Update README.md

DS-3915 RestResourceController hides not existing endpoints under other errors

.gitignore

@@ -6,8 +6,10 @@ tags
 
 ## Ignore project files created by Eclipse
 .settings/
+/bin/
 .project
 .classpath
+.checkstyle
 
 ## Ignore project files created by IntelliJ IDEA
 *.iml
@@ -24,7 +26,6 @@ dist/
 nbdist/
 nbactions.xml
 nb-configuration.xml
-META-INF/
 
 ## Ignore all *.properties file in root folder, EXCEPT build.properties (the default)
 ## KEPT FOR BACKWARDS COMPATIBILITY WITH 5.x (build.properties is now replaced with local.cfg)
@@ -38,3 +39,6 @@ META-INF/
 
 ##Mac noise
 .DS_Store
+
+##Ignore JRebel project configuration
+rebel.xml

.travis.yml

@@ -5,27 +5,23 @@ 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:
-  # Install Node.js 6.5.0 & print version info
-  - nvm install 6.5.0
-  - node --version
-  # Install npm 3.10.8 & print version info
-  - npm install -g npm@3.10.8
-  - npm --version
-  # Install Bower
-  - npm install -g bower
-  # Install Grunt & print version info
-  - npm install -g grunt && npm install -g grunt-cli
-  - grunt --version
-  # Print ruby version info (should be installed)
-  - ruby -v
-  # Install Sass & print version info
-  - gem install sass
-  - sass -v
-  # Install Compass & print version info
-  - gem install compass
-  - compass version
+  # Remove outdated settings.xml from Travis builds.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.'"
@@ -43,8 +39,6 @@ script:
   #        -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 assembly process works (from [src]/dspace/), including Mirage 2
-  #        -Dmirage2.on=true => Build Mirage2
-  #        -Dmirage2.deps.included=false => Don't include Mirage2 build dependencies (We installed them in before_install)
+  # 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 -Dmirage2.on=true -Dmirage2.deps.included=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
+  - "cd dspace && mvn package -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"

LICENSES_THIRD_PARTY

@@ -199,8 +199,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Woodstox (org.codehaus.woodstox:woodstox-core-asl:4.1.4 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.0 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.7 - http://woodstox.codehaus.org)
-        * databene ContiPerf (org.databene:contiperf:2.3.4 - http://databene.org/contiperf)
-        * elasticsearch (org.elasticsearch:elasticsearch:1.4.0 - http://nexus.sonatype.org/oss-repository-hosting.html/elasticsearch)
         * flyway-core (org.flywaydb:flyway-core:4.0.3 - https://flywaydb.org/flyway-core)
         * Ogg and Vorbis for Java, Core (org.gagravarr:vorbis-java-core:0.1 - https://github.com/Gagravarr/VorbisJava)
         * Apache Tika plugin for Ogg, Vorbis and FLAC (org.gagravarr:vorbis-java-tika:0.1 - https://github.com/Gagravarr/VorbisJava)
@@ -300,7 +298,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * 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-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
+        * 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/)

README.md

@@ -1,6 +1,9 @@
 
 # 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/) | 
@@ -9,9 +12,20 @@
 [Support](https://wiki.duraspace.org/display/DSPACE/Support)
 
 DSpace open source software is a turnkey repository application used by more than 
-1000+ organizations and institutions worldwide to provide durable access to digital resources.
+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).
@@ -53,6 +67,8 @@ We welcome everyone to participate in these lists:
 * [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 

checkstyle-suppressions.xml

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

checkstyle.xml

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

dspace-api/pom.xml

@@ -1,4 +1,5 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.dspace</groupId>
     <artifactId>dspace-api</artifactId>
@@ -12,7 +13,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>6.0-rc4</version>
+        <version>7.0-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -205,7 +206,8 @@
                         <executions>
                             <execution>
                                 <id>setproperty</id>
-                                <phase>generate-test-resources</phase> <!-- XXX I think this should be 'initialize' - MHW -->
+                                <phase>generate-test-resources
+                                </phase> <!-- XXX I think this should be 'initialize' - MHW -->
                                 <goals>
                                     <goal>execute</goal>
                                 </goals>
@@ -272,7 +274,6 @@
                     </plugin>
 
 
-
                     <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
                     <plugin>
                         <artifactId>maven-failsafe-plugin</artifactId>
@@ -291,7 +292,6 @@
         </profile>
     </profiles>
 
-
     <dependencies>
         <dependency>
             <groupId>org.hibernate</groupId>
@@ -307,10 +307,21 @@
             <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>
@@ -354,6 +365,10 @@
             <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>
@@ -434,10 +449,6 @@
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-scratchpad</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml</artifactId>
-        </dependency>
         <dependency>
             <groupId>rome</groupId>
             <artifactId>rome</artifactId>
@@ -501,10 +512,11 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>org.databene</groupId>
-            <artifactId>contiperf</artifactId>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-core</artifactId>
             <scope>test</scope>
         </dependency>
+
         <dependency>
             <groupId>org.rometools</groupId>
             <artifactId>rome-modules</artifactId>
@@ -568,9 +580,9 @@
             <artifactId>commons-configuration</artifactId>
         </dependency>
         <dependency>
-            <groupId>com.maxmind.geoip</groupId>
-            <artifactId>geoip-api</artifactId>
-            <version>1.3.0</version>
+            <groupId>com.maxmind.geoip2</groupId>
+            <artifactId>geoip2</artifactId>
+            <version>2.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
@@ -583,9 +595,9 @@
         </dependency>
 
         <dependency>
-            <groupId>org.elasticsearch</groupId>
-            <artifactId>elasticsearch</artifactId>
-            <version>1.4.0</version>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+            <version>4.10.4</version>
         </dependency>
 
         <dependency>
@@ -671,7 +683,6 @@
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
-            <version>2.9.2</version>
         </dependency>
         <dependency>
             <groupId>javax.inject</groupId>
@@ -696,7 +707,7 @@
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
-            <version>2.22.1</version>
+            <version>${jersey.version}</version>
         </dependency>
         <!-- S3 -->
         <dependency>
@@ -718,17 +729,10 @@
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>2.7.0</version>
         </dependency>
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.7.0</version>
-        </dependency>
-        <dependency>
-            <groupId>com.fasterxml.jackson.core</groupId>
-            <artifactId>jackson-annotations</artifactId>
-            <version>2.7.0</version>
         </dependency>
     </dependencies>
 

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

@@ -19,7 +19,6 @@ package org.apache.solr.handler.extraction;
 
 /**
  * The various Solr Parameters names to use when extracting content.
- *
  **/
 public interface ExtractingParams {
 
@@ -41,8 +40,6 @@ public interface ExtractingParams {
      * <pre>fmap.title=solr.title</pre>
      *
      * In this example, the tika "title" metadata value will be added to a Solr field named "solr.title"
-   *
-   *
      */
     public static final String MAP_PREFIX = "fmap.";
 
@@ -55,7 +52,6 @@ public interface ExtractingParams {
      * boost.solr.title=2.5
      * </pre>
      * will boost the solr.title field for this document by 2.5
-   *
      */
     public static final String BOOST_PREFIX = "boost.";
 
@@ -64,7 +60,6 @@ public interface ExtractingParams {
      * <pre>
      *  literal.myField=Foo
      * </pre>
-   *
      */
     public static final String LITERALS_PREFIX = "literal.";
 
@@ -72,10 +67,10 @@ public interface ExtractingParams {
     /**
      * Restrict the extracted parts of a document to be indexed
      * by passing in an XPath expression.  All content that satisfies the XPath expr.
-   * will be passed to the {@link SolrContentHandler}.
+     * will be passed to the {@link org.apache.solr.handler.extraction.SolrContentHandler}.
      * <p>
      * See Tika's docs for what the extracted document looks like.
-   * <p>
+     *
      * @see #CAPTURE_ELEMENTS
      */
     public static final String XPATH_EXPRESSION = "xpath";
@@ -92,20 +87,24 @@ public interface ExtractingParams {
     public static final String EXTRACT_FORMAT = "extractFormat";
 
     /**
-   * Capture attributes separately according to the name of the element, instead of just adding them to the string buffer
+     * Capture attributes separately according to the name of the element, instead of just adding them to the string
+     * buffer
      */
     public static final String CAPTURE_ATTRIBUTES = "captureAttr";
 
     /**
-   * Literal field values will by default override other values such as metadata and content. Set this to false to revert to pre-4.0 behaviour
+     * Literal field values will by default override other values such as metadata and content. Set this to false to
+     * revert to pre-4.0 behaviour
      */
     public static final String LITERALS_OVERRIDE = "literalsOverride";
 
     /**
-   * Capture the specified fields (and everything included below it that isn't capture by some other capture field) separately from the default.  This is different
+     * Capture the specified fields (and everything included below it that isn't capture by some other capture field)
+     * separately from the default.  This is different
      * then the case of passing in an XPath expression.
      * <p>
-   * The Capture field is based on the localName returned to the {@link SolrContentHandler}
+     * 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>
@@ -120,7 +119,6 @@ public interface ExtractingParams {
      * </pre>
      * By passing in the p tag, you could capture all P tags separately from the rest of the t
      * Thus, in the example, the capture of the P tag would be: "some text here.  more text"
-   *
      */
     public static final String CAPTURE_ELEMENTS = "capture";
 

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

@@ -35,8 +35,7 @@ import org.dspace.handle.service.HandleService;
  * @version $Revision$
  */
 
-public class CommunityFiliator
-{
+public class CommunityFiliator {
 
     protected CommunityService communityService;
     protected HandleService handleService;
@@ -47,12 +46,10 @@ public class CommunityFiliator
     }
 
     /**
-     *
-     * @param argv arguments
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
-    public static void main(String[] argv) throws Exception
-    {
+    public static void main(String[] argv) throws Exception {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -73,8 +70,7 @@ public class CommunityFiliator
         String parentID = null;
         String childID = null;
 
-        if (line.hasOption('h'))
-        {
+        if (line.hasOption('h')) {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("CommunityFiliator\n", options);
             System.out
@@ -85,45 +81,37 @@ public class CommunityFiliator
             System.exit(0);
         }
 
-        if (line.hasOption('s'))
-        {
+        if (line.hasOption('s')) {
             command = "set";
         }
 
-        if (line.hasOption('r'))
-        {
+        if (line.hasOption('r')) {
             command = "remove";
         }
 
-        if (line.hasOption('p')) // parent
-        {
+        if (line.hasOption('p')) { // parent
             parentID = line.getOptionValue('p');
         }
 
-        if (line.hasOption('c')) // child
-        {
+        if (line.hasOption('c')) { // child
             childID = line.getOptionValue('c');
         }
 
         // now validate
         // must have a command set
-        if (command == null)
-        {
+        if (command == null) {
             System.out
                 .println("Error - must run with either set or remove (run with -h flag for details)");
             System.exit(1);
         }
 
-        if ("set".equals(command) || "remove".equals(command))
-        {
-            if (parentID == null)
-            {
+        if ("set".equals(command) || "remove".equals(command)) {
+            if (parentID == null) {
                 System.out.println("Error - a parentID must be specified (run with -h flag for details)");
                 System.exit(1);
             }
 
-            if (childID == null)
-            {
+            if (childID == null) {
                 System.out.println("Error - a childID must be specified (run with -h flag for details)");
                 System.exit(1);
             }
@@ -135,52 +123,39 @@ public class CommunityFiliator
         // we are superuser!
         c.turnOffAuthorisationSystem();
 
-        try
-        {
+        try {
             // validate and resolve the parent and child IDs into commmunities
             Community parent = filiator.resolveCommunity(c, parentID);
             Community child = filiator.resolveCommunity(c, childID);
 
-            if (parent == null)
-            {
+            if (parent == null) {
                 System.out.println("Error, parent community cannot be found: "
                                        + parentID);
                 System.exit(1);
             }
 
-            if (child == null)
-            {
+            if (child == null) {
                 System.out.println("Error, child community cannot be found: "
                                        + childID);
                 System.exit(1);
             }
 
-            if ("set".equals(command))
-            {
+            if ("set".equals(command)) {
                 filiator.filiate(c, parent, child);
-            }
-            else
-            {
+            } else {
                 filiator.defiliate(c, parent, child);
             }
-        }
-        catch (SQLException sqlE)
-        {
+        } catch (SQLException sqlE) {
             System.out.println("Error - SQL exception: " + sqlE.toString());
-        }
-        catch (AuthorizeException authE)
-        {
+        } catch (AuthorizeException authE) {
             System.out.println("Error - Authorize exception: "
                                    + authE.toString());
-        }
-        catch (IOException ioE)
-        {
+        } catch (IOException ioE) {
             System.out.println("Error - IO exception: " + ioE.toString());
         }
     }
 
     /**
-     *
      * @param c      context
      * @param parent parent Community
      * @param child  child community
@@ -189,15 +164,14 @@ public class CommunityFiliator
      * @throws IOException        if IO error
      */
     public void filiate(Context c, Community parent, Community child)
-            throws SQLException, AuthorizeException, IOException
-    {
+        throws SQLException, AuthorizeException, IOException {
         // check that a valid filiation would be established
         // first test - proposed child must currently be an orphan (i.e.
         // top-level)
-        Community childDad = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities().iterator().next() : null;
+        Community childDad = CollectionUtils.isNotEmpty(child.getParentCommunities()) ? child.getParentCommunities()
+                                                                                             .iterator().next() : null;
 
-        if (childDad != null)
-        {
+        if (childDad != null) {
             System.out.println("Error, child community: " + child.getID()
                                    + " already a child of: " + childDad.getID());
             System.exit(1);
@@ -207,10 +181,8 @@ public class CommunityFiliator
         // child
         List<Community> parentDads = parent.getParentCommunities();
 
-        for (int i = 0; i < parentDads.size(); i++)
-        {
-            if (parentDads.get(i).getID().equals(child.getID()))
-            {
+        for (int i = 0; i < parentDads.size(); i++) {
+            if (parentDads.get(i).getID().equals(child.getID())) {
                 System.out
                     .println("Error, circular parentage - child is parent of parent");
                 System.exit(1);
@@ -227,7 +199,6 @@ public class CommunityFiliator
     }
 
     /**
-     *
      * @param c      context
      * @param parent parent Community
      * @param child  child community
@@ -236,24 +207,20 @@ public class CommunityFiliator
      * @throws IOException        if IO error
      */
     public void defiliate(Context c, Community parent, Community child)
-            throws SQLException, AuthorizeException, IOException
-    {
+        throws SQLException, AuthorizeException, IOException {
         // verify that child is indeed a child of parent
         List<Community> parentKids = parent.getSubcommunities();
         boolean isChild = false;
 
-        for (int i = 0; i < parentKids.size(); i++)
-        {
-            if (parentKids.get(i).getID().equals(child.getID()))
-            {
+        for (int i = 0; i < parentKids.size(); i++) {
+            if (parentKids.get(i).getID().equals(child.getID())) {
                 isChild = true;
 
                 break;
             }
         }
 
-        if (!isChild)
-        {
+        if (!isChild) {
             System.out
                 .println("Error, child community not a child of parent community");
             System.exit(1);
@@ -275,31 +242,27 @@ public class CommunityFiliator
 
     /**
      * Find a community by ID
+     *
      * @param c           context
      * @param communityID community ID
      * @return Community object
      * @throws SQLException if database error
      */
     protected Community resolveCommunity(Context c, String communityID)
-            throws SQLException
-    {
+        throws SQLException {
         Community community = null;
 
-        if (communityID.indexOf('/') != -1)
-        {
+        if (communityID.indexOf('/') != -1) {
             // has a / must be a handle
             community = (Community) handleService.resolveToObject(c,
                                                                   communityID);
 
             // ensure it's a community
             if ((community == null)
-                    || (community.getType() != Constants.COMMUNITY))
-            {
+                || (community.getType() != Constants.COMMUNITY)) {
                 community = null;
             }
-        }
-        else
-        {
+        } else {
             community = communityService.find(c, UUID.fromString(communityID));
         }
 

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

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

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

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

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

@@ -9,7 +9,6 @@ package org.dspace.administer;
 
 import java.io.IOException;
 import java.sql.SQLException;
-
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
@@ -18,9 +17,7 @@ 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;
@@ -31,11 +28,9 @@ 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;
 
 /**
@@ -61,17 +56,26 @@ import org.xml.sax.SAXException;
  * </dspace-dc-types>
  * }
  */
-public class MetadataImporter
-{
-    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
-    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
+public class MetadataImporter {
+    protected static MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance()
+                                                                                        .getMetadataSchemaService();
+    protected static MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance()
+                                                                                      .getMetadataFieldService();
 
-    /** logging category */
+    /**
+     * logging category
+     */
     private static final Logger log = LoggerFactory.getLogger(MetadataImporter.class);
 
+    /**
+     * Default constructor
+     */
+    private MetadataImporter() { }
+
     /**
      * main method for reading user input from the command line
-     * @param args arguments
+     *
+     * @param args the command line arguments given
      * @throws ParseException               if parse error
      * @throws SQLException                 if database error
      * @throws IOException                  if IO error
@@ -85,8 +89,7 @@ public class MetadataImporter
     public static void main(String[] args)
         throws ParseException, SQLException, IOException, TransformerException,
         ParserConfigurationException, AuthorizeException, SAXException,
-    			NonUniqueMetadataException, RegistryImportException
-    {
+        NonUniqueMetadataException, RegistryImportException {
         boolean forceUpdate = false;
 
         // create an options object and populate it
@@ -97,12 +100,9 @@ public class MetadataImporter
         CommandLine line = parser.parse(options, args);
 
         String file = null;
-        if (line.hasOption('f'))
-        {
+        if (line.hasOption('f')) {
             file = line.getOptionValue('f');
-        }
-        else
-        {
+        } else {
             usage();
             System.exit(0);
         }
@@ -127,12 +127,10 @@ public class MetadataImporter
      */
     public static void loadRegistry(String file, boolean forceUpdate)
         throws SQLException, IOException, TransformerException, ParserConfigurationException,
-    		AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException
-    {
+        AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException {
         Context context = null;
 
-        try
-        {
+        try {
             // create a context
             context = new Context();
             context.turnOffAuthorisationSystem();
@@ -144,8 +142,7 @@ public class MetadataImporter
             NodeList schemaNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-schema");
 
             // Add each one as a new format to the registry
-            for (int i = 0; i < schemaNodes.getLength(); i++)
-            {
+            for (int i = 0; i < schemaNodes.getLength(); i++) {
                 Node n = schemaNodes.item(i);
                 loadSchema(context, n, forceUpdate);
             }
@@ -154,31 +151,27 @@ public class MetadataImporter
             NodeList typeNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-type");
 
             // Add each one as a new format to the registry
-            for (int i = 0; i < typeNodes.getLength(); i++)
-            {
+            for (int i = 0; i < typeNodes.getLength(); i++) {
                 Node n = typeNodes.item(i);
                 loadType(context, n);
             }
 
             context.restoreAuthSystemState();
             context.complete();
-        }
-        finally
-        {
+        } finally {
             // Clean up our context, if it still exists & it was never completed
-            if(context!=null && context.isValid())
+            if (context != null && context.isValid()) {
                 context.abort();
             }
         }
+    }
 
