New location for DSpace Project

git-svn-id: http://scm.dspace.org/svn/repo/dspace/tags/dspace-1_3_2@3767 9c30dcfa-912a-0410-8fc2-9e0234be79fd

.gitattributes

@@ -1,14 +0,0 @@
-# Auto detect text files and perform LF normalization
-* text=auto
-
-# Standard to msysgit
-*.doc  diff=astextplain
-*.DOC  diff=astextplain
-*.docx diff=astextplain
-*.DOCX diff=astextplain
-*.dot  diff=astextplain
-*.DOT  diff=astextplain
-*.pdf  diff=astextplain
-*.PDF  diff=astextplain
-*.rtf  diff=astextplain
-*.RTF  diff=astextplain

.gitignore

@@ -1,44 +0,0 @@
-## Ignore the MVN compiled output directories from version tracking
-target/
-
-## Ignore tags index files created by Exuberant Ctags
-tags
-
-## Ignore project files created by Eclipse
-.settings/
-/bin/
-.project
-.classpath
-.checkstyle
-
-## Ignore project files created by IntelliJ IDEA
-*.iml
-*.ipr
-*.iws
-.idea/
-overlays/
-
-## Ignore project files created by NetBeans
-nbproject/private/
-build/
-nbbuild/
-dist/
-nbdist/
-nbactions.xml
-nb-configuration.xml
-
-## Ignore all *.properties file in root folder, EXCEPT build.properties (the default)
-## KEPT FOR BACKWARDS COMPATIBILITY WITH 5.x (build.properties is now replaced with local.cfg)
-/*.properties
-!/build.properties
-
-# Ignore a local.cfg file in root folder, if it exists
-/local.cfg
-# Also ignore it under dspace/config
-/dspace/config/local.cfg
-
-##Mac noise
-.DS_Store
-
-##Ignore JRebel project configuration
-rebel.xml

.travis.yml

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-  # Remove outdated settings.xml from Travis builds.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

LICENSE

@@ -1,40 +0,0 @@
-DSpace source code license:
-
-
-Copyright (c) 2002-2016, DuraSpace.  All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-- Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
-
-- Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-- Neither the name DuraSpace nor the name of the DSpace Foundation
-nor the names of its contributors may be used to endorse or promote
-products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
-
-
-DSpace uses third-party libraries which may be distributed under
-different licenses to the above. Information about these licenses 
-is detailed in the LICENSES_THIRD_PARTY file at the root of the source 
-tree.  You must agree to the terms of these licenses, in addition to 
-the above DSpace source code license, in order to use this software.

LICENSES_THIRD_PARTY

@@ -1,424 +0,0 @@
-
-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
-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
-"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
----------------------------------------------------
-
-    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/)
-        * AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.10.50 - https://aws.amazon.com/sdkforjava)
-        * AWS Java SDK for AWS KMS (com.amazonaws:aws-java-sdk-kms:1.10.50 - https://aws.amazon.com/sdkforjava)
-        * AWS Java SDK for Amazon S3 (com.amazonaws:aws-java-sdk-s3:1.10.50 - https://aws.amazon.com/sdkforjava)
-        * HPPC Collections (com.carrotsearch:hppc:0.5.2 - http://labs.carrotsearch.com/hppc.html/hppc)
-        * metadata-extractor (com.drewnoakes:metadata-extractor:2.6.2 - http://code.google.com/p/metadata-extractor/)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.5.4 - http://github.com/FasterXML/jackson)
-        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.7.0 - http://github.com/FasterXML/jackson)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.5.4 - https://github.com/FasterXML/jackson)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.7.0 - https://github.com/FasterXML/jackson-core)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.5.4 - http://github.com/FasterXML/jackson)
-        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.7.0 - http://github.com/FasterXML/jackson)
-        * Jackson-JAXRS-base (com.fasterxml.jackson.jaxrs:jackson-jaxrs-base:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-base)
-        * Jackson-JAXRS-JSON (com.fasterxml.jackson.jaxrs:jackson-jaxrs-json-provider:2.5.4 - http://wiki.fasterxml.com/JacksonHome/jackson-jaxrs-json-provider)
-        * Jackson-module-JAXB-annotations (com.fasterxml.jackson.module:jackson-module-jaxb-annotations:2.5.4 - http://wiki.fasterxml.com/JacksonJAXBAnnotations)
-        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.21.0 - https://github.com/google/google-api-java-client/google-api-client)
-        * Google Analytics API v3-rev123-1.21.0 (com.google.apis:google-api-services-analytics:v3-rev123-1.21.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-analytics)
-        * FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.1 - http://findbugs.sourceforge.net/)
-        * Gson (com.google.code.gson:gson:2.6.1 - https://github.com/google/gson/gson)
-        * Guava: Google Core Libraries for Java (com.google.guava:guava:14.0.1 - http://code.google.com/p/guava-libraries/guava)
-        * Guava: Google Core Libraries for Java (com.google.guava:guava:19.0 - https://github.com/google/guava/guava)
-        * Guava: Google Core Libraries for Java (JDK5 Backport) (com.google.guava:guava-jdk5:17.0 - http://code.google.com/p/guava-libraries/guava-jdk5)
-        * Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.21.0 - https://github.com/google/google-http-java-client/google-http-client)
-        * Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.21.0 - https://github.com/google/google-http-java-client/google-http-client-jackson2)
-        * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.21.0 - https://github.com/google/google-oauth-java-client/google-oauth-client)
-        * ConcurrentLinkedHashMap (com.googlecode.concurrentlinkedhashmap:concurrentlinkedhashmap-lru:1.2 - http://code.google.com/p/concurrentlinkedhashmap)
-        * ISO Parser (com.googlecode.mp4parser:isoparser:1.0-RC-1 - http://code.google.com/p/mp4parser/)
-        * builder-commons (com.lyncode:builder-commons:1.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/builder-commons)
-        * Jtwig Core (com.lyncode:jtwig-core:2.0.1 - http://www.lyncode.com/jtwig-core)
-        * Jtwig Core Functions (com.lyncode:jtwig-functions:2.0.1 - http://www.lyncode.com/jtwig-functions)
-        * Jtwig Spring (com.lyncode:jtwig-spring:2.0.1 - http://www.lyncode.com/jtwig-spring)
-        * Test Support (com.lyncode:test-support:1.0.3 - http://nexus.sonatype.org/oss-repository-hosting.html/test-support)
-        * Spatial4J (com.spatial4j:spatial4j:0.4.1 - https://github.com/spatial4j/spatial4j)
-        * Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.2 - http://commons.apache.org/proper/commons-beanutils/)
-        * Apache Commons CLI (commons-cli:commons-cli:1.3.1 - http://commons.apache.org/proper/commons-cli/)
-        * Apache Commons Codec (commons-codec:commons-codec:1.10 - http://commons.apache.org/proper/commons-codec/)
-        * Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
-        * Apache Commons Configuration (commons-configuration:commons-configuration:1.10 - http://commons.apache.org/configuration/)
-        * Commons Digester (commons-digester:commons-digester:1.8.1 - http://commons.apache.org/digester/)
-        * Apache Commons FileUpload (commons-fileupload:commons-fileupload:1.3.1 - http://commons.apache.org/proper/commons-fileupload/)
-        * HttpClient (commons-httpclient:commons-httpclient:3.1 - http://jakarta.apache.org/httpcomponents/httpclient-3.x/)
-        * Commons IO (commons-io:commons-io:2.4 - http://commons.apache.org/io/)
-        * commons-jexl (commons-jexl:commons-jexl:1.0 - no url defined)
-        * Commons JXPath (commons-jxpath:commons-jxpath:1.3 - http://commons.apache.org/jxpath/)
-        * Commons Lang (commons-lang:commons-lang:2.6 - http://commons.apache.org/lang/)
-        * Apache Commons Logging (commons-logging:commons-logging:1.2 - http://commons.apache.org/proper/commons-logging/)
-        * Apache Commons Validator (commons-validator:commons-validator:1.5.0 - http://commons.apache.org/proper/commons-validator/)
-        * Boilerpipe -- Boilerplate Removal and Fulltext Extraction from HTML pages (de.l3s.boilerpipe:boilerpipe:1.1.0 - http://code.google.com/p/boilerpipe/)
-        * The Netty Project (io.netty:netty:3.7.0.Final - http://netty.io/)
-        * jakarta-regexp (jakarta-regexp:jakarta-regexp:1.4 - no url defined)
-        * javax.inject (javax.inject:javax.inject:1 - http://code.google.com/p/atinject/)
-        * Bean Validation API (javax.validation:validation-api:1.1.0.Final - http://beanvalidation.org)
-        * jdbm (jdbm:jdbm:1.0 - no url defined)
-        * Joda time (joda-time:joda-time:2.2 - http://joda-time.sourceforge.net)
-        * Joda-Time (joda-time:joda-time:2.9.2 - http://www.joda.org/joda-time/)
-        * Apache Log4j (log4j:log4j:1.2.17 - http://logging.apache.org/log4j/1.2/)
-        * "Java Concurrency in Practice" book annotations (net.jcip:jcip-annotations:1.0 - http://jcip.net/)
-        * Ehcache Core (net.sf.ehcache:ehcache-core:2.4.3 - http://ehcache.org)
-        * opencsv (net.sf.opencsv:opencsv:2.3 - http://opencsv.sf.net)
-        * Abdera Client (org.apache.abdera:abdera-client:1.1.3 - http://abdera.apache.org/abdera-client)
-        * Abdera Core (org.apache.abdera:abdera-core:1.1.3 - http://abdera.apache.org/abdera-core)
-        * I18N Libraries (org.apache.abdera:abdera-i18n:1.1.3 - http://abdera.apache.org)
-        * Abdera Parser (org.apache.abdera:abdera-parser:1.1.3 - http://abdera.apache.org/abdera-parser)
-        * org.apache.tools.ant (org.apache.ant:ant:1.7.0 - http://ant.apache.org/ant/)
-        * ant-launcher (org.apache.ant:ant-launcher:1.7.0 - http://ant.apache.org/ant-launcher/)
-        * Avalon Framework API (org.apache.avalon.framework:avalon-framework-api:4.3.1 - http://www.apache.org/excalibur/avalon-framework/avalon-framework-api/)
-        * Avalon Framework Implementation (org.apache.avalon.framework:avalon-framework-impl:4.3.1 - http://www.apache.org/excalibur/avalon-framework/avalon-framework-impl/)
-        * Cocoon Configuration API (org.apache.cocoon:cocoon-configuration-api:1.0.2 - http://cocoon.apache.org/subprojects/configuration/1.0/configuration-api/1.0/)
-        * Cocoon Core (org.apache.cocoon:cocoon-core:2.2.0 - http://cocoon.apache.org/2.2/core-modules/core/2.2/)
-        * Cocoon Expression Language API (org.apache.cocoon:cocoon-expression-language-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/expression-language-api/1.0/)
-        * Cocoon Expression Language Implementation. (org.apache.cocoon:cocoon-expression-language-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/expression-language-impl/1.0/)
-        * Cocoon Flowscript Block Implementation (org.apache.cocoon:cocoon-flowscript-impl:1.0.0 - http://cocoon.apache.org/2.2/blocks/flowscript/1.0/)
-        * Cocoon Linkrewriter Block Implementation (org.apache.cocoon:cocoon-linkrewriter-impl:1.0.0 - http://cocoon.apache.org/2.2/blocks/linkrewriter/1.0/)
-        * Cocoon Pipeline API (org.apache.cocoon:cocoon-pipeline-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-api/1.0/)
-        * Cocoon Pipeline Components (org.apache.cocoon:cocoon-pipeline-components:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-components/1.0/)
-        * Cocoon Pipeline Implementation (org.apache.cocoon:cocoon-pipeline-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/pipeline-impl/1.0/)
-        * Cocoon Servlet Service Components (org.apache.cocoon:cocoon-servlet-service-components:1.0.0 - http://cocoon.apache.org/subprojects/servlet-service/1.0/servlet-service-components/1.0/)
-        * Cocoon Sitemap API (org.apache.cocoon:cocoon-sitemap-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-api/1.0/)
-        * Cocoon Sitemap Components (org.apache.cocoon:cocoon-sitemap-components:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-components/1.0/)
-        * Cocoon Sitemap Implementation (org.apache.cocoon:cocoon-sitemap-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/sitemap-impl/1.0/)
-        * Cocoon Spring Configurator (org.apache.cocoon:cocoon-spring-configurator:1.0.2 - http://cocoon.apache.org/cocoon-spring-configurator)
-        * Cocoon Store Implementation (org.apache.cocoon:cocoon-store-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/store-impl/1.0/)
-        * Cocoon Template Framework Block Implementation (org.apache.cocoon:cocoon-template-impl:1.1.0 - http://cocoon.apache.org/2.2/blocks/template/1.0/)
-        * Cocoon Thread API (org.apache.cocoon:cocoon-thread-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/thread-api/1.0/)
-        * Cocoon Thread Implementation (org.apache.cocoon:cocoon-thread-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/thread-impl/1.0/)
-        * Cocoon Util (org.apache.cocoon:cocoon-util:1.0.0 - http://cocoon.apache.org/2.2/core-modules/util/1.0/)
-        * Cocoon XML API (org.apache.cocoon:cocoon-xml-api:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-api/1.0/)
-        * Cocoon XML Implementation (org.apache.cocoon:cocoon-xml-impl:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-impl/1.0/)
-        * Cocoon XML Resolver (org.apache.cocoon:cocoon-xml-resolver:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-resolver/1.0/)
-        * Cocoon XML Utilities (org.apache.cocoon:cocoon-xml-util:1.0.0 - http://cocoon.apache.org/2.2/core-modules/xml-util/1.0/)
-        * Apache Commons Compress (org.apache.commons:commons-compress:1.7 - http://commons.apache.org/proper/commons-compress/)
-        * Apache Commons CSV (org.apache.commons:commons-csv:1.0 - http://commons.apache.org/proper/commons-csv/)
-        * Apache Commons DBCP (org.apache.commons:commons-dbcp2:2.1.1 - http://commons.apache.org/dbcp/)
-        * Apache Commons Lang (org.apache.commons:commons-lang3:3.3.2 - http://commons.apache.org/proper/commons-lang/)
-        * Apache Commons Pool (org.apache.commons:commons-pool2:2.4.2 - http://commons.apache.org/proper/commons-pool/)
-        * Excalibur Pool API (org.apache.excalibur.components:excalibur-pool-api:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-pool-modules/excalibur-pool-api/)
-        * Excalibur Sourceresolve (org.apache.excalibur.components:excalibur-sourceresolve:2.2.3 - http://www.apache.org/excalibur/excalibur-sourceresolve/)
-        * Excalibur Store (org.apache.excalibur.components:excalibur-store:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-store/)
-        * Excalibur XML Utilities (org.apache.excalibur.components:excalibur-xmlutil:2.2.1 - http://www.apache.org/excalibur/excalibur-components-modules/excalibur-xmlutil/)
-        * Excalibur Instrument API (org.apache.excalibur.containerkit:excalibur-instrument-api:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-instrument-modules/excalibur-instrument-api/)
-        * Excalibur Logger (org.apache.excalibur.containerkit:excalibur-logger:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-logger/)
-        * Activation 1.1 (org.apache.geronimo.specs:geronimo-activation_1.1_spec:1.1 - http://geronimo.apache.org/maven/specs/geronimo-activation_1.1_spec/1.1)
-        * JavaMail 1.4 (org.apache.geronimo.specs:geronimo-javamail_1.4_spec:1.7.1 - http://geronimo.apache.org/maven/specs/geronimo-javamail_1.4_spec/1.7.1)
-        * Streaming API for XML (STAX API 1.0) (org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:1.0.1 - http://geronimo.apache.org/specs/geronimo-stax-api_1.0_spec)
-        * Apache Hadoop Annotations (org.apache.hadoop:hadoop-annotations:2.2.0 - no url defined)
-        * Apache Hadoop Auth (org.apache.hadoop:hadoop-auth:2.2.0 - no url defined)
-        * Apache Hadoop Common (org.apache.hadoop:hadoop-common:2.2.0 - no url defined)
-        * Apache Hadoop HDFS (org.apache.hadoop:hadoop-hdfs:2.2.0 - no url defined)
-        * Apache HttpClient (org.apache.httpcomponents:httpclient:4.5.1 - http://hc.apache.org/httpcomponents-client)
-        * Apache HttpClient Cache (org.apache.httpcomponents:httpclient-cache:4.2.6 - http://hc.apache.org/httpcomponents-client)
-        * Apache HttpCore (org.apache.httpcomponents:httpcore:4.4.4 - http://hc.apache.org/httpcomponents-core-ga)
-        * Apache HttpClient Mime (org.apache.httpcomponents:httpmime:4.3.1 - http://hc.apache.org/httpcomponents-client)
-        * Apache JAMES Mime4j (Core) (org.apache.james:apache-mime4j-core:0.7.2 - http://james.apache.org/mime4j/apache-mime4j-core)
-        * Apache JAMES Mime4j (DOM) (org.apache.james:apache-mime4j-dom:0.7.2 - http://james.apache.org/mime4j/apache-mime4j-dom)
-        * Apache Jena - Libraries POM (org.apache.jena:apache-jena-libs:2.13.0 - http://jena.apache.org/apache-jena-libs/)
-        * Apache Jena - ARQ (SPARQL 1.1 Query Engine) (org.apache.jena:jena-arq:2.13.0 - http://jena.apache.org/jena-arq/)
-        * Apache Jena - Core (org.apache.jena:jena-core:2.13.0 - http://jena.apache.org/jena-core/)
-        * Apache Jena - IRI (org.apache.jena:jena-iri:1.1.2 - http://jena.apache.org/jena-iri/)
-        * Apache Jena - TDB (Native Triple Store) (org.apache.jena:jena-tdb:1.1.2 - http://jena.apache.org/jena-tdb/)
-        * Lucene Common Analyzers (org.apache.lucene:lucene-analyzers-common:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-analyzers-common)
-        * Lucene Common Analyzers (org.apache.lucene:lucene-analyzers-common:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-common)
-        * Lucene ICU Analysis Components (org.apache.lucene:lucene-analyzers-icu:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-icu)
-        * Lucene Kuromoji Japanese Morphological Analyzer (org.apache.lucene:lucene-analyzers-kuromoji:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-kuromoji)
-        * Lucene Morfologik Polish Lemmatizer (org.apache.lucene:lucene-analyzers-morfologik:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-morfologik)
-        * Lucene Phonetic Filters (org.apache.lucene:lucene-analyzers-phonetic:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-phonetic)
-        * Lucene Smart Chinese Analyzer (org.apache.lucene:lucene-analyzers-smartcn:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-smartcn)
-        * Lucene Stempel Analyzer (org.apache.lucene:lucene-analyzers-stempel:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-analyzers-stempel)
-        * Lucene codecs (org.apache.lucene:lucene-codecs:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-codecs)
-        * Lucene Core (org.apache.lucene:lucene-core:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-core)
-        * Lucene Core (org.apache.lucene:lucene-core:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-core)
-        * Lucene Expressions (org.apache.lucene:lucene-expressions:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-expressions)
-        * Lucene Grouping (org.apache.lucene:lucene-grouping:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-grouping)
-        * Lucene Grouping (org.apache.lucene:lucene-grouping:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-grouping)
-        * Lucene Highlighter (org.apache.lucene:lucene-highlighter:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-highlighter)
-        * Lucene Highlighter (org.apache.lucene:lucene-highlighter:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-highlighter)
-        * Lucene Join (org.apache.lucene:lucene-join:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-join)
-        * Lucene Join (org.apache.lucene:lucene-join:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-join)
-        * Lucene Memory (org.apache.lucene:lucene-memory:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-memory)
-        * Lucene Memory (org.apache.lucene:lucene-memory:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-memory)
-        * Lucene Miscellaneous (org.apache.lucene:lucene-misc:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-misc)
-        * Lucene Miscellaneous (org.apache.lucene:lucene-misc:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-misc)
-        * Lucene Queries (org.apache.lucene:lucene-queries:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-queries)
-        * Lucene Queries (org.apache.lucene:lucene-queries:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-queries)
-        * Lucene QueryParsers (org.apache.lucene:lucene-queryparser:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-queryparser)
-        * Lucene QueryParsers (org.apache.lucene:lucene-queryparser:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-queryparser)
-        * Lucene Sandbox (org.apache.lucene:lucene-sandbox:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-sandbox)
-        * Lucene Spatial (org.apache.lucene:lucene-spatial:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-spatial)
-        * Lucene Spatial (org.apache.lucene:lucene-spatial:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-spatial)
-        * Lucene Suggest (org.apache.lucene:lucene-suggest:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-suggest)
-        * Lucene Suggest (org.apache.lucene:lucene-suggest:4.10.4 - http://lucene.apache.org/lucene-parent/lucene-suggest)
-        * Apache FontBox (org.apache.pdfbox:fontbox:2.0.2 - http://pdfbox.apache.org/)
-        * Apache JempBox (org.apache.pdfbox:jempbox:1.8.4 - http://www.apache.org/pdfbox-parent/jempbox/)
-        * Apache PDFBox (org.apache.pdfbox:pdfbox:2.0.2 - http://www.apache.org/pdfbox-parent/pdfbox/)
-        * Apache POI (org.apache.poi:poi:3.13 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-ooxml:3.13 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-ooxml-schemas:3.10.1 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-ooxml-schemas:3.13 - http://poi.apache.org/)
-        * Apache POI (org.apache.poi:poi-scratchpad:3.13 - http://poi.apache.org/)
-        * Apache Solr Search Server (org.apache.solr:solr:4.10.4 - http://lucene.apache.org/solr-parent/solr)
-        * Apache Solr Analysis Extras (org.apache.solr:solr-analysis-extras:4.10.4 - http://lucene.apache.org/solr-parent/solr-analysis-extras)
-        * Apache Solr Content Extraction Library (org.apache.solr:solr-cell:4.10.4 - http://lucene.apache.org/solr-parent/solr-cell)
-        * Apache Solr Core (org.apache.solr:solr-core:4.10.4 - http://lucene.apache.org/solr-parent/solr-core)
-        * Apache Solr Solrj (org.apache.solr:solr-solrj:4.10.4 - http://lucene.apache.org/solr-parent/solr-solrj)
-        * Apache Thrift (org.apache.thrift:libthrift:0.9.2 - http://thrift.apache.org)
-        * Apache Tika core (org.apache.tika:tika-core:1.5 - http://tika.apache.org/)
-        * Apache Tika parsers (org.apache.tika:tika-parsers:1.5 - http://tika.apache.org/)
-        * Apache Tika XMP (org.apache.tika:tika-xmp:1.5 - http://tika.apache.org/)
-        * Axiom API (org.apache.ws.commons.axiom:axiom-api:1.2.14 - http://ws.apache.org/axiom/)
-        * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.14 - http://ws.apache.org/axiom/)
-        * XmlBeans (org.apache.xmlbeans:xmlbeans:2.6.0 - http://xmlbeans.apache.org)
-        * zookeeper (org.apache.zookeeper:zookeeper:3.4.6 - no url defined)
-        * Evo Inflector (org.atteo:evo-inflector:1.2.1 - http://atteo.org/static/evo-inflector)
-        * TagSoup (org.ccil.cowan.tagsoup:tagsoup:1.2.1 - http://home.ccil.org/~cowan/XML/tagsoup/)
-        * Jackson (org.codehaus.jackson:jackson-core-asl:1.9.13 - http://jackson.codehaus.org)
-        * Data Mapper for Jackson (org.codehaus.jackson:jackson-mapper-asl:1.9.13 - http://jackson.codehaus.org)
-        * Woodstox (org.codehaus.woodstox:woodstox-core-asl:4.1.4 - http://woodstox.codehaus.org)
-        * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.0 - http://woodstox.codehaus.org)
-        * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.7 - http://woodstox.codehaus.org)
-        * flyway-core (org.flywaydb:flyway-core:4.0.3 - https://flywaydb.org/flyway-core)
-        * Ogg and Vorbis for Java, Core (org.gagravarr:vorbis-java-core:0.1 - https://github.com/Gagravarr/VorbisJava)
-        * Apache Tika plugin for Ogg, Vorbis and FLAC (org.gagravarr:vorbis-java-tika:0.1 - https://github.com/Gagravarr/VorbisJava)
-        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
-        * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
-        * Jetty Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-servlet-tester)
-        * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
-        * Servlet Specification API (org.mortbay.jetty:servlet-api:2.5-20081211 - http://jetty.mortbay.org/servlet-api)
-        * Noggit (org.noggit:noggit:0.5 - http://noggit.org)
-        * Objenesis (org.objenesis:objenesis:2.1 - http://objenesis.org)
-        * parboiled-core (org.parboiled:parboiled-core:1.1.6 - http://parboiled.org)
-        * parboiled-java (org.parboiled:parboiled-java:1.1.6 - http://parboiled.org)
-        * org.restlet (org.restlet.jee:org.restlet:2.1.1 - no url defined)
-        * org.restlet.ext.servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - no url defined)
-        * rome-modules (org.rometools:rome-modules:1.0 - http://www.rometools.org)
-        * Spring AOP (org.springframework:spring-aop:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring AOP (org.springframework:spring-aop:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Beans (org.springframework:spring-beans:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Beans (org.springframework:spring-beans:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Context (org.springframework:spring-context:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Context (org.springframework:spring-context:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Context Support (org.springframework:spring-context-support:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Core (org.springframework:spring-core:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Core (org.springframework:spring-core:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Expression Language (SpEL) (org.springframework:spring-expression:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Expression Language (SpEL) (org.springframework:spring-expression:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring JDBC (org.springframework:spring-jdbc:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring JDBC (org.springframework:spring-jdbc:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Object/Relational Mapping (org.springframework:spring-orm:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Object/Relational Mapping (org.springframework:spring-orm:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring TestContext Framework (org.springframework:spring-test:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Transaction (org.springframework:spring-tx:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Transaction (org.springframework:spring-tx:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Web (org.springframework:spring-web:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Web (org.springframework:spring-web:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Web MVC (org.springframework:spring-webmvc:3.2.16.RELEASE - https://github.com/SpringSource/spring-framework)
-        * Spring Web MVC (org.springframework:spring-webmvc:3.2.5.RELEASE - https://github.com/SpringSource/spring-framework)
-        * spring-security-config (org.springframework.security:spring-security-config:3.2.9.RELEASE - http://spring.io/spring-security)
-        * spring-security-core (org.springframework.security:spring-security-core:3.2.9.RELEASE - http://spring.io/spring-security)
-        * spring-security-web (org.springframework.security:spring-security-web:3.2.9.RELEASE - http://spring.io/spring-security)
-        * SWORD Java API, GUI and CLI (org.swordapp:sword-common:1.1 - http://nexus.sonatype.org/oss-repository-hosting.html/sword-common)
-        * SWORD v2 :: Common Server Library (org.swordapp:sword2-server:1.0 - http://www.swordapp.org/)
-        * xml-matchers (org.xmlmatchers:xml-matchers:0.10 - http://code.google.com/p/xml-matchers/)
-        * oro (oro:oro:2.0.8 - no url defined)
-        * JUnitParams (pl.pragmatists:JUnitParams:1.0.2 - http://junitparams.googlecode.com)
-        * Rome A9 OpenSearch (rome:opensearch:0.1 - http://wiki.java.net/bin/view/Javawsxml/OpenSearch)
-        * ROME, RSS and atOM utilitiEs for Java (rome:rome:1.0 - https://rome.dev.java.net/)
-        * oai4j (se.kb:oai4j:0.6b1 - http://oai4j-client.sourceforge.net/)
-        * StAX API (stax:stax-api:1.0.1 - http://stax.codehaus.org/)
-        * standard (taglibs:standard:1.1.2 - no url defined)
-        * Xalan Java Serializer (xalan:serializer:2.7.2 - http://xml.apache.org/xalan-j/)
-        * Xalan Java (xalan:xalan:2.7.2 - http://xml.apache.org/xalan-j/)
-        * Xerces2-j (xerces:xercesImpl:2.11.0 - https://xerces.apache.org/xerces2-j/)
-        * xmlParserAPIs (xerces:xmlParserAPIs:2.6.2 - no url defined)
-        * XML Commons External Components XML APIs (xml-apis:xml-apis:1.4.01 - http://xml.apache.org/commons/components/external/)
-        * XML Commons Resolver Component (xml-resolver:xml-resolver:1.2 - http://xml.apache.org/commons/components/resolver/)
-
-    BSD License:
-
-        * AntLR Parser Generator (antlr:antlr:2.7.7 - http://www.antlr.org/)
-        * ASM Core (asm:asm:3.3.1 - http://asm.objectweb.org/asm/)
-        * XMP Library for Java (com.adobe.xmp:xmpcore:5.1.2 - http://www.adobe.com/devnet/xmp.html)
-        * coverity-escapers (com.coverity.security:coverity-escapers:1.1.1 - http://coverity.com/security)
-        * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.1 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
-        * Protocol Buffer Java API (com.google.protobuf:protobuf-java:2.5.0 - http://code.google.com/p/protobuf)
-        * Jena IRI (com.hp.hpl.jena:iri:0.8 - http://jena.sf.net/iri)
-        * Jena (com.hp.hpl.jena:jena:2.6.4 - http://www.openjena.org/)
-        * yui compressor (com.yahoo.platform.yui:yuicompressor:2.3.6 - http://developer.yahoo.com/yui/compressor/)
-        * dnsjava (dnsjava:dnsjava:2.1.7 - http://www.dnsjava.org)
-        * dom4j (dom4j:dom4j:1.6.1 - http://dom4j.org)
-        * Biblio Transformation Engine :: Core (gr.ekt.bte:bte-core:0.9.3.5 - http://github.com/EKT/Biblio-Transformation-Engine/bte-core)
-        * Biblio Transformation Engine :: Input/Output (gr.ekt.bte:bte-io:0.9.3.5 - http://github.com/EKT/Biblio-Transformation-Engine/bte-io)
-        * jaxen (jaxen:jaxen:1.1.6 - http://jaxen.codehaus.org/)
-        * JLine (jline:jline:0.9.94 - http://jline.sourceforge.net)
-        * ANTLR 3 Runtime (org.antlr:antlr-runtime:3.5 - http://www.antlr.org)
-        * Morfologik FSA (org.carrot2:morfologik-fsa:1.7.1 - http://morfologik.blogspot.com/morfologik-fsa/)
-        * Morfologik Stemming Dictionary for Polish (org.carrot2:morfologik-polish:1.7.1 - http://morfologik.blogspot.com/morfologik-polish/)
-        * Morfologik Stemming APIs (org.carrot2:morfologik-stemming:1.7.1 - http://morfologik.blogspot.com/morfologik-stemming/)
-        * Stax2 API (org.codehaus.woodstox:stax2-api:3.1.1 - http://woodstox.codehaus.org/StAX2)
-        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
-        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:6.0.3 - https://github.com/dspace/dspace-api-lang)
-        * DSpace JSP-UI (org.dspace:dspace-jspui:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
-        * DSpace OAI-PMH (org.dspace:dspace-oai:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
-        * DSpace RDF (org.dspace:dspace-rdf:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
-        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:6.0-rc4-SNAPSHOT - http://demo.dspace.org)
-        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
-        * Apache Solr Webapp (org.dspace:dspace-solr:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
-        * DSpace SWORD (org.dspace:dspace-sword:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
-        * DSpace SWORD v2 (org.dspace:dspace-swordv2:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
-        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
-        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:6.0.3 - https://github.com/dspace/dspace-xmlui-lang)
-        * handle (org.dspace:handle:6.2 - no url defined)
-        * jargon (org.dspace:jargon:1.4.25 - no url defined)
-        * mets (org.dspace:mets:1.5.2 - no url defined)
-        * oclc-harvester2 (org.dspace:oclc-harvester2:0.1.12 - no url defined)
-        * XOAI : OAI-PMH Java Toolkit (org.dspace:xoai:3.2.10 - http://nexus.sonatype.org/oss-repository-hosting.html/xoai)
-        * Repackaged Cocoon Servlet Service Implementation (org.dspace.dependencies.cocoon:dspace-cocoon-servlet-service-impl:1.0.3 - http://projects.dspace.org/dspace-pom/dspace-cocoon-servlet-service-impl)
-        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:6.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
-        * Hamcrest All (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
-        * Hamcrest Core (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
-        * JBibTeX (org.jbibtex:jbibtex:1.0.10 - http://www.jbibtex.org)
-        * ASM Core (org.ow2.asm:asm:4.1 - http://asm.objectweb.org/asm/)
-        * ASM Analysis (org.ow2.asm:asm-analysis:4.1 - http://asm.objectweb.org/asm-analysis/)
-        * ASM Commons (org.ow2.asm:asm-commons:4.1 - http://asm.objectweb.org/asm-commons/)
-        * ASM Tree (org.ow2.asm:asm-tree:4.1 - http://asm.objectweb.org/asm-tree/)
-        * ASM Util (org.ow2.asm:asm-util:4.1 - http://asm.objectweb.org/asm-util/)
-        * XMLUnit for Java (xmlunit:xmlunit:1.1 - http://xmlunit.sourceforge.net/)
-        * XMLUnit for Java (xmlunit:xmlunit:1.3 - http://xmlunit.sourceforge.net/)
-
-    Common Development and Distribution License (CDDL):
-
-        * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
-        * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
-        * JavaBeans(TM) Activation Framework (javax.activation:activation:1.1.1 - http://java.sun.com/javase/technologies/desktop/javabeans/jaf/index.jsp)
-        * javax.annotation API (javax.annotation:javax.annotation-api:1.2 - http://jcp.org/en/jsr/detail?id=250)
-        * JavaMail API (compat) (javax.mail:mail:1.4.7 - http://kenai.com/projects/javamail/mail)
-        * Java Servlet API (javax.servlet:javax.servlet-api:3.1.0 - http://servlet-spec.java.net)
-        * jsp-api (javax.servlet:jsp-api:2.0 - no url defined)
-        * jstl (javax.servlet:jstl:1.2 - no url defined)
-        * servlet-api (javax.servlet:servlet-api:2.5 - no url defined)
-        * javax.ws.rs-api (javax.ws.rs:javax.ws.rs-api:2.0.1 - http://jax-rs-spec.java.net)
-        * Class Model for Hk2 (org.glassfish.hk2:class-model:2.4.0-b31 - https://hk2.java.net/class-model)
-        * HK2 config types (org.glassfish.hk2:config-types:2.4.0-b31 - https://hk2.java.net/hk2-configuration/hk2-configuration-persistence/hk2-xml-dom/config-types)
-        * HK2 module of HK2 itself (org.glassfish.hk2:hk2:2.4.0-b31 - https://hk2.java.net/hk2)
-        * HK2 API module (org.glassfish.hk2:hk2-api:2.4.0-b31 - https://hk2.java.net/hk2-api)
-        * HK2 configuration module (org.glassfish.hk2:hk2-config:2.4.0-b31 - https://hk2.java.net/hk2-configuration/hk2-configuration-persistence/hk2-xml-dom/hk2-config)
-        * HK2 core module (org.glassfish.hk2:hk2-core:2.4.0-b31 - https://hk2.java.net/hk2-core)
-        * ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:2.4.0-b31 - https://hk2.java.net/hk2-locator)
-        * Run Level Service (org.glassfish.hk2:hk2-runlevel:2.4.0-b31 - https://hk2.java.net/hk2-runlevel)
-        * HK2 Implementation Utilities (org.glassfish.hk2:hk2-utils:2.4.0-b31 - https://hk2.java.net/hk2-utils)
-        * OSGi resource locator bundle - used by various API providers that rely on META-INF/services mechanism to locate providers. (org.glassfish.hk2:osgi-resource-locator:1.0.1 - http://glassfish.org/osgi-resource-locator/)
-        * HK2 Spring Bridge (org.glassfish.hk2:spring-bridge:2.4.0-b31 - https://hk2.java.net/spring-bridge)
-        * aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:2.4.0-b31 - https://hk2.java.net/external/aopalliance-repackaged)
-        * ASM library repackaged as OSGi bundle (org.glassfish.hk2.external:asm-all-repackaged:2.4.0-b31 - https://hk2.java.net/external/asm-all-repackaged)
-        * javax.validation:1.1.0.Final as OSGi bundle (org.glassfish.hk2.external:bean-validator:2.4.0-b31 - https://hk2.java.net/external/bean-validator)
-        * javax.inject:1 as OSGi bundle (org.glassfish.hk2.external:javax.inject:2.4.0-b31 - https://hk2.java.net/external/javax.inject)
-        * jersey-repackaged-guava (org.glassfish.jersey.bundles.repackaged:jersey-guava:2.22.1 - https://jersey.java.net/project/project/jersey-guava/)
-        * jersey-container-servlet (org.glassfish.jersey.containers:jersey-container-servlet:2.22.1 - https://jersey.java.net/project/jersey-container-servlet/)
-        * jersey-container-servlet-core (org.glassfish.jersey.containers:jersey-container-servlet-core:2.22.1 - https://jersey.java.net/project/jersey-container-servlet-core/)
-        * jersey-core-client (org.glassfish.jersey.core:jersey-client:2.22.1 - https://jersey.java.net/jersey-client/)
-        * jersey-core-common (org.glassfish.jersey.core:jersey-common:2.22.1 - https://jersey.java.net/jersey-common/)
-        * jersey-core-server (org.glassfish.jersey.core:jersey-server:2.22.1 - https://jersey.java.net/jersey-server/)
-        * jersey-ext-entity-filtering (org.glassfish.jersey.ext:jersey-entity-filtering:2.22.1 - https://jersey.java.net/project/jersey-entity-filtering/)
-        * jersey-spring3 (org.glassfish.jersey.ext:jersey-spring3:2.22.1 - https://jersey.java.net/project/jersey-spring3/)
-        * jersey-media-jaxb (org.glassfish.jersey.media:jersey-media-jaxb:2.22.1 - https://jersey.java.net/project/jersey-media-jaxb/)
-        * jersey-media-json-jackson (org.glassfish.jersey.media:jersey-media-json-jackson:2.22.1 - https://jersey.java.net/project/jersey-media-json-jackson/)
-        * Java Transaction API (org.jboss.spec.javax.transaction:jboss-transaction-api_1.1_spec:1.0.1.Final - http://www.jboss.org/jboss-transaction-api_1.1_spec)
-        * Type arithmetic library for Java5 (org.jvnet:tiger-types:1.4 - http://java.net/tiger-types/)
-
-    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)
-        * 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)
-
-    GNU General Public License, Version 2 with the Classpath Exception:
-
-        * 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)
-
-    GNU Lesser General Public License (LGPL):
-
-        * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.1u2 - http://findbugs.sourceforge.net/)
-        * MaxMind GeoIP Legacy API (com.maxmind.geoip:geoip-api:1.3.0 - https://github.com/maxmind/geoip-api-java)
-        * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
-        * DSpace TM-Extractors Dependency (org.dspace.dependencies:dspace-tm-extractors:1.0.1 - http://projects.dspace.org/dspace-pom/dspace-tm-extractors)
-        * A Hibernate O/RM Module (org.hibernate:hibernate-core:4.2.21.Final - http://hibernate.org)
-        * A Hibernate O/RM Module (org.hibernate:hibernate-ehcache:4.2.21.Final - http://hibernate.org)
-        * Hibernate Commons Annotations (org.hibernate.common:hibernate-commons-annotations:4.0.2.Final - http://hibernate.org)
-        * im4java (org.im4java:im4java:1.4.0 - http://sourceforge.net/projects/im4java/)
-        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
-        * JBoss Logging 3 (org.jboss.logging:jboss-logging:3.1.0.GA - http://www.jboss.org)
-        * org.jdesktop - Swing Worker (org.jdesktop:swing-worker:1.1 - no url defined)
-        * xom (xom:xom:1.1 - http://www.xom.nu)
-        * XOM (xom:xom:1.2.5 - http://xom.nu)
-
-    ICU License:
-
-        * ICU4J (com.ibm.icu:icu4j:56.1 - http://icu-project.org/)
-
-    JDOM License (Apache-style 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 Provider (org.bouncycastle:bcprov-jdk15:1.46 - http://www.bouncycastle.org/java.html)
-        * Main (org.jmockit:jmockit:1.21 - http://www.jmockit.org)
-        * OpenCloud (org.mcavallo:opencloud:0.3 - http://opencloud.mcavallo.org/)
-        * Mockito (org.mockito:mockito-core:1.10.19 - http://www.mockito.org)
-        * JCL 1.1.1 implemented over SLF4J (org.slf4j:jcl-over-slf4j:1.7.14 - http://www.slf4j.org)
-        * JUL to SLF4J bridge (org.slf4j:jul-to-slf4j:1.7.14 - http://www.slf4j.org)
-        * SLF4J API Module (org.slf4j:slf4j-api:1.7.14 - http://www.slf4j.org)
-        * SLF4J LOG4J-12 Binding (org.slf4j:slf4j-log4j12:1.7.14 - http://www.slf4j.org)
-
-    Mozilla Public License:
-
-        * juniversalchardet (com.googlecode.juniversalchardet:juniversalchardet:1.0.3 - http://juniversalchardet.googlecode.com/)
-        * h2 (com.h2database:h2:1.4.187 - no url defined)
-        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
-        * Rhino (rhino:js:1.6R7 - http://www.mozilla.org/rhino/)
-
-    Public Domain:
-
-        * AOP alliance (aopalliance:aopalliance:1.0 - http://aopalliance.sourceforge.net)
-        * Dough Lea's util.concurrent package (concurrent:concurrent:1.3.4 - no url defined)
-        * Reflections (org.reflections:reflections:0.9.9-RC1 - http://code.google.com/p/reflections/reflections/)
-        * XZ for Java (org.tukaani:xz:1.4 - http://tukaani.org/xz/java.html)
-
-    Similar to Apache License but with the acknowledgment clause removed:
-
-        * JDOM (org.jdom:jdom:1.1.3 - http://www.jdom.org)
-
-    The PostgreSQL License:
-
-        * PostgreSQL JDBC Driver - JDBC 4.2 (org.postgresql:postgresql:9.4.1211 - https://github.com/pgjdbc/pgjdbc)
-
-    license.txt:
-
-        * JPA 2.0 API (org.hibernate.javax.persistence:hibernate-jpa-2.0-api:1.0.1.Final - http://hibernate.org)

LICENSE_HEADER

@@ -1,5 +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/

NOTICE

@@ -1,15 +0,0 @@
-
-Licensing Notice
-
-Fedora Commons joined with the DSpace Foundation and began operating under
-the new name DuraSpace in July 2009.  DuraSpace holds the copyrights of
-the DSpace Foundation, Inc.
-
-The DSpace Foundation, Inc. is a 501(c)3 corporation established in July 2007 
-with a mission to promote and advance the dspace platform enabling management, 
-access and preservation of digital works. The Foundation was able to transfer 
-the legal copyright from Hewlett-Packard Company (HP) and Massachusetts 
-Institute of Technology (MIT) to the  DSpace Foundation in October 2007. Many 
-of the files in the source code may contain a copyright statement stating HP 
-and MIT possess the copyright, in these instances please note that the copy 
-right has transferred to the DSpace foundation, and subsequently to DuraSpace.

