */
-    private static void pingResponder(String server, String set, String metadataFormat) {
+    private static void pingResponder(String server, String set, String metadataFormat)
+    {
         List<String> errors;
 
         System.out.print("Testing basic PMH access:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", false);
+                (null != metadataFormat) ? metadataFormat : "dc", false);
-        if (errors.isEmpty()) {
+        if (errors.isEmpty())
             System.out.println("OK");
-        } else {
+        else
-            for (String error : errors) {
+        {
+            for (String error : errors)
                 System.err.println(error);
-            }
         }
 
         System.out.print("Testing ORE support:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", true);
+                (null != metadataFormat) ? metadataFormat : "dc", true);
-        if (errors.isEmpty()) {
+        if (errors.isEmpty())
             System.out.println("OK");
-        } else {
+        else
-            for (String error : errors) {
+        {
+            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

@@ -7,100 +7,87 @@
  */
 package org.dspace.app.itemimport;
 
+import gr.ekt.bte.core.DataLoader;
+import gr.ekt.bte.core.TransformationEngine;
+import gr.ekt.bte.dataloader.FileDataLoader;
+
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
-import gr.ekt.bte.core.DataLoader;
+
-import gr.ekt.bte.core.TransformationEngine;
-import gr.ekt.bte.dataloader.FileDataLoader;
 
 
 /**
- * This class acts as a Service in the procedure to batch import using the Biblio-Transformation-Engine
+ * This class acts as a Service in the procedure ot batch import using the Biblio-Transformation-Engine
  */
-public class BTEBatchImportService {
+public class BTEBatchImportService
+{
 
-    TransformationEngine transformationEngine;
+	TransformationEngine transformationEngine;
     Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
-    Map<String, String> outputMap = new HashMap<String, String>();
+    Map<String, String> outputMap = new HashMap<String,String>();
-
+    
     /**
      * Default constructor
      */
-    public BTEBatchImportService() {
+    public BTEBatchImportService()
+    {
         super();
     }
 
     /**
      * Setter method for dataLoaders parameter
-     *
+     * @param dataLoaders
-     * @param dataLoaders map of data loaders
      */
-    public void setDataLoaders(Map<String, DataLoader> dataLoaders) {
+    public void setDataLoaders(Map<String, DataLoader> dataLoaders)
+    {
         this.dataLoaders = dataLoaders;
     }
 
     /**
-     * Get data loaders
+     * 
-     *
      * @return the map of DataLoaders
      */
-    public Map<String, DataLoader> getDataLoaders() {
+    public Map<String, DataLoader> getDataLoaders()
+    {
         return dataLoaders;
     }
 
     /**
-     * Get output map
+     * 
-     *
      * @return the outputMapping
      */
-    public Map<String, String> getOutputMap() {
+	public Map<String, String> getOutputMap() {
-        return outputMap;
+		return outputMap;
-    }
+	}
 
-    /**
+	/**
-     * Setter method for the outputMapping
+	 * Setter method for the outputMapping
-     *
+	 * @param outputMapping
-     * @param outputMap the output mapping
+	 */
-     */
+	public void setOutputMap(Map<String, String> outputMap) {
-    public void setOutputMap(Map<String, String> outputMap) {
+		this.outputMap = outputMap;
-        this.outputMap = outputMap;
+	}
-    }
 
-    /**
+	public TransformationEngine getTransformationEngine() {
-     * Get transformation engine
+		return transformationEngine;
-     *
+	}
-     * @return transformation engine
-     */
-    public TransformationEngine getTransformationEngine() {
-        return transformationEngine;
-    }
 
-    /**
+	public void setTransformationEngine(TransformationEngine transformationEngine) {
-     * set transformation engine
+		this.transformationEngine = transformationEngine;
-     *
+	}
-     * @param transformationEngine transformation engine
+	
-     */
+	public List<String> getFileDataLoaders(){
-    public void setTransformationEngine(TransformationEngine transformationEngine) {
+		List<String> result = new ArrayList<String>();
-        this.transformationEngine = transformationEngine;
+				
-    }
+		for (String key : dataLoaders.keySet()){
-
+			DataLoader dl = dataLoaders.get(key);
-    /**
+			if (dl instanceof FileDataLoader){
-     * Getter of file data loaders
+				result.add(key);
-     *
+			}
-     * @return List of file data loaders
+		}
-     */
+		return result;
-    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

@@ -7,7 +7,9 @@
  */
 package org.dspace.app.itemimport;
 
+import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.LineNumberReader;
@@ -17,213 +19,147 @@ import java.util.Calendar;
 import java.util.Date;
 import java.util.GregorianCalendar;
 import java.util.List;
+import java.util.Scanner;
 
 /**
  * @author kstamatis
+ *
  */
 public class BatchUpload {
 
-    private Date date;
+	private Date date;
-    private File dir;
+	private File dir;
-    private boolean successful;
+	private boolean successful;
-    private int itemsImported;
+	private int itemsImported;
-    private int totalItems = 0;
+	private int totalItems = 0;
-    private List<String> handlesImported = new ArrayList<String>();
+	private List<String> handlesImported = new ArrayList<String>();
-    private String errorMsg = "";
+	private String errorMsg = "";
-    private String errorMsgHTML = "";
+	private String errorMsgHTML = "";
+	
+	/**
+	 * 
+	 */
+	public BatchUpload(String dirPath) {
+		
+		this.initializeWithFile(new File(dirPath));
+		
+	}
 
-    /**
+	public BatchUpload(File dir) {
-     * Initialize with directory
+		
-     *
+		this.initializeWithFile(dir);
-     * @param dirPath directory path
+		
-     */
+	}
-    public BatchUpload(String dirPath) {
 
-        this.initializeWithFile(new File(dirPath));
 
-    }
+	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();
+			}
+		}
+	}
+	
+	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(); 
-     * Initialize with directory
+	    reader.close();
-     *
+	    return cnt;
-     * @param dir directory path
+	}
-     */
+	
-    public BatchUpload(File dir) {
+	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();
+	}
 
-        this.initializeWithFile(dir);
+	public Date getDate() {
+		return date;
+	}
 
-    }
+	public File getDir() {
+		return dir;
+	}
 
-    /**
+	public boolean isSuccessful() {
-     * Initialize with directory
+		return successful;
-     *
+	}
-     * @param dir directory path
-     */
-    private void initializeWithFile(File dir) {
 
-        this.dir = dir;
+	public int getItemsImported() {
+		return itemsImported;
+	}
 
-        String dirName = dir.getName();
+	public int getTotalItems() {
-        long timeMillis = Long.parseLong(dirName);
+		return totalItems;
-        Calendar calendar = new GregorianCalendar();
+	}
-        calendar.setTimeInMillis(timeMillis);
+	
-        this.date = calendar.getTime();
+	public String getDateFormatted(){
+		SimpleDateFormat df = new SimpleDateFormat("dd/MM/yyyy - HH:mm");
+		
+		return df.format(date);
+	}
 
-        try {
+	public List<String> getHandlesImported() {
-            this.itemsImported = countLines(dir + File.separator + "mapfile");
+		return handlesImported;
-        } catch (IOException e) {
+	}
-            e.printStackTrace();
-        }
 
-        for (File file : dir.listFiles()) {
+	public String getErrorMsg() {
-            if (file.isDirectory()) {
+		return errorMsg;
-                this.totalItems = file.list().length;
+	}
-            }
-        }
 
-        this.successful = this.totalItems == this.itemsImported;
+	public String getErrorMsgHTML() {
-
+		return errorMsgHTML;
-        //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/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

@@ -9,85 +9,83 @@ 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 availableImageName;
-    private String nonAvailableImageName;
+	private String nonAvailableImageName;
+	
+	public ItemMarkingAvailabilityBitstreamStrategy() {
+	
+	}
 
-    @Autowired(required = true)
+	@Override
-    protected ItemService itemService;
+	public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-
+			throws SQLException {
-    public ItemMarkingAvailabilityBitstreamStrategy() {
+		
-
+		Bundle[] bundles = item.getBundles("ORIGINAL");
-    }
+		if (bundles.length == 0){
-
+			ItemMarkingInfo markInfo = new ItemMarkingInfo();
-    @Override
+			markInfo.setImageName(nonAvailableImageName);	
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+			
-        throws SQLException {
+			return markInfo;
-
+		}
-        List<Bundle> bundles = itemService.getBundles(item, "ORIGINAL");
+		else {
-        if (bundles.size() == 0) {
+			Bundle originalBundle = bundles[0];
-            ItemMarkingInfo markInfo = new ItemMarkingInfo();
+			if (originalBundle.getBitstreams().length == 0){
-            markInfo.setImageName(nonAvailableImageName);
+				ItemMarkingInfo markInfo = new ItemMarkingInfo();
-
+				markInfo.setImageName(nonAvailableImageName);
-            return markInfo;
+				
-        } else {
+				return markInfo;
-            Bundle originalBundle = bundles.iterator().next();
+			}
-            if (originalBundle.getBitstreams().size() == 0) {
+			else {
-                ItemMarkingInfo markInfo = new ItemMarkingInfo();
+				Bitstream bitstream = originalBundle.getBitstreams()[0];
-                markInfo.setImageName(nonAvailableImageName);
+				
-
+				ItemMarkingInfo signInfo = new ItemMarkingInfo();
-                return markInfo;
+				signInfo.setImageName(availableImageName);
-            } else {
+				signInfo.setTooltip(bitstream.getName());
-                Bitstream bitstream = originalBundle.getBitstreams().get(0);
+				
-
+				
-                ItemMarkingInfo signInfo = new ItemMarkingInfo();
+				
-                signInfo.setImageName(availableImageName);
+				String bsLink = "";
-                signInfo.setTooltip(bitstream.getName());
-
-
-                String bsLink = "";
 
                 bsLink = bsLink + "bitstream/"
-                    + item.getHandle() + "/"
+                            + item.getHandle() + "/"
-                    + bitstream.getSequenceID() + "/";
+                            + bitstream.getSequenceID() + "/";
-
+                
                 try {
-                    bsLink = bsLink + Util.encodeBitstreamName(bitstream.getName(), Constants.DEFAULT_ENCODING);
+					bsLink = bsLink + Util.encodeBitstreamName(bitstream.getName(),  Constants.DEFAULT_ENCODING);
-                } catch (UnsupportedEncodingException e) {
+				} catch (UnsupportedEncodingException e) {
+					
+					e.printStackTrace();
+				}
+                
+				signInfo.setLink(bsLink);
+				
+				return signInfo;
+			}
+		}
+	}
 
-                    e.printStackTrace();
+	public void setAvailableImageName(String availableImageName) {
-                }
+		this.availableImageName = availableImageName;
+	}
 
-                signInfo.setLink(bsLink);
+	public void setNonAvailableImageName(String nonAvailableImageName) {
-
+		this.nonAvailableImageName = nonAvailableImageName;
-                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

@@ -18,32 +18,33 @@ 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>();
+	Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
+	
+	public ItemMarkingCollectionStrategy() {
+	}
 
-    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;
+	}
 
-    @Override
+	public void setMapping(Map<String, ItemMarkingInfo> mapping) {
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+		this.mapping = mapping;
-        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

@@ -14,10 +14,11 @@ 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)
+	public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-        throws SQLException;
+			throws SQLException;
 }

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

@@ -9,48 +9,49 @@ 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 imageName;
-    private String classInfo;
+	private String classInfo;
-    private String tooltip;
+	private String tooltip;
-    private String link;
+	private String link;
 
-    public ItemMarkingInfo() {
+	public ItemMarkingInfo() {
-        super();
+		super();
-    }
+	}
 
-    public String getImageName() {
+	public String getImageName() {
-        return imageName;
+		return imageName;
-    }
+	}
 
-    public void setImageName(String imageName) {
+	public void setImageName(String imageName) {
-        this.imageName = imageName;
+		this.imageName = imageName;
-    }
+	}
 
-    public String getTooltip() {
+	public String getTooltip() {
-        return tooltip;
+		return tooltip;
-    }
+	}
 
-    public void setTooltip(String tooltip) {
+	public void setTooltip(String tooltip) {
-        this.tooltip = tooltip;
+		this.tooltip = tooltip;
-    }
+	}
+	
+	public String getLink() {
+		return link;
+	}
 
-    public String getLink() {
+	public void setLink(String link) {
-        return link;
+		this.link = link;
-    }
+	}
+	
+	public String getClassInfo() {
+		return classInfo;
+	}
 
-    public void setLink(String link) {
+	public void setClassInfo(String classInfo) {
-        this.link = link;
+		this.classInfo = classInfo;
-    }
+	}
-
-    public String getClassInfo() {
-        return classInfo;
-    }
-
-    public void setClassInfo(String classInfo) {
-        this.classInfo = classInfo;
-    }
 }

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

@@ -9,56 +9,53 @@ 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.Metadatum;
-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)
+	private String metadataField;
-    protected ItemService itemService;
+	Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
+	
+	public ItemMarkingMetadataStrategy() {
+	}
 
-    private String metadataField;
+	@Override
-    Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
+	public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+			throws SQLException {
+		
+		if (metadataField != null && mapping!=null)
+		{
+			Metadatum[] vals = item.getMetadataByMetadataString(metadataField);
+			if (vals.length > 0)
+			{
+				for (Metadatum value : vals){
+					String type = value.value;
+					if (mapping.containsKey(type)){
+						return mapping.get(type);
+					}
+				}
+			}
+		}
+		return null;
+	}
 
-    public ItemMarkingMetadataStrategy() {
+	public void setMetadataField(String metadataField) {
-    }
+		this.metadataField = metadataField;
+	}
 
-    @Override
+	public void setMapping(Map<String, ItemMarkingInfo> mapping) {
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
+		this.mapping = mapping;
-        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

@@ -12,70 +12,69 @@ import java.util.LinkedHashMap;
 import java.util.Map;
 
 /**
- * Container for UpdateActions
+ * 	 Container for UpdateActions      
- * Order of actions is very import for correct processing.  This implementation
+ *    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
+ *     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.
+ *     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>();
+                     = new LinkedHashMap<Class<? extends UpdateAction>, UpdateAction>();
-
+	
-    /**
+	public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass) 
-     * Get update action
+	throws InstantiationException, IllegalAccessException
-     *
+	{
-     * @param actionClass UpdateAction class
+		UpdateAction action =  registry.get(actionClass);
-     * @return instantiation of UpdateAction class
+		
-     * @throws InstantiationException if instantiation error
+		if (action == null)
-     * @throws IllegalAccessException if illegal access error
+		{
-     */
+			action = actionClass.newInstance();
-    public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass)
+			registry.put(actionClass, action);
-        throws InstantiationException, IllegalAccessException {
+		}
-        UpdateAction action = registry.get(actionClass);
+		
-
+		return action;		
-        if (action == null) {
+	}
-            action = actionClass.newInstance();
+	
-            registry.put(actionClass, action);
+	/**
-        }
+	 * 
-
+	 * @return whether any actions have been registered with this manager
-        return action;
+	 */
-    }
+	public boolean hasActions()
-
+	{
-    /**
+		return !registry.isEmpty();
-     * @return whether any actions have been registered with this manager
+	}
-     */
+	
-    public boolean hasActions() {
+	/**
-        return !registry.isEmpty();
+	 * 	 This implementation guarantees the iterator order is the same as the order
-    }
+	 *   in which updateActions have been added
-
+	 * 
-    /**
+	 * @return iterator for UpdateActions
-     * This implementation guarantees the iterator order is the same as the order
+	 */
-     * in which updateActions have been added
+	public Iterator<UpdateAction> iterator()
-     *
+	{
-     * @return iterator for UpdateActions
+		return new Iterator<UpdateAction>() 
-     */
+		{ 			
-    @Override
+			private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
-    public Iterator<UpdateAction> iterator() {
+			
-        return new Iterator<UpdateAction>() {
+			public boolean hasNext()
-            private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
+			{
-
+				return itr.hasNext();
-            @Override
+			}
-            public boolean hasNext() {
+			
-                return itr.hasNext();
+			public UpdateAction next()
-            }
+			{
-
+				return registry.get(itr.next());
-            @Override
+			}
-            public UpdateAction next() {
+			
-                return registry.get(itr.next());
+			//not supported
-            }
+			public void remove()
-
+			{
-            //not supported
+				throw new UnsupportedOperationException();
-            @Override
+			}
-            public void remove() {
+		};
-                throw new UnsupportedOperationException();
+		
-            }
+	}
-        };
-
-    }
 }

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

@@ -17,192 +17,196 @@ 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
+ * 	 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();
+		//empty	
-    protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
+	}
-    protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
+	
-
+	/**
-    public AddBitstreamsAction() {
+	 * 	Adds bitstreams from the archive as listed in the contents file.
-        //empty
+	 * 
-    }
+	 *  @param context
-
+	 *  @param itarch
-    /**
+	 *  @param isTest
-     * Adds bitstreams from the archive as listed in the contents file.
+	 *  @param suppressUndo
-     *
+	 *  @throws IllegalArgumentException
-     * @param context      DSpace Context
+	 *  @throws ParseException
-     * @param itarch       Item Archive
+	 *  @throws IOException
-     * @param isTest       test flag
+	 *  @throws AuthorizeException
-     * @param suppressUndo undo flag
+	 *  @throws SQLException
-     * @throws IOException              if IO error
+	 */
-     * @throws IllegalArgumentException if arg exception
+	public void execute(Context context, ItemArchive itarch, boolean isTest,
-     * @throws SQLException             if database error
+            boolean suppressUndo) throws IllegalArgumentException,
-     * @throws AuthorizeException       if authorization error
+            ParseException, IOException, AuthorizeException, SQLException 
-     * @throws ParseException           if parse error
+	{
-     */
+		Item item = itarch.getItem();
-    @Override
+		File dir = itarch.getDirectory();
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
+		
-                        boolean suppressUndo) throws IllegalArgumentException,
+		List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
-        ParseException, IOException, AuthorizeException, SQLException {
+		
-        Item item = itarch.getItem();
+		if (contents.isEmpty())
-        File dir = itarch.getDirectory();
+		{
-
+			ItemUpdate.pr("Contents is empty - no bitstreams to add");
-        List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
+			return;
-
+		}
-        if (contents.isEmpty()) {
+		
-            ItemUpdate.pr("Contents is empty - no bitstreams to add");
+		ItemUpdate.pr("Contents bitstream count: " + contents.size());
-            return;
+		
-        }
+		String[] files = dir.list(ItemUpdate.fileFilter);
-
+		List<String> fileList = new ArrayList<String>();
-        ItemUpdate.pr("Contents bitstream count: " + contents.size());
+		for (String filename : files)
-
+		{
-        String[] files = dir.list(ItemUpdate.fileFilter);
+			fileList.add(filename);
-        List<String> fileList = new ArrayList<String>();
+			ItemUpdate.pr("file: " + filename);
-        for (String filename : files) {
+		}
-            fileList.add(filename);
+		
-            ItemUpdate.pr("file: " + filename);
+		for (ContentsEntry ce : contents)
-        }
+		{
-
+			//validate match to existing file in archive
-        for (ContentsEntry ce : contents) {
+			if (!fileList.contains(ce.filename))
-            //validate match to existing file in archive
+			{
-            if (!fileList.contains(ce.filename)) {
+				throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
-                throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
+			}
-            }
+		}
-        }
+		int bitstream_bundles_updated = 0;
-        int bitstream_bundles_updated = 0;
+		
-
+		//now okay to add
-        //now okay to add
+		for (ContentsEntry ce : contents)
-        for (ContentsEntry ce : contents) {
+		{        				
-            String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
+			String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
-            if (!targetBundleName.equals("")
+			if (!targetBundleName.equals("")
-                && !targetBundleName.equals("THUMBNAIL")
+			    && !targetBundleName.equals("THUMBNAIL")
-                && !targetBundleName.equals("TEXT")) {
+			    && !targetBundleName.equals("TEXT"))
-                bitstream_bundles_updated++;
+			{
-            }
+				bitstream_bundles_updated++;
-        }
+			}
-
+		}
-        if (alterProvenance && bitstream_bundles_updated > 0) {
-            DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-
-            String append = ". Added " + Integer.toString(bitstream_bundles_updated)
-                + " bitstream(s) on " + DCDate.getCurrent() + " : "
-                + installItemService.getBitstreamProvenanceMessage(context, item);
-            MetadataUtilities.appendMetadata(context, item, dtom, false, append);
-        }
-    }
-
-    /**
-     * Add bitstream
-     *
-     * @param context      DSpace Context
-     * @param itarch       Item Archive
-     * @param item         DSpace Item
-     * @param dir          directory
-     * @param ce           contents entry for bitstream
-     * @param suppressUndo undo flag
-     * @param isTest       test flag
-     * @return bundle name
-     * @throws IOException              if IO error
-     * @throws IllegalArgumentException if arg exception
-     * @throws SQLException             if database error
-     * @throws AuthorizeException       if authorization error
-     * @throws ParseException           if parse error
-     */
-    protected String addBitstream(Context context, ItemArchive itarch, Item item, File dir,
-                                  ContentsEntry ce, boolean suppressUndo, boolean isTest)
-        throws IOException, IllegalArgumentException, SQLException, AuthorizeException, ParseException {
-        ItemUpdate.pr("contents entry for bitstream: " + ce.toString());
-        File f = new File(dir, ce.filename);
 