     /**
      * Process a node in the metadata registry XML file.  If the
      * schema already exists, it will not be recreated
      *
-     * @param context
-     *            DSpace context object
-     * @param node
-     *            the node in the DOM tree
+     * @param context DSpace context object
+     * @param node    the node in the DOM tree
      * @throws SQLException               if database error
      * @throws IOException                if IO error
      * @throws TransformerException       if transformer error
@@ -188,51 +181,43 @@ public class MetadataImporter
      */
     private static void loadSchema(Context context, Node node, boolean updateExisting)
         throws SQLException, IOException, TransformerException,
-            AuthorizeException, NonUniqueMetadataException, RegistryImportException
-    {
+        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
         // Get the values
         String name = RegistryImporter.getElementData(node, "name");
         String namespace = RegistryImporter.getElementData(node, "namespace");
 
-        if (name == null || "".equals(name))
-        {
+        if (name == null || "".equals(name)) {
             throw new RegistryImportException("Name of schema must be supplied");
         }
 
-        if (namespace == null || "".equals(namespace))
-        {
+        if (namespace == null || "".equals(namespace)) {
             throw new RegistryImportException("Namespace of schema must be supplied");
         }
 
         // check to see if the schema already exists
         MetadataSchema s = metadataSchemaService.find(context, name);
 
-        if (s == null)
-        {
+        if (s == null) {
             // Schema does not exist - create
             log.info("Registering Schema " + name + " (" + namespace + ")");
             metadataSchemaService.create(context, name, namespace);
-        }
-        else
-        {
+        } else {
             // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace))
-            {
+            if (s.getNamespace().equals(namespace)) {
                 // This schema already exists with this namespace, skipping it
                 return;
             }
 
             // It's a different namespace - have we been told to update?
-            if (updateExisting)
-            {
+            if (updateExisting) {
                 // Update the existing schema namespace and continue to type import
                 log.info("Updating Schema " + name + ": New namespace " + namespace);
                 s.setNamespace(namespace);
                 metadataSchemaService.update(context, s);
-            }
-            else
-            {
-                throw new RegistryImportException("Schema " + name + " already registered with different namespace " + namespace + ". Rerun with 'update' option enabled if you wish to update this schema.");
+            } else {
+                throw new RegistryImportException(
+                    "Schema " + name + " already registered with different namespace " + namespace + ". Rerun with " +
+                        "'update' option enabled if you wish to update this schema.");
             }
         }
 
@@ -243,10 +228,8 @@ public class MetadataImporter
      * be a "dc-type" node.  If the type already exists, then it
      * will not be reimported
      *
-     * @param context
-     *            DSpace context object
-     * @param node
-     *            the node in the DOM tree
+     * @param context DSpace context object
+     * @param node    the node in the DOM tree
      * @throws SQLException               if database error
      * @throws IOException                if IO error
      * @throws TransformerException       if transformer error
@@ -256,8 +239,7 @@ public class MetadataImporter
      */
     private static void loadType(Context context, Node node)
         throws SQLException, IOException, TransformerException,
-            AuthorizeException, NonUniqueMetadataException, RegistryImportException
-    {
+        AuthorizeException, NonUniqueMetadataException, RegistryImportException {
         // Get the values
         String schema = RegistryImporter.getElementData(node, "schema");
         String element = RegistryImporter.getElementData(node, "element");
@@ -265,8 +247,7 @@ public class MetadataImporter
         String scopeNote = RegistryImporter.getElementData(node, "scope_note");
 
         // If the schema is not provided default to DC
-        if (schema == null)
-        {
+        if (schema == null) {
             schema = MetadataSchema.DC_SCHEMA;
         }
 
@@ -274,22 +255,21 @@ public class MetadataImporter
         // Find the matching schema object
         MetadataSchema schemaObj = metadataSchemaService.find(context, schema);
 
-        if (schemaObj == null)
-        {
+        if (schemaObj == null) {
             throw new RegistryImportException("Schema '" + schema + "' is not registered and does not exist.");
         }
 
         MetadataField mf = metadataFieldService.findByElement(context, schemaObj, element, qualifier);
-        if (mf != null)
-        {
+        if (mf != null) {
             // Metadata field already exists, skipping it
             return;
         }
 
         // Actually create this metadata field as it doesn't yet exist
         String fieldName = schema + "." + element + "." + qualifier;
-        if(qualifier==null)
+        if (qualifier == null) {
             fieldName = schema + "." + element;
+        }
         log.info("Registering metadata field " + fieldName);
         MetadataField field = metadataFieldService.create(context, schemaObj, element, qualifier, scopeNote);
         metadataFieldService.update(context, field);
@@ -298,8 +278,7 @@ public class MetadataImporter
     /**
      * Print the usage message to stdout
      */
-    public static void usage()
-    {
+    public static void usage() {
         String usage = "Use this class with the following option:\n" +
             " -f <xml source file> : specify which xml source file " +
             "contains the DC fields to import.\n";

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

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

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

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

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

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

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

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

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

@@ -14,7 +14,6 @@ import java.io.IOException;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;
-
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -62,26 +61,34 @@ import org.xml.sax.SAXException;
  * documentation for more details
  *
  * @author Richard Jones
- *
  */
 
-public class StructBuilder
-{
-    /** the output xml document which will contain updated information about the 
+public class StructBuilder {
+    /**
+     * the output xml document which will contain updated information about the
      * imported structure
      */
     private static org.jdom.Document xmlOutput = new org.jdom.Document(new Element("imported_structure"));
 
-    /** a hashtable to hold metadata for the collection being worked on */
+    /**
+     * a hashtable to hold metadata for the collection being worked on
+     */
     private static Map<String, String> collectionMap = new HashMap<String, String>();
 
-    /** a hashtable to hold metadata for the community being worked on */
+    /**
+     * a hashtable to hold metadata for the community being worked on
+     */
     private static Map<String, String> communityMap = new HashMap<String, String>();
 
     protected static CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
     protected static EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
 
+    /**
+     * Default constructor
+     */
+    private StructBuilder() { }
+
     /**
      * Main method to be run from the command line to import a structure into
      * DSpace
@@ -92,12 +99,12 @@ public class StructBuilder
      *
      * 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 commandline arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if an error occurs
      */
     public static void main(String[] argv)
-    	throws Exception
-    {
+        throws Exception {
         CommandLineParser parser = new PosixParser();
 
         Options options = new Options();
@@ -112,23 +119,19 @@ public class StructBuilder
         String eperson = null;
         String output = null;
 
-    	if (line.hasOption('f'))
-    	{
+        if (line.hasOption('f')) {
             file = line.getOptionValue('f');
         }
 
-    	if (line.hasOption('e'))
-    	{
+        if (line.hasOption('e')) {
             eperson = line.getOptionValue('e');
         }
 
-    	if (line.hasOption('o'))
-    	{
+        if (line.hasOption('o')) {
             output = line.getOptionValue('o');
         }
 
-    	if (output == null || eperson == null || file == null)
-    	{
+        if (output == null || eperson == null || file == null) {
             usage();
             System.exit(0);
         }
@@ -169,20 +172,16 @@ public class StructBuilder
 
         // generate the output
         Element root = xmlOutput.getRootElement();
-        for (int i = 0; i < elements.length; i++)
-        {
+        for (int i = 0; i < elements.length; i++) {
             root.addContent(elements[i]);
         }
 
         // finally write the string into the output file
-        try 
-        {
+        try {
             BufferedWriter out = new BufferedWriter(new FileWriter(output));
             out.write(new XMLOutputter().outputString(xmlOutput));
             out.close();
-        } 
-        catch (IOException e) 
-        {
+        } catch (IOException e) {
             System.out.println("Unable to write to output file " + output);
             System.exit(0);
         }
@@ -193,10 +192,11 @@ public class StructBuilder
     /**
      * Output the usage information
      */
-    private static void usage()
-    {
+    private static void usage() {
         System.out.println("Usage: java StructBuilder -f <source XML file> -o <output file> -e <eperson email>");
-        System.out.println("Communities will be created from the top level, and a map of communities to handles will be returned in the output file");
+        System.out.println(
+            "Communities will be created from the top level, and a map of communities to handles will be returned in " +
+                "the output file");
         return;
     }
 
@@ -206,11 +206,9 @@ public class StructBuilder
      *
      * @param document the XML document object
      * @throws TransformerException if transformer error
-     * 
      */
     private static void validate(org.w3c.dom.Document document)
-    	throws TransformerException
-    {
+        throws TransformerException {
         StringBuffer err = new StringBuffer();
         boolean trip = false;
 
@@ -218,22 +216,19 @@ public class StructBuilder
         err.append("No changes have been made to the DSpace instance\n\n");
 
         NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
-        if (first.getLength() == 0)
-        {
+        if (first.getLength() == 0) {
             err.append("-There are no top level communities in the source document");
             System.out.println(err.toString());
             System.exit(0);
         }
 
         String errs = validateCommunities(first, 1);
-        if (errs != null)
-        {
+        if (errs != null) {
             err.append(errs);
             trip = true;
         }
 
-        if (trip)
-        {
+        if (trip) {
             System.out.println(err.toString());
             System.exit(0);
         }
@@ -246,23 +241,19 @@ public class StructBuilder
      * @param communities the NodeList of communities to validate
      * @param level       the level in the XML document that we are at, for the purposes
      *                    of error reporting
-     * 
      * @return the errors that need to be generated by the calling method, or null if
      * no errors.
      */
     private static String validateCommunities(NodeList communities, int level)
-    	throws TransformerException
-    {
+        throws TransformerException {
         StringBuffer err = new StringBuffer();
         boolean trip = false;
         String errs = null;
 
-        for (int i = 0; i < communities.getLength(); i++)
-        {
+        for (int i = 0; i < communities.getLength(); i++) {
             Node n = communities.item(i);
             NodeList name = XPathAPI.selectNodeList(n, "name");
-	        if (name.getLength() != 1)
-	        {
+            if (name.getLength() != 1) {
                 String pos = Integer.toString(i + 1);
                 err.append("-The level " + level + " community in position " + pos);
                 err.append(" does not contain exactly one name field\n");
@@ -272,8 +263,7 @@ public class StructBuilder
             // validate sub communities
             NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
             String comErrs = validateCommunities(subCommunities, level + 1);
-	        if (comErrs != null)
-	        {
+            if (comErrs != null) {
                 err.append(comErrs);
                 trip = true;
             }
@@ -281,15 +271,13 @@ public class StructBuilder
             // validate collections
             NodeList collections = XPathAPI.selectNodeList(n, "collection");
             String colErrs = validateCollections(collections, level + 1);
-	        if (colErrs != null)
-	        {
+            if (colErrs != null) {
                 err.append(colErrs);
                 trip = true;
             }
         }
 
-        if (trip)
-        {
+        if (trip) {
             errs = err.toString();
         }
 
@@ -302,22 +290,18 @@ public class StructBuilder
      *
      * @param collections a NodeList of collections to validate
      * @param level       the level in the XML document for the purposes of error reporting
-     * 
      * @return the errors to be generated by the calling method, or null if none
      */
     private static String validateCollections(NodeList collections, int level)
-    	throws TransformerException
-    {
+        throws TransformerException {
         StringBuffer err = new StringBuffer();
         boolean trip = false;
         String errs = null;
 
-        for (int i = 0; i < collections.getLength(); i++)
-        {
+        for (int i = 0; i < collections.getLength(); i++) {
             Node n = collections.item(i);
             NodeList name = XPathAPI.selectNodeList(n, "name");
-	        if (name.getLength() != 1)
-	        {
+            if (name.getLength() != 1) {
                 String pos = Integer.toString(i + 1);
                 err.append("-The level " + level + " collection in position " + pos);
                 err.append(" does not contain exactly one name field\n");
@@ -325,8 +309,7 @@ public class StructBuilder
             }
         }
 
-        if (trip)
-        {
+        if (trip) {
             errs = err.toString();
         }
 
@@ -336,14 +319,11 @@ public class StructBuilder
     /**
      * Load in the XML from file.
      *
-     * @param filename
-     *            the filename to load from
-     * 
+     * @param filename the filename to load from
      * @return the DOM representation of the XML file
      */
     private static org.w3c.dom.Document loadXML(String filename)
-    	throws IOException, ParserConfigurationException, SAXException
-    {
+        throws IOException, ParserConfigurationException, SAXException {
         DocumentBuilder builder = DocumentBuilderFactory.newInstance()
                                                         .newDocumentBuilder();
 
@@ -356,19 +336,15 @@ public class StructBuilder
      * Return the String value of a Node
      *
      * @param node the node from which we want to extract the string value
-     * 
      * @return the string value of the node
      */
-    public static String getStringValue(Node node)
-    {
+    public static String getStringValue(Node node) {
         String value = node.getNodeValue();
 
-        if (node.hasChildNodes())
-        {
+        if (node.hasChildNodes()) {
             Node first = node.getFirstChild();
 
-            if (first.getNodeType() == Node.TEXT_NODE)
-            {
+            if (first.getNodeType() == Node.TEXT_NODE) {
                 return first.getNodeValue().trim();
             }
         }
@@ -383,27 +359,21 @@ public class StructBuilder
      * @param context     the context of the request
      * @param communities a nodelist of communities to create along with their sub-structures
      * @param parent      the parent community of the nodelist of communities to create
-     * 
      * @return an element array containing additional information regarding the
      * created communities (e.g. the handles they have been assigned)
      */
     private static Element[] handleCommunities(Context context, NodeList communities, Community parent)
-    	throws TransformerException, SQLException, Exception
-    {
+        throws TransformerException, SQLException, Exception {
         Element[] elements = new Element[communities.getLength()];
 
-        for (int i = 0; i < communities.getLength(); i++)
-        {
+        for (int i = 0; i < communities.getLength(); i++) {
             Community community;
             Element element = new Element("community");
 
             // create the community or sub community
-            if (parent != null)
-            {
+            if (parent != null) {
                 community = communityService.create(parent, context);
-            }
-            else
-            {
+            } else {
                 community = communityService.create(null, context);
             }
 
@@ -412,11 +382,9 @@ public class StructBuilder
 
             // now update the metadata
             Node tn = communities.item(i);
-            for (Map.Entry<String, String> entry : communityMap.entrySet())
-            {
+            for (Map.Entry<String, String> entry : communityMap.entrySet()) {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1)
-                {
+                if (nl.getLength() == 1) {
                     communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
@@ -446,29 +414,25 @@ public class StructBuilder
             nameElement.setText(communityService.getMetadata(community, "name"));
             element.addContent(nameElement);
 
-            if (communityService.getMetadata(community, "short_description") != null)
-            {
+            if (communityService.getMetadata(community, "short_description") != null) {
                 Element descriptionElement = new Element("description");
                 descriptionElement.setText(communityService.getMetadata(community, "short_description"));
                 element.addContent(descriptionElement);
             }
 
-            if (communityService.getMetadata(community, "introductory_text") != null)
-            {
+            if (communityService.getMetadata(community, "introductory_text") != null) {
                 Element introElement = new Element("intro");
                 introElement.setText(communityService.getMetadata(community, "introductory_text"));
                 element.addContent(introElement);
             }
 
-            if (communityService.getMetadata(community, "copyright_text") != null)
-            {
+            if (communityService.getMetadata(community, "copyright_text") != null) {
                 Element copyrightElement = new Element("copyright");
                 copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
                 element.addContent(copyrightElement);
             }
 
-            if (communityService.getMetadata(community, "side_bar_text") != null)
-            {
+            if (communityService.getMetadata(community, "side_bar_text") != null) {
                 Element sidebarElement = new Element("sidebar");
                 sidebarElement.setText(communityService.getMetadata(community, "side_bar_text"));
                 element.addContent(sidebarElement);
@@ -483,12 +447,10 @@ public class StructBuilder
             Element[] collectionElements = handleCollections(context, collections, community);
 
             int j;
-            for (j = 0; j < subCommunityElements.length; j++)
-            {
+            for (j = 0; j < subCommunityElements.length; j++) {
                 element.addContent(subCommunityElements[j]);
             }
-            for (j = 0; j < collectionElements.length; j++)
-            {
+            for (j = 0; j < collectionElements.length; j++) {
                 element.addContent(collectionElements[j]);
             }
 
@@ -504,17 +466,14 @@ public class StructBuilder
      * @param context     the context of the request
      * @param collections the node list of collections to be created
      * @param parent      the parent community to whom the collections belong
-     * 
      * @return an Element array containing additional information about the
      * created collections (e.g. the handle)
      */
     private static Element[] handleCollections(Context context, NodeList collections, Community parent)
-    	throws TransformerException, SQLException, AuthorizeException, IOException, Exception
-    {
+        throws TransformerException, SQLException, AuthorizeException, IOException, Exception {
         Element[] elements = new Element[collections.getLength()];
 
-        for (int i = 0; i < collections.getLength(); i++)
-        {
+        for (int i = 0; i < collections.getLength(); i++) {
             Element element = new Element("collection");
             Collection collection = collectionService.create(context, parent);
 
@@ -523,11 +482,9 @@ public class StructBuilder
 
             // import the rest of the metadata
             Node tn = collections.item(i);
-            for (Map.Entry<String, String> entry : collectionMap.entrySet())
-            {
+            for (Map.Entry<String, String> entry : collectionMap.entrySet()) {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1)
-                {
+                if (nl.getLength() == 1) {
                     collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
                 }
             }
@@ -540,43 +497,37 @@ public class StructBuilder
             nameElement.setText(collectionService.getMetadata(collection, "name"));
             element.addContent(nameElement);
 
-            if (collectionService.getMetadata(collection, "short_description") != null)
-            {
+            if (collectionService.getMetadata(collection, "short_description") != null) {
                 Element descriptionElement = new Element("description");
                 descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
                 element.addContent(descriptionElement);
             }
 
-            if (collectionService.getMetadata(collection, "introductory_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "introductory_text") != null) {
                 Element introElement = new Element("intro");
                 introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
                 element.addContent(introElement);
             }
 
-            if (collectionService.getMetadata(collection, "copyright_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "copyright_text") != null) {
                 Element copyrightElement = new Element("copyright");
                 copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
                 element.addContent(copyrightElement);
             }
 
-            if (collectionService.getMetadata(collection, "side_bar_text") != null)
-            {
+            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
                 Element sidebarElement = new Element("sidebar");
                 sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
                 element.addContent(sidebarElement);
             }
 
-            if (collectionService.getMetadata(collection, "license") != null)
-            {
+            if (collectionService.getMetadata(collection, "license") != null) {
                 Element sidebarElement = new Element("license");
                 sidebarElement.setText(collectionService.getMetadata(collection, "license"));
                 element.addContent(sidebarElement);
             }
 
-            if (collectionService.getMetadata(collection, "provenance_description") != null)
-            {
+            if (collectionService.getMetadata(collection, "provenance_description") != null) {
                 Element sidebarElement = new Element("provenance");
                 sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
                 element.addContent(sidebarElement);

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

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

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

@@ -7,7 +7,26 @@
  */
 package org.dspace.app.bulkedit;
 
-import org.apache.commons.lang3.StringUtils;
+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;
@@ -16,19 +35,14 @@ import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
 import org.dspace.content.MetadataValue;
+import org.dspace.content.authority.Choices;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
-import org.dspace.content.authority.Choices;
 import org.dspace.core.Context;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.*;
-
 /**
  * Utility class to read and write CSV files
  *
@@ -43,45 +57,69 @@ import java.io.*;
  *
  * @author Stuart Lewis
  */
-public class DSpaceCSV implements Serializable
-{
-    /** The headings of the CSV file */
+public class DSpaceCSV implements Serializable {
+    /**
+     * The headings of the CSV file
+     */
     protected List<String> headings;
 
