New location for DSpace Project

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

.gitattributes

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

.gitignore

@@ -1,27 +0,0 @@
-## Ignore the MVN compiled output directories from version tracking
-target/
-
-## Ignore project files created by Eclipse
-.settings/
-.project
-.classpath
-
-## Ignore project files created by IntelliJ IDEA
-*.iml
-*.ipr
-*.iws
-.idea/
-
-## Ignore project files created by NetBeans
-nbproject/private/
-build/
-nbbuild/
-dist/
-nbdist/
-nbactions.xml
-nb-configuration.xml
-META-INF/
-
-## Ignore all *.properties file, EXCEPT build.properties (the default)
-*.properties
-!build.properties

LICENSE

@@ -1,40 +0,0 @@
-DSpace source code license:
-
-
-Copyright (c) 2002-2012, DuraSpace.  All rights reserved.
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are
-met:
-
-- Redistributions of source code must retain the above copyright
-notice, this list of conditions and the following disclaimer.
-
-- Redistributions in binary form must reproduce the above copyright
-notice, this list of conditions and the following disclaimer in the
-documentation and/or other materials provided with the distribution.
-
-- Neither the name DuraSpace nor the name of the DSpace Foundation
-nor the names of its contributors may be used to endorse or promote
-products derived from this software without specific prior written
-permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
-``AS IS'' AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
-LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
-A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
-HOLDERS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
-INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
-BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS
-OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
-ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR
-TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE
-USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
-DAMAGE.
-
-
-DSpace uses third-party libraries which may be distributed under
-different licenses to the above. Information about these licenses 
-is detailed in the LICENSES_THIRD_PARTY file at the root of the source 
-tree.  You must agree to the terms of these licenses, in addition to 
-the above DSpace source code license, in order to use this software.

LICENSES_THIRD_PARTY

@@ -1,144 +0,0 @@
-DSpace uses third-party libraries which may be distributed under different 
-licenses. We have attempted to list all of these third party libraries and 
-their licenses below (however the most up-to-date information can be found
-via Maven, see NOTE #2 at bottom of this page). 
-
-You must agree to the terms of these licenses, in addition to the DSpace 
-source code license, in order to use this software.
-
---------------------------------------------------
-Third party Java libraries listed by License type
-[Format: Name (Maven Project) - URL]
---------------------------------------------------
-
-Apache Software License, Version 2.0 (http://opensource.org/licenses/apache2.0)
-  * Ant-Contrib Tasks (ant-contrib:*) - http://ant-contrib.sourceforge.net/
-  * Apache Abdera (org.apache.abdera::*) - http://projects.apache.org/projects/abdera.html
-  * Apache Ant (org.apache.ant:*) - http://ant.apache.org/
-  * Apache Axis (axis:*) - http://axis.apache.org/axis/
-  * Apache Cocoon (org.apache.cocoon:*) - http://cocoon.apache.org/2.2/license.html
-  * Apache Commons BeanUtils (commons-beanutils:*) - http://commons.apache.org/beanutils/
-  * Apache Commons CLI (commons-cli:*) - http://commons.apache.org/cli/license.html
-  * Apache Commons Codec (commons-codec:*) - http://commons.apache.org/codec/license.html
-  * Apache Commons Collections (commons-collections:*) - http://commons.apache.org/collections/license.html
-  * Apache Commons Configuration (commons-configuration:*) - http://commons.apache.org/configuration/license.html
-  * Apache Commons DBCP (commons-dbcp:*) - http://commons.apache.org/dbcp/license.html
-  * Apache Commons Digester (commons-digester:*) - http://commons.apache.org/digester/
-  * Apache Commons Discovery (commons-discovery:*) - http://commons.apache.org/discovery/license.html
-  * Apache Commons FileUpload (commons-fileupload:*) - http://commons.apache.org/fileupload/license.html
-  * Apache Commons HTTP Client (commons-httpclient:*) - http://commons.apache.org/httpclient/license.html
-  * Apache Commons IO (commons-io:*) - http://commons.apache.org/io/license.html
-  * Apache Commons JXPath (commons-jxpath:*) - http://commons.apache.org/jxpath/license.html
-  * Apache Commons Lang (commons-lang:*) - http://commons.apache.org/lang/license.html
-  * Apache Commons Logging (commons-logging:*) - http://commons.apache.org/logging/license.html
-  * Apache Commons Pool (commons-pool:*) - http://commons.apache.org/pool/license.html
-  * Apache Commons Validator (commons-validator:*) - http://commons.apache.org/validator/license.html
-  * Apache Geronimo (org.apache.geronimo.specs:*) - http://geronimo.apache.org/
-  * Apache HTTPComponents (org.apache.httpcomponents:*) - http://hc.apache.org/
-  * Apache Jakarta ORO (oro:*) - http://svn.apache.org/repos/asf/jakarta/oro/trunk/LICENSE
-  * Apache Jakarta Regexp (jakarta-regexp:*) - http://jakarta.apache.org/regexp/
-  * Apache JaxMe (jaxme:jaxme-api) - http://ws.apache.org/old/jaxme-old/license.html
-  * Apache Jena (com.hp.hpl.jena:*) - http://jena.apache.org/
-  * Apache log4j (log4j:*) : http://logging.apache.org/log4j/
-  * Apache Lucene (org.apache.lucene:*) - http://lucene.apache.org/
-  * Apache PDFBox (org.apache.pdfbox:*) - http://pdfbox.apache.org/
-  * Apache POI (org.apache.poi:*) - http://poi.apache.org/
-  * Apache Solr (org.apache.solr:*) - http://lucene.apache.org/solr/
-  * Apache Xerces (xerces:*) - http://xerces.apache.org/
-  * Apache XML Commons (xml-apis:*) - http://xerces.apache.org/xml-commons/licenses.html
-  * Apache XML Project (xalan:*) - http://xml.apache.org/xalan-j/#license
-  * Apache XMLBeans (org.apache.xmlbeans:*) - http://xmlbeans.apache.org/
-  * Apache ZooKeeper (org.apache.zookeeper:*) - http://zookeeper.apache.org/
-  * Databene ContiPerf (org.databene:contiperf) - http://databene.org/contiperf
-  * Ehcache (net.sf.ehcache:*) - http://ehcache.org/about/license
-  * ElasticSearch (org.elasticsearch:*) - http://www.elasticsearch.org/
-  * flexjson (net.sf.flexjson:*) - http://sourceforge.net/projects/flexjson/
-  * Google GSON (com.google.code.gson:*) - http://code.google.com/p/google-gson/
-  * Google Guava (com.google.guava:*) - http://code.google.com/p/guava-libraries/
-  * Jetty (org.mortbay.jetty:*) - http://jetty.codehaus.org/jetty/license.html
-  * Lyncode XOAI (com.lyncode:xoai) - http://www.lyncode.com/
-  * OpenCSV (net.sf.opencsv:*) - http://opencsv.sourceforge.net/
-  * Rome (net.java.dev.rome:*, org.rometools:*, rome:*) - http://rometools.org/
-  * Spring Framework  (org.springframework:*) - http://www.springsource.org/spring-framework
-  * SWORD Libraries (org.swordapp:*) - http://mvnrepository.com/artifact/org.swordapp/server/2.0
-  * Woodstox (org.codehaus.woodstox:*) - http://woodstox.codehaus.org/Download
-
-BSD License (http://www.opensource.org/licenses/BSD-3-Clause)
-  * Biblio Transformation Engine (gr.ekt:biblio-transformation-engine) - http://code.google.com/p/biblio-transformation-engine/
-  * DNSJava (org.dspace.dnsjava:dnsjava)- http://www.xbill.org/dnsjava/dnsjava-current/README
-  * dom4j (dom4j:*, maven:dom4j) - http://dom4j.sourceforge.net/dom4j-1.6.1/license.html
-  * Foresite Toolkit (com.googlecode.foresite-toolkit:*) - http://code.google.com/p/foresite-toolkit/
-  * Java BibTeX Parser (org.jbibtex:*) - https://code.google.com/p/java-bibtex/
-  * Jaxen (jaxen:*) -  http://jaxen.codehaus.org/license.html
-  * JLine (jline:*) - http://jline.sourceforge.net/
-  * JUnitPerf (junitperf:*) - http://www.clarkware.com/software/JUnitPerf.html#license
-  * MSV (msv:*) - http://msv.java.net/
-  * StAX (Streaming API for XML) (stax:*) - http://stax.codehaus.org/
-  * XMLUnit (xmlunit:*) - http://xmlunit.sourceforge.net/
-  * YUI (com.yahoo.platform.yui:*) - http://yuilibrary.com/license/
-  
-Common Development and Distribution License (CDDL) v1.0 (http://www.opensource.org/licenses/CDDL-1.0)
-  * JavaBeans Activation Framework (javax.activation:*) - http://www.opensource.org/licenses/CDDL-1.0  
-  * Java Mail (javax.mail:*) - http://www.opensource.org/licenses/CDDL-1.0
-  * JAX-RPC (javax.xml:jaxrpc-api) - http://java.net/projects/jax-rpc/
-  * JAXB (com.sun.xml.bind:jaxb-impl) - http://jaxb.java.net/
-  
-Common Public License v1.0 (http://www.opensource.org/licenses/cpl1.0)
-  * JUnit (junit:*) - http://junit.org/license   
-  * WSDL4J (wsdl4j:*) - http://sourceforge.net/projects/wsdl4j/
-  
-Lesser GPL (http://www.opensource.org/licenses/LGPL-2.1)
-  * JExcelAPI (net.sourceforge.jexcelapi:*) - http://sourceforge.net/projects/jexcelapi/
-  * MaxMind GeoIP (org.dspace.dependencies:dspace-geoip) - http://geoip.cvs.sourceforge.net/viewvc/geoip/java/LICENSE
-  * Text-mining (org.dspace.dependencies:dspace-tm-extractors) - http://code.google.com/p/text-mining/
-  * XOM (xom:*) - http://www.xom.nu/
-
-MIT / X11 License (or adaptations) (http://www.opensource.org/licenses/MIT)
-  * Bouncy Castle (org.bouncycastle:*) - http://www.bouncycastle.org/licence.html
-  * jmockit (org.dspace.dependencies.jmockit:dspace-jmockit) - http://code.google.com/p/jmockit/
-  * SLF4J (org.slf4j:*) - http://www.slf4j.org/license.html
-  
-Mozilla Public License (http://www.opensource.org/licenses/MPL-2.0)
-  * H2 database (com.h2database:*) - http://www.h2database.com/html/license.html
-  
-Other Open Source Licenses:
-  * AOP Alliance (aopalliance:*) - Public Domain: http://aopalliance.sourceforge.net/
-  * ICU4J (com.ibm.icu:icu4j) - ICU License : http://source.icu-project.org/repos/icu/icu/trunk/license.html
-  * JDOM  (jdom:*) - JDOM License : https://github.com/hunterhacker/jdom/blob/master/LICENSE.txt
-  * PostgreSQL (postgresql:*) - PostgreSQL License (BSD-based): http://www.postgresql.org/about/licence/
-  * Pull-parser / XPP3 (pull-parser:*, xpp3:*) - Indiana University Extreme! Lab Software License (BSD-based): http://www.extreme.indiana.edu/xgws/xsoap/xpp/download/PullParser2/LICENSE.txt
-  
-----
-NOTE #1: Some individual web application files in DSpace (e.g. Javascript 
-libraries, CSS Frameworks) may have their own open source license. In that 
-scenario, we place a copy of the full text of the license alongside the 
-licensed files. You can locate these additional licenses in our codebase 
-by searching for files with a ".LICENSE" file extension.
-
-For example, on Linux you can use the 'find' command from the source directory:
-
-find . -type f -name "*.LICENSE"
-----
-
-----
-NOTE #2: Although we try to keep this libraries list current, the latest 
-information about DSpace third party libraries can be found by running the 
-following Maven command(s):
-
-mvn project-info-reports:dependencies
-
-This generates a "[project]/target/site/dependencies.html" report under every 
-DSpace project directory. This report lists all dependencies and their license
-(if it can be determined by Maven).
-
-Additionally, you may wish to run:
-
-mvn project-info-reports:dependency-convergence
-
-This generates a summary report at 
-"[dspace]/target/site/dependency-convergence.html" which lists all dependencies
-of all DSpace projects (though it does not list license information)
-
-For more information see the maven-project-info-reports-plugin:
-http://maven.apache.org/plugins/maven-project-info-reports-plugin/
-----

LICENSE_HEADER

@@ -1,5 +0,0 @@
-The contents of this file are subject to the license and copyright
-detailed in the LICENSE and NOTICE files at the root of the source
-tree and available online at
-
-http://www.dspace.org/license/

NOTICE

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

README

@@ -1,54 +0,0 @@
-Installation instructions are included in this release package under
-
- - dspace/docs/DSpace-Manual.pdf
-
-DSpace version information can be viewed online at
- - https://wiki.duraspace.org/display/DSDOC/
-
-Documentation for the most recent stable release(s) may be downloaded
-or viewed online at
- - http://www.dspace.org/latest-release/
- - https://wiki.duraspace.org/display/DSDOC/
-
-In addition, a listing of all known contributors to DSpace software can be
-found online at:
-https://wiki.duraspace.org/display/DSPACE/DSpaceContributors
-
-Installation instructions for other versions may be different, so you
-are encouraged to obtain the appropriate version of the Documentation
-(from the links above or from the source repository).
-
-To obtain files from the repository and build, please see:
-
- - https://github.com/DSpace/DSpace/
-
-or just:
-
- - git clone git://github.com/DSpace/DSpace.git
-
-Please refer any further problems to the dspace-tech@lists.sourceforge.net
-mailing list.
-
- - http://sourceforge.net/mail/?group_id=19984
-
-
-Detailed Issue Tracking for DSpace is done on our JIRA Issue Tracker
-
- - https://jira.duraspace.org/browse/DS
-
-
-To contribute to DSpace, please see:
-
- - https://wiki.duraspace.org/display/DSPACE/How+to+Contribute+to+DSpace
-
-
-For more details about DSpace, including a list of service providers,
-places to seek help, news articles and lists of other users, please see:
-
- - http://www.dspace.org/
-
-
-DSpace source code licensing information available online at:
- - http://www.dspace.org/license/
-
-Copyright (c) 2002-2012, DuraSpace.  All rights reserved.

build.properties

@@ -1,151 +0,0 @@
-# DSpace build.properties
-# This file should be customised to suit your build environment.
-# Note that not all configuration is handled here, only the most common
-# properties that tend to differ between build environments. 
-# For adjusting global settings or more complex settings, edit the relevant config file.
-#
-# IMPORTANT: Do not remove or comment out settings in build.properties
-# When you edit the "build.properties" file (or a custom *.properties file),
-# take care not to remove or comment out any settings. Doing so, may cause
-# your final "dspace.cfg" file to be misconfigured with regards to that
-# particular setting.  Instead, if you wish to remove/disable a particular
-# setting, just clear out its value.  For example, if you don't want to be
-# notified of new user registrations, ensure the "mail.registration.notify"
-# setting has no value, e.g. "mail.registration.notify="
-#
-
-##########################
-# SERVER CONFIGURATION #
-##########################
-
-# DSpace installation directory. This is the location where you want
-# to install DSpace. NOTE: this value will be copied over to the
-# "dspace.dir" setting in the final "dspace.cfg" file. It can be
-# modified later on in your "dspace.cfg", if needed.
-dspace.install.dir=/dspace
-
-# DSpace host name - should match base URL.  Do not include port number
-dspace.hostname = localhost
-
-# DSpace base host URL.  Include port number etc.
-dspace.baseUrl = http://localhost:8080
-
-# Name of the site
-dspace.name = DSpace at My University
-
-# Solr server
-solr.server=http://localhost:8080/solr
-
-# Default language for metadata values
-default.language = en_US
-
-##########################
-# DATABASE CONFIGURATION #
-##########################
-
-# Database name ("oracle", or "postgres")
-db.name=postgres
-
-# Uncomment the appropriate block below for your database.
-# postgres
-db.driver=org.postgresql.Driver
-db.url=jdbc:postgresql://localhost:5432/dspace
-db.username=dspace
-db.password=dspace
-
-# oracle
-#db.driver= oracle.jdbc.OracleDriver
-#db.url=jdbc:oracle:thin:@//localhost:1521/xe
-#db.username=dspace
-#db.password=dspace
-
-# Schema name - if your database contains multiple schemas, you can avoid problems with
-# retrieving the definitions of duplicate object names by specifying
-# the schema name here that is used for DSpace by uncommenting the following entry
-db.schema = 
-
-# Maximum number of DB connections in pool
-db.maxconnections = 30
-
-# Maximum time to wait before giving up if all connections in pool are busy (milliseconds)
-db.maxwait = 5000
-
-# Maximum number of idle connections in pool (-1 = unlimited)
-db.maxidle = -1
-
-# Determine if prepared statement should be cached. (default is true)
-db.statementpool = true
-
-# Specify a name for the connection pool (useful if you have multiple applications sharing Tomcat's dbcp)
-# If not specified, defaults to 'dspacepool'
-db.poolname = dspacepool
-
-#######################
-# EMAIL CONFIGURATION #
-#######################
-
-# SMTP mail server
-mail.server = smtp.example.com
-
-# SMTP mail server authentication username and password (if required)
-# mail.server.username = myusername
-# mail.server.password = mypassword
-mail.server.username=
-mail.server.password=
-
-# SMTP mail server alternate port (defaults to 25)
-mail.server.port = 25
-
-# From address for mail
-mail.from.address = dspace-noreply@myu.edu
-
-# Currently limited to one recipient!
-mail.feedback.recipient = dspace-help@myu.edu
-
-# General site administration (Webmaster) e-mail
-mail.admin = dspace-help@myu.edu
-
-# Recipient for server errors and alerts
-#mail.alert.recipient = email-address-here
-mail.alert.recipient=
-
-# Recipient for new user registration emails
-#mail.registration.notify = email-address-here
-mail.registration.notify=
-
-
-########################
-# HANDLE CONFIGURATION #
-########################
-
-# Canonical Handle URL prefix
-#
-# By default, DSpace is configured to use http://hdl.handle.net/
-# as the canonical URL prefix when generating dc.identifier.uri
-# during submission, and in the 'identifier' displayed in JSPUI
-# item record pages.
-#
-# If you do not subscribe to CNRI's handle service, you can change this
-# to match the persistent URL service you use, or you can force DSpace
-# to use your site's URL, eg.
-#handle.canonical.prefix = ${dspace.url}/handle/
-#
-# Note that this will not alter dc.identifer.uri metadata for existing
-# items (only for subsequent submissions), but it will alter the URL 
-# in JSPUI's 'identifier' message on item record pages for existing items.
-#
-# If omitted, the canonical URL prefix will be http://hdl.handle.net/
-handle.canonical.prefix = http://hdl.handle.net/
-
-# CNRI Handle prefix
-handle.prefix = 123456789
-
-#######################
-# PROXY CONFIGURATION #
-#######################
-# uncomment and specify both properties if proxy server required
-# proxy server for external http requests - use regular hostname without port number
-http.proxy.host =
-
-# port number of proxy server
-http.proxy.port =

dspace-api/pom.xml

@@ -1,441 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-    <modelVersion>4.0.0</modelVersion>
-    <groupId>org.dspace</groupId>
-    <artifactId>dspace-api</artifactId>
-    <name>DSpace Kernel :: API and Implementation</name>
-    <description>DSpace core data model and service APIs.</description>
-
-    <!--
-       A Parent POM that Maven inherits DSpace Defaults
-       POM attributes from.
-    -->
-    <parent>
-        <groupId>org.dspace</groupId>
-        <artifactId>dspace-parent</artifactId>
-        <version>3.1</version>
-        <relativePath>..</relativePath>
-    </parent>
-
-    <properties>
-        <!-- This is the path to the root [dspace-src] directory. -->
-        <root.basedir>${basedir}/..</root.basedir>
-    </properties>
-
-    <!--
-       Runtime and Compile Time dependencies for DSpace.
-    -->
-    <build>
-        <plugins>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-compiler-plugin</artifactId>
-                <configuration>
-                    <debug>true</debug>
-                    <showDeprecation>true</showDeprecation>
-                </configuration>
-            </plugin>
-            <plugin>
-                <groupId>org.apache.maven.plugins</groupId>
-                <artifactId>maven-jar-plugin</artifactId>
-                <configuration>
-                    <archive>
-                        <manifest>
-                            <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
-                            <addDefaultSpecificationEntries>true</addDefaultSpecificationEntries>
-                        </manifest>
-                    </archive>
-                </configuration>
-                <executions>
-                    <execution>
-                        <goals>
-                            <goal>test-jar</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-            <plugin>
-                <artifactId>maven-dependency-plugin</artifactId>
-                <version>2.3</version>
-                <executions>
-                    <execution>
-                        <id>setupTestEnvironment</id>
-                        <phase>generate-test-resources</phase>
-                        <goals>
-                            <goal>unpack</goal>
-                        </goals>
-                        <configuration>
-                            <outputDirectory>${project.build.directory}/testing</outputDirectory>
-                            <artifactItems>
-                                <artifactItem>
-                                    <groupId>org.dspace</groupId>
-                                    <artifactId>dspace-parent</artifactId>
-                                    <version>${project.version}</version>
-                                    <type>zip</type>
-                                    <classifier>testEnvironment</classifier>
-                                </artifactItem>
-                            </artifactItems>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-            <!-- This plugin allows us to run a Groovy script in our Maven POM
-                    (see: http://gmaven.codehaus.org/Executing+Groovy+Code )
-                    We are generating a OS-agnostic version (agnostic.build.dir) of
-                    the ${project.build.directory} property (full path of target dir).
-                    This is necessary so that the FileWeaver & Surefire plugins can
-                    use it to initialize the Unit Test Framework's dspace.cfg file.
-                    Otherwise, the Unit Test Framework will not work on Windows OS.
-                    This Groovy code was mostly borrowed from:
-                    http://stackoverflow.com/questions/3872355/how-to-convert-file-separator-in-maven
-            -->
-            <plugin>
-                <groupId>org.codehaus.gmaven</groupId>
-                <artifactId>gmaven-plugin</artifactId>
-                <version>1.4</version>
-                <executions>
-                    <execution>
-                        <id>setproperty</id>
-                        <phase>generate-test-resources</phase>
-                        <goals>
-                            <goal>execute</goal>
-                        </goals>
-                        <configuration>
-                            <source>
-                            pom.properties['agnostic.build.dir']=project.build.directory.replace('\\','/');
-                            println("Initializing Maven property 'agnostic.build.dir' to: " + project.properties['agnostic.build.dir']);
-                            </source>
-                        </configuration>
-                    </execution>
-                </executions>
-            </plugin>
-            <!-- FileWeaver plugin is in charge of initializing & "weaving" together
-                 the dspace.cfg file to be used by the Unit Testing framework -->
-            <plugin>
-                <groupId>edu.iu.ul.maven.plugins</groupId>
-                <artifactId>fileweaver</artifactId>
-                <version>1.0</version>
-                <configuration>
-                    <outputs>
-                        <output>
-                            <outputPath>${agnostic.build.dir}/testing</outputPath>
-                            <name>dspace.cfg.woven</name>
-                            <parts>
-                                <part>
-                                    <path>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</path>
-                                </part>
-                                <part>
-                                    <path>${agnostic.build.dir}/testing/dspace.cfg.more</path>
-                                </part>
-                            </parts>
-                            <properties>
-                                <dspace.install.dir>${agnostic.build.dir}/testing/dspace</dspace.install.dir>
-                            </properties>
-                        </output>
-                    </outputs>
-                </configuration>
-                <executions>
-                    <execution>
-                        <id>edit-dspace-cfg</id>
-                        <phase>process-test-resources</phase>
-                        <goals>
-                            <goal>weave</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
-            <!--
-                The ant plugin below ensures that the dspace "woven" configuration file ends up in the dspace directory
-                The dspace service manager needs this "woven" configuration file when it starts
-            -->
-            <plugin>
-              <artifactId>maven-antrun-plugin</artifactId>
-              <executions>
-                <execution>
-                  <phase>process-test-resources</phase>
-                  <configuration>
-                    <tasks>
-                        <copy file="${agnostic.build.dir}/testing/dspace.cfg.woven" tofile="${agnostic.build.dir}/testing/dspace/config/dspace.cfg" />
-                    </tasks>
-                  </configuration>
-                  <goals>
-                    <goal>run</goal>
-                  </goals>
-                </execution>
-              </executions>
-            </plugin>
-
-            <plugin>
-                <artifactId>maven-surefire-plugin</artifactId>
-                <configuration>
-                    <systemPropertyVariables>
-                        <dspace.dir>${agnostic.build.dir}/testing/dspace</dspace.dir>
-                        <dspace.dir.static>${basedir}/src/test/data/dspaceFolder</dspace.dir.static>
-                        <dspace.configuration>${agnostic.build.dir}/testing/dspace/config/dspace.cfg</dspace.configuration>
-                        <db.schema.path>${agnostic.build.dir}/testing/dspace/etc/h2/database_schema.sql</db.schema.path>
-                        <dspace.log.init.disable>true</dspace.log.init.disable>
-                    </systemPropertyVariables>
-                </configuration>
-            </plugin>
-        </plugins>
-    </build>
-
-    <dependencies>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>handle</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>jargon</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>mets</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>dspace-tm-extractors</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-core</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.lucene</groupId>
-            <artifactId>lucene-analyzers</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-cli</groupId>
-            <artifactId>commons-cli</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-codec</groupId>
-            <artifactId>commons-codec</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-collections</groupId>
-            <artifactId>commons-collections</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-dbcp</groupId>
-            <artifactId>commons-dbcp</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-fileupload</groupId>
-            <artifactId>commons-fileupload</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>commons-httpclient</groupId>
-            <artifactId>commons-httpclient</artifactId>
-        </dependency>
-
-        <dependency>
-            <groupId>commons-io</groupId>
-            <artifactId>commons-io</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-lang</groupId>
-            <artifactId>commons-lang</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>commons-pool</groupId>
-            <artifactId>commons-pool</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.mail</groupId>
-            <artifactId>mail</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>servlet-api</artifactId>
-            <scope>provided</scope>
-        </dependency>
-        <dependency>
-            <groupId>jaxen</groupId>
-            <artifactId>jaxen</artifactId>
-            <exclusions>
-                <exclusion>
-                    <artifactId>xom</artifactId>
-                    <groupId>xom</groupId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>jdom</groupId>
-            <artifactId>jdom</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>oro</groupId>
-            <artifactId>oro</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.pdfbox</groupId>
-            <artifactId>pdfbox</artifactId>
-        </dependency>
-        <dependency>
-           <groupId>org.apache.pdfbox</groupId>
-           <artifactId>fontbox</artifactId>
-        </dependency>
-        <dependency>
-           <groupId>org.apache.pdfbox</groupId>
-           <artifactId>jempbox</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcprov-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.bouncycastle</groupId>
-            <artifactId>bcmail-jdk15</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi-scratchpad</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.poi</groupId>
-            <artifactId>poi-ooxml</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>net.java.dev.rome</groupId>
-            <artifactId>rome</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>rome</groupId>
-            <artifactId>opensearch</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>xalan</groupId>
-            <artifactId>xalan</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>xerces</groupId>
-            <artifactId>xercesImpl</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>xml-apis</groupId>
-            <artifactId>xmlParserAPIs</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.activation</groupId>
-            <artifactId>activation</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>com.ibm.icu</groupId>
-            <artifactId>icu4j</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>oclc-harvester2</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>dspace-services</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace.dependencies.jmockit</groupId>
-            <artifactId>dspace-jmockit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>com.h2database</groupId>
-            <artifactId>h2</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.databene</groupId>
-            <artifactId>contiperf</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.rometools</groupId>
-            <artifactId>rome-modules</artifactId>
-            <version>1.0</version>
-        </dependency>
-        <dependency>
-            <groupId>gr.ekt</groupId>
-            <artifactId>biblio-transformation-engine</artifactId>
-            <version>0.82</version>
-        </dependency>
-        <dependency>
-            <groupId>net.sf.opencsv</groupId>
-            <artifactId>opencsv</artifactId>
-            <version>2.3</version>
-        </dependency>
-        <dependency>
-            <groupId>org.jbibtex</groupId>
-            <artifactId>jbibtex</artifactId>
-            <version>1.0.0</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.solr</groupId>
-            <artifactId>solr-solrj</artifactId>
-            <version>${lucene.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>jcl-over-slf4j</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.slf4j</groupId>
-                    <artifactId>slf4j-api</artifactId>
-                </exclusion>
-            </exclusions>
-        </dependency>
-        <dependency>
-            <groupId>commons-configuration</groupId>
-            <artifactId>commons-configuration</artifactId>
-            <version>1.8</version>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace.dependencies</groupId>
-            <artifactId>dspace-geoip</artifactId>
-            <version>1.2.3</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.ant</groupId>
-            <artifactId>ant</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>org.dspace.dnsjava</groupId>
-            <artifactId>dnsjava</artifactId>
-            <version>2.0.6</version>
-        </dependency>
-
-        <dependency>
-            <groupId>org.elasticsearch</groupId>
-            <artifactId>elasticsearch</artifactId>
-            <version>0.18.6</version>
-        </dependency>
-
-        <!--  Gson: Java to Json conversion -->
-        <dependency>
-            <groupId>com.google.code.gson</groupId>
-            <artifactId>gson</artifactId>
-            <version>2.2.1</version>
-            <scope>compile</scope>
-        </dependency>
-
-        <dependency>
-            <groupId>postgresql</groupId>
-            <artifactId>postgresql</artifactId>
-        </dependency>
-
-    </dependencies>
-
-</project>

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

@@ -1,268 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-import java.util.Locale;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-
-import org.apache.commons.lang.StringUtils;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.core.I18nUtil;
-import org.dspace.eperson.EPerson;
-import org.dspace.eperson.Group;
-
-/**
- * A command-line tool for creating an initial administrator for setting up a
- * DSpace site. Prompts for an e-mail address, last name, first name and
- * password from standard input. An administrator group is then created and the
- * data passed in used to create an e-person in that group.
- * <P>
- * Alternatively, it can be used to take the email, first name, last name and
- * desired password as arguments thus:
- * 
- * CreateAdministrator -e [email] -f [first name] -l [last name] -p [password]
- * 
- * This is particularly convenient for automated deploy scripts that require an 
- * initial administrator, for example, before deployment can be completed
- * 
- * @author Robert Tansley
- * @author Richard Jones
- * 
- * @version $Revision$
- */
-public final class CreateAdministrator
-{
-	/** DSpace Context object */
-	private Context context;
-	
-    /**
-     * 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
-     */
-    public static void main(String[] argv)
-    	throws Exception
-    {
-    	CommandLineParser parser = new PosixParser();
-    	Options options = new Options();
-    	
-    	CreateAdministrator ca = new CreateAdministrator();
-    	
-    	options.addOption("e", "email", true, "administrator email address");
-    	options.addOption("f", "first", true, "administrator first name");
-    	options.addOption("l", "last", true, "administrator last name");
-    	options.addOption("c", "language", true, "administrator language");
-    	options.addOption("p", "password", true, "administrator password");
-    	
-    	CommandLine line = parser.parse(options, argv);
-    	
-    	if (line.hasOption("e") && line.hasOption("f") && line.hasOption("l") &&
-    			line.hasOption("c") && line.hasOption("p"))
-    	{
-    		ca.createAdministrator(line.getOptionValue("e"),
-    				line.getOptionValue("f"), line.getOptionValue("l"),
-    				line.getOptionValue("c"), line.getOptionValue("p"));
-    	}
-    	else
-    	{
-    		ca.negotiateAdministratorDetails();
-    	}
-    }
-    
-    /** 
-     * constructor, which just creates and object with a ready context
-     * 
-     * @throws Exception
-     */
-    private CreateAdministrator()
-    	throws Exception
-    {
-    	context = new Context();
-    }
-    
-    /**
-     * Method which will negotiate with the user via the command line to 
-     * obtain the administrator's details
-     * 
-     * @throws Exception
-     */
-    private void negotiateAdministratorDetails()
-    	throws Exception
-    {
-    	// For easier reading of typing
-    	BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-    	
-    	System.out.println("Creating an initial administrator account");
-    	
-    	boolean dataOK = false;
-    	
-    	String email = null;
-    	String firstName = null;
-    	String lastName = null;
-    	String password1 = null;
-    	String password2 = null;
-    	String language = I18nUtil.DEFAULTLOCALE.getLanguage();
-    	
-    	while (!dataOK)
-    	{
-    		System.out.print("E-mail address: ");
-    		System.out.flush();
-    		
-    		email = input.readLine();
-            if (email != null)
-            {
-                email = email.trim();
-            }
-    		
-    		System.out.print("First name: ");
-    		System.out.flush();
-    		
-    		firstName = input.readLine();
-
-            if (firstName != null)
-            {
-                firstName = firstName.trim();
-            }
-    		
-    		System.out.print("Last name: ");
-    		System.out.flush();
-    		
-    		lastName = input.readLine();
-
-            if (lastName != null)
-            {
-                lastName = lastName.trim();
-            }
-   		
-            if (ConfigurationManager.getProperty("webui.supported.locales") != null)
-            {
-                System.out.println("Select one of the following languages: " + ConfigurationManager.getProperty("webui.supported.locales"));
-                System.out.print("Language: ");
-                System.out.flush();
-            
-    		    language = input.readLine();
-
-                if (language != null)
-                {
-                    language = language.trim();
-                    language = I18nUtil.getSupportedLocale(new Locale(language)).getLanguage();
-                }
-            }
-            
-    		System.out.println("WARNING: Password will appear on-screen.");
-    		System.out.print("Password: ");
-    		System.out.flush();
-    		
-    		password1 = input.readLine();
-
-            if (password1 != null)
-            {
-                password1 = password1.trim();
-            }
-    		
-    		System.out.print("Again to confirm: ");
-    		System.out.flush();
-    		
-    		password2 = input.readLine();
-
-            if (password2 != null)
-            {
-                password2 = password2.trim();
-            }
-    		
-    		if (!StringUtils.isEmpty(password1) && StringUtils.equals(password1, password2))
-    		{
-    			// password OK
-    			System.out.print("Is the above data correct? (y or n): ");
-    			System.out.flush();
-    			
-    			String s = input.readLine();
-
-                if (s != null)
-                {
-                    s = s.trim();
-                    if (s.toLowerCase().startsWith("y"))
-                    {
-                        dataOK = true;
-                    }
-                }
-    		}
-    		else
-    		{
-    			System.out.println("Passwords don't match");
-    		}
-    	}
-    	
-    	// if we make it to here, we are ready to create an administrator
-    	createAdministrator(email, firstName, lastName, language, password1);
-    }
-    
-    /**
-     * Create the administrator with the given details.  If the user
-     * already exists then they are simply upped to administrator status
-     * 
-     * @param email	the email for the user
-     * @param first	user's first name
-     * @param last	user's last name
-     * @param ps	desired password
-     * 
-     * @throws Exception
-     */
-    private void createAdministrator(String email, String first, String last,
-    		String language, String pw)
-    	throws Exception
-    {
-    	// Of course we aren't an administrator yet so we need to
-    	// circumvent authorisation
-    	context.setIgnoreAuthorization(true);
-    	
-    	// Find administrator group
-    	Group admins = Group.find(context, 1);
-    	
-    	if (admins == null)
-    	{
-    		throw new IllegalStateException("Error, no admin group (group 1) found");
-    	}
-    	
-    	// Create the administrator e-person
-        EPerson eperson = EPerson.findByEmail(context,email);
-        
-        // check if the email belongs to a registered user,
-        // if not create a new user with this email
-        if (eperson == null)
-        {
-            eperson = EPerson.create(context);
-            eperson.setEmail(email);
-            eperson.setCanLogIn(true);
-            eperson.setRequireCertificate(false);
-            eperson.setSelfRegistered(false);
-        }
-    	
-    	eperson.setLastName(last);
-    	eperson.setFirstName(first);
-    	eperson.setLanguage(language);
-    	eperson.setPassword(pw);
-    	eperson.update();
-    	
-    	admins.addMember(eperson);
-    	admins.update();
-    	
-    	context.complete();
-    	
-    	System.out.println("Administrator account created");
-    }
-}