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/

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

@@ -1,739 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-    <groupId>org.dspace</groupId>
-    <artifactId>dspace-api</artifactId>
-    <name>DSpace Kernel :: API and Implementation</name>
-    <description>DSpace core data model and service APIs.</description>
-
-    <!--
-       A Parent POM that Maven inherits DSpace Defaults
-       POM attributes from.
-    -->
-    <parent>
-        <groupId>org.dspace</groupId>
-        <artifactId>dspace-parent</artifactId>
-        <version>7.0-SNAPSHOT</version>
-        <relativePath>..</relativePath>
-    </parent>
-
-    <properties>
-        <!-- This is the path to the root [dspace-src] directory. -->
-        <root.basedir>${basedir}/..</root.basedir>
-    </properties>
-
-    <!--
-       Runtime and Compile Time dependencies for DSpace.
-    -->
-    <build>
-        <resources>
-            <resource>
-                <directory>src/main/resources</directory>
-                <includes>
-                    <include>maven.properties</include>
-                    <include>scm.properties</include>
-                </includes>
-                <filtering>true</filtering>
-            </resource>
-            <resource>
-                <directory>src/main/resources</directory>
-                <excludes>
-                    <exclude>maven.properties</exclude>
-                    <exclude>scm.properties</exclude>
-                </excludes>
-                <filtering>false</filtering>
-            </resource>
-        </resources>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <configuration>
-                    <debug>true</debug>
-                    <showDeprecation>true</showDeprecation>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <archive>
-                        <manifest>
-                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
-                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
-                        </manifest>
-                    </archive>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <!-- Verify OS license headers for all source code files -->
-            <plugin>
-                <groupId>com.mycila</groupId>
-                <artifactId>license-maven-plugin</artifactId>
-                <configuration>
-                    <excludes>
-                        <exclude>**/src/test/resources/**</exclude>
-                        <exclude>**/src/test/data/**</exclude>
-                        <exclude>**/.gitignore</exclude>
-                        <exclude>src/test/data/dspaceFolder/config/spiders/**</exclude>
-                        <exclude>src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java</exclude>
-                    </excludes>
-                </configuration>
-            </plugin>
-
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>build-helper-maven-plugin</artifactId>
-                <version>1.9.1</version>
-                <executions>
-                    <execution>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>maven-version</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-            <plugin>
-                <groupId>org.codehaus.mojo</groupId>
-                <artifactId>buildnumber-maven-plugin</artifactId>
-                <version>1.4</version>
-                <executions>
-                    <execution>
-                        <phase>validate</phase>
-                        <goals>
-                            <goal>create</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-        </plugins>
-    </build>
-
-
-    <profiles>
-        <profile>
-            <id>findbugs</id>
-            <activation>
-                <activeByDefault>false</activeByDefault>
-                <!-- property>
-                    <name>maven.test.skip</name>
-                    <value>false</value>
-                </property -->
-            </activation>
-            <build>
-                <plugins>
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>findbugs-maven-plugin</artifactId>
-                    </plugin>
-                </plugins>
-            </build>
-        </profile>
-
-        <!-- If Unit Testing is enabled, then setup the Unit Test Environment.
-             See also the 'skiptests' profile in Parent POM. -->
-        <profile>
-            <id>test-environment</id>
-            <activation>
-                <activeByDefault>false</activeByDefault>
-                <property>
-                    <name>maven.test.skip</name>
-                    <value>false</value>
-                </property>
-            </activation>
-            <build>
-                <plugins>
-                    <!-- Unit/Integration Testing setup: This plugin unzips the
-                         'testEnvironment.zip' file (created by dspace-parent POM), into
-                         the 'target/testing/' folder, to essentially create a test
-                         install of DSpace, against which Tests can be run. -->
-                    <plugin>
-                        <artifactId>maven-dependency-plugin</artifactId>
-                        <version>2.8</version>
-                        <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>
-                                <phase>generate-test-resources</phase>
-                                <goals>
-                                    <goal>unpack</goal>
-                                </goals>
-                            </execution>
-                            <execution>
-                                <id>setupIntegrationTestEnvironment</id>
-                                <phase>pre-integration-test</phase>
-                                <goals>
-                                    <goal>unpack</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                    </plugin>
-
-                    <!-- This plugin allows us to run a Groovy script in our Maven POM
-                         (see: http://gmaven.codehaus.org/Executing+Groovy+Code )
-                         We are generating a OS-agnostic version (agnostic.build.dir) of
-                         the ${project.build.directory} property (full path of target dir).
-                         This is needed by the FileWeaver & Surefire plugins (see below)
-                         to initialize the Unit Test environment's dspace.cfg file.
-                         Otherwise, the Unit Test Framework will not work on Windows OS.
-                         This Groovy code was mostly borrowed from:
-                         http://stackoverflow.com/questions/3872355/how-to-convert-file-separator-in-maven
-                    -->
-                    <plugin>
-                        <groupId>org.codehaus.gmaven</groupId>
-                        <artifactId>groovy-maven-plugin</artifactId>
-                        <version>2.0</version>
-                        <executions>
-                            <execution>
-                                <id>setproperty</id>
-                                <phase>generate-test-resources
-                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
-                                <goals>
-                                    <goal>execute</goal>
-                                </goals>
-                                <configuration>
-                                    <source>
-                                        project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
-                                        println("Initializing Maven property 'agnostic.build.dir' to: " + project.properties['agnostic.build.dir']);
-                                    </source>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-
-                    <!-- Run Unit Testing! This plugin just kicks off the tests (when enabled). -->
-                    <plugin>
-                        <artifactId>maven-surefire-plugin</artifactId>
-                        <configuration>
-                            <systemPropertyVariables>
-                                <!-- Specify the dspace.dir to use for test environment -->
-                                <!-- This system property is loaded by AbstractDSpaceTest to initialize the test environment -->
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
-                                <!-- Turn off any DSpace logging -->
-                                <dspace.log.init.disable>true</dspace.log.init.disable>
-                            </systemPropertyVariables>
-                        </configuration>
-                    </plugin>
-
-
-                    <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>xml-maven-plugin</artifactId>
-                        <version>1.0.1</version>
-                        <executions>
-                            <execution>
-                                <id>validate-ALL-xml-and-xsl</id>
-                                <phase>process-test-resources</phase>
-                                <goals>
-                                    <goal>validate</goal>
-                                </goals>
-                            </execution>
-                        </executions>
-                        <configuration>
-                            <validationSets>
-                                <!-- validate ALL XML and XSL config files in the testing folder -->
-                                <validationSet>
-                                    <dir>${agnostic.build.dir}/testing</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xconf</include>
-                                    </includes>
-                                </validationSet>
-                                <!-- validate ALL XML and XSL files throughout the project -->
-                                <validationSet>
-                                    <dir>${root.basedir}</dir>
-                                    <includes>
-                                        <include>**/*.xml</include>
-                                        <include>**/*.xsl</include>
-                                        <include>**/*.xmap</include>
-                                    </includes>
-                                </validationSet>
-                            </validationSets>
-                        </configuration>
-                    </plugin>
-
-
-                    <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
-                    <plugin>
-                        <artifactId>maven-failsafe-plugin</artifactId>
-                        <configuration>
-                            <systemPropertyVariables>
-                                <!-- Specify the dspace.dir to use for test environment -->
-                                <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
-                                <!-- Turn off any DSpace logging -->
-                                <dspace.log.init.disable>true</dspace.log.init.disable>
-                            </systemPropertyVariables>
-                        </configuration>
-                    </plugin>
-                </plugins>
-            </build>
-
-        </profile>
-    </profiles>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-core</artifactId>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.jboss.logging</groupId>
-                    <artifactId>jboss-logging</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>org.hibernate</groupId>
-            <artifactId>hibernate-ehcache</artifactId>
-        </dependency>
-        <dependency>
-           <groupId>org.hibernate</groupId>
-           <artifactId>hibernate-validator-cdi</artifactId>
-           <version>${hibernate-validator.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>org.springframework</groupId>
-            <artifactId>spring-orm</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>javax.el</artifactId>
-            <version>3.0.1-b10</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>handle</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>jargon</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>mets</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>dspace-tm-extractors</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.jena</groupId>
-            <artifactId>apache-jena-libs</artifactId>
-            <type>pom</type>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-core</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>commons-cli</groupId>
-            <artifactId>commons-cli</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-codec</groupId>
-            <artifactId>commons-codec</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-collections</groupId>
-            <artifactId>commons-collections</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-collections4</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-dbcp2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-fileupload</groupId>
-            <artifactId>commons-fileupload</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.commons</groupId>
-            <artifactId>commons-pool2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-validator</groupId>
-            <artifactId>commons-validator</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>mail</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
-            <scope>provided</scope>
-        </dependency>
-        <dependency>
-            <groupId>jaxen</groupId>
-            <artifactId>jaxen</artifactId>
-            <exclusions>
-                <exclusion>
-                    <artifactId>xom</artifactId>
-                    <groupId>xom</groupId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>org.jdom</groupId>
-            <artifactId>jdom</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>oro</groupId>
-            <artifactId>oro</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.pdfbox</groupId>
-            <artifactId>pdfbox</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.pdfbox</groupId>
-            <artifactId>fontbox</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcmail-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi-scratchpad</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>rome</groupId>
-            <artifactId>rome</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>rome</groupId>
-            <artifactId>opensearch</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>xalan</groupId>
-            <artifactId>xalan</artifactId>
-        </dependency>
-        <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>
-        </dependency>
-        <dependency>
-            <groupId>javax.activation</groupId>
-            <artifactId>activation</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.ibm.icu</groupId>
-            <artifactId>icu4j</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>oclc-harvester2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>dspace-services</artifactId>
-        </dependency>
-        <dependency> <!-- Keep jmockit before junit -->
-            <groupId>org.jmockit</groupId>
-            <artifactId>jmockit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>com.h2database</groupId>
-            <artifactId>h2</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.mockito</groupId>
-            <artifactId>mockito-core</artifactId>
-            <scope>test</scope>
-        </dependency>
-
-        <dependency>
-            <groupId>org.rometools</groupId>
-            <artifactId>rome-modules</artifactId>
-            <version>1.0</version>
-        </dependency>
-        <dependency>
-            <groupId>gr.ekt.bte</groupId>
-            <artifactId>bte-core</artifactId>
-            <version>0.9.3.5</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>gr.ekt.bte</groupId>
-            <artifactId>bte-io</artifactId>
-            <version>0.9.3.5</version>
-            <exclusions>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.apache.commons</groupId>
-                    <artifactId>commons-lang3</artifactId>
-                </exclusion>
-                <!-- A more recent version is retrieved from another dependency -->
-                <exclusion>
-                    <groupId>org.mockito</groupId>
-                    <artifactId>mockito-core</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpcore</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.httpcomponents</groupId>
-            <artifactId>httpclient</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr-solrj</artifactId>
-            <version>${solr.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>jcl-over-slf4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-api</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-
-        <dependency>
-            <groupId>commons-configuration</groupId>
-            <artifactId>commons-configuration</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.maxmind.geoip2</groupId>
-            <artifactId>geoip2</artifactId>
-            <version>2.11.0</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.ant</groupId>
-            <artifactId>ant</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>dnsjava</groupId>
-            <artifactId>dnsjava</artifactId>
-            <version>2.1.7</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-            <version>4.10.4</version>
-        </dependency>
-
-        <dependency>
-            <groupId>com.coverity.security</groupId>
-            <artifactId>coverity-escapers</artifactId>
-            <version>1.1.1</version>
-        </dependency>
-
-        <!--  Gson: Java to Json conversion -->
-        <dependency>
-            <groupId>com.google.code.gson</groupId>
-            <artifactId>gson</artifactId>
-            <scope>compile</scope>
-        </dependency>
-
-        <dependency>
-            <groupId>com.google.guava</groupId>
-            <artifactId>guava</artifactId>
-            <version>19.0</version>
-        </dependency>
-
-
-        <dependency>
-            <groupId>org.postgresql</groupId>
-            <artifactId>postgresql</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-api</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>jdbm</groupId>
-            <artifactId>jdbm</artifactId>
-            <version>1.0</version>
-        </dependency>
-
-        <!-- For ImageMagick MediaFilters -->
-        <dependency>
-            <groupId>org.im4java</groupId>
-            <artifactId>im4java</artifactId>
-            <version>1.4.0</version>
-        </dependency>
-
-        <!-- Flyway DB API (flywaydb.org) is used to manage DB upgrades automatically. -->
-        <dependency>
-            <groupId>org.flywaydb</groupId>
-            <artifactId>flyway-core</artifactId>
-            <version>4.0.3</version>
-        </dependency>
-
-        <!-- Google Analytics -->
-        <dependency>
-            <groupId>com.google.apis</groupId>
-            <artifactId>google-api-services-analytics</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.api-client</groupId>
-            <artifactId>google-api-client</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.http-client</groupId>
-            <artifactId>google-http-client</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.http-client</groupId>
-            <artifactId>google-http-client-jackson2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.oauth-client</groupId>
-            <artifactId>google-oauth-client</artifactId>
-        </dependency>
-        <!-- FindBugs -->
-        <dependency>
-            <groupId>com.google.code.findbugs</groupId>
-            <artifactId>jsr305</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.google.code.findbugs</groupId>
-            <artifactId>annotations</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>joda-time</groupId>
-            <artifactId>joda-time</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.inject</groupId>
-            <artifactId>javax.inject</artifactId>
-            <version>1</version>
-            <type>jar</type>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.ws.commons.axiom</groupId>
-            <artifactId>axiom-impl</artifactId>
-            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
-            <version>1.2.14</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.apache.ws.commons.axiom</groupId>
-            <artifactId>axiom-api</artifactId>
-            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
-            <version>1.2.14</version>
-        </dependency>
-        <dependency>
-            <groupId>org.glassfish.jersey.core</groupId>
-            <artifactId>jersey-client</artifactId>
-            <version>${jersey.version}</version>
-        </dependency>
-        <!-- S3 -->
-        <dependency>
-            <groupId>com.amazonaws</groupId>
-            <artifactId>aws-java-sdk-s3</artifactId>
-            <version>1.10.50</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>joda-time</groupId>
-                    <artifactId>joda-time</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <!-- S3 also wanted jackson... -->
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-core</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-databind</artifactId>
-        </dependency>
-    </dependencies>
-
-</project>

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

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

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

@@ -1,271 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import 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.service.HandleService;
-
-/**
- * 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 {
-
-    protected CommunityService communityService;
-    protected HandleService handleService;
-
-    public CommunityFiliator() {
-        communityService = ContentServiceFactory.getInstance().getCommunityService();
-        handleService = HandleServiceFactory.getInstance().getHandleService();
-    }
-
-    /**
-     * @param argv the command line arguments given
-     * @throws Exception if error
-     */
-    public static void main(String[] argv) throws Exception {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("s", "set", false, "set a parent/child relationship");
-        options.addOption("r", "remove", false,
-                          "remove a parent/child relationship");
-        options.addOption("p", "parent", true,
-                          "parent community (handle or database ID)");
-        options.addOption("c", "child", true,
-                          "child community (handle or databaseID)");
-        options.addOption("h", "help", false, "help");
-
-        CommandLine line = parser.parse(options, argv);
-
-        String command = null; // set or remove
-        String parentID = null;
-        String childID = null;
-
-        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");
-            System.out
-                .println("remove a relationship: CommunityFiliator -r -p parentID -c childID");
-
-            System.exit(0);
-        }
-
-        if (line.hasOption('s')) {
-            command = "set";
-        }
-
-        if (line.hasOption('r')) {
-            command = "remove";
-        }
-
-        if (line.hasOption('p')) { // parent
-            parentID = line.getOptionValue('p');
-        }
-
-        if (line.hasOption('c')) { // child
-            childID = line.getOptionValue('c');
-        }
-
-        // now validate
-        // must have a command set
-        if (command == null) {
-            System.out
-                .println("Error - must run with either set or remove (run with -h flag for details)");
-            System.exit(1);
-        }
-
-        if ("set".equals(command) || "remove".equals(command)) {
-            if (parentID == null) {
-                System.out.println("Error - a parentID must be specified (run with -h flag for details)");
-                System.exit(1);
-            }
-
-            if (childID == null) {
-                System.out.println("Error - a childID must be specified (run with -h flag for details)");
-                System.exit(1);
-            }
-        }
-
-        CommunityFiliator filiator = new CommunityFiliator();
-        Context c = new Context();
-
-        // we are superuser!
-        c.turnOffAuthorisationSystem();
-
-        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) {
-                System.out.println("Error, parent community cannot be found: "
-                                       + parentID);
-                System.exit(1);
-            }
-
-            if (child == null) {
-                System.out.println("Error, child community cannot be found: "
-                                       + childID);
-                System.exit(1);
-            }
-
-            if ("set".equals(command)) {
-                filiator.filiate(c, parent, child);
-            } else {
-                filiator.defiliate(c, parent, child);
-            }
-        } catch (SQLException sqlE) {
-            System.out.println("Error - SQL exception: " + sqlE.toString());
-        } catch (AuthorizeException authE) {
-            System.out.println("Error - Authorize exception: "
-                                   + authE.toString());
-        } 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 {
-        // check that a valid filiation would be established
-        // first test - proposed child must currently be an orphan (i.e.
-        // top-level)
-        Community childDad = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities()
-                                                                                             .iterator().next() : null;
-
-        if (childDad != null) {
-            System.out.println("Error, child community: " + child.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();
-
-        for (int i = 0; i < parentDads.size(); i++) {
-            if (parentDads.get(i).getID().equals(child.getID())) {
-                System.out
-                    .println("Error, circular parentage - child is parent of parent");
-                System.exit(1);
-            }
-        }
-
-        // everthing's OK
-        communityService.addSubcommunity(c, parent, child);
-
-        // complete the pending transaction
-        c.complete();
-        System.out.println("Filiation complete. Community: '" + parent.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 {
-        // verify that child is indeed a child of parent
-        List<Community> parentKids = parent.getSubcommunities();
-        boolean isChild = false;
-
-        for (int i = 0; i < parentKids.size(); i++) {
-            if (parentKids.get(i).getID().equals(child.getID())) {
-                isChild = true;
-
-                break;
-            }
-        }
-
-        if (!isChild) {
-            System.out
-                .println("Error, child community not a child of parent community");
-            System.exit(1);
-        }
-
-        // OK remove the mappings - but leave the community, which will become
-        // top-level
-        child.getParentCommunities().remove(parent);
-        parent.getSubcommunities().remove(child);
-        communityService.update(c, child);
-        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()
-                               + "'");
-    }
-
-    /**
-     * Find a community by ID
-     *
-     * @param c           context
-     * @param communityID community ID
-     * @return Community object
-     * @throws SQLException if database error
-     */
-    protected Community resolveCommunity(Context c, String communityID)
-        throws SQLException {
-        Community community = null;
-
-        if (communityID.indexOf('/') != -1) {
-            // has a / must be a handle
-            community = (Community) handleService.resolveToObject(c,
-                                                                  communityID);
-
-            // ensure it's a community
-            if ((community == null)
-                || (community.getType() != Constants.COMMUNITY)) {
-                community = null;
-            }
-        } else {
-            community = communityService.find(c, UUID.fromString(communityID));
-        }
-
-        return community;
-    }
-}

dspace-api/src/main/java/org/dspace/administer/CreateAdministrator.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.administer;
-
-import java.io.Console;
-import java.util.Arrays;
-import java.util.Locale;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.apache.commons.lang.StringUtils;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.core.I18nUtil;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.Group;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.EPersonService;
-import org.dspace.eperson.service.GroupService;
-
-/**
- * A command-line tool for creating an initial administrator for setting up a
- * DSpace site. Prompts for an e-mail address, last name, first name and
- * password from standard input. An administrator group is then created and the
- * data passed in used to create an e-person in that group.
- * <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
- * initial administrator, for example, before deployment can be completed
- *
- * @author Robert Tansley
- * @author Richard Jones
- * @version $Revision$
- */
-public final class CreateAdministrator {
-    /**
-     * DSpace Context object
-     */
-    private final Context context;
-
-    protected EPersonService ePersonService;
-    protected GroupService groupService;
-
-    /**
-     * For invoking via the command line.  If called with no command line arguments,
-     * it will negotiate with the user for the administrator details
-     *
-     * @param argv the command line arguments given
-     * @throws Exception if error
-     */
-    public static void main(String[] argv)
-        throws Exception {
-        CommandLineParser parser = new PosixParser();
-        Options options = new Options();
-
-        CreateAdministrator ca = new CreateAdministrator();
-
-        options.addOption("e", "email", true, "administrator email address");
-        options.addOption("f", "first", true, "administrator first name");
-        options.addOption("l", "last", true, "administrator last name");
-        options.addOption("c", "language", true, "administrator language");
-        options.addOption("p", "password", true, "administrator password");
-
-        CommandLine line = parser.parse(options, argv);
-
-        if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
-            line.hasOption("c") && line.hasOption("p")) {
-            ca.createAdministrator(line.getOptionValue("e"),
-                                   line.getOptionValue("f"), line.getOptionValue("l"),
-                                   line.getOptionValue("c"), line.getOptionValue("p"));
-        } else {
-            ca.negotiateAdministratorDetails();
-        }
-    }
-
-    /**
-     * constructor, which just creates and object with a ready context
-     *
-     * @throws Exception if error
-     */
-    protected CreateAdministrator()
-        throws Exception {
-        context = new Context();
-        groupService = EPersonServiceFactory.getInstance().getGroupService();
-        ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    }
-
-    /**
-     * Method which will negotiate with the user via the command line to
-     * obtain the administrator's details
-     *
-     * @throws Exception if error
-     */
-    protected void negotiateAdministratorDetails()
-        throws Exception {
-        Console console = System.console();
-
-        System.out.println("Creating an initial administrator account");
-
-        boolean dataOK = false;
-
-        String email = null;
-        String firstName = null;
-        String lastName = null;
-        char[] password1 = null;
-        char[] password2 = null;
-        String language = I18nUtil.DEFAULTLOCALE.getLanguage();
-
-        while (!dataOK) {
-            System.out.print("E-mail address: ");
-            System.out.flush();
-
-            email = console.readLine();
-            if (!StringUtils.isBlank(email)) {
-                email = email.trim();
-            } else {
-                System.out.println("Please provide an email address.");
-                continue;
-            }
-
-            System.out.print("First name: ");
-            System.out.flush();
-
-            firstName = console.readLine();
-
-            if (firstName != null) {
-                firstName = firstName.trim();
-            }
-
-            System.out.print("Last name: ");
-            System.out.flush();
-
-            lastName = console.readLine();
-
-            if (lastName != null) {
-                lastName = lastName.trim();
-            }
-
-            if (ConfigurationManager.getProperty("webui.supported.locales") != null) {
-                System.out.println("Select one of the following languages: " + ConfigurationManager
-                    .getProperty("webui.supported.locales"));
-                System.out.print("Language: ");
-                System.out.flush();
-
-                language = console.readLine();
-
-                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();
-
-            password1 = 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)) {
-                // password OK
-                System.out.print("Is the above data correct? (y or n): ");
-                System.out.flush();
-
-                String s = console.readLine();
-
-                if (s != null) {
-                    s = s.trim();
-                    if (s.toLowerCase().startsWith("y")) {
-                        dataOK = true;
-                    }
-                }
-            } 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));
-
-        //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 first    user's first name
-     * @param last     user's last name
-     * @param language preferred language
-     * @param pw       desired password
-     * @throws Exception if error
-     */
-    protected void createAdministrator(String email, String first, String last,
-                                       String language, String pw)
-        throws Exception {
-        // Of course we aren't an administrator yet so we need to
-        // circumvent authorisation
-        context.turnOffAuthorisationSystem();
-
-        // Find administrator group
-        Group admins = groupService.findByName(context, Group.ADMIN);
-
-        if (admins == null) {
-            throw new IllegalStateException("Error, no admin group (group 1) found");
-        }
-
-        // Create the administrator e-person
-        EPerson eperson = ePersonService.findByEmail(context, email);
-
-        // check if the email belongs to a registered user,
-        // if not create a new user with this email
-        if (eperson == null) {
-            eperson = ePersonService.create(context);
-            eperson.setEmail(email);
-            eperson.setCanLogIn(true);
-            eperson.setRequireCertificate(false);
-            eperson.setSelfRegistered(false);
-        }
-
-        eperson.setLastName(context, last);
-        eperson.setFirstName(context, first);
-        eperson.setLanguage(context, language);
-        ePersonService.setPassword(eperson, pw);
-        ePersonService.update(context, eperson);
-
-        groupService.addMember(context, admins, eperson);
-        groupService.update(context, admins);
-
-        context.complete();
-
-        System.out.println("Administrator account created");
-    }
-}

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

@@ -1,328 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.apache.xml.serialize.Method;
-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;
-
-
-/**
- * @author Graham Triggs
- *
- * 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>
- * <name>dc</name>
- * <namespace>http://dublincore.org/documents/dcmi-terms/</namespace>
- * </schema>
- * </metadata-schemas>
- * }
- */
-public class MetadataExporter {
-
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                        .getMetadataSchemaService();
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
-                                                                                      .getMetadataFieldService();
-
-    /**
-     * Default constructor
-     */
-    private MetadataExporter() { }
-
-    /**
-     * @param args commandline arguments
-     * @throws ParseException          if parser error
-     * @throws SAXException            if XML parse error
-     * @throws IOException             if IO error
-     * @throws SQLException            if database error
-     * @throws RegistryExportException if export error
-     */
-    public static void main(String[] args)
-        throws ParseException, SQLException, IOException, SAXException, RegistryExportException {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-        Options options = new Options();
-        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 schema = null;
-
-        if (line.hasOption('f')) {
-            file = line.getOptionValue('f');
-        } else {
-            usage();
-            System.exit(0);
-        }
-
-        if (line.hasOption('s')) {
-            schema = line.getOptionValue('s');
-        }
-
-        saveRegistry(file, schema);
-    }
-
-    /**
-     * 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();
-
-        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;
-
-        // If a single schema has been specified
-        if (schema != null && !"".equals(schema)) {
-            // Get the id of that schema
-            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
-            if (mdSchema == null) {
-                throw new RegistryExportException("no schema to export");
-            }
-
-            // Get the metadata fields only for the specified schema
-            mdFields = metadataFieldService.findAllInSchema(context, mdSchema);
-        } else {
-            // Get the metadata fields for all the schemas
-            mdFields = metadataFieldService.findAll(context);
-        }
-
-        // Output the metadata fields
-        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       DSpace Context
-     * @param xmlSerializer XML serializer
-     * @param schema        schema (may be null to save all)
-     * @throws SQLException            if database error
-     * @throws SAXException            if XML error
-     * @throws RegistryExportException if export error
-     */
-    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema)
-        throws SQLException, SAXException, RegistryExportException {
-        if (schema != null && !"".equals(schema)) {
-            // Find a single named schema
-            MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
-
-            saveSchema(xmlSerializer, mdSchema);
-        } else {
-            // Find all schemas
-            List<MetadataSchema> mdSchemas = metadataSchemaService.findAll(context);
-
-            for (MetadataSchema mdSchema : mdSchemas) {
-                saveSchema(xmlSerializer, mdSchema);
-            }
-        }
-    }
-
-    /**
-     * Serialize a single schema (namespace) registry entry
-     *
-     * @param xmlSerializer XML serializer
-     * @param mdSchema      DSpace metadata schema
-     * @throws SAXException            if XML error
-     * @throws RegistryExportException if export error
-     */
-    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema)
-        throws SAXException, RegistryExportException {
-        // If we haven't got a schema, it's an error
-        if (mdSchema == null) {
-            throw new RegistryExportException("no schema to export");
-        }
-
-        String name = mdSchema.getName();
-        String namespace = mdSchema.getNamespace();
-
-        if (name == null || "".equals(name)) {
-            System.out.println("name is null, skipping");
-            return;
-        }
-
-        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());
-        xmlSerializer.endElement("name");
-
-        // Output the schema namespace
-        xmlSerializer.startElement("namespace", null);
-        xmlSerializer.characters(namespace.toCharArray(), 0, namespace.length());
-        xmlSerializer.endElement("namespace");
-
-        xmlSerializer.endElement("dc-schema");
-    }
-
-    /**
-     * Serialize a single metadata field registry entry to xml
-     *
-     * @param context       DSpace context
-     * @param xmlSerializer xml serializer
-     * @param mdField       DSpace metadata field
-     * @throws SAXException            if XML error
-     * @throws RegistryExportException if export error
-     * @throws SQLException            if database error
-     * @throws IOException             if IO error
-     */
-    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField)
-        throws SAXException, RegistryExportException, SQLException, IOException {
-        // If we haven't been given a field, it's an error
-        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();
-        String qualifier = mdField.getQualifier();
-        String scopeNote = mdField.getScopeNote();
-
-        // We must have a schema and element
-        if (schemaName == null || element == null) {
-            throw new RegistryExportException("incomplete field information");
-        }
-
-        // Output the parent tag
-        xmlSerializer.startElement("dc-type", null);
-
-        // Output the schema name
-        xmlSerializer.startElement("schema", null);
-        xmlSerializer.characters(schemaName.toCharArray(), 0, schemaName.length());
-        xmlSerializer.endElement("schema");
-
-        // Output the element
-        xmlSerializer.startElement("element", null);
-        xmlSerializer.characters(element.toCharArray(), 0, element.length());
-        xmlSerializer.endElement("element");
-
-        // Output the qualifier, if present
-        if (qualifier != null) {
-            xmlSerializer.startElement("qualifier", null);
-            xmlSerializer.characters(qualifier.toCharArray(), 0, qualifier.length());
-            xmlSerializer.endElement("qualifier");
-        } else {
-            xmlSerializer.comment("unqualified");
-        }
-
-        // Output the scope note, if present
-        if (scopeNote != null) {
-            xmlSerializer.startElement("scope_note", null);
-            xmlSerializer.characters(scopeNote.toCharArray(), 0, scopeNote.length());
-            xmlSerializer.endElement("scope_note");
-        } 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)
-        throws SQLException, RegistryExportException {
-        // Get name from cache
-        String name = schemaMap.get(mdField.getMetadataSchema().getID());
-
-        if (name == null) {
-            // Name not retrieved before, so get the schema now
-            MetadataSchema mdSchema = metadataSchemaService.find(context, mdField.getMetadataSchema().getID());
-            if (mdSchema != null) {
-                name = mdSchema.getName();
-                schemaMap.put(mdSchema.getID(), name);
-            } 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() {
-        String usage = "Use this class with the following options:\n" +
-            " -f <xml output file> : specify the output file for the schemas\n" +
-            " -s <schema> : name of the schema to export\n";
-        System.out.println(usage);
-    }
-}

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

@@ -1,287 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.TransformerException;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.apache.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
- * they do not already exist
- *
- * The format of the XML file is as follows:
- *
- * {@code
- * <dspace-dc-types>
- * <dc-type>
- * <schema>icadmin</schema>
- * <element>status</element>
- * <qualifier>dateset</qualifier>
- * <scope_note>the workflow status of an item</scope_note>
- * </dc-type>
- *
- * [....]
- *
- * </dspace-dc-types>
- * }
- */
-public class MetadataImporter {
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                        .getMetadataSchemaService();
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
-                                                                                      .getMetadataFieldService();
-
-    /**
-     * logging category
-     */
-    private static final Logger log = LoggerFactory.getLogger(MetadataImporter.class);
-
-    /**
-     * Default constructor
-     */
-    private MetadataImporter() { }
-
-    /**
-     * main method for reading user input from the command line
-     *
-     * @param args the command line arguments given
-     * @throws ParseException               if parse error
-     * @throws SQLException                 if database error
-     * @throws IOException                  if IO error
-     * @throws TransformerException         if transformer error
-     * @throws ParserConfigurationException if config error
-     * @throws AuthorizeException           if authorization error
-     * @throws SAXException                 if parser error
-     * @throws NonUniqueMetadataException   if duplicate metadata
-     * @throws RegistryImportException      if import fails
-     **/
-    public static void main(String[] args)
-        throws ParseException, SQLException, IOException, TransformerException,
-        ParserConfigurationException, AuthorizeException, SAXException,
-        NonUniqueMetadataException, RegistryImportException {
-        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')) {
-            file = line.getOptionValue('f');
-        } else {
-            usage();
-            System.exit(0);
-        }
-
-        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 forceUpdate whether to force update
-     * @throws SQLException                 if database error
-     * @throws IOException                  if IO error
-     * @throws TransformerException         if transformer error
-     * @throws ParserConfigurationException if config error
-     * @throws AuthorizeException           if authorization error
-     * @throws SAXException                 if parser error
-     * @throws NonUniqueMetadataException   if duplicate metadata
-     * @throws RegistryImportException      if import fails
-     */
-    public static void loadRegistry(String file, boolean forceUpdate)
-        throws SQLException, IOException, TransformerException, ParserConfigurationException,
-        AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException {
-        Context context = null;
-
-        try {
-            // create a context
-            context = new Context();
-            context.turnOffAuthorisationSystem();
-
-            // read the XML
-            Document document = RegistryImporter.loadXML(file);
-
-            // Get the nodes corresponding to types
-            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++) {
-                Node n = schemaNodes.item(i);
-                loadSchema(context, n, forceUpdate);
-            }
-
-            // Get the nodes corresponding to types
-            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++) {
-                Node n = typeNodes.item(i);
-                loadType(context, n);
-            }
-
-            context.restoreAuthSystemState();
-            context.complete();
-        } finally {
-            // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
-    /**
-     * Process a node in the metadata registry XML file.  If the
-     * schema already exists, it will not be recreated
-     *
-     * @param context DSpace context object
-     * @param node    the node in the DOM tree
-     * @throws SQLException               if database error
-     * @throws IOException                if IO error
-     * @throws TransformerException       if transformer error
-     * @throws AuthorizeException         if authorization error
-     * @throws NonUniqueMetadataException if duplicate metadata
-     * @throws RegistryImportException    if import fails
-     */
-    private static void loadSchema(Context context, Node node, boolean updateExisting)
-        throws SQLException, IOException, TransformerException,
-        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
-        // Get the values
-        String name = RegistryImporter.getElementData(node, "name");
-        String namespace = RegistryImporter.getElementData(node, "namespace");
-
-        if (name == null || "".equals(name)) {
-            throw new RegistryImportException("Name of schema must be supplied");
-        }
-
-        if (namespace == null || "".equals(namespace)) {
-            throw new RegistryImportException("Namespace of schema must be supplied");
-        }
-
-        // check to see if the schema already exists
-        MetadataSchema s = metadataSchemaService.find(context, name);
-
-        if (s == null) {
-            // Schema does not exist - create
-            log.info("Registering Schema " + name + " (" + namespace + ")");
-            metadataSchemaService.create(context, name, namespace);
-        } else {
-            // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace)) {
-                // This schema already exists with this namespace, skipping it
-                return;
-            }
-
-            // It's a different namespace - have we been told to update?
-            if (updateExisting) {
-                // Update the existing schema namespace and continue to type import
-                log.info("Updating Schema " + name + ": New namespace " + namespace);
-                s.setNamespace(namespace);
-                metadataSchemaService.update(context, s);
-            } else {
-                throw new RegistryImportException(
-                    "Schema " + name + " already registered with different namespace " + namespace + ". Rerun with " +
-                        "'update' option enabled if you wish to update this schema.");
-            }
-        }
-
-    }
-
-    /**
-     * 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 node    the node in the DOM tree
-     * @throws SQLException               if database error
-     * @throws IOException                if IO error
-     * @throws TransformerException       if transformer error
-     * @throws AuthorizeException         if authorization error
-     * @throws NonUniqueMetadataException if duplicate metadata
-     * @throws RegistryImportException    if import fails
-     */
-    private static void loadType(Context context, Node node)
-        throws SQLException, IOException, TransformerException,
-        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
-        // Get the values
-        String schema = RegistryImporter.getElementData(node, "schema");
-        String element = RegistryImporter.getElementData(node, "element");
-        String qualifier = RegistryImporter.getElementData(node, "qualifier");
-        String scopeNote = RegistryImporter.getElementData(node, "scope_note");
-
-        // If the schema is not provided default to DC
-        if (schema == null) {
-            schema = MetadataSchema.DC_SCHEMA;
-        }
-
-
-        // Find the matching schema object
-        MetadataSchema schemaObj = metadataSchemaService.find(context, schema);
-
-        if (schemaObj == null) {
-            throw new RegistryImportException("Schema '" + schema + "' is not registered and does not exist.");
-        }
-
-        MetadataField mf = metadataFieldService.findByElement(context, schemaObj, element, qualifier);
-        if (mf != null) {
-            // 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) {
-            fieldName = schema + "." + element;
-        }
-        log.info("Registering metadata field " + fieldName);
-        MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
-        metadataFieldService.update(context, field);
-    }
-
-    /**
-     * Print the usage message to stdout
-     */
-    public static void usage() {
-        String usage = "Use this class with the following option:\n" +
-            " -f <xml source file> : specify which xml source file " +
-            "contains the DC fields to import.\n";
-        System.out.println(usage);
-    }
-}