-    /** An array list of CSV lines */
+    /**
+     * An array list of CSV lines
+     */
     protected List<DSpaceCSVLine> lines;
 
-    /** A counter of how many CSV lines this object holds */
+    /**
+     * A counter of how many CSV lines this object holds
+     */
     protected int counter;
 
-    /** The value separator (defaults to double pipe '||') */
+    /**
+     * The value separator (defaults to double pipe '||')
+     */
     protected String valueSeparator;
 
-    /** The value separator in an escaped form for using in regexes */
+    /**
+     * The value separator in an escaped form for using in regexes
+     */
     protected String escapedValueSeparator;
 
-    /** The field separator (defaults to comma) */
+    /**
+     * The field separator (defaults to comma)
+     */
     protected String fieldSeparator;
 
-    /** The field separator in an escaped form for using in regexes */
+    /**
+     * The field separator in an escaped form for using in regexes
+     */
     protected String escapedFieldSeparator;
 
-    /** The authority separator (defaults to double colon '::') */
+    /**
+     * The authority separator (defaults to double colon '::')
+     */
     protected String authoritySeparator;
 
-    /** The authority separator in an escaped form for using in regexes */
+    /**
+     * The authority separator in an escaped form for using in regexes
+     */
     protected String escapedAuthoritySeparator;
 
     protected transient final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    protected transient final MetadataSchemaService metadataSchemaService = ContentServiceFactory.getInstance().getMetadataSchemaService();
-    protected transient final MetadataFieldService metadataFieldService = ContentServiceFactory.getInstance().getMetadataFieldService();
-    protected transient final AuthorityValueService authorityValueService = AuthorityServiceFactory.getInstance().getAuthorityValueService();
+    protected transient final MetadataSchemaService metadataSchemaService =
+        ContentServiceFactory.getInstance().getMetadataSchemaService();
+    protected transient final MetadataFieldService metadataFieldService =
+        ContentServiceFactory.getInstance().getMetadataFieldService();
+    protected transient final AuthorityValueService authorityValueService =
+        AuthorityServiceFactory.getInstance().getAuthorityValueService();
 
 
-    /** Whether to export all metadata such as handles and provenance information */
+    /**
+     * Whether to export all metadata such as handles and provenance information
+     */
     protected boolean exportAll;
 
-    /** A list of metadata elements to ignore */
+    /**
+     * A list of metadata elements to ignore
+     */
     protected Map<String, String> ignore;
 
 
@@ -90,8 +128,7 @@ public class DSpaceCSV implements Serializable
      *
      * @param exportAll Whether to export all metadata such as handles and provenance information
      */
-    public DSpaceCSV(boolean exportAll)
-    {
+    public DSpaceCSV(boolean exportAll) {
         // Initialise the class
         init();
 
@@ -104,48 +141,37 @@ public class DSpaceCSV implements Serializable
      *
      * @param f The file to read from
      * @param c The DSpace Context
-     *
      * @throws Exception thrown if there is an error reading or processing the file
      */
-    public DSpaceCSV(File f, Context c) throws Exception
-    {
+    public DSpaceCSV(File f, Context c) throws Exception {
         // Initialise the class
         init();
 
         // Open the CSV file
         BufferedReader input = null;
-        try
-        {
+        try {
             input = new BufferedReader(new InputStreamReader(new FileInputStream(f), "UTF-8"));
 
             // Read the heading line
             String head = input.readLine();
             String[] headingElements = head.split(escapedFieldSeparator);
             int columnCounter = 0;
-            for (String element : headingElements)
-            {
+            for (String element : headingElements) {
                 columnCounter++;
 
                 // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\"")))
-                {
+                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
                     element = element.substring(1, element.length() - 1);
                 }
 
                 // Store the heading
-                if ("collection".equals(element))
-                {
+                if ("collection".equals(element)) {
                     // Store the heading
                     headings.add(element);
-                }
-                // Store the action
-                else if ("action".equals(element))
-                {
+                } else if ("action".equals(element)) { // Store the action
                     // Store the heading
                     headings.add(element);
-                }
-                else if (!"id".equals(element))
-                {
+                } else if (!"id".equals(element)) {
                     String authorityPrefix = "";
                     AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
                     if (authorityValueType != null) {
@@ -180,7 +206,8 @@ public class DSpaceCSV implements Serializable
                     }
 
                     // Check that the metadata element exists in the schema
-                    MetadataField foundField = metadataFieldService.findByElement(c, foundSchema, metadataElement, metadataQualifier);
+                    MetadataField foundField = metadataFieldService
+                        .findByElement(c, foundSchema, metadataElement, metadataQualifier);
                     if (foundField == null) {
                         throw new MetadataImportInvalidHeadingException(clean[0],
                                                                         MetadataImportInvalidHeadingException.ELEMENT,
@@ -196,8 +223,7 @@ public class DSpaceCSV implements Serializable
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while (StringUtils.isNotBlank(lineRead = input.readLine()))
-            {
+            while ((lineRead = input.readLine()) != null) {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line
                     lineBuilder.append("\n").append(lineRead);
@@ -236,11 +262,8 @@ public class DSpaceCSV implements Serializable
                     addItem(lineRead);
                 }
             }
-        }
-        finally
-        {
-            if (input != null)
-            {
+        } finally {
+            if (input != null) {
                 input.close();
             }
         }
@@ -249,8 +272,7 @@ public class DSpaceCSV implements Serializable
     /**
      * Initialise this class with values from dspace.cfg
      */
-    protected void init()
-    {
+    protected void init() {
         // Set the value separator
         setValueSeparator();
 
@@ -273,13 +295,16 @@ public class DSpaceCSV implements Serializable
         ignore = new HashMap<>();
 
         // Specify default values
-        String[] defaultValues = new String[]{"dc.date.accessioned, dc.date.available, " +
-                                              "dc.date.updated, dc.description.provenance"};
-        String[] toIgnoreArray = DSpaceServicesFactory.getInstance().getConfigurationService().getArrayProperty("bulkedit.ignore-on-export", defaultValues);
-        for (String toIgnoreString : toIgnoreArray)
-        {
-            if (!"".equals(toIgnoreString.trim()))
-            {
+        String[] defaultValues =
+            new String[] {
+                "dc.date.accessioned, dc.date.available, dc.date.updated, dc.description.provenance"
+            };
+        String[] toIgnoreArray =
+            DSpaceServicesFactory.getInstance()
+                                 .getConfigurationService()
+                                 .getArrayProperty("bulkedit.ignore-on-export", defaultValues);
+        for (String toIgnoreString : toIgnoreArray) {
+            if (!"".equals(toIgnoreString.trim())) {
                 ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
             }
         }
@@ -307,16 +332,13 @@ public class DSpaceCSV implements Serializable
      *
      * If not set, defaults to double pipe '||'
      */
-    private void setValueSeparator()
-    {
+    private void setValueSeparator() {
         // Get the value separator
-        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.valueseparator");
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim())))
-        {
+        valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+                                              .getProperty("bulkedit.valueseparator");
+        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim()))) {
             valueSeparator = valueSeparator.trim();
-        }
-        else
-        {
+        } else {
             valueSeparator = "||";
         }
 
@@ -336,32 +358,22 @@ public class DSpaceCSV implements Serializable
      * Special values are 'tab', 'hash' and 'semicolon' which will
      * get substituted from the text to the value.
      */
-    private void setFieldSeparator()
-    {
+    private void setFieldSeparator() {
         // Get the value separator
-        fieldSeparator =DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.fieldseparator");
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim())))
-        {
+        fieldSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+                                              .getProperty("bulkedit.fieldseparator");
+        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim()))) {
             fieldSeparator = fieldSeparator.trim();
-            if ("tab".equals(fieldSeparator))
-            {
+            if ("tab".equals(fieldSeparator)) {
                 fieldSeparator = "\t";
-            }
-            else if ("semicolon".equals(fieldSeparator))
-            {
+            } else if ("semicolon".equals(fieldSeparator)) {
                 fieldSeparator = ";";
-            }
-            else if ("hash".equals(fieldSeparator))
-            {
+            } else if ("hash".equals(fieldSeparator)) {
                 fieldSeparator = "#";
-            }
-            else
-            {
+            } else {
                 fieldSeparator = fieldSeparator.trim();
             }
-        }
-        else
-        {
+        } else {
             fieldSeparator = ",";
         }
 
@@ -378,16 +390,13 @@ public class DSpaceCSV implements Serializable
      *
      * If not set, defaults to double colon '::'
      */
-    private void setAuthoritySeparator()
-    {
+    private void setAuthoritySeparator() {
         // Get the value separator
-        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("bulkedit.authorityseparator");
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim())))
-        {
+        authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
+                                                  .getProperty("bulkedit.authorityseparator");
+        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim()))) {
             authoritySeparator = authoritySeparator.trim();
-        }
-        else
-        {
+        } else {
             authoritySeparator = "::";
         }
 
@@ -401,11 +410,9 @@ public class DSpaceCSV implements Serializable
      * Add a DSpace item to the CSV file
      *
      * @param i The DSpace item
-     *
      * @throws Exception if something goes wrong with adding the Item
      */
-    public final void addItem(Item i) throws Exception
-    {
+    public final void addItem(Item i) throws Exception {
         // If the item does not have an "owningCollection" the the below "getHandle()" call will fail
         // This should not happen but is here for safety.
         if (i.getOwningCollection() == null) {
@@ -421,49 +428,42 @@ public class DSpaceCSV implements Serializable
 
         // Add in any mapped collections
         List<Collection> collections = i.getCollections();
-        for (Collection c : collections)
-        {
+        for (Collection c : collections) {
             // Only add if it is not the owning collection
-            if (!c.getHandle().equals(owningCollectionHandle))
-            {
+            if (!c.getHandle().equals(owningCollectionHandle)) {
                 line.add("collection", c.getHandle());
             }
         }
 
         // Populate it
         List<MetadataValue> md = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (MetadataValue value : md)
-        {
+        for (MetadataValue value : md) {
             MetadataField metadataField = value.getMetadataField();
             MetadataSchema metadataSchema = metadataField.getMetadataSchema();
             // Get the key (schema.element)
             String key = metadataSchema.getName() + "." + metadataField.getElement();
 
             // Add the qualifier if there is one (schema.element.qualifier)
-            if (metadataField.getQualifier() != null)
-            {
+            if (metadataField.getQualifier() != null) {
                 key = key + "." + metadataField.getQualifier();
             }
 
             // Add the language if there is one (schema.element.qualifier[langauge])
             //if ((value.language != null) && (!"".equals(value.language)))
-            if (value.getLanguage() != null)
-            {
+            if (value.getLanguage() != null) {
                 key = key + "[" + value.getLanguage() + "]";
             }
 
             // Store the item
-            if (exportAll || okToExport(metadataField))
-            {
+            if (exportAll || okToExport(metadataField)) {
                 // Add authority and confidence if authority is not null
                 String mdValue = value.getValue();
-                if (value.getAuthority() != null && !"".equals(value.getAuthority()))
-                {
-                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value.getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
+                if (value.getAuthority() != null && !"".equals(value.getAuthority())) {
+                    mdValue += authoritySeparator + value.getAuthority() + authoritySeparator + (value
+                        .getConfidence() != -1 ? value.getConfidence() : Choices.CF_ACCEPTED);
                 }
                 line.add(key, mdValue);
-                if (!headings.contains(key))
-                {
+                if (!headings.contains(key)) {
                     headings.add(key);
                 }
             }
@@ -478,12 +478,10 @@ public class DSpaceCSV implements Serializable
      * @param line The line of elements
      * @throws Exception Thrown if an error occurs when adding the item
      */
-    public final void addItem(String line) throws Exception
-    {
+    public final void addItem(String line) throws Exception {
         // Check to see if the last character is a field separator, which hides the last empty column
         boolean last = false;
-        if (line.endsWith(fieldSeparator))
-        {
+        if (line.endsWith(fieldSeparator)) {
             // Add a space to the end, then remove it later
             last = true;
             line += " ";
@@ -496,15 +494,12 @@ public class DSpaceCSV implements Serializable
 
         // Merge parts with embedded separators
         boolean alldone = false;
-        while (!alldone)
-        {
+        while (!alldone) {
             boolean found = false;
             int i = 0;
-            for (String part : bits)
-            {
+            for (String part : bits) {
                 int bitcounter = part.length() - part.replaceAll("\"", "").length();
-                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1)))
-                {
+                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1))) {
                     found = true;
                     String add = bits.get(i) + fieldSeparator + bits.get(i + 1);
                     bits.remove(i);
@@ -519,10 +514,8 @@ public class DSpaceCSV implements Serializable
 
         // Deal with quotes around the elements
         int i = 0;
-        for (String part : bits)
-        {
-            if ((part.startsWith("\"")) && (part.endsWith("\"")))
-            {
+        for (String part : bits) {
+            if ((part.startsWith("\"")) && (part.endsWith("\""))) {
                 part = part.substring(1, part.length() - 1);
                 bits.set(i, part);
             }
@@ -531,10 +524,8 @@ public class DSpaceCSV implements Serializable
 
         // Remove embedded quotes
         i = 0;
-        for (String part : bits)
-        {
-            if (part.contains("\"\""))
-            {
+        for (String part : bits) {
+            if (part.contains("\"\"")) {
                 part = part.replaceAll("\"\"", "\"");
                 bits.set(i, part);
             }
@@ -546,18 +537,12 @@ public class DSpaceCSV implements Serializable
         DSpaceCSVLine csvLine;
 
         // Is this an existing item, or a new item (where id = '+')
-        if ("+".equals(id))
-        {
+        if ("+".equals(id)) {
             csvLine = new DSpaceCSVLine();
-        }
-        else
-        {
-            try
-            {
+        } else {
+            try {
                 csvLine = new DSpaceCSVLine(UUID.fromString(id));
-            }
-            catch (NumberFormatException nfe)
-            {
+            } catch (NumberFormatException nfe) {
                 System.err.println("Invalid item identifier: " + id);
                 System.err.println("Please check your CSV file for information. " +
                                        "Item id must be numeric, or a '+' to add a new item");
@@ -567,13 +552,10 @@ public class DSpaceCSV implements Serializable
 
         // Add the rest of the parts
         i = 0;
-        for (String part : bits)
-        {
-            if (i > 0)
-            {
+        for (String part : bits) {
+            if (i > 0) {
                 // Is this a last empty item?
-                if ((last) && (i == headings.size()))
-                {
+                if ((last) && (i == headings.size())) {
                     part = "";
                 }
 
@@ -585,10 +567,8 @@ public class DSpaceCSV implements Serializable
                 }
                 csvLine.add(headings.get(i - 1), null);
                 String[] elements = part.split(escapedValueSeparator);
-                for (String element : elements)
-                {
-                    if ((element != null) && (!"".equals(element)))
-                    {
+                for (String element : elements) {
+                    if ((element != null) && (!"".equals(element))) {
                         csvLine.add(headings.get(i - 1), element);
                     }
                 }
@@ -604,8 +584,7 @@ public class DSpaceCSV implements Serializable
      *
      * @return The lines
      */
-    public final List<DSpaceCSVLine> getCSVLines()
-    {
+    public final List<DSpaceCSVLine> getCSVLines() {
         // Return the lines
         return lines;
     }
@@ -615,22 +594,19 @@ public class DSpaceCSV implements Serializable
      *
      * @return the array of CSV formatted Strings
      */
-    public final String[] getCSVLinesAsStringArray()
-    {
+    public final String[] getCSVLinesAsStringArray() {
         // Create the headings line
         String[] csvLines = new String[counter + 1];
         csvLines[0] = "id" + fieldSeparator + "collection";
         List<String> headingsCopy = new ArrayList<>(headings);
         Collections.sort(headingsCopy);
-        for (String value : headingsCopy)
-        {
+        for (String value : headingsCopy) {
             csvLines[0] = csvLines[0] + fieldSeparator + value;
         }
 
         Iterator<DSpaceCSVLine> i = lines.iterator();
         int c = 1;
-        while (i.hasNext())
-        {
+        while (i.hasNext()) {
             csvLines[c++] = i.next().toCSV(headingsCopy, fieldSeparator, valueSeparator);
         }
 
@@ -641,11 +617,9 @@ public class DSpaceCSV implements Serializable
      * Save the CSV file to the given filename
      *
      * @param filename The filename to save the CSV file to
-     *
      * @throws IOException Thrown if an error occurs when writing the file
      */
-    public final void save(String filename) throws IOException
-    {
+    public final void save(String filename) throws IOException {
         // Save the file
         BufferedWriter out = new BufferedWriter(
             new OutputStreamWriter(
@@ -666,12 +640,10 @@ public class DSpaceCSV implements Serializable
      * @param md The Metadatum to examine
      * @return Whether or not it is OK to export this element
      */
-    protected boolean okToExport(MetadataField md)
-    {
+    protected boolean okToExport(MetadataField md) {
         // Now compare with the list to ignore
         String key = md.getMetadataSchema().getName() + "." + md.getElement();
-        if (md.getQualifier() != null)
-        {
+        if (md.getQualifier() != null) {
             key += "." + md.getQualifier();
         }
         if (ignore.get(key) != null) {
@@ -687,8 +659,7 @@ public class DSpaceCSV implements Serializable
      *
      * @return The headings
      */
-    public List<String> getHeadings()
-    {
+    public List<String> getHeadings() {
         return headings;
     }
 
@@ -698,13 +669,11 @@ public class DSpaceCSV implements Serializable
      * @return The formatted String as a csv
      */
     @Override
-    public final String toString()
-    {
+    public final String toString() {
         // Return the csv as one long string
         StringBuilder csvLines = new StringBuilder();
         String[] lines = this.getCSVLinesAsStringArray();
-        for (String line : lines)
-        {
+        for (String line : lines) {
             csvLines.append(line).append("\n");
         }
         return csvLines.toString();

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

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

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

@@ -7,34 +7,46 @@
  */
 package org.dspace.app.bulkedit;
 
-import com.google.common.collect.Iterators;
-import org.apache.commons.cli.*;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Iterator;
+import java.util.List;
 
-import org.dspace.content.*;
+import com.google.common.collect.Iterators;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
 
-import java.util.ArrayList;
-import java.sql.SQLException;
-import java.util.Iterator;
-import java.util.List;
-
 /**
  * Metadata exporter to allow the batch export of metadata into a file
  *
  * @author Stuart Lewis
  */
-public class MetadataExport
-{
-    /** The items to export */
+public class MetadataExport {
+    /**
+     * The items to export
+     */
     protected Iterator<Item> toExport;
 
     protected ItemService itemService;
 
-    /** Whether to export all metadata, or just normally edited metadata */
+    protected Context context;
+
+    /**
+     * Whether to export all metadata, or just normally edited metadata
+     */
     protected boolean exportAll;
 
     protected MetadataExport() {
@@ -48,13 +60,13 @@ public class MetadataExport
      * @param toExport  The ItemIterator of items to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll)
-    {
+    public MetadataExport(Context c, Iterator<Item> toExport, boolean exportAll) {
         itemService = ContentServiceFactory.getInstance().getItemService();
 
         // Store the export settings
         this.toExport = toExport;
         this.exportAll = exportAll;
+        this.context = c;
     }
 