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

@@ -1,325 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.BufferedWriter;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.apache.xml.serialize.Method;
-import org.apache.xml.serialize.OutputFormat;
-import org.apache.xml.serialize.XMLSerializer;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.core.Context;
-import org.xml.sax.SAXException;
-
-
-/**
- * @author Graham Triggs
- *
- * This class creates an xml document as passed in the arguments and
- * from the metadata schemas for the repository.
- * 
- * The form of the XML is as follows
- * 
- * <metadata-schemas>
- *   <schema>
- *     <name>dc</name>
- *     <namespace>http://dublincore.org/documents/dcmi-terms/</namespace>
- *   </schema>
- * </metadata-schemas>
- */
-public class MetadataExporter
-{
-
-    /**
-     * @param args
-     * @throws ParseException 
-     * @throws SAXException 
-     * @throws IOException 
-     * @throws SQLException 
-     * @throws 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();
-        options.addOption("f", "file",   true, "output xml file for registry");
-        options.addOption("s", "schema", true, "the name of the schema to export");
-        CommandLine line = parser.parse(options, args);
-        
-        String file   = null;
-        String schema = null;
-
-        if (line.hasOption('f'))
-        {
-            file   = line.getOptionValue('f');
-        }
-        else
-        {
-            usage();
-            System.exit(0);
-        }
-        
-        if (line.hasOption('s'))
-        {
-            schema = line.getOptionValue('s');
-        }
-
-        saveRegistry(file, schema);
-    }
-
-    public static void saveRegistry(String file, String schema) throws SQLException, IOException, SAXException, RegistryExportException
-    {
-        // create a context
-        Context context = new Context();
-        context.setIgnoreAuthorization(true);
-
-        OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
-        xmlFormat.setLineWidth(120);
-        xmlFormat.setIndent(4);
-        
-        XMLSerializer xmlSerializer = new XMLSerializer(new BufferedWriter(new FileWriter(file)), xmlFormat);
-        //        XMLSerializer xmlSerializer = new XMLSerializer(System.out, xmlFormat);
-        xmlSerializer.startDocument();
-        xmlSerializer.startElement("dspace-dc-types", null);
-        
-        // Save the schema definition(s)
-        saveSchema(context, xmlSerializer, schema);
-
-        MetadataField[] mdFields = null;
-
-        // If a single schema has been specified
-        if (schema != null && !"".equals(schema))
-        {
-            // Get the id of that schema
-            MetadataSchema mdSchema = MetadataSchema.find(context, schema);
-            if (mdSchema == null)
-            {
-                throw new RegistryExportException("no schema to export");
-            }
-            
-            // Get the metadata fields only for the specified schema
-            mdFields = MetadataField.findAllInSchema(context, mdSchema.getSchemaID());
-        }
-        else
-        {
-            // Get the metadata fields for all the schemas
-            mdFields = MetadataField.findAll(context);
-        }
-        
-        // Output the metadata fields
-        for (MetadataField mdField : mdFields)
-        {
-            saveType(context, xmlSerializer, mdField);
-        }
-        
-        xmlSerializer.endElement("dspace-dc-types");
-        xmlSerializer.endDocument();
-        
-        // abort the context, as we shouldn't have changed it!!
-        context.abort();
-    }
-    
-    /**
-     * Serialize the schema registry. If the parameter 'schema' is null or empty, save all schemas
-     * @param context
-     * @param xmlSerializer
-     * @param schema
-     * @throws SQLException
-     * @throws SAXException
-     * @throws RegistryExportException
-     */
-    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema) throws SQLException, SAXException, RegistryExportException
-    {
-        if (schema != null && !"".equals(schema))
-        {
-            // Find a single named schema
-            MetadataSchema mdSchema = MetadataSchema.find(context, schema);
-            
-            saveSchema(xmlSerializer, mdSchema);
-        }
-        else
-        {
-            // Find all schemas
-            MetadataSchema[] mdSchemas = MetadataSchema.findAll(context);
-            
-            for (MetadataSchema mdSchema : mdSchemas)
-            {
-                saveSchema(xmlSerializer, mdSchema);
-            }
-        }
-    }
-    
-    /**
-     * Serialize a single schema (namespace) registry entry
-     * 
-     * @param xmlSerializer
-     * @param mdSchema
-     * @throws SAXException
-     * @throws 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)
-        {
-            throw new RegistryExportException("no schema to export");
-        }
-        
-        String name      = mdSchema.getName();
-        String namespace = mdSchema.getNamespace();
-        
-        if (name == null || "".equals(name))
-        {
-            System.out.println("name is null, skipping");
-            return;
-        }
-
-        if (namespace == null || "".equals(namespace))
-        {
-            System.out.println("namespace is null, skipping");
-            return;
-        }
-
-        // Output the parent tag
-        xmlSerializer.startElement("dc-schema", null);
-        
-        // Output the schema name
-        xmlSerializer.startElement("name", null);
-        xmlSerializer.characters(name.toCharArray(), 0, name.length());
-        xmlSerializer.endElement("name");
-
-        // Output the schema namespace
-        xmlSerializer.startElement("namespace", null);
-        xmlSerializer.characters(namespace.toCharArray(), 0, namespace.length());
-        xmlSerializer.endElement("namespace");
-
-        xmlSerializer.endElement("dc-schema");
-    }
-    
-    /**
-     * Serialize a single metadata field registry entry to xml
-     * 
-     * @param context
-     * @param xmlSerializer
-     * @param mdField
-     * @throws SAXException
-     * @throws RegistryExportException
-     * @throws SQLException
-     * @throws 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)
-        {
-            throw new RegistryExportException("no field to export");
-        }
-        
-        // Get the data from the metadata field
-        String schemaName = getSchemaName(context, mdField);
-        String element = mdField.getElement();
-        String qualifier = mdField.getQualifier();
-        String scopeNote = mdField.getScopeNote();
-
-        // We must have a schema and element
-        if (schemaName == null || element == null)
-        {
-            throw new RegistryExportException("incomplete field information");
-        }
-
-        // Output the parent tag
-        xmlSerializer.startElement("dc-type", null);
-
-        // Output the schema name
-        xmlSerializer.startElement("schema", null);
-        xmlSerializer.characters(schemaName.toCharArray(), 0, schemaName.length());
-        xmlSerializer.endElement("schema");
-
-        // Output the element
-        xmlSerializer.startElement("element", null);
-        xmlSerializer.characters(element.toCharArray(), 0, element.length());
-        xmlSerializer.endElement("element");
-
-        // Output the qualifier, if present
-        if (qualifier != null)
-        {
-            xmlSerializer.startElement("qualifier", null);
-            xmlSerializer.characters(qualifier.toCharArray(), 0, qualifier.length());
-            xmlSerializer.endElement("qualifier");
-        }
-        else
-        {
-            xmlSerializer.comment("unqualified");
-        }
-        
-        // Output the scope note, if present
-        if (scopeNote != null)
-        {
-            xmlSerializer.startElement("scope_note", null);
-            xmlSerializer.characters(scopeNote.toCharArray(), 0, scopeNote.length());
-            xmlSerializer.endElement("scope_note");
-        }
-        else
-        {
-            xmlSerializer.comment("no scope note");
-        }
-        
-        xmlSerializer.endElement("dc-type");
-    }
-    
-    /**
-     * Helper method to retrieve a schema name for the field.
-     * Caches the name after looking up the id.
-     */
-    static Map<Integer, String> schemaMap = new HashMap<Integer, String>();
-    private static String getSchemaName(Context context, MetadataField mdField) throws SQLException, RegistryExportException
-    {
-        // Get name from cache
-        String name = schemaMap.get(Integer.valueOf(mdField.getSchemaID()));
-
-        if (name == null)
-        {
-            // Name not retrieved before, so get the schema now
-            MetadataSchema mdSchema = MetadataSchema.find(context, mdField.getSchemaID());
-            if (mdSchema != null)
-            {
-                name = mdSchema.getName();
-                schemaMap.put(Integer.valueOf(mdSchema.getSchemaID()), name);
-            }
-            else
-            {
-                // Can't find the schema
-                throw new RegistryExportException("Can't get schema name for field");
-            }
-        }
-        return name;
-    }
-    
-    /**
-     * Print the usage message to stdout
-     */
-    public static void usage()
-    {
-        String usage = "Use this class with the following options:\n" +
-                        " -f <xml output file> : specify the output file for the schemas\n" +
-                        " -s <schema> : name of the schema to export\n";
-        System.out.println(usage);
-    }
-}

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

@@ -1,264 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.IOException;
-import java.sql.SQLException;
-
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.TransformerException;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-
-import org.apache.xpath.XPathAPI;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-import org.dspace.content.NonUniqueMetadataException;
-import org.dspace.core.Context;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import org.xml.sax.SAXException;
-
-/**
- * @author Richard Jones
- *
- * This class takes an xml document as passed in the arguments and
- * uses it to create metadata elements in the Metadata Registry if 
- * they do not already exist
- * 
- * The format of the XML file is as follows:
- * 
- * <dspace-dc-types>
- *   <dc-type>
- *     <schema>icadmin</schema>
- *     <element>status</element>
- *     <qualifier>dateset</qualifier>
- *     <scope_note>the workflow status of an item</scope_note>
- *   </dc-type>
- *   
- *   [....]
- *   
- * </dspace-dc-types>
- */
-public class MetadataImporter
-{
-	/**
-	 * main method for reading user input from the command line
-	 */
-    public static void main(String[] args)
-    	throws ParseException, SQLException, IOException, TransformerException,
-    			ParserConfigurationException, AuthorizeException, SAXException,
-    			NonUniqueMetadataException, RegistryImportException
-    {
-        boolean forceUpdate = false;
-        
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-        Options options = new Options();
-        options.addOption("f", "file", true, "source xml file for DC fields");
-        options.addOption("u", "update", false, "update an existing schema");
-        CommandLine line = parser.parse(options, args);
-        
-        String file = null;
-        if (line.hasOption('f'))
-        {
-            file = line.getOptionValue('f');
-        }
-        else
-        {
-            usage();
-            System.exit(0);
-        }
-
-        forceUpdate = line.hasOption('u');
-        loadRegistry(file, forceUpdate);
-    }
-    
-    /**
-     * Load the data from the specified file path into the database
-     * 
-     * @param 	file	the file path containing the source data
-     */
-    public static void loadRegistry(String file, boolean forceUpdate)
-    	throws SQLException, IOException, TransformerException, ParserConfigurationException, 
-    		AuthorizeException, SAXException, NonUniqueMetadataException, RegistryImportException
-    {
-        // create a context
-        Context context = new Context();
-        context.setIgnoreAuthorization(true);
-        
-        // read the XML
-        Document document = RegistryImporter.loadXML(file);
-
-        // Get the nodes corresponding to types
-        NodeList schemaNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-schema");
-        
-        // Add each one as a new format to the registry
-        for (int i = 0; i < schemaNodes.getLength(); i++)
-        {
-            Node n = schemaNodes.item(i);
-            loadSchema(context, n, forceUpdate);
-        }
-        
-        // Get the nodes corresponding to types
-        NodeList typeNodes = XPathAPI.selectNodeList(document, "/dspace-dc-types/dc-type");
-
-        // Add each one as a new format to the registry
-        for (int i = 0; i < typeNodes.getLength(); i++)
-        {
-            Node n = typeNodes.item(i);
-            loadType(context, n);
-        }
-        
-        context.complete();
-    }
-    
-    /**
-     * Process a node in the metadata registry XML file.  If the
-     * schema already exists, it will not be recreated
-     * 
-     * @param context
-     *            DSpace context object
-     * @param node
-     *            the node in the DOM tree
-     * @throws NonUniqueMetadataException
-     */
-    private static void loadSchema(Context context, Node node, boolean updateExisting)
-        throws SQLException, IOException, TransformerException,
-            AuthorizeException, NonUniqueMetadataException, RegistryImportException
-    {
-        // Get the values
-        String name = RegistryImporter.getElementData(node, "name");
-        String namespace = RegistryImporter.getElementData(node, "namespace");
-        
-        if (name == null || "".equals(name))
-        {
-            throw new RegistryImportException("Name of schema must be supplied");
-        }
-
-        if (namespace == null || "".equals(namespace))
-        {
-            throw new RegistryImportException("Namespace of schema must be supplied");
-        }
-
-        System.out.print("Registering Schema: " + name + " - " + namespace + " ... ");
-        
-        // check to see if the schema already exists
-        MetadataSchema s = MetadataSchema.find(context, name);
-        
-        if (s == null)
-        {
-            // Schema does not exist - create
-            MetadataSchema schema = new MetadataSchema(namespace, name);
-            schema.create(context);
-            System.out.println("created");
-        }
-        else
-        {
-            // Schema exists - if it's the same namespace, allow the type imports to continue
-            if (s.getNamespace().equals(namespace))
-            {
-                System.out.println("already exists, skipping to type import");
-                return;
-            }
-            
-            // It's a different namespace - have we been told to update?
-            if (updateExisting)
-            {
-                // Update the existing schema namespace and continue to type import
-                s.setNamespace(namespace);
-                s.update(context);
-                System.out.println("namespace updated (" + name + " = " + namespace + ")");
-            }
-            else
-            {
-                // Don't update the existing namespace - abort abort abort
-                System.out.println("schema exists, but with different namespace");
-                System.out.println("was: " + s.getNamespace());
-                System.out.println("xml: " + namespace);
-                System.out.println("aborting - use -u to force the update");
-                
-                throw new RegistryImportException("schema already registered with different namespace - use -u to update");
-            }
-        }
-        
-    }
-    
-    /**
-     * Process a node in the metadata registry XML file. The node must
-     * be a "dc-type" node.  If the type already exists, then it
-     * will not be reimported
-     * 
-     * @param context
-     *            DSpace context object
-     * @param node
-     *            the node in the DOM tree
-     * @throws NonUniqueMetadataException
-     */
-    private static void loadType(Context context, Node node)
-            throws SQLException, IOException, TransformerException,
-            AuthorizeException, NonUniqueMetadataException, RegistryImportException
-    {
-        // Get the values
-        String schema = RegistryImporter.getElementData(node, "schema");
-        String element = RegistryImporter.getElementData(node, "element");
-        String qualifier = RegistryImporter.getElementData(node, "qualifier");
-        String scopeNote = RegistryImporter.getElementData(node, "scope_note");
-
-        // If the schema is not provided default to DC
-        if (schema == null)
-        {
-            schema = MetadataSchema.DC_SCHEMA;
-        }
-
-        System.out.print("Registering Metadata: " + schema + "." + element + "." + qualifier + " ... ");
-        
-        // Find the matching schema object
-        MetadataSchema schemaObj = MetadataSchema.find(context, schema);
-        
-        if (schemaObj == null)
-        {
-            throw new RegistryImportException("Schema '" + schema + "' is not registered");
-        }
-        
-        MetadataField mf = MetadataField.findByElement(context, schemaObj.getSchemaID(), element, qualifier);
-        if (mf != null)
-        {
-            System.out.println("already exists, skipping");
-            return;
-        }
-        
-        MetadataField field = new MetadataField();
-        field.setSchemaID(schemaObj.getSchemaID());
-        field.setElement(element);
-        field.setQualifier(qualifier);
-        field.setScopeNote(scopeNote);
-        field.create(context);
-        System.out.println("created");
-    }
-    
-    /**
-     * Print the usage message to stdout
-     */
-    public static void usage()
-    {
-        String usage = "Use this class with the following option:\n" +
-        				" -f <xml source file> : specify which xml source file " +
-        				"contains the DC fields to import.\n";
-        System.out.println(usage);
-    }
-}

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

@@ -1,56 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-/**
- * @author Graham Triggs
- *
- * An exception to report any problems with registry exports
- */
-public class RegistryExportException extends Exception
-{
-    /**
-     * Create an empty authorize exception
-     */
-    public RegistryExportException()
-    {
-        super();
-    }
-
-    /**
-     * create an exception with only a message
-     * 
-     * @param message
-     */
-    public RegistryExportException(String message)
-    {
-        super(message);
-    }
-    
-    /**
-     * create an exception with an inner exception and a message
-     * 
-     * @param   message
-     * @param   e
-     */
-    public RegistryExportException(String message, Throwable e)
-    {
-        super(message, e);
-    }
-    
-    /**
-     * create an exception with an inner exception
-     * 
-     * @param   e
-     */
-    public RegistryExportException(Throwable e)
-    {
-        super(e);
-    }
-    
-}

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

@@ -1,56 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-/**
- * @author Richard Jones
- *
- * An exception to report any problems with registry imports
- */
-public class RegistryImportException extends Exception
-{
-    /**
-     * Create an empty authorize exception
-     */
-    public RegistryImportException()
-    {
-        super();
-    }
-
-    /**
-     * create an exception with only a message
-     * 
-     * @param message
-     */
-    public RegistryImportException(String message)
-    {
-        super(message);
-    }
-    
-    /**
-     * create an exception with an inner exception and a message
-     * 
-     * @param	message
-     * @param	e
-     */
-    public RegistryImportException(String message, Throwable e)
-    {
-    	super(message, e);
-    }
-    
-    /**
-     * create an exception with an inner exception
-     * 
-     * @param	e
-     */
-    public RegistryImportException(Throwable e)
-    {
-    	super(e);
-    }
-    
-}

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

@@ -1,141 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.File;
-import java.io.IOException;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.TransformerException;
-
-import org.apache.xpath.XPathAPI;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import org.xml.sax.SAXException;
-
-/**
- * @author Richard Jones
- *
- * This class provides the tools that registry importers might need to
- * use.  Basically some utility methods.  And actually, although it says
- * I am the author, really I ripped these methods off from other
- * classes
- */
-public class RegistryImporter
-{
-    /**
-     * Load in the XML from file.
-     * 
-     * @param filename
-     *            the filename to load from
-     * 
-     * @return the DOM representation of the XML file
-     */
-    public static Document loadXML(String filename) 
-    	throws IOException, ParserConfigurationException, SAXException
-    {
-        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                .newDocumentBuilder();
-
-        Document document = builder.parse(new File(filename));
-        
-        return document;
-    }
-    
-    /**
-     * Get the CDATA of a particular element. For example, if the XML document
-     * contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;&lt;mimetype&gt;application/pdf&lt;/mimetype&gt;&lt;/foo&gt;
-     * </code>
-     * passing this the <code>foo</code> node and <code>mimetype</code> will
-     * return <code>application/pdf</code>.
-     * </P>
-     * Why this isn't a core part of the XML API I do not know...
-     * 
-     * @param parentElement
-     *            the element, whose child element you want the CDATA from
-     * @param childName
-     *            the name of the element you want the CDATA from
-     * 
-     * @return the CDATA as a <code>String</code>
-     */
-    public static String getElementData(Node parentElement, String childName)
-            throws TransformerException
-    {
-        // Grab the child node
-        Node childNode = XPathAPI.selectSingleNode(parentElement, childName);
-
-        if (childNode == null)
-        {
-            // No child node, so no values
-            return null;
-        }
-
-        // Get the #text
-        Node dataNode = childNode.getFirstChild();
-
-        if (dataNode == null)
-        {
-            return null;
-        }
-
-        // Get the data
-        String value = dataNode.getNodeValue().trim();
-
-        return value;
-    }
-
-    /**
-     * Get repeated CDATA for a particular element. For example, if the XML
-     * document contains:
-     * <P>
-     * <code>
-     * &lt;foo&gt;
-     *   &lt;bar&gt;val1&lt;/bar&gt;
-     *   &lt;bar&gt;val2&lt;/bar&gt;
-     * &lt;/foo&gt;
-     * </code>
-     * passing this the <code>foo</code> node and <code>bar</code> will
-     * return <code>val1</code> and <code>val2</code>.
-     * </P>
-     * Why this also isn't a core part of the XML API I do not know...
-     * 
-     * @param parentElement
-     *            the element, whose child element you want the CDATA from
-     * @param childName
-     *            the name of the element you want the CDATA from
-     * 
-     * @return the CDATA as a <code>String</code>
-     */
-    public static String[] getRepeatedElementData(Node parentElement,
-            String childName) throws TransformerException
-    {
-        // Grab the child node
-        NodeList childNodes = XPathAPI.selectNodeList(parentElement, childName);
-
-        String[] data = new String[childNodes.getLength()];
-
-        for (int i = 0; i < childNodes.getLength(); i++)
-        {
-            // Get the #text node
-            Node dataNode = childNodes.item(i).getFirstChild();
-
-            // Get the data
-            data[i] = dataNode.getNodeValue().trim();
-        }
-
-        return data;
-    }
-}

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

@@ -1,581 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.TransformerException;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.apache.xpath.XPathAPI;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-import org.jdom.Element;
-import org.jdom.output.XMLOutputter;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-/**
- * This class deals with importing community and collection structures from
- * an XML file.
- * 
- * The XML file structure needs to be:
- * 
- * <import_structure>
- *     <community>
- *         <name>....</name>
- *         <community>...</community>
- *         <collection>
- *             <name>....</name>
- *         </collection>
- *     </community>
- * </import_structure>
- * 
- * it can be arbitrarily deep, and supports all the metadata elements
- * that make up the community and collection metadata.  See the system
- * documentation for more details
- * 
- * @author Richard Jones
- *
- */
-
-public class StructBuilder
-{
-    /** the output xml document which will contain updated information about the 
-     * imported structure
-     */
-    private static org.jdom.Document xmlOutput = new org.jdom.Document(new Element("imported_structure"));
-    
-    /** a hashtable to hold metadata for the collection being worked on */
-    private static Map<String, String> collectionMap = new HashMap<String, String>();
-    
-    /** a hashtable to hold metadata for the community being worked on */
-    private static Map<String, String> communityMap = new HashMap<String, String>();
-    
-    /**
-     * Main method to be run from the command line to import a structure into
-     * DSpace
-     * 
-     * This is of the form:
-     * 
-     * StructBuilder -f [xml source] -e [administrator email] -o [output file]
-     * 
-     * 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.
-     */
-    public static void main(String[] argv) 
-    	throws Exception
-    {
-        CommandLineParser parser = new PosixParser();
-
-    	Options options = new Options();
-
-    	options.addOption( "f", "file", true, "file");
-    	options.addOption( "e", "eperson", true, "eperson");
-    	options.addOption("o", "output", true, "output");
-    	
-    	CommandLine line = parser.parse( options, argv );
-    	
-    	String file = null;
-    	String eperson = null;
-    	String output = null;
-    	
-    	if (line.hasOption('f'))
-    	{
-    	    file = line.getOptionValue('f');
-    	}
-    	
-    	if (line.hasOption('e'))
-    	{
-    	    eperson = line.getOptionValue('e');
-    	}
-    	
-    	if (line.hasOption('o'))
-    	{
-    	    output = line.getOptionValue('o');
-    	}
-    	
-    	if (output == null || eperson == null || file == null)
-    	{
-    	    usage();
-    	    System.exit(0);
-    	}
-    	
-        // create a context
-        Context context = new Context();
-        
-        // set the context
-        context.setCurrentUser(EPerson.findByEmail(context, eperson));
- 
-        // load the XML
-        Document document = loadXML(file);
-        
-        // run the preliminary validation, to be sure that the the XML document
-        // is properly structured
-        validate(document);
-        
-        // load the mappings into the member variable hashmaps
-        communityMap.put("name", "name");
-        communityMap.put("description", "short_description");
-        communityMap.put("intro", "introductory_text");
-        communityMap.put("copyright", "copyright_text");
-        communityMap.put("sidebar", "side_bar_text");
-        
-        collectionMap.put("name", "name");
-        collectionMap.put("description", "short_description");
-        collectionMap.put("intro", "introductory_text");
-        collectionMap.put("copyright", "copyright_text");
-        collectionMap.put("sidebar", "side_bar_text");
-        collectionMap.put("license", "license");
-        collectionMap.put("provenance", "provenance_description");
-        
-        // get the top level community list
-        NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
-        
-        // run the import starting with the top level communities
-        Element[] elements = handleCommunities(context, first, null);
-        
-        // generate the output
-        Element root = xmlOutput.getRootElement();
-        for (int i = 0; i < elements.length; i++)
-        {
-            root.addContent(elements[i]);
-        }
-        
-        // finally write the string into the output file
-        try 
-        {
-            BufferedWriter out = new BufferedWriter(new FileWriter(output));
-            out.write(new XMLOutputter().outputString(xmlOutput));
-            out.close();
-        } 
-        catch (IOException e) 
-        {
-            System.out.println("Unable to write to output file " + output);
-            System.exit(0);
-        }
-        
-        context.complete();
-    }
-    
-    /**
-     * Output the usage information
-     */
-    private static void usage()
-    {
-        System.out.println("Usage: java StructBuilder -f <source XML file> -o <output file> -e <eperson email>");
-        System.out.println("Communities will be created from the top level, and a map of communities to handles will be returned in the output file");
-        return;
-    }
-    
-    /**
-     * Validate the XML document.  This method does not return, but if validation
-     * fails it generates an error and ceases execution
-     * 
-     * @param	document	the XML document object
-     * @throws TransformerException
-     * 
-     */
-    private static void validate(org.w3c.dom.Document document)
-    	throws TransformerException
-    {
-        StringBuffer err = new StringBuffer();
-        boolean trip = false;
-        
-        err.append("The following errors were encountered parsing the source XML\n");
-        err.append("No changes have been made to the DSpace instance\n\n");
-        
-        NodeList first = XPathAPI.selectNodeList(document, "/import_structure/community");
-        if (first.getLength() == 0)
-        {
-            err.append("-There are no top level communities in the source document");
-            System.out.println(err.toString());
-            System.exit(0);
-        }
-        
-        String errs = validateCommunities(first, 1);
-        if (errs != null)
-        {
-            err.append(errs);
-            trip = true;
-        }
-        
-        if (trip)
-        {
-            System.out.println(err.toString());
-            System.exit(0);
-        }
-    }
-    
-    /**
-     * Validate the communities section of the XML document.  This returns a string
-     * containing any errors encountered, or null if there were no errors
-     * 
-     * @param communities the NodeList of communities to validate
-     * @param level the level in the XML document that we are at, for the purposes
-     * 			of error reporting
-     * 
-     * @return the errors that need to be generated by the calling method, or null if
-     * 			no errors.
-     */
-    private static String validateCommunities(NodeList communities, int level)
-    	throws TransformerException
-    {
-        StringBuffer err = new StringBuffer();
-        boolean trip = false;
-        String errs = null;
-        
-        for (int i = 0; i < communities.getLength(); i++)
-        {
-            Node n = communities.item(i);
-	        NodeList name = XPathAPI.selectNodeList(n, "name");
-	        if (name.getLength() != 1)
-	        {
-	            String pos = Integer.toString(i + 1);
-	            err.append("-The level " + level + " community in position " + pos);
-	            err.append(" does not contain exactly one name field\n");
-	            trip = true;
-	        }
-	        
-	        // validate sub communities
-	        NodeList subCommunities = XPathAPI.selectNodeList(n, "community");
-	        String comErrs = validateCommunities(subCommunities, level + 1);
-	        if (comErrs != null)
-	        {
-	            err.append(comErrs);
-	            trip = true;
-	        }
-	        
-	        // validate collections
-	        NodeList collections = XPathAPI.selectNodeList(n, "collection");
-	        String colErrs = validateCollections(collections, level + 1);
-	        if (colErrs != null)
-	        {
-	            err.append(colErrs);
-	            trip = true;
-	        }
-        }
-        
-        if (trip)
-        {
-            errs = err.toString();
-        }
-        
-        return errs;
-    }
-    
-    /**
-     * validate the collection section of the XML document.  This generates a
-     * string containing any errors encountered, or returns null if no errors
-     * 
-     * @param collections a NodeList of collections to validate
-     * @param level the level in the XML document for the purposes of error reporting
-     * 
-     * @return the errors to be generated by the calling method, or null if none
-     */
-    private static String validateCollections(NodeList collections, int level)
-    	throws TransformerException
-    {
-        StringBuffer err = new StringBuffer();
-        boolean trip = false;
-        String errs = null;
-        
-        for (int i = 0; i < collections.getLength(); i++)
-        {
-            Node n = collections.item(i);
-	        NodeList name = XPathAPI.selectNodeList(n, "name");
-	        if (name.getLength() != 1)
-	        {
-	            String pos = Integer.toString(i + 1);
-	            err.append("-The level " + level + " collection in position " + pos);
-	            err.append(" does not contain exactly one name field\n");
-	            trip = true;
-	        }
-        }
-        
-        if (trip)
-        {
-            errs = err.toString();
-        }
-        
-        return errs;
-    }
-    
-    /**
-     * Load in the XML from file.
-     * 
-     * @param filename
-     *            the filename to load from
-     * 
-     * @return the DOM representation of the XML file
-     */
-    private static org.w3c.dom.Document loadXML(String filename) 
-    	throws IOException, ParserConfigurationException, SAXException
-    {
-        DocumentBuilder builder = DocumentBuilderFactory.newInstance()
-                .newDocumentBuilder();
-
-        org.w3c.dom.Document document = builder.parse(new File(filename));
-        
-        return document;
-    }
-    
-    /**
-     * Return the String value of a Node
-     * 
-     * @param node the node from which we want to extract the string value
-     * 
-     * @return the string value of the node
-     */
-    public static String getStringValue(Node node)
-    {
-        String value = node.getNodeValue();
-
-        if (node.hasChildNodes())
-        {
-            Node first = node.getFirstChild();
-
-            if (first.getNodeType() == Node.TEXT_NODE)
-            {
-                return first.getNodeValue().trim();
-            }
-        }
-
-        return value;
-    }
-    
-    /**
-     * Take a node list of communities and build the structure from them, delegating
-     * to the relevant methods in this class for sub-communities and collections
-     * 
-     * @param context the context of the request
-     * @param communities a nodelist of communities to create along with their sub-structures
-     * @param parent the parent community of the nodelist of communities to create
-     * 
-     * @return an element array containing additional information regarding the 
-     * 			created communities (e.g. the handles they have been assigned)
-     */
-    private static Element[] handleCommunities(Context context, NodeList communities, Community parent)
-    	throws TransformerException, SQLException, Exception
-    {
-        Element[] elements = new Element[communities.getLength()];
-        
-        for (int i = 0; i < communities.getLength(); i++)
-        {
-            Community community;
-            Element element = new Element("community");
-            
-            // create the community or sub community
-            if (parent != null)
-            {
-                community = parent.createSubcommunity();
-            }
-            else
-            {
-                community = Community.create(null, context);
-            }
-            
-            // default the short description to be an empty string
-            community.setMetadata("short_description", " ");
-            
-            // now update the metadata
-            Node tn = communities.item(i);
-            for (Map.Entry<String, String> entry : communityMap.entrySet())
-            {
-                NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1)
-                {
-                    community.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
-                }
-            }
-            
-            // FIXME: at the moment, if the community already exists by name
-            // then this will throw a PSQLException on a duplicate key
-            // violation
-            // Ideally we'd skip this row and continue to create sub
-            // communities
-            // and so forth where they don't exist, but it's proving
-            // difficult
-            // to isolate the community that already exists without hitting
-            // the database directly.
-            community.update();
-            
-            // build the element with the handle that identifies the new
-            // community
-            // along with all the information that we imported here
-            // This looks like a lot of repetition of getting information
-            // from above
-            // but it's here to keep it separate from the create process in
-            // case
-            // we want to move it or make it switchable later
-            element.setAttribute("identifier", community.getHandle());
-            
-            Element nameElement = new Element("name");
-            nameElement.setText(community.getMetadata("name"));
-            element.addContent(nameElement);
-            
-            if (community.getMetadata("short_description") != null)
-            {
-                Element descriptionElement = new Element("description");
-                descriptionElement.setText(community.getMetadata("short_description"));
-                element.addContent(descriptionElement);
-            }
-            
-            if (community.getMetadata("introductory_text") != null)
-            {
-                Element introElement = new Element("intro");
-                introElement.setText(community.getMetadata("introductory_text"));
-                element.addContent(introElement);
-            }
-            
-            if (community.getMetadata("copyright_text") != null)
-            {
-                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(community.getMetadata("copyright_text"));
-                element.addContent(copyrightElement);
-            }
-            
-            if (community.getMetadata("side_bar_text") != null)
-            {
-                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(community.getMetadata("side_bar_text"));
-                element.addContent(sidebarElement);
-            }
-            
-            // handle sub communities
-            NodeList subCommunities = XPathAPI.selectNodeList(tn, "community");
-            Element[] subCommunityElements = handleCommunities(context, subCommunities, community);
-            
-            // handle collections
-            NodeList collections = XPathAPI.selectNodeList(tn, "collection");
-            Element[] collectionElements = handleCollections(context, collections, community);
-            
-            int j;
-            for (j = 0; j < subCommunityElements.length; j++)
-            {
-                element.addContent(subCommunityElements[j]);
-            }
-            for (j = 0; j < collectionElements.length; j++)
-            {
-                element.addContent(collectionElements[j]);
-            }
-            
-            elements[i] = element;
-        }
-        
-        return elements;
-    }
-    
-    /**
-     *  Take a node list of collections and create the structure from them
-     * 
-     * @param context the context of the request
-     * @param collections the node list of collections to be created
-     * @param parent the parent community to whom the collections belong
-     * 
-     * @return an Element array containing additional information about the
-     * 			created collections (e.g. the handle)
-     */
-    private static Element[] handleCollections(Context context, NodeList collections, Community parent)
-    	throws TransformerException, SQLException, AuthorizeException, IOException, Exception
-    {
-        Element[] elements = new Element[collections.getLength()];
-        
-        for (int i = 0; i < collections.getLength(); i++)
-        {
-            Element element = new Element("collection");
-            Collection collection = parent.createCollection();
-            
-            // default the short description to the empty string
-            collection.setMetadata("short_description", " ");
-            
-            // import the rest of the metadata
-            Node tn = collections.item(i);
-            for (Map.Entry<String, String> entry : collectionMap.entrySet())
-            {
-                NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
-                if (nl.getLength() == 1)
-                {
-                    collection.setMetadata(entry.getValue(), getStringValue(nl.item(0)));
-                }
-            }
-            
-            collection.update();
-            
-            element.setAttribute("identifier", collection.getHandle());
-            
-            Element nameElement = new Element("name");
-            nameElement.setText(collection.getMetadata("name"));
-            element.addContent(nameElement);
-            
-            if (collection.getMetadata("short_description") != null)
-            {
-                Element descriptionElement = new Element("description");
-                descriptionElement.setText(collection.getMetadata("short_description"));
-                element.addContent(descriptionElement);
-            }
-            
-            if (collection.getMetadata("introductory_text") != null)
-            {
-                Element introElement = new Element("intro");
-                introElement.setText(collection.getMetadata("introductory_text"));
-                element.addContent(introElement);
-            }
-            
-            if (collection.getMetadata("copyright_text") != null)
-            {
-                Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(collection.getMetadata("copyright_text"));
-                element.addContent(copyrightElement);
-            }
-            
-            if (collection.getMetadata("side_bar_text") != null)
-            {
-                Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(collection.getMetadata("side_bar_text"));
-                element.addContent(sidebarElement);
-            }
-            
-            if (collection.getMetadata("license") != null)
-            {
-                Element sidebarElement = new Element("license");
-                sidebarElement.setText(collection.getMetadata("license"));
-                element.addContent(sidebarElement);
-            }
-            
-            if (collection.getMetadata("provenance_description") != null)
-            {
-                Element sidebarElement = new Element("provenance");
-                sidebarElement.setText(collection.getMetadata("provenance_description"));
-                element.addContent(sidebarElement);
-            }
-            
-            elements[i] = element;
-        }
-        
-        return elements;
-    }
-    
-}

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

@@ -1,97 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import org.dspace.content.DCDate;
-import org.dspace.core.Context;
-import org.dspace.storage.rdbms.DatabaseManager;
-import org.dspace.storage.rdbms.TableRow;
-import org.dspace.storage.rdbms.TableRowIterator;
-
-/**
- * A command-line tool for performing necessary tweaks in the database for the
- * new last_modified column in the item table.
- * 
- * @author Robert Tansley
- * @version $Revision$
- */
-public class Upgrade101To11
-{
-    /**
-     * For invoking via the command line
-     * 
-     * @param argv
-     *            command-line arguments
-     */
-    public static void main(String[] argv)
-    {
-        Context context = null;
-
-        try
-        {
-            context = new Context();
-
-            // Deal with withdrawn items first.
-            // last_modified takes the value of the deletion date
-            TableRowIterator tri = DatabaseManager.queryTable(context, "item",
-                    "SELECT * FROM item WHERE withdrawal_date IS NOT NULL");
-
-            while (tri.hasNext())
-            {
-                TableRow row = tri.next();
-                DCDate d = new DCDate(row.getStringColumn("withdrawal_date"));
-                row.setColumn("last_modified", d.toDate());
-                DatabaseManager.update(context, row);
-            }
-            tri.close();
-
-            // Next, update those items with a date.available
-            tri = DatabaseManager.query(context,
-                        "SELECT item.item_id, dcvalue.text_value FROM item, dctyperegistry, "+
-                        "dcvalue WHERE item.item_id=dcvalue.item_id AND dcvalue.dc_type_id="+
-                        "dctyperegistry.dc_type_id AND dctyperegistry.element LIKE 'date' "+
-                        "AND dctyperegistry.qualifier LIKE 'available'");
-
-            while (tri.hasNext())
-            {
-                TableRow resultRow = tri.next();
-                DCDate d = new DCDate(resultRow.getStringColumn("text_value"));
-
-                // Can't update the row, have to do a separate query
-                TableRow itemRow = DatabaseManager.find(context, "item",
-                        resultRow.getIntColumn("item_id"));
-                itemRow.setColumn("last_modified", d.toDate());
-                DatabaseManager.update(context, itemRow);
-            }
-            tri.close();
-
-            // Finally, for all items that have no date.available or withdrawal
-            // date, set the update time to now!
-            DatabaseManager.updateQuery(context,
-                        "UPDATE item SET last_modified=now() WHERE last_modified IS NULL");
-
-            context.complete();
-
-            System.out.println("Last modified dates set");
-
-            System.exit(0);
-        }
-        catch (Exception e)
-        {
-            System.err.println("Exception occurred:" + e);
-            e.printStackTrace();
-
-            if (context != null)
-            {
-                context.abort();
-            }
-
-            System.exit(1);
-        }
-    }
-}

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

@@ -1,198 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.administer;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.core.Context;
-
-/**
- * Command-line tool for making changes to DSpace database when updating from
- * version 1.1/1.1.1 to 1.2.
- * <P>
- * The changes are:
- * <ul>
- * <li>Setting owning collection field for items
- * <li>Reorganising content bitstreams into one bundle named ORIGINAL, license
- * bitstreams into a bundle named LICENSE
- * <li>Setting the sequence_id numbers in the bitstream table. This happens as
- * item.update() is called on every item.
- * <li>If a (newly-reorganised) 'ORIGINAL' bundle contains a text/html
- * bitstream, that bitstream is set to the primary bitstream for HTML support.
- * </ul>
- */
-public class Upgrade11To12
-{
-    public static void main(String[] argv) throws Exception
-    {
-        Context c = new Context();
-
-        // ve are superuser!
-        c.setIgnoreAuthorization(true);
-
-        ItemIterator ii = null;
-
-        // first set owning Collections
-        Collection[] collections = Collection.findAll(c);
-
-        System.out.println("Setting item owningCollection fields in database");
-
-        for (int q = 0; q < collections.length; q++)
-        {
-            ii = collections[q].getItems();
-
-            while (ii.hasNext())
-            {
-                Item myItem = ii.next();
-
-                // set it if it's not already set
-                if (myItem.getOwningCollection() == null)
-                {
-                    myItem.setOwningCollection(collections[q]);
-                    myItem.update();
-                    System.out.println("Set owner of item " + myItem.getID()
-                            + " to collection " + collections[q].getID());
-                }
-            }
-        }
-
-        // commit pending transactions before continuing
-        c.commit();
-
-        // now combine some bundles
-        ii = Item.findAll(c);
-
-        while (ii.hasNext())
-        {
-            boolean skipItem = false;
-            Item myItem = ii.next();
-
-            int licenseBundleIndex = -1; // array index of license bundle (we'll
-                                         // skip this one often)
-            int primaryBundleIndex = -1; // array index of our primary bundle
-                                         // (all bitstreams assemble here)
-
-            System.out.println("Processing item #: " + myItem.getID());
-
-            Bundle[] myBundles = myItem.getBundles();
-
-            // look for bundles with multiple bitstreams
-            // (if any found, we'll skip this item)
-            for (int i = 0; i < myBundles.length; i++)
-            {
-                // skip if bundle is already named
-                if (myBundles[i].getName() != null)
-                {
-                    System.out
-                            .println("Skipping this item - named bundles already found");
-                    skipItem = true;
-
-                    break;
-                }
-
-                Bitstream[] bitstreams = myBundles[i].getBitstreams();
-
-                // skip this item if we already have bundles combined in this
-                // item
-                if (bitstreams.length > 1)
-                {
-                    System.out
-                            .println("Skipping this item - compound bundles already found");
-                    skipItem = true;
-
-                    break;
-                }
-
-                // is this the license? check the format
-                BitstreamFormat bf = bitstreams[0].getFormat();
-
-                if ("License".equals(bf.getShortDescription()))
-                {
-                    System.out.println("Found license!");
-
-                    if (licenseBundleIndex == -1)
-                    {
-                        licenseBundleIndex = i;
-                        System.out.println("License bundle set to: " + i);
-                    }
-                    else
-                    {
-                        System.out
-                                .println("ERROR - multiple license bundles in item - skipping");
-                        skipItem = true;
-
-                        break;
-                    }
-                }
-                else
-                {
-                    // not a license, if primary isn't set yet, set it
-                    if (primaryBundleIndex == -1)
-                    {
-                        primaryBundleIndex = i;
-                        System.out.println("Primary bundle set to: " + i);
-                    }
-                }
-            }
-
-            if (!skipItem)
-            {
-                // name the primary and license bundles
-                if (primaryBundleIndex != -1)
-                {
-                    myBundles[primaryBundleIndex].setName("ORIGINAL");
-                    myBundles[primaryBundleIndex].update();
-                }
-
-                if (licenseBundleIndex != -1)
-                {
-                    myBundles[licenseBundleIndex].setName("LICENSE");
-                    myBundles[licenseBundleIndex].update();
-                }
-
-                for (int i = 0; i < myBundles.length; i++)
-                {
-                    Bitstream[] bitstreams = myBundles[i].getBitstreams();
-
-                    // now we can safely assume no bundles with multiple
-                    // bitstreams
-                    if (bitstreams.length > 0 && (i != primaryBundleIndex) && (i != licenseBundleIndex))
-                    {
-                        // only option left is a bitstream to be combined
-                        // with primary bundle
-                        // and remove now-redundant bundle
-                        myBundles[primaryBundleIndex]
-                                .addBitstream(bitstreams[0]); // add to
-                                                              // primary
-                        myItem.removeBundle(myBundles[i]); // remove this
-                                                           // bundle
-
-                        System.out.println("Bitstream from bundle " + i
-                                + " moved to primary bundle");
-
-                        // flag if HTML bitstream
-                        if (bitstreams[0].getFormat().getMIMEType().equals(
-                                "text/html"))
-                        {
-                            System.out
-                                    .println("Set primary bitstream to HTML file in item #"
-                                            + myItem.getID()
-                                            + " for HTML support.");
-                        }
-                    }
-                }
-            }
-        }
-
-        c.complete();
-    }
-}