+	        if (alterProvenance && bitstream_bundles_updated > 0)
+	        {
+	        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
+	        
+	        	String append = ". Added " + Integer.toString(bitstream_bundles_updated)
+	        	                + " bitstream(s) on " + DCDate.getCurrent() + " : "
+	        	                + InstallItem.getBitstreamProvenanceMessage(item);
+	        	MetadataUtilities.appendMetadata(item, dtom, false, append);
+	        }
+	}
+		
+	private String addBitstream(Context context, ItemArchive itarch, Item item, File dir, 
+			                  ContentsEntry ce, boolean suppressUndo, boolean isTest)
+	throws IOException, IllegalArgumentException, SQLException, AuthorizeException, ParseException
+	{
+		ItemUpdate.pr("contents entry for bitstream: " + ce.toString());
+    	File f = new File(dir, ce.filename);
+    	
         // get an input stream
         BufferedInputStream bis = new BufferedInputStream(new FileInputStream(f));
 
         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)
+        {
+	        // find the bundle
+	        Bundle[] bundles = item.getBundles(newBundleName);
+	        Bundle targetBundle = null;
+	
+	        if (bundles.length < 1)
+	        {
+	            // not found, create a new one
+	            targetBundle = item.createBundle(newBundleName);
+	        }
+	        else
+	        {
+	    		//verify bundle + name are not duplicates
+	        	for (Bundle b : bundles)
+	        	{
+	        		Bitstream[] bitstreams = b.getBitstreams();
+	        		for (Bitstream bsm : bitstreams)
+	        		{
+	        			if (bsm.getName().equals(ce.filename))
+	        			{
+	        				throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: " 
+	        						+ b.getName() + " + " + bsm.getName());
+	        			}
+	        		}
+	        	}
 
-        if (!isTest) {
+	            // select first bundle
-            // find the bundle
+	            targetBundle = bundles[0];
-            List<Bundle> bundles = itemService.getBundles(item, newBundleName);
+	        }
-            Bundle targetBundle = null;
+	
-
+	        bs = targetBundle.createBitstream(bis);	
-            if (bundles.size() < 1) {
+	        bs.setName(ce.filename);
-                // not found, create a new one
+	
-                targetBundle = bundleService.create(context, item, newBundleName);
+	        // Identify the format
-            } else {
+	        // FIXME - guessing format guesses license.txt incorrectly as a text file format!
-                //verify bundle + name are not duplicates
+	        BitstreamFormat fmt = FormatIdentifier.guessFormat(context, bs);
-                for (Bundle b : bundles) {
+	    	bs.setFormat(fmt);
-                    List<Bitstream> bitstreams = b.getBitstreams();
+	    	
-                    for (Bitstream bsm : bitstreams) {
+	        if (ce.description != null)
-                        if (bsm.getName().equals(ce.filename)) {
+	        {
-                            throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: "
+	        	bs.setDescription(ce.description);
-                                                                   + b.getName() + " + " + bsm.getName());
+	        }
-                        }
+	        	        
-                    }
+	        if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null))
-                }
+	        {
-
+				Group group = Group.findByName(context, ce.permissionsGroupName);
-                // select first bundle
+				
-                targetBundle = bundles.iterator().next();
+				if (group != null)
-            }
+				{
-
+			        AuthorizeManager.removeAllPolicies(context, bs);  // remove the default policy
-            bs = bitstreamService.create(context, targetBundle, bis);
+			        ResourcePolicy rp = ResourcePolicy.create(context);
-            bs.setName(context, ce.filename);
+			        rp.setResource(bs);
-
+			        rp.setAction(ce.permissionsActionId);
-            // Identify the format
+			        rp.setGroup(group);		
-            // FIXME - guessing format guesses license.txt incorrectly as a text file format!
+			        rp.update();
-            BitstreamFormat fmt = bitstreamFormatService.guessFormat(context, bs);
+				}
-            bitstreamService.setFormat(context, bs, fmt);
+	        }
-
+	        
-            if (ce.description != null) {
+	        //update after all changes are applied
-                bs.setDescription(context, ce.description);
+	        bs.update();
-            }
+        
-
+	        if (!suppressUndo)
-            if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null)) {
+	        {
-                Group group = groupService.findByName(context, ce.permissionsGroupName);
+	        	itarch.addUndoDeleteContents(bs.getID());
-
+	        }
-                if (group != null) {
+		return targetBundle.getName();
-                    authorizeService.removeAllPolicies(context, bs);  // remove the default policy
-                    authorizeService.createResourcePolicy(context, bs, group, null, ce.permissionsActionId, null);
-                }
-            }
-
-            //update after all changes are applied
-            bitstreamService.update(context, bs);
-
-            if (!suppressUndo) {
-                itarch.addUndoDeleteContents(bs.getID());
-            }
-            return targetBundle.getName();
         }
-        return "";
+	return "";
     }
 
 }

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

@@ -8,110 +8,113 @@
 package org.dspace.app.itemupdate;
 
 import java.sql.SQLException;
-import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.Metadatum;
 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
+ *   Action to add metadata to item
+ *
  */
 public class AddMetadataAction extends UpdateMetadataAction {
-
+	
-    protected MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+	/**
-                                                                                 .getMetadataSchemaService();
+	 * 	Adds metadata specified in the source archive
-    protected MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
+	 * 
-
+	 *  @param context
-    /**
+	 *  @param itarch
-     * Adds metadata specified in the source archive
+	 *  @param isTest
-     *
+	 *  @param suppressUndo
-     * @param context      DSpace Context
+	 *  @throws AuthorizeException
-     * @param itarch       item archive
+	 *  @throws SQLException
-     * @param isTest       test flag
+	 */
-     * @param suppressUndo undo flag
+	public void execute(Context context, ItemArchive itarch, boolean isTest,
-     * @throws AuthorizeException if authorization error
+            boolean suppressUndo) throws AuthorizeException, SQLException
-     * @throws SQLException       if database error
+	{
-     */
+		Item item = itarch.getItem();
-    @Override
+		String dirname = itarch.getDirectoryName();
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
+	    	
-                        boolean suppressUndo) throws AuthorizeException, SQLException {
+		for (DtoMetadata dtom : itarch.getMetadataFields())
-        Item item = itarch.getItem();
+		{
-        String dirname = itarch.getDirectoryName();
+			for (String f : targetFields)
-
+			{
-        for (DtoMetadata dtom : itarch.getMetadataFields()) {
+				if (dtom.matches(f, false))
-            for (String f : targetFields) {
+				{
-                if (dtom.matches(f, false)) {
+					// match against metadata for this field/value in repository
-                    // match against metadata for this field/value in repository
+					// qualifier must be strictly matched, possibly null					
-                    // qualifier must be strictly matched, possibly null
+					Metadatum[] ardcv = null;
-                    List<MetadataValue> ardcv = null;
+					ardcv = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-                    ardcv = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+					
-
+					boolean found = false;
-                    boolean found = false;
+					for (Metadatum dcv : ardcv)
-                    for (MetadataValue dcv : ardcv) {
+					{
-                        if (dcv.getValue().equals(dtom.value)) {
+						if (dcv.value.equals(dtom.value))
-                            found = true;
+						{
-                            break;
+							found = true;
-                        }
+							break;
-                    }
+						}
-
+					}
-                    if (found) {
+					
-                        ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname
+					if (found)
-                                          + " for element " + f);
+					{
-                    } else {
+						ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname 
-                        if (isTest) {
+								+ " for element " + f);						
-                            ItemUpdate.pr("Metadata to add: " + dtom.toString());
+					}
-                            //validity tests that would occur in actual processing
+					else
-                            // If we're just test the import, let's check that the actual metadata field exists.
+					{
-                            MetadataSchema foundSchema = metadataSchemaService.find(context, dtom.schema);
+						if (isTest)
-
+						{
-                            if (foundSchema == null) {
+							ItemUpdate.pr("Metadata to add: " + dtom.toString());
-                                ItemUpdate.pr("ERROR: schema '"
+							   //validity tests that would occur in actual processing
-                                                  + dtom.schema + "' was not found in the registry; found on item " +
+	        	            // If we're just test the import, let's check that the actual metadata field exists.
-                                                  dirname);
+	        	        	MetadataSchema foundSchema = MetadataSchema.find(context, dtom.schema);
-                            } else {
+	        	        	
-                                MetadataField foundField = metadataFieldService
+	        	        	if (foundSchema == null)
-                                    .findByElement(context, foundSchema, dtom.element, dtom.qualifier);
+	        	        	{
-
+	        	        		ItemUpdate.pr("ERROR: schema '" 
-                                if (foundField == null) {
+	        	        			+ dtom.schema + "' was not found in the registry; found on item " + dirname);
-                                    ItemUpdate.pr("ERROR: Metadata field: '" + dtom.schema + "." + dtom.element + "."
+	        	        	}
-                                                      + dtom.qualifier + "' not found in registry; found on item " +
+	        	        	else
-                                                      dirname);
+	        	        	{
-                                }
+		        	        	int schemaID = foundSchema.getSchemaID();
-                            }
+		        	        	MetadataField foundField = MetadataField.findByElement(context, schemaID, dtom.element, dtom.qualifier);
-                        } else {
+		        	        	
-                            itemService
+		        	        	if (foundField == null)
-                                .addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language,
+		        	        	{
-                                             dtom.value);
+		        	        		ItemUpdate.pr("ERROR: Metadata field: '" + dtom.schema + "." + dtom.element + "." 
-                            ItemUpdate.pr("Metadata added: " + dtom.toString());
+		        	        				+ dtom.qualifier + "' not found in registry; found on item " + dirname);
-
+		        	            }		
-                            if (!suppressUndo) {
+	        				}						
-                                //itarch.addUndoDtom(dtom);
+						}
-                                //ItemUpdate.pr("Undo metadata: " + dtom);
+						else
-
+						{
-                                // add all as a replace record to be preceded by delete
+							item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, dtom.value);
-                                for (MetadataValue dcval : ardcv) {
+							ItemUpdate.pr("Metadata added: " + dtom.toString());
-                                    MetadataField metadataField = dcval.getMetadataField();
+	
-                                    MetadataSchema metadataSchema = metadataField.getMetadataSchema();
+							if (!suppressUndo)
-                                    itarch.addUndoMetadataField(
+							{
-                                        DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
+								//itarch.addUndoDtom(dtom);
-                                                           metadataField.getQualifier(), dcval.getLanguage(),
+								//ItemUpdate.pr("Undo metadata: " + dtom);
-                                                           dcval.getValue()));
+								
-                                }
+								// add all as a replace record to be preceded by delete
-
+								for (Metadatum dcval : ardcv)
-                            }
+								{							
-                        }
+									itarch.addUndoMetadataField(DtoMetadata.create(dcval.schema, dcval.element, 
-                    }
+											dcval.qualifier, dcval.language, dcval.value));
-                    break;  // don't need to check if this field matches any other target fields
+								}
-                }
+								
-            }
+							}
-        }
+						}
-    }
+					}
+					break;  // don't need to check if this field matches any other target fields
+				}
+			} 				
+		}   
+	}
 
 }

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

@@ -7,49 +7,55 @@
  */
 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
+ *   Filter interface to be used by ItemUpdate 
- * to determine which bitstreams in an Item
+ *   to determine which bitstreams in an Item
- * acceptable for removal.
+ *   acceptable for removal.
+ *
  */
 public abstract class BitstreamFilter {
 
-    protected Properties props = null;
+	protected Properties props = null; 
+	
+	/**
+	 *  The filter method 
+	 *  
+	 * @param bitstream
+	 * @return whether the bitstream matches the criteria
+	 * @throws BitstreamFilterException
+	 */
+	public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;
+	
+	/**
+	 * 
+	 * @param filepath - The complete path for the properties file
+	 * @throws IOException
+	 */
+	public void initProperties(String filepath)
+	throws IOException
+	{
+		props = new Properties();
+		
+		InputStream in = null;
 
-    /**
+        try
-     * The filter method
+        {
-     *
-     * @param bitstream Bitstream
-     * @return whether the bitstream matches the criteria
-     * @throws BitstreamFilterException if filter error
-     */
-    public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;
-
-    /**
-     * @param filepath - The complete path for the properties file
-     * @throws IOException if IO error
-     */
-    public void initProperties(String filepath)
-        throws IOException {
-        props = new Properties();
-
-        InputStream in = null;
-
-        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

@@ -8,50 +8,59 @@
 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
+ *   BitstreamFilter implementation to filter by bundle name
+ *
  */
 public class BitstreamFilterByBundleName extends BitstreamFilter {
 
-    protected String bundleName;
+	protected String bundleName;
-
+	
-    public BitstreamFilterByBundleName() {
+	public BitstreamFilterByBundleName()
-        //empty
+	{
-    }
+		//empty
-
+	}
-    /**
-     * Filter bitstream based on bundle name found in properties file
-     *
-     * @param bitstream Bitstream
-     * @return whether bitstream is in bundle
-     * @throws BitstreamFilterException if filter error
-     */
-    @Override
-    public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        if (bundleName == null) {
-            bundleName = props.getProperty("bundle");
-            if (bundleName == null) {
-                throw new BitstreamFilterException("Property 'bundle' not found.");
-            }
-        }
-
-        try {
-            List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle b : bundles) {
-                if (b.getName().equals(bundleName)) {
-                    return true;
-                }
-            }
-        } catch (SQLException e) {
-            throw new BitstreamFilterException(e);
-        }
-        return false;
-    }
 
+	/**
+	 *    Filter bitstream based on bundle name found in properties file
+	 *    
+	 *    @param bitstream
+	 *    @throws BitstreamFilterException
+	 *    @return whether bitstream is in bundle
+	 *    
+	 */
+	public boolean accept(Bitstream bitstream) 
+	throws BitstreamFilterException
+	{
+		if (bundleName == null)
+		{
+			bundleName = props.getProperty("bundle");
+			if (bundleName == null)
+			{
+				throw new BitstreamFilterException("Property 'bundle' not found.");
+			}			
+		}
+		
+		try
+		{
+			Bundle[] bundles = bitstream.getBundles();
+			for (Bundle b : bundles)
+			{
+				if (b.getName().equals(bundleName))
+				{
+					return true;
+				}
+			}		
+		}
+		catch(SQLException e)
+		{
+			throw new BitstreamFilterException(e);
+		}
+		return false;
+	}
+	
 }

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

@@ -7,43 +7,44 @@
  */
 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 {
+	
+	private Pattern pattern;
+	private String filenameRegex;
+	
+	public BitstreamFilterByFilename()
+	{
+		//empty
+	}
 
-    protected Pattern pattern;
+	/**
-    protected String filenameRegex;
+	 *   Tests bitstream by matching the regular expression in the 
-
+	 *   properties against the bitstream name
-    public BitstreamFilterByFilename() {
+	 * 
-        //empty
+	 *   @return whether bitstream name matches the regular expression
-    }
+	 */
-
+	public boolean accept(Bitstream bitstream) throws BitstreamFilterException
-    /**
+	{		
-     * Tests bitstream by matching the regular expression in the
+		if (filenameRegex == null)
-     * properties against the bitstream name
+		{
-     *
+			filenameRegex = props.getProperty("filename");
-     * @param bitstream Bitstream
+			if (filenameRegex == null)
-     * @return whether bitstream name matches the regular expression
+			{
-     * @throws BitstreamFilterException if filter error
+				throw new BitstreamFilterException("BitstreamFilter property 'filename' not found.");
-     */
+			}
-    @Override
+			pattern = Pattern.compile(filenameRegex);
-    public boolean accept(Bitstream bitstream) throws BitstreamFilterException {
+		}
-        if (filenameRegex == null) {
+		
-            filenameRegex = props.getProperty("filename");
+		Matcher m = pattern.matcher(bitstream.getName());
-            if (filenameRegex == null) {
+		return m.matches();
-                throw new BitstreamFilterException("BitstreamFilter property 'filename' not found.");
+	}	
-            }
+ 
-            pattern = Pattern.compile(filenameRegex);
-        }
-
-        Matcher m = pattern.matcher(bitstream.getName());
-        return m.matches();
-    }
-
 }

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

@@ -8,27 +8,22 @@
 package org.dspace.app.itemupdate;
 
 /**
- * Exception class for BitstreamFilters
+ *    Exception class for BitstreamFilters
+ *
  */
-public class BitstreamFilterException extends Exception {
+public class BitstreamFilterException extends Exception 
-
+{
-    private static final long serialVersionUID = 1L;
+	
-
+	private static final long serialVersionUID = 1L;
-    public BitstreamFilterException() {
+	
-    }
+	public BitstreamFilterException() {}
-
+	public BitstreamFilterException(String msg)
-    /**
+	{
-     * @param msg exception message
+		super(msg);
-     */
+	}
-    public BitstreamFilterException(String msg) {
+	public BitstreamFilterException(Exception e)
-        super(msg);
+	{
-    }
+		super(e);
-
+	}
-    /**
+	
-     * @param e exception
-     */
-    public BitstreamFilterException(Exception e) {
-        super(e);
-    }
-
 }

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

@@ -8,124 +8,146 @@
 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;
 