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

@@ -1,51 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-/**
- * @author Graham Triggs
- *
- * An exception to report any problems with registry exports
- */
-public class RegistryExportException extends Exception {
-    /**
-     * Create an empty authorize exception
-     */
-    public RegistryExportException() {
-        super();
-    }
-
-    /**
-     * create an exception with only a message
-     *
-     * @param message exception message
-     */
-    public RegistryExportException(String message) {
-        super(message);
-    }
-
-    /**
-     * create an exception with an inner exception and a message
-     *
-     * @param message exception message
-     * @param e       reference to Throwable
-     */
-    public RegistryExportException(String message, Throwable e) {
-        super(message, e);
-    }
-
-    /**
-     * create an exception with an inner exception
-     *
-     * @param e reference to Throwable
-     */
-    public RegistryExportException(Throwable e) {
-        super(e);
-    }
-
-}

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

@@ -1,51 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-/**
- * @author Richard Jones
- *
- * An exception to report any problems with registry imports
- */
-public class RegistryImportException extends Exception {
-    /**
-     * Create an empty authorize exception
-     */
-    public RegistryImportException() {
-        super();
-    }
-
-    /**
-     * create an exception with only a message
-     *
-     * @param message error message
-     */
-    public RegistryImportException(String message) {
-        super(message);
-    }
-
-    /**
-     * create an exception with an inner exception and a message
-     *
-     * @param message error message
-     * @param e       throwable
-     */
-    public RegistryImportException(String message, Throwable e) {
-        super(message, e);
-    }
-
-    /**
-     * create an exception with an inner exception
-     *
-     * @param e throwable
-     */
-    public RegistryImportException(Throwable e) {
-        super(e);
-    }
-
-}

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

@@ -1,134 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.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;
-
-/**
- * @author Richard Jones
- *
- * This class provides the tools that registry importers might need to
- * use.  Basically some utility methods.  And actually, although it says
- * I am the author, really I ripped these methods off from other
- * classes
- */
-public class RegistryImporter {
-
-    /**
-     * Default constructor
-     */
-    private RegistryImporter() { }
-
-    /**
-     * Load in the XML from file.
-     *
-     * @param filename the filename to load from
-     * @return the DOM representation of the XML file
-     * @throws IOException                  if IO error
-     * @throws ParserConfigurationException if configuration parse error
-     * @throws SAXException                 if XML parse error
-     */
-    public static Document loadXML(String filename)
-        throws IOException, ParserConfigurationException, SAXException {
-        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                                                        .newDocumentBuilder();
-
-        Document document = builder.parse(new File(filename));
-
-        return document;
-    }
-
-    /**
-     * Get the CDATA of a particular element. For example, if the XML document
-     * contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;&lt;mimetype&gt;application/pdf&lt;/mimetype&gt;&lt;/foo&gt;
-     * </code>
-     * passing this the <code>foo</code> node and <code>mimetype</code> will
-     * 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 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 {
-        // Grab the child node
-        Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
-
-        if (childNode == null) {
-            // No child node, so no values
-            return null;
-        }
-
-        // Get the #text
-        Node dataNode = childNode.getFirstChild();
-
-        if (dataNode == null) {
-            return null;
-        }
-
-        // Get the data
-        String value = dataNode.getNodeValue().trim();
-
-        return value;
-    }
-
-    /**
-     * Get repeated CDATA for a particular element. For example, if the XML
-     * document contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;
-     * &lt;bar&gt;val1&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 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 {
-        // Grab the child node
-        NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
-
-        String[] data = new String[childNodes.getLength()];
-
-        for (int i = 0; i < childNodes.getLength(); i++) {
-            // Get the #text node
-            Node dataNode = childNodes.item(i).getFirstChild();
-
-            // Get the data
-            data[i] = dataNode.getNodeValue().trim();
-        }
-
-        return data;
-    }
-}

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

@@ -1,293 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.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;
-import javax.xml.transform.TransformerException;
-
-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.service.BitstreamFormatService;
-import org.dspace.core.Context;
-import org.dspace.core.LogManager;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-/**
- * Loads the bitstream format and Dublin Core type registries into the database.
- * Intended for use as a command-line tool.
- * <P>
- * Example usage:
- * <P>
- * <code>RegistryLoader -bitstream bitstream-formats.xml</code>
- * <P>
- * <code>RegistryLoader -dc dc-types.xml</code>
- *
- * @author Robert Tansley
- * @version $Revision$
- */
-public class RegistryLoader {
-    /**
-     * log4j category
-     */
-    private static Logger log = Logger.getLogger(RegistryLoader.class);
-
-    protected static BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
-                                                                                          .getBitstreamFormatService();
-
-    /**
-     * Default constructor
-     */
-    private RegistryLoader() { }
-
-    /**
-     * For invoking via the command line
-     *
-     * @param argv the command line arguments given
-     * @throws Exception if error
-     */
-    public static void main(String[] argv) throws Exception {
-        String usage = "Usage: " + RegistryLoader.class.getName()
-            + " (-bitstream | -metadata) registry-file.xml";
-
-        Context context = null;
-
-        try {
-            context = new Context();
-
-            // Can't update registries anonymously, so we need to turn off
-            // authorisation
-            context.turnOffAuthorisationSystem();
-
-            // Work out what we're loading
-            if (argv[0].equalsIgnoreCase("-bitstream")) {
-                RegistryLoader.loadBitstreamFormats(context, argv[1]);
-            } else if (argv[0].equalsIgnoreCase("-metadata")) {
-                // Call MetadataImporter, as it handles Metadata schema updates
-                MetadataImporter.loadRegistry(argv[1], true);
-            } else {
-                System.err.println(usage);
-            }
-
-            // Commit changes and close Context
-            context.complete();
-
-            System.exit(0);
-        } catch (ArrayIndexOutOfBoundsException ae) {
-            System.err.println(usage);
-
-            System.exit(1);
-        } catch (Exception e) {
-            log.fatal(LogManager.getHeader(context, "error_loading_registries",
-                                           ""), e);
-
-            System.err.println("Error: \n - " + e.getMessage());
-            System.exit(1);
-        } finally {
-            // Clean up our context, if it still exists & it was never completed
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-        }
-    }
-
-    /**
-     * Load Bitstream Format metadata
-     *
-     * @param context  DSpace context object
-     * @param filename the filename of the XML file to load
-     * @throws SQLException                 if database error
-     * @throws IOException                  if IO error
-     * @throws TransformerException         if transformer error
-     * @throws ParserConfigurationException if config error
-     * @throws AuthorizeException           if authorization error
-     * @throws SAXException                 if parser error
-     */
-    public static void loadBitstreamFormats(Context context, String filename)
-        throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
-        Document document = loadXML(filename);
-
-        // Get the nodes corresponding to formats
-        NodeList typeNodes = XPathAPI.selectNodeList(document,
-                                                     "dspace-bitstream-types/bitstream-type");
-
-        // Add each one as a new format to the registry
-        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()));
-    }
-
-    /**
-     * Process a node in the bitstream format registry XML file. The node must
-     * be a "bitstream-type" node
-     *
-     * @param context DSpace context object
-     * @param node    the node in the DOM tree
-     * @throws SQLException         if database error
-     * @throws IOException          if IO error
-     * @throws TransformerException if transformer error
-     * @throws AuthorizeException   if authorization error
-     */
-    private static void loadFormat(Context context, Node node)
-        throws SQLException, IOException, TransformerException,
-        AuthorizeException {
-        // Get the values
-        String mimeType = getElementData(node, "mimetype");
-        String shortDesc = getElementData(node, "short_description");
-        String desc = getElementData(node, "description");
-
-        String supportLevelString = getElementData(node, "support_level");
-        int supportLevel = Integer.parseInt(supportLevelString);
-
-        String internalString = getElementData(node, "internal");
-        boolean internal = Boolean.valueOf(internalString).booleanValue();
-
-        String[] extensions = getRepeatedElementData(node, "extension");
-
-        // Check if this format already exists in our registry (by mime type)
-        BitstreamFormat exists = bitstreamFormatService.findByMIMEType(context, mimeType);
-
-        // If not found by mimeType, check by short description (since this must also be unique)
-        if (exists == null) {
-            exists = bitstreamFormatService.findByShortDescription(context, shortDesc);
-        }
-
-        // If it doesn't exist, create it..otherwise skip it.
-        if (exists == null) {
-            // Create the format object
-            BitstreamFormat format = bitstreamFormatService.create(context);
-
-            // Fill it out with the values
-            format.setMIMEType(mimeType);
-            bitstreamFormatService.setShortDescription(context, format, shortDesc);
-            format.setDescription(desc);
-            format.setSupportLevel(supportLevel);
-            format.setInternal(internal);
-            ArrayList<String> extensionList = new ArrayList<>();
-            extensionList.addAll(Arrays.asList(extensions));
-            format.setExtensions(extensionList);
-
-            // Write to database
-            bitstreamFormatService.update(context, format);
-        }
-    }
-
-    // ===================== XML Utility Methods =========================
-
-    /**
-     * Load in the XML from file.
-     *
-     * @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 {
-        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                                                        .newDocumentBuilder();
-
-        return builder.parse(new File(filename));
-    }
-
-    /**
-     * Get the CDATA of a particular element. For example, if the XML document
-     * contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;&lt;mimetype&gt;application/pdf&lt;/mimetype&gt;&lt;/foo&gt;
-     * </code>
-     * passing this the <code>foo</code> node and <code>mimetype</code> will
-     * 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 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 {
-        // Grab the child node
-        Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
-
-        if (childNode == null) {
-            // No child node, so no values
-            return null;
-        }
-
-        // Get the #text
-        Node dataNode = childNode.getFirstChild();
-
-        if (dataNode == null) {
-            return null;
-        }
-
-        // Get the data
-        String value = dataNode.getNodeValue().trim();
-
-        return value;
-    }
-
-    /**
-     * Get repeated CDATA for a particular element. For example, if the XML
-     * document contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;
-     * &lt;bar&gt;val1&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 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 {
-        // Grab the child node
-        NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
-
-        String[] data = new String[childNodes.getLength()];
-
-        for (int i = 0; i < childNodes.getLength(); i++) {
-            // Get the #text node
-            Node dataNode = childNodes.item(i).getFirstChild();
-
-            // Get the data
-            data[i] = dataNode.getNodeValue().trim();
-        }
-
-        return data;
-    }
-}

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

@@ -1,542 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-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;
-import javax.xml.transform.TransformerException;
-
-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.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.service.EPersonService;
-import org.jdom.Element;
-import org.jdom.output.XMLOutputter;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-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>
- * <name>....</name>
- * <community>...</community>
- * <collection>
- * <name>....</name>
- * </collection>
- * </community>
- * </import_structure>
- * }
- * it can be arbitrarily deep, and supports all the metadata elements
- * that make up the community and collection metadata.  See the system
- * documentation for more details
- *
- * @author Richard Jones
- */
-
-public class StructBuilder {
-    /**
-     * the output xml document which will contain updated information about the
-     * 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
-     */
-    private static Map<String, String> collectionMap = new HashMap<String, String>();
-
-    /**
-     * 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]}
-     *
-     * The output file will contain exactly the same as the source xml document, but
-     * with the handle for each imported item added as an attribute.
-     *
-     * @param argv the command line arguments given
-     * @throws Exception if an error occurs
-     */
-    public static void main(String[] argv)
-        throws Exception {
-        CommandLineParser parser = new PosixParser();
-
-        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);
-        }
-
-        // create a context
-        Context context = new Context();
-
-        // set the context
-        context.setCurrentUser(ePersonService.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");
-        collectionMap.put("copyright", "copyright_text");
-        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++) {
-            root.addContent(elements[i]);
-        }
-
-        // finally write the string into the output file
-        try {
-            BufferedWriter out = new BufferedWriter(new FileWriter(output));
-            out.write(new XMLOutputter().outputString(xmlOutput));
-            out.close();
-        } catch (IOException e) {
-            System.out.println("Unable to write to output file " + output);
-            System.exit(0);
-        }
-
-        context.complete();
-    }
-
-    /**
-     * Output the usage information
-     */
-    private static void usage() {
-        System.out.println("Usage: java StructBuilder -f <source XML file> -o <output file> -e <eperson email>");
-        System.out.println(
-            "Communities will be created from the top level, and a map of communities to handles will be returned in " +
-                "the output file");
-        return;
-    }
-
-    /**
-     * 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
-     * @throws TransformerException if transformer error
-     */
-    private static void validate(org.w3c.dom.Document document)
-        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) {
-            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) {
-            err.append(errs);
-            trip = true;
-        }
-
-        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
-     *                    of error reporting
-     * @return the errors that need to be generated by the calling method, or null if
-     * no errors.
-     */
-    private static String validateCommunities(NodeList communities, int level)
-        throws TransformerException {
-        StringBuffer err = new StringBuffer();
-        boolean trip = false;
-        String errs = null;
-
-        for (int i = 0; i < communities.getLength(); i++) {
-            Node n = communities.item(i);
-            NodeList name = XPathAPI.selectNodeList(n, "name");
-            if (name.getLength() != 1) {
-                String pos = Integer.toString(i + 1);
-                err.append("-The level " + level + " community in position " + pos);
-                err.append(" does not contain exactly one name field\n");
-                trip = true;
-            }
-
-            // validate sub communities
-            NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
-            String comErrs = validateCommunities(subCommunities, level + 1);
-            if (comErrs != null) {
-                err.append(comErrs);
-                trip = true;
-            }
-
-            // validate collections
-            NodeList collections = XPathAPI.selectNodeList(n, "collection");
-            String colErrs = validateCollections(collections, level + 1);
-            if (colErrs != null) {
-                err.append(colErrs);
-                trip = true;
-            }
-        }
-
-        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
-     * @return the errors to be generated by the calling method, or null if none
-     */
-    private static String validateCollections(NodeList collections, int level)
-        throws TransformerException {
-        StringBuffer err = new StringBuffer();
-        boolean trip = false;
-        String errs = null;
-
-        for (int i = 0; i < collections.getLength(); i++) {
-            Node n = collections.item(i);
-            NodeList name = XPathAPI.selectNodeList(n, "name");
-            if (name.getLength() != 1) {
-                String pos = Integer.toString(i + 1);
-                err.append("-The level " + level + " collection in position " + pos);
-                err.append(" does not contain exactly one name field\n");
-                trip = true;
-            }
-        }
-
-        if (trip) {
-            errs = err.toString();
-        }
-
-        return errs;
-    }
-
-    /**
-     * Load in the XML from file.
-     *
-     * @param filename the filename to load from
-     * @return the DOM representation of the XML file
-     */
-    private static org.w3c.dom.Document loadXML(String filename)
-        throws IOException, ParserConfigurationException, SAXException {
-        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                                                        .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) {
-        String value = node.getNodeValue();
-
-        if (node.hasChildNodes()) {
-            Node first = node.getFirstChild();
-
-            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 communities a nodelist of communities to create along with their sub-structures
-     * @param parent      the parent community of the nodelist of communities to create
-     * @return an element array containing additional information regarding the
-     * created communities (e.g. the handles they have been assigned)
-     */
-    private static Element[] handleCommunities(Context context, NodeList communities, Community parent)
-        throws TransformerException, SQLException, Exception {
-        Element[] elements = new Element[communities.getLength()];
-
-        for (int i = 0; i < communities.getLength(); i++) {
-            Community community;
-            Element element = new Element("community");
-
-            // create the community or sub community
-            if (parent != null) {
-                community = communityService.create(parent, context);
-            } else {
-                community = communityService.create(null, context);
-            }
-
-            // default the short description to be an empty string
-            communityService.setMetadata(context, community, "short_description", " ");
-
-            // now update the metadata
-            Node tn = communities.item(i);
-            for (Map.Entry<String, String> entry : communityMap.entrySet()) {
-                NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1) {
-                    communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
-                }
-            }
-
-            // FIXME: at the moment, if the community already exists by name
-            // then this will throw a PSQLException on a duplicate key
-            // violation
-            // Ideally we'd skip this row and continue to create sub
-            // communities
-            // and so forth where they don't exist, but it's proving
-            // difficult
-            // to isolate the community that already exists without hitting
-            // the database directly.
-            communityService.update(context, community);
-
-            // build the element with the handle that identifies the new
-            // community
-            // along with all the information that we imported here
-            // This looks like a lot of repetition of getting information
-            // from above
-            // but it's here to keep it separate from the create process in
-            // 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"));
-            element.addContent(nameElement);
-
-            if (communityService.getMetadata(community, "short_description") != null) {
-                Element descriptionElement = new Element("description");
-                descriptionElement.setText(communityService.getMetadata(community, "short_description"));
-                element.addContent(descriptionElement);
-            }
-
-            if (communityService.getMetadata(community, "introductory_text") != null) {
-                Element introElement = new Element("intro");
-                introElement.setText(communityService.getMetadata(community, "introductory_text"));
-                element.addContent(introElement);
-            }
-
-            if (communityService.getMetadata(community, "copyright_text") != null) {
-                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
-                element.addContent(copyrightElement);
-            }
-
-            if (communityService.getMetadata(community, "side_bar_text") != null) {
-                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(communityService.getMetadata(community, "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++) {
-                element.addContent(subCommunityElements[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
-     *
-     * @param context     the context of the request
-     * @param collections the node list of collections to be created
-     * @param parent      the parent community to whom the collections belong
-     * @return an Element array containing additional information about the
-     * created collections (e.g. the handle)
-     */
-    private static Element[] handleCollections(Context context, NodeList collections, Community parent)
-        throws TransformerException, SQLException, AuthorizeException, IOException, Exception {
-        Element[] elements = new Element[collections.getLength()];
-
-        for (int i = 0; i < collections.getLength(); i++) {
-            Element element = new Element("collection");
-            Collection collection = collectionService.create(context, parent);
-
-            // default the short description to the empty string
-            collectionService.setMetadata(context, collection, "short_description", " ");
-
-            // import the rest of the metadata
-            Node tn = collections.item(i);
-            for (Map.Entry<String, String> entry : collectionMap.entrySet()) {
-                NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1) {
-                    collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
-                }
-            }
-
-            collectionService.update(context, collection);
-
-            element.setAttribute("identifier", collection.getHandle());
-
-            Element nameElement = new Element("name");
-            nameElement.setText(collectionService.getMetadata(collection, "name"));
-            element.addContent(nameElement);
-
-            if (collectionService.getMetadata(collection, "short_description") != null) {
-                Element descriptionElement = new Element("description");
-                descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
-                element.addContent(descriptionElement);
-            }
-
-            if (collectionService.getMetadata(collection, "introductory_text") != null) {
-                Element introElement = new Element("intro");
-                introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
-                element.addContent(introElement);
-            }
-
-            if (collectionService.getMetadata(collection, "copyright_text") != null) {
-                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
-                element.addContent(copyrightElement);
-            }
-
-            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
-                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
-                element.addContent(sidebarElement);
-            }
-
-            if (collectionService.getMetadata(collection, "license") != null) {
-                Element sidebarElement = new Element("license");
-                sidebarElement.setText(collectionService.getMetadata(collection, "license"));
-                element.addContent(sidebarElement);
-            }
-
-            if (collectionService.getMetadata(collection, "provenance_description") != null) {
-                Element sidebarElement = new Element("provenance");
-                sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
-                element.addContent(sidebarElement);
-            }
-
-            elements[i] = element;
-        }
-
-        return elements;
-    }
-
-}

dspace-api/src/main/java/org/dspace/administer/package.html

@@ -1,23 +0,0 @@
-<!--
-
-    The contents of this file are subject to the license and copyright
-    detailed in the LICENSE and NOTICE files at the root of the source
-    tree and available online at
-
-    http://www.dspace.org/license/
-
--->
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head>
-<!--
-  Author:   Robert Tansley
-  Version:  $Revision$
-  Date:     $Date$
--->
-</head>
-<body bgcolor="white">
-Provides classes and methods for administrative functions that fall outside
-the regular use of other subsystems.
-</body>
-</html>

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

@@ -1,405 +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;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-
-/**
- * Utility class to store changes to item that may occur during a batch edit.
- *
- * @author Stuart Lewis
- */
-public class BulkEditChange {
-    /**
-     * The item these changes relate to
-     */
-    private Item item;
-
-    /**
-     * The List of hashtables with the new elements
-     */
-    private List<BulkEditMetadataValue> adds;
-
-    /**
-     * The List of hashtables with the removed elements
-     */
-    private List<BulkEditMetadataValue> removes;
-
-    /**
-     * The List of hashtables with the unchanged elements
-     */
-    private List<BulkEditMetadataValue> constant;
-
-    /**
-     * The List of the complete set of new values (constant + adds)
-     */
-    private List<BulkEditMetadataValue> complete;
-
-    /**
-     * 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
-     */
-    private List<Collection> newMappedCollections;
-
-    /**
-     * The old owning collection
-     */
-    private Collection oldOwningCollection;
-
-    /**
-     * The new owning collection
-     */
-    private Collection newOwningCollection;
-
-    /**
-     * Is this a new item
-     */
-    private boolean newItem;
-
-    /**
-     * Has this item been deleted?
-     */
-    private boolean deleted;
-
-    /**
-     * Has this item been withdrawn?
-     */
-    private boolean withdrawn;
-
-    /**
-     * Has this item been reinstated?
-     */
-    private boolean reinstated;
-
-    /**
-     * Have any changes actually been made?
-     */
-    private boolean empty;
-
-
-    /**
-     * Initialise a change holder for a new item
-     */
-    public BulkEditChange() {
-        // Set the item to be null
-        item = null;
-        newItem = true;
-        empty = true;
-        oldOwningCollection = null;
-        newOwningCollection = null;
-
-        // Initialise the arrays
-        adds = new ArrayList<>();
-        removes = new ArrayList<>();
-        constant = new ArrayList<>();
-        complete = new ArrayList<>();
-        oldMappedCollections = new ArrayList<>();
-        newMappedCollections = new ArrayList<>();
-    }
-
-    /**
-     * Initialise a new change holder for an existing item
-     *
-     * @param i The Item to store
-     */
-    public BulkEditChange(Item i) {
-        // Store the item
-        item = i;
-        newItem = false;
-        empty = true;
-
-        // Initialise the arrays
-        adds = new ArrayList<>();
-        removes = new ArrayList<>();
-        constant = new ArrayList<>();
-        complete = new ArrayList<>();
-        oldMappedCollections = new ArrayList<>();
-        newMappedCollections = new ArrayList<>();
-    }
-
-    /**
-     * Store the item - used when a new item is created
-     *
-     * @param i The item
-     */
-    public void setItem(Item i) {
-        // Store the item
-        item = i;
-    }
-
-    /**
-     * Add an added metadata value
-     *
-     * @param dcv The value to add
-     */
-    public void registerAdd(BulkEditMetadataValue dcv) {
-        // Add the added value
-        adds.add(dcv);
-        complete.add(dcv);
-        empty = false;
-    }
-
-    /**
-     * Add a removed metadata value
-     *
-     * @param dcv The value to remove
-     */
-    public void registerRemove(BulkEditMetadataValue dcv) {
-        // Add the removed value
-        removes.add(dcv);
-        empty = false;
-    }
-
-    /**
-     * Add an unchanged metadata value
-     *
-     * @param dcv The value to keep unchanged
-     */
-    public void registerConstant(BulkEditMetadataValue dcv) {
-        // Add the removed value
-        constant.add(dcv);
-        complete.add(dcv);
-    }
-
-    /**
-     * Add a new mapped Collection
-     *
-     * @param c The new mapped Collection
-     */
-    public void registerNewMappedCollection(Collection c) {
-        // Add the new owning Collection
-        newMappedCollections.add(c);
-        empty = false;
-    }
-
-    /**
-     * Add an old mapped Collection
-     *
-     * @param c The old mapped Collection
-     */
-    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()))) {
-            found = true;
-        }
-
-        for (Collection collection : oldMappedCollections) {
-            if (collection.getHandle().equals(c.getHandle())) {
-                found = true;
-            }
-        }
-
-        if (!found) {
-            oldMappedCollections.add(c);
-            empty = false;
-        }
-    }
-
-    /**
-     * Register a change to the owning collection
-     *
-     * @param oldC The old owning collection
-     * @param newC The new owning collection
-     */
-    public void changeOwningCollection(Collection oldC, Collection newC) {
-        // Store the old owning collection
-        oldOwningCollection = oldC;
-
-        // Store the new owning collection
-        newOwningCollection = newC;
-        empty = false;
-    }
-
-    /**
-     * Set the owning collection of an item
-     *
-     * @param newC The new owning collection
-     */
-    public void setOwningCollection(Collection newC) {
-        // Store the new owning collection
-        newOwningCollection = newC;
-        //empty = false;
-    }
-
-    /**
-     * Get the DSpace Item that these changes are applicable to.
-     *
-     * @return The item
-     */
-    public Item getItem() {
-        // Return the item
-        return item;
-    }
-
-    /**
-     * Get the list of elements and their values that have been added.
-     *
-     * @return the list of elements and their values that have been added.
-     */
-    public List<BulkEditMetadataValue> getAdds() {
-        // Return the array
-        return adds;
-    }
-
-    /**
-     * Get the list of elements and their values that have been removed.
-     *
-     * @return the list of elements and their values that have been removed.
-     */
-    public List<BulkEditMetadataValue> getRemoves() {
-        // Return the array
-        return removes;
-    }
-
-    /**
-     * Get the list of unchanged values
-     *
-     * @return the list of unchanged values
-     */
-    public List<BulkEditMetadataValue> getConstant() {
-        // Return the array
-        return constant;
-    }
-
-    /**
-     * Get the list of all values
-     *
-     * @return the list of all values
-     */
-    public List<BulkEditMetadataValue> getComplete() {
-        // Return the array
-        return complete;
-    }
-
-    /**
-     * Get the list of new mapped Collections
-     *
-     * @return the list of new mapped collections
-     */
-    public List<Collection> getNewMappedCollections() {
-        // Return the array
-        return newMappedCollections;
-    }
-
-    /**
-     * Get the list of old mapped Collections
-     *
-     * @return the list of old mapped collections
-     */
-    public List<Collection> getOldMappedCollections() {
-        // Return the array
-        return oldMappedCollections;
-    }
-
-    /**
-     * Get the old owning collection
-     *
-     * @return the old owning collection
-     */
-    public Collection getOldOwningCollection() {
-        // Return the old owning collection
-        return oldOwningCollection;
-    }
-
-    /**
-     * Get the new owning collection
-     *
-     * @return the new owning collection
-     */
-    public Collection getNewOwningCollection() {
-        // Return the new owning collection
-        return newOwningCollection;
-    }
-
-    /**
-     * Does this change object represent a new item?
-     *
-     * @return Whether or not this is for a new item
-     */
-    public boolean isNewItem() {
-        // Return the new item status
-        return newItem;
-    }
-
-    /**
-     * Does this change object represent a deleted item?
-     *
-     * @return Whether or not this is for a deleted item
-     */
-    public boolean isDeleted() {
-        // Return the new item status
-        return deleted;
-    }
-
-    /**
-     * Set that this item has been deleted
-     */
-    public void setDeleted() {
-        // Store the setting
-        deleted = true;
-        empty = false;
-    }
-
-    /**
-     * Does this change object represent a withdrawn item?
-     *
-     * @return Whether or not this is for a withdrawn item
-     */
-    public boolean isWithdrawn() {
-        // Return the new item status
-        return withdrawn;
-    }
-
-    /**
-     * Set that this item has been withdrawn
-     */
-    public void setWithdrawn() {
-        // Store the setting
-        withdrawn = true;
-        empty = false;
-    }
-
-    /**
-     * Does this change object represent a reinstated item?
-     *
-     * @return Whether or not this is for a reinstated item
-     */
-    public boolean isReinstated() {
-        // Return the new item status
-        return reinstated;
-    }
-
-    /**
-     * Set that this item has been deleted
-     */
-    public void setReinstated() {
-        // Store the setting
-        reinstated = true;
-        empty = false;
-    }
-
-    /**
-     * Have any changes actually been recorded, or is this empty?
-     *
-     * @return Whether or not changes have been made
-     */
-    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

@@ -1,689 +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;
-
-import java.io.BufferedReader;
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.factory.AuthorityServiceFactory;
-import org.dspace.authority.service.AuthorityValueService;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.MetadataValue;
-import org.dspace.content.authority.Choices;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.content.service.MetadataFieldService;
-import org.dspace.content.service.MetadataSchemaService;
-import org.dspace.core.Context;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Utility class to read and write CSV files
- *
- * **************
- * Important Note
- * **************
- *
- * 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?
- * b) holding an entire CSV upload in memory?
- *
- * @author Stuart Lewis
- */
-public class DSpaceCSV implements Serializable {
-    /**
-     * The headings of the CSV file
-     */
-    protected List<String> headings;
-
-    /**
-     * An array list of CSV lines
-     */
-    protected List<DSpaceCSVLine> lines;
-
-    /**
-     * A counter of how many CSV lines this object holds
-     */
-    protected int counter;
-
-    /**
-     * The value separator (defaults to double pipe '||')
-     */
-    protected String valueSeparator;
-
-    /**
-     * The value separator in an escaped form for using in regexes
-     */
-    protected String escapedValueSeparator;
-
-    /**
-     * The field separator (defaults to comma)
-     */
-    protected String fieldSeparator;
-
-    /**
-     * The field separator in an escaped form for using in regexes
-     */
-    protected String escapedFieldSeparator;
-
-    /**
-     * The authority separator (defaults to double colon '::')
-     */
-    protected String authoritySeparator;
-
-    /**
-     * The authority separator in an escaped form for using in regexes
-     */
-    protected String escapedAuthoritySeparator;
-
-    protected transient final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    protected transient final MetadataSchemaService metadataSchemaService =
-        ContentServiceFactory.getInstance().getMetadataSchemaService();
-    protected transient final MetadataFieldService metadataFieldService =
-        ContentServiceFactory.getInstance().getMetadataFieldService();
-    protected transient final AuthorityValueService authorityValueService =
-        AuthorityServiceFactory.getInstance().getAuthorityValueService();
-
-
-    /**
-     * Whether to export all metadata such as handles and provenance information
-     */
-    protected boolean exportAll;
-
-    /**
-     * A list of metadata elements to ignore
-     */
-    protected Map<String, String> ignore;
-
-
-    /**
-     * Create a new instance of a CSV line holder
-     *
-     * @param exportAll Whether to export all metadata such as handles and provenance information
-     */
-    public DSpaceCSV(boolean exportAll) {
-        // Initialise the class
-        init();
-
-        // Store the exportAll setting
-        this.exportAll = exportAll;
-    }
-
-    /**
-     * Create a new instance, reading the lines in from file
-     *
-     * @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 {
-        // Initialise the class
-        init();
-
-        // Open the CSV file
-        BufferedReader input = null;
-        try {
-            input = new BufferedReader(new InputStreamReader(new FileInputStream(f), "UTF-8"));
-
-            // Read the heading line
-            String head = input.readLine();
-            String[] headingElements = head.split(escapedFieldSeparator);
-            int columnCounter = 0;
-            for (String element : headingElements) {
-                columnCounter++;
-
-                // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
-                    element = element.substring(1, element.length() - 1);
-                }
-
-                // Store the heading
-                if ("collection".equals(element)) {
-                    // Store the heading
-                    headings.add(element);
-                } else if ("action".equals(element)) { // Store the action
-                    // Store the heading
-                    headings.add(element);
-                } else if (!"id".equals(element)) {
-                    String authorityPrefix = "";
-                    AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
-                    if (authorityValueType != null) {
-                        String authorityType = authorityValueType.getAuthorityType();
-                        authorityPrefix = element.substring(0, authorityType.length() + 1);
-                        element = element.substring(authorityPrefix.length());
-                    }
-
-                    // Verify that the heading is valid in the metadata registry
-                    String[] clean = element.split("\\[");
-                    String[] parts = clean[0].split("\\.");
-
-                    if (parts.length < 2) {
-                        throw new MetadataImportInvalidHeadingException(element,
-                                                                        MetadataImportInvalidHeadingException.ENTRY,
-                                                                        columnCounter);
-                    }
-
-                    String metadataSchema = parts[0];
-                    String metadataElement = parts[1];
-                    String metadataQualifier = null;
-                    if (parts.length > 2) {
-                        metadataQualifier = parts[2];
-                    }
-
-                    // Check that the scheme exists
-                    MetadataSchema foundSchema = metadataSchemaService.find(c, metadataSchema);
-                    if (foundSchema == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.SCHEMA,
-                                                                        columnCounter);
-                    }
-
-                    // Check that the metadata element exists in the schema
-                    MetadataField foundField = metadataFieldService
-                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
-                    if (foundField == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.ELEMENT,
-                                                                        columnCounter);
-                    }
-
-                    // Store the heading
-                    headings.add(authorityPrefix + element);
-                }
-            }
-
-            // Read each subsequent line
-            StringBuilder lineBuilder = new StringBuilder();
-            String lineRead;
-
-            while ((lineRead = input.readLine()) != null) {
-                if (lineBuilder.length() > 0) {
-                    // Already have a previously read value - add this line
-                    lineBuilder.append("\n").append(lineRead);
-
-                    // Count the number of quotes in the buffer
-                    int quoteCount = 0;
-                    for (int pos = 0; pos < lineBuilder.length(); pos++) {
-                        if (lineBuilder.charAt(pos) == '"') {
-                            quoteCount++;
-                        }
-                    }
-
-                    if (quoteCount % 2 == 0) {
-                        // Number of quotes is a multiple of 2, add the item
-                        addItem(lineBuilder.toString());
-                        lineBuilder = new StringBuilder();
-                    }
-                } else if (lineRead.indexOf('"') > -1) {
-                    // Get the number of quotes in the line
-                    int quoteCount = 0;
-                    for (int pos = 0; pos < lineRead.length(); pos++) {
-                        if (lineRead.charAt(pos) == '"') {
-                            quoteCount++;
-                        }
-                    }
-
-                    if (quoteCount % 2 == 0) {
-                        // Number of quotes is a multiple of 2, add the item
-                        addItem(lineRead);
-                    } else {
-                        // Uneven quotes - add to the buffer and leave for later
-                        lineBuilder.append(lineRead);
-                    }
-                } else {
-                    // No previously read line, and no quotes in the line - add item
-                    addItem(lineRead);
-                }
-            }
-        } finally {
-            if (input != null) {
-                input.close();
-            }
-        }
-    }
-
-    /**
-     * Initialise this class with values from dspace.cfg
-     */
-    protected void init() {
-        // Set the value separator
-        setValueSeparator();
-
-        // Set the field separator
-        setFieldSeparator();
-
-        // Set the authority separator
-        setAuthoritySeparator();
-
-        // Create the headings
-        headings = new ArrayList<>();
-
-        // Create the blank list of items
-        lines = new ArrayList<>();
-
-        // Initialise the counter
-        counter = 0;
-
-        // Set the metadata fields to ignore
-        ignore = new HashMap<>();
-
-        // Specify default values
-        String[] defaultValues =
-            new String[] {
-                "dc.date.accessioned, dc.date.available, dc.date.updated, dc.description.provenance"
-            };
-        String[] toIgnoreArray =
-            DSpaceServicesFactory.getInstance()
-                                 .getConfigurationService()
-                                 .getArrayProperty("bulkedit.ignore-on-export", defaultValues);
-        for (String toIgnoreString : toIgnoreArray) {
-            if (!"".equals(toIgnoreString.trim())) {
-                ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
-            }
-        }
-    }
-
-    /**
-     * Decide if this CSV file has an 'action' (case-dependent!) header.
-     *
-     * @return Whether or not there is an 'action' header
-     */
-    public boolean hasActions() {
-        // Look for a heading called 'action'
-        for (String header : headings) {
-            if (header.equals("action")) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    /**
-     * Set the value separator for multiple values stored in one csv value.
-     *
-     * Is set in bulkedit.cfg as valueseparator
-     *
-     * If not set, defaults to double pipe '||'
-     */
-    private void setValueSeparator() {
-        // Get the value separator
-        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                              .getProperty("bulkedit.valueseparator");
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim()))) {
-            valueSeparator = valueSeparator.trim();
-        } else {
-            valueSeparator = "||";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(valueSeparator);
-        escapedValueSeparator = match.replaceAll("\\\\$1");
-    }
-
-    /**
-     * Set the field separator use to separate fields in the csv.
-     *
-     * Is set in bulkedit.cfg as fieldseparator
-     *
-     * If not set, defaults to comma ','.
-     *
-     * Special values are 'tab', 'hash' and 'semicolon' which will
-     * get substituted from the text to the value.
-     */
-    private void setFieldSeparator() {
-        // Get the value separator
-        fieldSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                              .getProperty("bulkedit.fieldseparator");
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim()))) {
-            fieldSeparator = fieldSeparator.trim();
-            if ("tab".equals(fieldSeparator)) {
-                fieldSeparator = "\t";
-            } else if ("semicolon".equals(fieldSeparator)) {
-                fieldSeparator = ";";
-            } else if ("hash".equals(fieldSeparator)) {
-                fieldSeparator = "#";
-            } else {
-                fieldSeparator = fieldSeparator.trim();
-            }
-        } else {
-            fieldSeparator = ",";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(fieldSeparator);
-        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() {
-        // Get the value separator
-        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
-                                                  .getProperty("bulkedit.authorityseparator");
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim()))) {
-            authoritySeparator = authoritySeparator.trim();
-        } else {
-            authoritySeparator = "::";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(authoritySeparator);
-        escapedAuthoritySeparator = match.replaceAll("\\\\$1");
-    }
-
-    /**
-     * 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 {
-        // If the item does not have an "owningCollection" the the below "getHandle()" call will fail
-        // This should not happen but is here for safety.
-        if (i.getOwningCollection() == null) {
-            return;
-        }
-
-        // Create the CSV line
-        DSpaceCSVLine line = new DSpaceCSVLine(i.getID());
-
-        // Add in owning collection
-        String owningCollectionHandle = i.getOwningCollection().getHandle();
-        line.add("collection", owningCollectionHandle);
-
-        // Add in any mapped collections
-        List<Collection> collections = i.getCollections();
-        for (Collection c : collections) {
-            // Only add if it is not the owning collection
-            if (!c.getHandle().equals(owningCollectionHandle)) {
-                line.add("collection", c.getHandle());
-            }
-        }
-
-        // Populate it
-        List<MetadataValue> md = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (MetadataValue value : md) {
-            MetadataField metadataField = value.getMetadataField();
-            MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-            // Get the key (schema.element)
-            String key = metadataSchema.getName() + "." + metadataField.getElement();
-
-            // Add the qualifier if there is one (schema.element.qualifier)
-            if (metadataField.getQualifier() != null) {
-                key = key + "." + metadataField.getQualifier();
-            }
-
-            // Add the language if there is one (schema.element.qualifier[langauge])
-            //if ((value.language != null) && (!"".equals(value.language)))
-            if (value.getLanguage() != null) {
-                key = key + "[" + value.getLanguage() + "]";
-            }
-
-            // Store the item
-            if (exportAll || okToExport(metadataField)) {
-                // Add authority and confidence if authority is not null
-                String mdValue = value.getValue();
-                if (value.getAuthority() != null && !"".equals(value.getAuthority())) {
-                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value
-                        .getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
-                }
-                line.add(key, mdValue);
-                if (!headings.contains(key)) {
-                    headings.add(key);
-                }
-            }
-        }
-        lines.add(line);
-        counter++;
-    }
-
-    /**
-     * Add an item to the CSV file, from a CSV line of elements
-     *
-     * @param line The line of elements
-     * @throws Exception Thrown if an error occurs when adding the item
-     */
-    public final void addItem(String line) throws Exception {
-        // Check to see if the last character is a field separator, which hides the last empty column
-        boolean last = false;
-        if (line.endsWith(fieldSeparator)) {
-            // Add a space to the end, then remove it later
-            last = true;
-            line += " ";
-        }
-
-        // Split up on field separator
-        String[] parts = line.split(escapedFieldSeparator);
-        ArrayList<String> bits = new ArrayList<>();
-        bits.addAll(Arrays.asList(parts));
-
-        // Merge parts with embedded separators
-        boolean alldone = false;
-        while (!alldone) {
-            boolean found = false;
-            int i = 0;
-            for (String part : bits) {
-                int bitcounter = part.length() - part.replaceAll("\"", "").length();
-                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1))) {
-                    found = true;
-                    String add = bits.get(i) + fieldSeparator + bits.get(i + 1);
-                    bits.remove(i);
-                    bits.add(i, add);
-                    bits.remove(i + 1);
-                    break;
-                }
-                i++;
-            }
-            alldone = !found;
-        }
-
-        // Deal with quotes around the elements
-        int i = 0;
-        for (String part : bits) {
-            if ((part.startsWith("\"")) && (part.endsWith("\""))) {
-                part = part.substring(1, part.length() - 1);
-                bits.set(i, part);
-            }
-            i++;
-        }
-
-        // Remove embedded quotes
-        i = 0;
-        for (String part : bits) {
-            if (part.contains("\"\"")) {
-                part = part.replaceAll("\"\"", "\"");
-                bits.set(i, part);
-            }
-            i++;
-        }
-
-        // Add elements to a DSpaceCSVLine
-        String id = parts[0].replaceAll("\"", "");
-        DSpaceCSVLine csvLine;
-
-        // Is this an existing item, or a new item (where id = '+')
-        if ("+".equals(id)) {
-            csvLine = new DSpaceCSVLine();
-        } else {
-            try {
-                csvLine = new DSpaceCSVLine(UUID.fromString(id));
-            } catch (NumberFormatException nfe) {
-                System.err.println("Invalid item identifier: " + id);
-                System.err.println("Please check your CSV file for information. " +
-                                       "Item id must be numeric, or a '+' to add a new item");
-                throw (nfe);
-            }
-        }
-
-        // Add the rest of the parts
-        i = 0;
-        for (String part : bits) {
-            if (i > 0) {
-                // Is this a last empty item?
-                if ((last) && (i == headings.size())) {
-                    part = "";
-                }
-
-                // Make sure we register that this column was there
-                if (headings.size() < i) {
-                    throw new MetadataImportInvalidHeadingException("",
-                                                                    MetadataImportInvalidHeadingException.MISSING,
-                                                                    i + 1);
-                }
-                csvLine.add(headings.get(i - 1), null);
-                String[] elements = part.split(escapedValueSeparator);
-                for (String element : elements) {
-                    if ((element != null) && (!"".equals(element))) {
-                        csvLine.add(headings.get(i - 1), element);
-                    }
-                }
-            }
-            i++;
-        }
-        lines.add(csvLine);
-        counter++;
-    }
-
-    /**
-     * Get the lines in CSV holders
-     *
-     * @return The lines
-     */
-    public final List<DSpaceCSVLine> getCSVLines() {
-        // Return the lines
-        return lines;
-    }
-
-    /**
-     * Get the CSV lines as an array of CSV formatted strings
-     *
-     * @return the array of CSV formatted Strings
-     */
-    public final String[] getCSVLinesAsStringArray() {
-        // Create the headings line
-        String[] csvLines = new String[counter + 1];
-        csvLines[0] = "id" + fieldSeparator + "collection";
-        List<String> headingsCopy = new ArrayList<>(headings);
-        Collections.sort(headingsCopy);
-        for (String value : headingsCopy) {
-            csvLines[0] = csvLines[0] + fieldSeparator + value;
-        }
-
-        Iterator<DSpaceCSVLine> i = lines.iterator();
-        int c = 1;
-        while (i.hasNext()) {
-            csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
-        }
-
-        return csvLines;
-    }
-
-    /**
-     * 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 {
-        // Save the file
-        BufferedWriter out = new BufferedWriter(
-            new OutputStreamWriter(
-                new FileOutputStream(filename), "UTF-8"));
-        for (String csvLine : getCSVLinesAsStringArray()) {
-            out.write(csvLine + "\n");
-        }
-        out.flush();
-        out.close();
-    }
-
-    /**
-     * Is it Ok to export this value? When exportAll is set to false, we don't export
-     * some of the metadata elements.
-     *
-     * The list can be configured via the key ignore-on-export in bulkedit.cfg
-     *
-     * @param md The Metadatum to examine
-     * @return Whether or not it is OK to export this element
-     */
-    protected boolean okToExport(MetadataField md) {
-        // Now compare with the list to ignore
-        String key = md.getMetadataSchema().getName() + "." + md.getElement();
-        if (md.getQualifier() != null) {
-            key += "." + md.getQualifier();
-        }
-        if (ignore.get(key) != null) {
-            return false;
-        }
-
-        // Must be OK, so don't ignore
-        return true;
-    }
-
-    /**
-     * Get the headings used in this CSV file
-     *
-     * @return The headings
-     */
-    public List<String> getHeadings() {
-        return headings;
-    }
-
-    /**
-     * Return the csv file as one long formatted string
-     *
-     * @return The formatted String as a csv
-     */
-    @Override
-    public final String toString() {
-        // Return the csv as one long string
-        StringBuilder csvLines = new StringBuilder();
-        String[] lines = this.getCSVLinesAsStringArray();
-        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