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

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

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

@@ -1,407 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-import org.dspace.content.Item;
-import org.dspace.content.DCValue;
-import org.dspace.content.Collection;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Utility class to store changes to item that may occur during a batch edit.
- *
- * @author Stuart Lewis
- */
-public class BulkEditChange
-{
-    /** The item these changes relate to */
-    private Item item;
-
-    /** The List of hashtables with the new elements */
-    private List<DCValue> adds;
-
-    /** The List of hashtables with the removed elements */
-    private List<DCValue> removes;
-
-    /** The List of hashtables with the unchanged elements */
-    private List<DCValue> constant;
-
-    /** The List of the complete set of new values (constant + adds) */
-    private List<DCValue> complete;
-
-    /** The list of old collections the item used to be mapped to */
-    private List<Collection> oldMappedCollections;
-
-    /** The list of new collections the item has been mapped into */
-    private List<Collection> newMappedCollections;
-
-    /** The old owning collection */
-    private Collection oldOwningCollection;
-
-    /** The new owning collection */
-    private Collection newOwningCollection;
-
-    /** Is this a new item */
-    private boolean newItem;
-
-    /** Has this item been deleted? */
-    private boolean deleted;
-
-    /** Has this item been withdrawn? */
-    private boolean withdrawn;
-
-    /** Has this item been reinstated? */
-    private boolean reinstated;
-
-    /** Have any changes actually been made? */
-    private boolean empty;
-
-
-    /**
-     * Initialise a change holder for a new item 
-     */
-    public BulkEditChange()
-    {
-        // Set the item to be null
-        item = null;
-        newItem = true;
-        empty = true;
-        oldOwningCollection = null;
-        newOwningCollection = null;
-
-        // Initialise the arrays
-        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<Collection>();
-    }
-
-    /**
-     * Initialise a new change holder for an existing item
-     *
-     * @param i The Item to store
-     */
-    public BulkEditChange(Item i)
-    {
-        // Store the item
-        item = i;
-        newItem = false;
-        empty = true;
-
-        // Initialise the arrays
-        adds = new ArrayList<DCValue>();
-        removes = new ArrayList<DCValue>();
-        constant = new ArrayList<DCValue>();
-        complete = new ArrayList<DCValue>();
-        oldMappedCollections = new ArrayList<Collection>();
-        newMappedCollections = new ArrayList<Collection>();
-    }
-
-    /**
-     * Store the item - used when a new item is created
-     *
-     * @param i The item
-     */
-    public void setItem(Item i)
-    {
-        // Store the item
-        item = i;
-    }
-
-    /**
-     * Add an added metadata value
-     *
-     * @param dcv The value to add
-     */
-    public void registerAdd(DCValue dcv)
-    {
-        // Add the added value
-        adds.add(dcv);
-        complete.add(dcv);
-        empty = false;
-    }
-
-    /**
-     * Add a removed metadata value
-     *
-     * @param dcv The value to remove
-     */
-    public void registerRemove(DCValue dcv)
-    {
-        // Add the removed value
-        removes.add(dcv);
-        empty = false;
-    }
-
-    /**
-     * Add an unchanged metadata value
-     *
-     * @param dcv The value to keep unchanged
-     */
-    public void registerConstant(DCValue dcv)
-    {
-        // Add the removed value
-        constant.add(dcv);
-        complete.add(dcv);
-    }
-
-    /**
-     * Add a new mapped Collection
-     *
-     * @param c The new mapped Collection
-     */
-    public void registerNewMappedCollection(Collection c)
-    {
-        // Add the new owning Collection
-        newMappedCollections.add(c);
-        empty = false;
-    }
-
-    /**
-     * Add an old mapped Collection
-     *
-     * @param c The old mapped Collection
-     */
-    public void registerOldMappedCollection(Collection c)
-    {
-        // Add the old owning Collection (if it isn't there already, or is an old collection)
-        boolean found = false;
-
-        if ((this.getOldOwningCollection() != null) &&
-            (this.getOldOwningCollection().getHandle().equals(c.getHandle())))
-        {
-            found = true;
-        }
-
-        for (Collection collection : oldMappedCollections)
-        {
-            if (collection.getHandle().equals(c.getHandle()))
-            {
-                found = true;
-            }
-        }
-
-        if (!found)
-        {
-            oldMappedCollections.add(c);
-            empty = false;
-        }
-    }
-
-    /**
-     * Register a change to the owning collection
-     *
-     * @param oldC The old owning collection
-     * @param newC The new owning collection
-     */
-    public void changeOwningCollection(Collection oldC, Collection newC)
-    {
-        // Store the old owning collection
-        oldOwningCollection = oldC;
-
-        // Store the new owning collection
-        newOwningCollection = newC;
-        empty = false;
-    }
-
-    /**
-     * Set the owning collection of an item
-     *
-     * @param newC The new owning collection
-     */
-    public void setOwningCollection(Collection newC)
-    {
-        // Store the new owning collection
-        newOwningCollection = newC;
-        //empty = false;
-    }
-
-    /**
-     * Get the DSpace Item that these changes are applicable to.
-     *
-     * @return The item
-     */
-    public Item getItem()
-    {
-        // Return the item
-        return item;
-    }
-
-    /**
-     * Get the list of elements and their values that have been added.
-     *
-     * @return the list of elements and their values that have been added.
-     */
-    public List<DCValue> getAdds()
-    {
-        // Return the array
-        return adds;
-    }
-
-    /**
-     * Get the list of elements and their values that have been removed.
-     *
-     * @return the list of elements and their values that have been removed.
-     */
-    public List<DCValue> getRemoves()
-    {
-        // Return the array
-        return removes;
-    }
-
-    /**
-     * Get the list of unchanged values
-     *
-     * @return the list of unchanged values
-     */
-    public List<DCValue> getConstant()
-    {
-        // Return the array
-        return constant;
-    }
-
-    /**
-     * Get the list of all values
-     *
-     * @return the list of all values
-     */
-    public List<DCValue> getComplete()
-    {
-        // Return the array
-        return complete;
-    }
-
-    /**
-     * Get the list of new mapped Collections
-     *
-     * @return the list of new mapped collections
-     */
-    public List<Collection> getNewMappedCollections()
-    {
-        // Return the array
-        return newMappedCollections;
-    }
-
-    /**
-     * Get the list of old mapped Collections
-     *
-     * @return the list of old mapped collections
-     */
-    public List<Collection> getOldMappedCollections()
-    {
-        // Return the array
-        return oldMappedCollections;
-    }
-
-    /**
-     * Get the old owning collection
-     *
-     * @return the old owning collection
-     */
-    public Collection getOldOwningCollection()
-    {
-        // Return the old owning collection
-        return oldOwningCollection;
-    }
-
-    /**
-     * Get the new owning collection
-     *
-     * @return the new owning collection
-     */
-    public Collection getNewOwningCollection()
-    {
-        // Return the new owning collection
-        return newOwningCollection;
-    }
-
-    /**
-     * Does this change object represent a new item?
-     *
-     * @return Whether or not this is for a new item
-     */
-    public boolean isNewItem()
-    {
-        // Return the new item status
-        return newItem;
-    }
-
-    /**
-     * Does this change object represent a deleted item?
-     *
-     * @return Whether or not this is for a deleted item
-     */
-    public boolean isDeleted()
-    {
-        // Return the new item status
-        return deleted;
-    }
-
-    /**
-     * Set that this item has been deleted
-     */
-    public void setDeleted() {
-        // Store the setting
-        deleted = true;
-        empty = false;
-    }
-
-    /**
-     * Does this change object represent a withdrawn item?
-     *
-     * @return Whether or not this is for a withdrawn item
-     */
-    public boolean isWithdrawn()
-    {
-        // Return the new item status
-        return withdrawn;
-    }
-
-    /**
-     * Set that this item has been withdrawn
-     */
-    public void setWithdrawn() {
-        // Store the setting
-        withdrawn = true;
-        empty = false;
-    }
-
-    /**
-     * Does this change object represent a reinstated item?
-     *
-     * @return Whether or not this is for a reinstated item
-     */
-    public boolean isReinstated()
-    {
-        // Return the new item status
-        return reinstated;
-    }
-
-    /**
-     * Set that this item has been deleted
-     */
-    public void setReinstated() {
-        // Store the setting
-        reinstated = true;
-        empty = false;
-    }
-
-    /**
-     * Have any changes actually been recorded, or is this empty?
-     *
-     * @return Whether or not changes have been made
-     */
-    public boolean hasChanges()
-    {
-        return !empty;
-    }
-}

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

@@ -1,681 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-import org.dspace.content.*;
-import org.dspace.content.Collection;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.*;
-
-/**
- * Utility class to read and write CSV files
- *
- * **************
- * Important Note
- * **************
- *
- * This class has been made serializable, as it is stored in a Session.
- * Is it wise to:
- *    a) be putting this into a user's session?
- *    b) holding an entire CSV upload in memory?
- *
- * @author Stuart Lewis
- */
-public class DSpaceCSV implements Serializable
-{
-    /** The headings of the CSV file */
-    private List<String> headings;
-
-    /** An array list of CSV lines */
-    private List<DSpaceCSVLine> lines;
-
-    /** A counter of how many CSV lines this object holds */
-    private int counter;
-
-    /** The value separator (defaults to double pipe '||') */
-    protected static String valueSeparator;
-
-    /** The value separator in an escaped form for using in regexs */
-    protected static String escapedValueSeparator;
-
-    /** The field separator (defaults to comma) */
-    protected static String fieldSeparator;
-
-    /** The field separator in an escaped form for using in regexs */
-    protected static String escapedFieldSeparator;
-
-    /** The authority separator (defaults to dobule colon '::') */
-    protected static String authoritySeparator;
-
-    /** The authority separator in an escaped form for using in regexs */
-    protected static String escapedAuthoritySeparator;
-
-
-    /** Whether to export all metadata such as handles and provenance information */
-    private boolean exportAll;
-
-    /** A list of metadata elements to ignore */
-    private Map<String, String> ignore;
-
-
-    /**
-     * Create a new instance of a CSV line holder
-     *
-     * @param exportAll Whether to export all metadata such as handles and provenance information
-     */
-    public DSpaceCSV(boolean exportAll)
-    {
-        // Initialise the class
-        init();
-
-        // Store the exportAll setting
-        this.exportAll = exportAll;
-    }
-
-    /**
-     * Create a new instance, reading the lines in from file
-     *
-     * @param f The file to read from
-     * @param c The DSpace Context
-     *
-     * @throws Exception thrown if there is an error reading or processing the file
-     */
-    public DSpaceCSV(File f, Context c) throws Exception
-    {
-        // Initialise the class
-        init();
-
-        // Open the CSV file
-        BufferedReader input = null;
-        try
-        {
-            input = new BufferedReader(new InputStreamReader(new FileInputStream(f),"UTF-8"));
-
-            // Read the heading line
-            String head = input.readLine();
-            String[] headingElements = head.split(escapedFieldSeparator);
-            int columnCounter = 0;
-            for (String element : headingElements)
-            {
-                columnCounter++;
-
-                // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\"")))
-                {
-                    element = element.substring(1, element.length() - 1);
-                }
-
-                // Store the heading
-                if ("collection".equals(element))
-                {
-                    // Store the heading
-                    headings.add(element);
-                }
-                // Store the action
-                else if ("action".equals(element))
-                {
-                    // Store the heading
-                    headings.add(element);
-                }
-                else if (!"id".equals(element))
-                {
-                    // Verify that the heading is valid in the metadata registry
-                    String[] clean = element.split("\\[");
-                    String[] parts = clean[0].split("\\.");
-
-                    if (parts.length < 2) {
-                        throw new MetadataImportInvalidHeadingException(element,
-                                                                        MetadataImportInvalidHeadingException.ENTRY,
-                                                                        columnCounter);
-                    }
-
-                    String metadataSchema = parts[0];
-                    String metadataElement = parts[1];
-                    String metadataQualifier = null;
-                    if (parts.length > 2) {
-                        metadataQualifier = parts[2];
-                    }
-
-                    // Check that the scheme exists
-                    MetadataSchema foundSchema = MetadataSchema.find(c, metadataSchema);
-                    if (foundSchema == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.SCHEMA,
-                                                                        columnCounter);
-                    }
-
-                    // Check that the metadata element exists in the schema
-                    int schemaID = foundSchema.getSchemaID();
-                    MetadataField foundField = MetadataField.findByElement(c, schemaID, metadataElement, metadataQualifier);
-                    if (foundField == null) {
-                        throw new MetadataImportInvalidHeadingException(clean[0],
-                                                                        MetadataImportInvalidHeadingException.ELEMENT,
-                                                                        columnCounter);
-                    }
-
-                    // Store the heading
-                    headings.add(element);
-                }
-            }
-
-            // Read each subsequent line
-            StringBuilder lineBuilder = new StringBuilder();
-            String lineRead;
-
-            while ((lineRead = input.readLine()) != null)
-            {
-                if (lineBuilder.length() > 0) {
-                    // Already have a previously read value - add this line
-                    lineBuilder.append("\n").append(lineRead);
-
-                    // Count the number of quotes in the buffer
-                    int quoteCount = 0;
-                    for (int pos = 0; pos < lineBuilder.length(); pos++) {
-                        if (lineBuilder.charAt(pos) == '"') {
-                            quoteCount++;
-                        }
-                    }
-
-                    if (quoteCount % 2 == 0) {
-                        // Number of quotes is a multiple of 2, add the item
-                        addItem(lineBuilder.toString());
-                        lineBuilder = new StringBuilder();
-                    }
-                } else if (lineRead.indexOf('"') > -1) {
-                    // Get the number of quotes in the line
-                    int quoteCount = 0;
-                    for (int pos = 0; pos < lineRead.length(); pos++) {
-                        if (lineRead.charAt(pos) == '"') {
-                            quoteCount++;
-                        }
-                    }
-
-                    if (quoteCount % 2 == 0) {
-                        // Number of quotes is a multiple of 2, add the item
-                        addItem(lineRead);
-                    } else {
-                        // Uneven quotes - add to the buffer and leave for later
-                        lineBuilder.append(lineRead);
-                    }
-                } else {
-                    // No previously read line, and no quotes in the line - add item
-                    addItem(lineRead);
-                }
-            }
-        }
-        finally
-        {
-            if (input != null)
-            {
-                input.close();
-            }
-        }
-    }
-
-    /**
-     * Initialise this class with values from dspace.cfg
-     */
-    private void init()
-    {
-        // Set the value separator
-        setValueSeparator();
-
-        // Set the field separator
-        setFieldSeparator();
-
-        // Set the authority separator
-        setAuthoritySeparator();
-
-        // Create the headings
-        headings = new ArrayList<String>();
-
-        // Create the blank list of items
-        lines = new ArrayList<DSpaceCSVLine>();
-
-        // Initialise the counter
-        counter = 0;
-
-        // Set the metadata fields to ignore
-        ignore = new HashMap<String, String>();
-        String toIgnore = ConfigurationManager.getProperty("bulkedit", "ignore-on-export");
-        if ((toIgnore == null) || ("".equals(toIgnore.trim())))
-        {
-            // Set a default value
-            toIgnore = "dc.date.accessioned, dc.date.available, " +
-                       "dc.date.updated, dc.description.provenance";
-        }
-        String[] toIgnoreArray = toIgnore.split(",");
-        for (String toIgnoreString : toIgnoreArray)
-        {
-            if (!"".equals(toIgnoreString.trim()))
-            {
-                ignore.put(toIgnoreString.trim(), toIgnoreString.trim());
-            }
-        }
-    }
-
-    /**
-     * Decide if this CSV file has an 'action' (case-dependent!) header.
-     *
-     * @return Whether or not there is an 'action' header
-     */
-    public boolean hasActions() {
-        // Look for a heading called 'action'
-        for (String header : headings) {
-            if (header.equals("action")) {
-                return true;
-            }
-        }
-        return false;
-    }
-
-    /**
-     * Set the value separator for multiple values stored in one csv value.
-     *
-     * Is set in bulkedit.cfg as valueseparator
-     *
-     * If not set, defaults to double pipe '||'
-     */
-    private void setValueSeparator()
-    {
-        // Get the value separator
-        valueSeparator = ConfigurationManager.getProperty("bulkedit", "valueseparator");
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim())))
-        {
-            valueSeparator = valueSeparator.trim();
-        }
-        else
-        {
-            valueSeparator = "||";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(valueSeparator);
-        escapedValueSeparator = match.replaceAll("\\\\$1");
-    }
-
-    /**
-     * Set the field separator use to separate fields in the csv.
-     *
-     * Is set in bulkedit.cfg as fieldseparator
-     *
-     * If not set, defaults to comma ','.
-     *
-     * Special values are 'tab', 'hash' and 'semicolon' which will
-     * get substituted from the text to the value.
-     */
-    private void setFieldSeparator()
-    {
-        // Get the value separator
-        fieldSeparator = ConfigurationManager.getProperty("bulkedit", "fieldseparator");
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim())))
-        {
-            fieldSeparator = fieldSeparator.trim();
-            if ("tab".equals(fieldSeparator))
-            {
-                fieldSeparator = "\t";
-            }
-            else if ("semicolon".equals(fieldSeparator))
-            {
-                fieldSeparator = ";";
-            }
-            else if ("hash".equals(fieldSeparator))
-            {
-                fieldSeparator = "#";
-            }
-            else
-            {
-                fieldSeparator = fieldSeparator.trim();
-            }
-        }
-        else
-        {
-            fieldSeparator = ",";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(fieldSeparator);
-        escapedFieldSeparator = match.replaceAll("\\\\$1");
-    }
-
-     /**
-     * Set the authority separator for value with authority data.
-     *
-     * Is set in dspace.cfg as bulkedit.authorityseparator
-     *
-     * If not set, defaults to double colon '::'
-     */
-    private void setAuthoritySeparator()
-    {
-        // Get the value separator
-        authoritySeparator = ConfigurationManager.getProperty("bulkedit", "authorityseparator");
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim())))
-        {
-            authoritySeparator = authoritySeparator.trim();
-        }
-        else
-        {
-            authoritySeparator = "::";
-        }
-
-        // Now store the escaped version
-        Pattern spchars = Pattern.compile("([\\\\*+\\[\\](){}\\$.?\\^|])");
-        Matcher match = spchars.matcher(authoritySeparator);
-        escapedAuthoritySeparator = match.replaceAll("\\\\$1");
-    }
-
-    /**
-     * Add a DSpace item to the CSV file
-     *
-     * @param i The DSpace item
-     *
-     * @throws Exception if something goes wrong with adding the Item
-     */
-    public final void addItem(Item i) throws Exception
-    {
-        // Create the CSV line
-        DSpaceCSVLine line = new DSpaceCSVLine(i.getID());
-
-        // Add in owning collection
-        String owningCollectionHandle = i.getOwningCollection().getHandle();
-        line.add("collection", owningCollectionHandle);
-
-        // Add in any mapped collections
-        Collection[] collections = i.getCollections();
-        for (Collection c : collections)
-        {
-            // Only add if it is not the owning collection
-            if (!c.getHandle().equals(owningCollectionHandle))
-            {
-                line.add("collection", c.getHandle());
-            }
-        }
-
-        // Populate it
-        DCValue md[] = i.getMetadata(Item.ANY, Item.ANY, Item.ANY, Item.ANY);
-        for (DCValue value : md)
-        {
-            // Get the key (schema.element)
-            String key = value.schema + "." + value.element;
-
-            // Add the qualifier if there is one (schema.element.qualifier)
-            if (value.qualifier != null)
-            {
-                key = key + "." + value.qualifier;
-            }
-
-            // Add the language if there is one (schema.element.qualifier[langauge])
-            //if ((value.language != null) && (!"".equals(value.language)))
-            if (value.language != null)
-            {
-                key = key + "[" + value.language + "]";
-            }
-
-            // Store the item
-            if (exportAll || okToExport(value))
-            {
-                // Add authority and confidence if authority is not null
-                String mdValue = value.value;
-                if (value.authority != null && !"".equals(value.authority))
-                {
-                    mdValue += authoritySeparator + value.authority + authoritySeparator + value.confidence;
-                }
-                line.add(key, mdValue);
-                if (!headings.contains(key))
-                {
-                    headings.add(key);
-                }
-            }
-        }
-        lines.add(line);
-        counter++;
-    }
-
-    /**
-     * Add an item to the CSV file, from a CSV line of elements
-     *
-     * @param line The line of elements
-     * @throws Exception Thrown if an error occurs when adding the item
-     */
-    public final void addItem(String line) throws Exception
-    {
-        // Check to see if the last character is a field separator, which hides the last empy column
-        boolean last = false;
-        if (line.endsWith(fieldSeparator))
-        {
-            // Add a space to the end, then remove it later
-            last = true;
-            line += " ";
-        }
-
-        // Split up on field separator
-        String[] parts = line.split(escapedFieldSeparator);
-        ArrayList<String> bits = new ArrayList<String>();
-        bits.addAll(Arrays.asList(parts));
-
-        // Merge parts with embedded separators
-        boolean alldone = false;
-        while (!alldone)
-        {
-            boolean found = false;
-            int i = 0;
-            for (String part : bits)
-            {
-                int bitcounter = part.length() - part.replaceAll("\"", "").length();
-                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1)))
-                {
-                    found = true;
-                    String add = bits.get(i) + fieldSeparator + bits.get(i + 1);
-                    bits.remove(i);
-                    bits.add(i, add);
-                    bits.remove(i + 1);
-                    break;
-                }
-                i++;
-            }
-            alldone = !found;
-        }
-
-        // Deal with quotes around the elements
-        int i = 0;
-        for (String part : bits)
-        {
-            if ((part.startsWith("\"")) && (part.endsWith("\"")))
-            {
-                part = part.substring(1, part.length() - 1);
-                bits.set(i, part);
-            }
-            i++;
-        }
-
-        // Remove embedded quotes
-        i = 0;
-        for (String part : bits)
-        {
-            if (part.contains("\"\""))
-            {
-                part = part.replaceAll("\"\"", "\"");
-                bits.set(i, part);
-            }
-            i++;
-        }
-
-        // Add elements to a DSpaceCSVLine
-        String id = parts[0].replaceAll("\"", "");
-        DSpaceCSVLine csvLine;
-
-        // Is this an existing item, or a new item (where id = '+')
-        if ("+".equals(id))
-        {
-            csvLine = new DSpaceCSVLine();
-        }
-        else
-        {
-            try
-            {
-                csvLine = new DSpaceCSVLine(Integer.parseInt(id));
-            }
-            catch (NumberFormatException nfe)
-            {
-                System.err.println("Invalid item identifier: " + id);
-                System.err.println("Please check your CSV file for information. " +
-                                   "Item id must be numeric, or a '+' to add a new item");
-                throw(nfe);
-            }
-        }
-
-        // Add the rest of the parts
-        i = 0;
-        for (String part : bits)
-        {
-            if (i > 0)
-            {
-                // Is this a last empty item?
-                if ((last) && (i == headings.size()))
-                {
-                    part = "";
-                }
-
-                // Make sure we register that this column was there
-                if (headings.size() < i) {
-                    throw new MetadataImportInvalidHeadingException("",
-                                                                    MetadataImportInvalidHeadingException.MISSING,
-                                                                    i + 1);
-                }
-                csvLine.add(headings.get(i - 1), null);
-                String[] elements = part.split(escapedValueSeparator);
-                for (String element : elements)
-                {
-                    if ((element != null) && (!"".equals(element)))
-                    {
-                        csvLine.add(headings.get(i - 1), element);
-                    }
-                }
-            }
-            i++;
-        }
-        lines.add(csvLine);
-        counter++;
-    }
-
-    /**
-     * Get the lines in CSV holders
-     *
-     * @return The lines
-     */
-    public final List<DSpaceCSVLine> getCSVLines()
-    {
-        // Return the lines
-        return lines;
-    }
-
-    /**
-     * Get the CSV lines as an array of CSV formatted strings
-     *
-     * @return the array of CSV formatted Strings
-     */
-    public final String[] getCSVLinesAsStringArray()
-    {
-        // Create the headings line
-        String[] csvLines = new String[counter + 1];
-        csvLines[0] = "id" + fieldSeparator + "collection";
-        Collections.sort(headings);
-        for (String value : headings)
-        {
-            csvLines[0] = csvLines[0] + fieldSeparator + value;
-        }
-
-        Iterator<DSpaceCSVLine> i = lines.iterator();
-        int c = 1;
-        while (i.hasNext())
-        {
-            csvLines[c++] = i.next().toCSV(headings);
-        }
-
-        return csvLines;
-    }
-
-    /**
-     * Save the CSV file to the given filename
-     *
-     * @param filename The filename to save the CSV file to
-     *
-     * @throws IOException Thrown if an error occurs when writing the file
-     */
-    public final void save(String filename) throws IOException
-    {
-        // Save the file
-        BufferedWriter out = new BufferedWriter(
-                             new OutputStreamWriter(
-                             new FileOutputStream(filename), "UTF-8"));
-        for (String csvLine : getCSVLinesAsStringArray()) {
-            out.write(csvLine + "\n");
-        }
-        out.flush();
-        out.close();
-    }
-
-    /**
-     * Is it Ok to export this value? When exportAll is set to false, we don't export
-     * some of the metadata elements.
-     *
-     * The list can be configured via the key ignore-on-export in bulkedit.cfg
-     *
-     * @param md The DCValue to examine
-     * @return Whether or not it is OK to export this element
-     */
-    private final boolean okToExport(DCValue md)
-    {
-        // Now compare with the list to ignore
-        String key = md.schema + "." + md.element;
-        if (md.qualifier != null)
-        {
-            key += "." + md.qualifier;
-        }
-        if (ignore.get(key) != null) {
-            return false;
-        }
-
-        // Must be OK, so don't ignore
-        return true;
-    }
-
-    /**
-     * Get the headings used in this CSV file
-     *
-     * @return The headings
-     */
-    public List<String> getHeadings()
-    {
-        return headings;
-    }
-
-    /**
-     * Return the csv file as one long formatted string
-     *
-     * @return The formatted String as a csv
-     */
-    public final String toString()
-    {
-        // Return the csv as one long string
-        StringBuffer csvLines = new StringBuffer();
-        String[] lines = this.getCSVLinesAsStringArray();
-        for (String line : lines)
-        {
-            csvLines.append(line).append("\n");
-        }
-        return csvLines.toString();
-    }
-}

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

@@ -1,193 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-/**
- * Utility class to store a line from a CSV file
- *
- * @author Stuart Lewis
- */
-public class DSpaceCSVLine implements Serializable
-{
-    /** The item id of the item represented by this line. -1 is for a new item */
-    private int id;
-
-    /** The elements in this line in a hashtable, keyed by the metadata type */
-    private Map<String, ArrayList> items;
-
-    /**
-     * Create a new CSV line
-     *
-     * @param itemId The item ID of the line
-     */
-    public DSpaceCSVLine(int itemId)
-    {
-        // Store the ID + separator, and initialise the hashtable
-        this.id = itemId;
-        items = new HashMap<String, ArrayList>();
-    }
-
-    /**
-     * Create a new CSV line for a new item
-     */
-    public DSpaceCSVLine()
-    {
-        // Set the ID to be -1, and initialise the hashtable
-        this.id = -1;
-        this.items = new HashMap<String, ArrayList>();
-    }
-
-    /**
-     * Get the item ID that this line represents
-     *
-     * @return The item ID
-     */
-    public int getID()
-    {
-        // Return the ID
-        return id;
-    }
-
-    /**
-     * Add a new metadata value to this line
-     *
-     * @param key The metadata key (e.g. dc.contributor.author)
-     * @param value The metadata value
-     */
-    public void add(String key, String value)
-    {
-        // Create the array list if we need to
-        if (items.get(key) == null)
-        {
-            items.put(key, new ArrayList<String>());
-        }
-
-        // Store the item if it is not null
-        if (value != null)
-        {
-            items.get(key).add(value);
-        }
-    }
-
-    /**
-     * Get all the values that match the given metadata key. Will be null if none exist.
-     *
-     * @param key The metadata key
-     * @return All the elements that match
-     */
-    public List<String> get(String key)
-    {
-        // Return any relevant values
-        return items.get(key);
-    }
-
-    /**
-     * Get any action associated with this line
-     *
-     * @return The action (may be blank, 'withdraw', 'reinstate' or 'delete')
-     */
-    public String getAction()
-    {
-        if (items.containsKey("action")) {
-            ArrayList actions = items.get("action");
-            if (actions.size() > 0) {
-                return ((String)actions.get(0)).trim();
-            }
-        }
-        return "";
-    }
-
-    /**
-     * Get all the metadata keys that are represented in this line
-     *
-     * @return An enumeration of all the keys
-     */
-    public Set<String> keys()
-    {
-        // Return the keys
-        return items.keySet();
-    }
-
-    /**
-     * Write this line out as a CSV formatted string, in the order given by the headings provided
-     *
-     * @param headings The headings which define the order the elements must be presented in
-     * @return The CSV formatted String
-     */
-    protected String toCSV(List<String> headings)
-    {
-        StringBuilder bits = new StringBuilder();
-
-        // Add the id
-        bits.append("\"").append(id).append("\"").append(DSpaceCSV.fieldSeparator);
-        bits.append(valueToCSV(items.get("collection")));
-
-        // Add the rest of the elements
-        for (String heading : headings)
-        {
-            bits.append(DSpaceCSV.fieldSeparator);
-            List<String> values = items.get(heading);
-            if (values != null && !"collection".equals(heading))
-            {
-                bits.append(valueToCSV(values));
-            }
-        }
-
-        return bits.toString();
-    }
-
-    /**
-     * Internal method to create a CSV formatted String joining a given set of elements
-     *
-     * @param values The values to create the string from
-     * @return The line as a CSV formatted String
-     */
-    protected String valueToCSV(List<String> values)
-    {
-        // Check there is some content
-        if (values == null)
-        {
-            return "";
-        }
-
-        // Get on with the work
-        String s;
-        if (values.size() == 1)
-        {
-            s = values.get(0);
-        }
-        else
-        {
-            // Concatenate any fields together
-            StringBuilder str = new StringBuilder();
-
-            for (String value : values)
-            {
-                if (str.length() > 0)
-                {
-                    str.append(DSpaceCSV.valueSeparator);
-                }
-
-                str.append(value);
-            }
-
-            s = str.toString();
-        }
-
-        // Replace internal quotes with two sets of quotes
-        return "\"" + s.replaceAll("\"", "\"\"") + "\"";
-    }
-}
-

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

@@ -1,266 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-import org.apache.commons.cli.*;
-
-import org.dspace.content.*;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-
-import java.util.ArrayList;
-import java.sql.SQLException;
-import java.util.List;
-
-/**
- * Metadata exporter to allow the batch export of metadata into a file
- *
- * @author Stuart Lewis
- */
-public class MetadataExport
-{
-    /** The items to export */
-    private ItemIterator toExport;
-
-    /** Whether to export all metadata, or just normally edited metadata */
-    private boolean exportAll;
-
-    /**
-     * Set up a new metadata export
-     *
-     * @param c The Context
-     * @param toExport The ItemIterator of items to export
-     * @param exportAll whether to export all metadata or not (include handle, provenance etc)
-     */
-    public MetadataExport(Context c, ItemIterator toExport, boolean exportAll)
-    {
-        // Store the export settings
-        this.toExport = toExport;
-        this.exportAll = exportAll;
-    }
-
-    /**
-     * Method to export a community (and sub-communities and collections)
-     *
-     * @param c The Context
-     * @param toExport The Community to export
-     * @param exportAll whether to export all metadata or not (include handle, provenance etc)
-     */
-    public MetadataExport(Context c, Community toExport, boolean exportAll)
-    {
-        try
-        {
-            // Try to export the community
-            this.toExport = new ItemIterator(c, buildFromCommunity(toExport, new ArrayList<Integer>(), 0));
-            this.exportAll = exportAll;
-        }
-        catch (SQLException sqle)
-        {
-            // Something went wrong...
-            System.err.println("Error running exporter:");
-            sqle.printStackTrace(System.err);
-            System.exit(1);
-        }
-    }
-
-    /**
-     * Build an array list of item ids that are in a community (include sub-communities and collections)
-     *
-     * @param community The community to build from
-     * @param itemIDs The itemID (used for recursion - use an empty ArrayList)
-     * @param indent How many spaces to use when writing out the names of items added
-     * @return The list of item ids
-     * @throws SQLException
-     */
-    private List<Integer> buildFromCommunity(Community community, List<Integer> itemIDs, int indent)
-                                                                               throws SQLException
-    {
-        // Add all the collections
-        Collection[] collections = community.getCollections();
-        for (Collection collection : collections)
-        {
-            for (int i = 0; i < indent; i++)
-            {
-                System.out.print(" ");
-            }
-
-            ItemIterator items = collection.getAllItems();
-            while (items.hasNext())
-            {
-                int id = items.next().getID();
-                // Only add if not already included (so mapped items only appear once)
-                if (!itemIDs.contains(id))
-                {
-                    itemIDs.add(id);
-                }
-            }
-        }
-
-        // Add all the sub-communities
-        Community[] communities = community.getSubcommunities();
-        for (Community subCommunity : communities)
-        {
-            for (int i = 0; i < indent; i++)
-            {
-                System.out.print(" ");
-            }
-            buildFromCommunity(subCommunity, itemIDs, indent + 1);
-        }
-
-        return itemIDs;
-    }
-
-    /**
-     * Run the export
-     *
-     * @return the exported CSV lines
-     */
-    public DSpaceCSV export()
-    {
-        try
-        {
-            // Process each item
-            DSpaceCSV csv = new DSpaceCSV(exportAll);
-            while (toExport.hasNext())
-            {
-                csv.addItem(toExport.next());
-            }
-
-            // Return the results
-            return csv;
-        }
-        catch (Exception e)
-        {
-            return null;
-        }
-    }
-
-    /**
-     * Print the help message
-     *
-     * @param options The command line options the user gave
-     * @param exitCode the system exit code to use
-     */
-    private static void printHelp(Options options, int exitCode)
-    {
-        // print the help message
-        HelpFormatter myhelp = new HelpFormatter();
-        myhelp.printHelp("MetadataExport\n", options);
-        System.out.println("\nfull export: metadataexport -f filename");
-        System.out.println("partial export: metadataexport -i handle -f filename");
-        System.exit(exitCode);
-    }
-
-    /**
-	 * main method to run the metadata exporter
-	 *
-	 * @param argv the command line arguments given
-	 */
-    public static void main(String[] argv) throws Exception
-    {
-        // Create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
-        options.addOption("f", "file", true, "destination where you want file written");
-        options.addOption("a", "all", false, "include all metadata fields that are not normally changed (e.g. provenance)");
-        options.addOption("h", "help", false, "help");
-
-        CommandLine line = null;
-
-        try
-        {
-            line = parser.parse(options, argv);
-        }
-        catch (ParseException pe)
-        {
-            System.err.println("Error with commands.");
-            printHelp(options, 1);
-            System.exit(0);
-        }
-
-        if (line.hasOption('h'))
-        {
-            printHelp(options, 0);
-        }
-
-        // Check a filename is given
-        if (!line.hasOption('f'))
-        {
-            System.err.println("Required parameter -f missing!");
-            printHelp(options, 1);
-        }
-        String filename = line.getOptionValue('f');
-
-        // Create a context
-        Context c = new Context();
-        c.turnOffAuthorisationSystem();
-
-        // The things we'll export
-        ItemIterator toExport = null;
-        MetadataExport exporter = null;
-
-        // Export everything?
-        boolean exportAll = line.hasOption('a');
-
-        // Check we have an item OK
-        if (!line.hasOption('i'))
-        {
-            System.out.println("Exporting whole repository WARNING: May take some time!");
-            exporter = new MetadataExport(c, Item.findAll(c), exportAll);
-        }
-        else
-        {
-            String handle = line.getOptionValue('i');
-            DSpaceObject dso = HandleManager.resolveToObject(c, handle);
-            if (dso == null)
-            {
-                System.err.println("Item '" + handle + "' does not resolve to an item in your repository!");
-                printHelp(options, 1);
-            }
-
-            if (dso.getType() == Constants.ITEM)
-            {
-                System.out.println("Exporting item '" + dso.getName() + "' (" + handle + ")");
-                List<Integer> item = new ArrayList<Integer>();
-                item.add(dso.getID());
-                exporter = new MetadataExport(c, new ItemIterator(c, item), exportAll);
-            }
-            else if (dso.getType() == Constants.COLLECTION)
-            {
-                System.out.println("Exporting collection '" + dso.getName() + "' (" + handle + ")");
-                Collection collection = (Collection)dso;
-                toExport = collection.getAllItems();
-                exporter = new MetadataExport(c, toExport, exportAll);
-            }
-            else if (dso.getType() == Constants.COMMUNITY)
-            {
-                System.out.println("Exporting community '" + dso.getName() + "' (" + handle + ")");
-                exporter = new MetadataExport(c, (Community)dso, exportAll);
-            }
-            else
-            {
-                System.err.println("Error identifying '" + handle + "'");
-                System.exit(1);
-            }
-        }
-
-        // Perform the export
-        DSpaceCSV csv = exporter.export();
-
-        // Save the files to the file
-        csv.save(filename);        
-
-        // Finish off and tidy up
-        c.restoreAuthSystemState();
-        c.complete();
-    }
-}

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

@@ -1,37 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-/**
- * Metadata importer exception
- *
- * @author Stuart Lewis
- */
-public class MetadataImportException extends Exception
-{
-    /**
-     * Instantiate a new MetadataImportException
-     *
-     * @param message the error message
-     */
-    public MetadataImportException(String message)
-    {
-       super(message);
-    }
-
-    /**
-     * Instantiate a new MetadataImportException
-     *
-     * @param message the error message
-     * @param exception the root cause
-     */
-    public MetadataImportException(String message, Exception exception)
-    {
-       super(message, exception);
-    }
-}

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

@@ -1,104 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.bulkedit;
-
-/**
- * Metadata importer exception
- *
- * @author Stuart Lewis
- */
-public class MetadataImportInvalidHeadingException extends Exception
-{
-    /** The type of error (schema or element) */
-    private int type;
-
-    /** The bad heading */
-    private String badHeading;
-
-    /** The column number */
-    private int column;
-
-    /** Error with the schema */
-    public static final int SCHEMA = 0;
-
-    /** Error with the element */
-    public static final int ELEMENT = 1;
-
-    /** Error with a missing header */
-    public static final int MISSING = 98;
-
-    /** Error with the whole entry */
-    public static final int ENTRY = 99;
-
-
-    /**
-     * Instantiate a new MetadataImportInvalidHeadingException
-     *
-     * @param message the error message
-     * @param theType the type of the error
-     */
-    public MetadataImportInvalidHeadingException(String message, int theType, int theColumn)
-    {
-        super(message);
-        badHeading = message;
-        type = theType;
-        column = theColumn;
-    }
-
-    /**
-     * Get the type of the exception
-     *
-     *  @return the type of the exception
-     */
-    public String getType()
-    {
-        return "" + type;
-    }
-
-    /**
-     * Get the heading that was invalid
-     *
-     * @return the invalid heading
-     */
-    public String getBadHeader()
-    {
-        return badHeading;
-    }
-
-    /**
-     * Get the column number that was invalid
-     *
-     * @return the invalid column number
-     */
-    public int getColumn()
-    {
-        return column;
-    }
-
-    /**
-     * Get the exception message
-     *
-     * @return The exception message
-     */
-    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;
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/checker/package.html

@@ -1,19 +0,0 @@
-<!--
-
-    The contents of this file are subject to the license and copyright
-    detailed in the LICENSE and NOTICE files at the root of the source
-    tree and available online at
-
-    http://www.dspace.org/license/
-
--->
-<html>
-	<head>
-		<title>org.dspace.app.checker Package Documentation</title>
-	</head>
-  <body>
-      <p>org.dspace.app.checker provides user interfaces to the org.dspace.checker 
-		  package. Command line options are detailed in the ChecksumChecker javadoc.
-		  </p>
-  </body>
-</html>