     /**
@@ -64,18 +76,15 @@ public class MetadataExport
      * @param toExport  The Community to export
      * @param exportAll whether to export all metadata or not (include handle, provenance etc)
      */
-    public MetadataExport(Context c, Community toExport, boolean exportAll)
-    {
+    public MetadataExport(Context c, Community toExport, boolean exportAll) {
         itemService = ContentServiceFactory.getInstance().getItemService();
 
-        try
-        {
+        try {
             // Try to export the community
             this.toExport = buildFromCommunity(c, toExport, 0);
             this.exportAll = exportAll;
-        }
-        catch (SQLException sqle)
-        {
+            this.context = c;
+        } catch (SQLException sqle) {
             // Something went wrong...
             System.err.println("Error running exporter:");
             sqle.printStackTrace(System.err);
@@ -93,15 +102,12 @@ public class MetadataExport
      * @throws SQLException if database error
      */
     protected Iterator<Item> buildFromCommunity(Context context, Community community, int indent)
-                                                                               throws SQLException
-    {
+        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++)
-            {
+        for (Collection collection : collections) {
+            for (int i = 0; i < indent; i++) {
                 System.out.print(" ");
             }
 
@@ -111,10 +117,8 @@ public class MetadataExport
         }
         // Add all the sub-communities
         List<Community> communities = community.getSubcommunities();
-        for (Community subCommunity : communities)
-        {
-            for (int i = 0; i < indent; i++)
-            {
+        for (Community subCommunity : communities) {
+            for (int i = 0; i < indent; i++) {
                 System.out.print(" ");
             }
             Iterator<Item> items = buildFromCommunity(context, subCommunity, indent + 1);
@@ -125,8 +129,7 @@ public class MetadataExport
     }
 
     private Iterator<Item> addItemsToResult(Iterator<Item> result, Iterator<Item> items) {
-        if(result == null)
-        {
+        if (result == null) {
             result = items;
         } else {
             result = Iterators.concat(result, items);
@@ -140,22 +143,23 @@ public class MetadataExport
      *
      * @return the exported CSV lines
      */
-    public DSpaceCSV export()
-    {
-        try
-        {
+    public DSpaceCSV export() {
+        try {
+            Context.Mode originalMode = context.getCurrentMode();
+            context.setMode(Context.Mode.READ_ONLY);
+
             // Process each item
             DSpaceCSV csv = new DSpaceCSV(exportAll);
-            while (toExport.hasNext())
-            {
-                csv.addItem(toExport.next());
+            while (toExport.hasNext()) {
+                Item item = toExport.next();
+                csv.addItem(item);
+                context.uncacheEntity(item);
             }
 
+            context.setMode(originalMode);
             // Return the results
             return csv;
-        }
-        catch (Exception e)
-        {
+        } catch (Exception e) {
             // Something went wrong...
             System.err.println("Error exporting to CSV:");
             e.printStackTrace();
@@ -169,8 +173,7 @@ public class MetadataExport
      * @param options  The command line options the user gave
      * @param exitCode the system exit code to use
      */
-    private static void printHelp(Options options, int exitCode)
-    {
+    private static void printHelp(Options options, int exitCode) {
         // print the help message
         HelpFormatter myhelp = new HelpFormatter();
         myhelp.printHelp("MetadataExport\n", options);
@@ -185,8 +188,7 @@ public class MetadataExport
      * @param argv the command line arguments given
      * @throws Exception if error occurs
      */
-    public static void main(String[] argv) throws Exception
-    {
+    public static void main(String[] argv) throws Exception {
         // Create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -194,37 +196,33 @@ public class MetadataExport
 
         options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
         options.addOption("f", "file", true, "destination where you want file written");
-        options.addOption("a", "all", false, "include all metadata fields that are not normally changed (e.g. provenance)");
+        options.addOption("a", "all", false,
+                          "include all metadata fields that are not normally changed (e.g. provenance)");
         options.addOption("h", "help", false, "help");
 
         CommandLine line = null;
 
-        try
-        {
+        try {
             line = parser.parse(options, argv);
-        }
-        catch (ParseException pe)
-        {
+        } catch (ParseException pe) {
             System.err.println("Error with commands.");
             printHelp(options, 1);
             System.exit(0);
         }
 
-        if (line.hasOption('h'))
-        {
+        if (line.hasOption('h')) {
             printHelp(options, 0);
         }
 
         // Check a filename is given
-        if (!line.hasOption('f'))
-        {
+        if (!line.hasOption('f')) {
             System.err.println("Required parameter -f missing!");
             printHelp(options, 1);
         }
         String filename = line.getOptionValue('f');
 
         // Create a context
-        Context c = new Context();
+        Context c = new Context(Context.Mode.READ_ONLY);
         c.turnOffAuthorisationSystem();
 
         // The things we'll export
@@ -237,42 +235,31 @@ public class MetadataExport
         ContentServiceFactory contentServiceFactory = ContentServiceFactory.getInstance();
         // Check we have an item OK
         ItemService itemService = contentServiceFactory.getItemService();
-        if (!line.hasOption('i'))
-        {
+        if (!line.hasOption('i')) {
             System.out.println("Exporting whole repository WARNING: May take some time!");
             exporter = new MetadataExport(c, itemService.findAll(c), exportAll);
-        }
-        else
-        {
+        } else {
             String handle = line.getOptionValue('i');
             DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(c, handle);
-            if (dso == null)
-            {
+            if (dso == null) {
                 System.err.println("Item '" + handle + "' does not resolve to an item in your repository!");
                 printHelp(options, 1);
             }
 
-            if (dso.getType() == Constants.ITEM)
-            {
+            if (dso.getType() == Constants.ITEM) {
                 System.out.println("Exporting item '" + dso.getName() + "' (" + handle + ")");
                 List<Item> item = new ArrayList<>();
                 item.add((Item) dso);
                 exporter = new MetadataExport(c, item.iterator(), exportAll);
-            }
-            else if (dso.getType() == Constants.COLLECTION)
-            {
+            } else if (dso.getType() == Constants.COLLECTION) {
                 System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
                 Collection collection = (Collection) dso;
                 toExport = itemService.findByCollection(c, collection);
                 exporter = new MetadataExport(c, toExport, exportAll);
-            }
-            else if (dso.getType() == Constants.COMMUNITY)
-            {
+            } else if (dso.getType() == Constants.COMMUNITY) {
                 System.out.println("Exporting community '" + dso.getName() + "' (" + handle + ")");
                 exporter = new MetadataExport(c, (Community) dso, exportAll);
-            }
-            else
-            {
+            } else {
                 System.err.println("Error identifying '" + handle + "'");
                 System.exit(1);
             }

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

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

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

@@ -12,27 +12,40 @@ package org.dspace.app.bulkedit;
  *
  * @author Stuart Lewis
  */
-public class MetadataImportInvalidHeadingException extends Exception
-{
-    /** The type of error (schema or element) */
+public class MetadataImportInvalidHeadingException extends Exception {
+    /**
+     * The type of error (schema or element)
+     */
     private int type;
 
-    /** The bad heading */
+    /**
+     * The bad heading
+     */
     private String badHeading;
 
-    /** The column number */
+    /**
+     * The column number
+     */
     private int column;
 
-    /** Error with the schema */
+    /**
+     * Error with the schema
+     */
     public static final int SCHEMA = 0;
 
-    /** Error with the element */
+    /**
+     * Error with the element
+     */
     public static final int ELEMENT = 1;
 
-    /** Error with a missing header */
+    /**
+     * Error with a missing header
+     */
     public static final int MISSING = 98;
 
-    /** Error with the whole entry */
+    /**
+     * Error with the whole entry
+     */
     public static final int ENTRY = 99;
 
 
@@ -43,8 +56,7 @@ public class MetadataImportInvalidHeadingException extends Exception
      * @param theType   the type of the error
      * @param theColumn column number
      */
-    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn)
-    {
+    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn) {
         super(message);
         badHeading = message;
         type = theType;
@@ -56,8 +68,7 @@ public class MetadataImportInvalidHeadingException extends Exception
      *
      * @return the type of the exception
      */
-    public String getType()
-    {
+    public String getType() {
         return "" + type;
     }
 
@@ -66,8 +77,7 @@ public class MetadataImportInvalidHeadingException extends Exception
      *
      * @return the invalid heading
      */
-    public String getBadHeader()
-    {
+    public String getBadHeader() {
         return badHeading;
     }
 
@@ -76,8 +86,7 @@ public class MetadataImportInvalidHeadingException extends Exception
      *
      * @return the invalid column number
      */
-    public int getColumn()
-    {
+    public int getColumn() {
         return column;
     }
 
@@ -87,20 +96,15 @@ public class MetadataImportInvalidHeadingException extends Exception
      * @return The exception message
      */
     @Override
-    public String getMessage()
-    {
-        if (type == SCHEMA)
-        {
-            return "Unknown metadata schema in row " + column + ": " + badHeading;
-        } else if (type == ELEMENT)
-        {
-            return "Unknown metadata element in row " + column + ": " + badHeading;
-        } else if (type == MISSING)
-        {
-            return "Row with missing header: Row " + column;
-        } else
-        {
-            return "Bad metadata declaration in row " + column + ": " + badHeading;
+    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/checker/ChecksumChecker.java

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

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

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

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

@@ -21,19 +21,19 @@ 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.content.Item;
 import org.dspace.harvest.HarvestingException;
 import org.dspace.harvest.OAIHarvester;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
 import org.dspace.harvest.factory.HarvestServiceFactory;
 import org.dspace.harvest.service.HarvestedCollectionService;
 
@@ -42,16 +42,16 @@ import org.dspace.harvest.service.HarvestedCollectionService;
  *
  * @author Alexey Maslov
  */
-public class Harvest
-{
+public class Harvest {
     private static Context context;
 
-    private static final HarvestedCollectionService harvestedCollectionService = HarvestServiceFactory.getInstance().getHarvestedCollectionService();
+    private static final HarvestedCollectionService harvestedCollectionService =
+        HarvestServiceFactory.getInstance().getHarvestedCollectionService();
     private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    private static final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private static final CollectionService collectionService =
+        ContentServiceFactory.getInstance().getCollectionService();
 
-    public static void main(String[] argv) throws Exception
-    {
+    public static void main(String[] argv) throws Exception {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -67,12 +67,19 @@ public class Harvest
         options.addOption("P", "purge", false, "purge all harvestable collections");
 
 
-        options.addOption("e", "eperson", true, "eperson");
-        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
-        options.addOption("t", "type", true, "type of harvesting (0 for none)");
-        options.addOption("a", "address", true, "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true, "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
+        options.addOption("e", "eperson", true,
+                          "eperson");
+        options.addOption("c", "collection", true,
+                          "harvesting collection (handle or id)");
+        options.addOption("t", "type", true,
+                          "type of harvesting (0 for none)");
+        options.addOption("a", "address", true,
+                          "address of the OAI-PMH server");
+        options.addOption("i", "oai_set_id", true,
+                          "id of the PMH set representing the harvested collection");
+        options.addOption("m", "metadata_format", true,
+                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
+                              "crosswalk in dspace.cfg");
 
         options.addOption("h", "help", false, "help");
 
@@ -86,27 +93,21 @@ public class Harvest
         String metadataKey = null;
         int harvestType = 0;
 
-        if (line.hasOption('h'))
-        {
+        if (line.hasOption('h')) {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("Harvest\n", options);
-            System.out
-    				.println("\nPING OAI server: Harvest -g -s oai_source -i oai_set_id");
-            System.out
-					.println("RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
-            System.out
-                    .println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
-            System.out
-            		.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out
-    				.println("START harvest scheduler: Harvest -S");
-            System.out
-					.println("RESET all harvest status: Harvest -R");
-            System.out
-                    .println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            System.out
-					.println("PURGE all harvestable collections: Harvest -P -e eperson");
-            
+            System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
+            System.out.println(
+                "RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a " +
+                    "oai_source -i oai_set_id -m metadata_format");
+            System.out.println(
+                "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
+                    "oai_set_id -m metadata_format");
+            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
+            System.out.println("START harvest scheduler: Harvest -S");
+            System.out.println("RESET all harvest status: Harvest -R");
+            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
+            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
 
 
             System.exit(0);
@@ -162,21 +163,17 @@ public class Harvest
 
         // Instantiate our class
         Harvest harvester = new Harvest();
-        harvester.context = new Context();
+        harvester.context = new Context(Context.Mode.BATCH_EDIT);
 
 
         // Check our options
-        if (command == null)
-        {
+        if (command == null) {
             System.out
                 .println("Error - no parameters specified (run with -h flag for details)");
             System.exit(1);
-        }
+        } else if ("run".equals(command)) {
             // Run a single harvest cycle on a collection using saved settings.
-        else if ("run".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
+            if (collection == null || eperson == null) {
                 System.out
                     .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -184,22 +181,15 @@ public class Harvest
             }
 
             harvester.runHarvest(collection, eperson);
-        }
+        } else if ("start".equals(command)) {
             // start the harvest loop
-        else if ("start".equals(command))
-        {
             startHarvester();
-        }
+        } else if ("reset".equals(command)) {
             // reset harvesting status
-        else if ("reset".equals(command))
-        {
             resetHarvesting();
-        }
+        } else if ("purgeAll".equals(command)) {
             // purge all collections that are set up for harvesting (obviously for testing purposes only)
-        else if ("purgeAll".equals(command))
-        {
-        	if (eperson == null)
-            {
+            if (eperson == null) {
                 System.out
                     .println("Error - an eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -207,18 +197,17 @@ public class Harvest
             }
 
             List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-	    	for (HarvestedCollection harvestedCollection : harvestedCollections)
-	    	{
-                System.out.println("Purging the following collections (deleting items and resetting harvest status): " + harvestedCollection.getCollection().getID().toString());
+            for (HarvestedCollection harvestedCollection : harvestedCollections) {
+                System.out.println(
+                    "Purging the following collections (deleting items and resetting harvest status): " +
+                        harvestedCollection
+                            .getCollection().getID().toString());
                 harvester.purgeCollection(harvestedCollection.getCollection().getID().toString(), eperson);
             }
             context.complete();
-        }
+        } else if ("purge".equals(command)) {
             // Delete all items in a collection. Useful for testing fresh harvests.
-        else if ("purge".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
+            if (collection == null || eperson == null) {
                 System.out
                     .println("Error - a target collection and eperson must be provided");
                 System.out.println(" (run with -h flag for details)");
@@ -229,35 +218,28 @@ public class Harvest
             context.complete();
 
             //TODO: implement this... remove all items and remember to unset "last-harvested" settings
-        }
+        } else if ("config".equals(command)) {
             // Configure a collection with the three main settings
-        else if ("config".equals(command))
-        {
-            if (collection == null)
-            {
+            if (collection == null) {
                 System.out.println("Error -  a target collection must be provided");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (oaiSource == null || oaiSetID == null)
-            {
+            if (oaiSource == null || oaiSetID == null) {
                 System.out.println("Error - both the OAI server address and OAI set id must be specified");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
-            if (metadataKey == null)
-            {
-            	System.out.println("Error - a metadata key (commonly the prefix) must be specified for this collection");
+            if (metadataKey == null) {
+                System.out
+                    .println("Error - a metadata key (commonly the prefix) must be specified for this collection");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
             }
 
             harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
-        }
-        else if ("ping".equals(command))
-        {
-            if (oaiSource == null || oaiSetID == null)
-            {
+        } else if ("ping".equals(command)) {
+            if (oaiSource == null || oaiSetID == null) {
                 System.out.println("Error - both the OAI server address and OAI set id must be specified");
                 System.out.println(" (run with -h flag for details)");
                 System.exit(1);
@@ -278,39 +260,30 @@ public class Harvest
 
         try {
             // is the ID a handle?
-	        if (collectionID != null)
-            {
-                if (collectionID.indexOf('/') != -1)
-                {
+            if (collectionID != null) {
+                if (collectionID.indexOf('/') != -1) {
                     // string has a / so it must be a handle - try and resolve it
                     dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, collectionID);
 
                     // resolved, now make sure it's a collection
-                    if (dso == null || dso.getType() != Constants.COLLECTION)
-                    {
+                    if (dso == null || dso.getType() != Constants.COLLECTION) {
                         targetCollection = null;
-                    }
-                    else
-                    {
+                    } else {
                         targetCollection = (Collection) dso;
                     }
-                }
-                // not a handle, try and treat it as an integer collection
-                // database ID
-                else
-                {
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer.parseInt(collectionID) + "', " + "in context: " + context);
+                } else {
+                    // not a handle, try and treat it as an integer collection database ID
+                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer
+                        .parseInt(collectionID) + "', " + "in context: " + context);
                     targetCollection = collectionService.find(context, UUID.fromString(collectionID));
                 }
             }
             // was the collection valid?
-            if (targetCollection == null)
-            {
+            if (targetCollection == null) {
                 System.out.println("Cannot resolve " + collectionID + " to collection");
                 System.exit(1);
             }
-    	}
-    	catch (SQLException se) {
+        } catch (SQLException se) {
             se.printStackTrace();
         }
 
@@ -318,7 +291,8 @@ public class Harvest
     }
 
 
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) {
+    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId,
+                                     String mdConfigId) {
         System.out.println("Running: configure collection");
 
         Collection collection = resolveCollection(collectionID);
@@ -336,15 +310,12 @@ public class Harvest
             harvestedCollectionService.update(context, hc);
             context.restoreAuthSystemState();
             context.complete();
-    	} 
-    	catch (Exception e) {
+        } catch (Exception e) {
             System.out.println("Changes could not be committed");
             e.printStackTrace();
             System.exit(1);
-    	}
-    	finally {
-            if (context != null)
-            {
+        } finally {
+            if (context != null) {
                 context.restoreAuthSystemState();
             }
         }
@@ -358,11 +329,11 @@ public class Harvest
      * @param email
      */
     private void purgeCollection(String collectionID, String email) {
-    	System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
+        System.out.println(
+            "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
         Collection collection = resolveCollection(collectionID);
 
-    	try 
-    	{
+        try {
             EPerson eperson = ePersonService.findByEmail(context, email);
             context.setCurrentUser(eperson);
             context.turnOffAuthorisationSystem();
@@ -375,7 +346,7 @@ public class Harvest
                 Item item = it.next();
                 System.out.println("Deleting: " + item.getHandle());
                 collectionService.removeItem(context, collection, item);
-    			// Dispatch events every 50 items
+                context.uncacheEntity(item);// Dispatch events every 50 items
                 if (i % 50 == 0) {
                     context.dispatchEvents();
                     i = 0;
@@ -392,13 +363,11 @@ public class Harvest
             }
             context.restoreAuthSystemState();
             context.dispatchEvents();
-    	}
-    	catch (Exception e) {
+        } catch (Exception e) {
             System.out.println("Changes could not be committed");
             e.printStackTrace();
             System.exit(1);
-    	}
-    	finally {
+        } finally {
             context.restoreAuthSystemState();
         }
     }
@@ -417,8 +386,7 @@ public class Harvest
             HarvestedCollection hc = harvestedCollectionService.find(context, collection);
             harvester = new OAIHarvester(context, collection, hc);
             System.out.println("success. ");
-    	}
-    	catch (HarvestingException hex) {
+        } catch (HarvestingException hex) {
             System.out.print("failed. ");
             System.out.println(hex.getMessage());
             throw new IllegalStateException("Unable to harvest", hex);
@@ -435,14 +403,11 @@ public class Harvest
             context.setCurrentUser(eperson);
             harvester.runHarvest();
             context.complete();
-    	}
-        catch (SQLException e) {
+        } catch (SQLException e) {
             throw new IllegalStateException("Failed to run harvester", e);
-        }
-        catch (AuthorizeException e) {
+        } catch (AuthorizeException e) {
             throw new IllegalStateException("Failed to run harvester", e);
-        }
-        catch (IOException e) {
+        } catch (IOException e) {
             throw new IllegalStateException("Failed to run harvester", e);
         }
 