@@ -1,213 +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;
-
-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;
-
-/**
- * Utility class to store a line from a CSV file
- *
- * @author Stuart Lewis
- */
-public class DSpaceCSVLine implements Serializable {
-    /**
-     * The item id of the item represented by this line. -1 is for a new item
-     */
-    private final UUID id;
-
-    /**
-     * The elements in this line in a hashtable, keyed by the metadata type
-     */
-    private final Map<String, ArrayList> items;
-
-    protected transient final AuthorityValueService authorityValueService
-        = AuthorityServiceFactory.getInstance().getAuthorityValueService();
-
-    /**
-     * ensuring that the order-sensible columns of the csv are processed in the correct order
-     */
-    private transient final Comparator<? super String> headerComparator = new Comparator<String>() {
-        @Override
-        public int compare(String md1, String md2) {
-            // The metadata coming from an external source should be processed after the others
-            AuthorityValue source1 = authorityValueService.getAuthorityValueType(md1);
-            AuthorityValue source2 = authorityValueService.getAuthorityValueType(md2);
-
-            int compare;
-            if (source1 == null && source2 != null) {
-                compare = -1;
-            } else if (source1 != null && source2 == null) {
-                compare = 1;
-            } else {
-                // the order of the rest does not matter
-                compare = md1.compareTo(md2);
-            }
-            return compare;
-        }
-    };
-
-    /**
-     * Create a new CSV line
-     *
-     * @param itemId The item ID of the line
-     */
-    public DSpaceCSVLine(UUID itemId) {
-        // Store the ID + separator, and initialise the hashtable
-        this.id = itemId;
-        items = new TreeMap<>(headerComparator);
-//        this.items = new HashMap<String, ArrayList>();
-    }
-
-    /**
-     * Create a new CSV line for a new item
-     */
-    public DSpaceCSVLine() {
-        // Set the ID to be null, and initialise the hashtable
-        this.id = null;
-        this.items = new TreeMap<>(headerComparator);
-    }
-
-    /**
-     * Get the item ID that this line represents
-     *
-     * @return The item ID
-     */
-    public UUID getID() {
-        // Return the ID
-        return id;
-    }
-
-    /**
-     * Add a new metadata value to this line
-     *
-     * @param key   The metadata key (e.g. dc.contributor.author)
-     * @param value The metadata value
-     */
-    public void add(String key, String value) {
-        // Create the array list if we need to
-        if (items.get(key) == null) {
-            items.put(key, new ArrayList<String>());
-        }
-
-        // Store the item if it is not null
-        if (value != null) {
-            items.get(key).add(value);
-        }
-    }
-
-    /**
-     * Get all the values that match the given metadata key. Will be null if none exist.
-     *
-     * @param key The metadata key
-     * @return All the elements that match
-     */
-    public List<String> get(String key) {
-        // Return any relevant values
-        return items.get(key);
-    }
-
-    /**
-     * Get any action associated with this line
-     *
-     * @return The action (may be blank, 'withdraw', 'reinstate' or 'delete')
-     */
-    public String getAction() {
-        if (items.containsKey("action")) {
-            ArrayList actions = items.get("action");
-            if (actions.size() > 0) {
-                return ((String) actions.get(0)).trim();
-            }
-        }
-        return "";
-    }
-
-    /**
-     * Get all the metadata keys that are represented in this line
-     *
-     * @return An enumeration of all the keys
-     */
-    public Set<String> keys() {
-        // Return the keys
-        return items.keySet();
-    }
-
-    /**
-     * Write this line out as a CSV formatted string, in the order given by the headings provided
-     *
-     * @param headings       The headings which define the order the elements must be presented in
-     * @param fieldSeparator separator between metadata fields
-     * @param valueSeparator separator between metadata values (within a field)
-     * @return The CSV formatted String
-     */
-    protected String toCSV(List<String> headings, String fieldSeparator, String valueSeparator) {
-        StringBuilder bits = new StringBuilder();
-
-        // Add the id
-        bits.append("\"").append(id).append("\"").append(fieldSeparator);
-        bits.append(valueToCSV(items.get("collection"), valueSeparator));
-
-        // Add the rest of the elements
-        for (String heading : headings) {
-            bits.append(fieldSeparator);
-            List<String> values = items.get(heading);
-            if (values != null && !"collection".equals(heading)) {
-                bits.append(valueToCSV(values, valueSeparator));
-            }
-        }
-
-        return bits.toString();
-    }
-
-    /**
-     * Internal method to create a CSV formatted String joining a given set of elements
-     *
-     * @param values         The values to create the string from
-     * @param valueSeparator value separator
-     * @return The line as a CSV formatted String
-     */
-    protected String valueToCSV(List<String> values, String valueSeparator) {
-        // Check there is some content
-        if (values == null) {
-            return "";
-        }
-
-        // Get on with the work
-        String s;
-        if (values.size() == 1) {
-            s = values.get(0);
-        } else {
-            // Concatenate any fields together
-            StringBuilder str = new StringBuilder();
-
-            for (String value : values) {
-                if (str.length() > 0) {
-                    str.append(valueSeparator);
-                }
-
-                str.append(value);
-            }
-
-            s = str.toString();
-        }
-
-        // Replace internal quotes with two sets of quotes
-        return "\"" + s.replaceAll("\"", "\"\"") + "\"";
-    }
-}
-

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

@@ -1,278 +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;
-
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import com.google.common.collect.Iterators;
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.handle.factory.HandleServiceFactory;
-
-/**
- * Metadata exporter to allow the batch export of metadata into a file
- *
- * @author Stuart Lewis
- */
-public class MetadataExport {
-    /**
-     * The items to export
-     */
-    protected Iterator<Item> toExport;
-
-    protected ItemService itemService;
-
-    protected Context context;
-
-    /**
-     * Whether to export all metadata, or just normally edited metadata
-     */
-    protected boolean exportAll;
-
-    protected MetadataExport() {
-        itemService = ContentServiceFactory.getInstance().getItemService();
-    }
-
-    /**
-     * Set up a new metadata export
-     *
-     * @param c         The Context
-     * @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) {
-        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 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) {
-        itemService = ContentServiceFactory.getInstance().getItemService();
-
-        try {
-            // Try to export the community
-            this.toExport = buildFromCommunity(c, toExport, 0);
-            this.exportAll = exportAll;
-            this.context = c;
-        } catch (SQLException sqle) {
-            // Something went wrong...
-            System.err.println("Error running exporter:");
-            sqle.printStackTrace(System.err);
-            System.exit(1);
-        }
-    }
-
-    /**
-     * 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
-     * @return The list of item ids
-     * @throws SQLException if database error
-     */
-    protected Iterator<Item> buildFromCommunity(Context context, Community community, int indent)
-        throws SQLException {
-        // Add all the collections
-        List<Collection> collections = community.getCollections();
-        Iterator<Item> result = null;
-        for (Collection collection : collections) {
-            for (int i = 0; i < indent; i++) {
-                System.out.print(" ");
-            }
-
-            Iterator<Item> items = itemService.findByCollection(context, collection);
-            result = addItemsToResult(result, items);
-
-        }
-        // Add all the sub-communities
-        List<Community> communities = community.getSubcommunities();
-        for (Community subCommunity : communities) {
-            for (int i = 0; i < indent; i++) {
-                System.out.print(" ");
-            }
-            Iterator<Item> items = buildFromCommunity(context, subCommunity, indent + 1);
-            result = addItemsToResult(result, items);
-        }
-
-        return result;
-    }
-
-    private Iterator<Item> addItemsToResult(Iterator<Item> result, Iterator<Item> items) {
-        if (result == null) {
-            result = items;
-        } else {
-            result = Iterators.concat(result, items);
-        }
-
-        return result;
-    }
-
-    /**
-     * Run the export
-     *
-     * @return the exported CSV lines
-     */
-    public DSpaceCSV export() {
-        try {
-            Context.Mode originalMode = context.getCurrentMode();
-            context.setMode(Context.Mode.READ_ONLY);
-
-            // Process each item
-            DSpaceCSV csv = new DSpaceCSV(exportAll);
-            while (toExport.hasNext()) {
-                Item item = toExport.next();
-                csv.addItem(item);
-                context.uncacheEntity(item);
-            }
-
-            context.setMode(originalMode);
-            // Return the results
-            return csv;
-        } catch (Exception e) {
-            // Something went wrong...
-            System.err.println("Error exporting to CSV:");
-            e.printStackTrace();
-            return null;
-        }
-    }
-
-    /**
-     * Print the help message
-     *
-     * @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) {
-        // print the help message
-        HelpFormatter myhelp = new HelpFormatter();
-        myhelp.printHelp("MetadataExport\n", options);
-        System.out.println("\nfull export: metadataexport -f filename");
-        System.out.println("partial export: metadataexport -i handle -f filename");
-        System.exit(exitCode);
-    }
-
-    /**
-     * main method to run the metadata exporter
-     *
-     * @param argv the command line arguments given
-     * @throws Exception if error occurs
-     */
-    public static void main(String[] argv) throws Exception {
-        // Create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
-        options.addOption("f", "file", true, "destination where you want file written");
-        options.addOption("a", "all", false,
-                          "include all metadata fields that are not normally changed (e.g. provenance)");
-        options.addOption("h", "help", false, "help");
-
-        CommandLine line = null;
-
-        try {
-            line = parser.parse(options, argv);
-        } catch (ParseException pe) {
-            System.err.println("Error with commands.");
-            printHelp(options, 1);
-            System.exit(0);
-        }
-
-        if (line.hasOption('h')) {
-            printHelp(options, 0);
-        }
-
-        // Check a filename is given
-        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);
-        c.turnOffAuthorisationSystem();
-
-        // The things we'll export
-        Iterator<Item> 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')) {
-            System.out.println("Exporting whole repository WARNING: May take some time!");
-            exporter = new MetadataExport(c, itemService.findAll(c), exportAll);
-        } else {
-            String handle = line.getOptionValue('i');
-            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, handle);
-            if (dso == null) {
-                System.err.println("Item '" + handle + "' does not resolve to an item in your repository!");
-                printHelp(options, 1);
-            }
-
-            if (dso.getType() == Constants.ITEM) {
-                System.out.println("Exporting item '" + dso.getName() + "' (" + handle + ")");
-                List<Item> item = new ArrayList<>();
-                item.add((Item) dso);
-                exporter = new MetadataExport(c, item.iterator(), exportAll);
-            } else if (dso.getType() == Constants.COLLECTION) {
-                System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
-                Collection collection = (Collection) dso;
-                toExport = itemService.findByCollection(c, collection);
-                exporter = new MetadataExport(c, toExport, exportAll);
-            } else if (dso.getType() == Constants.COMMUNITY) {
-                System.out.println("Exporting community '" + dso.getName() + "' (" + handle + ")");
-                exporter = new MetadataExport(c, (Community) dso, exportAll);
-            } else {
-                System.err.println("Error identifying '" + handle + "'");
-                System.exit(1);
-            }
-        }
-
-        // Perform the export
-        DSpaceCSV csv = exporter.export();
-
-        // Save the files to the file
-        csv.save(filename);
-
-        // Finish off and tidy up
-        c.restoreAuthSystemState();
-        c.complete();
-    }
-}

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

@@ -1,34 +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;
-
-/**
- * Metadata importer exception
- *
- * @author Stuart Lewis
- */
-public class MetadataImportException extends Exception {
-    /**
-     * Instantiate a new MetadataImportException
-     *
-     * @param message the error message
-     */
-    public MetadataImportException(String message) {
-        super(message);
-    }
-
-    /**
-     * Instantiate a new MetadataImportException
-     *
-     * @param message   the error message
-     * @param exception the root cause
-     */
-    public MetadataImportException(String message, Exception exception) {
-        super(message, exception);
-    }
-}

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

@@ -1,110 +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;
-
-/**
- * Metadata importer exception
- *
- * @author Stuart Lewis
- */
-public class MetadataImportInvalidHeadingException extends Exception {
-    /**
-     * The type of error (schema or element)
-     */
-    private int type;
-
-    /**
-     * The bad heading
-     */
-    private String badHeading;
-
-    /**
-     * The column number
-     */
-    private int column;
-
-    /**
-     * Error with the schema
-     */
-    public static final int SCHEMA = 0;
-
-    /**
-     * Error with the element
-     */
-    public static final int ELEMENT = 1;
-
-    /**
-     * Error with a missing header
-     */
-    public static final int MISSING = 98;
-
-    /**
-     * Error with the whole entry
-     */
-    public static final int ENTRY = 99;
-
-
-    /**
-     * Instantiate a new MetadataImportInvalidHeadingException
-     *
-     * @param message   the error message
-     * @param theType   the type of the error
-     * @param theColumn column number
-     */
-    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn) {
-        super(message);
-        badHeading = message;
-        type = theType;
-        column = theColumn;
-    }
-
-    /**
-     * Get the type of the exception
-     *
-     * @return the type of the exception
-     */
-    public String getType() {
-        return "" + type;
-    }
-
-    /**
-     * Get the heading that was invalid
-     *
-     * @return the invalid heading
-     */
-    public String getBadHeader() {
-        return badHeading;
-    }
-
-    /**
-     * Get the column number that was invalid
-     *
-     * @return the invalid column number
-     */
-    public int getColumn() {
-        return column;
-    }
-
-    /**
-     * Get the exception message
-     *
-     * @return The exception message
-     */
-    @Override
-    public String getMessage() {
-        if (type == SCHEMA) {
-            return "Unknown metadata schema in column " + column + ": " + badHeading;
-        } else if (type == ELEMENT) {
-            return "Unknown metadata element in column " + column + ": " + badHeading;
-        } else if (type == MISSING) {
-            return "Row with missing header: column " + column;
-        } else {
-            return "Bad metadata declaration in column" + column + ": " + badHeading;
-        }
-    }
-}

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

@@ -1,21 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-/**
- * <p>The DSpace Batch Metadata Editor, which uses a CSV file to export/import
- * item metadata.</p>
- * <ul>
- *   <li>works on items, communities, collections or the whole site</li>
- *   <li>can also create new items, delete items and withdraw/restore them</li>
- *   <li>cannot export/import bitstreams</li>
- * </ul>
- */
-
-package org.dspace.app.bulkedit;
-
-

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

@@ -1,244 +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.checker;
-
-import java.io.FileNotFoundException;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.apache.log4j.Logger;
-import org.dspace.checker.BitstreamDispatcher;
-import org.dspace.checker.CheckerCommand;
-import org.dspace.checker.HandleDispatcher;
-import org.dspace.checker.IteratorDispatcher;
-import org.dspace.checker.LimitedCountDispatcher;
-import org.dspace.checker.LimitedDurationDispatcher;
-import org.dspace.checker.ResultsLogger;
-import org.dspace.checker.ResultsPruner;
-import org.dspace.checker.SimpleDispatcher;
-import org.dspace.content.Bitstream;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.BitstreamService;
-import org.dspace.core.Context;
-import org.dspace.core.Utils;
-
-/**
- * Command line access to the checksum checker. Options are listed in the
- * documentation for the main method.
- *
- * @author Jim Downing
- * @author Grace Carpenter
- * @author Nathan Sarr
- */
-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() {
-    }
-
-    /**
-     * Command line access to the checksum package.
-     *
-     * <dl>
-     * <dt>-h</dt>
-     * <dd>Print help on command line options</dd>
-     * <dt>-l</dt>
-     * <dd>loop through bitstreams once</dd>
-     * <dt>-L</dt>
-     * <dd>loop continuously through bitstreams</dd>
-     * <dt>-d</dt>
-     * <dd>specify duration of process run</dd>
-     * <dt>-b</dt>
-     * <dd>specify bitstream IDs</dd>
-     * <dt>-a [handle_id]</dt>
-     * <dd>check anything by handle</dd>
-     * <dt>-e</dt>
-     * <dd>Report only errors in the logs</dd>
-     * <dt>-p</dt>
-     * <dd>Don't prune results before running checker</dd>
-     * </dl>
-     *
-     * @param args the command line arguments given
-     * @throws SQLException if error
-     */
-    public static void main(String[] args) throws SQLException {
-        // set up command line parser
-        CommandLineParser parser = new PosixParser();
-        CommandLine line = null;
-
-        // create an options object and populate it
-        Options options = new Options();
-
-        options.addOption("l", "looping", false, "Loop once through bitstreams");
-        options.addOption("L", "continuous", false,
-                          "Loop continuously through bitstreams");
-        options.addOption("h", "help", false, "Help");
-        options.addOption("d", "duration", true, "Checking duration");
-        options.addOption("c", "count", true, "Check count");
-        options.addOption("a", "handle", true, "Specify a handle to check");
-        options.addOption("v", "verbose", false, "Report all processing");
-
-        OptionBuilder.withArgName("bitstream-ids").hasArgs().withDescription(
-            "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
-                              .withArgName("prune")
-                              .hasOptionalArgs(1)
-                              .withDescription(
-                                  "Prune old results (optionally using specified properties file for configuration)")
-                              .create('p'));
-
-        try {
-            line = parser.parse(options, args);
-        } catch (ParseException e) {
-            LOG.fatal(e);
-            System.exit(1);
-        }
-
-        // user asks for help
-        if (line.hasOption('h')) {
-            printHelp(options);
-        }
-        Context context = null;
-        try {
-            context = new Context();
-
-
-            // Prune stage
-            if (line.hasOption('p')) {
-                ResultsPruner rp = null;
-                try {
-                    rp = (line.getOptionValue('p') != null) ? ResultsPruner
-                        .getPruner(context, line.getOptionValue('p')) : ResultsPruner
-                        .getDefaultPruner(context);
-                } 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();
-
-            BitstreamDispatcher dispatcher = null;
-
-            // process should loop infinitely through
-            // most_recent_checksum table
-            if (line.hasOption('l')) {
-                dispatcher = new SimpleDispatcher(context, processStart, false);
-            } else if (line.hasOption('L')) {
-                dispatcher = new SimpleDispatcher(context, processStart, true);
-            } else if (line.hasOption('b')) {
-                // check only specified bitstream(s)
-                String[] ids = line.getOptionValues('b');
-                List<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());
-            } else if (line.hasOption('a')) {
-                dispatcher = new HandleDispatcher(context, line.getOptionValue('a'));
-            } else if (line.hasOption('d')) {
-                // 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);
-            }
-
-            ResultsLogger logger = new ResultsLogger(processStart);
-            CheckerCommand checker = new CheckerCommand(context);
-            // verbose reporting
-            if (line.hasOption('v')) {
-                checker.setReportVerbose(true);
-            }
-
-            checker.setProcessStartDate(processStart);
-            checker.setDispatcher(dispatcher);
-            checker.setCollector(logger);
-            checker.process();
-            context.complete();
-            context = null;
-        } finally {
-            if (context != null) {
-                context.abort();
-            }
-        }
-    }
-
-    /**
-     * Print the help options for the user
-     *
-     * @param options that are available for the user
-     */
-    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),"
-                               + "m(minutes), or h(hours): ChecksumChecker -d 30s"
-                               + " OR ChecksumChecker -d 30m"
-                               + " OR ChecksumChecker -d 2h");
-        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
-        System.out.println("\nLoop once through all bitstreams: "
-                               + "ChecksumChecker -l");
-        System.out.println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
-        System.out.println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
-        System.out.println("\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/checker/package.html

@@ -1,19 +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/
-
--->
-<html>
-	<head>
-		<title>org.dspace.app.checker Package Documentation</title>
-	</head>
-  <body>
-      <p>org.dspace.app.checker provides user interfaces to the org.dspace.checker 
-		  package. Command line options are detailed in the ChecksumChecker javadoc.
-		  </p>
-  </body>
-</html>

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

@@ -1,40 +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.configuration;
-
-import java.io.File;
-import java.net.MalformedURLException;
-
-import org.dspace.kernel.config.SpringLoader;
-import org.dspace.services.ConfigurationService;
-
-/**
- * @author Kevin Van de Velde (kevin at atmire dot com)
- */
-public class APISpringLoader implements SpringLoader {
-
-    @Override
-    public String[] getResourcePaths(ConfigurationService configurationService) {
-        StringBuffer filePath = new StringBuffer();
-        filePath.append(configurationService.getProperty("dspace.dir"));
-        filePath.append(File.separator);
-        filePath.append("config");
-        filePath.append(File.separator);
-        filePath.append("spring");
-        filePath.append(File.separator);
-        filePath.append("api");
-        filePath.append(File.separator);
-
-
-        try {
-            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

@@ -1,484 +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.harvest;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Collection;
-import org.dspace.content.DSpaceObject;
-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.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.EPersonService;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.harvest.HarvestedCollection;
-import org.dspace.harvest.HarvestingException;
-import org.dspace.harvest.OAIHarvester;
-import org.dspace.harvest.factory.HarvestServiceFactory;
-import org.dspace.harvest.service.HarvestedCollectionService;
-
-/**
- * Test class for harvested collections.
- *
- * @author Alexey Maslov
- */
-public class Harvest {
-    private static Context context;
-
-    private static final HarvestedCollectionService harvestedCollectionService =
-        HarvestServiceFactory.getInstance().getHarvestedCollectionService();
-    private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    private static final CollectionService collectionService =
-        ContentServiceFactory.getInstance().getCollectionService();
-
-    public static void main(String[] argv) throws Exception {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("p", "purge", false, "delete all items in the collection");
-        options.addOption("r", "run", false, "run the standard harvest procedure");
-        options.addOption("g", "ping", false, "test the OAI server and set");
-        options.addOption("o", "once", false, "run the harvest procedure with specified parameters");
-        options.addOption("s", "setup", false, "Set the collection up for harvesting");
-        options.addOption("S", "start", false, "start the harvest loop");
-        options.addOption("R", "reset", false, "reset harvest status on all collections");
-        options.addOption("P", "purge", false, "purge all harvestable collections");
-
-
-        options.addOption("e", "eperson", true,
-                          "eperson");
-        options.addOption("c", "collection", true,
-                          "harvesting collection (handle or id)");
-        options.addOption("t", "type", true,
-                          "type of harvesting (0 for none)");
-        options.addOption("a", "address", true,
-                          "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true,
-                          "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true,
-                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
-                              "crosswalk in dspace.cfg");
-
-        options.addOption("h", "help", false, "help");
-
-        CommandLine line = parser.parse(options, argv);
-
-        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')) {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("Harvest\n", options);
-            System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
-            System.out.println(
-                "RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a " +
-                    "oai_source -i oai_set_id -m metadata_format");
-            System.out.println(
-                "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
-                    "oai_set_id -m metadata_format");
-            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out.println("START harvest scheduler: Harvest -S");
-            System.out.println("RESET all harvest status: Harvest -R");
-            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
-
-
-            System.exit(0);
-        }
-
-        if (line.hasOption('s')) {
-            command = "config";
-        }
-        if (line.hasOption('p')) {
-            command = "purge";
-        }
-        if (line.hasOption('r')) {
-            command = "run";
-        }
-        if (line.hasOption('g')) {
-            command = "ping";
-        }
-        if (line.hasOption('o')) {
-            command = "runOnce";
-        }
-        if (line.hasOption('S')) {
-            command = "start";
-        }
-        if (line.hasOption('R')) {
-            command = "reset";
-        }
-        if (line.hasOption('P')) {
-            command = "purgeAll";
-        }
-
-
-        if (line.hasOption('e')) {
-            eperson = line.getOptionValue('e');
-        }
-        if (line.hasOption('c')) {
-            collection = line.getOptionValue('c');
-        }
-        if (line.hasOption('t')) {
-            harvestType = Integer.parseInt(line.getOptionValue('t'));
-        } else {
-            harvestType = 0;
-        }
-        if (line.hasOption('a')) {
-            oaiSource = line.getOptionValue('a');
-        }
-        if (line.hasOption('i')) {
-            oaiSetID = line.getOptionValue('i');
-        }
-        if (line.hasOption('m')) {
-            metadataKey = line.getOptionValue('m');
-        }
-
-
-        // Instantiate our class
-        Harvest harvester = new Harvest();
-        harvester.context = new Context(Context.Mode.BATCH_EDIT);
-
-
-        // Check our options
-        if (command == null) {
-            System.out
-                .println("Error - no parameters specified (run with -h flag for details)");
-            System.exit(1);
-        } else if ("run".equals(command)) {
-            // Run a single harvest cycle on a collection using saved settings.
-            if (collection == null || eperson == null) {
-                System.out
-                    .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
-            startHarvester();
-        } else if ("reset".equals(command)) {
-            // reset harvesting status
-            resetHarvesting();
-        } else if ("purgeAll".equals(command)) {
-            // purge all collections that are set up for harvesting (obviously for testing purposes only)
-            if (eperson == null) {
-                System.out
-                    .println("Error - an eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-
-            List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
-                System.out.println(
-                    "Purging the following collections (deleting items and resetting harvest status): " +
-                        harvestedCollection
-                            .getCollection().getID().toString());
-                harvester.purgeCollection(harvestedCollection.getCollection().getID().toString(), eperson);
-            }
-            context.complete();
-        } else if ("purge".equals(command)) {
-            // Delete all items in a collection. Useful for testing fresh harvests.
-            if (collection == null || eperson == null) {
-                System.out
-                    .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
-            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) {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-            if (metadataKey == null) {
-                System.out
-                    .println("Error - a metadata key (commonly the prefix) must be specified for this collection");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-
-            harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
-        } else if ("ping".equals(command)) {
-            if (oaiSource == null || oaiSetID == null) {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-
-            pingResponder(oaiSource, oaiSetID, metadataKey);
-        }
-    }
-
-    /*
-     * 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.
-     */
-    private Collection resolveCollection(String collectionID) {
-
-        DSpaceObject dso;
-        Collection targetCollection = null;
-
-        try {
-            // is the ID a handle?
-            if (collectionID != null) {
-                if (collectionID.indexOf('/') != -1) {
-                    // string has a / so it must be a handle - try and resolve it
-                    dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, collectionID);
-
-                    // resolved, now make sure it's a collection
-                    if (dso == null || dso.getType() != Constants.COLLECTION) {
-                        targetCollection = null;
-                    } else {
-                        targetCollection = (Collection) dso;
-                    }
-                } else {
-                    // not a handle, try and treat it as an integer collection database ID
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer
-                        .parseInt(collectionID) + "', " + "in context: " + context);
-                    targetCollection = collectionService.find(context, UUID.fromString(collectionID));
-                }
-            }
-            // was the collection valid?
-            if (targetCollection == null) {
-                System.out.println("Cannot resolve " + collectionID + " to collection");
-                System.exit(1);
-            }
-        } catch (SQLException se) {
-            se.printStackTrace();
-        }
-
-        return targetCollection;
-    }
-
-
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId,
-                                     String mdConfigId) {
-        System.out.println("Running: configure collection");
-
-        Collection collection = resolveCollection(collectionID);
-        System.out.println(collection.getID());
-
-        try {
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
-            if (hc == null) {
-                hc = harvestedCollectionService.create(context, collection);
-            }
-
-            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(
-            "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
-        Collection collection = resolveCollection(collectionID);
-
-        try {
-            EPerson eperson = ePersonService.findByEmail(context, email);
-            context.setCurrentUser(eperson);
-            context.turnOffAuthorisationSystem();
-
-            ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-            Iterator<Item> it = itemService.findByCollection(context, collection);
-            int i = 0;
-            while (it.hasNext()) {
-                i++;
-                Item item = it.next();
-                System.out.println("Deleting: " + item.getHandle());
-                collectionService.removeItem(context, collection, item);
-                context.uncacheEntity(item);// Dispatch events every 50 items
-                if (i % 50 == 0) {
-                    context.dispatchEvents();
-                    i = 0;
-                }
-            }
-
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
-            if (hc != null) {
-                hc.setLastHarvested(null);
-                hc.setHarvestMessage("");
-                hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-                hc.setHarvestStartTime(null);
-                harvestedCollectionService.update(context, hc);
-            }
-            context.restoreAuthSystemState();
-            context.dispatchEvents();
-        } catch (Exception e) {
-            System.out.println("Changes could not be committed");
-            e.printStackTrace();
-            System.exit(1);
-        } finally {
-            context.restoreAuthSystemState();
-        }
-    }
-
-
-    /**
-     * 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.print("Initializing the harvester... ");
-        OAIHarvester harvester = null;
-        try {
-            Collection collection = resolveCollection(collectionID);
-            HarvestedCollection hc = harvestedCollectionService.find(context, collection);
-            harvester = new OAIHarvester(context, collection, hc);
-            System.out.println("success. ");
-        } catch (HarvestingException hex) {
-            System.out.print("failed. ");
-            System.out.println(hex.getMessage());
-            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 = 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) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        }
-
-        System.out.println("Harvest complete. ");
-    }
-
-    /**
-     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the
-     * harvested_collections table
-     */
-    private static void resetHarvesting() {
-        System.out.print("Resetting harvest status flag on all collections... ");
-
-        try {
-            List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections) {
-                //hc.setHarvestResult(null,"");
-                harvestedCollection.setHarvestStartTime(null);
-                harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
-                harvestedCollectionService.update(context, harvestedCollection);
-            }
-            System.out.println("success. ");
-        } catch (Exception ex) {
-            System.out.println("failed. ");
-            ex.printStackTrace();
-        }
-    }
-
-    /**
-     * Starts up the harvest scheduler. Terminating this process will stop the scheduler.
-     */
-    private static void startHarvester() {
-        try {
-            System.out.print("Starting harvest loop... ");
-            HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
-            System.out.println("running. ");
-        } catch (Exception ex) {
-            ex.printStackTrace();
-        }
-    }
-
-    /**
-     * See if the responder is alive and working.
-     *
-     * @param server         address of the responder's host.
-     * @param set            name of an item set.
-     * @param metadataFormat local prefix name, or null for "dc".
-     */
-    private static void pingResponder(String server, String set, String metadataFormat) {
-        List<String> errors;
-
-        System.out.print("Testing basic PMH access:  ");
-        errors = OAIHarvester.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", false);
-        if (errors.isEmpty()) {
-            System.out.println("OK");
-        } else {
-            for (String error : errors) {
-                System.err.println(error);
-            }
-        }
-
-        System.out.print("Testing ORE support:  ");
-        errors = OAIHarvester.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", true);
-        if (errors.isEmpty()) {
-            System.out.println("OK");
-        } else {
-            for (String error : errors) {
-                System.err.println(error);
-            }
-        }
-    }
-}

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

@@ -1,246 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemexport;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.app.itemexport.factory.ItemExportServiceFactory;
-import org.dspace.app.itemexport.service.ItemExportService;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.CollectionService;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.handle.service.HandleService;
-
-/**
- * Item exporter to create simple AIPs for DSpace content. Currently exports
- * individual items, or entire collections. For instructions on use, see
- * printUsage() method.
- * <P>
- * ItemExport creates the simple AIP package that the importer also uses. It
- * consists of:
- * <P>
- * /exportdir/42/ (one directory per item) / dublin_core.xml - qualified dublin
- * core in RDF schema / contents - text file, listing one file per line / file1
- * - files contained in the item / file2 / ...
- * <P>
- * issues -doesn't handle special characters in metadata (needs to turn {@code &'s} into
- * {@code &amp;}, etc.)
- * <P>
- * Modified by David Little, UCSD Libraries 12/21/04 to allow the registration
- * of files (bitstreams) into DSpace.
- *
- * @author David Little
- * @author Jay Paz
- */
-public class ItemExportCLITool {
-
-    protected static ItemExportService itemExportService = ItemExportServiceFactory.getInstance()
-                                                                                   .getItemExportService();
-    protected static HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
-    protected static ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
-
-    /**
-     * Default constructor
-     */
-    private ItemExportCLITool() { }
-
-    /*
-     *
-     */
-    public static void main(String[] argv) throws Exception {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("t", "type", true, "type: COLLECTION or ITEM");
-        options.addOption("i", "id", true, "ID or handle of thing to export");
-        options.addOption("d", "dest", true,
-                          "destination where you want items to go");
-        options.addOption("m", "migrate", false,
-                          "export for migration (remove handle and metadata that will be re-created in new system)");
-        options.addOption("n", "number", true,
-                          "sequence number to begin exporting items with");
-        options.addOption("z", "zip", true, "export as zip file (specify filename e.g. export.zip)");
-        options.addOption("h", "help", false, "help");
-
-        // as pointed out by Peter Dietz this provides similar functionality to export metadata
-        // but it is needed since it directly exports to Simple Archive Format (SAF)
-        options.addOption("x", "exclude-bitstreams", false, "do not export bitstreams");
-
-        CommandLine line = parser.parse(options, argv);
-
-        String typeString = null;
-        String destDirName = null;
-        String myIDString = null;
-        int seqStart = -1;
-        int myType = -1;
-
-        Item myItem = null;
-        Collection mycollection = null;
-
-        if (line.hasOption('h')) {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("ItemExport\n", options);
-            System.out
-                .println("\nfull collection: ItemExport -t COLLECTION -i ID -d dest -n number");
-            System.out
-                .println("singleitem:       ItemExport -t ITEM -i ID -d dest -n number");
-
-            System.exit(0);
-        }
-
-        if (line.hasOption('t')) { // type
-            typeString = line.getOptionValue('t');
-
-            if ("ITEM".equals(typeString)) {
-                myType = Constants.ITEM;
-            } else if ("COLLECTION".equals(typeString)) {
-                myType = Constants.COLLECTION;
-            }
-        }
-
-        if (line.hasOption('i')) { // id
-            myIDString = line.getOptionValue('i');
-        }
-
-        if (line.hasOption('d')) { // dest
-            destDirName = line.getOptionValue('d');
-        }
-
-        if (line.hasOption('n')) { // number
-            seqStart = Integer.parseInt(line.getOptionValue('n'));
-        }
-
-        boolean migrate = false;
-        if (line.hasOption('m')) { // number
-            migrate = true;
-        }
-
-        boolean zip = false;
-        String zipFileName = "";
-        if (line.hasOption('z')) {
-            zip = true;
-            zipFileName = line.getOptionValue('z');
-        }
-
-        boolean excludeBitstreams = false;
-        if (line.hasOption('x')) {
-            excludeBitstreams = true;
-        }
-
-        // now validate the args
-        if (myType == -1) {
-            System.out
-                .println("type must be either COLLECTION or ITEM (-h for help)");
-            System.exit(1);
-        }
-
-        if (destDirName == null) {
-            System.out
-                .println("destination directory must be set (-h for help)");
-            System.exit(1);
-        }
-
-        if (seqStart == -1) {
-            System.out
-                .println("sequence start number must be set (-h for help)");
-            System.exit(1);
-        }
-
-        if (myIDString == null) {
-            System.out
-                .println("ID must be set to either a database ID or a handle (-h for help)");
-            System.exit(1);
-        }
-
-        Context c = new Context(Context.Mode.READ_ONLY);
-        c.turnOffAuthorisationSystem();
-
-        if (myType == Constants.ITEM) {
-            // first, is myIDString a handle?
-            if (myIDString.indexOf('/') != -1) {
-                myItem = (Item) handleService.resolveToObject(c, myIDString);
-
-                if ((myItem == null) || (myItem.getType() != Constants.ITEM)) {
-                    myItem = null;
-                }
-            } else {
-                myItem = itemService.find(c, UUID.fromString(myIDString));
-            }
-
-            if (myItem == null) {
-                System.out
-                    .println("Error, item cannot be found: " + myIDString);
-            }
-        } else {
-            if (myIDString.indexOf('/') != -1) {
-                // has a / must be a handle
-                mycollection = (Collection) handleService.resolveToObject(c,
-                                                                          myIDString);
-
-                // ensure it's a collection
-                if ((mycollection == null)
-                    || (mycollection.getType() != Constants.COLLECTION)) {
-                    mycollection = null;
-                }
-            } else if (myIDString != null) {
-                mycollection = collectionService.find(c, UUID.fromString(myIDString));
-            }
-
-            if (mycollection == null) {
-                System.out.println("Error, collection cannot be found: "
-                                       + myIDString);
-                System.exit(1);
-            }
-        }
-
-        if (zip) {
-            Iterator<Item> items;
-            if (myItem != null) {
-                List<Item> myItems = new ArrayList<>();
-                myItems.add(myItem);
-                items = myItems.iterator();
-            } else {
-                System.out.println("Exporting from collection: " + myIDString);
-                items = itemService.findByCollection(c, mycollection);
-            }
-            itemExportService.exportAsZip(c, items, destDirName, zipFileName, seqStart, migrate, excludeBitstreams);
-        } else {
-            if (myItem != null) {
-                // it's only a single item
-                itemExportService
-                    .exportItem(c, Collections.singletonList(myItem).iterator(), destDirName, seqStart, migrate,
-                                excludeBitstreams);
-            } else {
-                System.out.println("Exporting from collection: " + myIDString);
-
-                // it's a collection, so do a bunch of items
-                Iterator<Item> i = itemService.findByCollection(c, mycollection);
-                itemExportService.exportItem(c, i, destDirName, seqStart, migrate, excludeBitstreams);
-            }
-        }
-
-        c.complete();
-    }
-}