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

@@ -1,42 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.configuration;
-
-import org.dspace.kernel.config.SpringLoader;
-import org.dspace.services.ConfigurationService;
-
-import java.io.File;
-import java.net.MalformedURLException;
-
-/**
- * User: kevin (kevin at atmire.com)
- * Date: 3-aug-2011
- * Time: 11:31:21
- */
-public class APISpringLoader implements SpringLoader {
-
-    @Override
-    public String[] getResourcePaths(ConfigurationService configurationService) {
-        StringBuffer filePath = new StringBuffer();
-        filePath.append(configurationService.getProperty("dspace.dir"));
-        filePath.append(File.separator);
-        filePath.append("config");
-        filePath.append(File.separator);
-        filePath.append("spring");
-        filePath.append(File.separator);
-        filePath.append("api");
-        filePath.append(File.separator);
-
-
-        try {
-            return new String[]{new File(filePath.toString()).toURI().toURL().toString() + XML_SUFFIX};
-        } catch (MalformedURLException e) {
-            return new String[0];
-        }
-    }
-}

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

@@ -1,483 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.harvest;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.List;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.browse.IndexBrowse;
-import org.dspace.content.Collection;
-import org.dspace.content.DSpaceObject;
-import org.dspace.harvest.HarvestedCollection;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.harvest.OAIHarvester;
-import org.dspace.harvest.OAIHarvester.HarvestingException;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-import org.dspace.handle.HandleManager;
-
-/**
- *  Test class for harvested collections.
- *
- * @author Alexey Maslov
- */
-public class Harvest
-{
-	private static Context context;
-	
-    public static void main(String[] argv) throws Exception
-    {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-        options.addOption("p", "purge", false, "delete all items in the collection");
-        options.addOption("r", "run", false, "run the standard harvest procedure");
-        options.addOption("g", "ping", false, "test the OAI server and set");
-        options.addOption("o", "once", false, "run the harvest procedure with specified parameters");
-        options.addOption("s", "setup", false, "Set the collection up for harvesting");
-        options.addOption("S", "start", false, "start the harvest loop");
-        options.addOption("R", "reset", false, "reset harvest status on all collections");
-        options.addOption("P", "purge", false, "purge all harvestable collections");
-        
-
-        options.addOption("e", "eperson", true, "eperson");
-        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
-        options.addOption("t", "type", true, "type of harvesting (0 for none)");
-        options.addOption("a", "address", true, "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true, "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
-
-        options.addOption("h", "help", false, "help");
-
-        CommandLine line = parser.parse(options, argv);
-
-        String command = null; 
-        String eperson = null;
-        String collection = null;
-        String oaiSource = null;
-        String oaiSetID = null;
-        String metadataKey = null;
-        int harvestType = 0;
-        
-        if (line.hasOption('h'))
-        {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("Harvest\n", options);
-            System.out
-    				.println("\nPING OAI server: Harvest -g -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.exit(0);
-        }
-
-        if (line.hasOption('s')) {
-            command = "config";
-        }
-        if (line.hasOption('p')) {
-            command = "purge";
-        }
-        if (line.hasOption('r')) {
-            command = "run";
-        }
-        if (line.hasOption('g')) {
-            command = "ping";
-        }
-        if (line.hasOption('o')) {
-            command = "runOnce";
-        }
-        if (line.hasOption('S')) {
-            command = "start";
-        }
-        if (line.hasOption('R')) {
-            command = "reset";
-        }
-        if (line.hasOption('P')) {
-            command = "purgeAll";
-        }
-
-        
-        if (line.hasOption('e')) {
-            eperson = line.getOptionValue('e');
-        }
-        if (line.hasOption('c')) {
-            collection = line.getOptionValue('c');
-        }
-        if (line.hasOption('t')) {
-            harvestType = Integer.parseInt(line.getOptionValue('t'));
-        } else {
-        	harvestType = 0;
-        }
-        if (line.hasOption('a')) {
-            oaiSource = line.getOptionValue('a');
-        }
-        if (line.hasOption('i')) {
-            oaiSetID = line.getOptionValue('i');
-        }
-        if (line.hasOption('m')) {
-            metadataKey = line.getOptionValue('m');
-        }
-        
-
-        // Instantiate our class
-        Harvest harvester = new Harvest();
-        harvester.context = new Context();
-        
-        
-        // Check our options
-        if (command == null)
-        {
-            System.out
-                    .println("Error - no parameters specified (run with -h flag for details)");
-            System.exit(1);
-        }
-        // Run a single harvest cycle on a collection using saved settings.
-        else if ("run".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
-                System.out
-                        .println("Error - a target collection and eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-            
-            harvester.runHarvest(collection, eperson);
-        }
-        // start the harvest loop
-        else if ("start".equals(command))
-        {
-        	startHarvester();
-        }
-        // reset harvesting status
-        else if ("reset".equals(command))
-        {
-        	resetHarvesting();
-        }
-        // purge all collections that are set up for harvesting (obviously for testing purposes only)
-        else if ("purgeAll".equals(command))
-        {
-        	if (eperson == null)
-            {
-                System.out
-                        .println("Error - an eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-        	
-        	List<Integer> cids = HarvestedCollection.findAll(context);
-        	System.out.println("Purging the following collections (deleting items and resetting harvest status): " + cids.toString());
-	    	for (Integer cid : cids) 
-	    	{
-	    		harvester.purgeCollection(cid.toString(), eperson);
-	    	}
-	    	context.complete();
-        }
-        // Delete all items in a collection. Useful for testing fresh harvests.
-        else if ("purge".equals(command))
-        {
-            if (collection == null || eperson == null)
-            {
-                System.out
-                        .println("Error - a target collection and eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-            
-            harvester.purgeCollection(collection, eperson);
-            context.complete();
-            
-            //TODO: implement this... remove all items and remember to unset "last-harvested" settings
-        }
-        // Configure a collection with the three main settings 
-        else if ("config".equals(command))
-        {
-            if (collection == null)
-            {
-                System.out.println("Error -  a target collection must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-            if (oaiSource == null || oaiSetID == null)
-            {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-            if (metadataKey == null)
-            {
-            	System.out.println("Error - a metadata key (commonly the prefix) must be specified for this collection");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);            	
-            }
-            
-            harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
-        }
-        else if ("ping".equals(command))
-        {
-            if (oaiSource == null || oaiSetID == null)
-            {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
-            }
-        }
-    }
-    
-    /*
-     * Resolve the ID into a collection and check to see if its harvesting options are set. If so, return
-     * the collection, if not, bail out. 
-     */
-    private Collection resolveCollection(String collectionID) {
-    	
-    	DSpaceObject dso;
-    	Collection targetCollection = null;
-    	
-    	try {
-	    	// is the ID a handle?
-	        if (collectionID != null)
-            {
-                if (collectionID.indexOf('/') != -1)
-                {
-                    // string has a / so it must be a handle - try and resolve it
-                    dso = HandleManager.resolveToObject(context, collectionID);
-
-                    // resolved, now make sure it's a collection
-                    if (dso == null || dso.getType() != Constants.COLLECTION)
-                    {
-                        targetCollection = null;
-                    }
-                    else
-                    {
-                        targetCollection = (Collection) dso;
-                    }
-                }
-                // not a handle, try and treat it as an integer collection
-                // database ID
-                else
-                {
-                    System.out.println("Looking up by id: " + collectionID + ", parsed as '" + Integer.parseInt(collectionID) + "', " + "in context: " + context);
-                    targetCollection = Collection.find(context, Integer.parseInt(collectionID));
-                }
-            }
-            // was the collection valid?
-            if (targetCollection == null)
-            {
-                System.out.println("Cannot resolve " + collectionID + " to collection");
-                System.exit(1);
-            }
-    	}
-    	catch (SQLException se) {
-    		se.printStackTrace();
-    	}
-    	
-    	return targetCollection;
-    }
-    
-    
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId, String mdConfigId) {
-    	System.out.println("Running: configure collection");
-   	
-    	Collection collection = resolveCollection(collectionID);
-    	System.out.println(collection.getID());
-    	    	
-    	try {
-    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-        	if (hc == null) {
-        		hc = HarvestedCollection.create(context, collection.getID());
-        	}
-    		
-    		context.turnOffAuthorisationSystem();
-    		hc.setHarvestParams(type, oaiSource, oaiSetId, mdConfigId);
-    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-    		hc.update();
-    		context.restoreAuthSystemState();
-    		context.complete();
-    	} 
-    	catch (Exception e) {
-    		System.out.println("Changes could not be committed");
-    		e.printStackTrace();
-    		System.exit(1);
-    	}
-    	finally {
-            if (context != null)
-            {
-    		    context.restoreAuthSystemState();
-            }
-    	}
-    }
-    
-    
-    /**
-     * Purges a collection of all harvest-related data and settings. All items in the collection will be deleted.
-     * 
-     * @param collectionID
-     * @param email
-     */
-    private void purgeCollection(String collectionID, String email) {
-    	System.out.println("Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
-    	Collection collection = resolveCollection(collectionID);
-   	
-    	try 
-    	{
-    		EPerson eperson = EPerson.findByEmail(context, email);
-        	context.setCurrentUser(eperson);
-    		context.turnOffAuthorisationSystem();
-    		
-    		ItemIterator it = collection.getAllItems();
-    		IndexBrowse ib = new IndexBrowse(context);
-    		int i=0;
-    		while (it.hasNext()) {
-    			i++;
-    			Item item = it.next();
-    			System.out.println("Deleting: " + item.getHandle());
-    			ib.itemRemoved(item);
-    			collection.removeItem(item);
-    			// commit every 50 items
-    			if (i%50 == 0) {
-    				context.commit();
-    				i=0;
-    			}
-    		}
-    		
-    		HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-    		if (hc != null) {
-	    		hc.setHarvestResult(null,"");
-	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-	    		hc.setHarvestStartTime(null);
-	    		hc.update();
-    		}
-    		context.restoreAuthSystemState();    		
-    		context.commit();
-    	} 
-    	catch (Exception e) {
-    		System.out.println("Changes could not be committed");
-    		e.printStackTrace();
-    		System.exit(1);
-    	}
-    	finally {
-    		context.restoreAuthSystemState();
-    	}
-    }
-    
-    
-    /**
-     * Run a single harvest cycle on the specified collection under the authorization of the supplied EPerson 
-     */
-    private void runHarvest(String collectionID, String email) {
-    	System.out.println("Running: a harvest cycle on " + collectionID);
-    	
-    	System.out.print("Initializing the harvester... ");
-    	OAIHarvester harvester = null;
-    	try {
-    		Collection collection = resolveCollection(collectionID);
-        	HarvestedCollection hc = HarvestedCollection.find(context, collection.getID());
-    		harvester = new OAIHarvester(context, collection, hc);
-    		System.out.println("success. ");
-    	}
-    	catch (HarvestingException hex) {
-    		System.out.print("failed. ");
-    		System.out.println(hex.getMessage());
-    		throw new IllegalStateException("Unable to harvest", hex);
-    	} catch (SQLException se) {
-            System.out.print("failed. ");
-            System.out.println(se.getMessage());
-            throw new IllegalStateException("Unable to access database", se);
-		}
-    	    	
-    	try {
-    		// Harvest will not work for an anonymous user
-        	EPerson eperson = EPerson.findByEmail(context, email);
-        	System.out.println("Harvest started... ");
-        	context.setCurrentUser(eperson);
-    		harvester.runHarvest();
-    		context.complete();
-    	}
-        catch (SQLException e) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        }
-        catch (AuthorizeException e) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        }
-        catch (IOException e) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        }
-
-        System.out.println("Harvest complete. ");
-    }
-    
-    
-    /**
-     * Resets harvest_status and harvest_start_time flags for all collections that have a row in the harvested_collections table 
-     */
-    private static void resetHarvesting() {
-    	System.out.print("Resetting harvest status flag on all collections... ");
-    	
-    	try 
-    	{
-	    	List<Integer> cids = HarvestedCollection.findAll(context);
-	    	for (Integer cid : cids) 
-	    	{
-	    		HarvestedCollection hc = HarvestedCollection.find(context, cid);
-	    		//hc.setHarvestResult(null,"");
-	    		hc.setHarvestStartTime(null);
-	    		hc.setHarvestStatus(HarvestedCollection.STATUS_READY);
-	    		hc.update();
-	    	}
-	    	context.commit();
-	    	System.out.println("success. ");
-    	}
-    	catch (Exception ex) {
-    		System.out.println("failed. ");
-    		ex.printStackTrace();
-    	}    	
-    }
-    
-    
-    /**
-     * Starts up the harvest scheduler. Terminating this process will stop the scheduler.
-     */
-    private static void startHarvester() 
-    {
-	    try 
-	    {
-	    	System.out.print("Starting harvest loop... ");
-	    	OAIHarvester.startNewScheduler();
-	    	System.out.println("running. ");
-    	}
-    	catch (Exception ex) {
-    		ex.printStackTrace();
-    	}
-    }
-    
-}

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

@@ -1,29 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemexport;
-
-/**
- * An exception that can be thrown when error occur during item export
- */
-public class ItemExportException extends Exception
-{
-    public static final int EXPORT_TOO_LARGE = 0;
-
-    private int reason;
-
-    public ItemExportException(int r, String message)
-    {
-        super(message);
-        reason = r;
-    }
-
-    public int getReason()
-    {
-        return reason;
-    }
-}

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

@@ -1,52 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemimport;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import gr.ekt.transformationengine.core.DataLoader;
-
-
-
-
-/**
- * This class acts as a Service in the procedure ot batch import using the Biblio-Transformation-Engine
- */
-public class DataLoaderService
-{
-
-    Map<String, DataLoader> dataLoaders = new HashMap<String, DataLoader>();
-    
-    /**
-     * Default constructor
-     */
-    public DataLoaderService()
-    {
-        super();
-    }
-
-    /**
-     * Setter method for dataLoaders parameter
-     * @param dataLoaders
-     */
-    public void setDataLoaders(Map<String, DataLoader> dataLoaders)
-    {
-        this.dataLoaders = dataLoaders;
-    }
-
-    /**
-     * 
-     * @return the map of DataLoaders
-     */
-    public Map<String, DataLoader> getDataLoaders()
-    {
-        return dataLoaders;
-    }
-    
-}

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

@@ -1,80 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.Map;
-
-/**
- * 	 Container for UpdateActions      
- *    Order of actions is very import for correct processing.  This implementation
- *     supports an iterator that returns the actions in the order in which they are
- *     put in.  Adding the same action a second time has no effect on this order.
- * 
- *
- */
-public class ActionManager implements Iterable<UpdateAction> {
-	
-	private Map<Class<? extends UpdateAction>, UpdateAction> registry 
-                     = new LinkedHashMap<Class<? extends UpdateAction>, UpdateAction>();
-	
-	public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass) 
-	throws InstantiationException, IllegalAccessException
-	{
-		UpdateAction action =  registry.get(actionClass);
-		
-		if (action == null)
-		{
-			action = actionClass.newInstance();
-			registry.put(actionClass, action);
-		}
-		
-		return action;		
-	}
-	
-	/**
-	 * 
-	 * @return whether any actions have been registered with this manager
-	 */
-	public boolean hasActions()
-	{
-		return !registry.isEmpty();
-	}
-	
-	/**
-	 * 	 This implementation guarantees the iterator order is the same as the order
-	 *   in which updateActions have been added
-	 * 
-	 * @return iterator for UpdateActions
-	 */
-	public Iterator<UpdateAction> iterator()
-	{
-		return new Iterator<UpdateAction>() 
-		{ 			
-			private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
-			
-			public boolean hasNext()
-			{
-				return itr.hasNext();
-			}
-			
-			public UpdateAction next()
-			{
-				return registry.get(itr.next());
-			}
-			
-			//not supported
-			public void remove()
-			{
-				throw new UnsupportedOperationException();
-			}
-		};
-		
-	}
-}

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

@@ -1,203 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.authorize.ResourcePolicy;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.FormatIdentifier;
-import org.dspace.content.InstallItem;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-import org.dspace.eperson.Group;
-
-/**
- * 	 Action to add bitstreams listed in item contents file to the item in DSpace	
- *   
- *
- */
-public class AddBitstreamsAction extends UpdateBitstreamsAction {
-
-	public AddBitstreamsAction()
-	{
-		//empty	
-	}
-	
-	/**
-	 * 	Adds bitstreams from the archive as listed in the contents file.
-	 * 
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws IllegalArgumentException,
-            ParseException, IOException, AuthorizeException, SQLException 
-	{
-		Item item = itarch.getItem();
-		File dir = itarch.getDirectory();
-		
-		List<ContentsEntry> contents = MetadataUtilities.readContentsFile(new File(dir, ItemUpdate.CONTENTS_FILE));
-		
-		if (contents.isEmpty())
-		{
-			ItemUpdate.pr("Contents is empty - no bitstreams to add");
-			return;
-		}
-		
-		ItemUpdate.pr("Contents bitstream count: " + contents.size());
-		
-		String[] files = dir.list(ItemUpdate.fileFilter);
-		List<String> fileList = new ArrayList<String>();
-		for (String filename : files)
-		{
-			fileList.add(filename);
-			ItemUpdate.pr("file: " + filename);
-		}
-		
-		for (ContentsEntry ce : contents)
-		{
-			//validate match to existing file in archive
-			if (!fileList.contains(ce.filename))
-			{
-				throw new IllegalArgumentException("File listed in contents is missing: " + ce.filename);
-			}
-		}
-						
-		//now okay to add
-		for (ContentsEntry ce : contents)
-		{        				
-			addBitstream(context, itarch, item, dir, ce, suppressUndo, isTest);
-		}
-	}
-		
-	private void addBitstream(Context context, ItemArchive itarch, Item item, File dir, 
-			                  ContentsEntry ce, boolean suppressUndo, boolean isTest)
-	throws IOException, IllegalArgumentException, SQLException, AuthorizeException, ParseException
-	{
-		ItemUpdate.pr("contents entry for bitstream: " + ce.toString());
-    	File f = new File(dir, ce.filename);
-    	
-        // get an input stream
-        BufferedInputStream bis = new BufferedInputStream(new FileInputStream(f));
-
-        Bitstream bs = null;
-        String newBundleName = ce.bundlename;
-
-        if (ce.bundlename == null)  // should be required but default convention established
-        {
-            if (ce.filename.equals("license.txt"))
-            {
-                newBundleName = "LICENSE";
-            }
-            else  
-            {
-                newBundleName = "ORIGINAL";
-            }
-        }
-        ItemUpdate.pr("  Bitstream " + ce.filename + " to be added to bundle: " + newBundleName);
-        
-        if (!isTest)
-        {
-	        // find the bundle
-	        Bundle[] bundles = item.getBundles(newBundleName);
-	        Bundle targetBundle = null;
-	
-	        if (bundles.length < 1)
-	        {
-	            // not found, create a new one
-	            targetBundle = item.createBundle(newBundleName);
-	        }
-	        else
-	        {
-	    		//verify bundle + name are not duplicates
-	        	for (Bundle b : bundles)
-	        	{
-	        		Bitstream[] bitstreams = b.getBitstreams();
-	        		for (Bitstream bsm : bitstreams)
-	        		{
-	        			if (bsm.getName().equals(ce.filename))
-	        			{
-	        				throw new IllegalArgumentException("Duplicate bundle + filename cannot be added: " 
-	        						+ b.getName() + " + " + bsm.getName());
-	        			}
-	        		}
-	        	}
-
-	            // select first bundle
-	            targetBundle = bundles[0];
-	        }
-	
-	        bs = targetBundle.createBitstream(bis);	
-	        bs.setName(ce.filename);
-	
-	        // Identify the format
-	        // FIXME - guessing format guesses license.txt incorrectly as a text file format!
-	        BitstreamFormat fmt = FormatIdentifier.guessFormat(context, bs);
-	    	bs.setFormat(fmt);
-	    	
-	        if (ce.description != null)
-	        {
-	        	bs.setDescription(ce.description);
-	        }
-	        	        
-	        if ((ce.permissionsActionId != -1) && (ce.permissionsGroupName != null))
-	        {
-				Group group = Group.findByName(context, ce.permissionsGroupName);
-				
-				if (group != null)
-				{
-			        AuthorizeManager.removeAllPolicies(context, bs);  // remove the default policy
-			        ResourcePolicy rp = ResourcePolicy.create(context);
-			        rp.setResource(bs);
-			        rp.setAction(ce.permissionsActionId);
-			        rp.setGroup(group);		
-			        rp.update();
-				}
-	        }
-	        
-	        if (alterProvenance && !targetBundle.getName().equals("THUMBNAIL") 
-	        		&& !targetBundle.getName().equals("TEXT"))
-	        {
-	        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-	        	
-	        	String append = "Bitstream added on " + DCDate.getCurrent() + " : " 
-	        	                + InstallItem.getBitstreamProvenanceMessage(item);
-	        	MetadataUtilities.appendMetadata(item, dtom, false, append);
-	        }
-	        
-	        //update after all changes are applied, even metadata ones
-	        bs.update();
-        
-	        if (!suppressUndo)
-	        {
-	        	itarch.addUndoDeleteContents(bs.getID());
-	        }
-        }
-    }
-
-}

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

@@ -1,120 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.sql.SQLException;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataField;
-import org.dspace.content.MetadataSchema;
-
-import org.dspace.core.Context;
-
-/**
- *   Action to add metadata to item
- *
- */
-public class AddMetadataAction extends UpdateMetadataAction {
-	
-	/**
-	 * 	Adds metadata specified in the source archive
-	 * 
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws AuthorizeException, SQLException
-	{
-		Item item = itarch.getItem();
-		String dirname = itarch.getDirectoryName();
-	    	
-		for (DtoMetadata dtom : itarch.getMetadataFields())
-		{
-			for (String f : targetFields)
-			{
-				if (dtom.matches(f, false))
-				{
-					// match against metadata for this field/value in repository
-					// qualifier must be strictly matched, possibly null					
-					DCValue[] ardcv = null;
-					ardcv = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-					
-					boolean found = false;
-					for (DCValue dcv : ardcv)
-					{
-						if (dcv.value.equals(dtom.value))
-						{
-							found = true;
-							break;
-						}
-					}
-					
-					if (found)
-					{
-						ItemUpdate.pr("Warning:  No new metadata found to add to item " + dirname 
-								+ " for element " + f);						
-					}
-					else
-					{
-						if (isTest)
-						{
-							ItemUpdate.pr("Metadata to add: " + dtom.toString());
-							   //validity tests that would occur in actual processing
-	        	            // If we're just test the import, let's check that the actual metadata field exists.
-	        	        	MetadataSchema foundSchema = MetadataSchema.find(context, dtom.schema);
-	        	        	
-	        	        	if (foundSchema == null)
-	        	        	{
-	        	        		ItemUpdate.pr("ERROR: schema '" 
-	        	        			+ dtom.schema + "' was not found in the registry; found on item " + dirname);
-	        	        	}
-	        	        	else
-	        	        	{
-		        	        	int schemaID = foundSchema.getSchemaID();
-		        	        	MetadataField foundField = MetadataField.findByElement(context, schemaID, dtom.element, dtom.qualifier);
-		        	        	
-		        	        	if (foundField == null)
-		        	        	{
-		        	        		ItemUpdate.pr("ERROR: Metadata field: '" + dtom.schema + "." + dtom.element + "." 
-		        	        				+ dtom.qualifier + "' not found in registry; found on item " + dirname);
-		        	            }		
-	        				}						
-						}
-						else
-						{
-							item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, dtom.value);
-							ItemUpdate.pr("Metadata added: " + dtom.toString());
-	
-							if (!suppressUndo)
-							{
-								//itarch.addUndoDtom(dtom);
-								//ItemUpdate.pr("Undo metadata: " + dtom);
-								
-								// add all as a replace record to be preceded by delete
-								for (DCValue dcval : ardcv)
-								{							
-									itarch.addUndoMetadataField(DtoMetadata.create(dcval.schema, dcval.element, 
-											dcval.qualifier, dcval.language, dcval.value));
-								}
-								
-							}
-						}
-					}
-					break;  // don't need to check if this field matches any other target fields
-				}
-			} 				
-		}   
-	}
-
-}

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

@@ -1,61 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.IOException;
-import java.util.Properties;
-import java.io.InputStream;
-import java.io.FileInputStream;
-import org.dspace.content.Bitstream;
-
-/**
- *   Filter interface to be used by ItemUpdate 
- *   to determine which bitstreams in an Item
- *   acceptable for removal.
- *
- */
-public abstract class BitstreamFilter {
-
-	protected Properties props = null; 
-	
-	/**
-	 *  The filter method 
-	 *  
-	 * @param bitstream
-	 * @return whether the bitstream matches the criteria
-	 * @throws BitstreamFilterException
-	 */
-	public abstract boolean accept(Bitstream bitstream) throws BitstreamFilterException;
-	
-	/**
-	 * 
-	 * @param filepath - The complete path for the properties file
-	 * @throws IOException
-	 */
-	public void initProperties(String filepath)
-	throws IOException
-	{
-		props = new Properties();
-		
-		InputStream in = null;
-
-        try
-        {
-            in = new FileInputStream(filepath);
-            props.load(in);
-        }
-        finally
-        {
-            if (in != null)
-            {
-                in.close();
-            }
-        }
-	}
-	
-}

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

@@ -1,66 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.sql.SQLException;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-
-/**
- *   BitstreamFilter implementation to filter by bundle name
- *
- */
-public class BitstreamFilterByBundleName extends BitstreamFilter {
-
-	protected String bundleName;
-	
-	public BitstreamFilterByBundleName()
-	{
-		//empty
-	}
-
-	/**
-	 *    Filter bitstream based on bundle name found in properties file
-	 *    
-	 *    @param bitstream
-	 *    @throws BitstreamFilterException
-	 *    @return whether bitstream is in bundle
-	 *    
-	 */
-	public boolean accept(Bitstream bitstream) 
-	throws BitstreamFilterException
-	{
-		if (bundleName == null)
-		{
-			bundleName = props.getProperty("bundle");
-			if (bundleName == null)
-			{
-				throw new BitstreamFilterException("Property 'bundle' not found.");
-			}			
-		}
-		
-		try
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				if (b.getName().equals(bundleName))
-				{
-					return true;
-				}
-			}		
-		}
-		catch(SQLException e)
-		{
-			throw new BitstreamFilterException(e);
-		}
-		return false;
-	}
-	
-}

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

@@ -1,50 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.regex.*;
-
-import org.dspace.content.Bitstream;
-
-/**
- * BitstreamFilter implementation to filter by filename pattern
- *
- */
-public class BitstreamFilterByFilename extends BitstreamFilter {
-	
-	private Pattern pattern;
-	private String filenameRegex;
-	
-	public BitstreamFilterByFilename()
-	{
-		//empty
-	}
-
-	/**
-	 *   Tests bitstream by matching the regular expression in the 
-	 *   properties against the bitstream name
-	 * 
-	 *   @return whether bitstream name matches the regular expression
-	 */
-	public boolean accept(Bitstream bitstream) throws BitstreamFilterException
-	{		
-		if (filenameRegex == null)
-		{
-			filenameRegex = props.getProperty("filename");
-			if (filenameRegex == null)
-			{
-				throw new BitstreamFilterException("BitstreamFilter property 'filename' not found.");
-			}
-			pattern = Pattern.compile(filenameRegex);
-		}
-		
-		Matcher m = pattern.matcher(bitstream.getName());
-		return m.matches();
-	}	
- 
-}

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

@@ -1,29 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-/**
- *    Exception class for BitstreamFilters
- *
- */
-public class BitstreamFilterException extends Exception 
-{
-	
-	private static final long serialVersionUID = 1L;
-	
-	public BitstreamFilterException() {}
-	public BitstreamFilterException(String msg)
-	{
-		super(msg);
-	}
-	public BitstreamFilterException(Exception e)
-	{
-		super(e);
-	}
-	
-}

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

@@ -1,153 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.text.ParseException;
-import java.util.regex.*;
-
-import org.dspace.core.Constants;
-
-/**
- *   Holds the elements of a line in the Contents Entry file
- * 
- *   Based on private methods in ItemImport
- *   
- *   Lacking a spec or full documentation for the file format, 
- *   it looks from the source code that the ordering or elements is not fixed
- * 
- *   e.g.:    
- *      48217870-MIT.pdf\tbundle: bundlename\tpermissions: -r 'MIT Users'\tdescription: Full printable version (MIT only)
- *      permissions: -[r|w] ['group name']
- *      description: <the description of the file>
- * 
- *
- */
-public class ContentsEntry 
-{
-	public static final String HDR_BUNDLE = "bundle:";
-	public static final String HDR_PERMISSIONS = "permissions:";
-	public static final String HDR_DESCRIPTION = "description:";
-		
-	public static final Pattern permissionsPattern = Pattern.compile("-([rw])\\s*'?([^']+)'?");
-	
-	final String filename;
-	final String bundlename;
-	final String permissionsGroupName;
-	final int permissionsActionId;
-	final String description;
-	
-	private ContentsEntry(String filename, 
-			             String bundlename,
-			             int permissionsActionId,
-			             String permissionsGroupName,
-			             String description)
-	{
-		this.filename = filename;
-		this.bundlename = bundlename;
-		this.permissionsActionId = permissionsActionId;
-		this.permissionsGroupName = permissionsGroupName;
-		this.description = description;
-	}
-	
-	/**
-	 *   Factory method parses a line from the Contents Entry file
-	 *   
-	 * @param line
-	 * @return the parsed ContentsEntry object 
-	 * @throws ParseException
-	 */
-	public static ContentsEntry parse(String line)
-	throws ParseException
-	{
-		String[] ar = line.split("\t");
-		ItemUpdate.pr("ce line split: " + ar.length);
-		
-		String[] arp = new String[4];
-		arp[0] = ar[0];   //bitstream name doesn't have header and is always first
-		
-		String groupName = null;
-		int actionId = -1;
-
-		if (ar.length > 1)
-		{
-			for (int i=1; i < ar.length; i++)
-			{
-				ItemUpdate.pr("ce " + i + " : " + ar[i]);
-				if (ar[i].startsWith(HDR_BUNDLE))
-				{
-					arp[1] = ar[i].substring(HDR_BUNDLE.length()).trim();
-					
-				}
-				else if (ar[i].startsWith(HDR_PERMISSIONS))
-				{
-					arp[2] = ar[i].substring(HDR_PERMISSIONS.length()).trim();
-					
-					// parse into actionId and group name
-					
-					Matcher m = permissionsPattern.matcher(arp[2]);
-					if (m.matches())
-					{
-						String action = m.group(1); //
-						if (action.equals("r"))
-						{
-							 actionId = Constants.READ;
-						}
-						else if (action.equals("w"))
-						{
-							 actionId = Constants.WRITE;
-						}
-						
-						groupName = m.group(2).trim();
-					}
-					
-				}
-				else if (ar[i].startsWith(HDR_DESCRIPTION))
-				{
-					arp[3] = ar[i].substring(HDR_DESCRIPTION.length()).trim();
-					
-				}
-				else
-				{
-					throw new ParseException("Unknown text in contents file: " + ar[i], 0);				
-				}			
-			}
-		}
-		return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
-	}
-	
-	public String toString()
-	{
-		StringBuilder sb = new StringBuilder(filename);
-		if (bundlename != null)
-		{
-			sb.append(HDR_BUNDLE).append(" ").append(bundlename);
-		}
-		
-		if (permissionsGroupName != null)
-		{
-			sb.append(HDR_PERMISSIONS);
-			if (permissionsActionId == Constants.READ)
-			{
-				sb.append(" -r ");
-			}
-			else if (permissionsActionId == Constants.WRITE)
-			{
-				sb.append(" -w ");
-			}
-			sb.append(permissionsGroupName);
-		}
-		
-		if (description != null)
-		{
-			sb.append(HDR_DESCRIPTION).append(" ").append(description);
-		}		
-		
-		return sb.toString();
-	}
-	
-}

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

@@ -1,114 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.File;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * 	  Action to delete bitstreams	
- * 
- * 	  Undo not supported for this UpdateAction
- * 
- *    Derivatives of the bitstream to be deleted are not also deleted 
- *
- */
-public class DeleteBitstreamsAction extends UpdateBitstreamsAction 
-{
-	/**
-	 *   Delete bitstream from item
-	 * 
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws IllegalArgumentException, IOException,
-            SQLException, AuthorizeException, ParseException 
-	{
-		File f = new File(itarch.getDirectory(), ItemUpdate.DELETE_CONTENTS_FILE);
-		if (!f.exists())
-		{
-			ItemUpdate.pr("Warning: Delete_contents file for item " + itarch.getDirectoryName() + " not found.");
-		}
-		else
-		{
-			List<Integer> list = MetadataUtilities.readDeleteContentsFile(f);
-			if (list.isEmpty())
-			{
-				ItemUpdate.pr("Warning: empty delete_contents file for item " + itarch.getDirectoryName() );
-			}
-			else
-			{
-				for (int id : list)
-				{
-					try
-					{
-			    		Bitstream bs = Bitstream.find(context, id);
-			    		if (bs == null)
-			    		{
-			    			ItemUpdate.pr("Bitstream not found by id: " + id);
-			    		}
-			    		else
-			    		{
-				    		Bundle[] bundles = bs.getBundles();
-				    		for (Bundle b : bundles)
-				    		{
-				    			if (isTest)
-				    			{
-					    			ItemUpdate.pr("Delete bitstream with id = " + id);
-				    			}
-				    			else
-				    			{
-				    				b.removeBitstream(bs); 
-					    			ItemUpdate.pr("Deleted bitstream with id = " + id);
-					    			
-				    			}
-				    		}	
-			    		
-				            if (alterProvenance)
-				            {
-				            	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-				            	
-				            	String append = "Bitstream " + bs.getName() + " deleted on " + DCDate.getCurrent() + "; ";
-				            	Item item = bundles[0].getItems()[0];
-					    		ItemUpdate.pr("Append provenance with: " + append);
-					    		
-					    		if (!isTest)
-					    		{
-					    			MetadataUtilities.appendMetadata(item, dtom, false, append);
-					    		}
-				            }
-			    		}	
-					}
-					catch(SQLException e)
-					{
-						ItemUpdate.pr("Error finding bitstream from id: " + id + " : " + e.toString());
-					}
-				}
-			}
-		}
-	}
-
-}

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

@@ -1,130 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.DCDate;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * 		Action to delete bitstreams using a specified filter implementing BitstreamFilter
- *      Derivatives for the target bitstreams are not deleted.
- * 
- *      The dc.description.provenance field is amended to reflect the deletions
- *      
- *      Note:  Multiple filters are impractical if trying to manage multiple properties files
- *      in a commandline environment
- * 
- *
- */
-public class DeleteBitstreamsByFilterAction extends UpdateBitstreamsAction {
-
-	private BitstreamFilter filter;
-	
-	/**
-	 *   Set filter
-	 *   
-	 * @param filter
-	 */
-	public void setBitstreamFilter(BitstreamFilter filter)
-	{
-		this.filter = filter;
-	}
-	
-	/**
-	 *   Get filter
-	 * @return filter 
-	 */
-	public BitstreamFilter getBitstreamFilter()
-	{
-		return filter;
-	}
-	
-	/**
-	 * 	 Delete bitstream
-	 * 
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws IllegalArgumentException
-	 *  @throws ParseException
-	 *  @throws IOException
-	 *  @throws AuthorizeException
-	 *  @throws SQLException
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws AuthorizeException,
-            BitstreamFilterException, IOException, ParseException, SQLException 
-	{
-		
-		List<String> deleted = new ArrayList<String>();
-		
-		Item item = itarch.getItem();
-		Bundle[] bundles = item.getBundles();
-		
-		for (Bundle b : bundles)    
-		{
-			Bitstream[] bitstreams = b.getBitstreams();
-			String bundleName = b.getName();
-			
-			for (Bitstream bs : bitstreams)
-			{		
-			    if (filter.accept(bs))
-				{
-	    			if (isTest)
-	    			{
-		    			ItemUpdate.pr("Delete from bundle " + bundleName + " bitstream " + bs.getName() 
-		    					+ " with id = " + bs.getID());
-	    			}
-	    			else
-	    			{	    					    				
-	    				//provenance is not maintained for derivative bitstreams
-	    				if (!bundleName.equals("THUMBNAIL") && !bundleName.equals("TEXT"))
-	    				{
-	    					deleted.add(bs.getName());
-	    				}
-	    				b.removeBitstream(bs); 
-		    			ItemUpdate.pr("Deleted " + bundleName + " bitstream " + bs.getName() 
-		    					+ " with id = " + bs.getID());		    			
-	    			}
-				}
-			}			
-		}
-		
-        if (alterProvenance && !deleted.isEmpty())
-        {     	
-    		StringBuilder sb = new StringBuilder("  Bitstreams deleted on "); 	
-    		sb.append(DCDate.getCurrent()).append(": ");
-    		
-    		for (String s : deleted)
-    		{
-            	sb.append(s).append(", ");
-    		}
-    		        	
-        	DtoMetadata dtom = DtoMetadata.create("dc.description.provenance", "en", "");
-        	
-    		ItemUpdate.pr("Append provenance with: " + sb.toString());
-    		
-    		if (!isTest)
-    		{
-    			MetadataUtilities.appendMetadata(item, dtom, false, sb.toString());
-    		}
-        }
-	}
-	
-}

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

@@ -1,64 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.text.ParseException;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- *    Action to delete metadata 
- * 
- *
- */
-public class DeleteMetadataAction extends UpdateMetadataAction {
-
-	/**
-	 *   Delete metadata from item
-	 * 
-	 *  @param context
-	 *  @param itarch
-	 *  @param isTest
-	 *  @param suppressUndo
-	 *  @throws ParseException
-	 *  @throws AuthorizeException
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest,
-            boolean suppressUndo) throws AuthorizeException, ParseException 
-	{
-		Item item = itarch.getItem();
-		for (String f : targetFields)
-		{
-			DtoMetadata dummy = DtoMetadata.create(f, Item.ANY, "");
-			DCValue[] ardcv = item.getMetadata(f);
-
-			ItemUpdate.pr("Metadata to be deleted: ");
-			for (DCValue dcv : ardcv)
-			{
-				ItemUpdate.pr("  " + MetadataUtilities.getDCValueString(dcv));
-			}
-
-			if (!isTest)
-			{
-				if (!suppressUndo)
-				{
-					for (DCValue dcv : ardcv)
-					{
-						itarch.addUndoMetadataField(DtoMetadata.create(dcv.schema, dcv.element, 
-								dcv.qualifier, dcv.language, dcv.value));					
-					}
-				}
-				
-				item.clearMetadata(dummy.schema, dummy.element, dummy.qualifier, Item.ANY);	
-			}
-		}
-	}
-}

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

@@ -1,24 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.Properties;
-
-/**
- *   Bitstream filter to delete from TEXT bundle
- *
- */
-public class DerivativeTextBitstreamFilter extends BitstreamFilterByBundleName {
-	
-	public DerivativeTextBitstreamFilter()
-	{
-		props = new Properties();
-		props.setProperty("bundle", "TEXT");
-	}
-
-}