 /**
- * Holds the elements of a line in the Contents Entry file
+ *   Holds the elements of a line in the Contents Entry file
+ * 
+ *   Based on private methods in ItemImport
+ *   
+ *   Lacking a spec or full documentation for the file format, 
+ *   it looks from the source code that the ordering or elements is not fixed
+ * 
+ *   e.g.:    
+ *      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>
+ * 
  *
- * Based on private methods in ItemImport
- *
- * Lacking a spec or full documentation for the file format,
- * 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_BUNDLE = "bundle:";
-    public static final String HDR_DESCRIPTION = "description:";
+	public static final String HDR_PERMISSIONS = "permissions:";
-
+	public static final String HDR_DESCRIPTION = "description:";
-    public static final Pattern permissionsPattern = Pattern.compile("-([rw])\\s*'?([^']+)'?");
+		
-
+	public static final Pattern permissionsPattern = Pattern.compile("-([rw])\\s*'?([^']+)'?");
-    final String filename;
+	
-    final String bundlename;
+	final String filename;
-    final String permissionsGroupName;
+	final String bundlename;
-    final int permissionsActionId;
+	final String permissionsGroupName;
-    final String description;
+	final int permissionsActionId;
-
+	final String description;
-    protected ContentsEntry(String filename,
+	
-                            String bundlename,
+	private ContentsEntry(String filename, 
-                            int permissionsActionId,
+			             String bundlename,
-                            String permissionsGroupName,
+			             int permissionsActionId,
-                            String description) {
+			             String permissionsGroupName,
-        this.filename = filename;
+			             String description)
-        this.bundlename = bundlename;
+	{
-        this.permissionsActionId = permissionsActionId;
+		this.filename = filename;
-        this.permissionsGroupName = permissionsGroupName;
+		this.bundlename = bundlename;
-        this.description = description;
+		this.permissionsActionId = permissionsActionId;
-    }
+		this.permissionsGroupName = permissionsGroupName;
-
+		this.description = description;
-    /**
+	}
-     * Factory method parses a line from the Contents Entry file
+	
-     *
+	/**
-     * @param line line as string
+	 *   Factory method parses a line from the Contents Entry file
-     * @return the parsed ContentsEntry object
+	 *   
-     * @throws ParseException if parse error
+	 * @param line
-     */
+	 * @return the parsed ContentsEntry object 
-    public static ContentsEntry parse(String line)
+	 * @throws ParseException
-        throws ParseException {
+	 */
-        String[] ar = line.split("\t");
+	public static ContentsEntry parse(String line)
-        ItemUpdate.pr("ce line split: " + ar.length);
+	throws ParseException
-
+	{
-        String[] arp = new String[4];
+		String[] ar = line.split("\t");
-        arp[0] = ar[0];   //bitstream name doesn't have header and is always first
+		ItemUpdate.pr("ce line split: " + ar.length);
-
+		
-        String groupName = null;
+		String[] arp = new String[4];
-        int actionId = -1;
+		arp[0] = ar[0];   //bitstream name doesn't have header and is always first
-
+		
-        if (ar.length > 1) {
+		String groupName = null;
-            for (int i = 1; i < ar.length; i++) {
+		int actionId = -1;
-                ItemUpdate.pr("ce " + i + " : " + ar[i]);
-                if (ar[i].startsWith(HDR_BUNDLE)) {
-                    arp[1] = ar[i].substring(HDR_BUNDLE.length()).trim();
-
-                } 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()) {
-                        String action = m.group(1); //
-                        if (action.equals("r")) {
-                            actionId = Constants.READ;
-                        } else if (action.equals("w")) {
-                            actionId = Constants.WRITE;
-                        }
-
-                        groupName = m.group(2).trim();
-                    }
-
-                } else if (ar[i].startsWith(HDR_DESCRIPTION)) {
-                    arp[3] = ar[i].substring(HDR_DESCRIPTION.length()).trim();
-
-                } else {
-                    throw new ParseException("Unknown text in contents file: " + ar[i], 0);
-                }
-            }
-        }
-        return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
-    }
-
-    public String toString() {
-        StringBuilder sb = new StringBuilder(filename);
-        if (bundlename != null) {
-            sb.append(HDR_BUNDLE).append(" ").append(bundlename);
-        }
-
-        if (permissionsGroupName != null) {
-            sb.append(HDR_PERMISSIONS);
-            if (permissionsActionId == Constants.READ) {
-                sb.append(" -r ");
-            } else if (permissionsActionId == Constants.WRITE) {
-                sb.append(" -w ");
-            }
-            sb.append(permissionsGroupName);
-        }
-
-        if (description != null) {
-            sb.append(HDR_DESCRIPTION).append(" ").append(description);
-        }
-
-        return sb.toString();
-    }
 
+		if (ar.length > 1)
+		{
+			for (int i=1; i < ar.length; i++)
+			{
+				ItemUpdate.pr("ce " + i + " : " + ar[i]);
+				if (ar[i].startsWith(HDR_BUNDLE))
+				{
+					arp[1] = ar[i].substring(HDR_BUNDLE.length()).trim();
+					
+				}
+				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())
+					{
+						String action = m.group(1); //
+						if (action.equals("r"))
+						{
+							 actionId = Constants.READ;
+						}
+						else if (action.equals("w"))
+						{
+							 actionId = Constants.WRITE;
+						}
+						
+						groupName = m.group(2).trim();
+					}
+					
+				}
+				else if (ar[i].startsWith(HDR_DESCRIPTION))
+				{
+					arp[3] = ar[i].substring(HDR_DESCRIPTION.length()).trim();
+					
+				}
+				else
+				{
+					throw new ParseException("Unknown text in contents file: " + ar[i], 0);				
+				}			
+			}
+		}
+		return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
+	}
+	
+	public String toString()
+	{
+		StringBuilder sb = new StringBuilder(filename);
+		if (bundlename != null)
+		{
+			sb.append(HDR_BUNDLE).append(" ").append(bundlename);
+		}
+		
+		if (permissionsGroupName != null)
+		{
+			sb.append(HDR_PERMISSIONS);
+			if (permissionsActionId == Constants.READ)
+			{
+				sb.append(" -r ");
+			}
+			else if (permissionsActionId == Constants.WRITE)
+			{
+				sb.append(" -w ");
+			}
+			sb.append(permissionsGroupName);
+		}
+		
+		if (description != null)
+		{
+			sb.append(HDR_DESCRIPTION).append(" ").append(description);
+		}		
+		
+		return sb.toString();
+	}
+	
 }

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

@@ -21,74 +21,94 @@ import org.dspace.content.Item;
 import org.dspace.core.Context;
 
 /**
- * Action to delete bitstreams
+ * 	  Action to delete bitstreams	
+ * 
+ * 	  Undo not supported for this UpdateAction
+ * 
+ *    Derivatives of the bitstream to be deleted are not also deleted 
  *
- * 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
+	/**
-     *
+	 *   Delete bitstream from item
-     * @param context      DSpace Context
+	 * 
-     * @param itarch       item archive
+	 *  @param context
-     * @param isTest       test flag
+	 *  @param itarch
-     * @param suppressUndo undo flag
+	 *  @param isTest
-     * @throws IOException              if IO error
+	 *  @param suppressUndo
-     * @throws IllegalArgumentException if arg exception
+	 *  @throws IllegalArgumentException
-     * @throws SQLException             if database error
+	 *  @throws ParseException
-     * @throws AuthorizeException       if authorization error
+	 *  @throws IOException
-     * @throws ParseException           if parse error
+	 *  @throws AuthorizeException
-     */
+	 *  @throws SQLException
-    @Override
+	 */
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
+	public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws IllegalArgumentException, IOException,
+            boolean suppressUndo) throws IllegalArgumentException, IOException,
-        SQLException, AuthorizeException, ParseException {
+            SQLException, AuthorizeException, ParseException 
-        File f = new File(itarch.getDirectory(), ItemUpdate.DELETE_CONTENTS_FILE);
+	{
-        if (!f.exists()) {
+		File f = new File(itarch.getDirectory(), ItemUpdate.DELETE_CONTENTS_FILE);
-            ItemUpdate.pr("Warning: Delete_contents file for item " + itarch.getDirectoryName() + " not found.");
+		if (!f.exists())
-        } else {
+		{
-            List<String> list = MetadataUtilities.readDeleteContentsFile(f);
+			ItemUpdate.pr("Warning: Delete_contents file for item " + itarch.getDirectoryName() + " not found.");
-            if (list.isEmpty()) {
+		}
-                ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName());
+		else
-            } else {
+		{
-                for (String id : list) {
+			List<Integer> list = MetadataUtilities.readDeleteContentsFile(f);
-                    try {
+			if (list.isEmpty())
-                        Bitstream bs = bitstreamService.findByIdOrLegacyId(context, id);
+			{
-                        if (bs == null) {
+				ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName() );
-                            ItemUpdate.pr("Bitstream not found by id: " + id);
+			}
-                        } else {
+			else
-                            List<Bundle> bundles = bs.getBundles();
+			{
-                            for (Bundle b : bundles) {
+				for (int id : list)
-                                if (isTest) {
+				{
-                                    ItemUpdate.pr("Delete bitstream with id = " + id);
+					try
-                                } else {
+					{
-                                    bundleService.removeBitstream(context, b, bs);
+			    		Bitstream bs = Bitstream.find(context, id);
-                                    ItemUpdate.pr("Deleted bitstream with id = " + id);
+			    		if (bs == null)
-
+			    		{
-                                }
+			    			ItemUpdate.pr("Bitstream not found by id: " + id);
-                            }
+			    		}
-
+			    		else
-                            if (alterProvenance) {
+			    		{
-                                DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
+				    		Bundle[] bundles = bs.getBundles();
-
+				    		for (Bundle b : bundles)
-                                String append = "Bitstream " + bs.getName() + " deleted on " + DCDate
+				    		{
-                                    .getCurrent() + "; ";
+				    			if (isTest)
-                                Item item = bundles.iterator().next().getItems().iterator().next();
+				    			{
-                                ItemUpdate.pr("Append provenance with: " + append);
+					    			ItemUpdate.pr("Delete bitstream with id = " + id);
-
+				    			}
-                                if (!isTest) {
+				    			else
-                                    MetadataUtilities.appendMetadata(context, item, dtom, false, append);
+				    			{
-                                }
+				    				b.removeBitstream(bs); 
-                            }
+					    			ItemUpdate.pr("Deleted bitstream with id = " + id);
-                        }
+					    			
-                    } catch (SQLException e) {
+				    			}
-                        ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
+				    		}	
-                    }
+			    		
-                }
+				            if (alterProvenance)
-            }
+				            {
-        }
+				            	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-    }
+				            	
+				            	String append = "Bitstream " + bs.getName() + " deleted on " + DCDate.getCurrent() + "; ";
+				            	Item item = bundles[0].getItems()[0];
+					    		ItemUpdate.pr("Append provenance with: " + append);
+					    		
+					    		if (!isTest)
+					    		{
+					    			MetadataUtilities.appendMetadata(item, dtom, false, append);
+					    		}
+				            }
+			    		}	
+					}
+					catch(SQLException e)
+					{
+						ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
+					}
+				}
+			}
+		}
+	}
 
 }

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

@@ -21,97 +21,110 @@ import org.dspace.content.Item;
 import org.dspace.core.Context;
 
 /**
- * Action to delete bitstreams using a specified filter implementing BitstreamFilter
+ * 		Action to delete bitstreams using a specified filter implementing BitstreamFilter
- * Derivatives for the target bitstreams are not deleted.
+ *      Derivatives for the target bitstreams are not deleted.
+ * 
+ *      The dc.description.provenance field is amended to reflect the deletions
+ *      
+ *      Note:  Multiple filters are impractical if trying to manage multiple properties files
+ *      in a commandline environment
+ * 
  *
- * The dc.description.provenance field is amended to reflect the deletions
- *
- * 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
+	 *   Set filter
-     *
+	 *   
-     * @param filter BitstreamFilter
+	 * @param filter
-     */
+	 */
-    public void setBitstreamFilter(BitstreamFilter filter) {
+	public void setBitstreamFilter(BitstreamFilter filter)
-        this.filter = filter;
+	{
-    }
+		this.filter = filter;
-
+	}
-    /**
+	
-     * Get filter
+	/**
-     *
+	 *   Get filter
-     * @return filter
+	 * @return filter 
-     */
+	 */
-    public BitstreamFilter getBitstreamFilter() {
+	public BitstreamFilter getBitstreamFilter()
-        return filter;
+	{
-    }
+		return filter;
-
+	}
-    /**
+	
-     * Delete bitstream
+	/**
-     *
+	 * 	 Delete bitstream
-     * @param context      DSpace Context
+	 * 
-     * @param itarch       item archive
+	 *  @param context
-     * @param isTest       test flag
+	 *  @param itarch
-     * @param suppressUndo undo flag
+	 *  @param isTest
-     * @throws IOException              if IO error
+	 *  @param suppressUndo
-     * @throws SQLException             if database error
+	 *  @throws IllegalArgumentException
-     * @throws AuthorizeException       if authorization error
+	 *  @throws ParseException
-     * @throws ParseException           if parse error
+	 *  @throws IOException
-     * @throws BitstreamFilterException if filter error
+	 *  @throws AuthorizeException
-     */
+	 *  @throws SQLException
-    @Override
+	 */
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
+	public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException,
+            boolean suppressUndo) throws AuthorizeException,
-        BitstreamFilterException, IOException, ParseException, SQLException {
+            BitstreamFilterException, IOException, ParseException, SQLException 
-
+	{
-        List<String> deleted = new ArrayList<String>();
+		
-
+		List<String> deleted = new ArrayList<String>();
-        Item item = itarch.getItem();
+		
-        List<Bundle> bundles = item.getBundles();
+		Item item = itarch.getItem();
-
+		Bundle[] bundles = item.getBundles();
-        for (Bundle b : bundles) {
+		
-            List<Bitstream> bitstreams = b.getBitstreams();
+		for (Bundle b : bundles)    
-            String bundleName = b.getName();
+		{
-
+			Bitstream[] bitstreams = b.getBitstreams();
-            for (Bitstream bs : bitstreams) {
+			String bundleName = b.getName();
-                if (filter.accept(bs)) {
+			
-                    if (isTest) {
+			for (Bitstream bs : bitstreams)
-                        ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName()
+			{		
-                                          + " with id = " + bs.getID());
+			    if (filter.accept(bs))
-                    } else {
+				{
-                        //provenance is not maintained for derivative bitstreams
+	    			if (isTest)
-                        if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT")) {
+	    			{
-                            deleted.add(bs.getName());
+		    			ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName() 
-                        }
+		    					+ " with id = " + bs.getID());
-                        bundleService.removeBitstream(context, b, bs);
+	    			}
-                        ItemUpdate.pr("Deleted " + bundleName + " bitstream " + bs.getName()
+	    			else
-                                          + " with id = " + bs.getID());
+	    			{	    					    				
-                    }
+	    				//provenance is not maintained for derivative bitstreams
-                }
+	    				if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT"))
-            }
+	    				{
+	    					deleted.add(bs.getName());
+	    				}
+	    				b.removeBitstream(bs); 
+		    			ItemUpdate.pr("Deleted " + bundleName + " bitstream " + bs.getName() 
+		    					+ " with id = " + bs.getID());		    			
+	    			}
+				}
+			}			
+		}
+		
+        if (alterProvenance && !deleted.isEmpty())
+        {     	
+    		StringBuilder sb = new StringBuilder("  Bitstreams deleted on "); 	
+    		sb.append(DCDate.getCurrent()).append(": ");
+    		
+    		for (String s : deleted)
+    		{
+            	sb.append(s).append(", ");
+    		}
+    		        	
+        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
+        	
+    		ItemUpdate.pr("Append provenance with: " + sb.toString());
+    		
+    		if (!isTest)
+    		{
+    			MetadataUtilities.appendMetadata(item, dtom, false, sb.toString());
+    		}
         }
-
+	}
-        if (alterProvenance && !deleted.isEmpty()) {
+	
-            StringBuilder sb = new StringBuilder("  Bitstreams deleted on ");
-            sb.append(DCDate.getCurrent()).append(": ");
-
-            for (String s : deleted) {
-                sb.append(s).append(", ");
-            }
-
-            DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-
-            ItemUpdate.pr("Append provenance with: " + sb.toString());
-
-            if (!isTest) {
-                MetadataUtilities.appendMetadata(context, item, dtom, false, sb.toString());
-            }
-        }
-    }
-
 }

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

@@ -7,59 +7,58 @@
  */
 package org.dspace.app.itemupdate;
 
-import java.sql.SQLException;
 import java.text.ParseException;
-import java.util.List;
 
 import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.Metadatum;
 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
+ *    Action to delete metadata 
+ * 
+ *
  */
 public class DeleteMetadataAction extends UpdateMetadataAction {
 
-    /**
+	/**
-     * Delete metadata from item
+	 *   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
+	 */
-     */
+	public void execute(Context context, ItemArchive itarch, boolean isTest,
-    @Override
+            boolean suppressUndo) throws AuthorizeException, ParseException 
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
+	{
-                        boolean suppressUndo) throws AuthorizeException, ParseException, SQLException {
+		Item item = itarch.getItem();
-        Item item = itarch.getItem();
+		for (String f : targetFields)
-        for (String f : targetFields) {
+		{
-            DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
+			DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
-            List<MetadataValue> ardcv = itemService.getMetadataByMetadataString(item, f);
+			Metadatum[] ardcv = item.getMetadataByMetadataString(f);
 
-            ItemUpdate.pr("Metadata to be deleted: ");
+			ItemUpdate.pr("Metadata to be deleted: ");
-            for (MetadataValue dcv : ardcv) {
+			for (Metadatum dcv : ardcv)
-                ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
+			{
-            }
+				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 (Metadatum 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

@@ -10,13 +10,15 @@ package org.dspace.app.itemupdate;
 import java.util.Properties;
 
 /**
- * Bitstream filter to delete from TEXT bundle
+ *   Bitstream filter to delete from TEXT bundle
+ *
  */
 public class DerivativeTextBitstreamFilter extends BitstreamFilterByBundleName {
-
+	
-    public DerivativeTextBitstreamFilter() {
+	public DerivativeTextBitstreamFilter()
-        props = new Properties();
+	{
-        props.setProperty("bundle", "TEXT");
+		props = new Properties();
-    }
+		props.setProperty("bundle", "TEXT");
+	}
 
 }

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

@@ -8,131 +8,149 @@
 package org.dspace.app.itemupdate;
 
 import java.text.ParseException;
-
 import org.dspace.content.Item;
 
 /**
- * A data transfer object class enhancement of org.dspace.content.DCValue, which is deprecated
+ *   A data transfer object class enhancement of org.dspace.content.DCValue, which is deprecated
- * Name intended to not conflict with DSpace API classes for similar concepts but not usable in this context
+ *   Name intended to not conflict with DSpace API classes for similar concepts but not usable in this context
+ *   
+ *   Adds some utility methods
+ *   
+ *   Really not at all general enough but supports Dublin Core and the compound form notation <schema>.<element>[.<qualifier>]
+ *   
+ *   Does not support wildcard for qualifier
+ * 
  *
- * Adds some utility methods
- *
- * Really not at all general enough but supports Dublin Core and the compound form notation {@code <schema>
- * .<element>[.<qualifier>]}
- *
- * Does not support wildcard for qualifier
  */
-class DtoMetadata {
+class DtoMetadata 
-    final String schema;
+{
-    final String element;
+	final String schema;   
-    final String qualifier;
+	final String element;
-    final String language;
+	final String qualifier;
-    final String value;
+	final String language;
-
+	final String value;
-    protected DtoMetadata(String schema, String element, String qualifier, String language, String value) {
+	
-        this.schema = schema;
+	private DtoMetadata(String schema, String element, String qualifier, String language, String value) 
-        this.element = element;
+	{
-        this.qualifier = qualifier;
+		this.schema = schema;
-        this.language = language;
+		this.element = element;
-        this.value = value;
+		this.qualifier = qualifier;
+		this.language = language;
+		this.value = value;
+	}
+	
+	/**
+	 *  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      
+	 * @return DtoMetadata object
+	 */
+	public static DtoMetadata create(String schema,
+			    String element,
+			    String qualifier,
+			    String language,
+			    String value)
+	throws IllegalArgumentException
+    {
+		if ((qualifier != null) &&  (qualifier.equals(Item.ANY) || qualifier.equals("")))
+		{
+			throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
+		}
+		return new DtoMetadata(schema, element, qualifier, language, value);
     }
 
-    /**
+	/**
-     * Factory method
+	 *   Factory method to create metadata object
-     *
+	 *   
-     * @param schema    not null, not empty -  'dc' is the standard case
+	 * 
-     * @param element   not null, not empty
+	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>]
-     * @param qualifier null; don't allow empty string or * indicating 'any'
+	 * @param language   null or empty
-     * @param language  null or empty
+	 * @param value      
-     * @param value     value
+	 */
-     * @return DtoMetadata object
+	public static DtoMetadata create(String compoundForm, String language, String value)
-     * @throws IllegalArgumentException if arg error
+	throws ParseException, IllegalArgumentException  
-     */
+    {
-    public static DtoMetadata create(String schema,
+		String[] ar = MetadataUtilities.parseCompoundForm(compoundForm);
-                                     String element,
+		
-                                     String qualifier,
+		String qual = null;
-                                     String language,
+		if (ar.length > 2)
-                                     String value)
+		{
-        throws IllegalArgumentException {
+    		qual = ar[2];
-        if ((qualifier != null) && (qualifier.equals(Item.ANY) || qualifier.equals(""))) {
+		}
-            throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
+		
-        }
+		return create(ar[0], ar[1], qual, language, value);
-        return new DtoMetadata(schema, element, qualifier, language, value);
     }
 