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

@@ -1,26 +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;
-
-/**
- * An exception that can be thrown when error occur during item export
- */
-public class ItemExportException extends Exception {
-    public static final int EXPORT_TOO_LARGE = 0;
-
-    private int reason;
-
-    public ItemExportException(int r, String message) {
-        super(message);
-        reason = r;
-    }
-
-    public int getReason() {
-        return reason;
-    }
-}

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

@@ -1,27 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemexport.factory;
-
-import org.dspace.app.itemexport.service.ItemExportService;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Abstract factory to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to
- * retrieve an implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public abstract class ItemExportServiceFactory {
-
-    public abstract ItemExportService getItemExportService();
-
-    public static ItemExportServiceFactory getInstance() {
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("itemExportServiceFactory", ItemExportServiceFactory.class);
-    }
-}

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

@@ -1,28 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemexport.factory;
-
-import org.dspace.app.itemexport.service.ItemExportService;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Factory implementation to get services for the itemexport package, use ItemExportServiceFactory.getInstance() to
- * retrieve an implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public class ItemExportServiceFactoryImpl extends ItemExportServiceFactory {
-
-    @Autowired(required = true)
-    private ItemExportService itemExportService;
-
-    @Override
-    public ItemExportService getItemExportService() {
-        return itemExportService;
-    }
-}

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

@@ -1,270 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemexport.service;
-
-import java.io.InputStream;
-import java.util.Date;
-import java.util.Iterator;
-import java.util.List;
-import javax.mail.MessagingException;
-
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-
-/**
- * Item exporter to create simple AIPs for DSpace content. Currently exports
- * individual items, or entire collections. For instructions on use, see
- * printUsage() method.
- * <P>
- * ItemExport creates the simple AIP package that the importer also uses. It
- * consists of:
- * <P>
- * /exportdir/42/ (one directory per item) / dublin_core.xml - qualified dublin
- * core in RDF schema / contents - text file, listing one file per line / file1
- * - files contained in the item / file2 / ...
- * <P>
- * issues -doesn't handle special characters in metadata (needs to turn {@code &'s} into
- * {@code &amp;}, etc.)
- * <P>
- * Modified by David Little, UCSD Libraries 12/21/04 to allow the registration
- * of files (bitstreams) into DSpace.
- *
- * @author David Little
- * @author Jay Paz
- */
-public interface ItemExportService {
-
-    /**
-     * used for export download
-     */
-    public static final String COMPRESSED_EXPORT_MIME_TYPE = "application/zip";
-
-    public void exportItem(Context c, Iterator<Item> i,
-                           String destDirName, int seqStart, boolean migrate,
-                           boolean excludeBitstreams) throws Exception;
-
-    /**
-     * Method to perform an export and save it as a zip file.
-     *
-     * @param context           The DSpace Context
-     * @param items             The items to export
-     * @param destDirName       The directory to save the export in
-     * @param zipFileName       The name to save the zip file as
-     * @param seqStart          The first number in the sequence
-     * @param migrate           Whether to use the migrate option or not
-     * @param excludeBitstreams Whether to exclude bitstreams or not
-     * @throws Exception if error
-     */
-    public void exportAsZip(Context context, Iterator<Item> items,
-                            String destDirName, String zipFileName,
-                            int seqStart, boolean migrate,
-                            boolean excludeBitstreams) throws Exception;
-
-    /**
-     * Convenience methot to create export a single Community, Collection, or
-     * Item
-     *
-     * @param dso     - the dspace object to export
-     * @param context - the dspace context
-     * @param migrate Whether to use the migrate option or not
-     * @throws Exception if error
-     */
-    public void createDownloadableExport(DSpaceObject dso,
-                                         Context context, boolean migrate) throws Exception;
-
-    /**
-     * Convenience method to export a List of dspace objects (Community,
-     * Collection or Item)
-     *
-     * @param dsObjects - List containing dspace objects
-     * @param context   - the dspace context
-     * @param migrate   Whether to use the migrate option or not
-     * @throws Exception if error
-     */
-    public void createDownloadableExport(List<DSpaceObject> dsObjects,
-                                         Context context, boolean migrate) throws Exception;
-
-    /**
-     * Convenience methot to create export a single Community, Collection, or
-     * Item
-     *
-     * @param dso             - the dspace object to export
-     * @param context         - the dspace context
-     * @param additionalEmail - cc email to use
-     * @param migrate         Whether to use the migrate option or not
-     * @throws Exception if error
-     */
-    public void createDownloadableExport(DSpaceObject dso,
-                                         Context context, String additionalEmail, boolean migrate) throws Exception;
-
-    /**
-     * Convenience method to export a List of dspace objects (Community,
-     * Collection or Item)
-     *
-     * @param dsObjects       - List containing dspace objects
-     * @param context         - the dspace context
-     * @param additionalEmail - cc email to use
-     * @param migrate         Whether to use the migrate option or not
-     * @throws Exception if error
-     */
-    public void createDownloadableExport(List<DSpaceObject> dsObjects,
-                                         Context context, String additionalEmail, boolean migrate) throws Exception;
-
-
-    /**
-     * Create a file name based on the date and eperson
-     *
-     * @param type    Type of object (as string)
-     * @param eperson - eperson who requested export and will be able to download it
-     * @param date    - the date the export process was created
-     * @return String representing the file name in the form of
-     * 'export_yyy_MMM_dd_count_epersonID'
-     * @throws Exception if error
-     */
-    public String assembleFileName(String type, EPerson eperson,
-                                   Date date) throws Exception;
-
-
-    /**
-     * Use config file entry for org.dspace.app.itemexport.download.dir and id
-     * of the eperson to create a download directory name
-     *
-     * @param ePerson - the eperson who requested export archive
-     * @return String representing a directory in the form of
-     * org.dspace.app.itemexport.download.dir/epersonID
-     * @throws Exception if error
-     */
-    public String getExportDownloadDirectory(EPerson ePerson)
-        throws Exception;
-
-
-    /**
-     * Returns config file entry for org.dspace.app.itemexport.work.dir
-     *
-     * @return String representing config file entry for
-     * org.dspace.app.itemexport.work.dir
-     * @throws Exception if error
-     */
-    public String getExportWorkDirectory() throws Exception;
-
-    /**
-     * Used to read the export archived. Inteded for download.
-     *
-     * @param fileName the name of the file to download
-     * @param eperson  the eperson requesting the download
-     * @return an input stream of the file to be downloaded
-     * @throws Exception if error
-     */
-    public InputStream getExportDownloadInputStream(String fileName,
-                                                    EPerson eperson) throws Exception;
-
-    /**
-     * Get the file size of the export archive represented by the file name.
-     *
-     * @param context  DSpace context
-     * @param fileName name of the file to get the size.
-     * @return size as long
-     * @throws Exception if error
-     */
-    public long getExportFileSize(Context context, String fileName) throws Exception;
-
-    /**
-     * Get the last modified date of the export archive represented by the file name.
-     *
-     * @param context  DSpace context
-     * @param fileName name of the file to get the size.
-     * @return date as long
-     * @throws Exception if error
-     * @see java.io.File#lastModified()
-     */
-    public long getExportFileLastModified(Context context, String fileName)
-        throws Exception;
-
-    /**
-     * The file name of the export archive contains the eperson id of the person
-     * who created it When requested for download this method can check if the
-     * person requesting it is the same one that created it
-     *
-     * @param context  dspace context
-     * @param fileName the file name to check auths for
-     * @return true if it is the same person false otherwise
-     */
-    public boolean canDownload(Context context, String fileName);
-
-    /**
-     * Reads the download directory for the eperson to see if any export
-     * archives are available
-     *
-     * @param eperson EPerson object
-     * @return a list of file names representing export archives that have been
-     * processed
-     * @throws Exception if error
-     */
-    public List<String> getExportsAvailable(EPerson eperson)
-        throws Exception;
-
-    /**
-     * A clean up method that is ran before a new export archive is created. It
-     * uses the config file entry 'org.dspace.app.itemexport.life.span.hours' to
-     * determine if the current exports are too old and need pruging
-     *
-     * @param eperson - the eperson to clean up
-     * @throws Exception if error
-     */
-    public void deleteOldExportArchives(EPerson eperson) throws Exception;
-
-    /**
-     * A clean up method that is ran before a new export archive is created. It
-     * uses the config file entry 'org.dspace.app.itemexport.life.span.hours' to
-     * determine if the current exports are too old and need purgeing
-     * Removes all old exports, not just those for the person doing the export.
-     *
-     * @throws Exception if error
-     */
-    public void deleteOldExportArchives() throws Exception;
-
-    /**
-     * Since the archive is created in a new thread we are unable to communicate
-     * with calling method about success or failure. We accomplis this
-     * communication with email instead. Send a success email once the export
-     * archive is complete and ready for download
-     *
-     * @param context  - the current Context
-     * @param eperson  - eperson to send the email to
-     * @param fileName - the file name to be downloaded. It is added to the url in
-     *                 the email
-     * @throws MessagingException if error
-     */
-    public void emailSuccessMessage(Context context, EPerson eperson,
-                                    String fileName) throws MessagingException;
-
-    /**
-     * Since the archive is created in a new thread we are unable to communicate
-     * with calling method about success or failure. We accomplis this
-     * communication with email instead. Send an error email if the export
-     * archive fails
-     *
-     * @param eperson - EPerson to send the error message to
-     * @param error   - the error message
-     * @throws MessagingException if error
-     */
-    public void emailErrorMessage(EPerson eperson, String error)
-        throws MessagingException;
-
-    /**
-     * Zip source to target
-     *
-     * @param strSource source file
-     * @param target    target file
-     * @throws Exception if error
-     */
-    public void zip(String strSource, String target) throws Exception;
-
-}

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

@@ -1,106 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import gr.ekt.bte.core.DataLoader;
-import gr.ekt.bte.core.TransformationEngine;
-import gr.ekt.bte.dataloader.FileDataLoader;
-
-
-/**
- * This class acts as a Service in the procedure to batch import using the Biblio-Transformation-Engine
- */
-public class BTEBatchImportService {
-
-    TransformationEngine transformationEngine;
-    Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
-    Map<String, String> outputMap = new HashMap<String, String>();
-
-    /**
-     * Default constructor
-     */
-    public BTEBatchImportService() {
-        super();
-    }
-
-    /**
-     * Setter method for dataLoaders parameter
-     *
-     * @param dataLoaders map of data loaders
-     */
-    public void setDataLoaders(Map<String, DataLoader> dataLoaders) {
-        this.dataLoaders = dataLoaders;
-    }
-
-    /**
-     * Get data loaders
-     *
-     * @return the map of DataLoaders
-     */
-    public Map<String, DataLoader> getDataLoaders() {
-        return dataLoaders;
-    }
-
-    /**
-     * Get output map
-     *
-     * @return the outputMapping
-     */
-    public Map<String, String> getOutputMap() {
-        return outputMap;
-    }
-
-    /**
-     * Setter method for the outputMapping
-     *
-     * @param outputMap the output mapping
-     */
-    public void setOutputMap(Map<String, String> outputMap) {
-        this.outputMap = outputMap;
-    }
-
-    /**
-     * Get transformation engine
-     *
-     * @return transformation engine
-     */
-    public TransformationEngine getTransformationEngine() {
-        return transformationEngine;
-    }
-
-    /**
-     * set transformation engine
-     *
-     * @param transformationEngine transformation engine
-     */
-    public void setTransformationEngine(TransformationEngine transformationEngine) {
-        this.transformationEngine = transformationEngine;
-    }
-
-    /**
-     * Getter of file data loaders
-     *
-     * @return List of file data loaders
-     */
-    public List<String> getFileDataLoaders() {
-        List<String> result = new ArrayList<String>();
-
-        for (String key : dataLoaders.keySet()) {
-            DataLoader dl = dataLoaders.get(key);
-            if (dl instanceof FileDataLoader) {
-                result.add(key);
-            }
-        }
-        return result;
-    }
-}

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

@@ -1,229 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.LineNumberReader;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.GregorianCalendar;
-import java.util.List;
-
-/**
- * @author kstamatis
- */
-public class BatchUpload {
-
-    private Date date;
-    private File dir;
-    private boolean successful;
-    private int itemsImported;
-    private int totalItems = 0;
-    private List<String> handlesImported = new ArrayList<String>();
-    private String errorMsg = "";
-    private String errorMsgHTML = "";
-
-    /**
-     * Initialize with directory
-     *
-     * @param dirPath directory path
-     */
-    public BatchUpload(String dirPath) {
-
-        this.initializeWithFile(new File(dirPath));
-
-    }
-
-    /**
-     * Initialize with directory
-     *
-     * @param dir directory path
-     */
-    public BatchUpload(File dir) {
-
-        this.initializeWithFile(dir);
-
-    }
-
-    /**
-     * Initialize with directory
-     *
-     * @param dir directory path
-     */
-    private void initializeWithFile(File dir) {
-
-        this.dir = dir;
-
-        String dirName = dir.getName();
-        long timeMillis = Long.parseLong(dirName);
-        Calendar calendar = new GregorianCalendar();
-        calendar.setTimeInMillis(timeMillis);
-        this.date = calendar.getTime();
-
-        try {
-            this.itemsImported = countLines(dir + File.separator + "mapfile");
-        } catch (IOException e) {
-            e.printStackTrace();
-        }
-
-        for (File file : dir.listFiles()) {
-            if (file.isDirectory()) {
-                this.totalItems = file.list().length;
-            }
-        }
-
-        this.successful = this.totalItems == this.itemsImported;
-
-        //Parse possible error message
-
-        File errorFile = new File(dir + File.separator + "error.txt");
-        if (errorFile.exists()) {
-            try {
-                readFile(dir + File.separator + "error.txt");
-            } catch (IOException e) {
-                // TODO Auto-generated catch block
-                e.printStackTrace();
-            }
-        }
-    }
-
-    /**
-     * Count lines in file
-     *
-     * @param filename file name
-     * @return lines in file
-     * @throws IOException if IO error
-     */
-    private int countLines(String filename) throws IOException {
-        LineNumberReader reader = new LineNumberReader(new FileReader(filename));
-        int cnt = 0;
-        String lineRead = "";
-        while ((lineRead = reader.readLine()) != null) {
-            String[] parts = lineRead.split(" ");
-            if (parts.length > 1) {
-                handlesImported.add(parts[1].trim());
-            } else {
-                handlesImported.add(lineRead);
-            }
-        }
-
-        cnt = reader.getLineNumber();
-        reader.close();
-        return cnt;
-    }
-
-    /**
-     * Read a file
-     *
-     * @param filename file name
-     * @throws IOException if IO error
-     */
-    private void readFile(String filename) throws IOException {
-        LineNumberReader reader = new LineNumberReader(new FileReader(filename));
-        String lineRead = "";
-        while ((lineRead = reader.readLine()) != null) {
-            this.errorMsg += lineRead + "\n";
-
-            if (lineRead.startsWith("\tat ")) {
-                this.errorMsgHTML += "<span class=\"batchimport-error-tab\">" + lineRead + "</span><br/>";
-            } else if (lineRead.startsWith("Caused by")) {
-                this.errorMsgHTML += "<span class=\"batchimport-error-caused\">" + lineRead + "</span><br/>";
-            } else {
-                this.errorMsgHTML += lineRead + "<br/>";
-            }
-        }
-        reader.close();
-    }
-
-    /**
-     * Get date
-     *
-     * @return Date
-     */
-    public Date getDate() {
-        return date;
-    }
-
-    /**
-     * Get path to directory
-     *
-     * @return directory
-     */
-    public File getDir() {
-        return dir;
-    }
-
-    /**
-     * Whether successulf
-     *
-     * @return true or false
-     */
-    public boolean isSuccessful() {
-        return successful;
-    }
-
-    /**
-     * Get items imported
-     *
-     * @return number of items
-     */
-    public int getItemsImported() {
-        return itemsImported;
-    }
-
-    /**
-     * Get total items
-     *
-     * @return total
-     */
-    public int getTotalItems() {
-        return totalItems;
-    }
-
-    /**
-     * Get formatted date (DD/MM/YY)
-     *
-     * @return date as string
-     */
-    public String getDateFormatted() {
-        SimpleDateFormat df = new SimpleDateFormat("dd/MM/yyyy - HH:mm");
-
-        return df.format(date);
-    }
-
-    /**
-     * Get handles of imported files
-     *
-     * @return list of handles
-     */
-    public List<String> getHandlesImported() {
-        return handlesImported;
-    }
-
-    /**
-     * Get error message
-     *
-     * @return error message
-     */
-    public String getErrorMsg() {
-        return errorMsg;
-    }
-
-    /**
-     * Get error message as HTML
-     *
-     * @return error message string as HTML
-     */
-    public String getErrorMsgHTML() {
-        return errorMsgHTML;
-    }
-}

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

@@ -1,431 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport;
-
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.app.itemimport.factory.ItemImportServiceFactory;
-import org.dspace.app.itemimport.service.ItemImportService;
-import org.dspace.content.Collection;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.CollectionService;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.EPersonService;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.handle.service.HandleService;
-
-/**
- * Import items into DSpace. The conventional use is upload files by copying
- * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
- * also loaded to the DSpace database.
- * <P>
- * A second use assumes the bitstream files already exist in a storage
- * resource accessible to DSpace. In this case the bitstreams are 'registered'.
- * That is, the metadata is loaded to the DSpace database and DSpace is given
- * the location of the file which is subsumed into DSpace.
- * <P>
- * The distinction is controlled by the format of lines in the 'contents' file.
- * See comments in processContentsFile() below.
- * <P>
- * Modified by David Little, UCSD Libraries 12/21/04 to
- * allow the registration of files (bitstreams) into DSpace.
- */
-public class ItemImportCLITool {
-
-    private static boolean template = false;
-
-    private static final CollectionService collectionService = ContentServiceFactory.getInstance()
-                                                                                    .getCollectionService();
-    private static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    private static final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
-
-    /**
-     * Default constructor
-     */
-    private ItemImportCLITool() { }
-
-    public static void main(String[] argv) throws Exception {
-        Date startTime = new Date();
-        int status = 0;
-
-        try {
-            // create an options object and populate it
-            CommandLineParser parser = new PosixParser();
-
-            Options options = new Options();
-
-            options.addOption("a", "add", false, "add items to DSpace");
-            options.addOption("b", "add-bte", false, "add items to DSpace via Biblio-Transformation-Engine (BTE)");
-            options.addOption("r", "replace", false, "replace items in mapfile");
-            options.addOption("d", "delete", false,
-                              "delete items listed in mapfile");
-            options.addOption("i", "inputtype", true, "input type in case of BTE import");
-            options.addOption("s", "source", true, "source of items (directory)");
-            options.addOption("z", "zip", true, "name of zip file");
-            options.addOption("c", "collection", true,
-                              "destination collection(s) Handle or database ID");
-            options.addOption("m", "mapfile", true, "mapfile items in mapfile");
-            options.addOption("e", "eperson", true,
-                              "email of eperson doing importing");
-            options.addOption("w", "workflow", false,
-                              "send submission through collection's workflow");
-            options.addOption("n", "notify", false,
-                              "if sending submissions through the workflow, send notification emails");
-            options.addOption("t", "test", false,
-                              "test run - do not actually import items");
-            options.addOption("p", "template", false, "apply template");
-            options.addOption("R", "resume", false,
-                              "resume a failed import (add only)");
-            options.addOption("q", "quiet", false, "don't display metadata");
-
-            options.addOption("h", "help", false, "help");
-
-            CommandLine line = parser.parse(options, argv);
-
-            String command = null; // add replace remove, etc
-            String bteInputType = null; //ris, endnote, tsv, csv, bibtex
-            String sourcedir = null;
-            String mapfile = null;
-            String eperson = null; // db ID or email
-            String[] collections = null; // db ID or handles
-            boolean isTest = false;
-            boolean isResume = false;
-            boolean useWorkflow = false;
-            boolean useWorkflowSendEmail = false;
-            boolean isQuiet = false;
-
-            if (line.hasOption('h')) {
-                HelpFormatter myhelp = new HelpFormatter();
-                myhelp.printHelp("ItemImport\n", options);
-                System.out
-                    .println("\nadding items:    ItemImport -a -e eperson -c collection -s sourcedir -m mapfile");
-                System.out
-                    .println(
-                        "\nadding items from zip file:    ItemImport -a -e eperson -c collection -s sourcedir -z " +
-                            "filename.zip -m mapfile");
-                System.out
-                    .println("replacing items: ItemImport -r -e eperson -c collection -s sourcedir -m mapfile");
-                System.out
-                    .println("deleting items:  ItemImport -d -e eperson -m mapfile");
-                System.out
-                    .println(
-                        "If multiple collections are specified, the first collection will be the one that owns the " +
-                            "item.");
-
-                System.exit(0);
-            }
-
-            if (line.hasOption('a')) {
-                command = "add";
-            }
-
-            if (line.hasOption('r')) {
-                command = "replace";
-            }
-
-            if (line.hasOption('d')) {
-                command = "delete";
-            }
-
-            if (line.hasOption('b')) {
-                command = "add-bte";
-            }
-
-            if (line.hasOption('i')) {
-                bteInputType = line.getOptionValue('i');
-            }
-
-            if (line.hasOption('w')) {
-                useWorkflow = true;
-                if (line.hasOption('n')) {
-                    useWorkflowSendEmail = true;
-                }
-            }
-
-            if (line.hasOption('t')) {
-                isTest = true;
-                System.out.println("**Test Run** - not actually importing items.");
-            }
-
-            if (line.hasOption('p')) {
-                template = true;
-            }
-
-            if (line.hasOption('s')) { // source
-                sourcedir = line.getOptionValue('s');
-            }
-
-            if (line.hasOption('m')) { // mapfile
-                mapfile = line.getOptionValue('m');
-            }
-
-            if (line.hasOption('e')) { // eperson
-                eperson = line.getOptionValue('e');
-            }
-
-            if (line.hasOption('c')) { // collections
-                collections = line.getOptionValues('c');
-            }
-
-            if (line.hasOption('R')) {
-                isResume = true;
-                System.out
-                    .println("**Resume import** - attempting to import items not already imported");
-            }
-
-            if (line.hasOption('q')) {
-                isQuiet = true;
-            }
-
-            boolean zip = false;
-            String zipfilename = "";
-            if (line.hasOption('z')) {
-                zip = true;
-                zipfilename = line.getOptionValue('z');
-            }
-
-            //By default assume collections will be given on the command line
-            boolean commandLineCollections = true;
-            // now validate
-            // must have a command set
-            if (command == null) {
-                System.out
-                    .println("Error - must run with either add, replace, or remove (run with -h flag for details)");
-                System.exit(1);
-            } else if ("add".equals(command) || "replace".equals(command)) {
-                if (sourcedir == null) {
-                    System.out
-                        .println("Error - a source directory containing items must be set");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-
-                if (mapfile == null) {
-                    System.out
-                        .println("Error - a map file to hold importing results must be specified");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-
-                if (eperson == null) {
-                    System.out
-                        .println("Error - an eperson to do the importing must be specified");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-
-                if (collections == null) {
-                    System.out.println("No collections given. Assuming 'collections' file inside item directory");
-                    commandLineCollections = false;
-                }
-            } else if ("add-bte".equals(command)) {
-                //Source dir can be null, the user can specify the parameters for his loader in the Spring XML
-                // configuration file
-
-                if (mapfile == null) {
-                    System.out
-                        .println("Error - a map file to hold importing results must be specified");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-
-                if (eperson == null) {
-                    System.out
-                        .println("Error - an eperson to do the importing must be specified");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-
-                if (collections == null) {
-                    System.out.println("No collections given. Assuming 'collections' file inside item directory");
-                    commandLineCollections = false;
-                }
-
-                if (bteInputType == null) {
-                    System.out
-                        .println(
-                            "Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have " +
-                                "specified in BTE Spring XML configuration file) must be specified");
-                    System.out.println(" (run with -h flag for details)");
-                    System.exit(1);
-                }
-            } else if ("delete".equals(command)) {
-                if (eperson == null) {
-                    System.out
-                        .println("Error - an eperson to do the importing must be specified");
-                    System.exit(1);
-                }
-
-                if (mapfile == null) {
-                    System.out.println("Error - a map file must be specified");
-                    System.exit(1);
-                }
-            }
-
-            // can only resume for adds
-            if (isResume && !"add".equals(command) && !"add-bte".equals(command)) {
-                System.out
-                    .println("Error - resume option only works with the --add or the --add-bte commands");
-                System.exit(1);
-            }
-
-            // do checks around mapfile - if mapfile exists and 'add' is selected,
-            // resume must be chosen
-            File myFile = new File(mapfile);
-
-            if (!isResume && "add".equals(command) && myFile.exists()) {
-                System.out.println("Error - the mapfile " + mapfile
-                                       + " already exists.");
-                System.out
-                    .println("Either delete it or use --resume if attempting to resume an aborted import.");
-                System.exit(1);
-            }
-
-            ItemImportService myloader = ItemImportServiceFactory.getInstance().getItemImportService();
-            myloader.setTest(isTest);
-            myloader.setResume(isResume);
-            myloader.setUseWorkflow(useWorkflow);
-            myloader.setUseWorkflowSendEmail(useWorkflowSendEmail);
-            myloader.setQuiet(isQuiet);
-
-            // create a context
-            Context c = new Context(Context.Mode.BATCH_EDIT);
-
-            // find the EPerson, assign to context
-            EPerson myEPerson = null;
-
-            if (eperson.indexOf('@') != -1) {
-                // @ sign, must be an email
-                myEPerson = epersonService.findByEmail(c, eperson);
-            } else {
-                myEPerson = epersonService.find(c, UUID.fromString(eperson));
-            }
-
-            if (myEPerson == null) {
-                System.out.println("Error, eperson cannot be found: " + eperson);
-                System.exit(1);
-            }
-
-            c.setCurrentUser(myEPerson);
-
-            // find collections
-            List<Collection> mycollections = null;
-
-            // don't need to validate collections set if command is "delete"
-            // also if no collections are given in the command line
-            if (!"delete".equals(command) && commandLineCollections) {
-                System.out.println("Destination collections:");
-
-                mycollections = new ArrayList<>();
-
-                // validate each collection arg to see if it's a real collection
-                for (int i = 0; i < collections.length; i++) {
-                    // is the ID a handle?
-                    if (collections[i].indexOf('/') != -1) {
-                        // string has a / so it must be a handle - try and resolve
-                        // it
-                        mycollections.add((Collection) handleService
-                            .resolveToObject(c, collections[i]));
-
-                        // resolved, now make sure it's a collection
-                        if ((mycollections.get(i) == null)
-                            || (mycollections.get(i).getType() != Constants.COLLECTION)) {
-                            mycollections.set(i, null);
-                        }
-                    } else if (collections[i] != null) {
-                        // not a handle, try and treat it as an integer collection database ID
-                        mycollections.set(i, collectionService.find(c, UUID.fromString(collections[i])));
-                    }
-
-                    // was the collection valid?
-                    if (mycollections.get(i) == null) {
-                        throw new IllegalArgumentException("Cannot resolve "
-                                                               + collections[i] + " to collection");
-                    }
-
-                    // print progress info
-                    String owningPrefix = "";
-
-                    if (i == 0) {
-                        owningPrefix = "Owning ";
-                    }
-
-                    System.out.println(owningPrefix + " Collection: "
-                                           + mycollections.get(i).getName());
-                }
-            } // end of validating collections
-
-            try {
-                // If this is a zip archive, unzip it first
-                if (zip) {
-                    sourcedir = myloader.unzip(sourcedir, zipfilename);
-                }
-
-
-                c.turnOffAuthorisationSystem();
-
-                if ("add".equals(command)) {
-                    myloader.addItems(c, mycollections, sourcedir, mapfile, template);
-                } else if ("replace".equals(command)) {
-                    myloader.replaceItems(c, mycollections, sourcedir, mapfile, template);
-                } else if ("delete".equals(command)) {
-                    myloader.deleteItems(c, mapfile);
-                } else if ("add-bte".equals(command)) {
-                    myloader.addBTEItems(c, mycollections, sourcedir, mapfile, template, bteInputType, null);
-                }
-
-                // complete all transactions
-                c.complete();
-            } catch (Exception e) {
-                c.abort();
-                e.printStackTrace();
-                System.out.println(e);
-                status = 1;
-            }
-
-            // Delete the unzipped file
-            try {
-                if (zip) {
-                    System.gc();
-                    System.out.println(
-                        "Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
-                    myloader.cleanupZipTemp();
-                }
-            } catch (Exception ex) {
-                System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile()
-                                                                                                 .getAbsolutePath());
-            }
-
-
-            if (isTest) {
-                System.out.println("***End of Test Run***");
-            }
-        } finally {
-            Date endTime = new Date();
-            System.out.println("Started: " + startTime.getTime());
-            System.out.println("Ended: " + endTime.getTime());
-            System.out.println(
-                "Elapsed time: " + ((endTime.getTime() - startTime.getTime()) / 1000) + " secs (" + (endTime
-                    .getTime() - startTime.getTime()) + " msecs)");
-        }
-
-        System.exit(status);
-    }
-}

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

@@ -1,27 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport.factory;
-
-import org.dspace.app.itemimport.service.ItemImportService;
-import org.dspace.services.factory.DSpaceServicesFactory;
-
-/**
- * Abstract factory to get services for the itemimport package, use ItemImportService.getInstance() to retrieve an
- * implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public abstract class ItemImportServiceFactory {
-
-    public abstract ItemImportService getItemImportService();
-
-    public static ItemImportServiceFactory getInstance() {
-        return DSpaceServicesFactory.getInstance().getServiceManager()
-                                    .getServiceByName("itemImportServiceFactory", ItemImportServiceFactory.class);
-    }
-}

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

@@ -1,28 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport.factory;
-
-import org.dspace.app.itemimport.service.ItemImportService;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Factory implementation to get services for the itemimport package, use ItemImportService.getInstance() to retrieve
- * an implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public class ItemImportServiceFactoryImpl extends ItemImportServiceFactory {
-
-    @Autowired(required = true)
-    private ItemImportService itemImportService;
-
-    @Override
-    public ItemImportService getItemImportService() {
-        return itemImportService;
-    }
-}

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

@@ -1,253 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport.service;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.List;
-import javax.mail.MessagingException;
-
-import org.dspace.app.itemimport.BatchUpload;
-import org.dspace.content.Collection;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-
-/**
- * Import items into DSpace. The conventional use is upload files by copying
- * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
- * also loaded to the DSpace database.
- * <P>
- * A second use assumes the bitstream files already exist in a storage
- * resource accessible to DSpace. In this case the bitstreams are 'registered'.
- * That is, the metadata is loaded to the DSpace database and DSpace is given
- * the location of the file which is subsumed into DSpace.
- * <P>
- * The distinction is controlled by the format of lines in the 'contents' file.
- * See comments in processContentsFile() below.
- * <P>
- * Modified by David Little, UCSD Libraries 12/21/04 to
- * allow the registration of files (bitstreams) into DSpace.
- */
-public interface ItemImportService {
-
-
-    /**
-     * @param c             DSpace Context
-     * @param mycollections List of Collections
-     * @param sourceDir     source location
-     * @param mapFile       map file
-     * @param template      whether to use template item
-     * @throws Exception if error
-     */
-    public void addItemsAtomic(Context c, List<Collection> mycollections, String sourceDir, String mapFile,
-                               boolean template) throws Exception;
-
-    /**
-     * Add items
-     *
-     * @param c             DSpace Context
-     * @param mycollections List of Collections
-     * @param sourceDir     source location
-     * @param mapFile       map file
-     * @param template      whether to use template item
-     * @throws Exception if error
-     */
-    public void addItems(Context c, List<Collection> mycollections,
-                         String sourceDir, String mapFile, boolean template) throws Exception;
-
-    /**
-     * Unzip a file
-     *
-     * @param zipfile file
-     * @return unzip location
-     * @throws IOException if error
-     */
-    public String unzip(File zipfile) throws IOException;
-
-    /**
-     * Unzip a file to a destination
-     *
-     * @param zipfile file
-     * @param destDir destination directory
-     * @return unzip location
-     * @throws IOException if error
-     */
-    public String unzip(File zipfile, String destDir) throws IOException;
-
-    /**
-     * Unzip a file in a specific source directory
-     *
-     * @param sourcedir   source directory
-     * @param zipfilename file name
-     * @return unzip location
-     * @throws IOException if error
-     */
-    public String unzip(String sourcedir, String zipfilename) throws IOException;
-
-    /**
-     * Given a public URL to a zip file that has the Simple Archive Format, this method imports the contents to DSpace
-     *
-     * @param url              The public URL of the zip file
-     * @param owningCollection The owning collection the items will belong to
-     * @param collections      The collections the created items will be inserted to, apart from the owning one
-     * @param resumeDir        In case of a resume request, the directory that containsthe old mapfile and data
-     * @param inputType        The input type of the data (bibtex, csv, etc.), in case of local file
-     * @param context          The context
-     * @param template         whether to use template item
-     * @throws Exception if error
-     */
-    public void processUIImport(String url, Collection owningCollection, String[] collections, String resumeDir,
-                                String inputType, Context context, boolean template) throws Exception;
-
-    /**
-     * Since the BTE batch import is done in a new thread we are unable to communicate
-     * with calling method about success or failure. We accomplish this
-     * communication with email instead. Send a success email once the batch
-     * import is complete
-     *
-     * @param context  - the current Context
-     * @param eperson  - eperson to send the email to
-     * @param fileName - the filepath to the mapfile created by the batch import
-     * @throws MessagingException if error
-     */
-    public void emailSuccessMessage(Context context, EPerson eperson,
-                                    String fileName) throws MessagingException;
-
-    /**
-     * Since the BTE batch import is done in a new thread we are unable to communicate
-     * with calling method about success or failure. We accomplis this
-     * communication with email instead. Send an error email if the batch
-     * import fails
-     *
-     * @param eperson - EPerson to send the error message to
-     * @param error   - the error message
-     * @throws MessagingException if error
-     */
-    public void emailErrorMessage(EPerson eperson, String error)
-        throws MessagingException;
-
-
-    /**
-     * Get imports available for a person
-     *
-     * @param eperson EPerson object
-     * @return List of batch uploads
-     * @throws Exception if error
-     */
-    public List<BatchUpload> getImportsAvailable(EPerson eperson)
-        throws Exception;
-
-    /**
-     * Get import upload directory
-     *
-     * @param ePerson EPerson object
-     * @return directory
-     * @throws Exception if error
-     */
-    public String getImportUploadableDirectory(EPerson ePerson)
-        throws Exception;
-
-    /**
-     * Delete a batch by ID
-     *
-     * @param c        DSpace Context
-     * @param uploadId identifier
-     * @throws Exception if error
-     */
-    public void deleteBatchUpload(Context c, String uploadId) throws Exception;
-
-    /**
-     * Replace items
-     *
-     * @param c             DSpace Context
-     * @param mycollections List of Collections
-     * @param sourcedir     source directory
-     * @param mapfile       map file
-     * @param template      whether to use template item
-     * @throws Exception if error
-     */
-    public void replaceItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile,
-                             boolean template) throws Exception;
-
-    /**
-     * Delete items via mapfile
-     *
-     * @param c       DSpace Context
-     * @param mapfile map file
-     * @throws Exception if error
-     */
-    public void deleteItems(Context c, String mapfile) throws Exception;
-
-    /**
-     * Add items
-     *
-     * @param c             DSpace Context
-     * @param mycollections List of Collections
-     * @param sourcedir     source directory
-     * @param mapfile       map file
-     * @param template      whether to use template item
-     * @param bteInputType  The input type of the data (bibtex, csv, etc.), in case of local file
-     * @param workingDir    working directory
-     * @throws Exception if error
-     */
-    public void addBTEItems(Context c, List<Collection> mycollections, String sourcedir, String mapfile,
-                            boolean template, String bteInputType, String workingDir) throws Exception;
-
-    /**
-     * Get temporary work directory
-     *
-     * @return directory as string
-     */
-    public String getTempWorkDir();
-
-    /**
-     * Get temporary work directory (as File)
-     *
-     * @return directory as File
-     * @throws java.io.IOException if the directory cannot be created.
-     */
-    public File getTempWorkDirFile() throws IOException;
-
-    /**
-     * Cleanup
-     */
-    public void cleanupZipTemp();
-
-    /**
-     * Set test flag
-     *
-     * @param isTest true or false
-     */
-    public void setTest(boolean isTest);
-
-    /**
-     * Set resume flag
-     *
-     * @param isResume true or false
-     */
-    public void setResume(boolean isResume);
-
-    /**
-     * Set use workflow
-     *
-     * @param useWorkflow whether to enable workflow
-     */
-    public void setUseWorkflow(boolean useWorkflow);
-
-    /**
-     * @param useWorkflowSendMail whether to send mail
-     */
-    public void setUseWorkflowSendEmail(boolean useWorkflowSendMail);
-
-    /**
-     * Set quiet flag
-     *
-     * @param isQuiet true or false
-     */
-    public void setQuiet(boolean isQuiet);
-}

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

@@ -1,93 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemmarking;
-
-import java.io.UnsupportedEncodingException;
-import java.sql.SQLException;
-import java.util.List;
-
-import org.dspace.app.util.Util;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.Item;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This is an item marking Strategy class that tries to mark an item availability
- * based on the existence of bitstreams within the ORIGINAL bundle.
- *
- * @author Kostas Stamatis
- */
-public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtractor {
-
-    private String availableImageName;
-    private String nonAvailableImageName;
-
-    @Autowired(required = true)
-    protected ItemService itemService;
-
-    public ItemMarkingAvailabilityBitstreamStrategy() {
-
-    }
-
-    @Override
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-        throws SQLException {
-
-        List<Bundle> bundles = itemService.getBundles(item, "ORIGINAL");
-        if (bundles.size() == 0) {
-            ItemMarkingInfo markInfo = new ItemMarkingInfo();
-            markInfo.setImageName(nonAvailableImageName);
-
-            return markInfo;
-        } else {
-            Bundle originalBundle = bundles.iterator().next();
-            if (originalBundle.getBitstreams().size() == 0) {
-                ItemMarkingInfo markInfo = new ItemMarkingInfo();
-                markInfo.setImageName(nonAvailableImageName);
-
-                return markInfo;
-            } else {
-                Bitstream bitstream = originalBundle.getBitstreams().get(0);
-
-                ItemMarkingInfo signInfo = new ItemMarkingInfo();
-                signInfo.setImageName(availableImageName);
-                signInfo.setTooltip(bitstream.getName());
-
-
-                String bsLink = "";
-
-                bsLink = bsLink + "bitstream/"
-                    + item.getHandle() + "/"
-                    + bitstream.getSequenceID() + "/";
-
-                try {
-                    bsLink = bsLink + Util.encodeBitstreamName(bitstream.getName(), Constants.DEFAULT_ENCODING);
-                } catch (UnsupportedEncodingException e) {
-
-                    e.printStackTrace();
-                }
-
-                signInfo.setLink(bsLink);
-
-                return signInfo;
-            }
-        }
-    }
-
-    public void setAvailableImageName(String availableImageName) {
-        this.availableImageName = availableImageName;
-    }
-
-    public void setNonAvailableImageName(String nonAvailableImageName) {
-        this.nonAvailableImageName = nonAvailableImageName;
-    }
-}