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

@@ -1,156 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.text.ParseException;
-import org.dspace.content.Item;
-
-/**
- *   A data transfer object class enhancement of org.dspace.content.DCValue, which is deprecated
- *   Name intended to not conflict with DSpace API classes for similar concepts but not usable in this context
- *   
- *   Adds some utility methods
- *   
- *   Really not at all general enough but supports Dublin Core and the compound form notation <schema>.<element>[.<qualifier>]
- *   
- *   Does not support wildcard for qualifier
- * 
- *
- */
-class DtoMetadata 
-{
-	final String schema;   
-	final String element;
-	final String qualifier;
-	final String language;
-	final String value;
-	
-	private DtoMetadata(String schema, String element, String qualifier, String language, String value) 
-	{
-		this.schema = schema;
-		this.element = element;
-		this.qualifier = qualifier;
-		this.language = language;
-		this.value = value;
-	}
-	
-	/**
-	 *  Factory method
-	 *  
-	 *  
-	 * @param schema     not null, not empty -  'dc' is the standard case
-	 * @param element    not null, not empty
-	 * @param qualifier  null; don't allow empty string or * indicating 'any'
-	 * @param language   null or empty
-	 * @param value      
-	 * @return DtoMetadata object
-	 */
-	public static DtoMetadata create(String schema,
-			    String element,
-			    String qualifier,
-			    String language,
-			    String value)
-	throws IllegalArgumentException
-    {
-		if ((qualifier != null) &&  (qualifier.equals(Item.ANY) || qualifier.equals("")))
-		{
-			throw new IllegalArgumentException("Invalid qualifier: " + qualifier);
-		}
-		return new DtoMetadata(schema, element, qualifier, language, value);
-    }
-
-	/**
-	 *   Factory method to create metadata object
-	 *   
-	 * 
-	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>]
-	 * @param language   null or empty
-	 * @param value      
-	 */
-	public static DtoMetadata create(String compoundForm, String language, String value)
-	throws ParseException, IllegalArgumentException  
-    {
-		String[] ar = MetadataUtilities.parseCompoundForm(compoundForm);
-		
-		String qual = null;
-		if (ar.length > 2)
-		{
-    		qual = ar[2];
-		}
-		
-		return create(ar[0], ar[1], qual, language, value);
-    }
-
-	/**
-	 *   Determine if this metadata field matches the specified type:
-	 *    schema.element or schema.element.qualifier
-	 *    
-	 * 
-	 * @param compoundForm   of the form <schema>.<element>[.<qualifier>|.*]
-	 * @param wildcard       allow wildcards in compoundForm param
-	 * @return whether matches
-	 */
-	public boolean matches(String compoundForm, boolean wildcard)
-	{
-		String[] ar = compoundForm.split("\\s*\\.\\s*"); //MetadataUtilities.parseCompoundForm(compoundForm);
-		
-		if ((ar.length < 2) || (ar.length > 3))
-		{
-			return false;
-		}
-		
-		if (!this.schema.equals(ar[0]) || !this.element.equals(ar[1]))
-		{
-			return false;
-		}
-		
-		if (ar.length == 2)
-		{
-			if (this.qualifier != null)
-			{
-				return false;
-			}
-		}
-		
-		if (ar.length == 3)	
-		{
-			if (this.qualifier == null)
-			{
-				return false;
-			}
-			if (wildcard && ar[2].equals(Item.ANY))
-			{
-				return true;
-			}
-			if (!this.qualifier.equals(ar[2]))
-			{
-				return false;
-			}
-		}
-		return true;		
-	}
-	
-	public String toString()
-	{
-		String s =  "\tSchema: " + schema + " Element: " + element;
-		if (qualifier != null)
-		{
-			s+= " Qualifier: " + qualifier;
-		}
-		s+= " Language: " + ((language == null) ? "[null]" : language);
-        s += " Value: " + value;
-        
-        return s;
-	}
-	
-	public String getValue()
-	{
-		return value;
-	}
-		
-}

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

@@ -1,348 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileWriter;
-import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintWriter;
-import java.sql.SQLException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.TransformerConfigurationException;
-
-import org.apache.log4j.Logger;
-import org.dspace.content.ItemIterator;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-
-import org.w3c.dom.Document;
-
-
-/**
- *   Encapsulates the Item in the context of the DSpace Archive Format
- *
- */
-public class ItemArchive {
-    private static final Logger log = Logger.getLogger(ItemArchive.class); 
-
-	public static final String DUBLIN_CORE_XML = "dublin_core.xml";
-	
-    private static DocumentBuilder builder = null;
-    private static Transformer transformer = null;
-   
-	private List<DtoMetadata> dtomList = null; 
-	private List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
-	
-	private List<Integer> undoAddContents = new ArrayList<Integer>(); // for undo of add
-	
-	private Item item;
-	private File dir;  // directory name in source archive for this item
-	private String dirname; //convenience
-	
-//constructors
-	private ItemArchive() 
-	{
-		// nothing
-	}	
-	
-/** factory method
- * 
- * 	Minimal requirements for dublin_core.xml for this application
- *  is the presence of dc.identifier.uri
- *  which must contain the handle for the item
- *  
- *  @param context - The DSpace context
- *  @param dir     - The directory File in the source archive
- *  @param itemField - The metadata field in which the Item identifier is located
- *                     if null, the default is the handle in the dc.identifier.uri field
- * 
- */
-	public static ItemArchive create(Context context, File dir, String itemField)
-	throws Exception
-	{
-		ItemArchive itarch = new ItemArchive(); 
-		itarch.dir = dir;
-		itarch.dirname = dir.getName();
-        InputStream is = null;
-        try
-        {
-            is = new FileInputStream(new File(dir, DUBLIN_CORE_XML));
-            itarch.dtomList = MetadataUtilities.loadDublinCore(getDocumentBuilder(), is);
-        }
-        finally
-        {
-            if (is != null)
-            {
-                is.close();
-            }
-        }
-		ItemUpdate.pr("Loaded metadata with " + itarch.dtomList.size() + " fields");
-		
-		if (itemField == null)
-		{
-			itarch.item = itarch.itemFromHandleInput(context);  // sets the item instance var and seeds the undo list
-		}
-		else
-		{
-			itarch.item = itarch.itemFromMetadataField(context, itemField);  			
-		}
-		
-		if (itarch.item == null)
-		{
-			throw new Exception("Item not instantiated: " + itarch.dirname);
-		}
-		
-		ItemUpdate.prv("item instantiated: " + itarch.item.getHandle());
-
-		return itarch;
-	}
-		
-	private static DocumentBuilder getDocumentBuilder()
-	throws ParserConfigurationException
-	{
-		if (builder == null)
-		{
-		    builder = DocumentBuilderFactory.newInstance().newDocumentBuilder();
-		}
-		return builder;
-	}
-	
-	private static Transformer getTransformer()
-	throws TransformerConfigurationException
-	{
-		if (transformer == null)
-		{
-		    transformer = TransformerFactory.newInstance().newTransformer();
-		}
-		return transformer;
-	}
-
-	/**
-	 *   Getter for the DSpace item referenced in the archive
-	 * @return DSpace item 
-	 */
-	public Item getItem()
-	{
-		return item;
-	}
-	
-	/**
-	 *   Getter for directory in archive on disk
-	 * @return directory in archive
-	 */
-	public File getDirectory()
-	{
-		return dir;
-	}
-	
-	/**
-	 *   Getter for directory name in archive
-	 * @return directory name in archive
-	 */
-	public String getDirectoryName()
-	{
-		return dirname;
-	}
-	
-	/**
-	 *   Add metadata field to undo list
-	 * @param dtom
-	 */
-	public void addUndoMetadataField(DtoMetadata dtom)
-	{
-		this.undoDtomList.add(dtom);
-	}
-	
-	/**
-	 *    Getter for list of metadata fields 
-	 * @return list of metadata fields
-	 */
-	public List<DtoMetadata> getMetadataFields()
-	{
-		return dtomList;
-	}
-	
-	/**
-	 *   Add bitstream id to delete contents file
-	 * @param bitstreamId
-	 */
-	public void addUndoDeleteContents(int bitstreamId)
-	{
-		this.undoAddContents.add(bitstreamId);
-	}
-	
-	
-    /**
-	 *   Obtain item from DSpace based on handle
-     *   This is the default implementation
-     *   that uses the dc.identifier.uri metadatafield 
-     *   that contains the item handle as its value  
-     *   
-     */
-    private Item itemFromHandleInput(Context context)
-    throws SQLException, Exception
-    {
-    	DtoMetadata dtom = getMetadataField("dc.identifier.uri");
-    	if (dtom == null)
-    	{
-    		throw new Exception("No dc.identier.uri field found for handle"); 
-    	}
-    	
-    	this.addUndoMetadataField(dtom);  //seed the undo list with the uri
-    	
-		String uri = dtom.value;
-		
-    	if (!uri.startsWith(ItemUpdate.HANDLE_PREFIX))
-    	{
-    		throw new Exception("dc.identifier.uri for item " + uri 
-    				+ " does not begin with prefix: " + ItemUpdate.HANDLE_PREFIX);
-    	}
-    	
-    	String handle = uri.substring(ItemUpdate.HANDLE_PREFIX.length());
-    		
-		DSpaceObject dso = HandleManager.resolveToObject(context, handle);  
-		if (dso instanceof Item)
-		{
-			item =  (Item) dso;
-		}
-		else
-		{
-			ItemUpdate.pr("Warning: item not instantiated");
-			throw new IllegalArgumentException("Item " + handle + " not instantiated.");
-		}	
-		return item;
-    }
-    
-    /**
-     * 	 Find and instantiate Item from the dublin_core.xml based
-     *   on the specified itemField for the item identifier,
-     *   
-     * 
-     * @param context   - the DSpace context
-     * @param itemField - the compound form of the metadata element <schema>.<element>.<qualifier>
-     * @throws SQLException
-     * @throws Exception
-     */
-    private Item itemFromMetadataField(Context context, String itemField)
-    throws SQLException, AuthorizeException, Exception
-    {
-    	DtoMetadata dtom = getMetadataField(itemField);
-    	
-    	Item item = null;
-    	
-    	if (dtom == null)
-    	{
-    		throw new IllegalArgumentException("No field found for item identifier field: " + itemField);
-    	}  
-    	ItemUpdate.prv("Metadata field to match for item: " + dtom.toString());
-
-    	this.addUndoMetadataField(dtom);  //seed the undo list with the identifier field
-    	
-	    ItemIterator itr = Item.findByMetadataField(context, dtom.schema, dtom.element, dtom.qualifier, dtom.value);
-		int count = 0;
-		while (itr.hasNext())
-		{
-			item = itr.next();
-			count++;
-		}
-		
-		itr.close(); 
-		
-		ItemUpdate.prv("items matching = " + count );
-		
-		if (count != 1)
-		{
-			throw new Exception ("" + count + " items matching item identifier: " + dtom.value);
-		}
-        
-    	return item;    	
-    }  
-    
-    private DtoMetadata  getMetadataField(String compoundForm)
-    {
-    	for (DtoMetadata dtom : dtomList)
-    	{
-			if (dtom.matches(compoundForm, false))
-			{
-				return dtom;
-			}
-    	}
-    	return null;
-    }    
-
-    /**
-     * write undo directory and files to Disk in archive format
-     * 
-     * 
-     * @param undoDir - the root directory of the undo archive
-     */
-	public void writeUndo(File undoDir)
-	throws IOException, ParserConfigurationException, TransformerConfigurationException, 
-	       TransformerException, FileNotFoundException
-	{
-		// create directory for item
-		File dir = new File(undoDir, dirname);
-		if (!dir.exists() && !dir.mkdir())
-        {
-            log.error("Unable to create undo directory");
-        }
-		
-		OutputStream out = null;
-
-        try
-        {
-            out = new FileOutputStream(new File(dir, "dublin_core.xml"));
-            Document doc = MetadataUtilities.writeDublinCore(getDocumentBuilder(), undoDtomList);
-            MetadataUtilities.writeDocument(doc, getTransformer(), out);
-
-            // if undo has delete bitstream
-            if (undoAddContents.size() > 0)
-            {
-                PrintWriter pw = null;
-                try
-                {
-                    File f = new File(dir, ItemUpdate.DELETE_CONTENTS_FILE);
-                    pw = new PrintWriter(new BufferedWriter(new FileWriter(f)));
-                    for (Integer i : undoAddContents)
-                    {
-                        pw.println(i);
-                    }
-                }
-                finally
-                {
-                    pw.close();
-                }
-            }
-        }
-        finally
-        {
-            if (out != null)
-            {
-                out.close();
-            }
-        }
-	}
-	
-} //end class

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

@@ -1,610 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FilenameFilter;
-import java.io.FileNotFoundException;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.eperson.EPerson;
-
-/**
- *   
- *   Provides some batch editing capabilities for items in DSpace:
- *   	Metadata fields - Add, Delete
- *      Bitstreams - Add, Delete
- * 
- *   The design has been for compatibility with ItemImporter
- *      in the use of the DSpace archive format which is used to
- *      specify changes on a per item basis.  The directory names
- *      to correspond to each item are arbitrary and will only be
- *      used for logging purposes.  The reference to the item is
- *      from a required dc.identifier with the item handle to be 
- *      included in the dublin_core.xml (or similar metadata) file.
- *      
- *   Any combination of these actions is permitted in a single run of this class 
- *      The order of actions is important when used in combination.  
- *      It is the responsibility of the calling class (here, ItemUpdate)
- *      to register UpdateAction classes in the order to which they are
- *      to be performed.
- *      
- * 
- *   It is unfortunate that so much code needs to be borrowed 
- *      from ItemImport as it is not reusable in private methods, etc.
- *      Some of this has been placed into the MetadataUtilities class
- *      for possible reuse elsewhere. 
- *   
- * 
- * @author W. Hays based on a conceptual design by R. Rodgers
- *
- */
-public class ItemUpdate {
-	
-	public static final String SUPPRESS_UNDO_FILENAME = "suppress_undo";
-
-	public static final String CONTENTS_FILE = "contents";
-	public static final String DELETE_CONTENTS_FILE = "delete_contents";
-
-	public static String HANDLE_PREFIX = null;
-	public static final Map<String, String> filterAliases = new HashMap<String, String>();
-	
-	public static boolean verbose = false;
-	
-	static
-	{
-		filterAliases.put("ORIGINAL", "org.dspace.app.itemupdate.OriginalBitstreamFilter");
-		filterAliases.put("ORIGINAL_AND_DERIVATIVES", "org.dspace.app.itemupdate.OriginalWithDerivativesBitstreamFilter");
-		filterAliases.put("TEXT", "org.dspace.app.itemupdate.DerivativeTextBitstreamFilter");		
-		filterAliases.put("THUMBNAIL", "org.dspace.app.itemupdate.ThumbnailBitstreamFilter");		
-	}
-	          	                
-    // File listing filter to check for folders
-    static FilenameFilter directoryFilter = new FilenameFilter()
-    {
-        public boolean accept(File dir, String n)
-        {
-            File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
-            return f.isDirectory();
-        }
-    };
- 
-    // File listing filter to check for files (not directories)
-    static FilenameFilter fileFilter = new FilenameFilter()
-    {
-        public boolean accept(File dir, String n)
-        {
-            File f = new File(dir.getAbsolutePath() + File.separatorChar + n);
-            return (f.isFile());
-        }
-    };
-
-    // instance variables
-    private ActionManager actionMgr = new ActionManager(); 
-    private List<String> undoActionList = new ArrayList<String>();  
-    private String eperson;
-   
-    /**
-     * 
-     * @param argv
-     */
-    public static void main(String[] argv)
-    {
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        Options options = new Options();
-
-     //processing basis for determining items    
-        //item-specific changes with metadata in source directory with dublin_core.xml files  
-        options.addOption("s", "source", true, "root directory of source dspace archive ");
-      
-    //actions  on items     
-        options.addOption("a", "addmetadata", true, "add metadata specified for each item; multiples separated by semicolon ';'");
-        options.addOption("d", "deletemetadata", true, "delete metadata specified for each item");
-        
-        options.addOption("A", "addbitstreams", false, "add bitstreams as specified for each item");
-        
-        // extra work to get optional argument
-        Option delBitstreamOption = new Option("D", "deletebitstreams", true, "delete bitstreams as specified for each item");
-        delBitstreamOption.setOptionalArg(true);
-        delBitstreamOption.setArgName("BitstreamFilter");
-        options.addOption(delBitstreamOption);
-                               
-//other params        
-        options.addOption("e", "eperson", true, "email of eperson doing the update");
-        options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
-        options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");  
-        options.addOption("v", "verbose", false, "verbose logging");
-      
-//special run states        
-        options.addOption("t", "test", false, "test run - do not actually import items");
-        options.addOption("P", "provenance", false, "suppress altering provenance field for bitstream changes");
-        options.addOption("h", "help", false, "help");
-        
-        int status = 0;
-        boolean isTest = false;
-        boolean alterProvenance = true;
-        String itemField = null;
-        String metadataIndexName = null;
-        
-        Context context = null;
-        ItemUpdate iu = new ItemUpdate();	
-
-        try
-        {       
-	        CommandLine line = parser.parse(options, argv);
-	
-	        if (line.hasOption('h'))
-	        {
-	            HelpFormatter myhelp = new HelpFormatter();
-	            myhelp.printHelp("ItemUpdate", options);
-	            pr("");
-	            pr("Examples:");
-	            pr("  adding metadata:     ItemUpdate -e jsmith@mit.edu -s sourcedir -a dc.contributor -a dc.subject ");
-	            pr("  deleting metadata:   ItemUpdate -e jsmith@mit.edu -s sourcedir -d dc.description.other");
-	            pr("  adding bitstreams:   ItemUpdate -e jsmith@mit.edu -s sourcedir -A -i dc.identifier");
-	            pr("  deleting bitstreams: ItemUpdate -e jsmith@mit.edu -s sourcedir -D ORIGINAL ");
-	            pr("");
-	
-	            System.exit(0);
-	        }
-	        
-	        if (line.hasOption('v'))
-	        {
-	        	verbose = true;
-	        }
-
- 
-	        if (line.hasOption('P'))
-	        {
-	        	alterProvenance = false;
-	        	pr("Suppressing changes to Provenance field option");
-	        }
-
-	        iu.eperson = line.getOptionValue('e'); // db ID or email
-	        
-	        if (!line.hasOption('s')) // item specific changes from archive dir
-	        {
-	        	pr("Missing source archive option");
-	        	System.exit(1);
-	        }
-	        String sourcedir = line.getOptionValue('s');
-	        
-        	if (line.hasOption('t'))  //test
-        	{
-        		isTest = true;
-	            pr("**Test Run** - not actually updating items.");
-       		       	
-	        }
-        	
-        	if (line.hasOption('i'))
-        	{
-        		itemField = line.getOptionValue('i');      		
-        	}
-
-	        if (line.hasOption('d'))
-	        {
-	        	String[] targetFields = line.getOptionValues('d'); 
-	        	
-	        	DeleteMetadataAction delMetadataAction = (DeleteMetadataAction) iu.actionMgr.getUpdateAction(DeleteMetadataAction.class);
-	        	delMetadataAction.addTargetFields(targetFields);
-	        	
-	        	//undo is an add 
-	        	for (String field : targetFields)
-	        	{
-	        		iu.undoActionList.add(" -a " + field + " ");
-	        	}
-	        	
-	        	pr("Delete metadata for fields: ");
-	        	for (String s : targetFields)
-	        	{
-	        		pr("    " + s);
-	        	}
-	        }
-	        
-    		if (line.hasOption('a'))
-    		{
-    			String[] targetFields = line.getOptionValues('a'); 
-        	
-    			AddMetadataAction addMetadataAction = (AddMetadataAction) iu.actionMgr.getUpdateAction(AddMetadataAction.class); 
-    			addMetadataAction.addTargetFields(targetFields);
-        		
-        		//undo is a delete followed by an add of a replace record for target fields
-	        	for (String field : targetFields)
-	        	{
-	        		iu.undoActionList.add(" -d " + field + " ");
-	        	}
-    			
-	        	for (String field : targetFields)
-	        	{
-	        		iu.undoActionList.add(" -a " + field + " ");
-	        	}
-    			
-	        	pr("Add metadata for fields: ");
-	        	for (String s : targetFields)
-	        	{
-	        		pr("    " + s);
-	        	}
-        	}
-    		
-	        if (line.hasOption('D'))  // undo not supported 
-	        {
-	        	pr("Delete bitstreams ");
-	        	
-	        	String[] filterNames = line.getOptionValues('D');
-	        	if ((filterNames != null) && (filterNames.length > 1))
-	        	{
-	        		pr("Error: Only one filter can be a used at a time.");
-	        		System.exit(1);
-	        	}
-	        	
-	        	String filterName = line.getOptionValue('D');
-	        	pr("Filter argument: " + filterName);
-	        	
-	        	if (filterName == null)  // indicates using delete_contents files
-	        	{
-	        		DeleteBitstreamsAction delAction = (DeleteBitstreamsAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsAction.class);
-		        	delAction.setAlterProvenance(alterProvenance);
-	        	}
-	        	else
-	        	{
-	        	    // check if param is on ALIAS list
-	        		String filterClassname = filterAliases.get(filterName);
-	        		
-	        		if (filterClassname == null)
-	        		{
-	        			filterClassname = filterName;
-	        		}
-	        			        		
-	        	    BitstreamFilter filter = null; 
-
-	        	    try
-	        	    {
-		    			Class<?> cfilter = Class.forName(filterClassname);
-		    			pr("BitstreamFilter class to instantiate: " + cfilter.toString());
-		    			
-		    			filter =  (BitstreamFilter) cfilter.newInstance();  //unfortunate cast, an erasure consequence
-	        	    }
-	        	    catch(Exception e)
-	        	    {
-	        	    	pr("Error:  Failure instantiating bitstream filter class: " + filterClassname);
-	        	    	System.exit(1);
-	        	    }
-	        	    
-	        	    String filterPropertiesName = line.getOptionValue('F');
-	        	    if (filterPropertiesName != null)  //not always required
-	        	    {
-	        	    	try
-	        	    	{
-	        	    		// TODO try multiple relative locations, e.g. source dir
-	        	    		if (!filterPropertiesName.startsWith("/"))
-	        	    		{
-	        	    			filterPropertiesName = sourcedir + File.separator + filterPropertiesName;
-	        	    		}
-	        	    		
-	        	    		filter.initProperties(filterPropertiesName);
-	        	    	}
-	        	    	catch(Exception e)
-	        	    	{
-		        	    	pr("Error:  Failure finding properties file for bitstream filter class: " + filterPropertiesName);
-		        	    	System.exit(1);
-	        	    	}
-	        	    }
-	        	    
-	        		DeleteBitstreamsByFilterAction delAction = 
-	        			(DeleteBitstreamsByFilterAction) iu.actionMgr.getUpdateAction(DeleteBitstreamsByFilterAction.class);
-		        	delAction.setAlterProvenance(alterProvenance);
-		        	delAction.setBitstreamFilter(filter);
-	        	    //undo not supported
-	        	}        	
-	        }
-
-	        if (line.hasOption('A'))
-	        {
-	        	pr("Add bitstreams ");    	        	
-        		AddBitstreamsAction addAction = (AddBitstreamsAction) iu.actionMgr.getUpdateAction(AddBitstreamsAction.class);
-	        	addAction.setAlterProvenance(alterProvenance);
-	        	
-	        	iu.undoActionList.add(" -D ");  // delete_contents file will be written, no arg required	        	
-	        }    	        
-	        	        
-	        if (!iu.actionMgr.hasActions())
-	        {
-                pr("Error - an action must be specified");
-                System.exit(1);
-	        }
-	        else  
-	        {
-	        	pr("Actions to be performed: ");
-	        	
-	        	for (UpdateAction ua : iu.actionMgr)
-	        	{
-	        		pr("    " + ua.getClass().getName());
-	        	}
-	        }
-	        
-	        pr("ItemUpdate - initializing run on " + (new Date()).toString());
-	               	
-	        context = new Context();  
-	        iu.setEPerson(context, iu.eperson);	
-	        context.setIgnoreAuthorization(true);
-	        
-	    	HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
-	    	if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
-	    	{
-	    		HANDLE_PREFIX = "http://hdl.handle.net/";
-	    	}
-	    		        
-        	iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);		        	            
-
-	        context.complete();  // complete all transactions
-	        context.setIgnoreAuthorization(false);
-        }
-        catch (Exception e)
-        {
-            if (context != null && context.isValid())
-            {
-                context.abort();
-            	context.setIgnoreAuthorization(false);
-            }
-            e.printStackTrace();
-            pr(e.toString());
-            status = 1;
-        }
-
-        if (isTest)
-        {
-            pr("***End of Test Run***");
-        }
-        else
-        {
-        	pr("End.");
-        	
-        }
-        System.exit(status);
-    }
-    
-    private void processArchive(Context context, String sourceDirPath, String itemField,
-    		String metadataIndexName, boolean alterProvenance, boolean isTest)
-    throws Exception
-    {
-        // open and process the source directory
-        File sourceDir = new File(sourceDirPath);
-
-        if ((sourceDir == null) || !sourceDir.exists() || !sourceDir.isDirectory())
-        {
-            pr("Error, cannot open archive source directory " + sourceDirPath);
-            throw new Exception("error with archive source directory " + sourceDirPath);
-        }
-
-        String[] dircontents = sourceDir.list(directoryFilter);  //just the names, not the path
-        Arrays.sort(dircontents);
-       
-        //Undo is suppressed to prevent undo of undo
-        boolean suppressUndo = false;
-        File fSuppressUndo = new File(sourceDir, SUPPRESS_UNDO_FILENAME);
-        if (fSuppressUndo.exists())
-        {
-        	suppressUndo = true;
-        }
-
-        File undoDir = null;  //sibling directory of source archive
-        
-    	if (!suppressUndo && !isTest) 
-    	{
-    		undoDir = initUndoArchive(sourceDir);	
-    	}
-        
-    	int itemCount = 0;
-    	int successItemCount = 0;
-    	
-        for (String dirname : dircontents)
-        {
-        	itemCount++;
-    		pr("");
-    		pr("processing item " + dirname);
-    		
-    		try
-    		{
-	    		ItemArchive itarch = ItemArchive.create(context, new File(sourceDir, dirname), itemField);
-	    		
-	    		for (UpdateAction action : actionMgr)
-	    		{
-	    			pr("action: " + action.getClass().getName());
-	    			action.execute(context, itarch, isTest, suppressUndo);
-	    			if (!isTest && !suppressUndo)
-                    {
-                        itarch.writeUndo(undoDir);
-                    }
-	    		}
-	    		if (!isTest)
-	    		{
-    				Item item = itarch.getItem();
-    				item.update();  //need to update before commit
-    				context.commit();  
-	    			item.decache();
-	    		}
-    			ItemUpdate.pr("Item " + dirname + " completed");
-    			successItemCount++;
-    		}
-    		catch(Exception e)
-    		{
-    			pr("Exception processing item " + dirname + ": " + e.toString());
-                e.printStackTrace();
-    		}
-        }  
-        
-        if (!suppressUndo && !isTest)
-        {        	     	
-        	StringBuilder sb = new StringBuilder("dsrun org.dspace.app.itemupdate.ItemUpdate ");
-        	sb.append(" -e ").append(this.eperson);
-        	sb.append(" -s ").append(undoDir);
-        	
-        	if (itemField != null)
-        	{
-        		sb.append(" -i ").append(itemField);
-        	}
-        	
-         	if (!alterProvenance)
-        	{
-        		sb.append(" -P ");
-        	}
-        	if (isTest)
-        	{
-        		sb.append(" -t ");
-        	}
-        	
-        	for (String actionOption : undoActionList)
-        	{
-        		sb.append(actionOption);
-        	}   
-        	
-        	PrintWriter pw = null;
-        	try
-        	{
-               	File cmdFile = new File (undoDir.getParent(), undoDir.getName() + "_command.sh");
-	        	pw = new PrintWriter(new BufferedWriter(new FileWriter(cmdFile)));
-	        	pw.println(sb.toString());
-        	}
-        	finally
-        	{
-        		pw.close();
-        	}
-        }
-        
-        pr("");
-        pr("Done processing.  Successful items: " + successItemCount + " of " + itemCount + " items in source archive");
-        pr("");
-    }
-           
-    
-    /**
-     * 
-     * to avoid overwriting the undo source tree on repeated processing
-     * sequence numbers are added and checked 
-     * 
-     * @param sourceDir - the original source directory
-     * @return the directory of the undo archive
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-	private File initUndoArchive(File sourceDir)
-	throws FileNotFoundException, IOException
-	{				
-		File parentDir = sourceDir.getAbsoluteFile().getParentFile(); 
-		if (parentDir == null)
-		{
-			throw new FileNotFoundException("Parent directory of archive directory not found; unable to write UndoArchive; no processing performed");    			
-		}
-		
-		String sourceDirName = sourceDir.getName();
-		int seqNo = 1;
-		
-		File undoDir = new File(parentDir, "undo_" + sourceDirName + "_" + seqNo);
-		while (undoDir.exists())
-		{
-    		undoDir = new File(parentDir, "undo_" + sourceDirName+ "_" + ++seqNo); //increment
-		}
-		
-		// create root directory
-		if (!undoDir.mkdir())
-		{
-        	pr("ERROR creating  Undo Archive directory ");
-        	throw new IOException("ERROR creating  Undo Archive directory ");
-		}
-		
-        //Undo is suppressed to prevent undo of undo
-        File fSuppressUndo = new File(undoDir, ItemUpdate.SUPPRESS_UNDO_FILENAME);
-        try
-        {
-        	fSuppressUndo.createNewFile();
-        }
-        catch(IOException e)
-        {
-        	pr("ERROR creating Suppress Undo File " + e.toString());
-        	throw e;
-        }
-        return undoDir;		
-	}
-	
-	//private void write
-
-    private void setEPerson(Context context, String eperson)
-    throws Exception
-    {
-        if (eperson == null)
-        {
-            pr("Error - an eperson to do the importing must be specified");
-            pr(" (run with -h flag for details)");
-            throw new Exception("EPerson not specified.");        }
-
-        EPerson myEPerson = null;
-
-        if (eperson.indexOf('@') != -1)
-        {
-            // @ sign, must be an email
-            myEPerson = EPerson.findByEmail(context, eperson);
-        }
-        else
-        {
-            myEPerson = EPerson.find(context, Integer.parseInt(eperson));
-        }
-
-        if (myEPerson == null)
-        {
-            pr("Error, eperson cannot be found: " + eperson);
-            throw new Exception("Invalid EPerson");
-        }
-
-        context.setCurrentUser(myEPerson);
-    }
-    
-    /**
-     *   poor man's logging
-	 *   As with ItemImport, API logging goes through log4j to the DSpace.log files
-	 *   whereas the batch logging goes to the console to be captured there.
-     * @param s
-     */
-    static void pr(String s)
-    {
-    	System.out.println(s);
-    }
-    
-    /**
-     *  print if verbose flag is set
-     * @param s
-     */
-    static void prv(String s)
-    {
-    	if (verbose) 
-    	{
-        	System.out.println(s);
-    	}
-    }
-    
-} //end of class
-

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

@@ -1,529 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.InputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.ParserConfigurationException;
-import javax.xml.transform.Result;
-import javax.xml.transform.Source;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.xpath.XPathAPI;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.content.MetadataSchema;
-import org.dspace.core.ConfigurationManager;
-
-
-/**
- * 		Miscellaneous methods for metadata handling that build on the API
- *      which might have general utility outside of the specific use
- *      in context in ItemUpdate.
- *      
- *      The XML methods were based on those in ItemImport
- * 
- *
- */
-public class MetadataUtilities {
-	
-    /**      
-     * 
-     *  Working around Item API to delete a value-specific DCValue
-     *  For a given element/qualifier/lang:
-     *      get all DCValues
-     *      clear (i.e. delete) all of these DCValues
-     *      add them back, minus the one to actually delete
-     *  
-     * 
-     * @param item
-     * @param dtom
-     * @param isLanguageStrict - 
-     * 
-     * @return true if metadata field is found with matching value and was deleted
-     */
-    public static boolean deleteMetadataByValue(Item item, DtoMetadata dtom, boolean isLanguageStrict)
-    {   	
-    	DCValue[] ar = null;
-    	
-    	if (isLanguageStrict)
-    	{   // get all for given type
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-    	}
-    	else
-    	{
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
-    	}
-    	
-    	boolean found = false;
-    	
-    	//build new set minus the one to delete
-    	List<String> vals = new ArrayList<String>();
-    	for (DCValue dcv : ar)
-    	{
-    		if (dcv.value.equals(dtom.value))
-    		{
-    			found = true;
-    		}
-    		else
-    		{
-    			vals.add(dcv.value);
-    		}
-    	}
-    	
-    	if (found)  //remove all for given type  ??synchronize this block??
-    	{   
-        	if (isLanguageStrict)
-        	{           		
-        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-        	}
-        	else
-        	{
-        		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-        	}
-    	
-    		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
-    	}
-		return found;
-    }
-
-    /**
-     *   Append text to value metadata field to item
-     *   
-     * @param item
-     * @param dtom
-     * @param isLanguageStrict
-     * @param textToAppend
-     * @throws IllegalArgumentException  - When target metadata field is not found
-     */
-    public static void appendMetadata(Item item, DtoMetadata dtom, boolean isLanguageStrict, 
-    		String textToAppend)
-    throws IllegalArgumentException
-    {   	
-    	DCValue[] ar = null;
-    	
-    	// get all values for given element/qualifier
-    	if (isLanguageStrict)  // get all for given element/qualifier
-    	{   
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);  
-    	}
-    	else
-    	{
-    		ar = item.getMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);  
-    	}
-    	
-    	if (ar.length == 0)
-    	{
-    		throw new IllegalArgumentException("Metadata to append to not found");
-    	}
-    	
-    	int idx = 0;  //index of field to change
-    	if (ar.length > 1)  //need to pick one, can't be sure it's the last one
-    	{
-    		// TODO maybe get highest id ?
-    	}
-    	
-    	//build new set minus the one to delete
-    	List<String> vals = new ArrayList<String>();
-    	for (int i=0; i < ar.length; i++) 
-    	{
-    		if (i == idx)
-    		{
-    			vals.add(ar[i].value + textToAppend);
-    		}
-    		else
-    		{
-    			vals.add(ar[i].value);
-    		}
-    	}
-
-    	if (isLanguageStrict)
-    	{           		
-    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language);
-    	}
-    	else
-    	{
-    		item.clearMetadata(dtom.schema, dtom.element, dtom.qualifier, Item.ANY);
-    	}
-	
-		item.addMetadata(dtom.schema, dtom.element, dtom.qualifier, dtom.language, vals.toArray(new String[vals.size()]));   	
-    }
- 
-    /**
-     *  Modification of method from ItemImporter.loadDublinCore 
-     *  as a Factory method
-     * 
-     * @param docBuilder  - 
-     * @param is - InputStream of dublin_core.xml
-     * @return list of DtoMetadata representing the metadata fields relating to an Item
-     * @throws SQLException
-     * @throws IOException
-     * @throws ParserConfigurationException
-     * @throws SAXException
-     * @throws TransformerException
-     * @throws AuthorizeException
-     */
-    public static List<DtoMetadata> loadDublinCore(DocumentBuilder docBuilder, InputStream is)
-    throws SQLException, IOException, ParserConfigurationException,
-           SAXException, TransformerException, AuthorizeException
-	{    	
-		Document document = docBuilder.parse(is);
-		
-		List<DtoMetadata> dtomList = new ArrayList<DtoMetadata>();
-		
-		// Get the schema, for backward compatibility we will default to the
-		// dublin core schema if the schema name is not available in the import file		
-		String schema = null;
-		NodeList metadata = XPathAPI.selectNodeList(document, "/dublin_core");		
-		Node schemaAttr = metadata.item(0).getAttributes().getNamedItem("schema");
-		if (schemaAttr == null)
-		{
-		    schema = MetadataSchema.DC_SCHEMA;
-		}
-		else
-		{
-		    schema = schemaAttr.getNodeValue();
-		}
-
-		// Get the nodes corresponding to formats
-		NodeList dcNodes = XPathAPI.selectNodeList(document, "/dublin_core/dcvalue");
-		
-		for (int i = 0; i < dcNodes.getLength(); i++)
-		{
-		    Node n = dcNodes.item(i);		    
-	        String value = getStringValue(n).trim(); 
-	        // compensate for empty value getting read as "null", which won't display
-	        if (value == null)
-	        {
-	            value = "";
-	        }
-	        String element = getAttributeValue(n, "element");
-	        if (element != null)
-	        {
-	        	element = element.trim();
-	        }
-	        String qualifier = getAttributeValue(n, "qualifier"); 
-	        if (qualifier != null)
-	        {
-	        	qualifier = qualifier.trim();
-	        }
-	        String language = getAttributeValue(n, "language");
-	        if (language != null)
-	        {
-	        	language = language.trim();
-	        }
-
-	        if ("none".equals(qualifier) || "".equals(qualifier))
-	        {
-	            qualifier = null;
-	        }
-	        
-	        // a goofy default, but consistent with DSpace treatment elsewhere  
-	        if (language == null)
-	        {
-	            language = "en";
-	        }
-	        else if ("".equals(language))
-	        {
-	            language = ConfigurationManager.getProperty("default.language");
-	        }
-	        
-		    DtoMetadata dtom = DtoMetadata.create(schema, element, qualifier, language, value);
-		    ItemUpdate.pr(dtom.toString());
-		    dtomList.add(dtom);
-		}
-		return dtomList;
-	}
-
-    /**
-     *    Write dublin_core.xml 
-     * 
-     * @param docBuilder
-     * @param dtomList
-     * @return xml document
-     * @throws ParserConfigurationException
-     * @throws TransformerConfigurationException
-     * @throws TransformerException
-     */
-	public static Document writeDublinCore(DocumentBuilder docBuilder, List<DtoMetadata> dtomList)
-	throws ParserConfigurationException, TransformerConfigurationException, TransformerException
-	{		
-        Document doc = docBuilder.newDocument();
-        Element root = doc.createElement("dublin_core");
-        doc.appendChild(root);
-    
-        for (DtoMetadata dtom : dtomList)
-        {
-        	Element mel = doc.createElement("dcvalue");
-        	mel.setAttribute("element", dtom.element);
-        	if (dtom.qualifier == null)
-        	{
-        		mel.setAttribute("qualifier", "none");
-        	}
-        	else
-        	{
-        		mel.setAttribute("qualifier", dtom.qualifier);
-        	}
- 
-        	if (StringUtils.isEmpty(dtom.language))
-        	{
-        		mel.setAttribute("language", "en");
-        	}
-        	else
-        	{
-        		mel.setAttribute("language", dtom.language);
-        	}
-        	mel.setTextContent(dtom.value);
-        	root.appendChild(mel);
-        }
-        
-        return doc;       
-	}
-	
-    /**
-     *   write xml document to output stream
-     * @param doc
-     * @param transformer
-     * @param out
-     * @throws IOException
-     * @throws TransformerException
-     */
-	public static void writeDocument(Document doc, Transformer transformer, OutputStream out)
-	throws IOException, TransformerException
-	{
-        Source src = new DOMSource(doc); 
-        Result dest = new StreamResult(out); 
-        transformer.transform(src, dest); 
-	}
-    
-    
-    
-    // XML utility methods
-    /**
-     * Lookup an attribute from a DOM node.
-     * @param n
-     * @param name
-     * @return
-     */
-    private static String getAttributeValue(Node n, String name)
-    {
-        NamedNodeMap nm = n.getAttributes();
-
-        for (int i = 0; i < nm.getLength(); i++)
-        {
-            Node node = nm.item(i);
-
-            if (name.equals(node.getNodeName()))
-            {
-                return node.getNodeValue();
-            }
-        }
-
-        return "";
-    }
-    
-    /**
-     * Return the String value of a Node.
-     * @param node
-     * @return
-     */
-    private static String getStringValue(Node node)
-    {
-        String value = node.getNodeValue();
-
-        if (node.hasChildNodes())
-        {
-            Node first = node.getFirstChild();
-
-            if (first.getNodeType() == Node.TEXT_NODE)
-            {
-                return first.getNodeValue();
-            }
-        }
-
-        return value;
-    }
-    
-    /**
-     * Rewrite of ItemImport's functionality
-     * but just the parsing of the file, not the processing of its elements.
-     *      
-     * @validate  flag to verify matching files in tree
-     */
-    public static List<ContentsEntry> readContentsFile(File f)
-    throws FileNotFoundException, IOException, ParseException
-    {
-    	List<ContentsEntry> list = new ArrayList<ContentsEntry>();
-    	
-    	BufferedReader in = null;
-    	
-    	try
-    	{
-	    	in = new BufferedReader(new FileReader(f));
-	    	String line = null;
-	    	
-	    	while ((line = in.readLine()) != null)
-	    	{
-	    		line = line.trim();
-	            if ("".equals(line))
-	            {
-	                continue;
-	            }
-	            ItemUpdate.pr("Contents entry: " + line);	            
-	    		list.add(ContentsEntry.parse(line));	 
-	    	}
-    	}
-    	finally
-    	{
-    		try
-    		{
-    			in.close();
-    		}
-    		catch(IOException e)
-    		{
-    			//skip
-    		}
-    	}
-    	
-    	return list;
-    }
-
-    /**
-     * 
-     * @param f
-     * @throws FileNotFoundException
-     * @throws IOException
-     */
-    public static List<Integer> readDeleteContentsFile(File f)
-    throws FileNotFoundException, IOException
-    {
-    	List<Integer> list = new ArrayList<Integer>();
-    	
-    	BufferedReader in = null;
-    	
-    	try
-    	{
-	    	in = new BufferedReader(new FileReader(f));
-	    	String line = null;
-	    	
-	    	while ((line = in.readLine()) != null)
-	    	{
-	    		line = line.trim();
-	            if ("".equals(line))
-	            {
-	                continue;
-	            }
-	            
-	            int n = 0;
-	            try
-	            {
-	            	n = Integer.parseInt(line);
-		    		list.add(n);	    		
-	            }
-	            catch(NumberFormatException e)
-	            {
-	            	ItemUpdate.pr("Error reading delete contents line:" + e.toString());
-	            }            	
-	    	}
-    	}
-    	finally
-    	{
-    		try
-    		{
-    			in.close();
-    		}
-    		catch(IOException e)
-    		{
-    			//skip
-    		}
-    	}
-    	
-    	return list;
-    }
-
-    /**
-     *    Get display of DCValue    
-	 *
-     * @param dcv
-     * @return string displaying elements of the DCValue
-     */
-    public static String getDCValueString(DCValue dcv)
-    {
-    	return "schema: " + dcv.schema + "; element: " + dcv.element + "; qualifier: " + dcv.qualifier +
-    	       "; language: " + dcv.language + "; value: " + dcv.value;
-    }
-
-	/**
-	 * 
-	 * @return a String representation of the two- or three-part form of a metadata element
-	 *         e.g. dc.identifier.uri
-	 */
-	public static  String getCompoundForm(String schema, String element, String qualifier)
-	{
-		StringBuilder sb = new StringBuilder();
-		sb.append(schema).append(".").append(element);
-		
-		if (qualifier != null)
-		{
-			sb.append(".").append(qualifier);
-		}
-		return sb.toString();
-	}
-	
-	/**
-	 *    Parses metadata field given in the form <schema>.<element>[.<qualifier>|.*]
-	 *    checks for correct number of elements (2 or 3) and for empty strings
-	 *    
-	 *    @return String Array
-	 *    @throws ParseException if validity checks fail
-	 *    
-	 */
-	public static String[] parseCompoundForm(String compoundForm)
-	throws ParseException
-	{
-		String[] ar = compoundForm.split("\\s*\\.\\s*");  //trim ends
-				
-		if ("".equals(ar[0]))
-		{
-			throw new ParseException("schema is empty string: " + compoundForm, 0);
-		}
-		
-		if ((ar.length < 2) || (ar.length > 3) || "".equals(ar[1]))
-		{
-			throw new ParseException("element is malformed or empty string: " + compoundForm, 0);
-		}
-		
-		return ar;
-	}
-	
-} 