-    /**
+	/**
-     * Factory method to create metadata object
+	 *   Determine if this metadata field matches the specified type:
-     *
+	 *    schema.element or schema.element.qualifier
-     * @param compoundForm of the form <schema>.<element>[.<qualifier>]
+	 *    
-     * @param language     null or empty
+	 * 
-     * @param value        value
+	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>|.*]
-     * @throws ParseException           if parse error
+	 * @param wildcard       allow wildcards in compoundForm param
-     * @throws IllegalArgumentException if arg error
+	 * @return whether matches
-     */
+	 */
-    public static DtoMetadata create(String compoundForm, String language, String value)
+	public boolean matches(String compoundForm, boolean wildcard)
-        throws ParseException, IllegalArgumentException {
+	{
-        String[] ar = MetadataUtilities.parseCompoundForm(compoundForm);
+		String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
-
+		
-        String qual = null;
+		if ((ar.length < 2) || (ar.length > 3))
-        if (ar.length > 2) {
+		{
-            qual = ar[2];
+			return false;
-        }
+		}
-
+		
-        return create(ar[0], ar[1], qual, language, value);
+		if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1]))
-    }
+		{
-
+			return false;
-    /**
+		}
-     * Determine if this metadata field matches the specified type:
+		
-     * schema.element or schema.element.qualifier
+		if (ar.length == 2)
-     *
+		{
-     * @param compoundForm of the form <schema>.<element>[.<qualifier>|.*]
+			if (this.qualifier != null)
-     * @param wildcard     allow wildcards in compoundForm param
+			{
-     * @return whether matches
+				return false;
-     */
+			}
-    public boolean matches(String compoundForm, boolean wildcard) {
+		}
-        String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
+		
-
+		if (ar.length == 3)	
-        if ((ar.length < 2) || (ar.length > 3)) {
+		{
-            return false;
+			if (this.qualifier == null)
-        }
+			{
-
+				return false;
-        if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1])) {
+			}
-            return false;
+			if (wildcard && ar[2].equals(Item.ANY))
-        }
+			{
-
+				return true;
-        if (ar.length == 2) {
+			}
-            if (this.qualifier != null) {
+			if (!this.qualifier.equals(ar[2]))
-                return false;
+			{
-            }
+				return false;
-        }
+			}
-
+		}
-        if (ar.length == 3) {
+		return true;		
-            if (this.qualifier == null) {
+	}
-                return false;
+	
-            }
+	public String toString()
-            if (wildcard && ar[2].equals(Item.ANY)) {
+	{
-                return true;
+		String s =  "\tSchema: " + schema + " Element: " + element;
-            }
+		if (qualifier != null)
-            if (!this.qualifier.equals(ar[2])) {
+		{
-                return false;
+			s+= " Qualifier: " + qualifier;
-            }
+		}
-        }
+		s+= " Language: " + ((language == null) ? "[null]" : language);
-        return true;
-    }
-
-    public String toString() {
-        String s = "\tSchema: " + schema + " Element: " + element;
-        if (qualifier != null) {
-            s += " Qualifier: " + qualifier;
-        }
-        s += " Language: " + ((language == null) ? "[null]" : language);
         s += " Value: " + value;
-
+        
         return s;
-    }
+	}
-
+	
-    public String getValue() {
+	public String getValue()
-        return value;
+	{
-    }
+		return value;
-
+	}
+		
 }

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

@@ -10,334 +10,339 @@ 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
+ *   Encapsulates the Item in the context of the DSpace Archive Format
+ *
  */
 public class ItemArchive {
-    private static final Logger log = Logger.getLogger(ItemArchive.class);
+    private static final Logger log = Logger.getLogger(ItemArchive.class); 
 
-    public static final String DUBLIN_CORE_XML = "dublin_core.xml";
+	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;
+//constructors
-    protected ItemService itemService;
+	private ItemArchive() 
-
+	{
-    //constructors
+		// nothing
-    protected ItemArchive() {
+	}	
-        handleService = HandleServiceFactory.getInstance().getHandleService();
+	
-        itemService = ContentServiceFactory.getInstance().getItemService();
+/** factory method
-    }
+ * 
-
+ * 	Minimal requirements for dublin_core.xml for this application
-    /**
+ *  is the presence of dc.identifier.uri
-     * factory method
+ *  which must contain the handle for the item
-     *
+ *  
-     * Minimal requirements for dublin_core.xml for this application
+ *  @param context - The DSpace context
-     * is the presence of dc.identifier.uri
+ *  @param dir     - The directory File in the source archive
-     * which must contain the handle for the item
+ *  @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
-     * @param context   - The DSpace context
+ * 
-     * @param dir       - The directory File in the source archive
+ */
-     * @param itemField - The metadata field in which the Item identifier is located
+	public static ItemArchive create(Context context, File dir, String itemField)
-     *                  if null, the default is the handle in the dc.identifier.uri field
+	throws Exception
-     * @return ItemArchive object
+	{
-     * @throws Exception if error
+		ItemArchive itarch = new ItemArchive(); 
-     */
+		itarch.dir = dir;
-    public static ItemArchive create(Context context, File dir, String itemField)
+		itarch.dirname = dir.getName();
-        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
+        finally
-            // .ItemImportServiceImpl.java
+        {
-            File file[] = dir.listFiles(new LocalSchemaFilenameFilter());
+            if (is != null)
-            for (int i = 0; i < file.length; i++) {
+            {
-                is = new FileInputStream(file[i]);
-                itarch.dtomList.addAll(MetadataUtilities.loadDublinCore(getDocumentBuilder(), is));
-            }
-        } finally {
-            if (is != null) {
                 is.close();
             }
         }
-        ItemUpdate.pr("Loaded metadata with " + itarch.dtomList.size() + " fields");
+		ItemUpdate.pr("Loaded metadata with " + itarch.dtomList.size() + " fields");
+		
+		if (itemField == null)
+		{
+			itarch.item = itarch.itemFromHandleInput(context);  // sets the item instance var and seeds the undo list
+		}
+		else
+		{
+			itarch.item = itarch.itemFromMetadataField(context, itemField);  			
+		}
+		
+		if (itarch.item == null)
+		{
+			throw new Exception("Item not instantiated: " + itarch.dirname);
+		}
+		
+		ItemUpdate.prv("item instantiated: " + itarch.item.getHandle());
 
-        if (itemField == null) {
+		return itarch;
-            itarch.item = itarch.itemFromHandleInput(context);  // sets the item instance var and seeds the undo list
+	}
-        } else {
+		
-            itarch.item = itarch.itemFromMetadataField(context, itemField);
+	private static DocumentBuilder getDocumentBuilder()
-        }
+	throws ParserConfigurationException
-
+	{
-        if (itarch.item == null) {
+		if (builder == null)
-            throw new Exception("Item not instantiated: " + itarch.dirname);
+		{
-        }
+		    builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
-
+		}
-        ItemUpdate.prv("item instantiated: " + itarch.item.getHandle());
+		return builder;
-
+	}
-        return itarch;
+	
-    }
+	private static Transformer getTransformer()
-
+	throws TransformerConfigurationException
-    protected static DocumentBuilder getDocumentBuilder()
+	{
-        throws ParserConfigurationException {
+		if (transformer == null)
-        if (builder == null) {
+		{
-            builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
+		    transformer = TransformerFactory.newInstance().newTransformer();
-        }
+		}
-        return builder;
+		return transformer;
-    }
+	}
 
+	/**
+	 *   Getter for the DSpace item referenced in the archive
+	 * @return DSpace item 
+	 */
+	public Item getItem()
+	{
+		return item;
+	}
+	
+	/**
+	 *   Getter for directory in archive on disk
+	 * @return directory in archive
+	 */
+	public File getDirectory()
+	{
+		return dir;
+	}
+	
+	/**
+	 *   Getter for directory name in archive
+	 * @return directory name in archive
+	 */
+	public String getDirectoryName()
+	{
+		return dirname;
+	}
+	
+	/**
+	 *   Add metadata field to undo list
+	 * @param 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()
+	{
+		return dtomList;
+	}
+	
+	/**
+	 *   Add bitstream id to delete contents file
+	 * @param bitstreamId
+	 */
+	public void addUndoDeleteContents(int bitstreamId)
+	{
+		this.undoAddContents.add(bitstreamId);
+	}
+	
+	
     /**
-     * Getter for Transformer
+	 *   Obtain item from DSpace based on handle
-     *
+     *   This is the default implementation
-     * @return Transformer
+     *   that uses the dc.identifier.uri metadatafield 
-     * @throws TransformerConfigurationException if config error
+     *   that contains the item handle as its value  
-     */
+     *   
-    protected Transformer getTransformer()
-        throws TransformerConfigurationException {
-        if (transformer == null) {
-            transformer = TransformerFactory.newInstance().newTransformer();
-        }
-        return transformer;
-    }
-
-    /**
-     * Getter for the DSpace item referenced in the archive
-     *
-     * @return DSpace item
-     */
-    public Item getItem() {
-        return item;
-    }
-
-    /**
-     * Getter for directory in archive on disk
-     *
-     * @return directory in archive
-     */
-    public File getDirectory() {
-        return dir;
-    }
-
-    /**
-     * Getter for directory name in archive
-     *
-     * @return directory name in archive
-     */
-    public String getDirectoryName() {
-        return dirname;
-    }
-
-    /**
-     * Add metadata field to undo list
-     *
-     * @param dtom DtoMetadata (represents metadata field)
-     */
-    public void addUndoMetadataField(DtoMetadata dtom) {
-        this.undoDtomList.add(dtom);
-    }
-
-    /**
-     * Getter for list of metadata fields
-     *
-     * @return list of metadata fields
-     */
-    public List<DtoMetadata> getMetadataFields() {
-        return dtomList;
-    }
-
-    /**
-     * Add bitstream id to delete contents file
-     *
-     * @param bitstreamId bitstream ID
-     */
-    public void addUndoDeleteContents(UUID bitstreamId) {
-        this.undoAddContents.add(bitstreamId);
-    }
-
-
-    /**
-     * Obtain item from DSpace based on handle
-     * This is the default implementation
-     * that uses the dc.identifier.uri metadatafield
-     * that contains the item handle as its value
-     *
-     * @param context DSpace Context
-     * @throws SQLException if database error
-     * @throws Exception    if error
      */
     private Item itemFromHandleInput(Context context)
-        throws SQLException, Exception {
+    throws SQLException, Exception
-        DtoMetadata dtom = getMetadataField("dc.identifier.uri");
+    {
-        if (dtom == null) {
+    	DtoMetadata dtom = getMetadataField("dc.identifier.uri");
-            throw new Exception("No dc.identier.uri field found for handle");
+    	if (dtom == null)
-        }
+    	{
-
+    		throw new Exception("No dc.identier.uri field found for handle"); 
-        this.addUndoMetadataField(dtom);  //seed the undo list with the uri
+    	}
-
+    	
-        String uri = dtom.value;
+    	this.addUndoMetadataField(dtom);  //seed the undo list with the uri
-
+    	
-        if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX)) {
+		String uri = dtom.value;
-            throw new Exception("dc.identifier.uri for item " + uri
+		
-                                    + " does not begin with prefix: " + ItemUpdate.HANDLE_PREFIX);
+    	if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX))
-        }
+    	{
-
+    		throw new Exception("dc.identifier.uri for item " + uri 
-        String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());
+    				+ " does not begin with prefix: " + ItemUpdate.HANDLE_PREFIX);
-
+    	}
-        DSpaceObject dso = handleService.resolveToObject(context, handle);
+    	
-        if (dso instanceof Item) {
+    	String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());
-            item = (Item) dso;
+    		
-        } else {
+		DSpaceObject dso = HandleManager.resolveToObject(context, handle);  
-            ItemUpdate.pr("Warning: item not instantiated");
+		if (dso instanceof Item)
-            throw new IllegalArgumentException("Item " + handle + " not instantiated.");
+		{
-        }
+			item =  (Item) dso;
-        return item;
+		}
+		else
+		{
+			ItemUpdate.pr("Warning: item not instantiated");
+			throw new IllegalArgumentException("Item " + handle + " not instantiated.");
+		}	
+		return item;
     }
-
+    
     /**
-     * Find and instantiate Item from the dublin_core.xml based
+     * 	 Find and instantiate Item from the dublin_core.xml based
-     * on the specified itemField for the item identifier,
+     *   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);
+    {
+    	DtoMetadata dtom = getMetadataField(itemField);
+    	
+    	Item item = 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());
 
-        Item item = null;
+    	this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
-
+    	
-        if (dtom == null) {
+	    ItemIterator itr = Item.findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
-            throw new IllegalArgumentException("No field found for item identifier field: " + itemField);
+		int count = 0;
-        }
+		while (itr.hasNext())
-        ItemUpdate.prv("Metadata field to match for item: " + dtom.toString());
+		{
-
+			item = itr.next();
-        this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
+			count++;
-
+		}
-        Iterator<Item> itr = itemService
+		
-            .findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
+		itr.close(); 
-        int count = 0;
+		
-        while (itr.hasNext()) {
+		ItemUpdate.prv("items matching = " + count );
-            item = itr.next();
+		
-            count++;
+		if (count != 1)
-        }
+		{
-
+			throw new Exception ("" + count + " items matching item identifier: " + dtom.value);
-        ItemUpdate.prv("items matching = " + count);
+		}
-
+        
-        if (count != 1) {
+    	return item;    	
-            throw new Exception("" + count + " items matching item identifier: " + dtom.value);
+    }  
-        }
+    
-
+    private DtoMetadata  getMetadataField(String compoundForm)
-        return item;
+    {
-    }
+    	for (DtoMetadata dtom : dtomList)
-
+    	{
-    /**
+			if (dtom.matches(compoundForm, false))
-     * Get DtoMetadata field
+			{
-     *
+				return dtom;
-     * @param compoundForm compound form
+			}
-     * @return DtoMetadata field
+    	}
-     */
+    	return null;
-    private DtoMetadata getMetadataField(String compoundForm) {
+    }    
-        for (DtoMetadata dtom : dtomList) {
-            if (dtom.matches(compoundForm, false)) {
-                return dtom;
-            }
-        }
-        return null;
-    }
 
     /**
      * 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)
+	public void writeUndo(File undoDir)
-        throws IOException, ParserConfigurationException, TransformerConfigurationException,
+	throws IOException, ParserConfigurationException, TransformerConfigurationException, 
-        TransformerException, FileNotFoundException {
+	       TransformerException, FileNotFoundException
-        // create directory for item
+	{
-        File dir = new File(undoDir, dirname);
+		// create directory for item
-        if (!dir.exists() && !dir.mkdir()) {
+		File dir = new File(undoDir, dirname);
+		if (!dir.exists() && !dir.mkdir())
+        {
             log.error("Unable to create undo directory");
         }
+		
+		OutputStream out = null;
 
-        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();
             }
         }
-    }
+	}
-
+	
 } //end class

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;
@@ -46,420 +39,491 @@ import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.content.Metadatum;
+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
+ * 		Miscellaneous methods for metadata handling that build on the API
- * which might have general utility outside of the specific use
+ *      which might have general utility outside of the specific use
- * in context in ItemUpdate.
+ *      in context in ItemUpdate.
+ *      
+ *      The XML methods were based on those in ItemImport
+ * 
  *
- * The XML methods were based on those in ItemImport
  */
 public class MetadataUtilities {
-
+	
-    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    /**      
-
+     * 
-    /**
+     *  Working around Item API to delete a value-specific Metadatum
-     * Default constructor
+  For a given element/qualifier/lang:
-     */
+      get all DCValues
-    private MetadataUtilities() { }
+      clear (i.e. delete) all of these DCValues
-
+     *      add them back, minus the one to actually delete
-    /**
+     *  
-     * Working around Item API to delete a value-specific Metadatum
+     * 
-     * For a given element/qualifier/lang:
+     * @param item
-     * get all DCValues
+     * @param dtom
-     * clear (i.e. delete) all of these DCValues
+     * @param isLanguageStrict - 
-     * add them back, minus the one to actually delete
+     * 
-     *
-     * @param context          DSpace Context
-     * @param item             Item Object
-     * @param dtom             metadata field
-     * @param isLanguageStrict whether strict or not
      * @return true if metadata field is found with matching value and was deleted
-     * @throws SQLException if database error
      */
-    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;
+    	Metadatum[] 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
-
+    	{
-        boolean found = false;
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
-
+    	}
-        //build new set minus the one to delete
+    	
-        List<String> vals = new ArrayList<String>();
+    	boolean found = false;
-        for (MetadataValue dcv : ar) {
+    	
-            if (dcv.getValue().equals(dtom.value)) {
+    	//build new set minus the one to delete
-                found = true;
+    	List<String> vals = new ArrayList<String>();
-            } else {
+    	for (Metadatum dcv : ar)
-                vals.add(dcv.getValue());
+    	{
-            }
+    		if (dcv.value.equals(dtom.value))
-        }
+    		{
-
+    			found = true;
-        if (found) {  //remove all for given type  ??synchronize this block??
+    		}
-            if (isLanguageStrict) {
+    		else
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+    		{
-            } else {
+    			vals.add(dcv.value);
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+    		}
-            }
+    	}
-
+    	
-            itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
+    	if (found)  //remove all for given type  ??synchronize this block??
-        }
+    	{   
-        return found;
+        	if (isLanguageStrict)
+        	{           		
+        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+        	}
+        	else
+        	{
+        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+        	}
+    	
+    		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
+    	}
+		return found;
     }
 
     /**
-     * Append text to value metadata field to item
+     *   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 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)
+    		String textToAppend)
-        throws IllegalArgumentException, SQLException {
+    throws IllegalArgumentException
-        List<MetadataValue> ar = null;
+    {   	
+    	Metadatum[] ar = null;
+    	
+    	// get all values for given element/qualifier
+    	if (isLanguageStrict)  // get all for given element/qualifier
+    	{   
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
+    	}
+    	else
+    	{
+    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
+    	}
+    	
+    	if (ar.length == 0)
+    	{
+    		throw new IllegalArgumentException("Metadata to append to not found");
+    	}
+    	
+    	int idx = 0;  //index of field to change
+    	if (ar.length > 1)  //need to pick one, can't be sure it's the last one
+    	{
+    		// TODO maybe get highest id ?
+    	}
+    	
+    	//build new set minus the one to delete
+    	List<String> vals = new ArrayList<String>();
+    	for (int i=0; i < ar.length; i++) 
+    	{
+    		if (i == idx)
+    		{
+    			vals.add(ar[i].value + textToAppend);
+    		}
+    		else
+    		{
+    			vals.add(ar[i].value);
+    		}
+    	}
 
-        // get all values for given element/qualifier
+    	if (isLanguageStrict)
-        if (isLanguageStrict) {  // get all for given element/qualifier
+    	{           		
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
+    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
+    	}
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
+    	else
-        }
+    	{
-
+    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-        if (ar.size() == 0) {
+    	}
-            throw new IllegalArgumentException("Metadata to append to not found");
+	
-        }
+		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
-
-        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
-            // TODO maybe get highest id ?
-        }
-
-        //build new set minus the one to delete
-        List<String> vals = new ArrayList<String>();
-        for (int i = 0; i < ar.size(); i++) {
-            if (i == idx) {
-                vals.add(ar.get(i).getValue() + textToAppend);
-            } else {
-                vals.add(ar.get(i).getValue());
-            }
-        }
-
-        if (isLanguageStrict) {
-            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
-            itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-        }
-
-        itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
     }
-
+ 
     /**
-     * Modification of method from ItemImporter.loadDublinCore
+     *  Modification of method from ItemImporter.loadDublinCore 
-     * as a Factory method
+     *  as a Factory method
-     *
+     * 
-     * @param docBuilder DocumentBuilder
+     * @param docBuilder  - 
-     * @param is         - InputStream of dublin_core.xml
+     * @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,
+    throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
+           SAXException, TransformerException, AuthorizeException
-        Document document = docBuilder.parse(is);
+	{    	
+		Document document = docBuilder.parse(is);
+		
+		List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
+		
+		// Get the schema, for backward compatibility we will default to the
+		// dublin core schema if the schema name is not available in the import file		
+		String schema = null;
+		NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");		
+		Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
+		if (schemaAttr == null)
+		{
+		    schema = MetadataSchema.DC_SCHEMA;
+		}
+		else
+		{
+		    schema = schemaAttr.getNodeValue();
+		}
 