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

@@ -1,49 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemmarking;
-
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * This is an item marking Strategy class that tries to mark an item
- * based on the collection the items belong to
- *
- * @author Kostas Stamatis
- */
-public class ItemMarkingCollectionStrategy implements ItemMarkingExtractor {
-
-    Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
-
-    public ItemMarkingCollectionStrategy() {
-    }
-
-    @Override
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-        throws SQLException {
-
-        if (mapping != null) {
-            for (Collection collection : item.getCollections()) {
-                if (mapping.containsKey(collection.getHandle())) {
-                    return mapping.get(collection.getHandle());
-                }
-            }
-        }
-
-        return null;
-    }
-
-    public void setMapping(Map<String, ItemMarkingInfo> mapping) {
-        this.mapping = mapping;
-    }
-}

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

@@ -1,23 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemmarking;
-
-import java.sql.SQLException;
-
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * Interface to abstract the strategy for item signing
- *
- * @author Kostas Stamatis
- */
-public interface ItemMarkingExtractor {
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-        throws SQLException;
-}

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

@@ -1,56 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemmarking;
-
-/**
- * Simple DTO to transfer data about the marking info for an item
- *
- * @author Kostas Stamatis
- */
-public class ItemMarkingInfo {
-    private String imageName;
-    private String classInfo;
-    private String tooltip;
-    private String link;
-
-    public ItemMarkingInfo() {
-        super();
-    }
-
-    public String getImageName() {
-        return imageName;
-    }
-
-    public void setImageName(String imageName) {
-        this.imageName = imageName;
-    }
-
-    public String getTooltip() {
-        return tooltip;
-    }
-
-    public void setTooltip(String tooltip) {
-        this.tooltip = tooltip;
-    }
-
-    public String getLink() {
-        return link;
-    }
-
-    public void setLink(String link) {
-        this.link = link;
-    }
-
-    public String getClassInfo() {
-        return classInfo;
-    }
-
-    public void setClassInfo(String classInfo) {
-        this.classInfo = classInfo;
-    }
-}

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

@@ -1,64 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemmarking;
-
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.dspace.content.Item;
-import org.dspace.content.MetadataValue;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Context;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * This is an item marking Strategy class that tries to mark an item
- * based on the existence of a specific value within the values of a specific
- * metadata field
- *
- * @author Kostas Stamatis
- */
-public class ItemMarkingMetadataStrategy implements ItemMarkingExtractor {
-
-    @Autowired(required = true)
-    protected ItemService itemService;
-
-    private String metadataField;
-    Map<String, ItemMarkingInfo> mapping = new HashMap<String, ItemMarkingInfo>();
-
-    public ItemMarkingMetadataStrategy() {
-    }
-
-    @Override
-    public ItemMarkingInfo getItemMarkingInfo(Context context, Item item)
-        throws SQLException {
-
-        if (metadataField != null && mapping != null) {
-            List<MetadataValue> vals = itemService.getMetadataByMetadataString(item, metadataField);
-            if (vals.size() > 0) {
-                for (MetadataValue value : vals) {
-                    String type = value.getValue();
-                    if (mapping.containsKey(type)) {
-                        return mapping.get(type);
-                    }
-                }
-            }
-        }
-        return null;
-    }
-
-    public void setMetadataField(String metadataField) {
-        this.metadataField = metadataField;
-    }
-
-    public void setMapping(Map<String, ItemMarkingInfo> mapping) {
-        this.mapping = mapping;
-    }
-}

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

@@ -1,81 +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.itemupdate;
-
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-/**
- * Container for UpdateActions
- * Order of actions is very import for correct processing.  This implementation
- * supports an iterator that returns the actions in the order in which they are
- * put in.  Adding the same action a second time has no effect on this order.
- */
-public class ActionManager implements Iterable<UpdateAction> {
-
-    protected Map<Class<? extends UpdateAction>, UpdateAction> registry
-        = new LinkedHashMap<Class<? extends UpdateAction>, UpdateAction>();
-
-    /**
-     * Get update action
-     *
-     * @param actionClass UpdateAction class
-     * @return instantiation of UpdateAction class
-     * @throws InstantiationException if instantiation error
-     * @throws IllegalAccessException if illegal access error
-     */
-    public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass)
-        throws InstantiationException, IllegalAccessException {
-        UpdateAction action = registry.get(actionClass);
-
-        if (action == null) {
-            action = actionClass.newInstance();
-            registry.put(actionClass, action);
-        }
-
-        return action;
-    }
-
-    /**
-     * @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
-     */
-    @Override
-    public Iterator<UpdateAction> iterator() {
-        return new Iterator<UpdateAction>() {
-            private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
-
-            @Override
-            public boolean hasNext() {
-                return itr.hasNext();
-            }
-
-            @Override
-            public UpdateAction next() {
-                return registry.get(itr.next());
-            }
-
-            //not supported
-            @Override
-            public void remove() {
-                throw new UnsupportedOperationException();
-            }
-        };
-
-    }
-}

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

@@ -1,208 +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.itemupdate;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.authorize.factory.AuthorizeServiceFactory;
-import org.dspace.authorize.service.AuthorizeService;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.BitstreamFormatService;
-import org.dspace.content.service.InstallItemService;
-import org.dspace.core.Context;
-import org.dspace.eperson.Group;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.GroupService;
-
-/**
- * Action to add bitstreams listed in item contents file to the item in DSpace
- */
-public class AddBitstreamsAction extends UpdateBitstreamsAction {
-
-    protected AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
-    protected BitstreamFormatService bitstreamFormatService = ContentServiceFactory.getInstance()
-                                                                                   .getBitstreamFormatService();
-    protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
-    protected InstallItemService installItemService = ContentServiceFactory.getInstance().getInstallItemService();
-
-    public AddBitstreamsAction() {
-        //empty
-    }
-
-    /**
-     * Adds bitstreams from the archive as listed in the contents file.
-     *
-     * @param context      DSpace Context
-     * @param itarch       Item Archive
-     * @param isTest       test flag
-     * @param suppressUndo undo flag
-     * @throws IOException              if IO error
-     * @throws IllegalArgumentException if arg exception
-     * @throws SQLException             if database error
-     * @throws AuthorizeException       if authorization error
-     * @throws ParseException           if parse error
-     */
-    @Override
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws IllegalArgumentException,
-        ParseException, IOException, AuthorizeException, SQLException {
-        Item item = itarch.getItem();
-        File dir = itarch.getDirectory();
-
-        List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
-
-        if (contents.isEmpty()) {
-            ItemUpdate.pr("Contents is empty - no bitstreams to add");
-            return;
-        }
-
-        ItemUpdate.pr("Contents bitstream count: " + contents.size());
-
-        String[] files = dir.list(ItemUpdate.fileFilter);
-        List<String> fileList = new ArrayList<String>();
-        for (String filename : files) {
-            fileList.add(filename);
-            ItemUpdate.pr("file: " + filename);
-        }
-
-        for (ContentsEntry ce : contents) {
-            //validate match to existing file in archive
-            if (!fileList.contains(ce.filename)) {
-                throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
-            }
-        }
-        int bitstream_bundles_updated = 0;
-
-        //now okay to add
-        for (ContentsEntry ce : contents) {
-            String targetBundleName = addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
-            if (!targetBundleName.equals("")
-                && !targetBundleName.equals("THUMBNAIL")
-                && !targetBundleName.equals("TEXT")) {
-                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);
-
-        // 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.filename.equals("license.txt")) {
-                newBundleName = "LICENSE";
-            } else {
-                newBundleName = "ORIGINAL";
-            }
-        }
-        ItemUpdate.pr("  Bitstream " + ce.filename + " to be added to bundle: " + newBundleName);
-
-        if (!isTest) {
-            // find the bundle
-            List<Bundle> bundles = itemService.getBundles(item, newBundleName);
-            Bundle targetBundle = null;
-
-            if (bundles.size() < 1) {
-                // not found, create a new one
-                targetBundle = bundleService.create(context, item, newBundleName);
-            } else {
-                //verify bundle + name are not duplicates
-                for (Bundle b : bundles) {
-                    List<Bitstream> bitstreams = b.getBitstreams();
-                    for (Bitstream bsm : bitstreams) {
-                        if (bsm.getName().equals(ce.filename)) {
-                            throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: "
-                                                                   + b.getName() + " + " + bsm.getName());
-                        }
-                    }
-                }
-
-                // select first bundle
-                targetBundle = bundles.iterator().next();
-            }
-
-            bs = bitstreamService.create(context, targetBundle, bis);
-            bs.setName(context, ce.filename);
-
-            // Identify the format
-            // FIXME - guessing format guesses license.txt incorrectly as a text file format!
-            BitstreamFormat fmt = bitstreamFormatService.guessFormat(context, bs);
-            bitstreamService.setFormat(context, bs, fmt);
-
-            if (ce.description != null) {
-                bs.setDescription(context, ce.description);
-            }
-
-            if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null)) {
-                Group group = groupService.findByName(context, ce.permissionsGroupName);
-
-                if (group != null) {
-                    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 "";
-    }
-
-}

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

@@ -1,117 +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.itemupdate;
-
-import java.sql.SQLException;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.MetadataValue;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.MetadataFieldService;
-import org.dspace.content.service.MetadataSchemaService;
-import org.dspace.core.Context;
-
-/**
- * Action to add metadata to item
- */
-public class AddMetadataAction extends UpdateMetadataAction {
-
-    protected MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
-                                                                                 .getMetadataSchemaService();
-    protected MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
-
-    /**
-     * Adds metadata specified in the source archive
-     *
-     * @param context      DSpace Context
-     * @param itarch       item archive
-     * @param isTest       test flag
-     * @param suppressUndo undo flag
-     * @throws AuthorizeException if authorization error
-     * @throws SQLException       if database error
-     */
-    @Override
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException, SQLException {
-        Item item = itarch.getItem();
-        String dirname = itarch.getDirectoryName();
-
-        for (DtoMetadata dtom : itarch.getMetadataFields()) {
-            for (String f : targetFields) {
-                if (dtom.matches(f, false)) {
-                    // match against metadata for this field/value in repository
-                    // qualifier must be strictly matched, possibly null
-                    List<MetadataValue> ardcv = null;
-                    ardcv = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-
-                    boolean found = false;
-                    for (MetadataValue dcv : ardcv) {
-                        if (dcv.getValue().equals(dtom.value)) {
-                            found = true;
-                            break;
-                        }
-                    }
-
-                    if (found) {
-                        ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname
-                                          + " for element " + f);
-                    } else {
-                        if (isTest) {
-                            ItemUpdate.pr("Metadata to add: " + dtom.toString());
-                            //validity tests that would occur in actual processing
-                            // If we're just test the import, let's check that the actual metadata field exists.
-                            MetadataSchema foundSchema = metadataSchemaService.find(context, dtom.schema);
-
-                            if (foundSchema == null) {
-                                ItemUpdate.pr("ERROR: schema '"
-                                                  + dtom.schema + "' was not found in the registry; found on item " +
-                                                  dirname);
-                            } else {
-                                MetadataField foundField = metadataFieldService
-                                    .findByElement(context, foundSchema, dtom.element, dtom.qualifier);
-
-                                if (foundField == null) {
-                                    ItemUpdate.pr("ERROR: Metadata field: '" + dtom.schema + "." + dtom.element + "."
-                                                      + dtom.qualifier + "' not found in registry; found on item " +
-                                                      dirname);
-                                }
-                            }
-                        } else {
-                            itemService
-                                .addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language,
-                                             dtom.value);
-                            ItemUpdate.pr("Metadata added: " + dtom.toString());
-
-                            if (!suppressUndo) {
-                                //itarch.addUndoDtom(dtom);
-                                //ItemUpdate.pr("Undo metadata: " + dtom);
-
-                                // add all as a replace record to be preceded by delete
-                                for (MetadataValue dcval : ardcv) {
-                                    MetadataField metadataField = dcval.getMetadataField();
-                                    MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-                                    itarch.addUndoMetadataField(
-                                        DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
-                                                           metadataField.getQualifier(), dcval.getLanguage(),
-                                                           dcval.getValue()));
-                                }
-
-                            }
-                        }
-                    }
-                    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

@@ -1,55 +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.itemupdate;
-
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.Properties;
-
-import org.dspace.content.Bitstream;
-
-/**
- * Filter interface to be used by ItemUpdate
- * to determine which bitstreams in an Item
- * acceptable for removal.
- */
-public abstract class BitstreamFilter {
-
-    protected Properties props = null;
-
-    /**
-     * 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) {
-                in.close();
-            }
-        }
-    }
-
-}

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

@@ -1,57 +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.itemupdate;
-
-import java.sql.SQLException;
-import java.util.List;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-
-/**
- * BitstreamFilter implementation to filter by bundle name
- */
-public class BitstreamFilterByBundleName extends BitstreamFilter {
-
-    protected String bundleName;
-
-    public BitstreamFilterByBundleName() {
-        //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;
-    }
-
-}

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

@@ -1,49 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.dspace.content.Bitstream;
-
-/**
- * BitstreamFilter implementation to filter by filename pattern
- */
-public class BitstreamFilterByFilename extends BitstreamFilter {
-
-    protected Pattern pattern;
-    protected String filenameRegex;
-
-    public BitstreamFilterByFilename() {
-        //empty
-    }
-
-    /**
-     * Tests bitstream by matching the regular expression in the
-     * properties against the bitstream name
-     *
-     * @param bitstream Bitstream
-     * @return whether bitstream name matches the regular expression
-     * @throws BitstreamFilterException if filter error
-     */
-    @Override
-    public boolean accept(Bitstream bitstream) throws BitstreamFilterException {
-        if (filenameRegex == null) {
-            filenameRegex = props.getProperty("filename");
-            if (filenameRegex == null) {
-                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

@@ -1,34 +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.itemupdate;
-
-/**
- * Exception class for BitstreamFilters
- */
-public class BitstreamFilterException extends Exception {
-
-    private static final long serialVersionUID = 1L;
-
-    public BitstreamFilterException() {
-    }
-
-    /**
-     * @param msg exception message
-     */
-    public BitstreamFilterException(String msg) {
-        super(msg);
-    }
-
-    /**
-     * @param e exception
-     */
-    public BitstreamFilterException(Exception e) {
-        super(e);
-    }
-
-}

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

@@ -1,131 +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.itemupdate;
-
-import java.text.ParseException;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.dspace.core.Constants;
-
-/**
- * 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.:
- * {@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 static final String HDR_BUNDLE = "bundle:";
-    public static final String HDR_PERMISSIONS = "permissions:";
-    public static final String HDR_DESCRIPTION = "description:";
-
-    public static final Pattern permissionsPattern = Pattern.compile("-([rw])\\s*'?([^']+)'?");
-
-    final String filename;
-    final String bundlename;
-    final String permissionsGroupName;
-    final int permissionsActionId;
-    final String description;
-
-    protected ContentsEntry(String filename,
-                            String bundlename,
-                            int permissionsActionId,
-                            String permissionsGroupName,
-                            String description) {
-        this.filename = filename;
-        this.bundlename = bundlename;
-        this.permissionsActionId = permissionsActionId;
-        this.permissionsGroupName = permissionsGroupName;
-        this.description = description;
-    }
-
-    /**
-     * Factory method parses a line from the Contents Entry file
-     *
-     * @param line line as string
-     * @return the parsed ContentsEntry object
-     * @throws ParseException if parse error
-     */
-    public static ContentsEntry parse(String line)
-        throws ParseException {
-        String[] ar = line.split("\t");
-        ItemUpdate.pr("ce line split: " + ar.length);
-
-        String[] arp = new String[4];
-        arp[0] = ar[0];   //bitstream name doesn't have header and is always first
-
-        String groupName = null;
-        int actionId = -1;
-
-        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

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

@@ -1,117 +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.itemupdate;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * Action to delete bitstreams using a specified filter implementing BitstreamFilter
- * 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
- */
-public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
-
-    protected BitstreamFilter filter;
-
-    /**
-     * Set filter
-     *
-     * @param filter BitstreamFilter
-     */
-    public void setBitstreamFilter(BitstreamFilter filter) {
-        this.filter = filter;
-    }
-
-    /**
-     * Get filter
-     *
-     * @return filter
-     */
-    public BitstreamFilter getBitstreamFilter() {
-        return filter;
-    }
-
-    /**
-     * Delete bitstream
-     *
-     * @param context      DSpace Context
-     * @param itarch       item archive
-     * @param isTest       test flag
-     * @param suppressUndo undo flag
-     * @throws IOException              if IO error
-     * @throws SQLException             if database error
-     * @throws AuthorizeException       if authorization error
-     * @throws ParseException           if parse error
-     * @throws BitstreamFilterException if filter error
-     */
-    @Override
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException,
-        BitstreamFilterException, IOException, ParseException, SQLException {
-
-        List<String> deleted = new ArrayList<String>();
-
-        Item item = itarch.getItem();
-        List<Bundle> bundles = item.getBundles();
-
-        for (Bundle b : bundles) {
-            List<Bitstream> bitstreams = b.getBitstreams();
-            String bundleName = b.getName();
-
-            for (Bitstream bs : bitstreams) {
-                if (filter.accept(bs)) {
-                    if (isTest) {
-                        ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName()
-                                          + " with id = " + bs.getID());
-                    } else {
-                        //provenance is not maintained for derivative bitstreams
-                        if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT")) {
-                            deleted.add(bs.getName());
-                        }
-                        bundleService.removeBitstream(context, b, 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(context, item, dtom, false, sb.toString());
-            }
-        }
-    }
-
-}

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

@@ -1,65 +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.itemupdate;
-
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.MetadataValue;
-import org.dspace.core.Context;
-
-/**
- * Action to delete metadata
- */
-public class DeleteMetadataAction extends UpdateMetadataAction {
-
-    /**
-     * Delete metadata from item
-     *
-     * @param context      DSpace Context
-     * @param itarch       Item Archive
-     * @param isTest       test flag
-     * @param suppressUndo undo flag
-     * @throws SQLException       if database error
-     * @throws AuthorizeException if authorization error
-     * @throws ParseException     if parse error
-     */
-    @Override
-    public void execute(Context context, ItemArchive itarch, boolean isTest,
-                        boolean suppressUndo) throws AuthorizeException, ParseException, SQLException {
-        Item item = itarch.getItem();
-        for (String f : targetFields) {
-            DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
-            List<MetadataValue> ardcv = itemService.getMetadataByMetadataString(item, f);
-
-            ItemUpdate.pr("Metadata to be deleted: ");
-            for (MetadataValue dcv : ardcv) {
-                ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
-            }
-
-            if (!isTest) {
-                if (!suppressUndo) {
-                    for (MetadataValue dcv : ardcv) {
-                        MetadataField metadataField = dcv.getMetadataField();
-                        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-                        itarch.addUndoMetadataField(
-                            DtoMetadata.create(metadataSchema.getName(), metadataField.getElement(),
-                                               metadataField.getQualifier(), dcv.getLanguage(), dcv.getValue()));
-                    }
-                }
-
-                itemService.clearMetadata(context, item, dummy.schema, dummy.element, dummy.qualifier, Item.ANY);
-            }
-        }
-    }
-}

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

@@ -1,22 +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.itemupdate;
-
-import java.util.Properties;
-
-/**
- * Bitstream filter to delete from TEXT bundle
- */
-public class DerivativeTextBitstreamFilter extends BitstreamFilterByBundleName {
-
-    public DerivativeTextBitstreamFilter() {
-        props = new Properties();
-        props.setProperty("bundle", "TEXT");
-    }
-
-}

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

@@ -1,138 +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.itemupdate;
-
-import java.text.ParseException;
-
-import org.dspace.content.Item;
-
-/**
- * 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
- *
- * 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 {
-    final String schema;
-    final String element;
-    final String qualifier;
-    final String language;
-    final String value;
-
-    protected DtoMetadata(String schema, String element, String qualifier, String language, String value) {
-        this.schema = schema;
-        this.element = element;
-        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     value
-     * @return DtoMetadata object
-     * @throws IllegalArgumentException if arg error
-     */
-    public static DtoMetadata create(String schema,
-                                     String element,
-                                     String qualifier,
-                                     String language,
-                                     String value)
-        throws IllegalArgumentException {
-        if ((qualifier != null) && (qualifier.equals(Item.ANY) || qualifier.equals(""))) {
-            throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
-        }
-        return new DtoMetadata(schema, element, qualifier, language, value);
-    }
-
-    /**
-     * Factory method to create metadata object
-     *
-     * @param compoundForm of the form <schema>.<element>[.<qualifier>]
-     * @param language     null or empty
-     * @param value        value
-     * @throws ParseException           if parse error
-     * @throws IllegalArgumentException if arg error
-     */
-    public static DtoMetadata create(String compoundForm, String language, String value)
-        throws ParseException, IllegalArgumentException {
-        String[] ar = MetadataUtilities.parseCompoundForm(compoundForm);
-
-        String qual = null;
-        if (ar.length > 2) {
-            qual = ar[2];
-        }
-
-        return create(ar[0], ar[1], qual, language, value);
-    }
-
-    /**
-     * Determine if this metadata field matches the specified type:
-     * schema.element or schema.element.qualifier
-     *
-     * @param compoundForm of the form <schema>.<element>[.<qualifier>|.*]
-     * @param wildcard     allow wildcards in compoundForm param
-     * @return whether matches
-     */
-    public boolean matches(String compoundForm, boolean wildcard) {
-        String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
-
-        if ((ar.length < 2) || (ar.length > 3)) {
-            return false;
-        }
-
-        if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1])) {
-            return false;
-        }
-
-        if (ar.length == 2) {
-            if (this.qualifier != null) {
-                return false;
-            }
-        }
-
-        if (ar.length == 3) {
-            if (this.qualifier == null) {
-                return false;
-            }
-            if (wildcard && ar[2].equals(Item.ANY)) {
-                return true;
-            }
-            if (!this.qualifier.equals(ar[2])) {
-                return false;
-            }
-        }
-        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() {
-        return value;
-    }
-
-}

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

@@ -1,343 +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.itemupdate;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.UUID;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-
-import org.apache.log4j.Logger;
-import org.dspace.app.util.LocalSchemaFilenameFilter;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Context;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.handle.service.HandleService;
-import org.w3c.dom.Document;
-
-
-/**
- * Encapsulates the Item in the context of the DSpace Archive Format
- */
-public class ItemArchive {
-    private static final Logger log = Logger.getLogger(ItemArchive.class);
-
-    public static final String DUBLIN_CORE_XML = "dublin_core.xml";
-
-    protected static DocumentBuilder builder = null;
-    protected Transformer transformer = null;
-
-    protected List<DtoMetadata> dtomList = null;
-    protected List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
-
-    protected List<UUID> undoAddContents = new ArrayList<>(); // for undo of add
-
-    protected Item item;
-    protected File dir;  // directory name in source archive for this item
-    protected String dirname; //convenience
-
-    protected HandleService handleService;
-    protected ItemService itemService;
-
-    //constructors
-    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
-     * which must contain the handle for the item
-     *
-     * @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
-     *                  if null, the default is the handle in the dc.identifier.uri field
-     * @return ItemArchive object
-     * @throws Exception if error
-     */
-    public static ItemArchive create(Context context, File dir, String itemField)
-        throws Exception {
-        ItemArchive itarch = new ItemArchive();
-        itarch.dir = dir;
-        itarch.dirname = dir.getName();
-        InputStream is = null;
-        try {
-            is = new FileInputStream(new File(dir, DUBLIN_CORE_XML));
-            itarch.dtomList = MetadataUtilities.loadDublinCore(getDocumentBuilder(), is);
-
-            //The code to search for local schema files was copied from org.dspace.app.itemimport
-            // .ItemImportServiceImpl.java
-            File file[] = dir.listFiles(new LocalSchemaFilenameFilter());
-            for (int i = 0; i < file.length; i++) {
-                is = new FileInputStream(file[i]);
-                itarch.dtomList.addAll(MetadataUtilities.loadDublinCore(getDocumentBuilder(), is));
-            }
-        } finally {
-            if (is != null) {
-                is.close();
-            }
-        }
-        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());
-
-        return itarch;
-    }
-
-    protected static DocumentBuilder getDocumentBuilder()
-        throws ParserConfigurationException {
-        if (builder == null) {
-            builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
-        }
-        return builder;
-    }
-
-    /**
-     * Getter for Transformer
-     *
-     * @return Transformer
-     * @throws TransformerConfigurationException if config error
-     */
-    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 {
-        DtoMetadata dtom = getMetadataField("dc.identifier.uri");
-        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;
-
-        if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX)) {
-            throw new Exception("dc.identifier.uri for item " + uri
-                                    + " does not begin with prefix: " + ItemUpdate.HANDLE_PREFIX);
-        }
-
-        String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());
-
-        DSpaceObject dso = handleService.resolveToObject(context, handle);
-        if (dso instanceof Item) {
-            item = (Item) dso;
-        } 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
-     * on the specified itemField for the item identifier,
-     *
-     * @param context   - the DSpace context
-     * @param itemField - the compound form of the metadata element <schema>.<element>.<qualifier>
-     * @throws SQLException if database error
-     * @throws Exception    if error
-     */
-    private Item itemFromMetadataField(Context context, String itemField)
-        throws SQLException, AuthorizeException, Exception {
-        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());
-
-        this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
-
-        Iterator<Item> itr = itemService
-            .findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
-        int count = 0;
-        while (itr.hasNext()) {
-            item = itr.next();
-            count++;
-        }
-
-        ItemUpdate.prv("items matching = " + count);
-
-        if (count != 1) {
-            throw new Exception("" + count + " items matching item identifier: " + dtom.value);
-        }
-
-        return item;
-    }
-
-    /**
-     * Get DtoMetadata field
-     *
-     * @param compoundForm compound form
-     * @return DtoMetadata field
-     */
-    private DtoMetadata getMetadataField(String compoundForm) {
-        for (DtoMetadata dtom : dtomList) {
-            if (dtom.matches(compoundForm, false)) {
-                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)
-        throws IOException, ParserConfigurationException, TransformerConfigurationException,
-        TransformerException, FileNotFoundException {
-        // create directory for item
-        File dir = new File(undoDir, dirname);
-        if (!dir.exists() && !dir.mkdir()) {
-            log.error("Unable to create undo directory");
-        }
-
-        OutputStream out = null;
-
-        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) {
-                PrintWriter pw = null;
-                try {
-                    File f = new File(dir, ItemUpdate.DELETE_CONTENTS_FILE);
-                    pw = new PrintWriter(new BufferedWriter(new FileWriter(f)));
-                    for (UUID i : undoAddContents) {
-                        pw.println(i);
-                    }
-                } finally {
-                    pw.close();
-                }
-            }
-        } finally {
-            if (out != null) {
-                out.close();
-            }
-        }
-    }
-
-} //end class

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

@@ -1,566 +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.itemupdate;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.FilenameFilter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.UUID;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.eperson.service.EPersonService;
-
-/**
- * Provides some batch editing capabilities for items in DSpace:
- * Metadata fields - Add, Delete
- * Bitstreams - Add, Delete
- *
- * The design has been for compatibility with ItemImporter
- * in the use of the DSpace archive format which is used to
- * specify changes on a per item basis.  The directory names
- * to correspond to each item are arbitrary and will only be
- * used for logging purposes.  The reference to the item is
- * from a required dc.identifier with the item handle to be
- * included in the dublin_core.xml (or similar metadata) file.
- *
- * Any combination of these actions is permitted in a single run of this class
- * The order of actions is important when used in combination.
- * It is the responsibility of the calling class (here, ItemUpdate)
- * to register UpdateAction classes in the order to which they are
- * to be performed.
- *
- *
- * It is unfortunate that so much code needs to be borrowed
- * from ItemImport as it is not reusable in private methods, etc.
- * Some of this has been placed into the MetadataUtilities class
- * for possible reuse elsewhere.
- *
- * @author W. Hays based on a conceptual design by R. Rodgers
- */
-public class ItemUpdate {
-
-    public static final String SUPPRESS_UNDO_FILENAME = "suppress_undo";
-
-    public static final String CONTENTS_FILE = "contents";
-    public static final String DELETE_CONTENTS_FILE = "delete_contents";
-
-    public static String HANDLE_PREFIX = null;
-    public static final Map<String, String> filterAliases = new HashMap<String, String>();
-
-    public static boolean verbose = false;
-
-    protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
-    static {
-        filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
-        filterAliases
-            .put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
-        filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");
-        filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");
-    }
-
-    // File listing filter to check for folders
-    static FilenameFilter directoryFilter = new FilenameFilter() {
-        @Override
-        public boolean accept(File dir, String n) {
-            File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
-            return f.isDirectory();
-        }
-    };
-
-    // File listing filter to check for files (not directories)
-    static FilenameFilter fileFilter = new FilenameFilter() {
-        @Override
-        public boolean accept(File dir, String n) {
-            File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
-            return (f.isFile());
-        }
-    };
-
-    // instance variables
-    protected ActionManager actionMgr = new ActionManager();
-    protected List<String> undoActionList = new ArrayList<String>();
-    protected String eperson;
-
-    /**
-     * @param argv the command line arguments given
-     */
-    public static void main(String[] argv) {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        //processing basis for determining items
-        //item-specific changes with metadata in source directory with dublin_core.xml files
-        options.addOption("s", "source", true, "root directory of source dspace archive ");
-
-        //actions  on items
-        options.addOption("a", "addmetadata", true,
-                          "add metadata specified for each item; multiples separated by semicolon ';'");
-        options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
-
-        options.addOption("A", "addbitstreams", false, "add bitstreams as specified for each item");
-
-        // extra work to get optional argument
-        Option delBitstreamOption = new Option("D", "deletebitstreams", true,
-                                               "delete bitstreams as specified for each item");
-        delBitstreamOption.setOptionalArg(true);
-        delBitstreamOption.setArgName("BitstreamFilter");
-        options.addOption(delBitstreamOption);
-
-        //other params
-        options.addOption("e", "eperson", true, "email of eperson doing the update");
-        options.addOption("i", "itemfield", true,
-                          "optional metadata field that containing item identifier; default is dc.identifier.uri");
-        options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");
-        options.addOption("v", "verbose", false, "verbose logging");
-
-        //special run states
-        options.addOption("t", "test", false, "test run - do not actually import items");
-        options.addOption("P", "provenance", false, "suppress altering provenance field for bitstream changes");
-        options.addOption("h", "help", false, "help");
-
-        int status = 0;
-        boolean isTest = false;
-        boolean alterProvenance = true;
-        String itemField = null;
-        String metadataIndexName = null;
-
-        Context context = null;
-        ItemUpdate iu = new ItemUpdate();
-
-        try {
-            CommandLine line = parser.parse(options, argv);
-
-            if (line.hasOption('h')) {
-                HelpFormatter myhelp = new HelpFormatter();
-                myhelp.printHelp("ItemUpdate", options);
-                pr("");
-                pr("Examples:");
-                pr("  adding metadata:     ItemUpdate -e jsmith@mit.edu -s sourcedir -a dc.contributor -a dc.subject ");
-                pr("  deleting metadata:   ItemUpdate -e jsmith@mit.edu -s sourcedir -d dc.description.other");
-                pr("  adding bitstreams:   ItemUpdate -e jsmith@mit.edu -s sourcedir -A -i dc.identifier");
-                pr("  deleting bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -D ORIGINAL ");
-                pr("");
-
-                System.exit(0);
-            }
-
-            if (line.hasOption('v')) {
-                verbose = true;
-            }
-
-
-            if (line.hasOption('P')) {
-                alterProvenance = false;
-                pr("Suppressing changes to Provenance field option");
-            }
-
-            iu.eperson = line.getOptionValue('e'); // db ID or email
-
-            if (!line.hasOption('s')) { // item specific changes from archive dir
-                pr("Missing source archive option");
-                System.exit(1);
-            }
-            String sourcedir = line.getOptionValue('s');
-
-            if (line.hasOption('t')) { //test
-                isTest = true;
-                pr("**Test Run** - not actually updating items.");
-
-            }
-
-            if (line.hasOption('i')) {
-                itemField = line.getOptionValue('i');
-            }
-
-            if (line.hasOption('d')) {
-                String[] targetFields = line.getOptionValues('d');
-
-                DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr
-                    .getUpdateAction(DeleteMetadataAction.class);
-                delMetadataAction.addTargetFields(targetFields);
-
-                //undo is an add
-                for (String field : targetFields) {
-                    iu.undoActionList.add(" -a " + field + " ");
-                }
-
-                pr("Delete metadata for fields: ");
-                for (String s : targetFields) {
-                    pr("    " + s);
-                }
-            }
-
-            if (line.hasOption('a')) {
-                String[] targetFields = line.getOptionValues('a');
-
-                AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr
-                    .getUpdateAction(AddMetadataAction.class);
-                addMetadataAction.addTargetFields(targetFields);
-
-                //undo is a delete followed by an add of a replace record for target fields
-                for (String field : targetFields) {
-                    iu.undoActionList.add(" -d " + field + " ");
-                }
-
-                for (String field : targetFields) {
-                    iu.undoActionList.add(" -a " + field + " ");
-                }
-
-                pr("Add metadata for fields: ");
-                for (String s : targetFields) {
-                    pr("    " + s);
-                }
-            }
-
-            if (line.hasOption('D')) { // undo not supported
-                pr("Delete bitstreams ");
-
-                String[] filterNames = line.getOptionValues('D');
-                if ((filterNames != null) && (filterNames.length > 1)) {
-                    pr("Error: Only one filter can be a used at a time.");
-                    System.exit(1);
-                }
-
-                String filterName = line.getOptionValue('D');
-                pr("Filter argument: " + filterName);
-
-                if (filterName == null) { // indicates using delete_contents files
-                    DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr
-                        .getUpdateAction(DeleteBitstreamsAction.class);
-                    delAction.setAlterProvenance(alterProvenance);
-                } else {
-                    // check if param is on ALIAS list
-                    String filterClassname = filterAliases.get(filterName);
-
-                    if (filterClassname == null) {
-                        filterClassname = filterName;
-                    }
-
-                    BitstreamFilter filter = null;
-
-                    try {
-                        Class<?> cfilter = Class.forName(filterClassname);
-                        pr("BitstreamFilter class to instantiate: " + cfilter.toString());
-
-                        filter = (BitstreamFilter) cfilter.newInstance();  //unfortunate cast, an erasure consequence
-                    } catch (Exception e) {
-                        pr("Error:  Failure instantiating bitstream filter class: " + filterClassname);
-                        System.exit(1);
-                    }
-
-                    String filterPropertiesName = line.getOptionValue('F');
-                    if (filterPropertiesName != null) { //not always required
-                        try {
-                            // TODO try multiple relative locations, e.g. source dir
-                            if (!filterPropertiesName.startsWith("/")) {
-                                filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
-                            }
-
-                            filter.initProperties(filterPropertiesName);
-                        } catch (Exception e) {
-                            pr("Error:  Failure finding properties file for bitstream filter class: " +
-                                   filterPropertiesName);
-                            System.exit(1);
-                        }
-                    }
-
-                    DeleteBitstreamsByFilterAction delAction =
-                        (DeleteBitstreamsByFilterAction) iu.actionMgr
-                            .getUpdateAction(DeleteBitstreamsByFilterAction.class);
-                    delAction.setAlterProvenance(alterProvenance);
-                    delAction.setBitstreamFilter(filter);
-                    //undo not supported
-                }
-            }
-
-            if (line.hasOption('A')) {
-                pr("Add bitstreams ");
-                AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr
-                    .getUpdateAction(AddBitstreamsAction.class);
-                addAction.setAlterProvenance(alterProvenance);
-
-                iu.undoActionList.add(" -D ");  // delete_contents file will be written, no arg required
-            }
-
-            if (!iu.actionMgr.hasActions()) {
-                pr("Error - an action must be specified");
-                System.exit(1);
-            } else {
-                pr("Actions to be performed: ");
-
-                for (UpdateAction ua : iu.actionMgr) {
-                    pr("    " + ua.getClass().getName());
-                }
-            }
-
-            pr("ItemUpdate - initializing run on " + (new Date()).toString());
-
-            context = new Context(Context.Mode.BATCH_EDIT);
-            iu.setEPerson(context, iu.eperson);
-            context.turnOffAuthorisationSystem();
-
-            HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
-            if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
-                HANDLE_PREFIX = "http://hdl.handle.net/";
-            }
-
-            iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);
-
-            context.complete();  // complete all transactions
-        } catch (Exception e) {
-            if (context != null && context.isValid()) {
-                context.abort();
-            }
-            e.printStackTrace();
-            pr(e.toString());
-            status = 1;
-        } finally {
-            context.restoreAuthSystemState();
-        }
-
-        if (isTest) {
-            pr("***End of Test Run***");
-        } else {
-            pr("End.");
-
-        }
-        System.exit(status);
-    }
-
-    /**
-     * process an archive
-     *
-     * @param context           DSpace Context
-     * @param sourceDirPath     source path
-     * @param itemField         item field
-     * @param metadataIndexName index name
-     * @param alterProvenance   whether to alter provenance
-     * @param isTest            test flag
-     * @throws Exception if error
-     */
-    protected void processArchive(Context context, String sourceDirPath, String itemField,
-                                  String metadataIndexName, boolean alterProvenance, boolean isTest)
-        throws Exception {
-        // open and process the source directory
-        File sourceDir = new File(sourceDirPath);
-
-        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory()) {
-            pr("Error, cannot open archive source directory " + sourceDirPath);
-            throw new Exception("error with archive source directory " + sourceDirPath);
-        }
-
-        String[] dircontents = sourceDir.list(directoryFilter);  //just the names, not the path
-        Arrays.sort(dircontents);
-
-        //Undo is suppressed to prevent undo of undo
-        boolean suppressUndo = false;
-        File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
-        if (fSuppressUndo.exists()) {
-            suppressUndo = true;
-        }
-
-        File undoDir = null;  //sibling directory of source archive
-
-        if (!suppressUndo && !isTest) {
-            undoDir = initUndoArchive(sourceDir);
-        }
-
-        int itemCount = 0;
-        int successItemCount = 0;
-
-        for (String dirname : dircontents) {
-            itemCount++;
-            pr("");
-            pr("processing item " + dirname);
-
-            try {
-                ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
-
-                for (UpdateAction action : actionMgr) {
-                    pr("action: " + action.getClass().getName());
-                    action.execute(context, itarch, isTest, suppressUndo);
-                    if (!isTest && !suppressUndo) {
-                        itarch.writeUndo(undoDir);
-                    }
-                }
-                if (!isTest) {
-                    Item item = itarch.getItem();
-                    itemService.update(context, item);  //need to update before commit
-                    context.uncacheEntity(item);
-                }
-                ItemUpdate.pr("Item " + dirname + " completed");
-                successItemCount++;
-            } catch (Exception e) {
-                pr("Exception processing item " + dirname + ": " + e.toString());
-                e.printStackTrace();
-            }
-        }
-
-        if (!suppressUndo && !isTest) {
-            StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
-            sb.append(" -e ").append(this.eperson);
-            sb.append(" -s ").append(undoDir);
-
-            if (itemField != null) {
-                sb.append(" -i ").append(itemField);
-            }
-
-            if (!alterProvenance) {
-                sb.append(" -P ");
-            }
-            if (isTest) {
-                sb.append(" -t ");
-            }
-
-            for (String actionOption : undoActionList) {
-                sb.append(actionOption);
-            }
-
-            PrintWriter pw = null;
-            try {
-                File cmdFile = new File(undoDir.getParent(), undoDir.getName() + "_command.sh");
-                pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
-                pw.println(sb.toString());
-            } finally {
-                pw.close();
-            }
-        }
-
-        pr("");
-        pr("Done processing.  Successful items: " + successItemCount + " of " + itemCount + " items in source archive");
-        pr("");
-    }
-
-
-    /**
-     * to avoid overwriting the undo source tree on repeated processing
-     * sequence numbers are added and checked
-     *
-     * @param sourceDir - the original source directory
-     * @return the directory of the undo archive
-     * @throws FileNotFoundException if file doesn't exist
-     * @throws IOException           if IO error
-     */
-    protected File initUndoArchive(File sourceDir)
-        throws FileNotFoundException, IOException {
-        File parentDir = sourceDir.getCanonicalFile().getParentFile();
-        if (parentDir == null) {
-            throw new FileNotFoundException(
-                "Parent directory of archive directory not found; unable to write UndoArchive; no processing " +
-                    "performed");
-        }
-
-        String sourceDirName = sourceDir.getName();
-        int seqNo = 1;
-
-        File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
-        while (undoDir.exists()) {
-            undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + ++seqNo); //increment
-        }
-
-        // create root directory
-        if (!undoDir.mkdir()) {
-            pr("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
-            throw new IOException("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
-        }
-
-        //Undo is suppressed to prevent undo of undo
-        File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
-        try {
-            fSuppressUndo.createNewFile();
-        } catch (IOException e) {
-            pr("ERROR creating Suppress Undo File " + e.toString());
-            throw e;
-        }
-        return undoDir;
-    }
-
-    //private void write
-
-    /**
-     * Set EPerson doing import
-     *
-     * @param context DSpace Context
-     * @param eperson EPerson obj
-     * @throws Exception if error
-     */
-    protected void setEPerson(Context context, String eperson)
-        throws Exception {
-        if (eperson == null) {
-            pr("Error - an eperson to do the importing must be specified");
-            pr(" (run with -h flag for details)");
-            throw new Exception("EPerson not specified.");
-        }
-
-        EPerson myEPerson = null;
-
-        if (eperson.indexOf('@') != -1) {
-            // @ sign, must be an email
-            myEPerson = epersonService.findByEmail(context, eperson);
-        } else {
-            myEPerson = epersonService.find(context, UUID.fromString(eperson));
-        }
-
-        if (myEPerson == null) {
-            pr("Error, eperson cannot be found: " + eperson);
-            throw new Exception("Invalid EPerson");
-        }
-
-        context.setCurrentUser(myEPerson);
-    }
-
-    /**
-     * poor man's logging
-     * As with ItemImport, API logging goes through log4j to the DSpace.log files
-     * whereas the batch logging goes to the console to be captured there.
-     *
-     * @param s String
-     */
-    static void pr(String s) {
-        System.out.println(s);
-    }
-
-    /**
-     * print if verbose flag is set
-     *
-     * @param s String
-     */
-    static void prv(String s) {
-        if (verbose) {
-            System.out.println(s);
-        }
-    }
-
-} //end of class
-