@@ -450,24 +415,22 @@ public class Harvest
     }
 
     /**
-     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the harvested_collections table 
+     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the
+     * harvested_collections table
      */
     private static void resetHarvesting() {
         System.out.print("Resetting harvest status flag on all collections... ");
 
-    	try
-    	{
+        try {
             List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
-            for (HarvestedCollection harvestedCollection : harvestedCollections)
-            {
+            for (HarvestedCollection harvestedCollection : harvestedCollections) {
                 //hc.setHarvestResult(null,"");
                 harvestedCollection.setHarvestStartTime(null);
                 harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
                 harvestedCollectionService.update(context, harvestedCollection);
             }
             System.out.println("success. ");
-    	}
-    	catch (Exception ex) {
+        } catch (Exception ex) {
             System.out.println("failed. ");
             ex.printStackTrace();
         }
@@ -476,15 +439,12 @@ public class Harvest
     /**
      * Starts up the harvest scheduler. Terminating this process will stop the scheduler.
      */
-    private static void startHarvester()
-    {
-        try
-        {
+    private static void startHarvester() {
+        try {
             System.out.print("Starting harvest loop... ");
             HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
             System.out.println("running. ");
-    	}
-    	catch (Exception ex) {
+        } catch (Exception ex) {
             ex.printStackTrace();
         }
     }
@@ -496,30 +456,29 @@ public class Harvest
      * @param set            name of an item set.
      * @param metadataFormat local prefix name, or null for "dc".
      */
-    private static void pingResponder(String server, String set, String metadataFormat)
-    {
+    private static void pingResponder(String server, String set, String metadataFormat) {
         List<String> errors;
 
         System.out.print("Testing basic PMH access:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
                                                  (null != metadataFormat) ? metadataFormat : "dc", false);
-        if (errors.isEmpty())
+        if (errors.isEmpty()) {
             System.out.println("OK");
-        else
-        {
-            for (String error : errors)
+        } else {
+            for (String error : errors) {
                 System.err.println(error);
             }
+        }
 
         System.out.print("Testing ORE support:  ");
         errors = OAIHarvester.verifyOAIharvester(server, set,
                                                  (null != metadataFormat) ? metadataFormat : "dc", true);
-        if (errors.isEmpty())
+        if (errors.isEmpty()) {
             System.out.println("OK");
-        else
-        {
-            for (String error : errors)
+        } else {
+            for (String error : errors) {
                 System.err.println(error);
             }
         }
     }
+}

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

@@ -7,7 +7,17 @@
  */
 package org.dspace.app.itemexport;
 
-import org.apache.commons.cli.*;
+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;
@@ -20,8 +30,6 @@ import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 
-import java.util.*;
-
 /**
  * Item exporter to create simple AIPs for DSpace content. Currently exports
  * individual items, or entire collections. For instructions on use, see
@@ -45,17 +53,21 @@ import java.util.*;
  */
 public class ItemExportCLITool {
 
-    protected static ItemExportService itemExportService = ItemExportServiceFactory.getInstance().getItemExportService();
+    protected static ItemExportService itemExportService = ItemExportServiceFactory.getInstance()
+                                                                                   .getItemExportService();
     protected static HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
     protected static ItemService itemService = ContentServiceFactory.getInstance().getItemService();
     protected static CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
 
+    /**
+     * Default constructor
+     */
+    private ItemExportCLITool() { }
 
     /*
      *
      */
-    public static void main(String[] argv) throws Exception
-    {
+    public static void main(String[] argv) throws Exception {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -65,7 +77,8 @@ public class ItemExportCLITool {
         options.addOption("i", "id", true, "ID or handle of thing to export");
         options.addOption("d", "dest", true,
                           "destination where you want items to go");
-        options.addOption("m", "migrate", false, "export for migration (remove handle and metadata that will be re-created in new system)");
+        options.addOption("m", "migrate", false,
+                          "export for migration (remove handle and metadata that will be re-created in new system)");
         options.addOption("n", "number", true,
                           "sequence number to begin exporting items with");
         options.addOption("z", "zip", true, "export as zip file (specify filename e.g. export.zip)");
@@ -86,8 +99,7 @@ public class ItemExportCLITool {
         Item myItem = null;
         Collection mycollection = null;
 
-        if (line.hasOption('h'))
-        {
+        if (line.hasOption('h')) {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("ItemExport\n", options);
             System.out
@@ -98,163 +110,129 @@ public class ItemExportCLITool {
             System.exit(0);
         }
 
-        if (line.hasOption('t')) // type
-        {
+        if (line.hasOption('t')) { // type
             typeString = line.getOptionValue('t');
 
-            if ("ITEM".equals(typeString))
-            {
+            if ("ITEM".equals(typeString)) {
                 myType = Constants.ITEM;
-            }
-            else if ("COLLECTION".equals(typeString))
-            {
+            } else if ("COLLECTION".equals(typeString)) {
                 myType = Constants.COLLECTION;
             }
         }
 
-        if (line.hasOption('i')) // id
-        {
+        if (line.hasOption('i')) { // id
             myIDString = line.getOptionValue('i');
         }
 
-        if (line.hasOption('d')) // dest
-        {
+        if (line.hasOption('d')) { // dest
             destDirName = line.getOptionValue('d');
         }
 
-        if (line.hasOption('n')) // number
-        {
+        if (line.hasOption('n')) { // number
             seqStart = Integer.parseInt(line.getOptionValue('n'));
         }
 
         boolean migrate = false;
-        if (line.hasOption('m')) // number
-        {
+        if (line.hasOption('m')) { // number
             migrate = true;
         }
 
         boolean zip = false;
         String zipFileName = "";
-        if (line.hasOption('z'))
-        {
+        if (line.hasOption('z')) {
             zip = true;
             zipFileName = line.getOptionValue('z');
         }
 
         boolean excludeBitstreams = false;
-        if (line.hasOption('x'))
-        {
+        if (line.hasOption('x')) {
             excludeBitstreams = true;
         }
 
         // now validate the args
-        if (myType == -1)
-        {
+        if (myType == -1) {
             System.out
                 .println("type must be either COLLECTION or ITEM (-h for help)");
             System.exit(1);
         }
 
-        if (destDirName == null)
-        {
+        if (destDirName == null) {
             System.out
                 .println("destination directory must be set (-h for help)");
             System.exit(1);
         }
 
-        if (seqStart == -1)
-        {
+        if (seqStart == -1) {
             System.out
                 .println("sequence start number must be set (-h for help)");
             System.exit(1);
         }
 
-        if (myIDString == null)
-        {
+        if (myIDString == null) {
             System.out
                 .println("ID must be set to either a database ID or a handle (-h for help)");
             System.exit(1);
         }
 
-        Context c = new Context();
+        Context c = new Context(Context.Mode.READ_ONLY);
         c.turnOffAuthorisationSystem();
 
-        if (myType == Constants.ITEM)
-        {
+        if (myType == Constants.ITEM) {
             // first, is myIDString a handle?
-            if (myIDString.indexOf('/') != -1)
-            {
+            if (myIDString.indexOf('/') != -1) {
                 myItem = (Item) handleService.resolveToObject(c, myIDString);
 
-                if ((myItem == null) || (myItem.getType() != Constants.ITEM))
-                {
+                if ((myItem == null) || (myItem.getType() != Constants.ITEM)) {
                     myItem = null;
                 }
-            }
-            else
-            {
+            } else {
                 myItem = itemService.find(c, UUID.fromString(myIDString));
             }
 
-            if (myItem == null)
-            {
+            if (myItem == null) {
                 System.out
                     .println("Error, item cannot be found: " + myIDString);
             }
-        }
-        else
-        {
-            if (myIDString.indexOf('/') != -1)
-            {
+        } else {
+            if (myIDString.indexOf('/') != -1) {
                 // has a / must be a handle
                 mycollection = (Collection) handleService.resolveToObject(c,
                                                                           myIDString);
 
                 // ensure it's a collection
                 if ((mycollection == null)
-                        || (mycollection.getType() != Constants.COLLECTION))
-                {
+                    || (mycollection.getType() != Constants.COLLECTION)) {
                     mycollection = null;
                 }
-            }
-            else if (myIDString != null)
-            {
+            } else if (myIDString != null) {
                 mycollection = collectionService.find(c, UUID.fromString(myIDString));
             }
 
-            if (mycollection == null)
-            {
+            if (mycollection == null) {
                 System.out.println("Error, collection cannot be found: "
                                        + myIDString);
                 System.exit(1);
             }
         }
 
-        if (zip)
-        {
+        if (zip) {
             Iterator<Item> items;
-            if (myItem != null)
-            {
+            if (myItem != null) {
                 List<Item> myItems = new ArrayList<>();
                 myItems.add(myItem);
                 items = myItems.iterator();
-            }
-            else
-            {
+            } else {
                 System.out.println("Exporting from collection: " + myIDString);
                 items = itemService.findByCollection(c, mycollection);
             }
             itemExportService.exportAsZip(c, items, destDirName, zipFileName, seqStart, migrate, excludeBitstreams);
-        }
-        else
-        {
-            if (myItem != null)
-            {
+        } else {
+            if (myItem != null) {
                 // it's only a single item
-                itemExportService.exportItem(c, Collections.singletonList(myItem).iterator(), destDirName, seqStart, migrate, excludeBitstreams);
-            }
-            else
-            {
+                itemExportService
+                    .exportItem(c, Collections.singletonList(myItem).iterator(), destDirName, seqStart, migrate,
+                                excludeBitstreams);
+            } else {
                 System.out.println("Exporting from collection: " + myIDString);
 
                 // it's a collection, so do a bunch of items

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

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

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

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

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

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

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

@@ -7,16 +7,16 @@
  */
 package org.dspace.app.itemexport.service;
 
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-
-import javax.mail.MessagingException;
 import java.io.InputStream;
 import java.util.Date;
 import java.util.Iterator;
 import java.util.List;
+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
@@ -71,10 +71,8 @@ public interface ItemExportService {
      * Convenience methot to create export a single Community, Collection, or
      * Item
      *
-     * @param dso
-     *            - the dspace object to export
-     * @param context
-     *            - the dspace context
+     * @param dso     - the dspace object to export
+     * @param context - the dspace context
      * @param migrate Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -85,10 +83,8 @@ public interface ItemExportService {
      * Convenience method to export a List of dspace objects (Community,
      * Collection or Item)
      *
-     * @param dsObjects
-     *            - List containing dspace objects
-     * @param context
-     *            - the dspace context
+     * @param dsObjects - List containing dspace objects
+     * @param context   - the dspace context
      * @param migrate   Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -99,12 +95,9 @@ public interface ItemExportService {
      * Convenience methot to create export a single Community, Collection, or
      * Item
      *
-     * @param dso
-     *            - the dspace object to export
-     * @param context
-     *            - the dspace context
-     * @param additionalEmail
-     *            - cc email to use
+     * @param dso             - the dspace object to export
+     * @param context         - the dspace context
+     * @param additionalEmail - cc email to use
      * @param migrate         Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -115,12 +108,9 @@ public interface ItemExportService {
      * Convenience method to export a List of dspace objects (Community,
      * Collection or Item)
      *
-     * @param dsObjects
-     *            - List containing dspace objects
-     * @param context
-     *            - the dspace context
-     * @param additionalEmail
-     *            - cc email to use
+     * @param dsObjects       - List containing dspace objects
+     * @param context         - the dspace context
+     * @param additionalEmail - cc email to use
      * @param migrate         Whether to use the migrate option or not
      * @throws Exception if error
      */
@@ -132,10 +122,8 @@ public interface ItemExportService {
      * Create a file name based on the date and eperson
      *
      * @param type    Type of object (as string)
-     * @param eperson
-     *            - eperson who requested export and will be able to download it
-     * @param date
-     *            - the date the export process was created
+     * @param eperson - eperson who requested export and will be able to download it
+     * @param date    - the date the export process was created
      * @return String representing the file name in the form of
      * 'export_yyy_MMM_dd_count_epersonID'
      * @throws Exception if error
@@ -148,8 +136,7 @@ public interface ItemExportService {
      * Use config file entry for org.dspace.app.itemexport.download.dir and id
      * of the eperson to create a download directory name
      *
-     * @param ePerson
-     *            - the eperson who requested export archive
+     * @param ePerson - the eperson who requested export archive
      * @return String representing a directory in the form of
      * org.dspace.app.itemexport.download.dir/epersonID
      * @throws Exception if error
@@ -170,10 +157,8 @@ public interface ItemExportService {
     /**
      * Used to read the export archived. Inteded for download.
      *
-     * @param fileName
-     *            the name of the file to download
-     * @param eperson
-     *            the eperson requesting the download
+     * @param fileName the name of the file to download
+     * @param eperson  the eperson requesting the download
      * @return an input stream of the file to be downloaded
      * @throws Exception if error
      */
@@ -184,10 +169,9 @@ public interface ItemExportService {
      * Get the file size of the export archive represented by the file name.
      *
      * @param context  DSpace context
-     * @param fileName
-     *            name of the file to get the size.
-     * @throws Exception if error
+     * @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;
 
@@ -195,11 +179,10 @@ public interface ItemExportService {
      * Get the last modified date of the export archive represented by the file name.
      *
      * @param context  DSpace context
-     * @param fileName
-     *            name of the file to get the size.
+     * @param fileName name of the file to get the size.
      * @return date as long
-     * @see java.io.File#lastModified() 
      * @throws Exception if error
+     * @see java.io.File#lastModified()
      */
     public long getExportFileLastModified(Context context, String fileName)
         throws Exception;
@@ -209,10 +192,8 @@ public interface ItemExportService {
      * who created it When requested for download this method can check if the
      * person requesting it is the same one that created it
      *
-     * @param context
-     *            dspace context
-     * @param fileName
-     *            the file name to check auths for
+     * @param context  dspace context
+     * @param fileName the file name to check auths for
      * @return true if it is the same person false otherwise
      */
     public boolean canDownload(Context context, String fileName);
@@ -234,8 +215,7 @@ public interface ItemExportService {
      * uses the config file entry 'org.dspace.app.itemexport.life.span.hours' to
      * determine if the current exports are too old and need pruging
      *
-     * @param eperson
-     *            - the eperson to clean up
+     * @param eperson - the eperson to clean up
      * @throws Exception if error
      */
     public void deleteOldExportArchives(EPerson eperson) throws Exception;
@@ -256,12 +236,9 @@ public interface ItemExportService {
      * communication with email instead. Send a success email once the export
      * archive is complete and ready for download
      *
-     * @param context
-     *            - the current Context
-     * @param eperson
-     *            - eperson to send the email to
-     * @param fileName
-     *            - the file name to be downloaded. It is added to the url in
+     * @param context  - the current Context
+     * @param eperson  - eperson to send the email to
+     * @param fileName - the file name to be downloaded. It is added to the url in
      *                 the email
      * @throws MessagingException if error
      */
@@ -274,10 +251,8 @@ public interface ItemExportService {
      * communication with email instead. Send an error email if the export
      * archive fails
      *
-     * @param eperson
-     *            - EPerson to send the error message to
-     * @param error
-     *            - the error message
+     * @param eperson - EPerson to send the error message to
+     * @param error   - the error message
      * @throws MessagingException if error
      */
     public void emailErrorMessage(EPerson eperson, String error)
@@ -285,6 +260,7 @@ public interface ItemExportService {
 
     /**
      * Zip source to target
+     *
      * @param strSource source file
      * @param target    target file
      * @throws Exception if error

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

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

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

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

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

@@ -7,7 +7,17 @@
  */
 package org.dspace.app.itemimport;
 
-import org.apache.commons.cli.*;
+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;
@@ -21,12 +31,6 @@ import org.dspace.eperson.service.EPersonService;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 
-import java.io.File;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.List;
-import java.util.UUID;
-
 /**
  * Import items into DSpace. The conventional use is upload files by copying
  * them. DSpace writes the item's bitstreams into its assetstore. Metadata is
@@ -47,12 +51,17 @@ public class ItemImportCLITool {
 
     private static boolean template = false;
 
-    private static final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private static final CollectionService collectionService = ContentServiceFactory.getInstance()
+                                                                                    .getCollectionService();
     private static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
     private static final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
 
-    public static void main(String[] argv) throws Exception
-    {
+    /**
+     * Default constructor
+     */
+    private ItemImportCLITool() { }
+
+    public static void main(String[] argv) throws Exception {
         Date startTime = new Date();
         int status = 0;
 
@@ -108,13 +117,17 @@ public class ItemImportCLITool {
                 System.out
                     .println("\nadding items:    ItemImport -a -e eperson -c collection -s sourcedir -m mapfile");
                 System.out
-                        .println("\nadding items from zip file:    ItemImport -a -e eperson -c collection -s sourcedir -z filename.zip -m mapfile");
+                    .println(
+                        "\nadding items from zip file:    ItemImport -a -e eperson -c collection -s sourcedir -z " +
+                            "filename.zip -m mapfile");
                 System.out
                     .println("replacing items: ItemImport -r -e eperson -c collection -s sourcedir -m mapfile");
                 System.out
                     .println("deleting items:  ItemImport -d -e eperson -m mapfile");
                 System.out
-                        .println("If multiple collections are specified, the first collection will be the one that owns the item.");
+                    .println(
+                        "If multiple collections are specified, the first collection will be the one that owns the " +
+                            "item.");
 
                 System.exit(0);
             }
@@ -155,23 +168,19 @@ public class ItemImportCLITool {
                 template = true;
             }
 
-            if (line.hasOption('s')) // source
-            {
+            if (line.hasOption('s')) { // source
                 sourcedir = line.getOptionValue('s');
             }
 
-            if (line.hasOption('m')) // mapfile
-            {
+            if (line.hasOption('m')) { // mapfile
                 mapfile = line.getOptionValue('m');
             }
 
-            if (line.hasOption('e')) // eperson
-            {
+            if (line.hasOption('e')) { // eperson
                 eperson = line.getOptionValue('e');
             }
 
-            if (line.hasOption('c')) // collections
-            {
+            if (line.hasOption('c')) { // collections
                 collections = line.getOptionValues('c');
             }
 
@@ -189,7 +198,7 @@ public class ItemImportCLITool {
             String zipfilename = "";
             if (line.hasOption('z')) {
                 zip = true;
-                zipfilename = sourcedir + System.getProperty("file.separator") + line.getOptionValue('z');
+                zipfilename = line.getOptionValue('z');
             }
 