-        List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
+		// Get the nodes corresponding to formats
+		NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
+		
+		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)
+	        {
+	            value = "";
+	        }
+	        String element = getAttributeValue(n, "element");
+	        if (element != null)
+	        {
+	        	element = element.trim();
+	        }
+	        String qualifier = getAttributeValue(n, "qualifier"); 
+	        if (qualifier != null)
+	        {
+	        	qualifier = qualifier.trim();
+	        }
+	        String language = getAttributeValue(n, "language");
+	        if (language != null)
+	        {
+	        	language = language.trim();
+	        }
 
-        // Get the schema, for backward compatibility we will default to the
+	        if ("none".equals(qualifier) || "".equals(qualifier))
-        // dublin core schema if the schema name is not available in the import file
+	        {
-        String schema = null;
+	            qualifier = null;
-        NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");
+	        }
-        Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
+	        
-        if (schemaAttr == null) {
+	        // a goofy default, but consistent with DSpace treatment elsewhere  
-            schema = MetadataSchema.DC_SCHEMA;
+	        if (language == null)
-        } else {
+	        {
-            schema = schemaAttr.getNodeValue();
+	            language = "en";
-        }
+	        }
-
+	        else if ("".equals(language))
-        // Get the nodes corresponding to formats
+	        {
-        NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
+	            language = ConfigurationManager.getProperty("default.language");
-
+	        }
-        for (int i = 0; i < dcNodes.getLength(); i++) {
+	        
-            Node n = dcNodes.item(i);
+		    DtoMetadata dtom = DtoMetadata.create(schema, element, qualifier, language, value);
-            String value = getStringValue(n).trim();
+		    ItemUpdate.pr(dtom.toString());
-            // compensate for empty value getting read as "null", which won't display
+		    dtomList.add(dtom);
-            if (value == null) {
+		}
-                value = "";
+		return dtomList;
-            }
+	}
-            String element = getAttributeValue(n, "element");
-            if (element != null) {
-                element = element.trim();
-            }
-            String qualifier = getAttributeValue(n, "qualifier");
-            if (qualifier != null) {
-                qualifier = qualifier.trim();
-            }
-            String language = getAttributeValue(n, "language");
-            if (language != null) {
-                language = language.trim();
-            }
-
-            if ("none".equals(qualifier) || "".equals(qualifier)) {
-                qualifier = null;
-            }
-
-            // a goofy default, but consistent with DSpace treatment elsewhere
-            if (language == null) {
-                language = "en";
-            } else if ("".equals(language)) {
-                language = ConfigurationManager.getProperty("default.language");
-            }
-
-            DtoMetadata dtom = DtoMetadata.create(schema, element, qualifier, language, value);
-            ItemUpdate.pr(dtom.toString());
-            dtomList.add(dtom);
-        }
-        return dtomList;
-    }
 
     /**
-     * Write dublin_core.xml
+     *    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)
+	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);
+        	Element mel = doc.createElement("dcvalue");
-            if (dtom.qualifier == null) {
+        	mel.setAttribute("element", dtom.element);
-                mel.setAttribute("qualifier", "none");
+        	if (dtom.qualifier == null)
-            } else {
+        	{
-                mel.setAttribute("qualifier", dtom.qualifier);
+        		mel.setAttribute("qualifier", "none");
-            }
+        	}
-
+        	else
-            if (StringUtils.isEmpty(dtom.language)) {
+        	{
-                mel.setAttribute("language", "en");
+        		mel.setAttribute("qualifier", dtom.qualifier);
-            } else {
+        	}
-                mel.setAttribute("language", dtom.language);
+ 
-            }
+        	if (StringUtils.isEmpty(dtom.language))
-            mel.setTextContent(dtom.value);
+        	{
-            root.appendChild(mel);
+        		mel.setAttribute("language", "en");
+        	}
+        	else
+        	{
+        		mel.setAttribute("language", dtom.language);
+        	}
+        	mel.setTextContent(dtom.value);
+        	root.appendChild(mel);
         }
-
+        
-        return doc;
+        return doc;       
-    }
+	}
-
+	
     /**
-     * write xml document to output stream
+     *   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)
+	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);
+        Source src = new DOMSource(doc); 
-        transformer.transform(src, dest);
+        Result dest = new StreamResult(out); 
-    }
+        transformer.transform(src, dest); 
-
+	}
-
+    
+    
+    
     // 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();
             }
         }
 
         return "";
     }
-
+    
     /**
      * 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();
             }
         }
 
         return value;
     }
-
+    
     /**
      * 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>();
+    {
-
+    	List<ContentsEntry> list = new ArrayList<ContentsEntry>();
-        BufferedReader in = null;
+    	
-
+    	BufferedReader in = null;
-        try {
+    	
-            in = new BufferedReader(new FileReader(f));
+    	try
-            String line = null;
+    	{
-
+	    	in = new BufferedReader(new FileReader(f));
-            while ((line = in.readLine()) != null) {
+	    	String line = null;
-                line = line.trim();
+	    	
-                if ("".equals(line)) {
+	    	while ((line = in.readLine()) != null)
-                    continue;
+	    	{
-                }
+	    		line = line.trim();
-                ItemUpdate.pr("Contents entry: " + line);
+	            if ("".equals(line))
-                list.add(ContentsEntry.parse(line));
+	            {
-            }
+	                continue;
-        } finally {
+	            }
-            try {
+	            ItemUpdate.pr("Contents entry: " + line);	            
-                in.close();
+	    		list.add(ContentsEntry.parse(line));	 
-            } catch (IOException e) {
+	    	}
-                //skip
+    	}
-            }
+    	finally
-        }
+    	{
-
+    		try
-        return list;
+    		{
+    			in.close();
+    		}
+    		catch(IOException e)
+    		{
+    			//skip
+    		}
+    	}
+    	
+    	return list;
     }
 
     /**
-     * @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;
+    	
-
+    	BufferedReader in = null;
-        try {
+    	
-            in = new BufferedReader(new FileReader(f));
+    	try
-            String line = null;
+    	{
-
+	    	in = new BufferedReader(new FileReader(f));
-            while ((line = in.readLine()) != null) {
+	    	String line = null;
-                line = line.trim();
+	    	
-                if ("".equals(line)) {
+	    	while ((line = in.readLine()) != null)
-                    continue;
+	    	{
-                }
+	    		line = line.trim();
-
+	            if ("".equals(line))
-                list.add(line);
+	            {
-            }
+	                continue;
-        } finally {
+	            }
-            try {
+	            
-                in.close();
+	            int n = 0;
-            } catch (IOException e) {
+	            try
-                //skip
+	            {
-            }
+	            	n = Integer.parseInt(line);
-        }
+		    		list.add(n);	    		
-
+	            }
-        return list;
+	            catch(NumberFormatException e)
+	            {
+	            	ItemUpdate.pr("Error reading delete contents line:" + e.toString());
+	            }            	
+	    	}
+    	}
+    	finally
+    	{
+    		try
+    		{
+    			in.close();
+    		}
+    		catch(IOException e)
+    		{
+    			//skip
+    		}
+    	}
+    	
+    	return list;
     }
 
     /**
-     * Get display of Metadatum
+     *    Get display of Metadatum    
-     *
+	 *
-     * @param dcv MetadataValue
+     * @param dcv
      * @return string displaying elements of the Metadatum
      */
-    public static String getDCValueString(MetadataValue dcv) {
+    public static String getDCValueString(Metadatum 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)
+	 * 
-     *
+	 * @return a String representation of the two- or three-part form of a metadata element
-     * @param schema    schema
+	 *         e.g. dc.identifier.uri
-     * @param element   element
+	 */
-     * @param qualifier qualifier
+	public static  String getCompoundForm(String schema, String element, String qualifier)
-     * @return a String representation of the two- or three-part form of a metadata element
+	{
-     * e.g. dc.identifier.uri
+		StringBuilder sb = new StringBuilder();
-     */
+		sb.append(schema).append(".").append(element);
-    public static String getCompoundForm(String schema, String element, String qualifier) {
+		
-        StringBuilder sb = new StringBuilder();
+		if (qualifier != null)
-        sb.append(schema).append(".").append(element);
+		{
-
+			sb.append(".").append(qualifier);
-        if (qualifier != null) {
+		}
-            sb.append(".").append(qualifier);
+		return sb.toString();
-        }
+	}
-        return sb.toString();
+	
-    }
+	/**
-
+	 *    Parses metadata field given in the form <schema>.<element>[.<qualifier>|.*]
-    /**
+	 *    checks for correct number of elements (2 or 3) and for empty strings
-     * Parses metadata field given in the form {@code <schema>.<element>[.<qualifier>|.*]}
+	 *    
-     * checks for correct number of elements (2 or 3) and for empty strings
+	 *    @return String Array
-     *
+	 *    @throws ParseException if validity checks fail
-     * @param compoundForm compound form of metadata field
+	 *    
-     * @return String Array
+	 */
-     * @throws ParseException if validity checks fail
+	public static String[] parseCompoundForm(String compoundForm)
-     */
+	throws ParseException
-    public static String[] parseCompoundForm(String compoundForm)
+	{
-        throws ParseException {
+		String[] ar = compoundForm.split("\\s*\\.\\s*");  //trim ends
-        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);
+			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);
+		{
-        }
+			throw new ParseException("element is malformed or empty string: " + compoundForm, 0);
-
+		}
-        return ar;
+		
-    }
+		return ar;
-
+	}
-}
+	
+} 

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

@@ -8,42 +8,48 @@
 package org.dspace.app.itemupdate;
 
 import java.sql.SQLException;
-import java.util.List;
 
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 
-/**
+/** 
- * Filter all bitstreams in the ORIGINAL bundle
+ * 		Filter all bitstreams in the ORIGINAL bundle
- * Also delete all derivative bitstreams, i.e.
+ *      Also delete all derivative bitstreams, i.e.
- * all bitstreams in the TEXT and THUMBNAIL bundles
+ *      all bitstreams in the TEXT and THUMBNAIL bundles
  */
-public class OriginalBitstreamFilter extends BitstreamFilterByBundleName {
+public class OriginalBitstreamFilter extends BitstreamFilterByBundleName 
-    public OriginalBitstreamFilter() {
+{	
-        //empty
+	public OriginalBitstreamFilter()
-    }
+	{
-
+		//empty
-    /**
+	}
-     * Tests bitstreams for containment in an ORIGINAL bundle
+	
-     *
+	/**
-     * @param bitstream Bitstream
+	 *   Tests bitstreams for containment in an ORIGINAL bundle
-     * @return true if the bitstream is in the ORIGINAL bundle
+	 *  
-     * @throws BitstreamFilterException if filter error
+	 *  @return true if the bitstream is in the ORIGINAL bundle
-     */
+	 *  
-    @Override
+	 *  @throws BitstreamFilterException
-    public boolean accept(Bitstream bitstream)
+	 */
-        throws BitstreamFilterException {
+	public boolean accept(Bitstream bitstream) 
-        try {
+	throws BitstreamFilterException
-            List<Bundle> bundles = bitstream.getBundles();
+	{		
-            for (Bundle bundle : bundles) {
+		try
-                if (bundle.getName().equals("ORIGINAL")) {
+		{
-                    return true;
+			Bundle[] bundles = bitstream.getBundles();
-                }
+			for (Bundle b : bundles)
-            }
+			{
-        } catch (SQLException e) {
+				if (b.getName().equals("ORIGINAL"))
-            throw new BitstreamFilterException(e);
+				{
-        }
+					return true;
-        return false;
+				}
-    }
+			}		
+		}
+		catch(SQLException e)
+		{
+			throw new BitstreamFilterException(e);
+		}
+		return false;
+	}
 
 }

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

@@ -8,46 +8,52 @@
 package org.dspace.app.itemupdate;
 
 import java.sql.SQLException;
-import java.util.List;
-
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 
-/**
+/** 
- * Filter all bitstreams in the ORIGINAL bundle
+ * 		Filter all bitstreams in the ORIGINAL bundle
- * Also delete all derivative bitstreams, i.e.
+ *      Also delete all derivative bitstreams, i.e.
- * all bitstreams in the TEXT and THUMBNAIL bundles
+ *      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() {
+	
-        //empty
+	public OriginalWithDerivativesBitstreamFilter()
-    }
+	{
-
+		//empty
-    /**
+	}
-     * Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
+	
-     *
+	/**
-     * @param bitstream Bitstream
+	 * 	Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
-     * @return true if bitstream is in specified bundles
+	 * 
-     * @throws BitstreamFilterException if error
+	 * @param bitstream
-     */
+	 * @throws BitstreamFilterException
-    @Override
+	 * @return true if bitstream is in specified bundles
-    public boolean accept(Bitstream bitstream)
+	 */
-        throws BitstreamFilterException {
+	public boolean accept(Bitstream bitstream) 
-        try {
+	throws BitstreamFilterException
-            List<Bundle> bundles = bitstream.getBundles();
+	{		
-            for (Bundle b : bundles) {
+		try
-                for (String bn : bundlesToEmpty) {
+		{
-                    if (b.getName().equals(bn)) {
+			Bundle[] bundles = bitstream.getBundles();
-                        return true;
+			for (Bundle b : bundles)
-                    }
+			{
-                }
+				for (String bn : bundlesToEmpty)
-            }
+				{
-        } catch (SQLException e) {
+					if (b.getName().equals(bn))
-            throw new BitstreamFilterException(e);
+					{
-        }
+						return true;
-        return false;
+					}
-    }
+				}
+			}		
+		}
+		catch(SQLException e)
+		{
+			throw new BitstreamFilterException(e);
+		}
+		return false;
+	}
 
 }

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

@@ -10,13 +10,15 @@ package org.dspace.app.itemupdate;
 import java.util.Properties;
 
 /**
- * Bitstream filter targetting the THUMBNAIL bundle
+ *    Bitstream filter targetting the THUMBNAIL bundle
+ *
  */
 public class ThumbnailBitstreamFilter extends BitstreamFilterByBundleName {
-
+	
-    public ThumbnailBitstreamFilter() {
+	public ThumbnailBitstreamFilter()
-        props = new Properties();
+	{
-        props.setProperty("bundle", "THUMBNAIL");
+		props = new Properties();
-    }
+		props.setProperty("bundle", "THUMBNAIL");
+	}
 
 }

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

@@ -7,27 +7,24 @@
  */
 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
+ *    Interface for actions to update an item
+ *
  */
-public interface UpdateAction {
+public interface UpdateAction 
-    public ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+{
-
+	/**
-
+	 *   Action to update item
-    /**
+	 * 
-     * Action to update item
+	 * @param context
-     *
+	 * @param itarch
-     * @param context      DSpace context
+	 * @param isTest
-     * @param itarch       item archive
+	 * @param suppressUndo
-     * @param isTest       test flag
+	 * @throws Exception
-     * @param suppressUndo undo flag
+	 */
-     * @throws Exception if error
+	public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo) 
-     */
+	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

@@ -7,37 +7,33 @@
  */
 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
+ * 	  Base class for Bitstream actions
+ * 
+ *
  */
 public abstract class UpdateBitstreamsAction implements UpdateAction {
 
-    protected boolean alterProvenance = true;
+	protected boolean alterProvenance = true;
 
-
+	/**
-    protected BundleService bundleService = ContentServiceFactory.getInstance().getBundleService();
+	 *        Set variable to indicate that the dc.description.provenance field may 
-    protected BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
+	 *        be changed as a result of Bitstream changes by ItemUpdate
-
+	 * @param alterProvenance
-    /**
+	 */
-     * Set variable to indicate that the dc.description.provenance field may
+	public void setAlterProvenance(boolean alterProvenance)
-     * be changed as a result of Bitstream changes by ItemUpdate
+	{
-     *
+		this.alterProvenance = alterProvenance;
-     * @param alterProvenance whether to alter provenance
+	}
-     */
+	
-    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
-    /**
+	 */
-     * @return boolean value to indicate whether the dc.description.provenance field may
+	public boolean getAlterProvenance()
-     * be changed as a result of Bitstream changes by ItemUpdate
+	{
-     */
+		return alterProvenance;
-    public boolean getAlterProvenance() {
+	}
-        return alterProvenance;
-    }
 
 }

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

@@ -11,57 +11,60 @@ import java.util.HashSet;
 import java.util.Set;
 
 /**
- * This abstract subclass for metadata actions
+ *   This abstract subclass for metadata actions
- * maintains a collection for the target metadata fields
+ *   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.
+ *   on which to apply the action when the method execute is called.
+ * 
+ *   Implemented as a Set to avoid problems with duplicates
+ * 
  *
- * Implemented as a Set to avoid problems with duplicates
  */
 public abstract class UpdateMetadataAction implements UpdateAction {
 
-    protected Set<String> targetFields = new HashSet<String>();
+	protected Set<String> targetFields = new HashSet<String>();
-
+	
     /**
-     * Get target fields
+     *   Get target fields
-     *
+     *   
      * @return set of fields to update
      */
-    public Set<String> getTargetFields() {
+	public Set<String> getTargetFields() {
-        return targetFields;
+		return targetFields;
-    }
+	}
 
-    /**
+	/**
-     * Set target fields
+	 *   Set target fields
-     *
+	 *   
-     * @param targetFields Set of target fields to update
+	 * @param targetFields
-     */
+	 */
-    public void addTargetFields(Set<String> targetFields) {
+	public void addTargetFields(Set<String> targetFields) {
-        for (String tf : targetFields) {
+		for (String tf : targetFields)
-            this.targetFields.add(tf);
+		{
-        }
+			this.targetFields.add(tf);
+		}
+		
+	}
 
-    }
+	/**
+	 *    Add array of target fields to update
+	 * @param targetFields
+	 */
+	public void addTargetFields(String[] targetFields) {
+		for (String tf : targetFields)
+		{
+			this.targetFields.add(tf);
+		}
+		
+	}
 
-    /**
+	/**
-     * Add array of target fields to update
+	 *   Add single field to update
-     *
+	 * 
-     * @param targetFields array of target fields to update
+	 * @param targetField
-     */
+	 */
-    public void addTargetFields(String[] targetFields) {
+	public void addTargetField(String targetField) {
-        for (String tf : targetFields) {
+			this.targetFields.add(targetField);
-            this.targetFields.add(tf);
+	}
-        }
-
-    }
-
-    /**
-     * Add single field to update
-     *
-     * @param targetField target field to update
-     */
-    public void addTargetField(String targetField) {
-        this.targetFields.add(targetField);
-    }
 
 }

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

@@ -16,28 +16,21 @@ import java.io.StreamTokenizer;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.jdom.Document;
-
 /**
+ *
  * @author mwood
  */
-public class CommandRunner {
+public class CommandRunner
-
+{
-    /**
-     * Default constructor
-     */
-    private CommandRunner() { }
-
-    /**
-     * @param args the command line arguments given
-     * @throws IOException           if IO error
-     * @throws FileNotFoundException if file doesn't exist
-     */
     public static void main(String[] args)
-        throws FileNotFoundException, IOException {
+            throws FileNotFoundException, IOException
-        if (args.length > 0) {
+    {
+        if (args.length > 0)
+        {
             runManyCommands(args[0]);
-        } else {
+        }
+        else
+        {
             runManyCommands("-");
         }
         // There is no sensible way to use the status returned by runManyCommands().
@@ -52,17 +45,22 @@ public class CommandRunner {
     /**
      * Read a file of command lines and execute each in turn.
      *
+     * @param doc details of recognized commands.
      * @param script the file of command lines to be executed.
-     * @return status code
+     * @return
-     * @throws IOException           if IO error
+     * @throws FileNotFoundException
-     * @throws FileNotFoundException if file doesn't exist
+     * @throws IOException 
      */
     static int runManyCommands(String script)
-        throws FileNotFoundException, IOException {
+            throws FileNotFoundException, IOException
+    {
         Reader input;
-        if ("-".equals(script)) {
+        if ("-".equals(script))
+        {
             input = new InputStreamReader(System.in);
-        } else {
+        }
+        else
+        {
             input = new FileReader(script);
         }
 