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

@@ -1,55 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.sql.SQLException;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-
-/** 
- * 		Filter all bitstreams in the ORIGINAL bundle
- *      Also delete all derivative bitstreams, i.e.
- *      all bitstreams in the TEXT and THUMBNAIL bundles
- */
-public class OriginalBitstreamFilter extends BitstreamFilterByBundleName 
-{	
-	public OriginalBitstreamFilter()
-	{
-		//empty
-	}
-	
-	/**
-	 *   Tests bitstreams for containment in an ORIGINAL bundle
-	 *  
-	 *  @return true if the bitstream is in the ORIGINAL bundle
-	 *  
-	 *  @throws BitstreamFilterException
-	 */
-	public boolean accept(Bitstream bitstream) 
-	throws BitstreamFilterException
-	{		
-		try
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				if (b.getName().equals("ORIGINAL"))
-				{
-					return true;
-				}
-			}		
-		}
-		catch(SQLException e)
-		{
-			throw new BitstreamFilterException(e);
-		}
-		return false;
-	}
-
-}

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

@@ -1,59 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.sql.SQLException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-
-/** 
- * 		Filter all bitstreams in the ORIGINAL bundle
- *      Also delete all derivative bitstreams, i.e.
- *      all bitstreams in the TEXT and THUMBNAIL bundles
- */
-public class OriginalWithDerivativesBitstreamFilter extends BitstreamFilter 
-{
-	private String[] bundlesToEmpty = { "ORIGINAL", "TEXT", "THUMBNAIL" };	
-	
-	public OriginalWithDerivativesBitstreamFilter()
-	{
-		//empty
-	}
-	
-	/**
-	 * 	Tests bitstream for membership in specified bundles (ORIGINAL, TEXT, THUMBNAIL)
-	 * 
-	 * @param bitstream
-	 * @throws BitstreamFilterException
-	 * @return true if bitstream is in specified bundles
-	 */
-	public boolean accept(Bitstream bitstream) 
-	throws BitstreamFilterException
-	{		
-		try
-		{
-			Bundle[] bundles = bitstream.getBundles();
-			for (Bundle b : bundles)
-			{
-				for (String bn : bundlesToEmpty)
-				{
-					if (b.getName().equals(bn))
-					{
-						return true;
-					}
-				}
-			}		
-		}
-		catch(SQLException e)
-		{
-			throw new BitstreamFilterException(e);
-		}
-		return false;
-	}
-
-}

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

@@ -1,24 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.Properties;
-
-/**
- *    Bitstream filter targetting the THUMBNAIL bundle
- *
- */
-public class ThumbnailBitstreamFilter extends BitstreamFilterByBundleName {
-	
-	public ThumbnailBitstreamFilter()
-	{
-		props = new Properties();
-		props.setProperty("bundle", "THUMBNAIL");
-	}
-
-}

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

@@ -1,30 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import org.dspace.core.Context;
-
-/**
- *    Interface for actions to update an item
- *
- */
-public interface UpdateAction 
-{
-	/**
-	 *   Action to update item
-	 * 
-	 * @param context
-	 * @param itarch
-	 * @param isTest
-	 * @param suppressUndo
-	 * @throws Exception
-	 */
-	public void execute(Context context, ItemArchive itarch, boolean isTest, boolean suppressUndo) 
-	throws Exception;
-	
-}

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

@@ -1,39 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-/**
- * 	  Base class for Bitstream actions
- * 
- *
- */
-public abstract class UpdateBitstreamsAction implements UpdateAction {
-
-	protected boolean alterProvenance = true;
-
-	/**
-	 *        Set variable to indicate that the dc.description.provenance field may 
-	 *        be changed as a result of Bitstream changes by ItemUpdate
-	 * @param 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()
-	{
-		return alterProvenance;
-	}
-
-}

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

@@ -1,70 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.itemupdate;
-
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- *   This abstract subclass for metadata actions
- *   maintains a collection for the target metadata fields
- *   expressed as a string in the compound notation ( <schema>.<element>.<qualifier> )
- *   on which to apply the action when the method execute is called.
- * 
- *   Implemented as a Set to avoid problems with duplicates
- * 
- *
- */
-public abstract class UpdateMetadataAction implements UpdateAction {
-
-	protected Set<String> targetFields = new HashSet<String>();
-	
-    /**
-     *   Get target fields
-     *   
-     * @return set of fields to update
-     */
-	public Set<String> getTargetFields() {
-		return targetFields;
-	}
-
-	/**
-	 *   Set target fields
-	 *   
-	 * @param targetFields
-	 */
-	public void addTargetFields(Set<String> targetFields) {
-		for (String tf : targetFields)
-		{
-			this.targetFields.add(tf);
-		}
-		
-	}
-
-	/**
-	 *    Add array of target fields to update
-	 * @param targetFields
-	 */
-	public void addTargetFields(String[] targetFields) {
-		for (String tf : targetFields)
-		{
-			this.targetFields.add(tf);
-		}
-		
-	}
-
-	/**
-	 *   Add single field to update
-	 * 
-	 * @param targetField
-	 */
-	public void addTargetField(String targetField) {
-			this.targetFields.add(targetField);
-	}
-
-}

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

@@ -1,273 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.launcher;
-
-import org.dspace.core.ConfigurationManager;
-import org.dspace.servicemanager.DSpaceKernelImpl;
-import org.dspace.servicemanager.DSpaceKernelInit;
-import org.dspace.services.RequestService;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-import java.util.List;
-import java.lang.reflect.Method;
-
-/**
- * A DSpace script launcher.
- *
- * @author Stuart Lewis
- * @author Mark Diggory
- */
-public class ScriptLauncher
-{
-    /** The service manager kernel */
-    private static transient DSpaceKernelImpl kernelImpl;
-
-    /**
-     * Execute the DSpace script launcher
-     *
-     * @param args Any parameters required to be passed to the scripts it executes
-     */
-    public static void main(String[] args)
-    {
-        // Check that there is at least one argument
-        if (args.length < 1)
-        {
-            System.err.println("You must provide at least one command argument");
-            display();
-            System.exit(1);
-        }
-
-        // Initialise the service manager kernel
-        try {
-            kernelImpl = DSpaceKernelInit.getKernel(null);
-            if (!kernelImpl.isRunning())
-            {
-                kernelImpl.start(ConfigurationManager.getProperty("dspace.dir"));
-            }
-        } catch (Exception e)
-        {
-            // Failed to start so destroy it and log and throw an exception
-            try
-            {
-                kernelImpl.destroy();
-            }
-            catch (Exception e1)
-            {
-                // Nothing to do
-            }
-            String message = "Failure during filter init: " + e.getMessage();
-            System.err.println(message + ":" + e);
-            throw new IllegalStateException(message, e);
-        }
-
-        // Parse the configuration file looking for the command entered
-        Document doc = getConfig();
-        String request = args[0];
-        Element root = doc.getRootElement();
-        List<Element> commands = root.getChildren("command");
-        for (Element command : commands)
-        {
-            if (request.equalsIgnoreCase(command.getChild("name").getValue()))
-            {
-                // Run each step
-                List<Element> steps = command.getChildren("step");
-                for (Element step : steps)
-                {
-                    // Instantiate the class
-                    Class target = null;
-
-                    // Is it the special case 'dsrun' where the user provides the class name?
-                    String className;
-                    if ("dsrun".equals(request))
-                    {
-                        if (args.length < 2)
-                        {
-                            System.err.println("Error in launcher.xml: Missing class name");
-                            System.exit(1);
-                        }
-                        className = args[1];
-                    }
-                    else {
-                        className = step.getChild("class").getValue();
-                    }
-                    try
-                    {
-                        target = Class.forName(className,
-                                               true,
-                                               Thread.currentThread().getContextClassLoader());
-                    }
-                    catch (ClassNotFoundException e)
-                    {
-                        System.err.println("Error in launcher.xml: Invalid class name: " + className);
-                        System.exit(1);
-                    }
-
-                    // Strip the leading argument from the args, and add the arguments
-                    // Set <passargs>false</passargs> if the arguments should not be passed on
-                    String[] useargs = args.clone();
-                    Class[] argTypes = {useargs.getClass()};
-                    boolean passargs = true;
-                    if ((step.getAttribute("passuserargs") != null) &&
-                        ("false".equalsIgnoreCase(step.getAttribute("passuserargs").getValue())))
-                    {
-                        passargs = false;
-                    }
-                    if ((args.length == 1) || (("dsrun".equals(request)) && (args.length == 2)) || (!passargs))
-                    {
-                        useargs = new String[0];
-                    }
-                    else
-                    {
-                        // The number of arguments to ignore
-                        // If dsrun is the command, ignore the next, as it is the class name not an arg
-                        int x = 1;
-                        if ("dsrun".equals(request))
-                        {
-                            x = 2;
-                        }
-                        String[] argsnew = new String[useargs.length - x];
-                        for (int i = x; i < useargs.length; i++)
-                        {
-                            argsnew[i - x] = useargs[i];
-                        }
-                        useargs = argsnew;
-                    }
-
-                    // Add any extra properties
-                    List<Element> bits = step.getChildren("argument");
-                    if (step.getChild("argument") != null)
-                    {
-                        String[] argsnew = new String[useargs.length + bits.size()];
-                        int i = 0;
-                        for (Element arg : bits)
-                        {
-                            argsnew[i++] = arg.getValue();
-                        }
-                        for (; i < bits.size() + useargs.length; i++)
-                        {
-                            argsnew[i] = useargs[i - bits.size()];
-                        }
-                        useargs = argsnew;
-                    }
-
-                    // Establish the request service startup
-                    RequestService requestService = kernelImpl.getServiceManager().getServiceByName(RequestService.class.getName(), RequestService.class);
-                    if (requestService == null) {
-                        throw new IllegalStateException("Could not get the DSpace RequestService to start the request transaction");
-                    }
-
-                    // Establish a request related to the current session
-                    // that will trigger the various request listeners
-                    requestService.startRequest();
-
-                    // Run the main() method
-                    try
-                    {
-                        Object[] arguments = {useargs};
-
-                        // Useful for debugging, so left in the code...
-                        /**System.out.print("About to execute: " + className);
-                        for (String param : useargs)
-                        {
-                            System.out.print(" " + param);
-                        }
-                        System.out.println("");**/
-
-                        Method main = target.getMethod("main", argTypes);
-                        main.invoke(null, arguments);
-
-                        // ensure we close out the request (happy request)
-                        requestService.endRequest(null);
-                    }
-                    catch (Exception e)
-                    {
-                        // Failure occurred in the request so we destroy it
-                        requestService.endRequest(e);
-
-                    	if (kernelImpl != null)
-                        {
-                            kernelImpl.destroy();
-                            kernelImpl = null;
-                        }
-
-                        // Exceptions from the script are reported as a 'cause'
-                        Throwable cause = e.getCause();
-                        System.err.println("Exception: " + cause.getMessage());
-                        cause.printStackTrace();
-                        System.exit(1);
-                    }
-
-                }
-
-                // Destroy the service kernel
-                if (kernelImpl != null)
-                {
-                    kernelImpl.destroy();
-                    kernelImpl = null;
-                }
-
-                // Everything completed OK
-                System.exit(0);
-            }
-        }
-
-        // Destroy the service kernel if it is still alive
-        if (kernelImpl != null)
-        {
-            kernelImpl.destroy();
-            kernelImpl = null;
-        }
-
-        // The command wasn't found
-        System.err.println("Command not found: " + args[0]);
-        display();
-        System.exit(1);
-    }
-
-    /**
-     * Load the launcher configuration file
-     *
-     * @return The XML configuration file Document
-     */
-    private static Document getConfig()
-    {
-        // Load the launcher configuration file
-        String config = ConfigurationManager.getProperty("dspace.dir") +
-                        System.getProperty("file.separator") + "config" +
-                        System.getProperty("file.separator") + "launcher.xml";
-        SAXBuilder saxBuilder = new SAXBuilder();
-        Document doc = null;
-        try
-        {
-            doc = saxBuilder.build(config);
-        }
-        catch (Exception e)
-        {
-            System.err.println("Unable to load the launcher configuration file: [dspace]/config/launcher.xml");
-            System.err.println(e.getMessage());
-            System.exit(1);
-        }
-        return doc;
-    }
-
-    /**
-     * Display the commands that the current launcher config file knows about
-     */
-    private static void display()
-    {
-        Document doc = getConfig();
-        List<Element> commands = doc.getRootElement().getChildren("command");
-        System.out.println("Usage: dspace [command-name] {parameters}");
-        for (Element command : commands)
-        {
-            System.out.println(" - " + command.getChild("name").getValue() +
-                               ": " + command.getChild("description").getValue());
-        }
-    }
-}

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

@@ -1,162 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.awt.image.BufferedImage;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Graphics2D;
-import java.awt.Rectangle;
-
-/**
- * Class to attach a footer to an image using ImageMagick.
- * Thanks Ninh Nguyen from the National Library of Australia for providing the source code.
- * This version of the code is basically Ninh's but reorganised a little. Used with permission.
- */
-
-public class Brand
-{
-	private int brandWidth;
-	private int brandHeight;
-	private Font font;
-	private int xOffset;
-
-	/**
-	 * Constructor to set up footer image attributes.
-	 *
-	 * @param brandWidth length of the footer in pixels
-	 * @param brandHeight height of the footer in pixels
-	 * @param font font to use for text on the footer
-	 * @param xOffset number of pixels text should be indented from left-hand side of footer
-	 *
-	 */
-	public Brand(int brandWidth,
-		      int brandHeight,
-		      Font font,
-		      int xOffset)
-	{
-		this.brandWidth = brandWidth;
-		this.brandHeight = brandHeight;
-		this.font = font;
-		this.xOffset = xOffset;
-	}
-
-	/**
-	 * Create the brand image
-	 *
-	 * @param brandLeftText text that should appear in the bottom left of the image
-	 * @param shortLeftText abbreviated form of brandLeftText that will be substituted if
-	 *	the image is resized such that brandLeftText will not fit. <code>null</code> if not
-	 *	required
-	 * @param brandRightText text that should appear in the bottom right of the image
-	 *
-	 * @return BufferedImage a BufferedImage object describing the brand image file
-	 */
-	public BufferedImage create(String brandLeftText,
-			   String shortLeftText,
-			   String brandRightText)
-	{
-		BrandText[] allBrandText = null;
-
-		BufferedImage brandImage =
-			new BufferedImage(brandWidth, brandHeight, BufferedImage.TYPE_INT_RGB);
-
-		if (brandWidth >= 350)
-		{
-			allBrandText = new BrandText[]
-			{
-				new BrandText(BrandText.BL, brandLeftText),
-				new BrandText(BrandText.BR, brandRightText)
-			};
-		} 
-		else if (brandWidth >= 190)
-		{
-			allBrandText = new BrandText[]
-			{
-				new BrandText(BrandText.BL, shortLeftText),
-				new BrandText(BrandText.BR, brandRightText)
-			};
-		}
-		else
-		{
-			allBrandText = new BrandText[]
-			{
-				new BrandText(BrandText.BR, brandRightText)
-			};
-		}
-
-		if (allBrandText != null && allBrandText.length > 0)
-		{
-      		for (int i = 0; i < allBrandText.length; ++i)
-			{
-        		drawImage(brandImage, allBrandText[i]);
-      		}
-    	}
-
-		return brandImage;
-	}
-
-
-	/**
-	 * do the text placements and preparatory work for the brand image generation
-	 *
-	 * @param brandImage a BufferedImage object where the image is created
-	 * @param identifier and Identifier object describing what text is to be placed in what
-	 *	position within the brand
-	 */
-	private void drawImage(BufferedImage brandImage,
-			BrandText brandText)
-	{
-		int imgWidth = brandImage.getWidth();
-		int imgHeight = brandImage.getHeight();
-
-		int bx, by, tx, ty, bWidth, bHeight;
-
-		Graphics2D g2 = brandImage.createGraphics();
-		g2.setFont(font);
-		FontMetrics fm = g2.getFontMetrics();
-
-
-		bWidth = fm.stringWidth(brandText.getText()) + xOffset * 2 + 1;
-		bHeight = fm.getHeight();
-
-		bx = 0;
-        by = 0;
-
-		if (brandText.getLocation().equals(BrandText.TL))
-		{
-			bx = 0;
-			by = 0;
-		}
-		else if (brandText.getLocation().equals(BrandText.TR))
-		{
-			bx = imgWidth - bWidth;
-			by = 0;
-		}
-		else if (brandText.getLocation().equals(BrandText.BL))
-		{
-			bx = 0;
-			by = imgHeight - bHeight;
-		}
-		else if (brandText.getLocation().equals(BrandText.BR))
-		{
-			bx = imgWidth - bWidth;
-			by = imgHeight - bHeight;
-		}
-
-		Rectangle box = new Rectangle(bx, by, bWidth, bHeight);
-		tx = bx + xOffset;
-		ty = by + fm.getAscent();
-
-    	g2.setColor(Color.black);
-		g2.fill(box);
-		g2.setColor(Color.white);
-		g2.drawString(brandText.getText(), tx, ty);
-	}
-}

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

@@ -1,85 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-/**
- * Identifier class, holding a single item of text and its location
- * within a rectangular areas. Allowable locations are any of the four corners.
- * This is a copy of Picture Australia's PiObj class re-organised with methods.
- * Thanks to Ninh Nguyen at the National Library for providing the original source.
- */
-class BrandText
-{
-	/** Bottom Left */
-	public static final String BL = "bl";
-	/** Bottom Right */
-	public static final String BR = "br";
-	/** Top Left */
-	public static final String TL = "tl";
-	/** Top Right */
-	public static final String TR = "tr";
-
-	private String location;
-	private String text;
-
-	/**
-	 * Constructor for an Identifier object containing a text string and
-	 * its location within a rectangular area.
-	 *
-	 * @param location one of the class location constants e.g. <code>Identifier.BL</code>
-	 * @param the text associated with the location
-	 */
-	public BrandText(String location, String text)
-	{
-		this.location = location;
-		this.text = text;
-	}
-
-	/**
-	 * get the location the text of the Identifier object is associated with
-	 *
-	 * @return String one the class location constants e.g. <code>Identifier.BL</code>
-	 */
-	public String getLocation()
-	{
-		return location;
-	}
-
-
-	/**
-	 * get the text associated with the Identifier object
-	 *
-	 * @return String the text associated with the Identifier object
-	 */
-	public String getText()
-	{
-		return text;
-	}
-
-
-	/**
-	 * set the location associated with the Identifier object
-	 *
-	 * @param location one of the class location constants
-	 */
-	public void setLocation(String location)
-	{
-		this.location = location;
-	}
-
-
-	/**
-	 * set the text associated with the Identifier object
-	 *
-	 * @param text any text string (typically a branding or identifier)
-	 */
-	public void setText(String text)
-	{
-		this.text = text;
-	}
-}

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

@@ -1,161 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.awt.Font;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-
-import javax.imageio.ImageIO;
-
-import org.dspace.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 class BrandedPreviewJPEGFilter extends MediaFilter
-{
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".preview.jpg";
-    }
-
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "BRANDED_PREVIEW";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "JPEG";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Generated Branded Preview";
-    }
-
-   
-    /**
-     * @param source
-     *            source input stream
-     * 
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        // read in bitstream's image
-        BufferedImage buf = ImageIO.read(source);
-
-        // get config params
-        float xmax = (float) ConfigurationManager
-                .getIntProperty("webui.preview.maxwidth");
-        float ymax = (float) ConfigurationManager
-                .getIntProperty("webui.preview.maxheight");
-        int brandHeight = ConfigurationManager.getIntProperty("webui.preview.brand.height");
-        String brandFont = ConfigurationManager.getProperty("webui.preview.brand.font");
-        int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");
-        
-        // now get the image dimensions
-        float xsize = (float) buf.getWidth(null);
-        float ysize = (float) buf.getHeight(null);
-
-        // if verbose flag is set, print out dimensions
-        // to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("original size: " + xsize + "," + ysize);
-        }
-
-        // scale by x first if needed
-        if (xsize > xmax)
-        {
-            // calculate scaling factor so that xsize * scale = new size (max)
-            float scaleFactor = xmax / xsize;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("x scale factor: " + scaleFactor);
-            }
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scaleFactor;
-            ysize = ysize * scaleFactor;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("new size: " + xsize + "," + ysize);
-            }
-        }
-
-        // scale by y if needed
-        if (ysize > ymax)
-        {
-            float scaleFactor = ymax / ysize;
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scaleFactor;
-            ysize = ysize * scaleFactor;
-        }
-
-        // if verbose flag is set, print details to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("created thumbnail size: " + xsize + ", "
-                    + ysize);
-        }
-
-        // create an image buffer for the preview with the new xsize, ysize
-        // we add
-        BufferedImage branded = new BufferedImage((int) xsize, (int) ysize + brandHeight,
-                BufferedImage.TYPE_INT_RGB);
-
-        // now render the image into the preview buffer
-        Graphics2D g2d = branded.createGraphics();
-        g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);
-        
-        Brand brand = new Brand((int) xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
-		BufferedImage brandImage = brand.create(ConfigurationManager.getProperty("webui.preview.brand"),
-												ConfigurationManager.getProperty("webui.preview.brand.abbrev"),
-												MediaFilterManager.getCurrentItem() == null ? "" : "hdl:" + MediaFilterManager.getCurrentItem().getHandle());
-		
-		g2d.drawImage(brandImage, (int)0, (int)ysize, (int) xsize, (int) 20, null);
-
-        // now create an input stream for the thumbnail buffer and return it
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-
-        ImageIO.write(branded, "jpeg", baos);
-
-        // now get the array
-        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
-
-        return bais; // hope this gets written out before its garbage collected!
-	}
-}

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

@@ -1,103 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.InputStream;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-/**
- * Public interface for any class which transforms or converts content/bitstreams 
- * from one format to another.  This interface should be implemented by any class
- * which defines a "filter" to be run by the MediaFilterManager.
- */
-public interface FormatFilter
-{
-    /**
-     * Get a filename for a newly created filtered bitstream
-     * 
-     * @param sourceName
-     *            name of source bitstream
-     * @return filename generated by the filter - for example, document.pdf
-     *         becomes document.pdf.txt
-     */
-    public String getFilteredName(String sourceName);
-
-    /**
-     * @return name of the bundle this filter will stick its generated
-     *         Bitstreams
-     */
-    public String getBundleName();
-
-    /**
-     * @return name of the bitstream format (say "HTML" or "Microsoft Word")
-     *         returned by this filter look in the bitstream format registry or
-     *         mediafilter.cfg for valid format strings.
-     */
-    public String getFormatString();
-
-    /**
-     * @return string to describe the newly-generated Bitstream's - how it was
-     *         produced is a good idea
-     */
-    public String getDescription();
-
-    /**
-     * @param source
-     *            input stream
-     * 
-     * @return result of filter's transformation, written out to a bitstream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception;
-
-    /**
-     * Perform any pre-processing of the source bitstream *before* the actual 
-     * filtering takes place in MediaFilterManager.processBitstream().
-     * <p>
-     * Return true if pre-processing is successful (or no pre-processing
-     * is necessary).  Return false if bitstream should be skipped
-     * for any reason.
-     * 
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param source
-     *            source bitstream to be processed
-     * 
-     * @return true if bitstream processing should continue, 
-     * 			false if this bitstream should be skipped
-     */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-            throws Exception;
-        
-    /**
-     * Perform any post-processing of the generated bitstream *after* this
-     * filter has already been run.
-     * <p>
-     * Return true if pre-processing is successful (or no pre-processing
-     * is necessary).  Return false if bitstream should be skipped
-     * for some reason.
-     * 
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param generatedBitstream
-     *            the bitstream which was generated by
-     *            this filter.
-     */
-    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-            throws Exception;
-}
-

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

@@ -1,81 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-
-import javax.swing.text.Document;
-import javax.swing.text.html.HTMLEditorKit;
-
-/*
- * 
- * 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 String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Extracted text";
-    }
-
-    /**
-     * @param source
-     *            source input stream
-     * 
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        // try and read the document - set to ignore character set directive,
-        // assuming that the input stream is already set properly (I hope)
-        HTMLEditorKit kit = new HTMLEditorKit();
-        Document doc = kit.createDefaultDocument();
-
-        doc.putProperty("IgnoreCharsetDirective", Boolean.TRUE);
-
-        kit.read(source, doc, 0);
-
-        String extractedText = doc.getText(0, doc.getLength());
-
-        // generate an input stream with the extracted text
-        byte[] textBytes = extractedText.getBytes();
-        ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-        return bais; // will this work? or will the byte array be out of scope?
-    }
-}

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

@@ -1,166 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.InputStream;
-
-import javax.imageio.ImageIO;
-
-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 class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
-{
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".jpg";
-    }
-
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "THUMBNAIL";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "JPEG";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Generated Thumbnail";
-    }
-
-    /**
-     * @param source
-     *            source input stream
-     * 
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        // read in bitstream's image
-        BufferedImage buf = ImageIO.read(source);
-
-        // get config params
-        float xmax = (float) ConfigurationManager
-                .getIntProperty("thumbnail.maxwidth");
-        float ymax = (float) ConfigurationManager
-                .getIntProperty("thumbnail.maxheight");
-
-        // now get the image dimensions
-        float xsize = (float) buf.getWidth(null);
-        float ysize = (float) buf.getHeight(null);
-
-        // if verbose flag is set, print out dimensions
-        // to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("original size: " + xsize + "," + ysize);
-        }
-
-        // scale by x first if needed
-        if (xsize > xmax)
-        {
-            // calculate scaling factor so that xsize * scale = new size (max)
-            float scale_factor = xmax / xsize;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("x scale factor: " + scale_factor);
-            }
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scale_factor;
-            ysize = ysize * scale_factor;
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println("new size: " + xsize + "," + ysize);
-            }
-        }
-
-        // scale by y if needed
-        if (ysize > ymax)
-        {
-            float scale_factor = ymax / ysize;
-
-            // now reduce x size
-            // and y size
-            xsize = xsize * scale_factor;
-            ysize = ysize * scale_factor;
-        }
-
-        // if verbose flag is set, print details to STDOUT
-        if (MediaFilterManager.isVerbose)
-        {
-            System.out.println("created thumbnail size: " + xsize + ", "
-                    + ysize);
-        }
-
-        // create an image buffer for the thumbnail with the new xsize, ysize
-        BufferedImage thumbnail = new BufferedImage((int) xsize, (int) ysize,
-                BufferedImage.TYPE_INT_RGB);
-
-        // now render the image into the thumbnail buffer
-        Graphics2D g2d = thumbnail.createGraphics();
-        g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);
-
-        // now create an input stream for the thumbnail buffer and return it
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-
-        ImageIO.write(thumbnail, "jpeg", baos);
-
-        // now get the array
-        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
-
-        return bais; // hope this gets written out before its garbage collected!
-    }
-
-
-    public String[] getInputMIMETypes()
-    {
-        return ImageIO.getReaderMIMETypes();
-    }
-
-    public String[] getInputDescriptions()
-    {
-        return null;
-    }
-
-    public String[] getInputExtensions()
-    {
-        // Temporarily disabled as JDK 1.6 only
-        // return ImageIO.getReaderFileSuffixes();
-        return null;
-    }
-}

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

@@ -1,70 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import org.dspace.content.Bitstream;
-import org.dspace.content.Item;
-import org.dspace.core.Context;
-
-
-/**
- * Abstract class which defines the default settings for a *simple* Media or Format Filter. 
- * This class may be extended by any class which wishes to define a simple filter to be run 
- * by the MediaFilterManager.  More complex filters should likely implement the FormatFilter
- * interface directly, so that they can define their own pre/postProcessing methods.
- */
-public abstract class MediaFilter implements FormatFilter
-{
-	/**
-     * Perform any pre-processing of the source bitstream *before* the actual 
-     * filtering takes place in MediaFilterManager.processBitstream().
-     * <p>
-     * Return true if pre-processing is successful (or no pre-processing
-     * is necessary).  Return false if bitstream should be skipped
-     * for any reason.
-     * 
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param source
-     *            source bitstream to be processed
-     * 
-     * @return true if bitstream processing should continue, 
-     *          false if this bitstream should be skipped
-     */
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-            throws Exception
-    {
-        return true;  //default to no pre-processing
-    }
-     
-    /**
-     * Perform any post-processing of the generated bitstream *after* this
-     * filter has already been run.
-     * <p>
-     * Return true if pre-processing is successful (or no pre-processing
-     * is necessary).  Return false if bitstream should be skipped
-     * for some reason.
-     * 
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param generatedBitstream
-     *            the bitstream which was generated by
-     *            this filter.
-     */
-    public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)
-            throws Exception
-    {
-        //default to no post-processing necessary
-    }
-}