             //By default assume collections will be given on the command line
@@ -227,7 +236,8 @@ public class ItemImportCLITool {
                     commandLineCollections = false;
                 }
             } else if ("add-bte".equals(command)) {
-                //Source dir can be null, the user can specify the parameters for his loader in the Spring XML configuration file
+                //Source dir can be null, the user can specify the parameters for his loader in the Spring XML
+                // configuration file
 
                 if (mapfile == null) {
                     System.out
@@ -250,7 +260,9 @@ public class ItemImportCLITool {
 
                 if (bteInputType == null) {
                     System.out
-                            .println("Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have specified in BTE Spring XML configuration file) must be specified");
+                        .println(
+                            "Error - an input type (tsv, csv, ris, endnote, bibtex or any other type you have " +
+                                "specified in BTE Spring XML configuration file) must be specified");
                     System.out.println(" (run with -h flag for details)");
                     System.exit(1);
                 }
@@ -294,7 +306,7 @@ public class ItemImportCLITool {
             myloader.setQuiet(isQuiet);
 
             // create a context
-            Context c = new Context();
+            Context c = new Context(Context.Mode.BATCH_EDIT);
 
             // find the EPerson, assign to context
             EPerson myEPerson = null;
@@ -337,10 +349,8 @@ public class ItemImportCLITool {
                             || (mycollections.get(i).getType() != Constants.COLLECTION)) {
                             mycollections.set(i, null);
                         }
-                    }
-                    // not a handle, try and treat it as an integer collection
-                    // database ID
-                    else if (collections[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])));
                     }
 
@@ -394,11 +404,13 @@ public class ItemImportCLITool {
             try {
                 if (zip) {
                     System.gc();
-                    System.out.println("Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
+                    System.out.println(
+                        "Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
                     myloader.cleanupZipTemp();
                 }
             } catch (Exception ex) {
-                System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile().getAbsolutePath());
+                System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile()
+                                                                                                 .getAbsolutePath());
             }
 
 
@@ -409,7 +421,9 @@ public class ItemImportCLITool {
             Date endTime = new Date();
             System.out.println("Started: " + startTime.getTime());
             System.out.println("Ended: " + endTime.getTime());
-            System.out.println("Elapsed time: " + ((endTime.getTime() - startTime.getTime()) / 1000) + " secs (" + (endTime.getTime() - startTime.getTime()) + " msecs)");
+            System.out.println(
+                "Elapsed time: " + ((endTime.getTime() - startTime.getTime()) / 1000) + " secs (" + (endTime
+                    .getTime() - startTime.getTime()) + " msecs)");
         }
 
         System.exit(status);

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -9,12 +9,18 @@ package org.dspace.app.itemupdate;
 
 import java.io.BufferedWriter;
 import java.io.File;
-import java.io.FilenameFilter;
 import java.io.FileNotFoundException;
 import java.io.FileWriter;
+import java.io.FilenameFilter;
 import java.io.IOException;
 import java.io.PrintWriter;
-import java.util.*;
+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;
@@ -32,7 +38,6 @@ 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
@@ -57,9 +62,7 @@ import org.dspace.eperson.service.EPersonService;
  * Some of this has been placed into the MetadataUtilities class
  * for possible reuse elsewhere.
  *
- * 
  * @author W. Hays based on a conceptual design by R. Rodgers
- *
  */
 public class ItemUpdate {
 
@@ -76,31 +79,27 @@ public class ItemUpdate {
     protected static final EPersonService epersonService = EPersonServiceFactory.getInstance().getEPersonService();
     protected static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
-	static
-	{
+    static {
         filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
-		filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
+        filterAliases
+            .put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
         filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");
         filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");
     }
 
     // File listing filter to check for folders
-    static FilenameFilter directoryFilter = new FilenameFilter()
-    {
+    static FilenameFilter directoryFilter = new FilenameFilter() {
         @Override
-		public boolean accept(File dir, String n)
-        {
+        public boolean accept(File dir, String n) {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return f.isDirectory();
         }
     };
 
     // File listing filter to check for files (not directories)
-    static FilenameFilter fileFilter = new FilenameFilter()
-    {
+    static FilenameFilter fileFilter = new FilenameFilter() {
         @Override
-		public boolean accept(File dir, String n)
-        {
+        public boolean accept(File dir, String n) {
             File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
             return (f.isFile());
         }
@@ -112,11 +111,9 @@ public class ItemUpdate {
     protected String eperson;
 
     /**
-     * 
-     * @param argv commandline args
+     * @param argv the command line arguments given
      */
-    public static void main(String[] argv)
-    {
+    public static void main(String[] argv) {
         // create an options object and populate it
         CommandLineParser parser = new PosixParser();
 
@@ -127,20 +124,23 @@ public class ItemUpdate {
         options.addOption("s", "source", true, "root directory of source dspace archive ");
 
         //actions  on items
-        options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'");
+        options.addOption("a", "addmetadata", true,
+                          "add metadata specified for each item; multiples separated by semicolon ';'");
         options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
 
         options.addOption("A", "addbitstreams", false, "add bitstreams as specified for each item");
 
         // extra work to get optional argument
-        Option delBitstreamOption = new Option("D", "deletebitstreams", true, "delete bitstreams as specified for each item");
+        Option delBitstreamOption = new Option("D", "deletebitstreams", true,
+                                               "delete bitstreams as specified for each item");
         delBitstreamOption.setOptionalArg(true);
         delBitstreamOption.setArgName("BitstreamFilter");
         options.addOption(delBitstreamOption);
 
         //other params
         options.addOption("e", "eperson", true, "email of eperson doing the update");
-        options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
+        options.addOption("i", "itemfield", true,
+                          "optional metadata field that containing item identifier; default is dc.identifier.uri");
         options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");
         options.addOption("v", "verbose", false, "verbose logging");
 
@@ -158,12 +158,10 @@ public class ItemUpdate {
         Context context = null;
         ItemUpdate iu = new ItemUpdate();
 
-        try
-        {       
+        try {
             CommandLine line = parser.parse(options, argv);
 
-	        if (line.hasOption('h'))
-	        {
+            if (line.hasOption('h')) {
                 HelpFormatter myhelp = new HelpFormatter();
                 myhelp.printHelp("ItemUpdate", options);
                 pr("");
@@ -177,91 +175,79 @@ public class ItemUpdate {
                 System.exit(0);
             }
 
-	        if (line.hasOption('v'))
-	        {
+            if (line.hasOption('v')) {
                 verbose = true;
             }
 
 
-	        if (line.hasOption('P'))
-	        {
+            if (line.hasOption('P')) {
                 alterProvenance = false;
                 pr("Suppressing changes to Provenance field option");
             }
 
             iu.eperson = line.getOptionValue('e'); // db ID or email
 
-	        if (!line.hasOption('s')) // item specific changes from archive dir
-	        {
+            if (!line.hasOption('s')) { // item specific changes from archive dir
                 pr("Missing source archive option");
                 System.exit(1);
             }
             String sourcedir = line.getOptionValue('s');
 
-        	if (line.hasOption('t'))  //test
-        	{
+            if (line.hasOption('t')) { //test
                 isTest = true;
                 pr("**Test Run** - not actually updating items.");
 
             }
 
-        	if (line.hasOption('i'))
-        	{
+            if (line.hasOption('i')) {
                 itemField = line.getOptionValue('i');
             }
 
-	        if (line.hasOption('d'))
-	        {
+            if (line.hasOption('d')) {
                 String[] targetFields = line.getOptionValues('d');
 
-	        	DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
+                DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr
+                    .getUpdateAction(DeleteMetadataAction.class);
                 delMetadataAction.addTargetFields(targetFields);
 
                 //undo is an add
-	        	for (String field : targetFields)
-	        	{
+                for (String field : targetFields) {
                     iu.undoActionList.add(" -a " + field + " ");
                 }
 
                 pr("Delete metadata for fields: ");
-	        	for (String s : targetFields)
-	        	{
+                for (String s : targetFields) {
                     pr("    " + s);
                 }
             }
 
-    		if (line.hasOption('a'))
-    		{
+            if (line.hasOption('a')) {
                 String[] targetFields = line.getOptionValues('a');
 
-    			AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class); 
+                AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr
+                    .getUpdateAction(AddMetadataAction.class);
                 addMetadataAction.addTargetFields(targetFields);
 
                 //undo is a delete followed by an add of a replace record for target fields
-	        	for (String field : targetFields)
-	        	{
+                for (String field : targetFields) {
                     iu.undoActionList.add(" -d " + field + " ");
                 }
 
-	        	for (String field : targetFields)
-	        	{
+                for (String field : targetFields) {
                     iu.undoActionList.add(" -a " + field + " ");
                 }
 
                 pr("Add metadata for fields: ");
-	        	for (String s : targetFields)
-	        	{
+                for (String s : targetFields) {
                     pr("    " + s);
                 }
             }
 
-	        if (line.hasOption('D'))  // undo not supported 
-	        {
+            if (line.hasOption('D')) { // undo not supported
                 pr("Delete bitstreams ");
 
                 String[] filterNames = line.getOptionValues('D');
-	        	if ((filterNames != null) && (filterNames.length > 1))
-	        	{
+                if ((filterNames != null) && (filterNames.length > 1)) {
                     pr("Error: Only one filter can be a used at a time.");
                     System.exit(1);
                 }
@@ -269,124 +255,103 @@ public class ItemUpdate {
                 String filterName = line.getOptionValue('D');
                 pr("Filter argument: " + filterName);
 
-	        	if (filterName == null)  // indicates using delete_contents files
-	        	{
-	        		DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class);
+                if (filterName == null) { // indicates using delete_contents files
+                    DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr
+                        .getUpdateAction(DeleteBitstreamsAction.class);
                     delAction.setAlterProvenance(alterProvenance);
-	        	}
-	        	else
-	        	{
+                } else {
                     // check if param is on ALIAS list
                     String filterClassname = filterAliases.get(filterName);
 
-	        		if (filterClassname == null)
-	        		{
+                    if (filterClassname == null) {
                         filterClassname = filterName;
                     }
 
                     BitstreamFilter filter = null;
 
-	        	    try
-	        	    {
+                    try {
                         Class<?> cfilter = Class.forName(filterClassname);
                         pr("BitstreamFilter class to instantiate: " + cfilter.toString());
 
                         filter = (BitstreamFilter) cfilter.newInstance();  //unfortunate cast, an erasure consequence
-	        	    }
-	        	    catch(Exception e)
-	        	    {
+                    } catch (Exception e) {
                         pr("Error:  Failure instantiating bitstream filter class: " + filterClassname);
                         System.exit(1);
                     }
 
                     String filterPropertiesName = line.getOptionValue('F');
-	        	    if (filterPropertiesName != null)  //not always required
-	        	    {
-	        	    	try
-	        	    	{
+                    if (filterPropertiesName != null) { //not always required
+                        try {
                             // TODO try multiple relative locations, e.g. source dir
-	        	    		if (!filterPropertiesName.startsWith("/"))
-	        	    		{
+                            if (!filterPropertiesName.startsWith("/")) {
                                 filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
                             }
 
                             filter.initProperties(filterPropertiesName);
-	        	    	}
-	        	    	catch(Exception e)
-	        	    	{
-		        	    	pr("Error:  Failure finding properties file for bitstream filter class: " + filterPropertiesName);
+                        } catch (Exception e) {
+                            pr("Error:  Failure finding properties file for bitstream filter class: " +
+                                   filterPropertiesName);
                             System.exit(1);
                         }
                     }
 
                     DeleteBitstreamsByFilterAction delAction =
-	        			(DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
+                        (DeleteBitstreamsByFilterAction) iu.actionMgr
+                            .getUpdateAction(DeleteBitstreamsByFilterAction.class);
                     delAction.setAlterProvenance(alterProvenance);
                     delAction.setBitstreamFilter(filter);
                     //undo not supported
                 }
             }
 
-	        if (line.hasOption('A'))
-	        {
+            if (line.hasOption('A')) {
                 pr("Add bitstreams ");
-        		AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
+                AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr
+                    .getUpdateAction(AddBitstreamsAction.class);
                 addAction.setAlterProvenance(alterProvenance);
 
                 iu.undoActionList.add(" -D ");  // delete_contents file will be written, no arg required
             }
 
-	        if (!iu.actionMgr.hasActions())
-	        {
+            if (!iu.actionMgr.hasActions()) {
                 pr("Error - an action must be specified");
                 System.exit(1);
-	        }
-	        else  
-	        {
+            } else {
                 pr("Actions to be performed: ");
 
-	        	for (UpdateAction ua : iu.actionMgr)
-	        	{
+                for (UpdateAction ua : iu.actionMgr) {
                     pr("    " + ua.getClass().getName());
                 }
             }
 
             pr("ItemUpdate - initializing run on " + (new Date()).toString());
 
-	        context = new Context();  
+            context = new Context(Context.Mode.BATCH_EDIT);
             iu.setEPerson(context, iu.eperson);
             context.turnOffAuthorisationSystem();
 
             HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
-	    	if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
-	    	{
+            if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0) {
                 HANDLE_PREFIX = "http://hdl.handle.net/";
             }
 
             iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);
 
             context.complete();  // complete all transactions
-        }
-        catch (Exception e)
-        {
-            if (context != null && context.isValid())
-            {
+        } catch (Exception e) {
+            if (context != null && context.isValid()) {
                 context.abort();
             }
             e.printStackTrace();
             pr(e.toString());
             status = 1;
-        }
-        finally {
+        } finally {
             context.restoreAuthSystemState();
         }
 
-        if (isTest)
-        {
+        if (isTest) {
             pr("***End of Test Run***");
-        }
-        else
-        {
+        } else {
             pr("End.");
 
         }
@@ -395,6 +360,7 @@ public class ItemUpdate {
 
     /**
      * process an archive
+     *
      * @param context           DSpace Context
      * @param sourceDirPath     source path
      * @param itemField         item field
@@ -405,13 +371,11 @@ public class ItemUpdate {
      */
     protected void processArchive(Context context, String sourceDirPath, String itemField,
                                   String metadataIndexName, boolean alterProvenance, boolean isTest)
-    throws Exception
-    {
+        throws Exception {
         // open and process the source directory
         File sourceDir = new File(sourceDirPath);
 
-        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory())
-        {
+        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory()) {
             pr("Error, cannot open archive source directory " + sourceDirPath);
             throw new Exception("error with archive source directory " + sourceDirPath);
         }
@@ -422,89 +386,73 @@ public class ItemUpdate {
         //Undo is suppressed to prevent undo of undo
         boolean suppressUndo = false;
         File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
-        if (fSuppressUndo.exists())
-        {
+        if (fSuppressUndo.exists()) {
             suppressUndo = true;
         }
 
         File undoDir = null;  //sibling directory of source archive
 
-    	if (!suppressUndo && !isTest) 
-    	{
+        if (!suppressUndo && !isTest) {
             undoDir = initUndoArchive(sourceDir);
         }
 
         int itemCount = 0;
         int successItemCount = 0;
 
-        for (String dirname : dircontents)
-        {
+        for (String dirname : dircontents) {
             itemCount++;
             pr("");
             pr("processing item " + dirname);
 
-    		try
-    		{
+            try {
                 ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
 
-	    		for (UpdateAction action : actionMgr)
-	    		{
+                for (UpdateAction action : actionMgr) {
                     pr("action: " + action.getClass().getName());
                     action.execute(context, itarch, isTest, suppressUndo);
-	    			if (!isTest && !suppressUndo)
-                    {
+                    if (!isTest && !suppressUndo) {
                         itarch.writeUndo(undoDir);
                     }
                 }
-	    		if (!isTest)
-	    		{
+                if (!isTest) {
                     Item item = itarch.getItem();
                     itemService.update(context, item);  //need to update before commit
+                    context.uncacheEntity(item);
                 }
                 ItemUpdate.pr("Item " + dirname + " completed");
                 successItemCount++;
-    		}
-    		catch(Exception e)
-    		{
+            } catch (Exception e) {
                 pr("Exception processing item " + dirname + ": " + e.toString());
                 e.printStackTrace();
             }
         }
 
-        if (!suppressUndo && !isTest)
-        {        	     	
+        if (!suppressUndo && !isTest) {
             StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
             sb.append(" -e ").append(this.eperson);
             sb.append(" -s ").append(undoDir);
 
-        	if (itemField != null)
-        	{
+            if (itemField != null) {
                 sb.append(" -i ").append(itemField);
             }
 
-         	if (!alterProvenance)
-        	{
+            if (!alterProvenance) {
                 sb.append(" -P ");
             }
-        	if (isTest)
-        	{
+            if (isTest) {
                 sb.append(" -t ");
             }
 
-        	for (String actionOption : undoActionList)
-        	{
+            for (String actionOption : undoActionList) {
                 sb.append(actionOption);
             }
 
             PrintWriter pw = null;
-        	try
-        	{
+            try {
                 File cmdFile = new File(undoDir.getParent(), undoDir.getName() + "_command.sh");
                 pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
                 pw.println(sb.toString());
-        	}
-        	finally
-        	{
+            } finally {
                 pw.close();
             }
         }
@@ -516,7 +464,6 @@ public class ItemUpdate {
 
 
     /**
-     * 
      * to avoid overwriting the undo source tree on repeated processing
      * sequence numbers are added and checked
      *
@@ -526,38 +473,33 @@ public class ItemUpdate {
      * @throws IOException           if IO error
      */
     protected File initUndoArchive(File sourceDir)
-	throws FileNotFoundException, IOException
-	{				
+        throws FileNotFoundException, IOException {
         File parentDir = sourceDir.getCanonicalFile().getParentFile();
-		if (parentDir == null)
-		{
-			throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");    			
+        if (parentDir == null) {
+            throw new FileNotFoundException(
+                "Parent directory of archive directory not found; unable to write UndoArchive; no processing " +
+                    "performed");
         }
 
         String sourceDirName = sourceDir.getName();
         int seqNo = 1;
 
         File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
-		while (undoDir.exists())
-		{
+        while (undoDir.exists()) {
             undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + ++seqNo); //increment
         }
 
         // create root directory
-		if (!undoDir.mkdir())
-		{
+        if (!undoDir.mkdir()) {
             pr("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
             throw new IOException("ERROR creating  Undo Archive directory " + undoDir.getCanonicalPath());
         }
 
         //Undo is suppressed to prevent undo of undo
         File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
-        try
-        {
+        try {
             fSuppressUndo.createNewFile();
-        }
-        catch(IOException e)
-        {
+        } catch (IOException e) {
             pr("ERROR creating Suppress Undo File " + e.toString());
             throw e;
         }
@@ -568,33 +510,29 @@ public class ItemUpdate {
 
     /**
      * Set EPerson doing import
+     *
      * @param context DSpace Context
      * @param eperson EPerson obj
      * @throws Exception if error
      */
     protected void setEPerson(Context context, String eperson)
-    throws Exception
-    {
-        if (eperson == null)
-        {
+        throws Exception {
+        if (eperson == null) {
             pr("Error - an eperson to do the importing must be specified");
             pr(" (run with -h flag for details)");
-            throw new Exception("EPerson not specified.");        }
+            throw new Exception("EPerson not specified.");
+        }
 
         EPerson myEPerson = null;
 
-        if (eperson.indexOf('@') != -1)
-        {
+        if (eperson.indexOf('@') != -1) {
             // @ sign, must be an email
             myEPerson = epersonService.findByEmail(context, eperson);
-        }
-        else
-        {
+        } else {
             myEPerson = epersonService.find(context, UUID.fromString(eperson));
         }
 
-        if (myEPerson == null)
-        {
+        if (myEPerson == null) {
             pr("Error, eperson cannot be found: " + eperson);
             throw new Exception("Invalid EPerson");
         }
@@ -606,21 +544,20 @@ public class ItemUpdate {
      * poor man's logging
      * As with ItemImport, API logging goes through log4j to the DSpace.log files
      * whereas the batch logging goes to the console to be captured there.
+     *
      * @param s String
      */
-    static void pr(String s)
-    {
+    static void pr(String s) {
         System.out.println(s);
     }
 