@@ -84,17 +82,22 @@ public class CommandRunner {
 
         int status = 0;
         List<String> tokens = new ArrayList<String>();
-        Document commandConfigs = ScriptLauncher.getConfig();
+        while (StreamTokenizer.TT_EOF != tokenizer.nextToken())
-        while (StreamTokenizer.TT_EOF != tokenizer.nextToken()) {
+        {
-            if (StreamTokenizer.TT_EOL == tokenizer.ttype) {
+            if (StreamTokenizer.TT_EOL == tokenizer.ttype)
-                if (tokens.size() > 0) {
+            {
-                    status = ScriptLauncher.runOneCommand(commandConfigs, tokens.toArray(new String[tokens.size()]));
+                if (tokens.size() > 0)
-                    if (status > 0) {
+                {
+                    status = ScriptLauncher.runOneCommand(tokens.toArray(new String[tokens.size()]));
+                    if (status > 0)
+                    {
                         break;
                     }
                     tokens.clear();
                 }
-            } else {
+            }
+            else
+            {
                 tokens.add(tokenizer.sval);
             }
         }

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

@@ -12,7 +12,7 @@ import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.List;
 import java.util.TreeMap;
-
+import org.dspace.core.ConfigurationManager;
 import org.dspace.servicemanager.DSpaceKernelImpl;
 import org.dspace.servicemanager.DSpaceKernelInit;
 import org.dspace.services.RequestService;
@@ -26,61 +26,60 @@ 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;
 
-    /**
+    /** Definitions of all commands. */
-     * Default constructor
+    private static final Document commandConfigs = getConfig();
-     */
-    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 {
+            throws FileNotFoundException, IOException
+    {
+        // Check that there is at least one argument
+        if (args.length < 1)
+        {
+            System.err.println("You must provide at least one command argument");
+            display();
+            System.exit(1);
+        }
+
         // Initialise the service manager kernel
         try {
             kernelImpl = DSpaceKernelInit.getKernel(null);
-            if (!kernelImpl.isRunning()) {
+            if (!kernelImpl.isRunning())
-                kernelImpl.start();
+            {
+                kernelImpl.start(ConfigurationManager.getProperty("dspace.dir"));
             }
-        } catch (Exception e) {
+        } catch (Exception e)
+        {
             // Failed to start so destroy it and log and throw an exception
-            try {
+            try
+            {
                 kernelImpl.destroy();
-            } catch (Exception e1) {
+            }
+            catch (Exception e1)
+            {
                 // Nothing to do
             }
-            String message = "Failure during kernel init: " + e.getMessage();
+            String message = "Failure during filter init: " + e.getMessage();
-            System.err.println(message);
+            System.err.println(message + ":" + e);
-            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);
-            System.exit(1);
-        }
-
         // Look up command in the configuration, and execute.
         int status;
-        status = runOneCommand(commandConfigs, args);
+        status = runOneCommand(args);
 
         // Destroy the service kernel if it is still alive
-        if (kernelImpl != null) {
+        if (kernelImpl != null)
+        {
             kernelImpl.destroy();
             kernelImpl = null;
         }
@@ -88,57 +87,63 @@ public class ScriptLauncher {
         System.exit(status);
     }
 
-    protected static int runOneCommand(Document commandConfigs, String[] args) {
-        return runOneCommand(commandConfigs, args, kernelImpl);
-    }
-
     /**
      * Recognize and execute a single command.
-     *
+     * @param doc
-     * @param commandConfigs  Document
+     * @param args
-     * @param args the command line arguments given
      */
-    public static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
+    static int runOneCommand(String[] args)
+    {
         String request = args[0];
         Element root = commandConfigs.getRootElement();
         List<Element> commands = root.getChildren("command");
         Element command = null;
-        for (Element candidate : commands) {
+        for (Element candidate : commands)
-            if (request.equalsIgnoreCase(candidate.getChild("name").getValue())) {
+        {
+            if (request.equalsIgnoreCase(candidate.getChild("name").getValue()))
+            {
                 command = candidate;
                 break;
             }
         }
 
-        if (null == command) {
+        if (null == command)
+        {
             // The command wasn't found
             System.err.println("Command not found: " + args[0]);
-            display(commandConfigs);
+            display();
             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;
                 }
                 className = args[1];
-            } else {
+            }
+            else {
                 className = step.getChild("class").getValue();
             }
-            try {
+            try
+            {
                 target = Class.forName(className,
                                        true,
                                        Thread.currentThread().getContextClassLoader());
-            } catch (ClassNotFoundException e) {
+            }
+            catch (ClassNotFoundException e)
+            {
                 System.err.println("Error in launcher.xml: Invalid class name: " + className);
                 return 1;
             }
@@ -149,20 +154,26 @@ public class ScriptLauncher {
             Class[] argTypes = {useargs.getClass()};
             boolean passargs = true;
             if ((step.getAttribute("passuserargs") != null) &&
-                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue()))) {
+                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue())))
+            {
                 passargs = false;
             }
-            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs)) {
+            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs))
+            {
                 useargs = new String[0];
-            } else {
+            }
+            else
+            {
                 // The number of arguments to ignore
                 // If dsrun is the command, ignore the next, as it is the class name not an arg
                 int x = 1;
-                if ("dsrun".equals(request)) {
+                if ("dsrun".equals(request))
+                {
                     x = 2;
                 }
                 String[] argsnew = new String[useargs.length - x];
-                for (int i = x; i < useargs.length; i++) {
+                for (int i = x; i < useargs.length; i++)
+                {
                     argsnew[i - x] = useargs[i];
                 }
                 useargs = argsnew;
@@ -170,13 +181,16 @@ public class ScriptLauncher {
 
             // Add any extra properties
             List<Element> bits = step.getChildren("argument");
-            if (step.getChild("argument") != null) {
+            if (step.getChild("argument") != null)
+            {
                 String[] argsnew = new String[useargs.length + bits.size()];
                 int i = 0;
-                for (Element arg : bits) {
+                for (Element arg : bits)
+                {
                     argsnew[i++] = arg.getValue();
                 }
-                for (; i < bits.size() + useargs.length; i++) {
+                for (; i < bits.size() + useargs.length; i++)
+                {
                     argsnew[i] = useargs[i - bits.size()];
                 }
                 useargs = argsnew;
@@ -184,10 +198,11 @@ public class ScriptLauncher {
 
             // Establish the request service startup
             RequestService requestService = kernelImpl.getServiceManager().getServiceByName(
-                RequestService.class.getName(), RequestService.class);
+                    RequestService.class.getName(), RequestService.class);
-            if (requestService == null) {
+            if (requestService == null)
+            {
                 throw new IllegalStateException(
-                    "Could not get the DSpace RequestService to start the request transaction");
+                        "Could not get the DSpace RequestService to start the request transaction");
             }
 
             // Establish a request related to the current session
@@ -195,23 +210,26 @@ public class ScriptLauncher {
             requestService.startRequest();
 
             // Run the main() method
-            try {
+            try
+            {
                 Object[] arguments = {useargs};
 
                 // Useful for debugging, so left in the code...
                 /**System.out.print("About to execute: " + className);
-                 for (String param : useargs)
+                for (String param : useargs)
-                 {
+                {
-                 System.out.print(" " + param);
+                    System.out.print(" " + param);
-                 }
+                }
-                 System.out.println("");**/
+                System.out.println("");**/
 
                 Method main = target.getMethod("main", argTypes);
                 main.invoke(null, arguments);
 
                 // ensure we close out the request (happy request)
                 requestService.endRequest(null);
-            } catch (Exception e) {
+            }
+            catch (Exception e)
+            {
                 // Failure occurred in the request so we destroy it
                 requestService.endRequest(e);
 
@@ -232,23 +250,22 @@ 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") + "config" +
-            System.getProperty("file.separator") + "launcher.xml";
+                        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;
@@ -256,10 +273,9 @@ 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");
 
@@ -267,15 +283,17 @@ public class ScriptLauncher {
         // We cannot just use commands.sort() because it tries to remove and
         // reinsert Elements within other Elements, and that doesn't work.
         TreeMap<String, Element> sortedCommands = new TreeMap<>();
-        for (Element command : commands) {
+        for (Element command : commands)
+        {
             sortedCommands.put(command.getChild("name").getValue(), command);
         }
 
         // Display the sorted list
         System.out.println("Usage: dspace [command-name] {parameters}");
-        for (Element command : sortedCommands.values()) {
+        for (Element command : sortedCommands.values())
+        {
             System.out.println(" - " + command.getChild("name").getValue() +
-                                   ": " + command.getChild("description").getValue());
+                               ": " + 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.
@@ -20,117 +20,143 @@ 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 int brandWidth;
-    private Font font;
+	private int brandHeight;
-    private int xOffset;
+	private Font font;
+	private int xOffset;
 
-    /**
+	/**
-     * Constructor to set up footer image attributes.
+	 * Constructor to set up footer image attributes.
-     *
+	 *
-     * @param brandWidth  length of the footer in pixels
+	 * @param brandWidth length of the footer in pixels
-     * @param brandHeight height of the footer in pixels
+	 * @param brandHeight height of the footer in pixels
-     * @param font        font to use for text on the footer
+	 * @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
+	 * @param xOffset number of pixels text should be indented from left-hand side of footer
-     */
+	 *
-    public Brand(int brandWidth,
+	 */
-                 int brandHeight,
+	public Brand(int brandWidth,
-                 Font font,
+		      int brandHeight,
-                 int xOffset) {
+		      Font font,
-        this.brandWidth = brandWidth;
+		      int xOffset)
-        this.brandHeight = brandHeight;
+	{
-        this.font = font;
+		this.brandWidth = brandWidth;
-        this.xOffset = xOffset;
+		this.brandHeight = brandHeight;
-    }
+		this.font = font;
+		this.xOffset = xOffset;
+	}
 
-    /**
+	/**
-     * Create the brand image
+	 * Create the brand image
-     *
+	 *
-     * @param brandLeftText  text that should appear in the bottom left of the image
+	 * @param brandLeftText text that should appear in the bottom left of the image
-     * @param shortLeftText  abbreviated form of brandLeftText that will be substituted if
+	 * @param shortLeftText abbreviated form of brandLeftText that will be substituted if
-     *                       the image is resized such that brandLeftText will not fit. <code>null</code> if not
+	 *	the image is resized such that brandLeftText will not fit. <code>null</code> if not
-     *                       required
+	 *	required
-     * @param brandRightText text that should appear in the bottom right of the image
+	 * @param brandRightText text that should appear in the bottom right of the image
-     * @return BufferedImage a BufferedImage object describing the brand image file
+	 *
-     */
+	 * @return BufferedImage a BufferedImage object describing the brand image file
-    public BufferedImage create(String brandLeftText,
+	 */
-                                String shortLeftText,
+	public BufferedImage create(String brandLeftText,
-                                String brandRightText) {
+			   String shortLeftText,
-        BrandText[] allBrandText = null;
+			   String brandRightText)
+	{
+		BrandText[] allBrandText = null;
 
-        BufferedImage brandImage =
+		BufferedImage brandImage =
-            new BufferedImage(brandWidth, brandHeight, BufferedImage.TYPE_INT_RGB);
+			new BufferedImage(brandWidth, brandHeight, BufferedImage.TYPE_INT_RGB);
 
-        if (brandWidth >= 350) {
+		if (brandWidth >= 350)
-            allBrandText = new BrandText[] {
+		{
-                new BrandText(BrandText.BL, brandLeftText),
+			allBrandText = new BrandText[]
-                new BrandText(BrandText.BR, brandRightText)
+			{
-            };
+				new BrandText(BrandText.BL, brandLeftText),
-        } else if (brandWidth >= 190) {
+				new BrandText(BrandText.BR, brandRightText)
-            allBrandText = new BrandText[] {
+			};
-                new BrandText(BrandText.BL, shortLeftText),
+		} 
-                new BrandText(BrandText.BR, brandRightText)
+		else if (brandWidth >= 190)
-            };
+		{
-        } else {
+			allBrandText = new BrandText[]
-            allBrandText = new BrandText[] {
+			{
-                new BrandText(BrandText.BR, brandRightText)
+				new BrandText(BrandText.BL, shortLeftText),
-            };
+				new BrandText(BrandText.BR, brandRightText)
-        }
+			};
+		}
+		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) {
+		{
-                drawImage(brandImage, allBrandText[i]);
+      		for (int i = 0; i < allBrandText.length; ++i)
-            }
+			{
-        }
+        		drawImage(brandImage, allBrandText[i]);
+      		}
+    	}
 
-        return brandImage;
+		return brandImage;
-    }
+	}
 
 
-    /**
+	/**
-     * do the text placements and preparatory work for the brand image generation
+	 * do the text placements and preparatory work for the brand image generation
-     *
+	 *
-     * @param brandImage a BufferedImage object where the image is created
+	 * @param brandImage a BufferedImage object where the image is created
-     * @param identifier and Identifier object describing what text is to be placed in what
+	 * @param identifier and Identifier object describing what text is to be placed in what
-     *                   position within the brand
+	 *	position within the brand
-     */
+	 */
-    private void drawImage(BufferedImage brandImage,
+	private void drawImage(BufferedImage brandImage,
-                           BrandText brandText) {
+			BrandText brandText)
-        int imgWidth = brandImage.getWidth();
+	{
-        int imgHeight = brandImage.getHeight();
+		int imgWidth = brandImage.getWidth();
+		int imgHeight = brandImage.getHeight();
 
-        Graphics2D g2 = brandImage.createGraphics();
+		int bx, by, tx, ty, bWidth, bHeight;
-        g2.setFont(font);
-        FontMetrics fm = g2.getFontMetrics();
 
-        int bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
+		Graphics2D g2 = brandImage.createGraphics();
-        int bHeight = fm.getHeight();
+		g2.setFont(font);
+		FontMetrics fm = g2.getFontMetrics();
 
-        int bx = 0;
-        int by = 0;
 
-        if (brandText.getLocation().equals(BrandText.TL)) {
+		bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
-            bx = 0;
+		bHeight = fm.getHeight();
-            by = 0;
-        } else if (brandText.getLocation().equals(BrandText.TR)) {
-            bx = imgWidth - bWidth;
-            by = 0;
-        } else if (brandText.getLocation().equals(BrandText.BL)) {
-            bx = 0;
-            by = imgHeight - bHeight;
-        } else if (brandText.getLocation().equals(BrandText.BR)) {
-            bx = imgWidth - bWidth;
-            by = imgHeight - bHeight;
-        }
 
-        Rectangle box = new Rectangle(bx, by, bWidth, bHeight);
+		bx = 0;
-        int tx = bx + xOffset;
+        by = 0;
-        int ty = by + fm.getAscent();
 
-        g2.setColor(Color.black);
+		if (brandText.getLocation().equals(BrandText.TL))
-        g2.fill(box);
+		{
-        g2.setColor(Color.white);
+			bx = 0;
-        g2.drawString(brandText.getText(), tx, ty);
+			by = 0;
-    }
+		}
+		else if (brandText.getLocation().equals(BrandText.TR))
+		{
+			bx = imgWidth - bWidth;
+			by = 0;
+		}
+		else if (brandText.getLocation().equals(BrandText.BL))
+		{
+			bx = 0;
+			by = imgHeight - bHeight;
+		}
+		else if (brandText.getLocation().equals(BrandText.BR))
+		{
+			bx = imgWidth - bWidth;
+			by = imgHeight - bHeight;
+		}
+
+		Rectangle box = new Rectangle(bx, by, bWidth, bHeight);
+		tx = bx + xOffset;
+		ty = by + fm.getAscent();
+
+    	g2.setColor(Color.black);
+		g2.fill(box);
+		g2.setColor(Color.white);
+		g2.drawString(brandText.getText(), tx, ty);
+	}
 }

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

@@ -13,75 +13,73 @@ 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";
-    public static final String BL = "bl";
+	/** Bottom Right */
-    /**
+	public static final String BR = "br";
-     * Bottom Right
+	/** Top Left */
-     */
+	public static final String TL = "tl";
-    public static final String BR = "br";
+	/** Top Right */
-    /**
+	public static final String TR = "tr";
-     * Top Left
-     */
-    public static final String TL = "tl";
-    /**
-     * Top Right
-     */
-    public static final String TR = "tr";
 
-    private String location;
+	private String location;
-    private String text;
+	private String text;
 
-    /**
+	/**
-     * Constructor for an Identifier object containing a text string and
+	 * Constructor for an Identifier object containing a text string and
-     * its location within a rectangular area.
+	 * its location within a rectangular area.
-     *
+	 *
-     * @param location one of the class location constants e.g. <code>Identifier.BL</code>
+	 * @param location one of the class location constants e.g. <code>Identifier.BL</code>
-     * @param the      text associated with the location
+	 * @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;
+		this.location = location;
-    }
+		this.text = text;
+	}
 
-    /**
+	/**
-     * get the location the text of the Identifier object is associated with
+	 * get the location the text of the Identifier object is associated with
-     *
+	 *
-     * @return String one the class location constants e.g. <code>Identifier.BL</code>
+	 * @return String one the class location constants e.g. <code>Identifier.BL</code>
-     */
+	 */
-    public String getLocation() {
+	public String getLocation()
-        return location;
+	{
-    }
+		return location;
+	}
 
 
-    /**
+	/**
-     * get the text associated with the Identifier object
+	 * get the text associated with the Identifier object
-     *
+	 *
-     * @return String the text associated with the Identifier object
+	 * @return String the text associated with the Identifier object
-     */
+	 */
-    public String getText() {
+	public String getText()
-        return text;
+	{
-    }
+		return text;
+	}
 
 
-    /**
+	/**
-     * set the location associated with the Identifier object
+	 * set the location associated with the Identifier object
-     *
+	 *
-     * @param location one of the class location constants
+	 * @param location one of the class location constants
-     */
+	 */
-    public void setLocation(String location) {
+	public void setLocation(String location)
-        this.location = location;
+	{
-    }
+		this.location = location;
+	}
 
 
-    /**
+	/**
-     * set the text associated with the Identifier object
+	 * set the text associated with the Identifier object
-     *
+	 *
-     * @param text any text string (typically a branding or identifier)
+	 * @param text any text string (typically a branding or identifier)
-     */
+	 */
-    public void setText(String text) {
+	public void setText(String text)
-        this.text = text;
+	{
-    }
+		this.text = text;
+	}
 }

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

@@ -7,11 +7,18 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.image.BufferedImage;
+import java.awt.Graphics2D;
+import java.awt.Color;
+import java.awt.image.*;
+import java.awt.RenderingHints;
+import java.awt.Transparency;
+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;
 
 /**
@@ -19,68 +26,271 @@ import org.dspace.core.ConfigurationManager;
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  *
- * @author Jason Sherman jsherman@usao.edu
+ * @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);
 
         // get config params
         float xmax = (float) ConfigurationManager
-            .getIntProperty("webui.preview.maxwidth");
+                .getIntProperty("webui.preview.maxwidth");
         float ymax = (float) ConfigurationManager
-            .getIntProperty("webui.preview.maxheight");
+                .getIntProperty("webui.preview.maxheight");
         boolean blurring = (boolean) ConfigurationManager
-            .getBooleanProperty("webui.preview.blurring");
+                .getBooleanProperty("webui.preview.blurring");
         boolean hqscaling = (boolean) ConfigurationManager
-            .getBooleanProperty("webui.preview.hqscaling");
+                .getBooleanProperty("webui.preview.hqscaling");
         int brandHeight = ConfigurationManager.getIntProperty("webui.preview.brand.height");
         String brandFont = ConfigurationManager.getProperty("webui.preview.brand.font");
         int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");
+        
+        // now get the image dimensions
+        float xsize = (float) buf.getWidth(null);
+        float ysize = (float) buf.getHeight(null);
 