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

@@ -1,838 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.InputStream;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.List;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.MissingArgumentException;
-import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-
-import org.apache.commons.lang.ArrayUtils;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DCDate;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.core.PluginManager;
-import org.dspace.core.SelfNamedPlugin;
-import org.dspace.handle.HandleManager;
-import org.dspace.search.DSIndexer;
-
-/**
- * MediaFilterManager is the class that invokes the media/format filters over the
- * repository's content. A few command line flags affect the operation of the
- * MFM: -v verbose outputs all extracted text to STDOUT; -f force forces all
- * bitstreams to be processed, even if they have been before; -n noindex does not
- * recreate index after processing bitstreams; -i [identifier] limits processing 
- * scope to a community, collection or item; and -m [max] limits processing to a
- * maximum number of items.
- */
-public class MediaFilterManager
-{
-	//key (in dspace.cfg) which lists all enabled filters by name
-    public static final String MEDIA_FILTER_PLUGINS_KEY = "filter.plugins";
-	
-    //prefix (in dspace.cfg) for all filter properties
-    public static final String FILTER_PREFIX = "filter";
-    
-    //suffix (in dspace.cfg) for input formats supported by each filter
-    public static final String INPUT_FORMATS_SUFFIX = "inputFormats";
-    
-    static boolean updateIndex = true; // default to updating index
-
-    static boolean isVerbose = false; // default to not verbose
-
-    static boolean isQuiet = false; // default is noisy
-
-    static boolean isForce = false; // default to not forced
-    
-    static String identifier = null; // object scope limiter
-    
-    static int max2Process = Integer.MAX_VALUE;  // maximum number items to process
-    
-    static int processed = 0;   // number items processed
-    
-    private static Item currentItem = null;   // current item being processed
-    
-    private static FormatFilter[] filterClasses = null;
-    
-    private static Map<String, List<String>> filterFormats = new HashMap<String, List<String>>();
-    
-    private static List<String> skipList = null; //list of identifiers to skip during processing
-    
-    //separator in filterFormats Map between a filter class name and a plugin name,
-    //for MediaFilters which extend SelfNamedPlugin (\034 is "file separator" char)
-    public static final String FILTER_PLUGIN_SEPARATOR = "\034";
-    
-    public static void main(String[] argv) throws Exception
-    {
-        // set headless for non-gui workstations
-        System.setProperty("java.awt.headless", "true");
-
-        // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
-
-        int status = 0;
-
-        Options options = new Options();
-        
-        options.addOption("v", "verbose", false,
-                "print all extracted text and other details to STDOUT");
-        options.addOption("q", "quiet", false,
-                "do not print anything except in the event of errors.");
-        options.addOption("f", "force", false,
-                "force all bitstreams to be processed");
-        options.addOption("n", "noindex", false,
-                "do NOT update the search index after filtering bitstreams");
-        options.addOption("i", "identifier", true,
-        		"ONLY process bitstreams belonging to identifier");
-        options.addOption("m", "maximum", true,
-				"process no more than maximum items");
-        options.addOption("h", "help", false, "help");
-
-        //create a "plugin" option (to specify specific MediaFilter plugins to run)
-        OptionBuilder.withLongOpt("plugins");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-                       "ONLY run the specified Media Filter plugin(s)\n" +
-                       "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" + 
-                       "Separate multiple with a comma (,)\n" +
-                       "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")");                
-        Option pluginOption = OptionBuilder.create('p');
-        pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
-        options.addOption(pluginOption);	
-        
-         //create a "skip" option (to specify communities/collections/items to skip)
-        OptionBuilder.withLongOpt("skip");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-                "SKIP the bitstreams belonging to identifier\n" + 
-                "Separate multiple identifiers with a comma (,)\n" +
-                "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)");                
-        Option skipOption = OptionBuilder.create('s');
-        skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
-        options.addOption(skipOption);    
-        
-        CommandLine line = null;
-        try
-        {
-            line = parser.parse(options, argv);
-        }
-        catch(MissingArgumentException e)
-        {
-            System.out.println("ERROR: " + e.getMessage());
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("MediaFilterManager\n", options);
-            System.exit(1);
-        }          
-
-        if (line.hasOption('h'))
-        {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("MediaFilterManager\n", options);
-
-            System.exit(0);
-        }
-
-        if (line.hasOption('v'))
-        {
-            isVerbose = true;
-        }
-
-        isQuiet = line.hasOption('q');
-
-        if (line.hasOption('n'))
-        {
-            updateIndex = false;
-        }
-
-        if (line.hasOption('f'))
-        {
-            isForce = true;
-        }
-        
-        if (line.hasOption('i'))
-        {
-        	identifier = line.getOptionValue('i');
-        }
-        
-        if (line.hasOption('m'))
-        {
-        	max2Process = Integer.parseInt(line.getOptionValue('m'));
-        	if (max2Process <= 1)
-        	{
-        		System.out.println("Invalid maximum value '" + 
-        				     		line.getOptionValue('m') + "' - ignoring");
-        		max2Process = Integer.MAX_VALUE;
-        	}
-        }
-
-        String filterNames[] = null;
-        if(line.hasOption('p'))
-        {
-            //specified which media filter plugins we are using
-            filterNames = line.getOptionValues('p');
-        
-            if(filterNames==null || filterNames.length==0)
-            {   //display error, since no plugins specified
-                System.err.println("\nERROR: -p (-plugin) option requires at least one plugin to be specified.\n" +
-                                          "(e.g. MediaFilterManager -p \"Word Text Extractor\",\"PDF Text Extractor\")\n");
-                HelpFormatter myhelp = new HelpFormatter();
-                myhelp.printHelp("MediaFilterManager\n", options);
-                System.exit(1);
-             }
-        }
-        else
-        { 
-            //retrieve list of all enabled media filter plugins!
-            String enabledPlugins = ConfigurationManager.getProperty(MEDIA_FILTER_PLUGINS_KEY);
-            filterNames = enabledPlugins.split(",\\s*");
-        }
-                
-        //initialize an array of our enabled filters
-        List<FormatFilter> filterList = new ArrayList<FormatFilter>();
-                
-        //set up each filter
-        for(int i=0; i< filterNames.length; i++)
-        {
-            //get filter of this name & add to list of filters
-            FormatFilter filter = (FormatFilter) PluginManager.getNamedPlugin(FormatFilter.class, filterNames[i]);
-            if(filter==null)
-            {   
-                System.err.println("\nERROR: Unknown MediaFilter specified (either from command-line or in dspace.cfg): '" + filterNames[i] + "'");
-                System.exit(1);
-            }
-            else
-            {   
-                filterList.add(filter);
-                       
-                String filterClassName = filter.getClass().getName();
-                           
-                String pluginName = null;
-                           
-                //If this filter is a SelfNamedPlugin,
-                //then the input formats it accepts may differ for
-                //each "named" plugin that it defines.
-                //So, we have to look for every key that fits the
-                //following format: filter.<class-name>.<plugin-name>.inputFormats
-                if( SelfNamedPlugin.class.isAssignableFrom(filter.getClass()) )
-                {
-                    //Get the plugin instance name for this class
-                    pluginName = ((SelfNamedPlugin) filter).getPluginInstanceName();
-                }
-            
-                
-                //Retrieve our list of supported formats from dspace.cfg
-                //For SelfNamedPlugins, format of key is:  
-                //  filter.<class-name>.<plugin-name>.inputFormats
-                //For other MediaFilters, format of key is: 
-                //  filter.<class-name>.inputFormats
-                String formats = ConfigurationManager.getProperty(
-                    FILTER_PREFIX + "." + filterClassName + 
-                    (pluginName!=null ? "." + pluginName : "") +
-                    "." + INPUT_FORMATS_SUFFIX);
-            
-                //add to internal map of filters to supported formats	
-                if (formats != null)
-                {
-                    //For SelfNamedPlugins, map key is:  
-                    //  <class-name><separator><plugin-name>
-                    //For other MediaFilters, map key is just:
-                    //  <class-name>
-                    filterFormats.put(filterClassName + 
-        	            (pluginName!=null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""),
-        	            Arrays.asList(formats.split(",[\\s]*")));
-                }
-            }//end if filter!=null
-        }//end for
-        
-        //If verbose, print out loaded mediafilter info
-        if(isVerbose)
-        {   
-            System.out.println("The following MediaFilters are enabled: ");
-            Iterator<String> i = filterFormats.keySet().iterator();
-            while(i.hasNext())
-            {
-                String filterName = i.next();
-                System.out.println("Full Filter Name: " + filterName);
-                String pluginName = null;
-                if(filterName.contains(FILTER_PLUGIN_SEPARATOR))
-                {
-                    String[] fields = filterName.split(FILTER_PLUGIN_SEPARATOR);
-                    filterName=fields[0];
-                    pluginName=fields[1];
-                }
-                 
-                System.out.println(filterName +
-                        (pluginName!=null? " (Plugin: " + pluginName + ")": ""));
-             }
-        }
-              
-        //store our filter list into an internal array
-        filterClasses = (FormatFilter[]) filterList.toArray(new FormatFilter[filterList.size()]);
-        
-        
-        //Retrieve list of identifiers to skip (if any)
-        String skipIds[] = null;
-        if(line.hasOption('s'))
-        {
-            //specified which identifiers to skip when processing
-            skipIds = line.getOptionValues('s');
-            
-            if(skipIds==null || skipIds.length==0)
-            {   //display error, since no identifiers specified to skip
-                System.err.println("\nERROR: -s (-skip) option requires at least one identifier to SKIP.\n" +
-                                    "Make sure to separate multiple identifiers with a comma!\n" +
-                                    "(e.g. MediaFilterManager -s 123456789/34,123456789/323)\n");
-                HelpFormatter myhelp = new HelpFormatter();
-                myhelp.printHelp("MediaFilterManager\n", options);
-                System.exit(0);
-            }
-            
-            //save to a global skip list
-            skipList = Arrays.asList(skipIds);
-        }
-        
-        Context c = null;
-
-        try
-        {
-            c = new Context();
-
-            // have to be super-user to do the filtering
-            c.turnOffAuthorisationSystem();
-
-            // now apply the filters
-            if (identifier == null)
-            {
-            	applyFiltersAllItems(c);
-            }
-            else  // restrict application scope to identifier
-            {
-            	DSpaceObject dso = HandleManager.resolveToObject(c, identifier);
-            	if (dso == null)
-            	{
-            		throw new IllegalArgumentException("Cannot resolve "
-                                + identifier + " to a DSpace object");
-            	}
-            	
-            	switch (dso.getType())
-            	{
-            		case Constants.COMMUNITY:
-            						applyFiltersCommunity(c, (Community)dso);
-            						break;					
-            		case Constants.COLLECTION:
-            						applyFiltersCollection(c, (Collection)dso);
-            						break;						
-            		case Constants.ITEM:
-            						applyFiltersItem(c, (Item)dso);
-            						break;
-            	}
-            }
-          
-            // update search index?
-            if (updateIndex)
-            {
-                if (!isQuiet)
-                {
-                    System.out.println("Updating search index:");
-                }
-                DSIndexer.setBatchProcessingMode(true);
-                try
-                {
-                    DSIndexer.updateIndex(c);
-                }
-                finally
-                {
-                    DSIndexer.setBatchProcessingMode(false);
-                }
-            }
-
-            c.complete();
-            c = null;
-        }
-        catch (Exception e)
-        {
-            status = 1;
-        }
-        finally
-        {
-            if (c != null)
-            {
-                c.abort();
-            }
-        }
-        System.exit(status);
-    }
-
-    public static void applyFiltersAllItems(Context c) throws Exception
-    {
-        if(skipList!=null)
-        {    
-            //if a skip-list exists, we need to filter community-by-community
-            //so we can respect what is in the skip-list
-            Community[] topLevelCommunities = Community.findAllTop(c);
-          
-            for(int i=0; i<topLevelCommunities.length; i++)
-            {
-                applyFiltersCommunity(c, topLevelCommunities[i]);
-            }
-        }
-        else 
-        {
-            //otherwise, just find every item and process
-            ItemIterator i = Item.findAll(c);
-            try
-            {
-                while (i.hasNext() && processed < max2Process)
-                {
-                    applyFiltersItem(c, i.next());
-                }
-            }
-            finally
-            {
-                if (i != null)
-                {
-                    i.close();
-                }
-            }
-        }
-    }
-    
-    public static void applyFiltersCommunity(Context c, Community community)
-                                             throws Exception
-    {   //only apply filters if community not in skip-list
-        if(!inSkipList(community.getHandle()))
-        {    
-           	Community[] subcommunities = community.getSubcommunities();
-           	for (int i = 0; i < subcommunities.length; i++)
-           	{
-           		applyFiltersCommunity(c, subcommunities[i]);
-           	}
-           	
-           	Collection[] collections = community.getCollections();
-           	for (int j = 0; j < collections.length; j++)
-           	{
-           		applyFiltersCollection(c, collections[j]);
-           	}
-        }
-    }
-        
-    public static void applyFiltersCollection(Context c, Collection collection)
-                                              throws Exception
-    {
-        //only apply filters if collection not in skip-list
-        if(!inSkipList(collection.getHandle()))
-        {
-            ItemIterator i = collection.getItems();
-            try
-            {
-                while (i.hasNext() && processed < max2Process)
-                {
-                    applyFiltersItem(c, i.next());
-                }
-            }
-            finally
-            {
-                if (i != null)
-                {
-                    i.close();
-                }
-            }
-        }
-    }
-       
-    public static void applyFiltersItem(Context c, Item item) throws Exception
-    {
-        //only apply filters if item not in skip-list
-        if(!inSkipList(item.getHandle()))
-        {
-    	  //cache this item in MediaFilterManager
-    	  //so it can be accessed by MediaFilters as necessary
-    	  currentItem = item;
-    	
-          if (filterItem(c, item))
-          {
-        	  // commit changes after each filtered item
-        	  c.commit();
-              // increment processed count
-              ++processed;
-          }
-          // clear item objects from context cache and internal cache
-          item.decache();
-          currentItem = null;
-        }  
-    }
-
-    /**
-     * Iterate through the item's bitstreams in the ORIGINAL bundle, applying
-     * filters if possible.
-     * 
-     * @return true if any bitstreams processed, 
-     *         false if none
-     */
-    public static boolean filterItem(Context c, Item myItem) throws Exception
-    {
-        // get 'original' bundles
-        Bundle[] myBundles = myItem.getBundles("ORIGINAL");
-        boolean done = false;
-        for (int i = 0; i < myBundles.length; i++)
-        {
-        	// now look at all of the bitstreams
-            Bitstream[] myBitstreams = myBundles[i].getBitstreams();
-            
-            for (int k = 0; k < myBitstreams.length; k++)
-            {
-            	done |= filterBitstream(c, myItem, myBitstreams[k]);
-            }
-        }
-        return done;
-    }
-
-    /**
-     * Attempt to filter a bitstream.
-     * 
-     * An exception will be thrown if the media filter class cannot be
-     * instantiated.  Exceptions from filtering will be logged to STDOUT and
-     * swallowed.
-     * 
-     * @return true if bitstream processed, 
-     *         false if no applicable filter or already processed
-     */
-    public static boolean filterBitstream(Context c, Item myItem,
-            Bitstream myBitstream) throws Exception
-    {
-    	boolean filtered = false;
-    	
-    	// iterate through filter classes. A single format may be actioned
-    	// by more than one filter
-    	for (int i = 0; i < filterClasses.length; i++)
-    	{
-    		//List fmts = (List)filterFormats.get(filterClasses[i].getClass().getName());
-    	    String pluginName = null;
-    	               
-    	    //if this filter class is a SelfNamedPlugin,
-    	    //its list of supported formats is different for
-    	    //differently named "plugin"
-    	    if( SelfNamedPlugin.class.isAssignableFrom(filterClasses[i].getClass()) )
-    	    {
-    	        //get plugin instance name for this media filter
-    	        pluginName = ((SelfNamedPlugin)filterClasses[i]).getPluginInstanceName();
-    	    }
-    	               
-    	    //Get list of supported formats for the filter (and possibly named plugin)
-    	    //For SelfNamedPlugins, map key is:  
-    	    //  <class-name><separator><plugin-name>
-    	    //For other MediaFilters, map key is just:
-    	    //  <class-name>
-    	    List<String> fmts = filterFormats.get(filterClasses[i].getClass().getName() +
-    	                       (pluginName!=null ? FILTER_PLUGIN_SEPARATOR + pluginName : ""));
-    	   
-    	    if (fmts.contains(myBitstream.getFormat().getShortDescription()))
-    		{
-            	try
-            	{
-		            // only update item if bitstream not skipped
-		            if (processBitstream(c, myItem, myBitstream, filterClasses[i]))
-            	    {
-		           		myItem.update(); // Make sure new bitstream has a sequence
-		                                 	// number
-		           		filtered = true;
-		            }
-            	}
-                catch (Exception e)
-                {
-                	String handle = myItem.getHandle();
-                	Bundle[] bundles = myBitstream.getBundles();
-                	long size = myBitstream.getSize();
-                	String checksum = myBitstream.getChecksum() + " ("+myBitstream.getChecksumAlgorithm()+")";
-                	int assetstore = myBitstream.getStoreNumber();
-   
-                	// Printout helpful information to find the errored bitstream.
-                	System.out.println("ERROR filtering, skipping bitstream:\n");
-                	System.out.println("\tItem Handle: "+ handle);
-                	for (Bundle bundle : bundles)
-                	{
-                		System.out.println("\tBundle Name: " + bundle.getName());
-                	}
-                	System.out.println("\tFile Size: " + size);
-                	System.out.println("\tChecksum: " + checksum);
-                	System.out.println("\tAsset Store: " + assetstore);
-                	System.out.println(e);
-                    e.printStackTrace();
-                }
-    		}
-            else if (filterClasses[i] instanceof SelfRegisterInputFormats)
-            {
-                // Filter implements self registration, so check to see if it should be applied
-                // given the formats it claims to support
-                SelfRegisterInputFormats srif = (SelfRegisterInputFormats)filterClasses[i];
-                boolean applyFilter = false;
-
-                // Check MIME type
-                String[] mimeTypes = srif.getInputMIMETypes();
-                if (mimeTypes != null)
-                {
-                    for (String mimeType : mimeTypes)
-                    {
-                        if (mimeType.equalsIgnoreCase(myBitstream.getFormat().getMIMEType()))
-                        {
-                            applyFilter = true;
-                        }
-                    }
-                }
-
-                // Check description
-                if (!applyFilter)
-                {
-                    String[] descriptions = srif.getInputDescriptions();
-                    if (descriptions != null)
-                    {
-                        for (String desc : descriptions)
-                        {
-                            if (desc.equalsIgnoreCase(myBitstream.getFormat().getShortDescription()))
-                            {
-                                applyFilter = true;
-                            }
-                        }
-                    }
-                }
-
-                // Check extensions
-                if (!applyFilter)
-                {
-                    String[] extensions = srif.getInputExtensions();
-                    if (extensions != null)
-                    {
-                        for (String ext : extensions)
-                        {
-                            String[] formatExtensions = myBitstream.getFormat().getExtensions();
-                            if (formatExtensions != null && ArrayUtils.contains(formatExtensions, ext))
-                            {
-                                applyFilter = true;
-                            }
-                        }
-                    }
-                }
-
-                // Filter claims to handle this type of file, so attempt to apply it
-                if (applyFilter)
-                {
-                    try
-                    {
-                        // only update item if bitstream not skipped
-                        if (processBitstream(c, myItem, myBitstream, filterClasses[i]))
-                        {
-                               myItem.update(); // Make sure new bitstream has a sequence
-                                                 // number
-                               filtered = true;
-                        }
-                    }
-                    catch (Exception e)
-                    {
-                        System.out.println("ERROR filtering, skipping bitstream #"
-                                + myBitstream.getID() + " " + e);
-                        e.printStackTrace();
-                    }
-                }
-            }
-    	}
-        return filtered;
-    }
-    
-    /**
-     * A utility class that calls the virtual methods
-     * from the current MediaFilter class.
-     * It scans the bitstreams in an item, and decides if a bitstream has 
-     * already been filtered, and if not or if overWrite is set, invokes the 
-     * filter.
-     * 
-     * @param c
-     *            context
-     * @param item
-     *            item containing bitstream to process
-     * @param source
-     *            source bitstream to process
-     * @param formatFilter
-     *            FormatFilter to perform filtering
-     * 
-     * @return true if new rendition is created, false if rendition already
-     *         exists and overWrite is not set
-     */
-    public static boolean processBitstream(Context c, Item item, Bitstream source, FormatFilter formatFilter)
-            throws Exception
-    {
-        //do pre-processing of this bitstream, and if it fails, skip this bitstream!
-    	if(!formatFilter.preProcessBitstream(c, item, source))
-        {
-            return false;
-        }
-        	
-    	boolean overWrite = MediaFilterManager.isForce;
-        
-        // get bitstream filename, calculate destination filename
-        String newName = formatFilter.getFilteredName(source.getName());
-
-        Bitstream existingBitstream = null; // is there an existing rendition?
-        Bundle targetBundle = null; // bundle we're modifying
-
-        Bundle[] bundles = item.getBundles(formatFilter.getBundleName());
-
-        // check if destination bitstream exists
-        if (bundles.length > 0)
-        {
-            // only finds the last match (FIXME?)
-            for (int i = 0; i < bundles.length; i++)
-            {
-                Bitstream[] bitstreams = bundles[i].getBitstreams();
-
-                for (int j = 0; j < bitstreams.length; j++)
-                {
-                    if (bitstreams[j].getName().equals(newName))
-                    {
-                        targetBundle = bundles[i];
-                        existingBitstream = bitstreams[j];
-                    }
-                }
-            }
-        }
-
-        // if exists and overwrite = false, exit
-        if (!overWrite && (existingBitstream != null))
-        {
-            if (!isQuiet)
-            {
-                System.out.println("SKIPPED: bitstream " + source.getID()
-                        + " (item: " + item.getHandle() + ") because '" + newName + "' already exists");
-            }
-
-            return false;
-        }
-        
-        InputStream destStream = formatFilter.getDestinationStream(source.retrieve());
-        if (destStream == null)
-        {
-            if (!isQuiet)
-            {
-                System.out.println("SKIPPED: bitstream " + source.getID()
-                        + " (item: " + item.getHandle() + ") because filtering was unsuccessful");
-            }
-
-            return false;
-        }
-
-        // create new bundle if needed
-        if (bundles.length < 1)
-        {
-            targetBundle = item.createBundle(formatFilter.getBundleName());
-        }
-        else
-        {
-            // take the first match
-            targetBundle = bundles[0];
-        }
-
-        Bitstream b = targetBundle.createBitstream(destStream);
-
-        // Now set the format and name of the bitstream
-        b.setName(newName);
-        b.setSource("Written by FormatFilter " + formatFilter.getClass().getName() +
-        			" on " + DCDate.getCurrent() + " (GMT)."); 
-        b.setDescription(formatFilter.getDescription());
-
-        // Find the proper format
-        BitstreamFormat bf = BitstreamFormat.findByShortDescription(c,
-                formatFilter.getFormatString());
-        b.setFormat(bf);
-        b.update();
-        
-        //Inherit policies from the source bitstream
-        //(first remove any existing policies)
-        AuthorizeManager.removeAllPolicies(c, b);
-        AuthorizeManager.inheritPolicies(c, source, b);
-
-        // fixme - set date?
-        // we are overwriting, so remove old bitstream
-        if (existingBitstream != null)
-        {
-            targetBundle.removeBitstream(existingBitstream);
-        }
-
-        if (!isQuiet)
-        {
-            System.out.println("FILTERED: bitstream " + source.getID()
-                    + " (item: " + item.getHandle() + ") and created '" + newName + "'");
-        }
-
-        //do post-processing of the generated bitstream
-        formatFilter.postProcessBitstream(c, item, b);
-        
-        return true;
-    }
-    
-    /**
-     * Return the item that is currently being processed/filtered
-     * by the MediaFilterManager.
-     * <p>
-     * This allows FormatFilters to retrieve the Item object
-     * in case they need access to item-level information for their format
-     * transformations/conversions.
-     * 
-     * @return current Item being processed by MediaFilterManager
-     */
-    public static Item getCurrentItem()
-    {
-        return currentItem;
-    }
-    
-    /**
-     * Check whether or not to skip processing the given identifier.
-     * 
-     * @param identifier
-     *            identifier (handle) of a community, collection or item
-     *            
-     * @return true if this community, collection or item should be skipped
-     *          during processing.  Otherwise, return false.
-     */
-    public static boolean inSkipList(String identifier)
-    {
-        if(skipList!=null && skipList.contains(identifier))
-        {
-            if (!isQuiet)
-            {
-                System.out.println("SKIP-LIST: skipped bitstreams within identifier " + identifier);
-            }
-            return true;
-        }    
-        else
-        {
-            return false;
-        }
-    }
-    
-}

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

@@ -1,148 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.InputStream;
-import java.io.OutputStreamWriter;
-import java.io.Writer;
-
-import org.apache.log4j.Logger;
-import org.apache.pdfbox.pdmodel.PDDocument;
-import org.apache.pdfbox.util.PDFTextStripper;
-import org.dspace.core.ConfigurationManager;
-
-/*
- *
- * to do: helpful error messages - can't find mediafilter.cfg - can't
- * instantiate filter - bitstream format doesn't exist
- *
- */
-public class PDFFilter extends MediaFilter
-{
-
-    private static Logger log = Logger.getLogger(PDFFilter.class);
-
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     *
-     */
-    public String getBundleName()
-    {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Extracted text";
-    }
-
-    /**
-     * @param source
-     *            source input stream
-     *
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        try
-        {
-            boolean useTemporaryFile = ConfigurationManager.getBooleanProperty("pdffilter.largepdfs", false);
-
-            // get input stream from bitstream
-            // pass to filter, get string back
-            PDFTextStripper pts = new PDFTextStripper();
-            PDDocument pdfDoc = null;
-            Writer writer = null;
-            File tempTextFile = null;
-            ByteArrayOutputStream byteStream = null;
-
-            if (useTemporaryFile)
-            {
-                tempTextFile = File.createTempFile("dspacepdfextract" + source.hashCode(), ".txt");
-                tempTextFile.deleteOnExit();
-                writer = new OutputStreamWriter(new FileOutputStream(tempTextFile));
-            }
-            else
-            {
-                byteStream = new ByteArrayOutputStream();
-                writer = new OutputStreamWriter(byteStream);
-            }
-            
-            try
-            {
-                pdfDoc = PDDocument.load(source);
-                pts.writeText(pdfDoc, writer);
-            }
-            finally
-            {
-                try
-                {
-                    if (pdfDoc != null)
-                    {
-                        pdfDoc.close();
-                    }
-                }
-                catch(Exception e)
-                {
-                   log.error("Error closing PDF file: " + e.getMessage(), e);
-                }
-
-                try
-                {
-                    writer.close();
-                }
-                catch(Exception e)
-                {
-                   log.error("Error closing temporary extract file: " + e.getMessage(), e);
-                }
-            }
-
-            if (useTemporaryFile)
-            {
-                return new FileInputStream(tempTextFile);
-            }
-            else
-            {
-                byte[] bytes = byteStream.toByteArray();
-                return new ByteArrayInputStream(bytes);
-            }
-        }
-        catch (OutOfMemoryError oome)
-        {
-            log.error("Error parsing PDF document " + oome.getMessage(), oome);
-            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false))
-            {
-                throw oome;
-            }
-        }
-
-        return null;
-    }
-}

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

@@ -1,124 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-
-import org.apache.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;
-
-/*
- * TODO: Allow user to configure extraction of only text or only notes
- * 
- */
-public class PowerPointFilter extends MediaFilter
-{
-
-    private static Logger log = Logger.getLogger(PowerPointFilter.class);
-
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     * 
-     */
-    public String getBundleName()
-    {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstream format
-     * 
-     *         TODO: Check that this is correct
-     */
-    public String getFormatString()
-    {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Extracted text";
-    }
-
-    /**
-     * @param source
-     *            source input stream
-     * 
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-
-        try
-        {
-
-            String extractedText = null;
-            new ExtractorFactory();
-            POITextExtractor pptExtractor = ExtractorFactory
-                    .createExtractor(source);
-
-            // PowerPoint XML files and legacy format PowerPoint files
-            // require different classes and APIs for text extraction
-
-            // If this is a PowerPoint XML file, extract accordingly
-            if (pptExtractor instanceof XSLFPowerPointExtractor)
-            {
-
-                // The true method arguments indicate that text from
-                // the slides and the notes is desired
-                extractedText = ((XSLFPowerPointExtractor) pptExtractor)
-                        .getText(true, true);
-            }
-
-            // Legacy PowerPoint files
-            else if (pptExtractor instanceof PowerPointExtractor)
-            {
-
-                extractedText = ((PowerPointExtractor) pptExtractor).getText()
-                        + " " + ((PowerPointExtractor) pptExtractor).getNotes();
-
-            }
-            if (extractedText != null)
-            {
-                // if verbose flag is set, print out extracted text
-                // to STDOUT
-                if (MediaFilterManager.isVerbose)
-                {
-                    System.out.println(extractedText);
-                }
-
-                // generate an input stream with the extracted text
-                byte[] textBytes = extractedText.getBytes();
-                ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-                return bais;
-            }
-        }
-        catch (Exception e)
-        {
-            log.error("Error filtering bitstream: " + e.getMessage(), e);
-            throw e;
-        }
-
-        return null;
-    }
-}

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

@@ -1,21 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-/**
- * Interface to allow filters to register the input formats they handle
- * (useful for exposing underlying capabilities of libraries used)
- */
-public interface SelfRegisterInputFormats
-{
-    public String[] getInputMIMETypes();
-
-    public String[] getInputDescriptions();
-
-    public String[] getInputExtensions();
-}

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

@@ -1,98 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.io.IOException;
-
-import org.apache.log4j.Logger;
-
-import org.textmining.extraction.TextExtractor;
-import org.textmining.extraction.word.WordTextExtractorFactory;
-
-/*
- * 
- * to do: helpful error messages - can't find mediafilter.cfg - can't
- * instantiate filter - bitstream format doesn't exist.
- *  
- */
-public class WordFilter extends MediaFilter
-{
-
-    private static Logger log = Logger.getLogger(WordFilter.class);
-
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".txt";
-    }
-
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "TEXT";
-    }
-
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "Text";
-    }
-
-    /**
-     * @return String description
-     */
-    public String getDescription()
-    {
-        return "Extracted text";
-    }
-
-    /**
-     * @param source
-     *            source input stream
-     * 
-     * @return InputStream the resulting input stream
-     */
-    public InputStream getDestinationStream(InputStream source)
-            throws Exception
-    {
-        // get input stream from bitstream
-        // pass to filter, get string back
-        try  
-        {
-            WordTextExtractorFactory factory = new WordTextExtractorFactory();
-            TextExtractor e = factory.textExtractor(source);
-            String extractedText = e.getText();
-
-            // if verbose flag is set, print out extracted text
-            // to STDOUT
-            if (MediaFilterManager.isVerbose)
-            {
-                System.out.println(extractedText);
-            }
-
-            // generate an input stream with the extracted text
-            byte[] textBytes = extractedText.getBytes();
-            ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
-
-            return bais; // will this work? or will the byte array be out of scope?
-        } 
-        catch (IOException ioe)
-        {
-            System.out.println("Invalid Word Format");
-            log.error("Error detected - Word File format not recognized: "
-                    + ioe.getMessage(), ioe);
-            throw ioe;
-        }
-    }
-}

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

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

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

@@ -1,318 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.mediafilter;
-
-import java.awt.Graphics2D;
-import java.awt.image.BufferedImage;
-import java.io.BufferedReader;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.OutputStream;
-import java.util.Arrays;
-import java.util.regex.MatchResult;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import javax.imageio.ImageIO;
-
-import org.apache.log4j.Logger;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Utils;
-
-/**
- * Thumbnail MediaFilter for PDF sources
- *
- * This filter generates thumbnail images for PDF documents, _including_
- * 3D PDF documents with 2D "poster" images.  Since the PDFBox library
- * does not understand these, and fails to render a lot of other PDFs,
- * this filter forks a process running the "pdftoppm" program from the
- * XPdf suite -- see http://www.foolabs.com/xpdf/
- * This is a suite of open-source PDF tools that has been widely ported
- * to Unix platforms and the ones we use (pdftoppm, pdfinfo) even
- * run on Win32.
- *
- * This was written for the FACADE project but it is not directly connected
- * to any of the other FACADE-specific software.  The FACADE UI expects
- * to find thumbnail images for 3D PDFs generated by this filter.
- *
- * Requires DSpace config properties keys:
- *
- *  xpdf.path.pdftoppm -- absolute path to "pdftoppm" executable (required!)
- *  xpdf.path.pdfinfo -- absolute path to "pdfinfo" executable (required!)
- *  thumbnail.maxwidth  -- borrowed from thumbnails, max dim of generated image
- *
- * @author Larry Stone
- * @see org.dspace.app.mediafilter.MediaFilter
- */
-public class XPDF2Thumbnail extends MediaFilter
-{
-    private static Logger log = Logger.getLogger(XPDF2Thumbnail.class);
-
-    // maximum size of either preview image dimension
-    private static final int MAX_PX = 800;
-
-    // maxium DPI - use common screen res, 100dpi.
-    private static final int MAX_DPI = 100;
-
-    // command to get image from PDF; @FILE@, @OUTPUT@ are placeholders
-    private static final String XPDF_PDFTOPPM_COMMAND[] =
-    {
-        "@COMMAND@", "-q", "-f", "1", "-l", "1",
-        "-r", "@DPI@", "@FILE@", "@OUTPUTFILE@"
-    };
-
-    // command to get image from PDF; @FILE@, @OUTPUT@ are placeholders
-    private static final String XPDF_PDFINFO_COMMAND[] =
-    {
-        "@COMMAND@", "-f", "1", "-l", "1", "-box", "@FILE@"
-    };
-
-    // executable path for "pdftoppm", comes from DSpace config at runtime.
-    private String pdftoppmPath = null;
-
-    // executable path for "pdfinfo", comes from DSpace config at runtime.
-    private String pdfinfoPath = null;
-
-    // match line in pdfinfo output that describes file's MediaBox
-    private static final Pattern MEDIABOX_PATT = Pattern.compile(
-        "^Page\\s+\\d+\\s+MediaBox:\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)\\s+([\\.\\d-]+)");
-
-    // also from thumbnail.maxwidth in config
-    private int maxwidth = 0;
-
-    // backup default for size, on the large side.
-    private static final int DEFAULT_MAXWIDTH = 500;
-
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".jpg";
-    }
-
-    public String getBundleName()
-    {
-        return "THUMBNAIL";
-    }
-
-    public String getFormatString()
-    {
-        return "JPEG";
-    }
-
-    public String getDescription()
-    {
-        return "Generated Thumbnail";
-    }
-
-    // canonical MediaFilter method to generate the thumbnail as stream.
-    public InputStream getDestinationStream(InputStream sourceStream)
-            throws Exception
-    {
-        // sanity check: xpdf paths are required. can cache since it won't change
-        if (pdftoppmPath == null || pdfinfoPath == null)
-        {
-            pdftoppmPath = ConfigurationManager.getProperty("xpdf.path.pdftoppm");
-            pdfinfoPath = ConfigurationManager.getProperty("xpdf.path.pdfinfo");
-            if (pdftoppmPath == null)
-            {
-                throw new IllegalStateException("No value for key \"xpdf.path.pdftoppm\" in DSpace configuration!  Should be path to XPDF pdftoppm executable.");
-            }
-            if (pdfinfoPath == null)
-            {
-                throw new IllegalStateException("No value for key \"xpdf.path.pdfinfo\" in DSpace configuration!  Should be path to XPDF pdfinfo executable.");
-            }
-            maxwidth = ConfigurationManager.getIntProperty("thumbnail.maxwidth");
-            if (maxwidth == 0)
-            {
-                maxwidth = DEFAULT_MAXWIDTH;
-            }
-        }
-
-        // make local file copy of source PDF since the PDF tools
-        // require a file for random access.
-        // XXX fixme would be nice to optimize this if we ever get
-        // XXX  a DSpace method to access (optionally!) the _file_ of
-        //     a Bitstream in the asset store, only when there is one of course.
-        File sourceTmp = File.createTempFile("DSfilt",".pdf");
-        sourceTmp.deleteOnExit();
-        int status = 0;
-        BufferedImage source = null;
-        try
-        {
-            OutputStream sto = new FileOutputStream(sourceTmp);
-            Utils.copy(sourceStream, sto);
-            sto.close();
-            sourceStream.close();
-
-            // First get max physical dim of bounding box of first page
-            // to compute the DPI to ask for..  otherwise some AutoCAD
-            // drawings can produce enormous files even at 75dpi, for
-            // 48" drawings..
-
-            // run pdfinfo, look for MediaBox description in the output, e.g.
-            // "Page    1 MediaBox:     0.00     0.00   612.00   792.00"
-            //
-            int dpi = 0;
-            String pdfinfoCmd[] = XPDF_PDFINFO_COMMAND.clone();
-            pdfinfoCmd[0] = pdfinfoPath;
-            pdfinfoCmd[pdfinfoCmd.length-1] = sourceTmp.toString();
-            BufferedReader lr = null;
-            try
-            {
-                MatchResult mediaBox = null;
-                Process pdfProc = Runtime.getRuntime().exec(pdfinfoCmd);
-                lr = new BufferedReader(new InputStreamReader(pdfProc.getInputStream()));
-                String line;
-                for (line = lr.readLine(); line != null; line = lr.readLine())
-                {
-                    // if (line.matches(MEDIABOX_PATT))
-                    Matcher mm = MEDIABOX_PATT.matcher(line);
-                    if (mm.matches())
-                    {
-                        mediaBox = mm.toMatchResult();
-                    }
-                }
-                int istatus = pdfProc.waitFor();
-                if (istatus != 0)
-                {
-                    log.error("XPDF pdfinfo proc failed, exit status=" + istatus + ", file=" + sourceTmp);
-                }
-                if (mediaBox == null)
-                {
-                    log.error("Sanity check: Did not find \"MediaBox\" line in output of XPDF pdfinfo, file="+sourceTmp);
-                    throw new IllegalArgumentException("Failed to get MediaBox of PDF with pdfinfo, cannot compute thumbnail.");
-                }
-                else
-                {
-                    double x0 = Double.parseDouble(mediaBox.group(1));
-                    double y0 = Double.parseDouble(mediaBox.group(2));
-                    double x1 = Double.parseDouble(mediaBox.group(3));
-                    double y1 = Double.parseDouble(mediaBox.group(4));
-                    int maxdim = (int)Math.max(Math.abs(x1 - x0), Math.abs(y1 - y0));
-                    dpi = Math.min(MAX_DPI, (MAX_PX * 72 / maxdim));
-                    log.debug("DPI: pdfinfo method got dpi="+dpi+" for max dim="+maxdim+" (points, 1/72\")");
-                }
-            }
-            catch (InterruptedException e)
-            {
-                log.error("Failed transforming file for preview: ",e);
-                throw new IllegalArgumentException("Failed transforming file for thumbnail: ",e);
-            }
-            catch (NumberFormatException e)
-            {
-                log.error("Failed interpreting pdfinfo results, check regexp: ",e);
-                throw new IllegalArgumentException("Failed transforming file for thumbnail: ",e);
-            }
-            finally
-            {
-                if (lr != null)
-                {
-                    lr.close();
-                }
-            }
-
-            // Render page 1 using xpdf's pdftoppm
-            // Requires Sun JAI imageio additions to read ppm directly.
-            // this will get "-000001.ppm" appended to it by pdftoppm
-            File outPrefixF = File.createTempFile("prevu","out");
-            String outPrefix = outPrefixF.toString();
-            if (!outPrefixF.delete())
-            {
-                log.error("Unable to delete output file");
-            }
-            String pdfCmd[] = XPDF_PDFTOPPM_COMMAND.clone();
-            pdfCmd[0] = pdftoppmPath;
-            pdfCmd[pdfCmd.length-3] = String.valueOf(dpi);
-            pdfCmd[pdfCmd.length-2] = sourceTmp.toString();
-            pdfCmd[pdfCmd.length-1] = outPrefix;
-            File outf = new File(outPrefix+"-000001.ppm");
-            log.debug("Running xpdf command: "+Arrays.deepToString(pdfCmd));
-            try
-            {
-                Process pdfProc = Runtime.getRuntime().exec(pdfCmd);
-                status = pdfProc.waitFor();
-                if (!outf.exists()) outf = new File(outPrefix+"-00001.ppm");
-                if (!outf.exists()) outf = new File(outPrefix+"-0001.ppm");
-                if (!outf.exists()) outf = new File(outPrefix+"-001.ppm");
-                if (!outf.exists()) outf = new File(outPrefix+"-01.ppm");
-                if (!outf.exists()) outf = new File(outPrefix+"-1.ppm");
-                log.debug("PDFTOPPM output is: "+outf+", exists="+outf.exists());
-                source = ImageIO.read(outf);
-            }
-            catch (InterruptedException e)
-            {
-                log.error("Failed transforming file for preview: ",e);
-                throw new IllegalArgumentException("Failed transforming file for preview: ",e);
-            }
-            finally
-            {
-                if (!outf.delete())
-                {
-                    log.error("Unable to delete file");
-                }
-            }
-        }
-        finally
-        {
-            if (!sourceTmp.delete())
-            {
-                log.error("Unable to delete temporary source");
-            }
-            
-            if (status != 0)
-            {
-                log.error("PDF conversion proc failed, exit status=" + status + ", file=" + sourceTmp);
-            }
-        }
-
-        if (source == null)
-        {
-            throw new IOException("Unknown failure while transforming file to preview: no image produced.");
-        }
-
-        // Scale image and return in-memory stream
-        BufferedImage toenail = scaleImage(source, maxwidth*3/4, maxwidth);
-        ByteArrayOutputStream baos = new ByteArrayOutputStream();
-        ImageIO.write(toenail, "jpeg", baos);
-        return new ByteArrayInputStream(baos.toByteArray());
-    }
-
-    // scale the image, preserving aspect ratio, if at least one
-    // dimension is not between min and max.
-    private static BufferedImage scaleImage(BufferedImage source,
-                                            int min, int max)
-    {
-        int xsize = source.getWidth(null);
-        int ysize = source.getHeight(null);
-        int msize = Math.max(xsize, ysize);
-        BufferedImage result = null;
-
-        // scale the image if it's outside of requested range.
-        // ALSO pass through if min and max are both 0
-        if ((min == 0 && max == 0) ||
-            (msize >= min && Math.min(xsize, ysize) <= max))
-        {
-            return source;
-        }
-        else
-        {
-            int xnew = xsize * max / msize;
-            int ynew = ysize * max / msize;
-            result = new BufferedImage(xnew, ynew, BufferedImage.TYPE_INT_RGB);
-            Graphics2D g2d = result.createGraphics();
-            g2d.drawImage(source, 0, 0, xnew, ynew, null);
-            return result;
-        }
-    }
-}
-
- 	  	 