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

@@ -1,465 +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.itemupdate;
-
-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.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;
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.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;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-
-/**
- * Miscellaneous methods for metadata handling that build on the API
- * which might have general utility outside of the specific use
- * in context in ItemUpdate.
- *
- * The XML methods were based on those in ItemImport
- */
-public class MetadataUtilities {
-
-    protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
-    /**
-     * Default constructor
-     */
-    private MetadataUtilities() { }
-
-    /**
-     * Working around Item API to delete a value-specific Metadatum
-     * For a given element/qualifier/lang:
-     * get all DCValues
-     * clear (i.e. delete) all of these DCValues
-     * 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)
-        throws SQLException {
-        List<MetadataValue> ar = null;
-
-        if (isLanguageStrict) {   // get all for given type
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-        }
-
-        boolean found = false;
-
-        //build new set minus the one to delete
-        List<String> vals = new ArrayList<String>();
-        for (MetadataValue dcv : ar) {
-            if (dcv.getValue().equals(dtom.value)) {
-                found = true;
-            } else {
-                vals.add(dcv.getValue());
-            }
-        }
-
-        if (found) {  //remove all for given type  ??synchronize this block??
-            if (isLanguageStrict) {
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-            } else {
-                itemService.clearMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-            }
-
-            itemService.addMetadata(context, item, dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals);
-        }
-        return found;
-    }
-
-    /**
-     * Append text to value metadata field to item
-     *
-     * @param context          DSpace Context
-     * @param item             DSpace Item
-     * @param dtom             metadata field
-     * @param isLanguageStrict if strict
-     * @param textToAppend     text to append
-     * @throws IllegalArgumentException - When target metadata field is not found
-     * @throws SQLException             if database error
-     */
-    public static void appendMetadata(Context context, Item item, DtoMetadata dtom, boolean isLanguageStrict,
-                                      String textToAppend)
-        throws IllegalArgumentException, SQLException {
-        List<MetadataValue> ar = null;
-
-        // get all values for given element/qualifier
-        if (isLanguageStrict) {  // get all for given element/qualifier
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        } else {
-            ar = itemService.getMetadata(item, dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-        }
-
-        if (ar.size() == 0) {
-            throw new IllegalArgumentException("Metadata to append to not found");
-        }
-
-        int idx = 0;  //index of field to change
-        if (ar.size() > 1) { //need to pick one, can't be sure it's the last one
-            // 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
-     * as a Factory method
-     *
-     * @param docBuilder DocumentBuilder
-     * @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 IOException                  if IO error
-     * @throws ParserConfigurationException if parser config error
-     * @throws SAXException                 if XML error
-     * @throws TransformerException         if transformer error
-     * @throws AuthorizeException           if authorization error
-     */
-    public static List<DtoMetadata> loadDublinCore(DocumentBuilder docBuilder, InputStream is)
-        throws SQLException, IOException, ParserConfigurationException,
-        SAXException, TransformerException, AuthorizeException {
-        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();
-        }
-
-        // 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();
-            }
-
-            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
-     *
-     * @param docBuilder DocumentBuilder
-     * @param dtomList   List of metadata fields
-     * @return xml document
-     * @throws ParserConfigurationException      if parser config error
-     * @throws TransformerConfigurationException if transformer config error
-     * @throws TransformerException              if transformer error
-     */
-    public static Document writeDublinCore(DocumentBuilder docBuilder, List<DtoMetadata> dtomList)
-        throws ParserConfigurationException, TransformerConfigurationException, TransformerException {
-        Document doc = docBuilder.newDocument();
-        Element root = doc.createElement("dublin_core");
-        doc.appendChild(root);
-
-        for (DtoMetadata dtom : dtomList) {
-            Element mel = doc.createElement("dcvalue");
-            mel.setAttribute("element", dtom.element);
-            if (dtom.qualifier == null) {
-                mel.setAttribute("qualifier", "none");
-            } else {
-                mel.setAttribute("qualifier", dtom.qualifier);
-            }
-
-            if (StringUtils.isEmpty(dtom.language)) {
-                mel.setAttribute("language", "en");
-            } else {
-                mel.setAttribute("language", dtom.language);
-            }
-            mel.setTextContent(dtom.value);
-            root.appendChild(mel);
-        }
-
-        return doc;
-    }
-
-    /**
-     * write xml document to output stream
-     *
-     * @param doc         XML Document
-     * @param transformer XML Transformer
-     * @param out         OutputStream
-     * @throws IOException          if IO Error
-     * @throws TransformerException if Transformer error
-     */
-    public static void writeDocument(Document doc, Transformer transformer, OutputStream out)
-        throws IOException, TransformerException {
-        Source src = new DOMSource(doc);
-        Result dest = new StreamResult(out);
-        transformer.transform(src, dest);
-    }
-
-
-    // XML utility methods
-
-    /**
-     * Lookup an attribute from a DOM node.
-     *
-     * @param n    Node
-     * @param name name
-     * @return attribute value
-     */
-    private static String getAttributeValue(Node n, String name) {
-        NamedNodeMap nm = n.getAttributes();
-
-        for (int i = 0; i < nm.getLength(); i++) {
-            Node node = nm.item(i);
-
-            if (name.equals(node.getNodeName())) {
-                return node.getNodeValue();
-            }
-        }
-
-        return "";
-    }
-
-    /**
-     * Return the String value of a Node.
-     *
-     * @param node node
-     * @return string value
-     */
-    private static String getStringValue(Node node) {
-        String value = node.getNodeValue();
-
-        if (node.hasChildNodes()) {
-            Node first = node.getFirstChild();
-
-            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
-     * @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 {
-        List<ContentsEntry> list = new ArrayList<ContentsEntry>();
-
-        BufferedReader in = null;
-
-        try {
-            in = new BufferedReader(new FileReader(f));
-            String line = null;
-
-            while ((line = in.readLine()) != null) {
-                line = line.trim();
-                if ("".equals(line)) {
-                    continue;
-                }
-                ItemUpdate.pr("Contents entry: " + line);
-                list.add(ContentsEntry.parse(line));
-            }
-        } finally {
-            try {
-                in.close();
-            } catch (IOException e) {
-                //skip
-            }
-        }
-
-        return list;
-    }
-
-    /**
-     * @param f file
-     * @return list of lines as strings
-     * @throws FileNotFoundException if file doesn't exist
-     * @throws IOException           if IO Error
-     */
-    public static List<String> readDeleteContentsFile(File f)
-        throws FileNotFoundException, IOException {
-        List<String> list = new ArrayList<>();
-
-        BufferedReader in = null;
-
-        try {
-            in = new BufferedReader(new FileReader(f));
-            String line = null;
-
-            while ((line = in.readLine()) != null) {
-                line = line.trim();
-                if ("".equals(line)) {
-                    continue;
-                }
-
-                list.add(line);
-            }
-        } finally {
-            try {
-                in.close();
-            } catch (IOException e) {
-                //skip
-            }
-        }
-
-        return list;
-    }
-
-    /**
-     * Get display of Metadatum
-     *
-     * @param dcv MetadataValue
-     * @return string displaying elements of the Metadatum
-     */
-    public static String getDCValueString(MetadataValue dcv) {
-        MetadataField metadataField = dcv.getMetadataField();
-        MetadataSchema metadataSchema = metadataField.getMetadataSchema();
-        return "schema: " + metadataSchema.getName() + "; element: " + metadataField
-            .getElement() + "; qualifier: " + metadataField.getQualifier() +
-            "; language: " + dcv.getLanguage() + "; value: " + dcv.getValue();
-    }
-
-    /**
-     * Return compound form of a metadata field (i.e. schema.element.qualifier)
-     *
-     * @param schema    schema
-     * @param element   element
-     * @param qualifier qualifier
-     * @return a String representation of the two- or three-part form of a metadata element
-     * e.g. dc.identifier.uri
-     */
-    public static String getCompoundForm(String schema, String element, String qualifier) {
-        StringBuilder sb = new StringBuilder();
-        sb.append(schema).append(".").append(element);
-
-        if (qualifier != null) {
-            sb.append(".").append(qualifier);
-        }
-        return sb.toString();
-    }
-
-    /**
-     * Parses metadata field given in the form {@code <schema>.<element>[.<qualifier>|.*]}
-     * checks for correct number of elements (2 or 3) and for empty strings
-     *
-     * @param compoundForm compound form of metadata field
-     * @return String Array
-     * @throws ParseException if validity checks fail
-     */
-    public static String[] parseCompoundForm(String compoundForm)
-        throws ParseException {
-        String[] ar = compoundForm.split("\\s*\\.\\s*");  //trim ends
-
-        if ("".equals(ar[0])) {
-            throw new ParseException("schema is empty string: " + compoundForm, 0);
-        }
-
-        if ((ar.length < 2) || (ar.length > 3) || "".equals(ar[1])) {
-            throw new ParseException("element is malformed or empty string: " + compoundForm, 0);
-        }
-
-        return ar;
-    }
-
-}

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

@@ -1,49 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.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
- * Also delete all derivative bitstreams, i.e.
- * all bitstreams in the TEXT and THUMBNAIL bundles
- */
-public class OriginalBitstreamFilter extends BitstreamFilterByBundleName {
-    public OriginalBitstreamFilter() {
-        //empty
-    }
-
-    /**
-     * Tests bitstreams for containment in an ORIGINAL bundle
-     *
-     * @param bitstream Bitstream
-     * @return true if the bitstream is in the ORIGINAL bundle
-     * @throws BitstreamFilterException if filter error
-     */
-    @Override
-    public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        try {
-            List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle bundle : bundles) {
-                if (bundle.getName().equals("ORIGINAL")) {
-                    return true;
-                }
-            }
-        } catch (SQLException e) {
-            throw new BitstreamFilterException(e);
-        }
-        return false;
-    }
-
-}

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

@@ -1,53 +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.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
- * Also delete all derivative bitstreams, i.e.
- * all bitstreams in the TEXT and THUMBNAIL bundles
- */
-public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter {
-    protected String[] bundlesToEmpty = {"ORIGINAL", "TEXT", "THUMBNAIL"};
-
-    public OriginalWithDerivativesBitstreamFilter() {
-        //empty
-    }
-
-    /**
-     * Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
-     *
-     * @param bitstream Bitstream
-     * @return true if bitstream is in specified bundles
-     * @throws BitstreamFilterException if error
-     */
-    @Override
-    public boolean accept(Bitstream bitstream)
-        throws BitstreamFilterException {
-        try {
-            List<Bundle> bundles = bitstream.getBundles();
-            for (Bundle b : bundles) {
-                for (String bn : bundlesToEmpty) {
-                    if (b.getName().equals(bn)) {
-                        return true;
-                    }
-                }
-            }
-        } catch (SQLException e) {
-            throw new BitstreamFilterException(e);
-        }
-        return false;
-    }
-
-}

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

@@ -1,22 +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.itemupdate;
-
-import java.util.Properties;
-
-/**
- * Bitstream filter targetting the THUMBNAIL bundle
- */
-public class ThumbnailBitstreamFilter extends BitstreamFilterByBundleName {
-
-    public ThumbnailBitstreamFilter() {
-        props = new Properties();
-        props.setProperty("bundle", "THUMBNAIL");
-    }
-
-}

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

@@ -1,33 +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.itemupdate;
-
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.Context;
-
-/**
- * Interface for actions to update an item
- */
-public interface UpdateAction {
-    public ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
-
-    /**
-     * Action to update item
-     *
-     * @param context      DSpace context
-     * @param itarch       item archive
-     * @param isTest       test flag
-     * @param suppressUndo undo flag
-     * @throws Exception if error
-     */
-    public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo)
-        throws Exception;
-
-}

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

@@ -1,43 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.BitstreamService;
-import org.dspace.content.service.BundleService;
-
-/**
- * Base class for Bitstream actions
- */
-public abstract class UpdateBitstreamsAction implements UpdateAction {
-
-    protected boolean alterProvenance = true;
-
-
-    protected BundleService bundleService = ContentServiceFactory.getInstance().getBundleService();
-    protected BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
-
-    /**
-     * Set variable to indicate that the dc.description.provenance field may
-     * be changed as a result of Bitstream changes by ItemUpdate
-     *
-     * @param alterProvenance 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
-     */
-    public boolean getAlterProvenance() {
-        return alterProvenance;
-    }
-
-}

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

@@ -1,67 +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.itemupdate;
-
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * This abstract subclass for metadata actions
- * maintains a collection for the target metadata fields
- * expressed as a string in the compound notation ( {@code <schema>.<element>.<qualifier>} )
- * on which to apply the action when the method execute is called.
- *
- * Implemented as a Set to avoid problems with duplicates
- */
-public abstract class UpdateMetadataAction implements UpdateAction {
-
-    protected Set<String> targetFields = new HashSet<String>();
-
-    /**
-     * Get target fields
-     *
-     * @return set of fields to update
-     */
-    public Set<String> getTargetFields() {
-        return targetFields;
-    }
-
-    /**
-     * Set target fields
-     *
-     * @param targetFields Set of target fields to update
-     */
-    public void addTargetFields(Set<String> targetFields) {
-        for (String tf : targetFields) {
-            this.targetFields.add(tf);
-        }
-
-    }
-
-    /**
-     * Add array of target fields to update
-     *
-     * @param targetFields array of target fields to update
-     */
-    public void addTargetFields(String[] targetFields) {
-        for (String tf : targetFields) {
-            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

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

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

@@ -1,281 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.launcher;
-
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.lang.reflect.Method;
-import java.util.List;
-import java.util.TreeMap;
-
-import org.dspace.servicemanager.DSpaceKernelImpl;
-import org.dspace.servicemanager.DSpaceKernelInit;
-import org.dspace.services.RequestService;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-
-/**
- * A DSpace script launcher.
- *
- * @author Stuart Lewis
- * @author Mark Diggory
- */
-public class ScriptLauncher {
-    /**
-     * The service manager kernel
-     */
-    private static transient DSpaceKernelImpl kernelImpl;
-
-    /**
-     * Default constructor
-     */
-    private ScriptLauncher() { }
-
-    /**
-     * Execute the DSpace script launcher
-     *
-     * @param args Any parameters required to be passed to the scripts it executes
-     * @throws IOException           if IO error
-     * @throws FileNotFoundException if file doesn't exist
-     */
-    public static void main(String[] args)
-        throws FileNotFoundException, IOException {
-        // Initialise the service manager kernel
-        try {
-            kernelImpl = DSpaceKernelInit.getKernel(null);
-            if (!kernelImpl.isRunning()) {
-                kernelImpl.start();
-            }
-        } catch (Exception e) {
-            // Failed to start so destroy it and log and throw an exception
-            try {
-                kernelImpl.destroy();
-            } catch (Exception e1) {
-                // Nothing to do
-            }
-            String message = "Failure during kernel init: " + e.getMessage();
-            System.err.println(message);
-            e.printStackTrace();
-            throw new IllegalStateException(message, e);
-        }
-
-        // Load up the ScriptLauncher's configuration
-        Document commandConfigs = getConfig();
-
-        // Check that there is at least one argument (if not display command options)
-        if (args.length < 1) {
-            System.err.println("You must provide at least one command argument");
-            display(commandConfigs);
-            System.exit(1);
-        }
-
-        // Look up command in the configuration, and execute.
-        int status;
-        status = runOneCommand(commandConfigs, args);
-
-        // Destroy the service kernel if it is still alive
-        if (kernelImpl != null) {
-            kernelImpl.destroy();
-            kernelImpl = null;
-        }
-
-        System.exit(status);
-    }
-
-    protected static int runOneCommand(Document commandConfigs, String[] args) {
-        return runOneCommand(commandConfigs, args, kernelImpl);
-    }
-
-    /**
-     * Recognize and execute a single command.
-     *
-     * @param commandConfigs  Document
-     * @param args the command line arguments given
-     */
-    public static int runOneCommand(Document commandConfigs, String[] args, DSpaceKernelImpl kernelImpl) {
-        String request = args[0];
-        Element root = commandConfigs.getRootElement();
-        List<Element> commands = root.getChildren("command");
-        Element command = null;
-        for (Element candidate : commands) {
-            if (request.equalsIgnoreCase(candidate.getChild("name").getValue())) {
-                command = candidate;
-                break;
-            }
-        }
-
-        if (null == command) {
-            // The command wasn't found
-            System.err.println("Command not found: " + args[0]);
-            display(commandConfigs);
-            return 1;
-        }
-
-        // Run each step
-        List<Element> steps = command.getChildren("step");
-        for (Element step : steps) {
-            // Instantiate the class
-            Class target = null;
-
-            // Is it the special case 'dsrun' where the user provides the class name?
-            String className;
-            if ("dsrun".equals(request)) {
-                if (args.length < 2) {
-                    System.err.println("Error in launcher.xml: Missing class name");
-                    return 1;
-                }
-                className = args[1];
-            } else {
-                className = step.getChild("class").getValue();
-            }
-            try {
-                target = Class.forName(className,
-                                       true,
-                                       Thread.currentThread().getContextClassLoader());
-            } catch (ClassNotFoundException e) {
-                System.err.println("Error in launcher.xml: Invalid class name: " + className);
-                return 1;
-            }
-
-            // Strip the leading argument from the args, and add the arguments
-            // Set <passargs>false</passargs> if the arguments should not be passed on
-            String[] useargs = args.clone();
-            Class[] argTypes = {useargs.getClass()};
-            boolean passargs = true;
-            if ((step.getAttribute("passuserargs") != null) &&
-                ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue()))) {
-                passargs = false;
-            }
-            if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs)) {
-                useargs = new String[0];
-            } 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)) {
-                    x = 2;
-                }
-                String[] argsnew = new String[useargs.length - x];
-                for (int i = x; i < useargs.length; i++) {
-                    argsnew[i - x] = useargs[i];
-                }
-                useargs = argsnew;
-            }
-
-            // Add any extra properties
-            List<Element> bits = step.getChildren("argument");
-            if (step.getChild("argument") != null) {
-                String[] argsnew = new String[useargs.length + bits.size()];
-                int i = 0;
-                for (Element arg : bits) {
-                    argsnew[i++] = arg.getValue();
-                }
-                for (; i < bits.size() + useargs.length; i++) {
-                    argsnew[i] = useargs[i - bits.size()];
-                }
-                useargs = argsnew;
-            }
-
-            // Establish the request service startup
-            RequestService requestService = kernelImpl.getServiceManager().getServiceByName(
-                RequestService.class.getName(), RequestService.class);
-            if (requestService == null) {
-                throw new IllegalStateException(
-                    "Could not get the DSpace RequestService to start the request transaction");
-            }
-
-            // Establish a request related to the current session
-            // that will trigger the various request listeners
-            requestService.startRequest();
-
-            // Run the main() method
-            try {
-                Object[] arguments = {useargs};
-
-                // Useful for debugging, so left in the code...
-                /**System.out.print("About to execute: " + className);
-                 for (String param : useargs)
-                 {
-                 System.out.print(" " + param);
-                 }
-                 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) {
-                // Failure occurred in the request so we destroy it
-                requestService.endRequest(e);
-
-                // Exceptions from the script are reported as a 'cause'
-                Throwable cause = e.getCause();
-                System.err.println("Exception: " + cause.getMessage());
-                cause.printStackTrace();
-                return 1;
-            }
-        }
-
-        // Everything completed OK
-        return 0;
-    }
-
-    /**
-     * Load the launcher configuration file
-     *
-     * @return The XML configuration file Document
-     */
-    protected static Document getConfig() {
-        return getConfig(kernelImpl);
-    }
-
-    public static Document getConfig(DSpaceKernelImpl kernelImpl) {
-        // Load the launcher configuration file
-        String config = kernelImpl.getConfigurationService().getProperty("dspace.dir") +
-            System.getProperty("file.separator") + "config" +
-            System.getProperty("file.separator") + "launcher.xml";
-        SAXBuilder saxBuilder = new SAXBuilder();
-        Document doc = null;
-        try {
-            doc = saxBuilder.build(config);
-        } 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;
-    }
-
-    /**
-     * Display the commands that the current launcher config file knows about
-     *
-     * @param commandConfigs configs as Document
-     */
-    private static void display(Document commandConfigs) {
-        // List all command elements
-        List<Element> commands = commandConfigs.getRootElement().getChildren("command");
-
-        // Sort the commands by name.
-        // We cannot just use commands.sort() because it tries to remove and
-        // reinsert Elements within other Elements, and that doesn't work.
-        TreeMap<String, Element> sortedCommands = new TreeMap<>();
-        for (Element command : commands) {
-            sortedCommands.put(command.getChild("name").getValue(), command);
-        }
-
-        // Display the sorted list
-        System.out.println("Usage: dspace [command-name] {parameters}");
-        for (Element command : sortedCommands.values()) {
-            System.out.println(" - " + command.getChild("name").getValue() +
-                                   ": " + command.getChild("description").getValue());
-        }
-    }
-}

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

@@ -1,136 +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.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.
- * Thanks Ninh Nguyen from the National Library of Australia for providing the source code.
- * This version of the code is basically Ninh's but reorganised a little. Used with permission.
- */
-
-public class Brand {
-    private int brandWidth;
-    private int brandHeight;
-    private Font font;
-    private int xOffset;
-
-    /**
-     * Constructor to set up footer image attributes.
-     *
-     * @param brandWidth  length of the footer in pixels
-     * @param brandHeight height of the footer in pixels
-     * @param font        font to use for text on the footer
-     * @param xOffset     number of pixels text should be indented from left-hand side of footer
-     */
-    public Brand(int brandWidth,
-                 int brandHeight,
-                 Font font,
-                 int xOffset) {
-        this.brandWidth = brandWidth;
-        this.brandHeight = brandHeight;
-        this.font = font;
-        this.xOffset = xOffset;
-    }
-
-    /**
-     * Create the brand 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
-     *                       the image is resized such that brandLeftText will not fit. <code>null</code> if not
-     *                       required
-     * @param brandRightText text that should appear in the bottom right of the image
-     * @return BufferedImage a BufferedImage object describing the brand image file
-     */
-    public BufferedImage create(String brandLeftText,
-                                String shortLeftText,
-                                String brandRightText) {
-        BrandText[] allBrandText = null;
-
-        BufferedImage brandImage =
-            new BufferedImage(brandWidth, brandHeight, BufferedImage.TYPE_INT_RGB);
-
-        if (brandWidth >= 350) {
-            allBrandText = new BrandText[] {
-                new BrandText(BrandText.BL, brandLeftText),
-                new BrandText(BrandText.BR, brandRightText)
-            };
-        } else if (brandWidth >= 190) {
-            allBrandText = new BrandText[] {
-                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) {
-            for (int i = 0; i < allBrandText.length; ++i) {
-                drawImage(brandImage, allBrandText[i]);
-            }
-        }
-
-        return brandImage;
-    }
-
-
-    /**
-     * do the text placements and preparatory work for the brand image generation
-     *
-     * @param brandImage a BufferedImage object where the image is created
-     * @param identifier and Identifier object describing what text is to be placed in what
-     *                   position within the brand
-     */
-    private void drawImage(BufferedImage brandImage,
-                           BrandText brandText) {
-        int imgWidth = brandImage.getWidth();
-        int imgHeight = brandImage.getHeight();
-
-        Graphics2D g2 = brandImage.createGraphics();
-        g2.setFont(font);
-        FontMetrics fm = g2.getFontMetrics();
-
-        int bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
-        int bHeight = fm.getHeight();
-
-        int bx = 0;
-        int by = 0;
-
-        if (brandText.getLocation().equals(BrandText.TL)) {
-            bx = 0;
-            by = 0;
-        } else if (brandText.getLocation().equals(BrandText.TR)) {
-            bx = imgWidth - bWidth;
-            by = 0;
-        } else if (brandText.getLocation().equals(BrandText.BL)) {
-            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);
-        int tx = bx + xOffset;
-        int 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

@@ -1,87 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-/**
- * Identifier class, holding a single item of text and its location
- * within a rectangular areas. Allowable locations are any of the four corners.
- * This is a copy of Picture Australia's PiObj class re-organised with methods.
- * Thanks to Ninh Nguyen at the National Library for providing the original source.
- */
-class BrandText {
-    /**
-     * Bottom Left
-     */
-    public static final String BL = "bl";
-    /**
-     * Bottom Right
-     */
-    public static final String BR = "br";
-    /**
-     * Top Left
-     */
-    public static final String TL = "tl";
-    /**
-     * Top Right
-     */
-    public static final String TR = "tr";
-
-    private String location;
-    private String text;
-
-    /**
-     * Constructor for an Identifier object containing a text string and
-     * its location within a rectangular area.
-     *
-     * @param location one of the class location constants e.g. <code>Identifier.BL</code>
-     * @param the      text associated with the location
-     */
-    public BrandText(String location, String text) {
-        this.location = location;
-        this.text = text;
-    }
-
-    /**
-     * 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>
-     */
-    public String getLocation() {
-        return location;
-    }
-
-
-    /**
-     * get the text associated with the Identifier object
-     *
-     * @return String the text associated with the Identifier object
-     */
-    public String getText() {
-        return text;
-    }
-
-
-    /**
-     * set the location associated with the Identifier object
-     *
-     * @param location one of the class location constants
-     */
-    public void setLocation(String location) {
-        this.location = location;
-    }
-
-
-    /**
-     * set the text associated with the Identifier object
-     *
-     * @param text any text string (typically a branding or identifier)
-     */
-    public void setText(String text) {
-        this.text = text;
-    }
-}

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

@@ -1,86 +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.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
-
-/**
- * Filter image bitstreams, scaling the image to be within the bounds of
- * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
- * no bigger than. Creates only JPEGs.
- *
- * @author Jason Sherman jsherman@usao.edu
- */
-public class BrandedPreviewJPEGFilter extends MediaFilter {
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".preview.jpg";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "BRANDED_PREVIEW";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "JPEG";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Generated Branded Preview";
-    }
-
-
-    /**
-     * @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 {
-        // read in bitstream's image
-        BufferedImage buf = ImageIO.read(source);
-
-        // get config params
-        float xmax = (float) ConfigurationManager
-            .getIntProperty("webui.preview.maxwidth");
-        float ymax = (float) ConfigurationManager
-            .getIntProperty("webui.preview.maxheight");
-        boolean blurring = (boolean) ConfigurationManager
-            .getBooleanProperty("webui.preview.blurring");
-        boolean hqscaling = (boolean) ConfigurationManager
-            .getBooleanProperty("webui.preview.hqscaling");
-        int brandHeight = ConfigurationManager.getIntProperty("webui.preview.brand.height");
-        String brandFont = ConfigurationManager.getProperty("webui.preview.brand.font");
-        int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");
-
-        JPEGFilter jpegFilter = new JPEGFilter();
-        return jpegFilter
-            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
-                         brandFont);
-    }
-}

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

@@ -1,98 +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 org.dspace.content.Bitstream;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * 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 {
-    /**
-     * Get a filename for a newly created filtered bitstream
-     *
-     * @param sourceName name of source bitstream
-     * @return filename generated by the filter - for example, document.pdf
-     * becomes document.pdf.txt
-     */
-    public String getFilteredName(String sourceName);
-
-    /**
-     * @return name of the bundle this filter will stick its generated
-     * 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
-     * mediafilter.cfg for valid format strings.
-     */
-    public String getFormatString();
-
-    /**
-     * @return string to describe the newly-generated Bitstream - how it was
-     * produced is a good idea
-     */
-    public String getDescription();
-
-    /**
-     * Read the source stream and produce the filtered content.
-     *
-     * @param item    Item
-     * @param source  input stream
-     * @param verbose verbosity flag
-     * @return result of filter's transformation as a byte stream.
-     * @throws Exception if error
-     */
-    public InputStream getDestinationStream(Item item, InputStream source, boolean verbose)
-        throws Exception;
-
-    /**
-     * 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 source  source bitstream to be processed
-     * @param verbose verbose mode
-     * @return true if bitstream processing should continue,
-     * false if this bitstream should be skipped
-     * @throws Exception if error
-     */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
-        throws Exception;
-
-    /**
-     * Perform any post-processing of the generated bitstream *after* this
-     * filter has already been run.
-     * <p>
-     * 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 generatedBitstream the bitstream which was generated by
-     *                           this filter.
-     * @throws Exception if error
-     */
-    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-        throws Exception;
-}
-

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

@@ -1,81 +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.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 {
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Extracted text";
-    }
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        // 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();
-        Document doc = kit.createDefaultDocument();
-
-        doc.putProperty("IgnoreCharsetDirective", Boolean.TRUE);
-
-        kit.read(source, doc, 0);
-
-        String extractedText = doc.getText(0, doc.getLength());
-
-        // generate an input stream with the extracted text
-        byte[] textBytes = extractedText.getBytes();
-        ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-        return bais; // will this work? or will the byte array be out of scope?
-    }
-}

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

@@ -1,52 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.nio.file.Files;
-
-import org.dspace.content.Item;
-
-
-/**
- * Filter image bitstreams, scaling the image to be within the bounds of
- * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
- * no bigger than. Creates only JPEGs.
- */
-public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter {
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        File f = inputStreamToTempFile(source, "imthumb", ".tmp");
-        File f2 = null;
-        try {
-            f2 = getThumbnailFile(f, verbose);
-            byte[] bytes = Files.readAllBytes(f2.toPath());
-            return new ByteArrayInputStream(bytes);
-        } finally {
-            //noinspection ResultOfMethodCallIgnored
-            f.delete();
-            if (f2 != null) {
-                //noinspection ResultOfMethodCallIgnored
-                f2.delete();
-            }
-        }
-    }
-
-
-}

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

@@ -1,43 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.InputStream;
-import java.nio.file.Files;
-
-import org.dspace.content.Item;
-
-public class ImageMagickPdfThumbnailFilter extends ImageMagickThumbnailFilter {
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
-        File f2 = null;
-        File f3 = null;
-        try {
-            f2 = getImageFile(f, 0, verbose);
-            f3 = getThumbnailFile(f2, verbose);
-            byte[] bytes = Files.readAllBytes(f3.toPath());
-            return new ByteArrayInputStream(bytes);
-        } finally {
-            //noinspection ResultOfMethodCallIgnored
-            f.delete();
-            if (f2 != null) {
-                //noinspection ResultOfMethodCallIgnored
-                f2.delete();
-            }
-            if (f3 != null) {
-                //noinspection ResultOfMethodCallIgnored
-                f3.delete();
-            }
-        }
-    }
-
-}

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

@@ -1,202 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.util.regex.Pattern;
-import java.util.regex.PatternSyntaxException;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.Item;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.im4java.core.ConvertCmd;
-import org.im4java.core.IM4JavaException;
-import org.im4java.core.IMOperation;
-import org.im4java.core.Info;
-import org.im4java.process.ProcessStarter;
-
-/**
- * Filter image bitstreams, scaling the image to be within the bounds of
- * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
- * no bigger than. Creates only JPEGs.
- */
-public abstract class ImageMagickThumbnailFilter extends MediaFilter {
-    protected static int width = 180;
-    protected static int height = 120;
-    private static boolean flatten = true;
-    static String bitstreamDescription = "IM Thumbnail";
-    static final String defaultPattern = "Generated Thumbnail";
-    static Pattern replaceRegex = Pattern.compile(defaultPattern);
-    protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-
-    static String cmyk_profile;
-    static String srgb_profile;
-
-    static {
-        String pre = ImageMagickThumbnailFilter.class.getName();
-        String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
-        ProcessStarter.setGlobalSearchPath(s);
-        width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
-        height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
-        flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
-        String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
-        cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
-        srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
-        if (description != null) {
-            bitstreamDescription = description;
-        }
-        try {
-            String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
-            replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
-        } catch (PatternSyntaxException e) {
-            System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
-        }
-    }
-
-    public ImageMagickThumbnailFilter() {
-    }
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".jpg";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "THUMBNAIL";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "JPEG";
-    }
-
-    /**
-     * @return String bitstreamDescription
-     */
-    @Override
-    public String getDescription() {
-        return bitstreamDescription;
-    }
-
-    public File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
-        File f = File.createTempFile(prefix, suffix);
-        f.deleteOnExit();
-        FileOutputStream fos = new FileOutputStream(f);
-
-        byte[] buffer = new byte[1024];
-        int len = source.read(buffer);
-        while (len != -1) {
-            fos.write(buffer, 0, len);
-            len = source.read(buffer);
-        }
-        fos.close();
-        return f;
-    }
-
-    public File getThumbnailFile(File f, boolean verbose)
-        throws IOException, InterruptedException, IM4JavaException {
-        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-        f2.deleteOnExit();
-        ConvertCmd cmd = new ConvertCmd();
-        IMOperation op = new IMOperation();
-        op.autoOrient();
-        op.addImage(f.getAbsolutePath());
-        op.thumbnail(width, height);
-        op.addImage(f2.getAbsolutePath());
-        if (verbose) {
-            System.out.println("IM Thumbnail Param: " + op);
-        }
-        cmd.run(op);
-        return f2;
-    }
-
-    public File getImageFile(File f, int page, boolean verbose)
-        throws IOException, InterruptedException, IM4JavaException {
-        File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-        f2.deleteOnExit();
-        ConvertCmd cmd = new ConvertCmd();
-        IMOperation op = new IMOperation();
-        String s = "[" + page + "]";
-        op.addImage(f.getAbsolutePath() + s);
-        if (flatten) {
-            op.flatten();
-        }
-        // PDFs using the CMYK color system can be handled specially if
-        // profiles are defined
-        if (cmyk_profile != null && srgb_profile != null) {
-            Info imageInfo = new Info(f.getAbsolutePath(), true);
-            String imageClass = imageInfo.getImageClass();
-            if (imageClass.contains("CMYK")) {
-                op.profile(cmyk_profile);
-                op.profile(srgb_profile);
-            }
-        }
-        op.addImage(f2.getAbsolutePath());
-        if (verbose) {
-            System.out.println("IM Image Param: " + op);
-        }
-        cmd.run(op);
-        return f2;
-    }
-
-    @Override
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose) throws Exception {
-        String nsrc = source.getName();
-        for (Bundle b : itemService.getBundles(item, "THUMBNAIL")) {
-            for (Bitstream bit : b.getBitstreams()) {
-                String n = bit.getName();
-                if (n != null) {
-                    if (nsrc != null) {
-                        if (!n.startsWith(nsrc)) {
-                            continue;
-                        }
-                    }
-                }
-                String description = bit.getDescription();
-                // If anything other than a generated thumbnail
-                // is found, halt processing
-                if (description != null) {
-                    if (replaceRegex.matcher(description).matches()) {
-                        if (verbose) {
-                            System.out.println(description + " " + nsrc
-                                                   + " matches pattern and is replacable.");
-                        }
-                        continue;
-                    }
-                    if (description.equals(bitstreamDescription)) {
-                        if (verbose) {
-                            System.out.println(bitstreamDescription + " " + nsrc
-                                                   + " is replacable.");
-                        }
-                        continue;
-                    }
-                }
-                System.out.println("Custom Thumbnail exists for " + nsrc + " for item "
-                                       + item.getHandle() + ".  Thumbnail will not be generated. ");
-                return false;
-            }
-        }
-
-        return true; // assume that the thumbnail is a custom one
-    }
-
-}