-        JPEGFilter jpegFilter = new JPEGFilter();
+        // if verbose flag is set, print out dimensions
-        return jpegFilter
+        // to STDOUT
-            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
+        if (MediaFilterManager.isVerbose)
-                         brandFont);
+        {
+            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);
+
+        // 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 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!
+	}
+
+    public BufferedImage getNormalizedInstance(BufferedImage buf)
+    {
+     int type = (buf.getTransparency() == Transparency.OPAQUE) ?
+            BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB_PRE;
+     int w, h;
+     w = buf.getWidth();
+     h = buf.getHeight();
+     BufferedImage normal = new BufferedImage(w, h, type);
+     Graphics2D g2d = normal.createGraphics();
+     g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
+     g2d.dispose();
+     return normal;
+    }
+
+    public BufferedImage getBlurredInstance(BufferedImage buf)
+    {
+    /**
+     * Convenience method that returns a blurred instance of the
+     * provided {@code BufferedImage}.
+     *
+     */
+
+     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, 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/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

@@ -14,70 +14,72 @@ import org.dspace.content.Item;
 import org.dspace.core.Context;
 
 /**
- * Public interface for any class which transforms or converts content/bitstreams
+ * Public interface for any class which transforms or converts content/bitstreams 
  * 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
+     *         becomes document.pdf.txt
      */
     public String getFilteredName(String sourceName);
 
     /**
      * @return name of the bundle this filter will stick its generated
-     * Bitstreams
+     *         Bitstreams
      */
     public String getBundleName();
 
     /**
      * @return name of the bitstream format (say "HTML" or "Microsoft Word")
-     * returned by this filter look in the bitstream format registry or
+     *         returned by this filter look in the bitstream format registry or
-     * mediafilter.cfg for valid format strings.
+     *         mediafilter.cfg for valid format strings.
      */
     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
+     *         produced is a good idea
      */
     public String getDescription();
 
     /**
-     * Read the source stream and produce the filtered content.
+     * @param source
-     *
+     *            input stream
-     * @param item    Item
+     * 
-     * @param source  input stream
+     * @return result of filter's transformation, written out to a bitstream
-     * @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;
+            throws Exception;
 
     /**
-     * Perform any pre-processing of the source bitstream *before* the actual
+     * Perform any pre-processing of the source bitstream *before* the actual 
      * filtering takes place in MediaFilterManager.processBitstream().
      * <p>
      * Return true if pre-processing is successful (or no pre-processing
      * 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
-     * @return true if bitstream processing should continue,
+     *            item containing bitstream to process
-     * false if this bitstream should be skipped
+     * @param source
-     * @throws Exception if error
+     *            source bitstream to be processed
+     * 
+     * @return true if bitstream processing should continue, 
+     * 			false if this bitstream should be skipped
      */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-        throws Exception;
+            throws Exception;
-
+        
     /**
      * Perform any post-processing of the generated bitstream *after* this
      * filter has already been run.
@@ -85,14 +87,17 @@ public interface FormatFilter {
      * Return true if pre-processing is successful (or no pre-processing
      * 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
-     *                           this filter.
+     * @param item
-     * @throws Exception if error
+     *            item containing bitstream to process
+     * @param generatedBitstream
+     *            the bitstream which was generated by
+     *            this filter.
      */
     public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-        throws Exception;
+            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

@@ -12,41 +12,43 @@ import java.io.File;
 import java.io.InputStream;
 import java.nio.file.Files;
 
-import org.dspace.content.Item;
-
 
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  */
-public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter {
+public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter 
+{
 
     /**
-     * @param currentItem item
+     * @param source
-     * @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 {
+    {
-        File f = inputStreamToTempFile(source, "imthumb", ".tmp");
+		File f = inputStreamToTempFile(source, "imthumb", ".tmp");
-        File f2 = null;
+    	File f2 = null;
-        try {
+	    try
-            f2 = getThumbnailFile(f, verbose);
+	    {
-            byte[] bytes = Files.readAllBytes(f2.toPath());
+		    f2 = getThumbnailFile(f);
-            return new ByteArrayInputStream(bytes);
+		    byte[] bytes = Files.readAllBytes(f2.toPath());
-        } finally {
+		    return new ByteArrayInputStream(bytes);
-            //noinspection ResultOfMethodCallIgnored
+	    }
-            f.delete();
+	    finally
-            if (f2 != null) {
+	    {
-                //noinspection ResultOfMethodCallIgnored
+		    //noinspection ResultOfMethodCallIgnored
-                f2.delete();
+		    f.delete();
-            }
+		    if (f2 != null)
-        }
+		    {
-    }
+			    //noinspection ResultOfMethodCallIgnored
+			    f2.delete();
+		    }
+	    }
+	}
 
 
 }

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

@@ -12,32 +12,41 @@ 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(InputStream source)
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception
-        throws Exception {
+    {
-        File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
+		File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
-        File f2 = null;
+		File f2 = null;
-        File f3 = null;
+	    File f3 = null;
-        try {
+	    try
-            f2 = getImageFile(f, 0, verbose);
+	    {
-            f3 = getThumbnailFile(f2, verbose);
+		    f2 = getImageFile(f, 0);
-            byte[] bytes = Files.readAllBytes(f3.toPath());
+		    f3 = getThumbnailFile(f2);
-            return new ByteArrayInputStream(bytes);
+		    byte[] bytes = Files.readAllBytes(f3.toPath());
-        } finally {
+		    return new ByteArrayInputStream(bytes);
-            //noinspection ResultOfMethodCallIgnored
+	    }
-            f.delete();
+		finally
-            if (f2 != null) {
+	    {
-                //noinspection ResultOfMethodCallIgnored
+		    //noinspection ResultOfMethodCallIgnored
-                f2.delete();
+		    f.delete();
-            }
+		    if (f2 != null)
-            if (f3 != null) {
+		    {
-                //noinspection ResultOfMethodCallIgnored
+			    //noinspection ResultOfMethodCallIgnored
-                f3.delete();
+			    f2.delete();
-            }
+		    }
-        }
+		    if (f3 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f3.delete();
+		    }
+	    }
     }
 
+   public static final String[] PDF = {"Adobe PDF"};
+   public String[] getInputMIMETypes()
+  {
+      return PDF;
+  }
+
 }

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

@@ -14,189 +14,187 @@ import java.io.InputStream;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
+import javax.imageio.ImageIO;
+
+import org.dspace.app.mediafilter.MediaFilter;
+import org.dspace.app.mediafilter.SelfRegisterInputFormats;
 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;
 
+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.
  */
-public abstract class ImageMagickThumbnailFilter extends MediaFilter {
+public abstract class ImageMagickThumbnailFilter extends MediaFilter implements SelfRegisterInputFormats
-    protected static int width = 180;
+{
-    protected static int height = 120;
+	private static int width = 180;
-    private static boolean flatten = true;
+	private static int height = 120;
-    static String bitstreamDescription = "IM Thumbnail";
+        private static boolean flatten = true;
-    static final String defaultPattern = "Generated Thumbnail";
+	static String bitstreamDescription = "IM Thumbnail";
-    static Pattern replaceRegex = Pattern.compile(defaultPattern);
+	static final String defaultPattern = "Generated Thumbnail";
-    protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+	static Pattern replaceRegex = Pattern.compile(defaultPattern);
-
+	
-    static String cmyk_profile;
+	static {
-    static String srgb_profile;
+		String pre = ImageMagickThumbnailFilter.class.getName();
-
+		String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
-    static {
+		ProcessStarter.setGlobalSearchPath(s);
-        String pre = ImageMagickThumbnailFilter.class.getName();
+		width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
-        String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
+		height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
-        ProcessStarter.setGlobalSearchPath(s);
+                flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
-        width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
+		String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
-        height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
+		if (description != null) {
-        flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
+			bitstreamDescription = description;
-        String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
+		}
-        cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
+		try {
-        srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
+			String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
-        if (description != null) {
+		    replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
-            bitstreamDescription = description;
+		} catch(PatternSyntaxException e) {
-        }
+			System.err.println("Invalid thumbnail replacement pattern: "+e.getMessage());
-        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() {
-        }
+	}
-    }
+	
-
+	
-    public ImageMagickThumbnailFilter() {
+    public String getFilteredName(String oldFilename)
-    }
+    {
-
-    @Override
-    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 bitstreamDescription
      */
-    @Override
+    public String getDescription()
-    public String getDescription() {
+    {
         return bitstreamDescription;
     }
 
-    public File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
+    public static File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
-        File f = File.createTempFile(prefix, suffix);
+		File f = File.createTempFile(prefix, suffix);
-        f.deleteOnExit();
+		f.deleteOnExit();
-        FileOutputStream fos = new FileOutputStream(f);
+    	FileOutputStream fos = new FileOutputStream(f);
-
+    	
-        byte[] buffer = new byte[1024];
+    	byte[] buffer = new byte[1024];
-        int len = source.read(buffer);
+    	int len = source.read(buffer);
-        while (len != -1) {
+    	while (len != -1) {
-            fos.write(buffer, 0, len);
+    		fos.write(buffer, 0, len);
-            len = source.read(buffer);
+    		len = source.read(buffer);
-        }
+    	}
-        fos.close();
+    	fos.close();
-        return f;
+		return f;
     }
-
+    
-    public File getThumbnailFile(File f, boolean verbose)
+    public static File getThumbnailFile(File f) throws IOException, InterruptedException, IM4JavaException {
-        throws IOException, InterruptedException, IM4JavaException {
+    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+    	f2.deleteOnExit();
-        f2.deleteOnExit();
+    	ConvertCmd cmd = new ConvertCmd();
-        ConvertCmd cmd = new ConvertCmd();
+		IMOperation op = new IMOperation();
-        IMOperation op = new IMOperation();
+		op.addImage(f.getAbsolutePath());
-        op.autoOrient();
+		op.thumbnail(width, height);
-        op.addImage(f.getAbsolutePath());
+		op.addImage(f2.getAbsolutePath());
-        op.thumbnail(width, height);
+        if (MediaFilterManager.isVerbose) {
-        op.addImage(f2.getAbsolutePath());
+		    System.out.println("IM Thumbnail Param: "+op);
-        if (verbose) {
-            System.out.println("IM Thumbnail Param: " + op);
         }
-        cmd.run(op);
+		cmd.run(op);
-        return f2;
+		return f2;
     }
-
+    
-    public File getImageFile(File f, int page, boolean verbose)
+    public static File getImageFile(File f, int page) throws IOException, InterruptedException, IM4JavaException {
-        throws IOException, InterruptedException, IM4JavaException {
+    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+    	f2.deleteOnExit();
-        f2.deleteOnExit();
+    	ConvertCmd cmd = new ConvertCmd();
-        ConvertCmd cmd = new ConvertCmd();
+		IMOperation op = new IMOperation();
-        IMOperation op = new IMOperation();
+		String s = "[" + page + "]";
-        String s = "[" + page + "]";
+		op.addImage(f.getAbsolutePath()+s);
-        op.addImage(f.getAbsolutePath() + s);
+                if (flatten)
-        if (flatten) {
+                {
-            op.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();
+		op.addImage(f2.getAbsolutePath());
-                // If anything other than a generated thumbnail
+        if (MediaFilterManager.isVerbose) {
-                // is found, halt processing
+		    System.out.println("IM Image Param: "+op);
-                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;
-            }
         }
-
+		cmd.run(op);
-        return true; // assume that the thumbnail is a custom one
+		return f2;
+    }
+    
+    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
+            throws Exception
+    {
+    	String nsrc = source.getName();
+    	for(Bundle b: item.getBundles("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 (MediaFilterManager.isVerbose) {
+        	    		    System.out.println(description + " " + nsrc + " matches pattern and is replacable.");
+        	            }
+        	    		continue;
+        	    	}
+        	    	if (description.equals(bitstreamDescription)) {
+        	            if (MediaFilterManager.isVerbose) {
+        	    		    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
     }
 
+     public String[] getInputMIMETypes()
+    {
+        return ImageIO.getReaderMIMETypes();
+    }
+
+    public String[] getInputDescriptions()
+    {
+        return null;
+    }
+
+    public String[] getInputExtensions()
+    {
+        return ImageIO.getReaderFileSuffixes();
+    }
 }

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

@@ -7,21 +7,17 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.Color;
-import java.awt.Font;
 import java.awt.Graphics2D;
+import java.awt.Color;
+import java.awt.image.*;
 import java.awt.RenderingHints;
 import java.awt.Transparency;
-import java.awt.image.BufferedImage;
-import java.awt.image.BufferedImageOp;
-import java.awt.image.ConvolveOp;
-import java.awt.image.Kernel;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.InputStream;
+
 import javax.imageio.ImageIO;
 
-import org.dspace.content.Item;
 import org.dspace.core.ConfigurationManager;
 
 /**
@@ -29,91 +25,83 @@ import org.dspace.core.ConfigurationManager;
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  *
- * @author Jason Sherman jsherman@usao.edu
+ * @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");
+                .getIntProperty("thumbnail.maxwidth");
         float ymax = (float) ConfigurationManager
-            .getIntProperty("thumbnail.maxheight");
+                .getIntProperty("thumbnail.maxheight");
         boolean blurring = (boolean) ConfigurationManager
-            .getBooleanProperty("thumbnail.blurring");
+                .getBooleanProperty("thumbnail.blurring");
         boolean hqscaling = (boolean) ConfigurationManager
-            .getBooleanProperty("thumbnail.hqscaling");
+                .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 +112,15 @@ 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
@@ -140,43 +130,37 @@ 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 + ", "
+        {
-                                   + ysize);
+            System.out.println("created thumbnail size: " + xsize + ", "
+                    + ysize);
         }
 
         // create an image buffer for the thumbnail with the new xsize, ysize
         BufferedImage thumbnail = new BufferedImage((int) xsize, (int) ysize,
-                                                    BufferedImage.TYPE_INT_RGB);
+                BufferedImage.TYPE_INT_RGB);
 
         // Use blurring if selected in config.
         // a little blur before scaling does wonders for keeping moire in check.
-        if (blurring) {
+        if (blurring)
-            // send the buffered image off to get blurred.
+        {
-            buf = getBlurredInstance((BufferedImage) buf);
+                // send the buffered image off to get blurred.
+                buf = getBlurredInstance((BufferedImage) buf);
         }
 
         // Use high quality scaling method if selected in config.
         // this has a definite performance penalty.
-        if (hqscaling) {
+        if (hqscaling)
-            // send the buffered image off to get an HQ downscale.
+        {
-            buf = getScaledInstance((BufferedImage) buf, (int) xsize, (int) ysize,
+                // send the buffered image off to get an HQ downscale.
-                                    (Object) RenderingHints.VALUE_INTERPOLATION_BICUBIC, (boolean) true);
+                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();
 
@@ -189,90 +173,92 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
     }
 
 
-    @Override
+    public String[] getInputMIMETypes()
-    public String[] getInputMIMETypes() {
+    {
         return ImageIO.getReaderMIMETypes();
     }
 
-    @Override
+    public String[] getInputDescriptions()
-    public String[] getInputDescriptions() {
+    {
         return null;
     }
 
-    @Override
+    public String[] getInputExtensions()
-    public String[] getInputExtensions() {
+    {
         // Temporarily disabled as JDK 1.6 only
         // return ImageIO.getReaderFileSuffixes();
         return null;
     }
 
-    public BufferedImage getNormalizedInstance(BufferedImage buf) {
+    public BufferedImage getNormalizedInstance(BufferedImage buf)
-        int type = (buf.getTransparency() == Transparency.OPAQUE) ?
+    {
+     int type = (buf.getTransparency() == Transparency.OPAQUE) ?
             BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB_PRE;
-        int w = buf.getWidth();
+     int w, h;
-        int h = buf.getHeight();
+     w = buf.getWidth();
-        BufferedImage normal = new BufferedImage(w, h, type);
+     h = buf.getHeight();
-        Graphics2D g2d = normal.createGraphics();
+     BufferedImage normal = new BufferedImage(w, h, type);
-        g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
+     Graphics2D g2d = normal.createGraphics();
-        g2d.dispose();
+     g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
-        return normal;
+     g2d.dispose();
+     return normal;
     }
 
+    public BufferedImage getBlurredInstance(BufferedImage buf)
+    {
     /**
      * 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
+     buf = getNormalizedInstance(buf);
-        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.
+     // kernel for blur op
-        BufferedImageOp blur = new ConvolveOp(new Kernel(3, 3, matrix));
+     float[] matrix = {
-        BufferedImage blurbuf = blur.filter(buf, null);
+        0.111f, 0.111f, 0.111f,
-        return blurbuf;
+        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 buf the original image to be scaled
-     * @param targetWidth   the desired width of the scaled instance,
+     * @param targetWidth the desired width of the scaled instance,
-     *                      in pixels
+     *    in pixels
-     * @param targetHeight  the desired height of the scaled instance,
+     * @param targetHeight the desired height of the scaled instance,
-     *                      in pixels
+     *    in pixels
-     * @param hint          one of the rendering hints that corresponds to
+     * @param hint one of the rendering hints that corresponds to
-     *                      {@code RenderingHints.KEY_INTERPOLATION} (e.g.
+     *    {@code RenderingHints.KEY_INTERPOLATION} (e.g.
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR},
+     *    {@code RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR},
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_BILINEAR},
+     *    {@code RenderingHints.VALUE_INTERPOLATION_BILINEAR},
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_BICUBIC})
+     *    {@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
+     *    scaling technique that provides higher quality than the usual
-     *                      one-step technique (only useful in downscaling cases, where
+     *    one-step technique (only useful in downscaling cases, where
-     *                      {@code targetWidth} or {@code targetHeight} is
+     *    {@code targetWidth} or {@code targetHeight} is
-     *                      smaller than the original dimensions, and generally only when
+     *    smaller than the original dimensions, and generally only when
-     *                      the {@code BILINEAR} hint is specified)
+     *    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) {
+                                           boolean higherQuality)
+    {
         int type = (buf.getTransparency() == Transparency.OPAQUE) ?
             BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB;
-        BufferedImage scalebuf = (BufferedImage) buf;
+        BufferedImage scalebuf = (BufferedImage)buf;
-        int w;
+        int w, h;
-        int h;
         if (higherQuality) {
             // Use multi-step technique: start with original size, then
             // scale down in multiple passes with drawImage()

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

@@ -13,34 +13,38 @@ import org.dspace.core.Context;
 
 
 /**
- * Abstract class which defines the default settings for a *simple* Media or Format Filter.
+ * Abstract class which defines the default settings for a *simple* Media or Format Filter. 
- * This class may be extended by any class which wishes to define a simple filter to be run
+ * This class may be extended by any class which wishes to define a simple filter to be run 
  * 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
+	/**
+     * Perform any pre-processing of the source bitstream *before* the actual 
      * filtering takes place in MediaFilterManager.processBitstream().
      * <p>
      * Return true if pre-processing is successful (or no pre-processing
      * 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
-     * @return true if bitstream processing should continue,
+     *            item containing bitstream to process
-     * false if this bitstream should be skipped
+     * @param source
-     * @throws Exception if error
+     *            source bitstream to be processed
+     * 
+     * @return true if bitstream processing should continue, 
+     *          false if this bitstream should be skipped
      */
-    @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
     }
-
+     
     /**
      * Perform any post-processing of the generated bitstream *after* this
      * filter has already been run.
@@ -48,16 +52,19 @@ public abstract class MediaFilter implements FormatFilter {
      * Return true if pre-processing is successful (or no pre-processing
      * 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
-     *                           this filter.
+     * @param item
-     * @throws Exception if error
+     *            item containing bitstream to process
+     * @param generatedBitstream
+     *            the bitstream which was generated by
+     *            this filter.
      */
-    @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 +1,850 @@
+/**
+ * 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.apache.log4j.Logger;
+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.eperson.Group;
+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
+{
+    private static final Logger log = Logger.getLogger(MediaFilterManager.class);
+
+	//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 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 final Map<String, List<String>> filterFormats = new HashMap<>();
+
+    private static List<String> skipList = null; //list of identifiers to skip during processing
+
+    private static final List<String> publicFiltersClasses = new ArrayList<>();
+
+    //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";
+
+    static {
+        String publicPermissionFilters = ConfigurationManager.getProperty("filter.org.dspace.app.mediafilter.publicPermission");
+        if(publicPermissionFilters != null) {
+            String[] publicPermisionFiltersArray = publicPermissionFilters.split(",");
+            for(String filter : publicPermisionFiltersArray) {
+                publicFiltersClasses.add(filter.trim());
+            }
+        }
+    }
+    
+    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);    
+        
+        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!
+            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;
+            	}
+            }
+
+            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;
+        }
+        
+        if(isVerbose) {
+            System.out.println("PROCESSING: bitstream " + source.getID()
+                + " (item: " + item.getHandle() + ")");
+        }
+
+        InputStream destStream;
+        try {
+            System.out.println("File: " + newName);
+            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;
+            }
+        }
+        catch (OutOfMemoryError oome)
+        {
+            System.out.println("!!! OutOfMemoryError !!!");
+            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();
+        
+        //Set permissions on the derivative bitstream
+        //- First remove any existing policies
+        AuthorizeManager.removeAllPolicies(c, b);
+
+        //- Determine if this is a public-derivative format
+        if(publicFiltersClasses.contains(formatFilter.getClass().getSimpleName())) {
+            //- Set derivative bitstream to be publicly accessible
+            Group anonymous = Group.find(c, 0);
+            AuthorizeManager.addPolicy(c, b, Constants.READ, anonymous);
+        } else {
+            //- Inherit policies from the source bitstream
+            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) {
+                }
-                    log.error("Error closing PDF file: " + e.getMessage(), e);
+                catch(Exception e)
+                {
+                   log.error("Error closing PDF file: " + e.getMessage(), e);
                 }
 