     /**
      * print if verbose flag is set
+     *
      * @param s String
      */
-    static void prv(String s)
-    {
-    	if (verbose) 
-    	{
+    static void prv(String s) {
+        if (verbose) {
             System.out.println(s);
         }
     }

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@@ -18,13 +18,11 @@ import org.dspace.core.Context;
  * from one format to another.  This interface should be implemented by any class
  * which defines a "filter" to be run by the MediaFilterManager.
  */
-public interface FormatFilter
-{
+public interface FormatFilter {
     /**
      * Get a filename for a newly created filtered bitstream
      *
-     * @param sourceName
-     *            name of source bitstream
+     * @param sourceName name of source bitstream
      * @return filename generated by the filter - for example, document.pdf
      * becomes document.pdf.txt
      */
@@ -44,18 +42,18 @@ public interface FormatFilter
     public String getFormatString();
 
     /**
-     * @return string to describe the newly-generated Bitstream's - how it was
+     * @return string to describe the newly-generated Bitstream - how it was
      * produced is a good idea
      */
     public String getDescription();
 
     /**
-     * @param item Item
-     * @param source
-     *            input stream
-     * @param verbose verbosity flag
+     * Read the source stream and produce the filtered content.
      *
-     * @return result of filter's transformation, written out to a bitstream
+     * @param item    Item
+     * @param source  input stream
+     * @param verbose verbosity flag
+     * @return result of filter's transformation as a byte stream.
      * @throws Exception if error
      */
     public InputStream getDestinationStream(Item item, InputStream source, boolean verbose)
@@ -69,12 +67,10 @@ public interface FormatFilter
      * is necessary).  Return false if bitstream should be skipped
      * for any reason.
      *
-     * 
      * @param c       context
      * @param item    item containing bitstream to process
      * @param source  source bitstream to be processed
      * @param verbose verbose mode
-     * 
      * @return true if bitstream processing should continue,
      * false if this bitstream should be skipped
      * @throws Exception if error
@@ -90,13 +86,9 @@ public interface FormatFilter
      * is necessary).  Return false if bitstream should be skipped
      * for some reason.
      *
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param generatedBitstream
-     *            the bitstream which was generated by
+     * @param c                  context
+     * @param item               item containing bitstream to process
+     * @param generatedBitstream the bitstream which was generated by
      *                           this filter.
      * @throws Exception if error
      */

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

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

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

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

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

@@ -7,50 +7,37 @@
  */
 package org.dspace.app.mediafilter;
 
-import org.dspace.content.Item;
-
 import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.InputStream;
 import java.nio.file.Files;
 
+import org.dspace.content.Item;
+
 public class ImageMagickPdfThumbnailFilter extends ImageMagickThumbnailFilter {
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-        throws Exception
-    {
+        throws Exception {
         File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
         File f2 = null;
         File f3 = null;
-	    try
-	    {
+        try {
             f2 = getImageFile(f, 0, verbose);
             f3 = getThumbnailFile(f2, verbose);
             byte[] bytes = Files.readAllBytes(f3.toPath());
             return new ByteArrayInputStream(bytes);
-	    }
-		finally
-	    {
+        } finally {
             //noinspection ResultOfMethodCallIgnored
             f.delete();
-		    if (f2 != null)
-		    {
+            if (f2 != null) {
                 //noinspection ResultOfMethodCallIgnored
                 f2.delete();
             }
-		    if (f3 != null)
-		    {
+            if (f3 != null) {
                 //noinspection ResultOfMethodCallIgnored
                 f3.delete();
             }
         }
     }
 
-   public static final String[] PDF = {"Adobe PDF"};
-   @Override
-   public String[] getInputMIMETypes()
-  {
-      return PDF;
-  }
-
 }

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

@@ -14,28 +14,25 @@ import java.io.InputStream;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
-import javax.imageio.ImageIO;
-
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
+import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.im4java.core.ConvertCmd;
 import org.im4java.core.IM4JavaException;
 import org.im4java.core.IMOperation;
+import org.im4java.core.Info;
 import org.im4java.process.ProcessStarter;
 
-import org.dspace.core.ConfigurationManager;
-
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  */
-public abstract class ImageMagickThumbnailFilter extends MediaFilter implements SelfRegisterInputFormats
-{
+public abstract class ImageMagickThumbnailFilter extends MediaFilter {
     protected static int width = 180;
     protected static int height = 120;
     private static boolean flatten = true;
@@ -44,6 +41,9 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
     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");
@@ -52,6 +52,8 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
         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;
         }
@@ -66,20 +68,16 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
     public ImageMagickThumbnailFilter() {
     }
 
-	
     @Override
-    public String getFilteredName(String oldFilename)
-    {
+    public String getFilteredName(String oldFilename) {
         return oldFilename + ".jpg";
     }
 
     /**
      * @return String bundle name
-     *  
      */
     @Override
-    public String getBundleName()
-    {
+    public String getBundleName() {
         return "THUMBNAIL";
     }
 
@@ -87,8 +85,7 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString()
-    {
+    public String getFormatString() {
         return "JPEG";
     }
 
@@ -96,8 +93,7 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
      * @return String bitstreamDescription
      */
     @Override
-    public String getDescription()
-    {
+    public String getDescription() {
         return bitstreamDescription;
     }
 
@@ -116,11 +112,13 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
         return f;
     }
 
-    public File getThumbnailFile(File f, boolean verbose) throws IOException, InterruptedException, IM4JavaException {
+    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());
@@ -131,17 +129,27 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
         return f2;
     }
 
-    public File getImageFile(File f, int page, boolean verbose) throws IOException, InterruptedException, IM4JavaException {
+    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)
-                {
+        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);
@@ -151,58 +159,44 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter implements
     }
 
     @Override
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source, boolean verbose)
-            throws Exception
-    {
+    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;
+                        if (!n.startsWith(nsrc)) {
+                            continue;
+                        }
                     }
                 }
                 String description = bit.getDescription();
-    	    	//If anything other than a generated thumbnail is found, halt processing
+                // 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.");
+                            System.out.println(description + " " + nsrc
+                                                   + " matches pattern and is replacable.");
                         }
                         continue;
                     }
                     if (description.equals(bitstreamDescription)) {
                         if (verbose) {
-        	    		    System.out.println(bitstreamDescription + " " + nsrc + " is replacable.");
+                            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. ");
+                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
     }
 
-     @Override
-     public String[] getInputMIMETypes()
-    {
-        return ImageIO.getReaderMIMETypes();
-    }
-
-    @Override
-    public String[] getInputDescriptions()
-    {
-        return null;
-    }
-
-    @Override
-    public String[] getInputExtensions()
-    {
-        return ImageIO.getReaderFileSuffixes();
-    }
 }

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

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

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

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

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

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

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

@@ -8,13 +8,27 @@
 package org.dspace.app.mediafilter;
 
 import java.io.InputStream;
-import java.util.*;
+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.*;
+import org.dspace.content.Bitstream;
+import org.dspace.content.BitstreamFormat;
+import org.dspace.content.Bundle;
 import org.dspace.content.Collection;
-import org.dspace.content.service.*;
+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;
@@ -33,8 +47,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  * scope to a community, collection or item; and -m [max] limits processing to a
  * maximum number of items.
  */
-public class MediaFilterServiceImpl implements MediaFilterService, InitializingBean
-{
+public class MediaFilterServiceImpl implements MediaFilterService, InitializingBean {
     @Autowired(required = true)
     protected AuthorizeService authorizeService;
     @Autowired(required = true)
@@ -72,14 +85,14 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     protected boolean isQuiet = false;
     protected boolean isForce = false; // default to not forced
 
-    protected MediaFilterServiceImpl()
-    {
+    protected MediaFilterServiceImpl() {
 
     }
 
     @Override
     public void afterPropertiesSet() throws Exception {
-        String[] publicPermissionFilters = configurationService.getArrayProperty("filter.org.dspace.app.mediafilter.publicPermission");
+        String[] publicPermissionFilters = configurationService
+            .getArrayProperty("filter.org.dspace.app.mediafilter.publicPermission");
 
         if (publicPermissionFilters != null) {
             for (String filter : publicPermissionFilters) {
@@ -89,10 +102,8 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     }
 
     @Override
-    public void applyFiltersAllItems(Context context) throws Exception
-    {
-        if(skipList!=null)
-        {    
+    public void applyFiltersAllItems(Context context) throws Exception {
+        if (skipList != null) {
             //if a skip-list exists, we need to filter community-by-community
             //so we can respect what is in the skip-list
             List<Community> topLevelCommunities = communityService.findAllTop(context);
@@ -100,13 +111,10 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
             for (Community topLevelCommunity : topLevelCommunities) {
                 applyFiltersCommunity(context, topLevelCommunity);
             }
-        }
-        else 
-        {
+        } else {
             //otherwise, just find every item and process
             Iterator<Item> itemIterator = itemService.findAll(context);
-            while (itemIterator.hasNext() && processed < max2Process)
-            {
+            while (itemIterator.hasNext() && processed < max2Process) {
                 applyFiltersItem(context, itemIterator.next());
             }
         }
@@ -114,10 +122,8 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public void applyFiltersCommunity(Context context, Community community)
-                                             throws Exception
-    {   //only apply filters if community not in skip-list
-        if(!inSkipList(community.getHandle()))
-        {    
+        throws Exception {   //only apply filters if community not in skip-list
+        if (!inSkipList(community.getHandle())) {
             List<Community> subcommunities = community.getSubcommunities();
             for (Community subcommunity : subcommunities) {
                 applyFiltersCommunity(context, subcommunity);
@@ -132,42 +138,36 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public void applyFiltersCollection(Context context, Collection collection)
-                                              throws Exception
-    {
+        throws Exception {
         //only apply filters if collection not in skip-list
-        if(!inSkipList(collection.getHandle()))
-        {
+        if (!inSkipList(collection.getHandle())) {
             Iterator<Item> itemIterator = itemService.findAllByCollection(context, collection);
-            while (itemIterator.hasNext() && processed < max2Process)
-            {
+            while (itemIterator.hasNext() && processed < max2Process) {
                 applyFiltersItem(context, itemIterator.next());
             }
         }
     }
 
     @Override
-    public void applyFiltersItem(Context c, Item item) throws Exception
-    {
+    public void applyFiltersItem(Context c, Item item) throws Exception {
         //only apply filters if item not in skip-list
-        if(!inSkipList(item.getHandle()))
-        {
+        if (!inSkipList(item.getHandle())) {
             //cache this item in MediaFilterManager
             //so it can be accessed by MediaFilters as necessary
             currentItem = item;
 
-          if (filterItem(c, item))
-          {
+            if (filterItem(c, item)) {
                 // increment processed count
                 ++processed;
             }
             // clear item objects from context cache and internal cache
+            c.uncacheEntity(currentItem);
             currentItem = null;
         }
     }
 
     @Override
-    public boolean filterItem(Context context, Item myItem) throws Exception
-    {
+    public boolean filterItem(Context context, Item myItem) throws Exception {
         // get 'original' bundles
         List<Bundle> myBundles = itemService.getBundles(myItem, "ORIGINAL");
         boolean done = false;
@@ -184,8 +184,7 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public boolean filterBitstream(Context context, Item myItem,
-            Bitstream myBitstream) throws Exception
-    {
+                                   Bitstream myBitstream) throws Exception {
         boolean filtered = false;
 
         // iterate through filter classes. A single format may be actioned
@@ -300,11 +299,9 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
     @Override
     public boolean processBitstream(Context context, Item item, Bitstream source, FormatFilter formatFilter)
-            throws Exception
-    {
+        throws Exception {
         //do pre-processing of this bitstream, and if it fails, skip this bitstream!
-    	if(!formatFilter.preProcessBitstream(context, item, source, isVerbose))
-        {
+        if (!formatFilter.preProcessBitstream(context, item, source, isVerbose)) {
             return false;
         }
 
@@ -319,14 +316,13 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
         List<Bundle> bundles = itemService.getBundles(item, formatFilter.getBundleName());
 
         // check if destination bitstream exists
-        if (bundles.size() > 0)
-        {
+        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().equals(newName)) {
+                    if (bitstream.getName().trim().equals(newName.trim())) {
                         targetBundle = bundle;
                         existingBitstream = bitstream;
                     }
@@ -335,10 +331,8 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
         }
 
         // if exists and overwrite = false, exit
-        if (!overWrite && (existingBitstream != null))
-        {
-            if (!isQuiet)
-            {
+        if (!overWrite && (existingBitstream != null)) {
+            if (!isQuiet) {
                 System.out.println("SKIPPED: bitstream " + source.getID()
                                        + " (item: " + item.getHandle() + ") because '" + newName + "' already exists");
             }
@@ -369,12 +363,9 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
         }
 
         // create new bundle if needed
-        if (bundles.size() < 1)
-        {
+        if (bundles.size() < 1) {
             targetBundle = bundleService.create(context, item, formatFilter.getBundleName());
-        }
-        else
-        {
+        } else {
             // take the first match
             targetBundle = bundles.get(0);
         }
@@ -409,13 +400,11 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
 
         // fixme - set date?
         // we are overwriting, so remove old bitstream
-        if (existingBitstream != null)
-        {
+        if (existingBitstream != null) {
             bundleService.removeBitstream(context, targetBundle, existingBitstream);
         }
 
-        if (!isQuiet)
-        {
+        if (!isQuiet) {
             System.out.println("FILTERED: bitstream " + source.getID()
                                    + " (item: " + item.getHandle() + ") and created '" + newName + "'");
         }
@@ -427,24 +416,18 @@ public class MediaFilterServiceImpl implements MediaFilterService, InitializingB
     }
 
     @Override
-    public Item getCurrentItem()
-    {
+    public Item getCurrentItem() {
         return currentItem;
     }
 
     @Override
-    public boolean inSkipList(String identifier)
-    {
-        if(skipList!=null && skipList.contains(identifier))
-        {
-            if (!isQuiet)
-            {
+    public boolean inSkipList(String identifier) {
+        if (skipList != null && skipList.contains(identifier)) {
+            if (!isQuiet) {
                 System.out.println("SKIP-LIST: skipped bitstreams within identifier " + identifier);
             }
             return true;
-        }    
-        else
-        {
+        } else {
             return false;
         }
     }

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

@@ -7,18 +7,14 @@
  */
 package org.dspace.app.mediafilter;
 
-import java.awt.image.*;
+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;
 
-import org.dspace.app.mediafilter.JPEGFilter;
-
 /**
  * Create JPEG thumbnails from PDF cover page using PDFBox.
  * Based on JPEGFilter:
@@ -29,21 +25,17 @@ import org.dspace.app.mediafilter.JPEGFilter;
  * @author Ivan Masár helix84@centrum.sk
  * @author Jason Sherman jsherman@usao.edu
  */
-public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFormats
-{
+public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFormats {
     @Override
-    public String getFilteredName(String oldFilename)
-    {
+    public String getFilteredName(String oldFilename) {
         return oldFilename + ".jpg";
     }
 
     /**
      * @return String bundle name
-     *  
      */
     @Override
-    public String getBundleName()
-    {
+    public String getBundleName() {
         return "THUMBNAIL";
     }
 
@@ -51,8 +43,7 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @return String bitstreamformat
      */
     @Override
-    public String getFormatString()
-    {
+    public String getFormatString() {
         return "JPEG";
     }
 
@@ -60,8 +51,7 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @return String description
      */
     @Override
-    public String getDescription()
-    {
+    public String getDescription() {
         return "Generated Thumbnail";
     }
 
@@ -69,14 +59,12 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
      * @param currentItem item
      * @param source      source input stream
      * @param verbose     verbose mode
-     * 
      * @return InputStream the resulting input stream
      * @throws Exception if error
      */
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
-            throws Exception
-    {
+        throws Exception {
         PDDocument doc = PDDocument.load(source);
         PDFRenderer renderer = new PDFRenderer(doc);
         BufferedImage buf = renderer.renderImage(0);
@@ -88,20 +76,17 @@ public class PDFBoxThumbnail extends MediaFilter implements SelfRegisterInputFor
     }
 
     @Override
-    public String[] getInputMIMETypes()
-    {
+    public String[] getInputMIMETypes() {
         return ImageIO.getReaderMIMETypes();
     }
 
     @Override
-    public String[] getInputDescriptions()
-    {
+    public String[] getInputDescriptions() {
         return null;
     }
 
     @Override
-    public String[] getInputExtensions()
-    {
+    public String[] getInputExtensions() {
         // Temporarily disabled as JDK 1.6 only
         // return ImageIO.getReaderFileSuffixes();
         return null;

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

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

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

@@ -0,0 +1,71 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.mediafilter;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+
+import org.apache.poi.POITextExtractor;
+import org.apache.poi.extractor.ExtractorFactory;
+import org.apache.poi.openxml4j.exceptions.OpenXML4JException;
+import org.apache.xmlbeans.XmlException;
+import org.dspace.content.Item;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+/**
+ * Extract flat text from Microsoft Word documents (.doc, .docx).
+ */
+public class PoiWordFilter
+    extends MediaFilter {
+    private static final Logger LOG = LoggerFactory.getLogger(PoiWordFilter.class);
+
+    @Override
+    public String getFilteredName(String oldFilename) {
+        return oldFilename + ".txt";
+    }
+
+    @Override
+    public String getBundleName() {
+        return "TEXT";
+    }
+
+    @Override
+    public String getFormatString() {
+        return "Text";
+    }
+
+    @Override
+    public String getDescription() {
+        return "Extracted text";
+    }
+
+    @Override
+    public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
+        throws Exception {
+        String text;
+        try {
+            // get input stream from bitstream, pass to filter, get string back
+            POITextExtractor extractor = ExtractorFactory.createExtractor(source);
+            text = extractor.getText();
+        } catch (IOException | OpenXML4JException | XmlException e) {
+            System.err.format("Invalid File Format:  %s%n", e.getMessage());
+            LOG.error("Unable to parse the bitstream:  ", e);
+            throw e;
+        }
+
+        // if verbose flag is set, print out extracted text to STDOUT
+        if (verbose) {
+            System.out.println(text);
+        }
+
+        // return the extracted text as a stream.
+        return new ByteArrayInputStream(text.getBytes());
+    }
+}

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

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

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

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

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

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

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

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

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

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

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

@@ -7,6 +7,9 @@
  */
 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;
@@ -14,9 +17,6 @@ import org.dspace.content.Community;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 
-import java.util.List;
-import java.util.Map;
-
 /**
  * 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
@@ -79,17 +79,13 @@ public interface MediaFilterService {
      * 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
-     * @throws Exception if error occurs
+     * @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;
@@ -109,9 +105,7 @@ public interface MediaFilterService {
     /**
      * Check whether or not to skip processing the given identifier.
      *
-     * @param identifier
-     *            identifier (handle) of a community, collection or item
-     *
+     * @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.
      */