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

@@ -1,315 +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.Color;
-import java.awt.Font;
-import java.awt.Graphics2D;
-import java.awt.RenderingHints;
-import java.awt.Transparency;
-import java.awt.image.BufferedImage;
-import java.awt.image.BufferedImageOp;
-import java.awt.image.ConvolveOp;
-import java.awt.image.Kernel;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-import javax.imageio.ImageIO;
-
-import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
-
-/**
- * Filter image bitstreams, scaling the image to be within the bounds of
- * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
- * no bigger than. Creates only JPEGs.
- *
- * @author Jason Sherman jsherman@usao.edu
- */
-public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats {
-    @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 {
-        // read in bitstream's image
-        BufferedImage buf = ImageIO.read(source);
-
-        return getThumb(currentItem, buf, verbose);
-    }
-
-    public InputStream getThumb(Item currentItem, BufferedImage buf, boolean verbose)
-        throws Exception {
-        // get config params
-        float xmax = (float) ConfigurationManager
-            .getIntProperty("thumbnail.maxwidth");
-        float ymax = (float) ConfigurationManager
-            .getIntProperty("thumbnail.maxheight");
-        boolean blurring = (boolean) ConfigurationManager
-            .getBooleanProperty("thumbnail.blurring");
-        boolean hqscaling = (boolean) ConfigurationManager
-            .getBooleanProperty("thumbnail.hqscaling");
-
-        return getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, 0, 0, null);
-    }
-
-    public InputStream getThumbDim(Item currentItem, BufferedImage buf, boolean verbose, float xmax, float ymax,
-                                   boolean blurring, boolean hqscaling, int brandHeight, int brandFontPoint,
-                                   String brandFont)
-        throws Exception {
-        // now get the image dimensions
-        float xsize = (float) buf.getWidth(null);
-        float ysize = (float) buf.getHeight(null);
-
-        // if verbose flag is set, print out dimensions
-        // to STDOUT
-        if (verbose) {
-            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 (verbose) {
-                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 (verbose) {
-                System.out.println("size after fitting to maximum width: " + 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 (verbose) {
-            System.out.println("size after fitting to maximum height: " + 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);
-
-        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();
-
-        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!
-    }
-
-
-    @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;
-    }
-
-    public BufferedImage getNormalizedInstance(BufferedImage buf) {
-        int type = (buf.getTransparency() == Transparency.OPAQUE) ?
-            BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB_PRE;
-        int w = buf.getWidth();
-        int h = buf.getHeight();
-        BufferedImage normal = new BufferedImage(w, h, type);
-        Graphics2D g2d = normal.createGraphics();
-        g2d.drawImage(buf, 0, 0, w, h, Color.WHITE, null);
-        g2d.dispose();
-        return normal;
-    }
-
-    /**
-     * Convenience method that returns a blurred instance of the
-     * provided {@code BufferedImage}.
-     *
-     * @param buf buffered image
-     * @return updated BufferedImage
-     */
-    public BufferedImage getBlurredInstance(BufferedImage buf) {
-        buf = getNormalizedInstance(buf);
-
-        // kernel for blur op
-        float[] matrix = {
-            0.111f, 0.111f, 0.111f,
-            0.111f, 0.111f, 0.111f,
-            0.111f, 0.111f, 0.111f,
-        };
-
-        // perform the blur and return the blurred version.
-        BufferedImageOp blur = new ConvolveOp(new Kernel(3, 3, matrix));
-        BufferedImage blurbuf = blur.filter(buf, null);
-        return blurbuf;
-    }
-
-    /**
-     * Convenience method that returns a scaled instance of the
-     * provided {@code BufferedImage}.
-     *
-     * @param buf           the original image to be scaled
-     * @param targetWidth   the desired width of the scaled instance,
-     *                      in pixels
-     * @param targetHeight  the desired height of the scaled instance,
-     *                      in pixels
-     * @param hint          one of the rendering hints that corresponds to
-     *                      {@code RenderingHints.KEY_INTERPOLATION} (e.g.
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_NEAREST_NEIGHBOR},
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_BILINEAR},
-     *                      {@code RenderingHints.VALUE_INTERPOLATION_BICUBIC})
-     * @param higherQuality if true, this method will use a multi-step
-     *                      scaling technique that provides higher quality than the usual
-     *                      one-step technique (only useful in downscaling cases, where
-     *                      {@code targetWidth} or {@code targetHeight} is
-     *                      smaller than the original dimensions, and generally only when
-     *                      the {@code BILINEAR} hint is specified)
-     * @return a scaled version of the original {@code BufferedImage}
-     */
-    public BufferedImage getScaledInstance(BufferedImage buf,
-                                           int targetWidth,
-                                           int targetHeight,
-                                           Object hint,
-                                           boolean higherQuality) {
-        int type = (buf.getTransparency() == Transparency.OPAQUE) ?
-            BufferedImage.TYPE_INT_RGB : BufferedImage.TYPE_INT_ARGB;
-        BufferedImage scalebuf = (BufferedImage) buf;
-        int w;
-        int h;
-        if (higherQuality) {
-            // Use multi-step technique: start with original size, then
-            // scale down in multiple passes with drawImage()
-            // until the target size is reached
-            w = buf.getWidth();
-            h = buf.getHeight();
-        } else {
-            // Use one-step technique: scale directly from original
-            // size to target size with a single drawImage() call
-            w = targetWidth;
-            h = targetHeight;
-        }
-
-        do {
-            if (higherQuality && w > targetWidth) {
-                w /= 2;
-                if (w < targetWidth) {
-                    w = targetWidth;
-                }
-            }
-
-            if (higherQuality && h > targetHeight) {
-                h /= 2;
-                if (h < targetHeight) {
-                    h = targetHeight;
-                }
-            }
-
-            BufferedImage tmp = new BufferedImage(w, h, type);
-            Graphics2D g2d = tmp.createGraphics();
-            g2d.setRenderingHint(RenderingHints.KEY_INTERPOLATION, hint);
-            g2d.drawImage(scalebuf, 0, 0, w, h, Color.WHITE, null);
-            g2d.dispose();
-
-            scalebuf = tmp;
-        } while (w != targetWidth || h != targetHeight);
-
-        return scalebuf;
-    }
-}

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

@@ -1,63 +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 org.dspace.content.Bitstream;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-
-/**
- * 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
- * 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 {
-    /**
-     * 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 source  source bitstream to be processed
-     * @param verbose verbose mode
-     * @return true if bitstream processing should continue,
-     * false if this bitstream should be skipped
-     * @throws Exception if error
-     */
-    @Override
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
-        throws Exception {
-        return true;  //default to no pre-processing
-    }
-
-    /**
-     * Perform any post-processing of the generated bitstream *after* this
-     * filter has already been run.
-     * <p>
-     * 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 generatedBitstream the bitstream which was generated by
-     *                           this filter.
-     * @throws Exception if error
-     */
-    @Override
-    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-        throws Exception {
-        //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/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

@@ -1,129 +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.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
-import java.io.Writer;
-
-import org.apache.log4j.Logger;
-import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.text.PDFTextStripper;
-import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
-
-/*
- *
- * to do: helpful error messages - can't find mediafilter.cfg - can't
- * instantiate filter - bitstream format doesn't exist
- *
- */
-public class PDFFilter extends MediaFilter {
-
-    private static Logger log = Logger.getLogger(PDFFilter.class);
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Extracted text";
-    }
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        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) {
-                tempTextFile = File.createTempFile("dspacepdfextract" + source.hashCode(), ".txt");
-                tempTextFile.deleteOnExit();
-                writer = new OutputStreamWriter(new FileOutputStream(tempTextFile));
-            } else {
-                byteStream = new ByteArrayOutputStream();
-                writer = new OutputStreamWriter(byteStream);
-            }
-
-            try {
-                pdfDoc = PDDocument.load(source);
-                pts.writeText(pdfDoc, writer);
-            } finally {
-                try {
-                    if (pdfDoc != null) {
-                        pdfDoc.close();
-                    }
-                } catch (Exception e) {
-                    log.error("Error closing PDF file: " + e.getMessage(), e);
-                }
-
-                try {
-                    writer.close();
-                } catch (Exception e) {
-                    log.error("Error closing temporary extract file: " + e.getMessage(), e);
-                }
-            }
-
-            if (useTemporaryFile) {
-                return new FileInputStream(tempTextFile);
-            } else {
-                byte[] bytes = byteStream.toByteArray();
-                return new ByteArrayInputStream(bytes);
-            }
-        } catch (OutOfMemoryError oome) {
-            log.error("Error parsing PDF document " + oome.getMessage(), oome);
-            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
-                throw oome;
-            }
-        }
-
-        return null;
-    }
-}

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

@@ -1,113 +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.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;
-
-/*
- * TODO: Allow user to configure extraction of only text or only notes
- *
- */
-public class PowerPointFilter extends MediaFilter {
-
-    private static Logger log = Logger.getLogger(PowerPointFilter.class);
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstream format
-     *
-     * TODO: Check that this is correct
-     */
-    @Override
-    public String getFormatString() {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Extracted text";
-    }
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-
-        try {
-
-            String extractedText = null;
-            new ExtractorFactory();
-            POITextExtractor pptExtractor = ExtractorFactory
-                .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) {
-
-                // The true method arguments indicate that text from
-                // the slides and the notes is desired
-                extractedText = ((XSLFPowerPointExtractor) pptExtractor)
-                    .getText(true, true);
-            } else if (pptExtractor instanceof PowerPointExtractor) { // Legacy PowerPoint files
-
-                extractedText = ((PowerPointExtractor) pptExtractor).getText()
-                    + " " + ((PowerPointExtractor) pptExtractor).getNotes();
-
-            }
-            if (extractedText != null) {
-                // if verbose flag is set, print out extracted text
-                // to STDOUT
-                if (verbose) {
-                    System.out.println(extractedText);
-                }
-
-                // generate an input stream with the extracted text
-                byte[] textBytes = extractedText.getBytes();
-                ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-                return bais;
-            }
-        } catch (Exception e) {
-            log.error("Error filtering bitstream: " + e.getMessage(), e);
-            throw e;
-        }
-
-        return null;
-    }
-}

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

@@ -1,20 +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;
-
-/**
- * Interface to allow filters to register the input formats they handle
- * (useful for exposing underlying capabilities of libraries used)
- */
-public interface SelfRegisterInputFormats {
-    public String[] getInputMIMETypes();
-
-    public String[] getInputDescriptions();
-
-    public String[] getInputExtensions();
-}

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

@@ -1,93 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-
-import org.apache.log4j.Logger;
-import org.dspace.content.Item;
-import org.textmining.extraction.TextExtractor;
-import org.textmining.extraction.word.WordTextExtractorFactory;
-
-/*
- *
- * to do: helpful error messages - can't find mediafilter.cfg - can't
- * instantiate filter - bitstream format doesn't exist.
- *
- */
-public class WordFilter extends MediaFilter {
-
-    private static Logger log = Logger.getLogger(WordFilter.class);
-
-    @Override
-    public String getFilteredName(String oldFilename) {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     */
-    @Override
-    public String getBundleName() {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    @Override
-    public String getFormatString() {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    @Override
-    public String getDescription() {
-        return "Extracted text";
-    }
-
-    /**
-     * @param currentItem item
-     * @param source      source input stream
-     * @param verbose     verbose mode
-     * @return InputStream the resulting input stream
-     * @throws Exception if error
-     */
-    @Override
-    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        // get input stream from bitstream
-        // pass to filter, get string back
-        try {
-            WordTextExtractorFactory factory = new WordTextExtractorFactory();
-            TextExtractor e = factory.textExtractor(source);
-            String extractedText = e.getText();
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (verbose) {
-                System.out.println(extractedText);
-            }
-
-            // generate an input stream with the extracted text
-            byte[] textBytes = extractedText.getBytes();
-            ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-            return bais; // will this work? or will the byte array be out of scope?
-        } catch (IOException ioe) {
-            System.out.println("Invalid Word Format");
-            log.error("Error detected - Word File format not recognized: "
-                          + ioe.getMessage(), ioe);
-            throw ioe;
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/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);
-    }
-}

dspace-api/src/main/java/org/dspace/app/mediafilter/factory/MediaFilterServiceFactoryImpl.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.mediafilter.factory;
-
-import org.dspace.app.mediafilter.service.MediaFilterService;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Factory implementation to get services for the mediafilter package, use MediaFilterServiceFactory.getInstance() to
- * retrieve an implementation
- *
- * @author kevinvandevelde at atmire.com
- */
-public class MediaFilterServiceFactoryImpl extends MediaFilterServiceFactory {
-
-    @Autowired(required = true)
-    private MediaFilterService mediaFilterService;
-
-    @Override
-    public MediaFilterService getMediaFilterService() {
-        return mediaFilterService;
-    }
-}

dspace-api/src/main/java/org/dspace/app/mediafilter/service/MediaFilterService.java

@@ -1,127 +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.service;
-
-import java.util.List;
-import java.util.Map;
-
-import org.dspace.app.mediafilter.FormatFilter;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * 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 interface MediaFilterService {
-
-    //separator in filterFormats Map between a filter class name and a plugin name,
-    //for MediaFilters which extend SelfNamedPlugin (\034 is "file separator" char)
-    public static final String FILTER_PLUGIN_SEPARATOR = "\034";
-
-
-    public void applyFiltersAllItems(Context context) throws Exception;
-
-    public void applyFiltersCommunity(Context context, Community community)
-        throws Exception;
-
-    public void applyFiltersCollection(Context context, Collection collection)
-        throws Exception;
-
-    public void applyFiltersItem(Context c, Item item) throws Exception;
-
-
-    /**
-     * Iterate through the item's bitstreams in the ORIGINAL bundle, applying
-     * filters if possible.
-     *
-     * @param context context
-     * @param myItem  item
-     * @return true if any bitstreams processed,
-     * false if none
-     * @throws Exception if error
-     */
-    public boolean filterItem(Context context, Item myItem) throws Exception;
-
-    /**
-     * 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.
-     *
-     * @param c           context
-     * @param myItem      item
-     * @param myBitstream bitstream
-     * @return true if bitstream processed,
-     * false if no applicable filter or already processed
-     * @throws Exception if error
-     */
-    public boolean filterBitstream(Context c, Item myItem, Bitstream myBitstream) throws Exception;
-
-    /**
-     * 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 context      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
-     * @throws Exception if error occurs
-     */
-    public boolean processBitstream(Context context, Item item, Bitstream source, FormatFilter formatFilter)
-        throws Exception;
-
-    /**
-     * 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 Item getCurrentItem();
-
-    /**
-     * 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 boolean inSkipList(String identifier);
-
-    public void setVerbose(boolean isVerbose);
-
-    public void setQuiet(boolean isQuiet);
-
-    public void setForce(boolean isForce);
-
-    public void setMax2Process(int max2Process);
-
-    public void setFilterClasses(List<FormatFilter> filterClasses);
-
-    public void setSkipList(List<String> skipList);
-
-    public void setFilterFormats(Map<String, List<String>> filterFormats);
-}

dspace-api/src/main/java/org/dspace/app/packager/Packager.java

@@ -1,731 +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.packager;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.sql.SQLException;
-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.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.crosswalk.CrosswalkException;
-import org.dspace.content.packager.PackageDisseminator;
-import org.dspace.content.packager.PackageException;
-import org.dspace.content.packager.PackageIngester;
-import org.dspace.content.packager.PackageParameters;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.core.factory.CoreServiceFactory;
-import org.dspace.core.service.PluginService;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.factory.EPersonServiceFactory;
-import org.dspace.handle.factory.HandleServiceFactory;
-import org.dspace.workflow.WorkflowException;
-
-/**
- * Command-line interface to the Packager plugin.
- * <p>
- * This class ONLY exists to provide a CLI for the packager plugins. It does not
- * "manage" the plugins and it is not called from within DSpace, but the name
- * follows a DSpace convention.
- * <p>
- * It can invoke one of the Submission (SIP) packagers to create a new DSpace
- * Item out of a package, or a Dissemination (DIP) packager to write an Item out
- * as a package.
- * <p>
- * Usage is as follows:<br>
- * (Add the -h option to get the command to show its own help)
- *
- * <pre>
- *  1. To submit a SIP  (submissions tend to create a *new* object, with a new handle.  If you want to restore an
- *  object, see -r option below)
- *   dspace packager
- *       -e {ePerson}
- *       -t {PackagerType}
- *       -p {parent-handle} [ -p {parent2} ...]
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       [-a] --- also recursively ingest all child packages of the initial package
- *                (child pkgs must be referenced from parent pkg)
- *       [-w]   --- skip Workflow
- *       {package-filename}
- *
- *   {PackagerType} must match one of the aliases of the chosen Packager
- *   plugin.
- *
- *   The &quot;-w&quot; option circumvents Workflow, and is optional.  The &quot;-o&quot;
- *   option, which may be repeated, passes options to the packager
- *   (e.g. &quot;metadataOnly&quot; to a DIP packager).
- *
- *  2. To restore an AIP  (similar to submit mode, but attempts to restore with the handles/parents specified in AIP):
- *   dspace packager
- *       -r     --- restores a object from a package info, including the specified handle (will throw an error if
- *       handle is already in use)
- *       -e {ePerson}
- *       -t {PackagerType}
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       [-a] --- also recursively restore all child packages of the initial package
- *                (child pkgs must be referenced from parent pkg)
- *       [-k]   --- Skip over errors where objects already exist and Keep Existing objects by default.
- *                  Use with -r to only restore objects which do not already exist.  By default, -r will throw an error
- *                  and rollback all changes when an object is found that already exists.
- *       [-f]   --- Force a restore (even if object already exists).
- *                  Use with -r to replace an existing object with one from a package (essentially a delete and
- *                  restore).
- *                  By default, -r will throw an error and rollback all changes when an object is found that already
- *                  exists.
- *       [-i {identifier-handle-of-object}] -- Optional when -f is specified.  When replacing an object, you can
- *       specify the
- *                  object to replace if it cannot be easily determined from the package itself.
- *       {package-filename}
- *
- *   Restoring is very similar to submitting, except that you are recreating pre-existing objects.  So, in a restore,
- *   the object(s) are
- *   being recreated based on the details in the AIP.  This means that the object is recreated with the same handle
- *   and same parent/children
- *   objects.  Not all {PackagerTypes} may support a "restore".
- *
- *  3. To write out a DIP:
- *   dspace packager
- *       -d
- *       -e {ePerson}
- *       -t {PackagerType}
- *       -i {identifier-handle-of-object}
- *       [-a] --- also recursively disseminate all child objects of this object
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       {package-filename}
- *
- *   The &quot;-d&quot; switch chooses a Dissemination packager, and is required.
- *   The &quot;-o&quot; option, which may be repeated, passes options to the packager
- *   (e.g. &quot;metadataOnly&quot; to a DIP packager).
- * </pre>
- *
- * Note that {package-filename} may be "-" for standard input or standard
- * output, respectively.
- *
- * @author Larry Stone
- * @author Tim Donohue
- * @version $Revision$
- */
-public class Packager {
-    /* Various private global settings/options */
-    protected String packageType = null;
-    protected boolean submit = true;
-    protected boolean userInteractionEnabled = true;
-
-    // die from illegal command line
-    protected static void usageError(String msg) {
-        System.out.println(msg);
-        System.out.println(" (run with -h flag for details)");
-        System.exit(1);
-    }
-
-    public static void main(String[] argv) throws Exception {
-        Options options = new Options();
-        options.addOption("p", "parent", true,
-                          "Handle(s) of parent Community or Collection into which to ingest object (repeatable)");
-        options.addOption("e", "eperson", true,
-                          "email address of eperson doing importing");
-        options
-            .addOption(
-                "w",
-                "install",
-                false,
-                "disable workflow; install immediately without going through collection's workflow");
-        options.addOption("r", "restore", false,
-                          "ingest in \"restore\" mode.  Restores a missing object based on the contents in a package.");
-        options.addOption("k", "keep-existing", false,
-                          "if an object is found to already exist during a restore (-r), then keep the existing " +
-                              "object and continue processing.  Can only be used with '-r'.  This avoids " +
-                              "object-exists errors which are thrown by -r by default.");
-        options.addOption("f", "force-replace", false,
-                          "if an object is found to already exist during a restore (-r), then remove it and replace " +
-                              "it with the contents of the package.  Can only be used with '-r'.  This REPLACES the " +
-                              "object(s) in the repository with the contents from the package(s).");
-        options.addOption("t", "type", true, "package type or MIMEtype");
-        options
-            .addOption("o", "option", true,
-                       "Packager option to pass to plugin, \"name=value\" (repeatable)");
-        options.addOption("d", "disseminate", false,
-                          "Disseminate package (output); default is to submit.");
-        options.addOption("s", "submit", false,
-                          "Submission package (Input); this is the default. ");
-        options.addOption("i", "identifier", true, "Handle of object to disseminate.");
-        options.addOption("a", "all", false,
-                          "also recursively ingest/disseminate any child packages, e.g. all Items within a Collection" +
-                              " (not all packagers may support this option!)");
-        options.addOption("h", "help", false,
-                          "help (you may also specify '-h -t [type]' for additional help with a specific type of " +
-                              "packager)");
-        options.addOption("u", "no-user-interaction", false,
-                          "Skips over all user interaction (i.e. [y/n] question prompts) within this script. This " +
-                              "flag can be used if you want to save (pipe) a report of all changes to a file, and " +
-                              "therefore need to bypass all user interaction.");
-
-        CommandLineParser parser = new PosixParser();
-        CommandLine line = parser.parse(options, argv);
-
-        String sourceFile = null;
-        String eperson = null;
-        String[] parents = null;
-        String identifier = null;
-        PackageParameters pkgParams = new PackageParameters();
-        PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
-
-        //initialize a new packager -- we'll add all our current params as settings
-        Packager myPackager = new Packager();
-
-        if (line.hasOption('h')) {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("Packager  [options]  package-file|-\n",
-                             options);
-            //If user specified a type, also print out the SIP and DIP options
-            // that are specific to that type of packager
-            if (line.hasOption('t')) {
-                System.out.println("\n--------------------------------------------------------------");
-                System.out.println("Additional options for the " + line.getOptionValue('t') + " packager:");
-                System.out.println("--------------------------------------------------------------");
-                System.out.println("(These options may be specified using --option as described above)");
-
-                PackageIngester sip = (PackageIngester) pluginService
-                    .getNamedPlugin(PackageIngester.class, line.getOptionValue('t'));
-
-                if (sip != null) {
-                    System.out.println("\n\n" + line.getOptionValue('t') + " Submission (SIP) plugin options:\n");
-                    System.out.println(sip.getParameterHelp());
-                } else {
-                    System.out.println("\nNo valid Submission plugin found for " + line.getOptionValue('t') + " type.");
-                }
-
-                PackageDisseminator dip = (PackageDisseminator) pluginService
-                    .getNamedPlugin(PackageDisseminator.class, line.getOptionValue('t'));
-
-                if (dip != null) {
-                    System.out.println("\n\n" + line.getOptionValue('t') + " Dissemination (DIP) plugin options:\n");
-                    System.out.println(dip.getParameterHelp());
-                } else {
-                    System.out
-                        .println("\nNo valid Dissemination plugin found for " + line.getOptionValue('t') + " type.");
-                }
-
-            } else {
-                //otherwise, display list of valid packager types
-                System.out.println("\nAvailable Submission Package (SIP) types:");
-                String pn[] = pluginService
-                    .getAllPluginNames(PackageIngester.class);
-                for (int i = 0; i < pn.length; ++i) {
-                    System.out.println("  " + pn[i]);
-                }
-                System.out
-                    .println("\nAvailable Dissemination Package (DIP) types:");
-                pn = pluginService.getAllPluginNames(PackageDisseminator.class);
-                for (int i = 0; i < pn.length; ++i) {
-                    System.out.println("  " + pn[i]);
-                }
-            }
-            System.exit(0);
-        }
-
-        //look for flag to disable all user interaction
-        if (line.hasOption('u')) {
-            myPackager.userInteractionEnabled = false;
-        }
-        if (line.hasOption('w')) {
-            pkgParams.setWorkflowEnabled(false);
-        }
-        if (line.hasOption('r')) {
-            pkgParams.setRestoreModeEnabled(true);
-        }
-        //keep-existing is only valid in restoreMode (-r) -- otherwise ignore -k option.
-        if (line.hasOption('k') && pkgParams.restoreModeEnabled()) {
-            pkgParams.setKeepExistingModeEnabled(true);
-        }
-        //force-replace is only valid in restoreMode (-r) -- otherwise ignore -f option.
-        if (line.hasOption('f') && pkgParams.restoreModeEnabled()) {
-            pkgParams.setReplaceModeEnabled(true);
-        }
-        if (line.hasOption('e')) {
-            eperson = line.getOptionValue('e');
-        }
-        if (line.hasOption('p')) {
-            parents = line.getOptionValues('p');
-        }
-        if (line.hasOption('t')) {
-            myPackager.packageType = line.getOptionValue('t');
-        }
-        if (line.hasOption('i')) {
-            identifier = line.getOptionValue('i');
-        }
-        if (line.hasOption('a')) {
-            //enable 'recursiveMode' param to packager implementations, in case it helps with packaging or ingestion
-            // process
-            pkgParams.setRecursiveModeEnabled(true);
-        }
-        String files[] = line.getArgs();
-        if (files.length > 0) {
-            sourceFile = files[0];
-        }
-        if (line.hasOption('d')) {
-            myPackager.submit = false;
-        }
-        if (line.hasOption('o')) {
-            String popt[] = line.getOptionValues('o');
-            for (int i = 0; i < popt.length; ++i) {
-                String pair[] = popt[i].split("\\=", 2);
-                if (pair.length == 2) {
-                    pkgParams.addProperty(pair[0].trim(), pair[1].trim());
-                } else if (pair.length == 1) {
-                    pkgParams.addProperty(pair[0].trim(), "");
-                } else {
-                    System.err
-                        .println("Warning: Illegal package option format: \""
-                                     + popt[i] + "\"");
-                }
-            }
-        }
-
-        // Sanity checks on arg list: required args
-        // REQUIRED: sourceFile, ePerson (-e), packageType (-t)
-        if (sourceFile == null || eperson == null || myPackager.packageType == null) {
-            System.err.println("Error - missing a REQUIRED argument or option.\n");
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("PackageManager  [options]  package-file|-\n", options);
-            System.exit(0);
-        }
-
-        // find the EPerson, assign to context
-        Context context = new Context();
-        EPerson myEPerson = null;
-        myEPerson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(context, eperson);
-        if (myEPerson == null) {
-            usageError("Error, eperson cannot be found: " + eperson);
-        }
-        context.setCurrentUser(myEPerson);
-
-
-        //If we are in REPLACE mode
-        if (pkgParams.replaceModeEnabled()) {
-            context.setMode(Context.Mode.BATCH_EDIT);
-            PackageIngester sip = (PackageIngester) pluginService
-                .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null) {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            DSpaceObject objToReplace = null;
-
-            //if a specific identifier was specified, make sure it is valid
-            if (identifier != null && identifier.length() > 0) {
-                objToReplace = HandleServiceFactory.getInstance().getHandleService()
-                                                   .resolveToObject(context, identifier);
-                if (objToReplace == null) {
-                    throw new IllegalArgumentException("Bad identifier/handle -- "
-                                                           + "Cannot resolve handle \"" + identifier + "\"");
-                }
-            }
-
-            String choiceString = null;
-            if (myPackager.userInteractionEnabled) {
-                BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                System.out.println("\n\nWARNING -- You are running the packager in REPLACE mode.");
-                System.out.println(
-                    "\nREPLACE mode may be potentially dangerous as it will automatically remove and replace contents" +
-                        " within DSpace.");
-                System.out.println(
-                    "We highly recommend backing up all your DSpace contents (files & database) before continuing.");
-                System.out.print("\nWould you like to continue? [y/n]: ");
-                choiceString = input.readLine();
-            } else {
-                //user interaction disabled -- default answer to 'yes', otherwise script won't continue
-                choiceString = "y";
-            }
-
-            if (choiceString.equalsIgnoreCase("y")) {
-                System.out.println("Beginning replacement process...");
-
-                try {
-                    //replace the object from the source file
-                    myPackager.replace(context, sip, pkgParams, sourceFile, objToReplace);
-
-                    //commit all changes & exit successfully
-                    context.complete();
-                    System.exit(0);
-                } catch (Exception e) {
-                    // abort all operations
-                    e.printStackTrace();
-                    context.abort();
-                    System.out.println(e);
-                    System.exit(1);
-                }
-            }
-
-        } else if (myPackager.submit || pkgParams.restoreModeEnabled()) {
-            //else if normal SUBMIT mode (or basic RESTORE mode -- which is a special type of submission)
-            context.setMode(Context.Mode.BATCH_EDIT);
-
-            PackageIngester sip = (PackageIngester) pluginService
-                .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null) {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            // validate each parent arg (if any)
-            DSpaceObject parentObjs[] = null;
-            if (parents != null) {
-                System.out.println("Destination parents:");
-
-                parentObjs = new DSpaceObject[parents.length];
-                for (int i = 0; i < parents.length; i++) {
-                    // sanity check: did handle resolve?
-                    parentObjs[i] = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context,
-                                                                                                          parents[i]);
-                    if (parentObjs[i] == null) {
-                        throw new IllegalArgumentException(
-                            "Bad parent list -- "
-                                + "Cannot resolve parent handle \""
-                                + parents[i] + "\"");
-                    }
-                    System.out.println((i == 0 ? "Owner: " : "Parent: ")
-                                           + parentObjs[i].getHandle());
-                }
-            }
-
-            try {
-                //ingest the object from the source file
-                myPackager.ingest(context, sip, pkgParams, sourceFile, parentObjs);
-
-                //commit all changes & exit successfully
-                context.complete();
-                System.exit(0);
-            } catch (Exception e) {
-                // abort all operations
-                e.printStackTrace();
-                context.abort();
-                System.out.println(e);
-                System.exit(1);
-            }
-        } else {
-            // else, if DISSEMINATE mode
-            context.setMode(Context.Mode.READ_ONLY);
-
-            //retrieve specified package disseminator
-            PackageDisseminator dip = (PackageDisseminator) pluginService
-                .getNamedPlugin(PackageDisseminator.class, myPackager.packageType);
-            if (dip == null) {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
-                                                   .resolveToObject(context, identifier);
-            if (dso == null) {
-                throw new IllegalArgumentException("Bad identifier/handle -- "
-                                                       + "Cannot resolve handle \"" + identifier + "\"");
-            }
-
-            //disseminate the requested object
-            myPackager.disseminate(context, dip, dso, pkgParams, sourceFile);
-        }
-        System.exit(0);
-    }
-
-    /**
-     * Ingest one or more DSpace objects from package(s) based on the
-     * options passed to the 'packager' script.  This method is called
-     * for both 'submit' (-s) and 'restore' (-r) modes.
-     * <p>
-     * Please note that replace (-r -f) mode calls the replace() method instead.
-     *
-     * @param context    DSpace Context
-     * @param sip        PackageIngester which will actually ingest the package
-     * @param pkgParams  Parameters to pass to individual packager instances
-     * @param sourceFile location of the source package to ingest
-     * @param parentObjs Parent DSpace object(s) to attach new object to
-     * @throws IOException           if IO error
-     * @throws SQLException          if database error
-     * @throws FileNotFoundException if file doesn't exist
-     * @throws AuthorizeException    if authorization error
-     * @throws CrosswalkException    if crosswalk error
-     * @throws PackageException      if packaging error
-     */
-    protected void ingest(Context context, PackageIngester sip, PackageParameters pkgParams, String sourceFile,
-                          DSpaceObject parentObjs[])
-        throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException,
-        PackageException {
-        // make sure we have an input file
-        File pkgFile = new File(sourceFile);
-
-        if (!pkgFile.exists()) {
-            System.out.println("\nERROR: Package located at " + sourceFile + " does not exist!");
-            System.exit(1);
-        }
-
-        System.out.println("\nIngesting package located at " + sourceFile);
-
-        //find first parent (if specified) -- this will be the "owner" of the object
-        DSpaceObject parent = null;
-        if (parentObjs != null && parentObjs.length > 0) {
-            parent = parentObjs[0];
-        }
-        //NOTE: at this point, Parent may be null -- in which case it is up to the PackageIngester
-        // to either determine the Parent (from package contents) or throw an error.
-
-        try {
-            //If we are doing a recursive ingest, call ingestAll()
-            if (pkgParams.recursiveModeEnabled()) {
-                System.out.println("\nAlso ingesting all referenced packages (recursive mode)..");
-                System.out.println(
-                    "This may take a while, please check your logs for ongoing status while we process each package.");
-
-                //ingest first package & recursively ingest anything else that package references (child packages, etc)
-                List<String> hdlResults = sip.ingestAll(context, parent, pkgFile, pkgParams, null);
-
-                if (hdlResults != null) {
-                    //Report total objects created
-                    System.out.println("\nCREATED a total of " + hdlResults.size() + " DSpace Objects.");
-
-                    String choiceString = null;
-                    //Ask if user wants full list printed to command line, as this may be rather long.
-                    if (this.userInteractionEnabled) {
-                        BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                        System.out.print("\nWould you like to view a list of all objects that were created? [y/n]: ");
-                        choiceString = input.readLine();
-                    } else {
-                        // user interaction disabled -- default answer to 'yes', as
-                        // we want to provide user with as detailed a report as possible.
-                        choiceString = "y";
-                    }
-
-                    // Provide detailed report if user answered 'yes'
-                    if (choiceString.equalsIgnoreCase("y")) {
-                        System.out.println("\n\n");
-                        for (String result : hdlResults) {
-                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
-                                                                   .resolveToObject(context, result);
-
-                            if (dso != null) {
-
-                                if (pkgParams.restoreModeEnabled()) {
-                                    System.out.println("RESTORED DSpace " + Constants.typeText[dso.getType()] +
-                                                           " [ hdl=" + dso.getHandle() + ", dbID=" + dso
-                                        .getID() + " ] ");
-                                } else {
-                                    System.out.println("CREATED new DSpace " + Constants.typeText[dso.getType()] +
-                                                           " [ hdl=" + dso.getHandle() + ", dbID=" + dso
-                                        .getID() + " ] ");
-                                }
-                            }
-                        }
-                    }
-                }
-
-            } else {
-                //otherwise, just one package to ingest
-                try {
-                    DSpaceObject dso = sip.ingest(context, parent, pkgFile, pkgParams, null);
-
-                    if (dso != null) {
-                        if (pkgParams.restoreModeEnabled()) {
-                            System.out.println("RESTORED DSpace " + Constants.typeText[dso.getType()] +
-                                                   " [ hdl=" + dso.getHandle() + ", dbID=" + dso.getID() + " ] ");
-                        } else {
-                            System.out.println("CREATED new DSpace " + Constants.typeText[dso.getType()] +
-                                                   " [ hdl=" + dso.getHandle() + ", dbID=" + dso.getID() + " ] ");
-                        }
-                    }
-                } catch (IllegalStateException ie) {
-                    // NOTE: if we encounter an IllegalStateException, this means the
-                    // handle is already in use and this object already exists.
-
-                    //if we are skipping over (i.e. keeping) existing objects
-                    if (pkgParams.keepExistingModeEnabled()) {
-                        System.out.println(
-                            "\nSKIPPED processing package '" + pkgFile + "', as an Object already exists with this " +
-                                "handle.");
-                    } else {
-                        // Pass this exception on -- which essentially causes a full rollback of all changes (this
-                        // is the default)
-                        throw ie;
-                    }
-                }
-            }
-        } catch (WorkflowException e) {
-            throw new PackageException(e);
-        }
-    }
-
-
-    /**
-     * Disseminate one or more DSpace objects into package(s) based on the
-     * options passed to the 'packager' script
-     *
-     * @param context    DSpace context
-     * @param dip        PackageDisseminator which will actually create the package
-     * @param dso        DSpace Object to disseminate as a package
-     * @param pkgParams  Parameters to pass to individual packager instances
-     * @param outputFile File where final package should be saved
-     * @throws IOException           if IO error
-     * @throws SQLException          if database error
-     * @throws FileNotFoundException if file doesn't exist
-     * @throws AuthorizeException    if authorization error
-     * @throws CrosswalkException    if crosswalk error
-     * @throws PackageException      if packaging error
-     */
-    protected void disseminate(Context context, PackageDisseminator dip,
-                               DSpaceObject dso, PackageParameters pkgParams,
-                               String outputFile)
-        throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException,
-        PackageException {
-        // initialize output file
-        File pkgFile = new File(outputFile);
-
-        System.out.println("\nDisseminating DSpace " + Constants.typeText[dso.getType()] +
-                               " [ hdl=" + dso.getHandle() + " ] to " + outputFile);
-
-        //If we are doing a recursive dissemination of this object & all its child objects, call disseminateAll()
-        if (pkgParams.recursiveModeEnabled()) {
-            System.out.println("\nAlso disseminating all child objects (recursive mode)..");
-            System.out.println(
-                "This may take a while, please check your logs for ongoing status while we process each package.");
-
-            //disseminate initial object & recursively disseminate all child objects as well
-            List<File> fileResults = dip.disseminateAll(context, dso, pkgParams, pkgFile);
-
-            if (fileResults != null) {
-                //Report total files created
-                System.out.println("\nCREATED a total of " + fileResults.size() + " dissemination package files.");
-
-                String choiceString = null;
-                //Ask if user wants full list printed to command line, as this may be rather long.
-                if (this.userInteractionEnabled) {
-                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                    System.out.print("\nWould you like to view a list of all files that were created? [y/n]: ");
-                    choiceString = input.readLine();
-                } else {
-                    // user interaction disabled -- default answer to 'yes', as
-                    // we want to provide user with as detailed a report as possible.
-                    choiceString = "y";
-                }
-
-                // Provide detailed report if user answered 'yes'
-                if (choiceString.equalsIgnoreCase("y")) {
-                    System.out.println("\n\n");
-                    for (File result : fileResults) {
-                        System.out.println("CREATED package file: " + result.getCanonicalPath());
-                    }
-                }
-            }
-        } else {
-            //otherwise, just disseminate a single object to a single package file
-            dip.disseminate(context, dso, pkgParams, pkgFile);
-
-            if (pkgFile != null && pkgFile.exists()) {
-                System.out.println("\nCREATED package file: " + pkgFile.getCanonicalPath());
-            }
-        }
-    }
-
-
-    /**
-     * Replace an one or more existing DSpace objects with the contents of
-     * specified package(s) based on the options passed to the 'packager' script.
-     * This method is only called for full replaces ('-r -f' options specified)
-     *
-     * @param context      DSpace Context
-     * @param sip          PackageIngester which will actually replace the object with the package
-     * @param pkgParams    Parameters to pass to individual packager instances
-     * @param sourceFile   location of the source package to ingest as the replacement
-     * @param objToReplace DSpace object to replace (may be null if it will be specified in the package itself)
-     * @throws IOException           if IO error
-     * @throws SQLException          if database error
-     * @throws FileNotFoundException if file doesn't exist
-     * @throws AuthorizeException    if authorization error
-     * @throws CrosswalkException    if crosswalk error
-     * @throws PackageException      if packaging error
-     */
-    protected void replace(Context context, PackageIngester sip, PackageParameters pkgParams, String sourceFile,
-                           DSpaceObject objToReplace)
-        throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException,
-        PackageException {
-
-        // make sure we have an input file
-        File pkgFile = new File(sourceFile);
-
-        if (!pkgFile.exists()) {
-            System.out.println("\nPackage located at " + sourceFile + " does not exist!");
-            System.exit(1);
-        }
-
-        System.out.println("\nReplacing DSpace object(s) with package located at " + sourceFile);
-        if (objToReplace != null) {
-            System.out.println("Will replace existing DSpace " + Constants.typeText[objToReplace.getType()] +
-                                   " [ hdl=" + objToReplace.getHandle() + " ]");
-        }
-        // NOTE: At this point, objToReplace may be null.  If it is null, it is up to the PackageIngester
-        // to determine which Object needs to be replaced (based on the handle specified in the pkg, etc.)
-
-        try {
-            //If we are doing a recursive replace, call replaceAll()
-            if (pkgParams.recursiveModeEnabled()) {
-                //ingest first object using package & recursively replace anything else that package references
-                // (child objects, etc)
-                List<String> hdlResults = sip.replaceAll(context, objToReplace, pkgFile, pkgParams);
-
-                if (hdlResults != null) {
-                    //Report total objects replaced
-                    System.out.println("\nREPLACED a total of " + hdlResults.size() + " DSpace Objects.");
-
-                    String choiceString = null;
-                    //Ask if user wants full list printed to command line, as this may be rather long.
-                    if (this.userInteractionEnabled) {
-                        BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                        System.out.print("\nWould you like to view a list of all objects that were replaced? [y/n]: ");
-                        choiceString = input.readLine();
-                    } else {
-                        // user interaction disabled -- default answer to 'yes', as
-                        // we want to provide user with as detailed a report as possible.
-                        choiceString = "y";
-                    }
-
-                    // Provide detailed report if user answered 'yes'
-                    if (choiceString.equalsIgnoreCase("y")) {
-                        System.out.println("\n\n");
-                        for (String result : hdlResults) {
-                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
-                                                                   .resolveToObject(context, result);
-
-                            if (dso != null) {
-                                System.out.println("REPLACED DSpace " + Constants.typeText[dso.getType()] +
-                                                       " [ hdl=" + dso.getHandle() + " ] ");
-                            }
-                        }
-                    }
-
-
-                }
-            } else {
-                //otherwise, just one object to replace
-                DSpaceObject dso = sip.replace(context, objToReplace, pkgFile, pkgParams);
-
-                if (dso != null) {
-                    System.out.println("REPLACED DSpace " + Constants.typeText[dso.getType()] +
-                                           " [ hdl=" + dso.getHandle() + " ] ");
-                }
-            }
-        } catch (WorkflowException e) {
-            throw new PackageException(e);
-        }
-    }
-}