-                try {
+                try
+                {
                     writer.close();
-                } catch (Exception e) {
+                }
-                    log.error("Error closing temporary extract file: " + e.getMessage(), 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

@@ -10,90 +10,99 @@ 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";
     }
 
     /**
      * @return String bitstream format
-     *
+     * 
-     * TODO: Check that this is correct
+     *         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();
             POITextExtractor pptExtractor = ExtractorFactory
-                .createExtractor(source);
+                    .createExtractor(source);
 
             // PowerPoint XML files and legacy format PowerPoint files
             // 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);
+                        .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();
+                        + " " + ((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

@@ -8,73 +8,76 @@
 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;
 
 /*
- *
+ * 
  * to do: helpful error messages - can't find mediafilter.cfg - can't
  * 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);
             }
 
@@ -83,10 +86,12 @@ 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);
+                    + ioe.getMessage(), ioe);
             throw ioe;
         }
     }

dspace-api/src/main/java/org/dspace/app/mediafilter/XPDF2Text.java

@@ -0,0 +1,160 @@
+/**
+ * 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.BufferedInputStream;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.Arrays;
+
+import org.apache.log4j.Logger;
+import org.dspace.core.ConfigurationManager;
+import org.dspace.core.Utils;
+
+/**
+ * Text MediaFilter for PDF sources
+ *
+ * This filter produces extracted text suitable for building an index,
+ * but not for display to end users.
+ * It forks a process running the "pdftotext" program from the
+ * XPdf suite -- see http://www.foolabs.com/xpdf/
+ * This is a suite of open-source PDF tools that has been widely ported
+ * to Unix platforms and the ones we use (pdftoppm, pdftotext) even
+ * run on Win32.
+ *
+ * This was written for the FACADE project but it is not directly connected
+ * to any of the other FACADE-specific software.  The FACADE UI expects
+ * to find thumbnail images for 3D PDFs generated by this filter.
+ *
+ * Requires DSpace config properties keys:
+ *
+ *  xpdf.path.pdftotext -- path to "pdftotext" executable (required!)
+ *
+ * @author Larry Stone
+ * @see org.dspace.app.mediafilter.MediaFilter
+ */
+public class XPDF2Text extends MediaFilter
+{
+    private static Logger log = Logger.getLogger(XPDF2Text.class);
+
+    // Command to get text from pdf; @infile@, @COMMAND@ are placeholders
+    private static final String XPDF_PDFTOTEXT_COMMAND[] =
+    {
+        "@COMMAND@", "-q", "-enc", "UTF-8", "@infile@", "-"
+    };
+
+
+    // executable path that comes from DSpace config at runtime.
+    private String pdftotextPath = null;
+
+    public String getFilteredName(String oldFilename)
+    {
+        return oldFilename + ".txt";
+    }
+
+    public String getBundleName()
+    {
+        return "TEXT";
+    }
+
+    public String getFormatString()
+    {
+        return "Text";
+    }
+
+    public String getDescription()
+    {
+        return "Extracted Text";
+    }
+
+    public InputStream getDestinationStream(InputStream sourceStream)
+            throws Exception
+    {
+        // get configured value for path to XPDF command:
+        if (pdftotextPath == null)
+        {
+            pdftotextPath = ConfigurationManager.getProperty("xpdf.path.pdftotext");
+            if (pdftotextPath == null)
+            {
+                throw new IllegalStateException("No value for key \"xpdf.path.pdftotext\" in DSpace configuration!  Should be path to XPDF pdftotext executable.");
+            }
+        }
+
+        File sourceTmp = File.createTempFile("DSfilt",".pdf");
+        sourceTmp.deleteOnExit();  // extra insurance, we'll delete it here.
+        int status = -1;
+        try
+        {
+            // make local temp copy of source PDF since PDF tools
+            // require a file for random access.
+            // XXX fixme could optimize if we ever get an interface to grab asset *files*
+            OutputStream sto = new FileOutputStream(sourceTmp);
+            Utils.copy(sourceStream, sto);
+            sto.close();
+            sourceStream.close();
+
+            String pdfCmd[] = XPDF_PDFTOTEXT_COMMAND.clone();
+            pdfCmd[0] = pdftotextPath;
+            pdfCmd[4] = sourceTmp.toString();
+
+            log.debug("Running command: "+Arrays.deepToString(pdfCmd));
+            Process pdfProc = Runtime.getRuntime().exec(pdfCmd);
+            InputStream stdout = pdfProc.getInputStream();
+            ByteArrayOutputStream baos = new ByteArrayOutputStream();
+            Utils.copy(new BufferedInputStream(stdout), baos);
+            stdout.close();
+            baos.close();
+
+            status = pdfProc.waitFor();
+            String msg = null;
+            if (status == 1)
+            {
+                msg = "pdftotext failed opening input: file=" + sourceTmp.toString();
+            }
+            else if (status == 3)
+            {
+                msg = "pdftotext permission failure (perhaps copying of text from this document is not allowed - check PDF file's internal permissions): file=" + sourceTmp.toString();
+            }
+            else if (status != 0)
+            {
+                msg = "pdftotext failed, maybe corrupt PDF? status=" + String.valueOf(status);
+            }
+
+            if (msg != null)
+            {
+                log.error(msg);
+                throw new IOException(msg);
+            }
+
+            return new ByteArrayInputStream(baos.toByteArray());
+        }
+        catch (InterruptedException e)
+        {
+            log.error("Failed in pdftotext subprocess: ",e);
+            throw e;
+        }
+        finally
+        {
+            if (!sourceTmp.delete())
+            {
+                log.error("Unable to delete temporary file");
+            }
+            if (status != 0)
+            {
+                log.error("PDF conversion proc failed, returns=" + status + ", file=" + sourceTmp);
+            }
+        }
+    }
+}
+
+ 	  	 

dspace-api/src/main/java/org/dspace/app/mediafilter/XPDF2Thumbnail.java

@@ -0,0 +1,514 @@
+/**
+ * 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.Graphics2D;
+import java.awt.Color;
+import java.awt.image.*;
+import java.awt.RenderingHints;
+import java.awt.Transparency;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.util.Arrays;
+import java.util.regex.MatchResult;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import javax.imageio.ImageIO;
+
+import org.apache.log4j.Logger;
+import org.dspace.core.ConfigurationManager;
+import org.dspace.core.Utils;
+
+/**
+ * Thumbnail MediaFilter for PDF sources
+ *
+ * This filter generates thumbnail images for PDF documents, _including_
+ * 3D PDF documents with 2D "poster" images.  Since the PDFBox library
+ * does not understand these, and fails to render a lot of other PDFs,
+ * this filter forks a process running the "pdftoppm" program from the
+ * XPdf suite -- see http://www.foolabs.com/xpdf/
+ * This is a suite of open-source PDF tools that has been widely ported
+ * to Unix platforms and the ones we use (pdftoppm, pdfinfo) even
+ * run on Win32.
+ *
+ * This was written for the FACADE project but it is not directly connected
+ * to any of the other FACADE-specific software.  The FACADE UI expects
+ * to find thumbnail images for 3D PDFs generated by this filter.
+ *
+ * Requires DSpace config properties keys:
+ *
+ *  xpdf.path.pdftoppm -- absolute path to "pdftoppm" executable (required!)
+ *  xpdf.path.pdfinfo -- absolute path to "pdfinfo" executable (required!)
+ *  thumbnail.maxwidth  -- borrowed from thumbnails, max dim of generated image
+ *
+ * @author Larry Stone
+ * @see org.dspace.app.mediafilter.MediaFilter
+ */
+public class XPDF2Thumbnail extends MediaFilter
+{
+    private static Logger log = Logger.getLogger(XPDF2Thumbnail.class);
+
+    // maximum size of either preview image dimension
+    private static final int MAX_PX = 800;
+
+    // maxium DPI - use common screen res, 100dpi.
+    private static final int MAX_DPI = 100;
+
+    // command to get image from PDF; @FILE@, @OUTPUT@ are placeholders
+    private static final String XPDF_PDFTOPPM_COMMAND[] =
+    {
+        "@COMMAND@", "-q", "-f", "1", "-l", "1",
+        "-r", "@DPI@", "@FILE@", "@OUTPUTFILE@"
+    };
+
+    // command to get image from PDF; @FILE@, @OUTPUT@ are placeholders
+    private static final String XPDF_PDFINFO_COMMAND[] =
+    {
+        "@COMMAND@", "-f", "1", "-l", "1", "-box", "@FILE@"
+    };
+
+    // executable path for "pdftoppm", comes from DSpace config at runtime.
+    private String pdftoppmPath = null;
+
+    // executable path for "pdfinfo", comes from DSpace config at runtime.
+    private String pdfinfoPath = null;
+
+    // match line in pdfinfo output that describes file's MediaBox
+    private static final Pattern MEDIABOX_PATT = Pattern.compile(
+        "^Page\\s+\\d+\\s+MediaBox:\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)");
+
+    // also from thumbnail.maxwidth in config
+    private int xmax = 0;
+
+    // backup default for size, on the large side.
+    private static final int DEFAULT_XMAX = 500;
+
+    public String getFilteredName(String oldFilename)
+    {
+        return oldFilename + ".jpg";
+    }
+
+    public String getBundleName()
+    {
+        return "THUMBNAIL";
+    }
+
+    public String getFormatString()
+    {
+        return "JPEG";
+    }
+
+    public String getDescription()
+    {
+        return "Generated Thumbnail";
+    }
+
+    // canonical MediaFilter method to generate the thumbnail as stream.
+    public InputStream getDestinationStream(InputStream sourceStream)
+            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");
+        
+        // sanity check: xpdf paths are required. can cache since it won't change
+        if (pdftoppmPath == null || pdfinfoPath == null)
+        {
+            pdftoppmPath = ConfigurationManager.getProperty("xpdf.path.pdftoppm");
+            pdfinfoPath = ConfigurationManager.getProperty("xpdf.path.pdfinfo");
+            if (pdftoppmPath == null)
+            {
+                throw new IllegalStateException("No value for key \"xpdf.path.pdftoppm\" in DSpace configuration!  Should be path to XPDF pdftoppm executable.");
+            }
+            if (pdfinfoPath == null)
+            {
+                throw new IllegalStateException("No value for key \"xpdf.path.pdfinfo\" in DSpace configuration!  Should be path to XPDF pdfinfo executable.");
+            }
+                
+            if (xmax == 0)
+            {
+                xmax = DEFAULT_XMAX;
+            }
+        }
+
+        // make local file copy of source PDF since the PDF tools
+        // require a file for random access.
+        // XXX fixme would be nice to optimize this if we ever get
+        // XXX  a DSpace method to access (optionally!) the _file_ of
+        //     a Bitstream in the asset store, only when there is one of course.
+        File sourceTmp = File.createTempFile("DSfilt",".pdf");
+        sourceTmp.deleteOnExit();
+        int status = 0;
+        BufferedImage source = null;
+        try
+        {
+            OutputStream sto = new FileOutputStream(sourceTmp);
+            Utils.copy(sourceStream, sto);
+            sto.close();
+            sourceStream.close();
+
+            // First get max physical dim of bounding box of first page
+            // to compute the DPI to ask for..  otherwise some AutoCAD
+            // drawings can produce enormous files even at 75dpi, for
+            // 48" drawings..
+
+            // run pdfinfo, look for MediaBox description in the output, e.g.
+            // "Page    1 MediaBox:     0.00     0.00   612.00   792.00"
+            //
+            int dpi = 0;
+            String pdfinfoCmd[] = XPDF_PDFINFO_COMMAND.clone();
+            pdfinfoCmd[0] = pdfinfoPath;
+            pdfinfoCmd[pdfinfoCmd.length-1] = sourceTmp.toString();
+            BufferedReader lr = null;
+            try
+            {
+                MatchResult mediaBox = null;
+                Process pdfProc = Runtime.getRuntime().exec(pdfinfoCmd);
+                lr = new BufferedReader(new InputStreamReader(pdfProc.getInputStream()));
+                String line;
+                for (line = lr.readLine(); line != null; line = lr.readLine())
+                {
+                    // if (line.matches(MEDIABOX_PATT))
+                    Matcher mm = MEDIABOX_PATT.matcher(line);
+                    if (mm.matches())
+                    {
+                        mediaBox = mm.toMatchResult();
+                    }
+                }
+                int istatus = pdfProc.waitFor();
+                if (istatus != 0)
+                {
+                    log.error("XPDF pdfinfo proc failed, exit status=" + istatus + ", file=" + sourceTmp);
+                }
+                if (mediaBox == null)
+                {
+                    log.error("Sanity check: Did not find \"MediaBox\" line in output of XPDF pdfinfo, file="+sourceTmp);
+                    throw new IllegalArgumentException("Failed to get MediaBox of PDF with pdfinfo, cannot compute thumbnail.");
+                }
+                else
+                {
+                    double x0 = Double.parseDouble(mediaBox.group(1));
+                    double y0 = Double.parseDouble(mediaBox.group(2));
+                    double x1 = Double.parseDouble(mediaBox.group(3));
+                    double y1 = Double.parseDouble(mediaBox.group(4));
+                    int maxdim = (int)Math.max(Math.abs(x1 - x0), Math.abs(y1 - y0));
+                    dpi = Math.min(MAX_DPI, (MAX_PX * 72 / maxdim));
+                    log.debug("DPI: pdfinfo method got dpi="+dpi+" for max dim="+maxdim+" (points, 1/72\")");
+                }
+            }
+            catch (InterruptedException e)
+            {
+                log.error("Failed transforming file for preview: ",e);
+                throw new IllegalArgumentException("Failed transforming file for thumbnail: ",e);
+            }
+            catch (NumberFormatException e)
+            {
+                log.error("Failed interpreting pdfinfo results, check regexp: ",e);
+                throw new IllegalArgumentException("Failed transforming file for thumbnail: ",e);
+            }
+            finally
+            {
+                if (lr != null)
+                {
+                    lr.close();
+                }
+            }
+
+            // Render page 1 using xpdf's pdftoppm
+            // Requires Sun JAI imageio additions to read ppm directly.
+            // this will get "-000001.ppm" appended to it by pdftoppm
+            File outPrefixF = File.createTempFile("prevu","out");
+            String outPrefix = outPrefixF.toString();
+            if (!outPrefixF.delete())
+            {
+                log.error("Unable to delete output file");
+            }
+            String pdfCmd[] = XPDF_PDFTOPPM_COMMAND.clone();
+            pdfCmd[0] = pdftoppmPath;
+            pdfCmd[pdfCmd.length-3] = String.valueOf(dpi);
+            pdfCmd[pdfCmd.length-2] = sourceTmp.toString();
+            pdfCmd[pdfCmd.length-1] = outPrefix;
+            File outf = new File(outPrefix+"-000001.ppm");
+            log.debug("Running xpdf command: "+Arrays.deepToString(pdfCmd));
+            try
+            {
+                Process pdfProc = Runtime.getRuntime().exec(pdfCmd);
+                status = pdfProc.waitFor();
+                if (!outf.exists()) outf = new File(outPrefix+"-00001.ppm");
+                if (!outf.exists()) outf = new File(outPrefix+"-0001.ppm");
+                if (!outf.exists()) outf = new File(outPrefix+"-001.ppm");
+                if (!outf.exists()) outf = new File(outPrefix+"-01.ppm");
+                if (!outf.exists()) outf = new File(outPrefix+"-1.ppm");
+                log.debug("PDFTOPPM output is: "+outf+", exists="+outf.exists());
+                source = ImageIO.read(outf);
+            }
+            catch (InterruptedException e)
+            {
+                log.error("Failed transforming file for preview: ",e);
+                throw new IllegalArgumentException("Failed transforming file for preview: ",e);
+            }
+            finally
+            {
+                if (!outf.delete())
+                {
+                    log.error("Unable to delete file");
+                }
+            }
+        }
+        finally
+        {
+            if (!sourceTmp.delete())
+            {
+                log.error("Unable to delete temporary source");
+            }
+            
+            if (status != 0)
+            {
+                log.error("PDF conversion proc failed, exit status=" + status + ", file=" + sourceTmp);
+            }
+        }
+
+        if (source == null)
+        {
+            throw new IOException("Unknown failure while transforming file to preview: no image produced.");
+        }
+        
+        // read in bitstream's image
+        BufferedImage buf = source;
+
+        // now get the image dimensions
+        float xsize = (float) buf.getWidth(null);
+        float ysize = (float) buf.getHeight(null);
+        
+        // if verbose flag is set, print out dimensions
+        // to STDOUT
+        if (MediaFilterManager.isVerbose)
+        {
+            System.out.println("original size: " + xsize + "," + ysize);
+        }
+        
+        // scale by x first if needed
+        if (xsize > xmax)
+        {
+            // calculate scaling factor so that xsize * scale = new size (max)
+            float scale_factor = xmax / xsize;
+
+            // if verbose flag is set, print out extracted text
+            // to STDOUT
+            if (MediaFilterManager.isVerbose)
+            {
+                System.out.println("x scale factor: " + scale_factor);
+            }
+
+            // now reduce x size
+            // and y size
+            xsize = xsize * scale_factor;
+            ysize = ysize * scale_factor;
+
+            // 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 scale_factor = ymax / ysize;
+
+            // now reduce x size
+            // and y size
+            xsize = xsize * scale_factor;
+            ysize = ysize * scale_factor;
+        }
+
+        // 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 thumbnail with the new xsize, ysize
+        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);
+
+        // now create an input stream for the thumbnail buffer and return it
+        ByteArrayOutputStream baos = new ByteArrayOutputStream();
+
+        ImageIO.write(thumbnail, "jpeg", baos);
+
+        // now get the array
+        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
+
+        return bais; // hope this gets written out before its garbage collected!
+    }
+    
+   public String[] getInputMIMETypes()
+    {
+        return ImageIO.getReaderMIMETypes();
+    }
+
+    public String[] getInputDescriptions()
+    {
+        return null;
+    }
+
+    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, h;
+     w = buf.getWidth();
+     h = buf.getHeight();
+     BufferedImage normal = new BufferedImage(w, h, type);
+     Graphics2D g2d = normal.createGraphics();
+     g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
+     g2d.dispose();
+     return normal;
+    }
+
+    public BufferedImage getBlurredInstance(BufferedImage buf)
+    {
+    /**
+     * Convenience method that returns a blurred instance of the
+     * provided {@code BufferedImage}.
+     *
+     */
+
+     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, 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/factory/MediaFilterServiceFactory.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.mediafilter.factory;
-
-import org.dspace.app.mediafilter.service.MediaFilterService;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Abstract factory to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to
- * retrieve an implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public abstract class MediaFilterServiceFactory {
-
-    public abstract MediaFilterService getMediaFilterService();
-
-    public static MediaFilterServiceFactory getInstance() {
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("mediaFilterServiceFactory", MediaFilterServiceFactory.class);
-    }
-}