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

@@ -25,8 +25,8 @@ 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.PackageParameters;
 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;
@@ -51,7 +51,8 @@ import org.dspace.workflow.WorkflowException;
  * (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)
+ *  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}
@@ -71,7 +72,8 @@ import org.dspace.workflow.WorkflowException;
  *
  *  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)
+ *       -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} ..]]
@@ -81,14 +83,19 @@ import org.dspace.workflow.WorkflowException;
  *                  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
+ *                  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
+ *   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:
@@ -113,23 +120,20 @@ import org.dspace.workflow.WorkflowException;
  * @author Tim Donohue
  * @version $Revision$
  */
-public class Packager
-{
+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)
-    {
+    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
-    {
+    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)");
@@ -141,9 +145,16 @@ public class Packager
                 "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("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,
@@ -153,9 +164,16 @@ public class Packager
         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.");
+        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);
@@ -170,15 +188,13 @@ public class Packager
         //initialize a new packager -- we'll add all our current params as settings
         Packager myPackager = new Packager();
 
-        if (line.hasOption('h'))
-        {
+        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'))
-            {
+            if (line.hasOption('t')) {
                 System.out.println("\n--------------------------------------------------------------");
                 System.out.println("Additional options for the " + line.getOptionValue('t') + " packager:");
                 System.out.println("--------------------------------------------------------------");
@@ -187,44 +203,36 @@ public class Packager
                 PackageIngester sip = (PackageIngester) pluginService
                     .getNamedPlugin(PackageIngester.class, line.getOptionValue('t'));
 
-                if (sip != null)
-                {
+                if (sip != null) {
                     System.out.println("\n\n" + line.getOptionValue('t') + " Submission (SIP) plugin options:\n");
                     System.out.println(sip.getParameterHelp());
-                }
-                else
-                {
+                } 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)
-                {
+                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 {
+                    System.out
+                        .println("\nNo valid Dissemination plugin found for " + line.getOptionValue('t') + " type.");
                 }
 
-            }
-            else  //otherwise, display list of valid packager types
-            {
+            } 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)
-                {
+                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)
-                {
+                for (int i = 0; i < pn.length; ++i) {
                     System.out.println("  " + pn[i]);
                 }
             }
@@ -232,74 +240,56 @@ public class Packager
         }
 
         //look for flag to disable all user interaction
-        if(line.hasOption('u'))
-        {
+        if (line.hasOption('u')) {
             myPackager.userInteractionEnabled = false;
         }
-        if (line.hasOption('w'))
-        {
+        if (line.hasOption('w')) {
             pkgParams.setWorkflowEnabled(false);
         }
-        if (line.hasOption('r'))
-        {
+        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())
-        {
+        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())
-        {
+        if (line.hasOption('f') && pkgParams.restoreModeEnabled()) {
             pkgParams.setReplaceModeEnabled(true);
         }
-        if (line.hasOption('e'))
-        {
+        if (line.hasOption('e')) {
             eperson = line.getOptionValue('e');
         }
-        if (line.hasOption('p'))
-        {
+        if (line.hasOption('p')) {
             parents = line.getOptionValues('p');
         }
-        if (line.hasOption('t'))
-        {
+        if (line.hasOption('t')) {
             myPackager.packageType = line.getOptionValue('t');
         }
-        if (line.hasOption('i'))
-        {
+        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
+        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)
-        {
+        if (files.length > 0) {
             sourceFile = files[0];
         }
-        if (line.hasOption('d'))
-        {
+        if (line.hasOption('d')) {
             myPackager.submit = false;
         }
-        if (line.hasOption('o'))
-        {
+        if (line.hasOption('o')) {
             String popt[] = line.getOptionValues('o');
-            for (int i = 0; i < popt.length; ++i)
-            {
+            for (int i = 0; i < popt.length; ++i) {
                 String pair[] = popt[i].split("\\=", 2);
-                if (pair.length == 2)
-                {
+                if (pair.length == 2) {
                     pkgParams.addProperty(pair[0].trim(), pair[1].trim());
-                }
-                else if (pair.length == 1)
-                {
+                } else if (pair.length == 1) {
                     pkgParams.addProperty(pair[0].trim(), "");
-                }
-                else
-                {
+                } else {
                     System.err
                         .println("Warning: Illegal package option format: \""
                                      + popt[i] + "\"");
@@ -309,8 +299,7 @@ public class Packager
 
         // Sanity checks on arg list: required args
         // REQUIRED: sourceFile, ePerson (-e), packageType (-t)
-        if (sourceFile == null || eperson == null || myPackager.packageType == null)
-        {
+        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);
@@ -321,67 +310,60 @@ public class Packager
         Context context = new Context();
         EPerson myEPerson = null;
         myEPerson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(context, eperson);
-        if (myEPerson == null)
-        {
+        if (myEPerson == null) {
             usageError("Error, eperson cannot be found: " + eperson);
         }
         context.setCurrentUser(myEPerson);
 
 
         //If we are in REPLACE mode
-        if(pkgParams.replaceModeEnabled())
-        {
+        if (pkgParams.replaceModeEnabled()) {
+            context.setMode(Context.Mode.BATCH_EDIT);
             PackageIngester sip = (PackageIngester) pluginService
                 .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null)
-            {
+            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)
-                {
+            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)
-            {
+            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.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
-            {
+            } else {
                 //user interaction disabled -- default answer to 'yes', otherwise script won't continue
                 choiceString = "y";
             }
 
-            if (choiceString.equalsIgnoreCase("y"))
-            {
+            if (choiceString.equalsIgnoreCase("y")) {
                 System.out.println("Beginning replacement process...");
 
-                try
-                {
+                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)
-                {
+                } catch (Exception e) {
                     // abort all operations
                     e.printStackTrace();
                     context.abort();
@@ -390,31 +372,27 @@ public class Packager
                 }
             }
 
-        }
+        } else if (myPackager.submit || pkgParams.restoreModeEnabled()) {
             //else if normal SUBMIT mode (or basic RESTORE mode -- which is a special type of submission)
-        else if (myPackager.submit || pkgParams.restoreModeEnabled())
-        {
+            context.setMode(Context.Mode.BATCH_EDIT);
+
             PackageIngester sip = (PackageIngester) pluginService
                 .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null)
-            {
+            if (sip == null) {
                 usageError("Error, Unknown package type: " + myPackager.packageType);
             }
 
             // validate each parent arg (if any)
             DSpaceObject parentObjs[] = null;
-            if(parents!=null)
-            {
+            if (parents != null) {
                 System.out.println("Destination parents:");
 
                 parentObjs = new DSpaceObject[parents.length];
-                for (int i = 0; i < parents.length; i++)
-                {
+                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)
-                    {
+                    if (parentObjs[i] == null) {
                         throw new IllegalArgumentException(
                             "Bad parent list -- "
                                 + "Cannot resolve parent handle \""
@@ -425,37 +403,34 @@ public class Packager
                 }
             }
 
-            try
-            {
+            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)
-            {
+            } catch (Exception e) {
                 // abort all operations
                 e.printStackTrace();
                 context.abort();
                 System.out.println(e);
                 System.exit(1);
             }
-        }// else, if DISSEMINATE mode
-        else
-        {
+        } 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)
-            {
+            if (dip == null) {
                 usageError("Error, Unknown package type: " + myPackager.packageType);
             }
 
-            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, identifier);
-            if (dso == null)
-            {
+            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
+                                                   .resolveToObject(context, identifier);
+            if (dso == null) {
                 throw new IllegalArgumentException("Bad identifier/handle -- "
                                                        + "Cannot resolve handle \"" + identifier + "\"");
             }
@@ -485,14 +460,14 @@ public class Packager
      * @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
-    {
+    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())
-        {
+        if (!pkgFile.exists()) {
             System.out.println("\nERROR: Package located at " + sourceFile + " does not exist!");
             System.exit(1);
         }
@@ -501,55 +476,67 @@ public class Packager
 
         //find first parent (if specified) -- this will be the "owner" of the object
         DSpaceObject parent = null;
-        if(parentObjs!=null && parentObjs.length>0)
-        {
+        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
-        {
+        try {
             //If we are doing a recursive ingest, call ingestAll()
-            if(pkgParams.recursiveModeEnabled())
-            {
+            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.");
+                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)
-                {
+                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)
-                    {
+                    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
-                    {
+                    } 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"))
-                    {
+                    if (choiceString.equalsIgnoreCase("y")) {
                         System.out.println("\n\n");
-                        for (String result : hdlResults)
-                        {
-                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, result);
+                        for (String result : hdlResults) {
+                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
+                                                                   .resolveToObject(context, result);
 
-                            if(dso!=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() + " ] ");
+                                }
+                            }
+                        }
+                    }
+                }
+
+            } 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() + " ] ");
@@ -558,51 +545,23 @@ public class Packager
                                                    " [ 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)
-                {
+                } 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)
-                    {
+                    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)
-        {
+        } catch (WorkflowException e) {
             throw new PackageException(e);
         }
     }
@@ -627,8 +586,8 @@ public class Packager
     protected void disseminate(Context context, PackageDisseminator dip,
                                DSpaceObject dso, PackageParameters pkgParams,
                                String outputFile)
-            throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException, PackageException
-    {
+        throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException,
+        PackageException {
         // initialize output file
         File pkgFile = new File(outputFile);
 
@@ -636,59 +595,49 @@ public class Packager
                                " [ hdl=" + dso.getHandle() + " ] to " + outputFile);
 
         //If we are doing a recursive dissemination of this object & all its child objects, call disseminateAll()
-        if(pkgParams.recursiveModeEnabled())
-        {
+        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.");
+            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)
-            {
+            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)
-                {
+                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
-                {
+                } 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"))
-                {
+                if (choiceString.equalsIgnoreCase("y")) {
                     System.out.println("\n\n");
-                    for(File result : fileResults)
-                    {
+                    for (File result : fileResults) {
                         System.out.println("CREATED package file: " + result.getCanonicalPath());
                     }
                 }
             }
-        }
-        else
-        {
+        } else {
             //otherwise, just disseminate a single object to a single package file
             dip.disseminate(context, dso, pkgParams, pkgFile);
 
-            if(pkgFile!=null && pkgFile.exists())
-            {
+            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.
@@ -706,34 +655,32 @@ public class Packager
      * @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
-    {
+    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())
-        {
+        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)
-        {
+        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
-        {
+        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)
+            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) {
@@ -742,29 +689,24 @@ public class Packager
 
                     String choiceString = null;
                     //Ask if user wants full list printed to command line, as this may be rather long.
-                    if (this.userInteractionEnabled)
-                    {
+                    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
-                    {
+                    } 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"))
-                    {
+                    if (choiceString.equalsIgnoreCase("y")) {
                         System.out.println("\n\n");
-                        for (String result : hdlResults)
-                        {
-                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, result);
+                        for (String result : hdlResults) {
+                            DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService()
+                                                                   .resolveToObject(context, result);
 
-                            if (dso != null)
-                            {
+                            if (dso != null) {
                                 System.out.println("REPLACED DSpace " + Constants.typeText[dso.getType()] +
                                                        " [ hdl=" + dso.getHandle() + " ] ");
                             }
@@ -773,21 +715,16 @@ public class Packager
 
 
                 }
-            }
-            else
-            {
+            } else {
                 //otherwise, just one object to replace
                 DSpaceObject dso = sip.replace(context, objToReplace, pkgFile, pkgParams);
 
-                if (dso != null)
-                {
+                if (dso != null) {
                     System.out.println("REPLACED DSpace " + Constants.typeText[dso.getType()] +
                                            " [ hdl=" + dso.getHandle() + " ] ");
                 }
             }
-        }
-        catch (WorkflowException e)
-        {
+        } catch (WorkflowException e) {
             throw new PackageException(e);
         }
     }

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItem.java

@@ -7,14 +7,25 @@
  */
 package org.dspace.app.requestitem;
 
+import java.util.Date;
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.persistence.SequenceGenerator;
+import javax.persistence.Table;
+import javax.persistence.Temporal;
+import javax.persistence.TemporalType;
+
 import org.dspace.content.Bitstream;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.core.ReloadableEntity;
 
-import javax.persistence.*;
-import java.util.Date;
-
 /**
  * Object representing an Item Request
  */
@@ -71,10 +82,10 @@ public class RequestItem implements ReloadableEntity<Integer> {
 
     /**
      * Protected constructor, create object using:
-     * {@link org.dspace.app.requestitem.service.RequestItemService#createRequest(Context, Bitstream, Item, boolean, String, String, String)}
+     * {@link org.dspace.app.requestitem.service.RequestItemService#createRequest(Context, Bitstream, Item,
+     * boolean, String, String, String)}
      */
-    protected RequestItem()
-    {
+    protected RequestItem() {
     }
 
     public Integer getID() {

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemAuthor.java

@@ -14,7 +14,6 @@ import org.dspace.eperson.EPerson;
  * Copy feature
  *
  * @author Andrea Bollini
- * 
  */
 public class RequestItemAuthor {
     private String fullName;

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemAuthorExtractor.java

@@ -17,7 +17,6 @@ import org.dspace.core.Context;
  * request copy
  *
  * @author Andrea Bollini
- * 
  */
 public interface RequestItemAuthorExtractor {
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item)

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemHelpdeskStrategy.java

@@ -7,6 +7,8 @@
  */
 package org.dspace.app.requestitem;
 
+import java.sql.SQLException;
+
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.content.Item;
@@ -17,13 +19,12 @@ import org.dspace.eperson.EPerson;
 import org.dspace.eperson.service.EPersonService;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import java.sql.SQLException;
-
 /**
  * RequestItem strategy to allow DSpace support team's helpdesk to receive requestItem request
  * With this enabled, then the Item author/submitter doesn't receive the request, but the helpdesk instead does.
  *
- * Failover to the RequestItemSubmitterStrategy, which means the submitter would get the request if there is no specified helpdesk email.
+ * Failover to the RequestItemSubmitterStrategy, which means the submitter would get the request if there is no
+ * specified helpdesk email.
  *
  * @author Sam Ottenhoff
  * @author Peter Dietz
@@ -35,11 +36,13 @@ public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
     @Autowired(required = true)
     protected EPersonService ePersonService;
 
-    public RequestItemHelpdeskStrategy() {}
+    public RequestItemHelpdeskStrategy() {
+    }
 
     @Override
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item) throws SQLException {
-        boolean helpdeskOverridesSubmitter = ConfigurationManager.getBooleanProperty("request.item.helpdesk.override", false);
+        boolean helpdeskOverridesSubmitter = ConfigurationManager
+            .getBooleanProperty("request.item.helpdesk.override", false);
         String helpDeskEmail = ConfigurationManager.getProperty("mail.helpdesk");
 
         if (helpdeskOverridesSubmitter && StringUtils.isNotBlank(helpDeskEmail)) {
@@ -54,6 +57,7 @@ public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
      * Return a RequestItemAuthor object for the specified helpdesk email address.
      * It makes an attempt to find if there is a matching eperson for the helpdesk address, to use the name,
      * Otherwise it falls back to a helpdeskname key in the Messages.props.
+     *
      * @param context       context
      * @param helpDeskEmail email
      * @return RequestItemAuthor

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemMetadataStrategy.java

@@ -11,8 +11,8 @@ import java.sql.SQLException;
 import java.util.List;
 
 import org.apache.commons.lang.StringUtils;
-import org.dspace.content.MetadataValue;
 import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
@@ -23,7 +23,6 @@ import org.springframework.beans.factory.annotation.Autowired;
  * Failover to the RequestItemSubmitterStrategy
  *
  * @author Andrea Bollini
- * 
  */
 public class RequestItemMetadataStrategy extends RequestItemSubmitterStrategy {
 
@@ -39,24 +38,19 @@ public class RequestItemMetadataStrategy extends RequestItemSubmitterStrategy {
     @Override
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item)
         throws SQLException {
-		if (emailMetadata != null)
-		{
+        if (emailMetadata != null) {
             List<MetadataValue> vals = itemService.getMetadataByMetadataString(item, emailMetadata);
-			if (vals.size() > 0)
-			{
+            if (vals.size() > 0) {
                 String email = vals.iterator().next().getValue();
                 String fullname = null;
-				if (fullNameMetadata != null)
-				{
+                if (fullNameMetadata != null) {
                     List<MetadataValue> nameVals = itemService.getMetadataByMetadataString(item, fullNameMetadata);
-					if (nameVals.size() > 0)
-					{
+                    if (nameVals.size() > 0) {
                         fullname = nameVals.iterator().next().getValue();
                     }
                 }
 
-				if (StringUtils.isBlank(fullname))
-				{
+                if (StringUtils.isBlank(fullname)) {
                     fullname = I18nUtil
                         .getMessage(
                             "org.dspace.app.requestitem.RequestItemMetadataStrategy.unnamed",

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemServiceImpl.java

@@ -7,6 +7,9 @@
  */
 package org.dspace.app.requestitem;
 
+import java.sql.SQLException;
+import java.util.Date;
+
 import org.apache.log4j.Logger;
 import org.dspace.app.requestitem.dao.RequestItemDAO;
 import org.dspace.app.requestitem.service.RequestItemService;
@@ -16,9 +19,6 @@ import org.dspace.core.Context;
 import org.dspace.core.Utils;
 import org.springframework.beans.factory.annotation.Autowired;
 
-import java.sql.SQLException;
-import java.util.Date;
-
 /**
  * Service implementation for the RequestItem object.
  * This class is responsible for all business logic calls for the RequestItem object and is autowired by spring.
@@ -33,13 +33,13 @@ public class RequestItemServiceImpl implements RequestItemService {
     @Autowired(required = true)
     protected RequestItemDAO requestItemDAO;
 
-    protected RequestItemServiceImpl()
-    {
+    protected RequestItemServiceImpl() {
 
     }
 
     @Override
-    public String createRequest(Context context, Bitstream bitstream, Item item, boolean allFiles, String reqEmail, String reqName, String reqMessage) throws SQLException {
+    public String createRequest(Context context, Bitstream bitstream, Item item, boolean allFiles, String reqEmail,
+                                String reqName, String reqMessage) throws SQLException {
         RequestItem requestItem = requestItemDAO.create(context, new RequestItem());
 
         requestItem.setToken(Utils.generateHexKey());
@@ -53,8 +53,7 @@ public class RequestItemServiceImpl implements RequestItemService {
 
         requestItemDAO.save(context, requestItem);
 
-        if (log.isDebugEnabled())
-        {
+        if (log.isDebugEnabled()) {
             log.debug("Created requestitem_token " + requestItem.getID()
                           + " with token " + requestItem.getToken() + "\"");
         }

dspace-api/src/main/java/org/dspace/app/requestitem/RequestItemSubmitterStrategy.java

@@ -17,7 +17,6 @@ import org.dspace.eperson.EPerson;
  * Basic strategy that looks to the original submitter.
  *
  * @author Andrea Bollini
- *
  */
 public class RequestItemSubmitterStrategy implements RequestItemAuthorExtractor {
 

dspace-api/src/main/java/org/dspace/app/requestitem/dao/RequestItemDAO.java

@@ -7,15 +7,16 @@
  */
 package org.dspace.app.requestitem.dao;
 
+import java.sql.SQLException;
+
 import org.dspace.app.requestitem.RequestItem;
 import org.dspace.core.Context;
 import org.dspace.core.GenericDAO;
 
-import java.sql.SQLException;
-
 /**
  * Database Access Object interface class for the RequestItem object.
- * The implementation of this class is responsible for all database calls for the RequestItem object and is autowired by spring
+ * The implementation of this class is responsible for all database calls for the RequestItem object and is autowired
+ * by spring
  * This class should only be accessed from a single service and should never be exposed outside of the API
  *
  * @author kevinvandevelde at atmire.com