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

@@ -1,776 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.packager;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.sql.SQLException;
-import java.util.List;
-
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.crosswalk.CrosswalkException;
-import org.dspace.content.packager.PackageDisseminator;
-import org.dspace.content.packager.PackageException;
-import org.dspace.content.packager.PackageParameters;
-import org.dspace.content.packager.PackageIngester;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.core.PluginManager;
-import org.dspace.eperson.EPerson;
-import org.dspace.handle.HandleManager;
-
-/**
- * Command-line interface to the Packager plugin.
- * <p>
- * This class ONLY exists to provide a CLI for the packager plugins. It does not
- * "manage" the plugins and it is not called from within DSpace, but the name
- * follows a DSpace convention.
- * <p>
- * It can invoke one of the Submission (SIP) packagers to create a new DSpace
- * Item out of a package, or a Dissemination (DIP) packager to write an Item out
- * as a package.
- * <p>
- * Usage is as follows:<br>
- * (Add the -h option to get the command to show its own help)
- *
- * <pre>
- *  1. To submit a SIP  (submissions tend to create a *new* object, with a new handle.  If you want to restore an object, see -r option below)
- *   dspace packager
- *       -e {ePerson}
- *       -t {PackagerType}
- *       -p {parent-handle} [ -p {parent2} ...]
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       [-a] --- also recursively ingest all child packages of the initial package
- *                (child pkgs must be referenced from parent pkg)
- *       [-w]   --- skip Workflow
- *       {package-filename}
- *
- *   {PackagerType} must match one of the aliases of the chosen Packager
- *   plugin.
- *
- *   The &quot;-w&quot; option circumvents Workflow, and is optional.  The &quot;-o&quot;
- *   option, which may be repeated, passes options to the packager
- *   (e.g. &quot;metadataOnly&quot; to a DIP packager).
- *
- *  2. To restore an AIP  (similar to submit mode, but attempts to restore with the handles/parents specified in AIP):
- *   dspace packager
- *       -r     --- restores a object from a package info, including the specified handle (will throw an error if handle is already in use)
- *       -e {ePerson}
- *       -t {PackagerType}
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       [-a] --- also recursively restore all child packages of the initial package
- *                (child pkgs must be referenced from parent pkg)
- *       [-k]   --- Skip over errors where objects already exist and Keep Existing objects by default.
- *                  Use with -r to only restore objects which do not already exist.  By default, -r will throw an error
- *                  and rollback all changes when an object is found that already exists.
- *       [-f]   --- Force a restore (even if object already exists).
- *                  Use with -r to replace an existing object with one from a package (essentially a delete and restore).
- *                  By default, -r will throw an error and rollback all changes when an object is found that already exists.
- *       [-i {identifier-handle-of-object}] -- Optional when -f is specified.  When replacing an object, you can specify the
- *                  object to replace if it cannot be easily determined from the package itself.
- *       {package-filename}
- *
- *   Restoring is very similar to submitting, except that you are recreating pre-existing objects.  So, in a restore, the object(s) are
- *   being recreated based on the details in the AIP.  This means that the object is recreated with the same handle and same parent/children
- *   objects.  Not all {PackagerTypes} may support a "restore".
- *
- *  3. To write out a DIP:
- *   dspace packager
- *       -d
- *       -e {ePerson}
- *       -t {PackagerType}
- *       -i {identifier-handle-of-object}
- *       [-a] --- also recursively disseminate all child objects of this object
- *       [-o {name}={value} [ -o {name}={value} ..]]
- *       {package-filename}
- *
- *   The &quot;-d&quot; switch chooses a Dissemination packager, and is required.
- *   The &quot;-o&quot; option, which may be repeated, passes options to the packager
- *   (e.g. &quot;metadataOnly&quot; to a DIP packager).
- * </pre>
- *
- * Note that {package-filename} may be "-" for standard input or standard
- * output, respectively.
- *
- * @author Larry Stone
- * @author Tim Donohue
- * @version $Revision$
- */
-public class Packager
-{
-    /* Various private global settings/options */
-    private String packageType = null;
-    private boolean submit = true;
-    private boolean userInteractionEnabled = true;
-
-    // die from illegal command line
-    private static void usageError(String msg)
-    {
-        System.out.println(msg);
-        System.out.println(" (run with -h flag for details)");
-        System.exit(1);
-    }
-
-    public static void main(String[] argv) throws Exception
-    {
-        Options options = new Options();
-        options.addOption("p", "parent", true,
-                "Handle(s) of parent Community or Collection into which to ingest object (repeatable)");
-        options.addOption("e", "eperson", true,
-                "email address of eperson doing importing");
-        options
-                .addOption(
-                        "w",
-                        "install",
-                        false,
-                        "disable workflow; install immediately without going through collection's workflow");
-        options.addOption("r", "restore", false, "ingest in \"restore\" mode.  Restores a missing object based on the contents in a package.");
-        options.addOption("k", "keep-existing", false, "if an object is found to already exist during a restore (-r), then keep the existing object and continue processing.  Can only be used with '-r'.  This avoids object-exists errors which are thrown by -r by default.");
-        options.addOption("f", "force-replace", false, "if an object is found to already exist during a restore (-r), then remove it and replace it with the contents of the package.  Can only be used with '-r'.  This REPLACES the object(s) in the repository with the contents from the package(s).");
-        options.addOption("t", "type", true, "package type or MIMEtype");
-        options
-                .addOption("o", "option", true,
-                        "Packager option to pass to plugin, \"name=value\" (repeatable)");
-        options.addOption("d", "disseminate", false,
-                "Disseminate package (output); default is to submit.");
-        options.addOption("s", "submit", false,
-                "Submission package (Input); this is the default. ");
-        options.addOption("i", "identifier", true, "Handle of object to disseminate.");
-        options.addOption("a", "all", false, "also recursively ingest/disseminate any child packages, e.g. all Items within a Collection (not all packagers may support this option!)");
-        options.addOption("h", "help", false, "help (you may also specify '-h -t [type]' for additional help with a specific type of packager)");
-        options.addOption("u", "no-user-interaction", false, "Skips over all user interaction (i.e. [y/n] question prompts) within this script. This flag can be used if you want to save (pipe) a report of all changes to a file, and therefore need to bypass all user interaction.");
-
-        CommandLineParser parser = new PosixParser();
-        CommandLine line = parser.parse(options, argv);
-
-        String sourceFile = null;
-        String eperson = null;
-        String[] parents = null;
-        String identifier = null;
-        PackageParameters pkgParams = new PackageParameters();
-
-        //initialize a new packager -- we'll add all our current params as settings
-        Packager myPackager = new Packager();
-
-        if (line.hasOption('h'))
-        {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("Packager  [options]  package-file|-\n",
-                    options);
-            //If user specified a type, also print out the SIP and DIP options
-            // that are specific to that type of packager
-            if (line.hasOption('t'))
-            {
-                System.out.println("\n--------------------------------------------------------------");
-                System.out.println("Additional options for the " + line.getOptionValue('t') + " packager:");
-                System.out.println("--------------------------------------------------------------");
-                System.out.println("(These options may be specified using --option as described above)");
-
-                PackageIngester sip = (PackageIngester) PluginManager
-                    .getNamedPlugin(PackageIngester.class, line.getOptionValue('t'));
-
-                if (sip != null)
-                {
-                    System.out.println("\n\n" + line.getOptionValue('t') + " Submission (SIP) plugin options:\n");
-                    System.out.println(sip.getParameterHelp());
-                }
-                else
-                {
-                    System.out.println("\nNo valid Submission plugin found for " + line.getOptionValue('t') + " type.");
-                }
-
-                PackageDisseminator dip = (PackageDisseminator) PluginManager
-                    .getNamedPlugin(PackageDisseminator.class, line.getOptionValue('t'));
-
-                if (dip != null)
-                {
-                    System.out.println("\n\n" + line.getOptionValue('t') + " Dissemination (DIP) plugin options:\n");
-                    System.out.println(dip.getParameterHelp());
-                }
-                else
-                {
-                    System.out.println("\nNo valid Dissemination plugin found for " + line.getOptionValue('t') + " type.");
-                }
-
-            }
-            else  //otherwise, display list of valid packager types
-            {
-                System.out.println("\nAvailable Submission Package (SIP) types:");
-                String pn[] = PluginManager
-                        .getAllPluginNames(PackageIngester.class);
-                for (int i = 0; i < pn.length; ++i)
-                {
-                    System.out.println("  " + pn[i]);
-                }
-                System.out
-                        .println("\nAvailable Dissemination Package (DIP) types:");
-                pn = PluginManager.getAllPluginNames(PackageDisseminator.class);
-                for (int i = 0; i < pn.length; ++i)
-                {
-                    System.out.println("  " + pn[i]);
-                }
-            }
-            System.exit(0);
-        }
-
-        //look for flag to disable all user interaction
-        if(line.hasOption('u'))
-        {
-            myPackager.userInteractionEnabled = false;
-        }
-        if (line.hasOption('w'))
-        {
-            pkgParams.setWorkflowEnabled(false);
-        }
-        if (line.hasOption('r'))
-        {
-            pkgParams.setRestoreModeEnabled(true);
-        }
-        //keep-existing is only valid in restoreMode (-r) -- otherwise ignore -k option.
-        if (line.hasOption('k') && pkgParams.restoreModeEnabled())
-        {
-            pkgParams.setKeepExistingModeEnabled(true);
-        }
-        //force-replace is only valid in restoreMode (-r) -- otherwise ignore -f option.
-        if (line.hasOption('f') && pkgParams.restoreModeEnabled())
-        {
-            pkgParams.setReplaceModeEnabled(true);
-        }
-        if (line.hasOption('e'))
-        {
-            eperson = line.getOptionValue('e');
-        }
-        if (line.hasOption('p'))
-        {
-            parents = line.getOptionValues('p');
-        }
-        if (line.hasOption('t'))
-        {
-            myPackager.packageType = line.getOptionValue('t');
-        }
-        if (line.hasOption('i'))
-        {
-            identifier = line.getOptionValue('i');
-        }
-        if (line.hasOption('a'))
-        {
-            //enable 'recursiveMode' param to packager implementations, in case it helps with packaging or ingestion process
-            pkgParams.setRecursiveModeEnabled(true);
-        }
-        String files[] = line.getArgs();
-        if (files.length > 0)
-        {
-            sourceFile = files[0];
-        }
-        if (line.hasOption('d'))
-        {
-            myPackager.submit = false;
-        }
-        if (line.hasOption('o'))
-        {
-            String popt[] = line.getOptionValues('o');
-            for (int i = 0; i < popt.length; ++i)
-            {
-                String pair[] = popt[i].split("\\=", 2);
-                if (pair.length == 2)
-                {
-                    pkgParams.addProperty(pair[0].trim(), pair[1].trim());
-                }
-                else if (pair.length == 1)
-                {
-                    pkgParams.addProperty(pair[0].trim(), "");
-                }
-                else
-                {
-                    System.err
-                            .println("Warning: Illegal package option format: \""
-                                    + popt[i] + "\"");
-                }
-            }
-        }
-
-        // Sanity checks on arg list: required args
-        // REQUIRED: sourceFile, ePerson (-e), packageType (-t)
-        if (sourceFile == null || eperson == null || myPackager.packageType == null)
-        {
-            System.err.println("Error - missing a REQUIRED argument or option.\n");
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("PackageManager  [options]  package-file|-\n", options);
-            System.exit(0);
-        }
-
-        // find the EPerson, assign to context
-        Context context = new Context();
-        EPerson myEPerson = null;
-        myEPerson = EPerson.findByEmail(context, eperson);
-        if (myEPerson == null)
-        {
-            usageError("Error, eperson cannot be found: " + eperson);
-        }
-        context.setCurrentUser(myEPerson);
-
-
-        //If we are in REPLACE mode
-        if(pkgParams.replaceModeEnabled())
-        {
-            PackageIngester sip = (PackageIngester) PluginManager
-                    .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null)
-            {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            DSpaceObject objToReplace = null;
-
-            //if a specific identifier was specified, make sure it is valid
-            if(identifier!=null && identifier.length()>0)
-            {
-                objToReplace = HandleManager.resolveToObject(context, identifier);
-                if (objToReplace == null)
-                {
-                    throw new IllegalArgumentException("Bad identifier/handle -- "
-                            + "Cannot resolve handle \"" + identifier + "\"");
-                }
-            }
-
-            String choiceString = null;
-            if(myPackager.userInteractionEnabled)
-            {
-                BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                System.out.println("\n\nWARNING -- You are running the packager in REPLACE mode.");
-                System.out.println("\nREPLACE mode may be potentially dangerous as it will automatically remove and replace contents within DSpace.");
-                System.out.println("We highly recommend backing up all your DSpace contents (files & database) before continuing.");
-                System.out.print("\nWould you like to continue? [y/n]: ");
-                choiceString = input.readLine();
-            }
-            else
-            {
-                //user interaction disabled -- default answer to 'yes', otherwise script won't continue
-                choiceString = "y";
-            }
-
-            if (choiceString.equalsIgnoreCase("y"))
-            {
-                System.out.println("Beginning replacement process...");
-
-                try
-                {
-                    //replace the object from the source file
-                    myPackager.replace(context, sip, pkgParams, sourceFile, objToReplace);
-
-                    //commit all changes & exit successfully
-                    context.complete();
-                    System.exit(0);
-                }
-                catch (Exception e)
-                {
-                    // abort all operations
-                    e.printStackTrace();
-                    context.abort();
-                    System.out.println(e);
-                    System.exit(1);
-                }
-            }
-
-        }
-        //else if normal SUBMIT mode (or basic RESTORE mode -- which is a special type of submission)
-        else if (myPackager.submit || pkgParams.restoreModeEnabled())
-        {
-            PackageIngester sip = (PackageIngester) PluginManager
-                    .getNamedPlugin(PackageIngester.class, myPackager.packageType);
-            if (sip == null)
-            {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            // validate each parent arg (if any)
-            DSpaceObject parentObjs[] = null;
-            if(parents!=null)
-            {
-                System.out.println("Destination parents:");
-
-                parentObjs = new DSpaceObject[parents.length];
-                for (int i = 0; i < parents.length; i++)
-                {
-                    // sanity check: did handle resolve?
-                    parentObjs[i] = HandleManager.resolveToObject(context,
-                            parents[i]);
-                    if (parentObjs[i] == null)
-                    {
-                        throw new IllegalArgumentException(
-                                "Bad parent list -- "
-                                        + "Cannot resolve parent handle \""
-                                        + parents[i] + "\"");
-                    }
-                    System.out.println((i == 0 ? "Owner: " : "Parent: ")
-                            + parentObjs[i].getHandle());
-                }
-            }
-
-            try
-            {
-                //ingest the object from the source file
-                myPackager.ingest(context, sip, pkgParams, sourceFile, parentObjs);
-
-                //commit all changes & exit successfully
-                context.complete();
-                System.exit(0);
-            }
-            catch (Exception e)
-            {
-                // abort all operations
-                e.printStackTrace();
-                context.abort();
-                System.out.println(e);
-                System.exit(1);
-            }
-        }// else, if DISSEMINATE mode
-        else
-        {
-            //retrieve specified package disseminator
-            PackageDisseminator dip = (PackageDisseminator) PluginManager
-                .getNamedPlugin(PackageDisseminator.class, myPackager.packageType);
-            if (dip == null)
-            {
-                usageError("Error, Unknown package type: " + myPackager.packageType);
-            }
-
-            DSpaceObject dso = HandleManager.resolveToObject(context, identifier);
-            if (dso == null)
-            {
-                throw new IllegalArgumentException("Bad identifier/handle -- "
-                        + "Cannot resolve handle \"" + identifier + "\"");
-            }
-
-            //disseminate the requested object
-            myPackager.disseminate(context, dip, dso, pkgParams, sourceFile);
-        }
-        System.exit(0);
-    }
-
-    /**
-     * Ingest one or more DSpace objects from package(s) based on the
-     * options passed to the 'packager' script.  This method is called
-     * for both 'submit' (-s) and 'restore' (-r) modes.
-     * <p>
-     * Please note that replace (-r -f) mode calls the replace() method instead.
-     *
-     * @param context DSpace Context
-     * @param sip PackageIngester which will actually ingest the package
-     * @param pkgParams Parameters to pass to individual packager instances
-     * @param sourceFile location of the source package to ingest
-     * @param parentObjs Parent DSpace object(s) to attach new object to
-     * @throws IOException
-     * @throws SQLException
-     * @throws FileNotFoundException
-     * @throws AuthorizeException
-     * @throws CrosswalkException
-     * @throws 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())
-        {
-            System.out.println("\nERROR: Package located at " + sourceFile + " does not exist!");
-            System.exit(1);
-        }
-
-        System.out.println("\nIngesting package located at " + sourceFile);
-
-        //find first parent (if specified) -- this will be the "owner" of the object
-        DSpaceObject parent = null;
-        if(parentObjs!=null && parentObjs.length>0)
-        {
-            parent = parentObjs[0];
-        }
-        //NOTE: at this point, Parent may be null -- in which case it is up to the PackageIngester
-        // to either determine the Parent (from package contents) or throw an error.
-
-
-        //If we are doing a recursive ingest, call ingestAll()
-        if(pkgParams.recursiveModeEnabled())
-        {
-            System.out.println("\nAlso ingesting all referenced packages (recursive mode)..");
-            System.out.println("This may take a while, please check your logs for ongoing status while we process each package.");
-
-            //ingest first package & recursively ingest anything else that package references (child packages, etc)
-            List<DSpaceObject> dsoResults = sip.ingestAll(context, parent, pkgFile, pkgParams, null);
-
-            if(dsoResults!=null)
-            {
-                //Report total objects created
-                System.out.println("\nCREATED a total of " + dsoResults.size() + " DSpace Objects.");
-
-                String choiceString = null;
-                //Ask if user wants full list printed to command line, as this may be rather long.
-                if(this.userInteractionEnabled)
-                {
-                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                    System.out.print("\nWould you like to view a list of all objects that were created? [y/n]: ");
-                    choiceString = input.readLine();
-                }
-                else
-                {
-                    // user interaction disabled -- default answer to 'yes', as
-                    // we want to provide user with as detailed a report as possible.
-                    choiceString = "y";
-                }
-
-                // Provide detailed report if user answered 'yes'
-                if (choiceString.equalsIgnoreCase("y"))
-                {
-                    System.out.println("\n\n");
-                    for(DSpaceObject result : dsoResults)
-                    {
-                        if(pkgParams.restoreModeEnabled())
-                        {
-                            System.out.println("RESTORED DSpace " + Constants.typeText[result.getType()] +
-                                    " [ hdl=" + result.getHandle() + ", dbID=" + result.getID() + " ] ");
-                        }
-                        else
-                        {
-                            System.out.println("CREATED new DSpace " + Constants.typeText[result.getType()] +
-                                    " [ hdl=" + result.getHandle() + ", dbID=" + result.getID() + " ] ");
-                        }
-                    }
-                }
-
-            }
-        }
-        else
-        {
-
-            //otherwise, just one package to ingest
-            try
-            {
-
-                DSpaceObject dso = sip.ingest(context, parent, pkgFile, pkgParams, null);
-
-                if(dso!=null)
-                {
-                    if(pkgParams.restoreModeEnabled())
-                    {
-                        System.out.println("RESTORED DSpace " + Constants.typeText[dso.getType()] +
-                                " [ hdl=" + dso.getHandle() + ", dbID=" + dso.getID() + " ] ");
-                    }
-                    else
-                    {
-                        System.out.println("CREATED new DSpace " + Constants.typeText[dso.getType()] +
-                                " [ hdl=" + dso.getHandle() + ", dbID=" + dso.getID() + " ] ");
-                    }
-                }
-            }
-            catch(IllegalStateException ie)
-            {
-                // NOTE: if we encounter an IllegalStateException, this means the
-                // handle is already in use and this object already exists.
-
-                //if we are skipping over (i.e. keeping) existing objects
-                if(pkgParams.keepExistingModeEnabled())
-                {
-                    System.out.println("\nSKIPPED processing package '" + pkgFile + "', as an Object already exists with this handle.");
-                }
-                else // Pass this exception on -- which essentially causes a full rollback of all changes (this is the default)
-                {
-                    throw ie;
-                }
-            }
-
-        }
-
-    }
-
-
-    /**
-     * Disseminate one or more DSpace objects into package(s) based on the
-     * options passed to the 'packager' script
-     *
-     * @param context DSpace context
-     * @param dip PackageDisseminator which will actually create the package
-     * @param dso DSpace Object to disseminate as a package
-     * @param pkgParams Parameters to pass to individual packager instances
-     * @param outputFile File where final package should be saved
-     * @throws IOException
-     * @throws SQLException
-     * @throws FileNotFoundException
-     * @throws AuthorizeException
-     * @throws CrosswalkException
-     * @throws PackageException
-     */
-    protected void disseminate(Context context, PackageDisseminator dip,
-			       DSpaceObject dso, PackageParameters pkgParams,
-			       String outputFile)
-            throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException, PackageException
-    {
-        // initialize output file
-        File pkgFile = new File(outputFile);
-
-        System.out.println("\nDisseminating DSpace " + Constants.typeText[dso.getType()] +
-                            " [ hdl=" + dso.getHandle() + " ] to " + outputFile);
-
-        //If we are doing a recursive dissemination of this object & all its child objects, call disseminateAll()
-        if(pkgParams.recursiveModeEnabled())
-        {
-            System.out.println("\nAlso disseminating all child objects (recursive mode)..");
-            System.out.println("This may take a while, please check your logs for ongoing status while we process each package.");
-
-            //disseminate initial object & recursively disseminate all child objects as well
-            List<File> fileResults = dip.disseminateAll(context, dso, pkgParams, pkgFile);
-
-            if(fileResults!=null)
-            {
-                //Report total files created
-                System.out.println("\nCREATED a total of " + fileResults.size() + " dissemination package files.");
-
-                String choiceString = null;
-                //Ask if user wants full list printed to command line, as this may be rather long.
-                if(this.userInteractionEnabled)
-                {
-                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                    System.out.print("\nWould you like to view a list of all files that were created? [y/n]: ");
-                    choiceString = input.readLine();
-                }
-                else
-                {
-                    // user interaction disabled -- default answer to 'yes', as
-                    // we want to provide user with as detailed a report as possible.
-                    choiceString = "y";
-                }
-
-                // Provide detailed report if user answered 'yes'
-                if (choiceString.equalsIgnoreCase("y"))
-                {
-                    System.out.println("\n\n");
-                    for(File result : fileResults)
-                    {
-                        System.out.println("CREATED package file: " + result.getCanonicalPath());
-                    }
-                }
-            }
-        }
-        else
-        {
-            //otherwise, just disseminate a single object to a single package file
-            dip.disseminate(context, dso, pkgParams, pkgFile);
-
-            if(pkgFile!=null && pkgFile.exists())
-            {
-                System.out.println("\nCREATED package file: " + pkgFile.getCanonicalPath());
-            }
-        }
-    }
-
-
-
-    /**
-     * Replace an one or more existing DSpace objects with the contents of
-     * specified package(s) based on the options passed to the 'packager' script.
-     * This method is only called for full replaces ('-r -f' options specified)
-     *
-     * @param context DSpace Context
-     * @param sip PackageIngester which will actually replace the object with the package
-     * @param pkgParams Parameters to pass to individual packager instances
-     * @param sourceFile location of the source package to ingest as the replacement
-     * @param objToReplace DSpace object to replace (may be null if it will be specified in the package itself)
-     * @throws IOException
-     * @throws SQLException
-     * @throws FileNotFoundException
-     * @throws AuthorizeException
-     * @throws CrosswalkException
-     * @throws 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())
-        {
-            System.out.println("\nPackage located at " + sourceFile + " does not exist!");
-            System.exit(1);
-        }
-
-        System.out.println("\nReplacing DSpace object(s) with package located at " + sourceFile);
-        if(objToReplace!=null)
-        {
-            System.out.println("Will replace existing DSpace " + Constants.typeText[objToReplace.getType()] +
-                            " [ hdl=" + objToReplace.getHandle() + " ]");
-        }
-        // NOTE: At this point, objToReplace may be null.  If it is null, it is up to the PackageIngester
-        // to determine which Object needs to be replaced (based on the handle specified in the pkg, etc.)
-
-
-        //If we are doing a recursive replace, call replaceAll()
-        if(pkgParams.recursiveModeEnabled())
-        {
-            //ingest first object using package & recursively replace anything else that package references (child objects, etc)
-            List<DSpaceObject> dsoResults = sip.replaceAll(context, objToReplace, pkgFile, pkgParams);
-
-            if(dsoResults!=null)
-            {
-                //Report total objects replaced
-                System.out.println("\nREPLACED a total of " + dsoResults.size() + " DSpace Objects.");
-
-                String choiceString = null;
-                //Ask if user wants full list printed to command line, as this may be rather long.
-                if(this.userInteractionEnabled)
-                {
-                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
-                    System.out.print("\nWould you like to view a list of all objects that were replaced? [y/n]: ");
-                    choiceString = input.readLine();
-                }
-                else
-                {
-                    // user interaction disabled -- default answer to 'yes', as
-                    // we want to provide user with as detailed a report as possible.
-                    choiceString = "y";
-                }
-
-                // Provide detailed report if user answered 'yes'
-                if (choiceString.equalsIgnoreCase("y"))
-                {
-                    System.out.println("\n\n");
-                    for(DSpaceObject result : dsoResults)
-                    {
-                        System.out.println("REPLACED DSpace " + Constants.typeText[result.getType()] +
-                                    " [ hdl=" + result.getHandle() + " ] ");
-                    }
-                }
-
-
-            }
-        }
-        else
-        {
-            //otherwise, just one object to replace
-            DSpaceObject dso = sip.replace(context, objToReplace, pkgFile, pkgParams);
-
-            if(dso!=null)
-            {
-                System.out.println("REPLACED DSpace " + Constants.typeText[dso.getType()] +
-                        " [ hdl=" + dso.getHandle() + " ] ");
-            }
-        }
-    }
-
-}

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

@@ -1,16 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-/**
- * <p>Tools for exporting and importing DSpace objects (Community, Collection,
- * Item, etc.) wrapped in various kinds of packaging.</p>
- * 
- * @see org.dspace.content.packager
- */
-
-package org.dspace.app.packager;

dspace-api/src/main/java/org/dspace/app/sfx/SFXFileReader.java

@@ -1,324 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sfx;
-
-import java.io.File;
-import java.io.IOException;
-import java.net.URLEncoder;
-
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-
-import org.dspace.content.DCPersonName;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.core.Constants;
-
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.ParserConfigurationException;
-
-import org.w3c.dom.NamedNodeMap;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.SAXException;
-
-
-public class SFXFileReader {
-
-    /** The SFX configuration file */
-    private static Document doc;
-
-    /** log4j logger */
-    private static final Logger log = Logger.getLogger(SFXFileReader.class);
-
-
-    /**
-     * Loads the SFX configuraiton file
-     *
-     * @param fileName The name of the SFX configuration file
-     * @param item The item to process
-     *
-     * @return the SFX string
-     * @throws IOException
-     */
-    public static String loadSFXFile(String fileName, Item item) throws IOException
-    {
-        // Parse XML file -> XML document will be build
-        if (doc == null)
-        {
-            doc = parseFile(fileName);
-        }
-
-        // Return final sfx Query String
-        return  doNodes(doc, item);
-    }
-
-   /** Parses XML file and returns XML document.
-    * @param fileName XML file to parse
-    * @return XML document or <B>null</B> if error occured
-    */
-
-   public static Document parseFile(String fileName) {
-	log.info("Parsing XML file... " + fileName);
-       DocumentBuilder docBuilder;
-       Document doc = null;
-       DocumentBuilderFactory docBuilderFactory = DocumentBuilderFactory.newInstance();
-       docBuilderFactory.setIgnoringElementContentWhitespace(true);
-       try {
-           docBuilder = docBuilderFactory.newDocumentBuilder();
-       }
-       catch (ParserConfigurationException e) {
-	    log.error("Wrong parser configuration: " + e.getMessage());
-           return null;
-       }
-       File sourceFile = new File(fileName);
-       try {
-           doc = docBuilder.parse(sourceFile);
-       }
-       catch (SAXException e) {
-           log.error("Wrong XML file structure: " + e.getMessage());
-           return null;
-       }
-       catch (IOException e) {
-           log.error("Could not read source file: " + e.getMessage());
-       }
-       log.info("XML file parsed");
-       return doc;
-   }
-
-    /**
-     * Process the item.
-     *
-     * @param node
-     * @param item
-     * @return processed fields.
-     * @throws IOException
-     */
-   public static String doNodes(Node node, Item item) throws IOException
-   {
-        if (node == null)
-        {
-	    log.error (" Empty Node ");
-            return null;
-        }
-        Node e = getElement(node);
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        String sfxfield = "";
-        int i = 0;
-
-        while ((i < len) && StringUtils.isEmpty(sfxfield))
-        {
-            Node nd = nl.item(i);
-            if ((nd == null) || isEmptyTextNode(nd))
-            {
-                i++;
-                continue;
-            }
-            String tagName = nd.getNodeName();
-            if (tagName.equals("query-pairs"))
-            {
-                sfxfield = processFields(nd, item);
-
-            }
-            i++;
-        }
-           log.info("Process fields : " + sfxfield);
-        return sfxfield;
-   }
-
-    /**
-     * Process the fields.
-     *
-     * @param e
-     * @param item
-     * @return assembled query.
-     * @throws IOException
-     */
-   private static String processFields(Node e, Item item) throws IOException
-   {
-        NodeList cl = e.getChildNodes();
-        int lench = cl.getLength();
-        String  myquery = "";
-
-        for (int j = 0; j < lench; j++)
-        {
-            Node nch = cl.item(j);
-            String querystring = "";
-            String schema = "";
-            String qualifier = "";
-            String element = "";
-
-            if (nch.getNodeName().equals("field"))
-            {
-                NodeList pl = nch.getChildNodes();
-                int plen = pl.getLength();
-                int finish = 0;
-                for (int k = 0; k < plen; k++)
-                {
-                    Node vn= pl.item(k);
-                    String vName = vn.getNodeName();
-                    if (vName.equals("querystring"))
-                    {
-                        querystring = getValue(vn);
-                        finish ++;
-                    }
-                    else if (vName.equals("dc-schema"))
-                    {
-                        schema = getValue(vn);
-                        finish ++;
-                        }
-                        else if (vName.equals("dc-element"))
-                        {
-                            element = getValue(vn);
-                            finish ++;
-                        }
-                        else if (vName.equals("dc-qualifier"))
-                        {
-                            qualifier = getValue(vn);
-                            finish ++;
-                            if (StringUtils.isEmpty(qualifier))
-                            {
-                                qualifier = null;
-                            }
-                        }
-                        if (finish == 4)
-                        {
-                        DCValue[] dcvalue = item.getMetadata(schema, element, qualifier, Item.ANY);
-                        if (dcvalue.length > 0)
-                            {
-                            // Issued Date
-                                if (element.equals("date") && qualifier.equals("issued"))
-                            {
-                            String fullDate = dcvalue[0].value;
-                            // Remove the time if there is one - day is greatest granularity for SFX
-                                if (fullDate.length() > 10)
-                                {
-                                     fullDate = fullDate.substring(0, 10);
-                                }
-                                if (myquery.equals(""))
-                                { myquery = querystring + URLEncoder.encode(fullDate, Constants.DEFAULT_ENCODING); }
-                                else
-                                { myquery =  myquery + "&" + querystring + URLEncoder.encode(fullDate, Constants.DEFAULT_ENCODING); }
-                            }
-                            else
-                            {
-                                // Contributor Author
-                                if (element.equals("contributor") && qualifier.equals("author"))
-                                    {
-                                    DCPersonName dpn = new DCPersonName(dcvalue[0].value);
-                                        String dpnName = dcvalue[0].value;
-
-                                        if (querystring.endsWith("aulast="))  { dpnName = dpn.getLastName(); }
-                                        else { if (querystring.endsWith("aufirst=")) { dpnName = dpn.getFirstNames(); }}
-
-                                    if (myquery.equals(""))
-                                    { myquery = querystring + URLEncoder.encode(dpnName, Constants.DEFAULT_ENCODING); }
-                                            else
-                                    { myquery =  myquery + "&" + querystring + URLEncoder.encode(dpnName, Constants.DEFAULT_ENCODING); }
-                                }
-                                else
-                                {
-                                    if (myquery.equals(""))
-                                    { myquery =  querystring + URLEncoder.encode(dcvalue[0].value, Constants.DEFAULT_ENCODING);}
-                                    else
-                                        { myquery =  myquery + "&" + querystring + URLEncoder.encode(dcvalue[0].value, Constants.DEFAULT_ENCODING);}
-                                    }
-                                }
-                            } // if dc.length > 0
-
-                    finish = 0;
-                        querystring = "";
-                    schema = "";
-                        element = "";
-                    qualifier = "";
-                    } // if finish == 4
-                } //for k
-            } // if field
-        } // for j
-        return myquery;
-   }
-
-   /** Returns element node
-    * @param node element (it is XML tag)
-    * @return Element node otherwise null
-    */
-  public static Node getElement(Node node)
-  {
-       NodeList child = node.getChildNodes();
-       int length = child.getLength();
-       for (int i = 0; i < length; i++)
-       {
-   	    Node kid = child.item(i);
-   	    if (kid.getNodeType() == Node.ELEMENT_NODE)
-   	    {
-   	    	return kid;
-         }
-       }
-       return null;
-  }
-
-		/** Is Empty text Node **/
-   public static boolean isEmptyTextNode(Node nd)
-   {
-   	boolean isEmpty = false;
-   	if (nd.getNodeType() == Node.TEXT_NODE)
-   	{
-   		String text = nd.getNodeValue().trim();
-   		if (text.length() == 0)
-   		{
-   			isEmpty = true;
-   		}
-   	}
-   	return isEmpty;
-   }
-
-   /**
-    * Returns the value of the node's attribute named <name>
-   **/
-   public static String getAttribute(Node e, String name)
-   {
-   	NamedNodeMap attrs = e.getAttributes();
-   	int len = attrs.getLength();
-   	if (len > 0)
-   	{
-   		for (int i = 0; i < len; i++)
-   		{
-   			Node attr = attrs.item(i);
-   			if (name.equals(attr.getNodeName()))
-   			{
-   				return attr.getNodeValue().trim();
-   			}
-   		}
-   	}
-   	//no such attribute
-   	return null;
-   }
-
-   /**
-    * Returns the value found in the Text node (if any) in the
-    * node list that's passed in.
-   */
-   public static String getValue(Node node)
-   {
-   	NodeList child = node.getChildNodes();
-   	for (int i = 0; i < child.getLength(); i++)
-   	{
-   		Node kid = child.item(i);
-   		short type = kid.getNodeType();
-   		if (type == Node.TEXT_NODE)
-   		{
-		    return kid.getNodeValue().trim();
-   		}
-   	}
-   	// Didn't find a text node
-   	return null;
-   }
-}

dspace-api/src/main/java/org/dspace/app/sitemap/AbstractGenerator.java

@@ -1,251 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sitemap;
-
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
-import java.util.Date;
-import java.util.zip.GZIPOutputStream;
-
-/**
- * Base class for creating sitemaps of various kinds. A sitemap consists of one
- * or more files which list significant URLs on a site for search engines to
- * efficiently crawl. Dates of modification may also be included. A sitemap
- * index file that links to each of the sitemap files is also generated. It is
- * this index file that search engines should be directed towards.
- * <P>
- * Provides most of the required functionality, subclasses need just implement a
- * few methods that specify the "boilerplate" and text for including URLs.
- * <P>
- * Typical usage:
- * <pre>
- *   AbstractGenerator g = new FooGenerator(...);
- *   while (...) {
- *     g.addURL(url, date);
- *   }
- *   g.finish();
- * </pre>
- * 
- * @author Robert Tansley
- */
-public abstract class AbstractGenerator
-{
-    /** Number of files written so far */
-    protected int fileCount;
-
-    /** Number of bytes written to current file */
-    protected int bytesWritten;
-
-    /** Number of URLs written to current file */
-    protected int urlsWritten;
-
-    /** Directory files are written to */
-    protected File outputDir;
-
-    /** Current output */
-    protected PrintStream currentOutput;
-
-    /** Size in bytes of trailing boilerplate */
-    private int trailingByteCount;
-
-    /**
-     * Initialize this generator to write to the given directory. This must be
-     * called by any subclass constructor.
-     * 
-     * @param outputDirIn
-     *            directory to write sitemap files to
-     */
-    public AbstractGenerator(File outputDirIn)
-    {
-        fileCount = 0;
-        outputDir = outputDirIn;
-        trailingByteCount = getTrailingBoilerPlate().length();
-        currentOutput = null;
-    }
-
-    /**
-     * Start writing a new sitemap file.
-     * 
-     * @throws IOException
-     *             if an error occurs creating the file
-     */
-    protected void startNewFile() throws IOException
-    {
-        String lbp = getLeadingBoilerPlate();
-
-        OutputStream fo = new FileOutputStream(new File(outputDir,
-                getFilename(fileCount)));
-
-        if (useCompression())
-        {
-            fo = new GZIPOutputStream(fo);
-        }
-
-        currentOutput = new PrintStream(fo);
-        currentOutput.print(lbp);
-        bytesWritten = lbp.length();
-        urlsWritten = 0;
-    }
-
-    /**
-     * Add the given URL to the sitemap.
-     * 
-     * @param url
-     *            Full URL to add
-     * @param lastMod
-     *            Date URL was last modified, or {@code null}
-     * @throws IOException
-     *             if an error occurs writing
-     */
-    public void addURL(String url, Date lastMod) throws IOException
-    {
-        // Kick things off if this is the first call
-        if (currentOutput == null)
-        {
-            startNewFile();
-        }
-
-        String newURLText = getURLText(url, lastMod);
-
-        if (bytesWritten + newURLText.length() + trailingByteCount > getMaxSize()
-                || urlsWritten + 1 > getMaxURLs())
-        {
-            closeCurrentFile();
-            startNewFile();
-        }
-
-        currentOutput.print(newURLText);
-        bytesWritten += newURLText.length();
-        urlsWritten++;
-    }
-
-    /**
-     * Finish with the current sitemap file.
-     * 
-     * @throws IOException
-     *             if an error occurs writing
-     */
-    protected void closeCurrentFile() throws IOException
-    {
-        currentOutput.print(getTrailingBoilerPlate());
-        currentOutput.close();
-        fileCount++;
-    }
-
-    /**
-     * Complete writing sitemap files and write the index files. This is invoked
-     * when all calls to {@link AbstractGenerator#addURL(String, Date)} have
-     * been completed, and invalidates the generator.
-     * 
-     * @return number of sitemap files written.
-     * 
-     * @throws IOException
-     *             if an error occurs writing
-     */
-    public int finish() throws IOException
-    {
-        closeCurrentFile();
-
-        OutputStream fo = new FileOutputStream(new File(outputDir,
-                getIndexFilename()));
-
-        if (useCompression())
-        {
-            fo = new GZIPOutputStream(fo);
-        }
-
-        PrintStream out = new PrintStream(fo);
-        writeIndex(out, fileCount);
-        out.close();
-        
-        return fileCount;
-    }
-
-    /**
-     * Return marked-up text to be included in a sitemap about a given URL.
-     * 
-     * @param url
-     *            URL to add information about
-     * @param lastMod
-     *            date URL was last modified, or {@code null} if unknown or not
-     *            applicable
-     * @return the mark-up to include
-     */
-    public abstract String getURLText(String url, Date lastMod);
-
-    /**
-     * Return the boilerplate at the top of a sitemap file.
-     * 
-     * @return The boilerplate markup.
-     */
-    public abstract String getLeadingBoilerPlate();
-
-    /**
-     * Return the boilerplate at the end of a sitemap file.
-     * 
-     * @return The boilerplate markup.
-     */
-    public abstract String getTrailingBoilerPlate();
-
-    /**
-     * Return the maximum size in bytes that an individual sitemap file should
-     * be.
-     * 
-     * @return the size in bytes.
-     */
-    public abstract int getMaxSize();
-
-    /**
-     * Return the maximum number of URLs that an individual sitemap file should
-     * contain.
-     * 
-     * @return the maximum number of URLs.
-     */
-    public abstract int getMaxURLs();
-
-    /**
-     * Return whether the written sitemap files and index should be
-     * GZIP-compressed.
-     * 
-     * @return {@code true} if GZIP compression should be used, {@code false}
-     *         otherwise.
-     */
-    public abstract boolean useCompression();
-
-    /**
-     * Return the filename a sitemap at the given index should be stored at.
-     * 
-     * @param number
-     *            index of the sitemap file (zero is first).
-     * @return the filename to write the sitemap to.
-     */
-    public abstract String getFilename(int number);
-
-    /**
-     * Get the filename the index should be written to.
-     * 
-     * @return the filename of the index.
-     */
-    public abstract String getIndexFilename();
-
-    /**
-     * Write the index file.
-     * 
-     * @param output
-     *            stream to write the index to
-     * @param sitemapCount
-     *            number of sitemaps that were generated
-     * @throws IOException
-     *             if an IO error occurs
-     */
-    public abstract void writeIndex(PrintStream output, int sitemapCount)
-            throws IOException;
-}

dspace-api/src/main/java/org/dspace/app/sitemap/GenerateSitemaps.java

@@ -1,365 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sitemap;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.UnsupportedEncodingException;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLEncoder;
-import java.sql.SQLException;
-import java.util.Date;
-
-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.apache.log4j.Logger;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.Item;
-import org.dspace.content.ItemIterator;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.core.LogManager;
-
-/**
- * Command-line utility for generating HTML and Sitemaps.org protocol Sitemaps.
- * 
- * @author Robert Tansley
- * @author Stuart Lewis
- */
-public class GenerateSitemaps
-{
-    /** Logger */
-    private static Logger log = Logger.getLogger(GenerateSitemaps.class);
-
-    public static void main(String[] args) throws Exception
-    {
-        final String usage = GenerateSitemaps.class.getCanonicalName();
-
-        CommandLineParser parser = new PosixParser();
-        HelpFormatter hf = new HelpFormatter();
-
-        Options options = new Options();
-
-        options.addOption("h", "help", false, "help");
-        options.addOption("s", "no_sitemaps", false,
-                "do not generate sitemaps.org protocol sitemap");
-        options.addOption("b", "no_htmlmap", false,
-                "do not generate a basic HTML sitemap");
-        options.addOption("a", "ping_all", false,
-                "ping configured search engines");
-        options
-                .addOption("p", "ping", true,
-                        "ping specified search engine URL");
-
-        CommandLine line = null;
-
-        try
-        {
-            line = parser.parse(options, args);
-        }
-        catch (ParseException pe)
-        {
-            hf.printHelp(usage, options);
-            System.exit(1);
-        }
-
-        if (line.hasOption('h'))
-        {
-            hf.printHelp(usage, options);
-            System.exit(0);
-        }
-
-        if (line.getArgs().length != 0)
-        {
-            hf.printHelp(usage, options);
-            System.exit(1);
-        }
-
-        /*
-         * Sanity check -- if no sitemap generation or pinging to do, print
-         * usage
-         */
-        if (line.getArgs().length != 0 || line.hasOption('b')
-                && line.hasOption('s') && !line.hasOption('g')
-                && !line.hasOption('m') && !line.hasOption('y')
-                && !line.hasOption('p'))
-        {
-            System.err
-                    .println("Nothing to do (no sitemap to generate, no search engines to ping)");
-            hf.printHelp(usage, options);
-            System.exit(1);
-        }
-
-        // Note the negation (CLI options indicate NOT to generate a sitemap)
-        if (!line.hasOption('b') || !line.hasOption('s'))
-        {
-            generateSitemaps(!line.hasOption('b'), !line.hasOption('s'));
-        }
-
-        if (line.hasOption('a'))
-        {
-            pingConfiguredSearchEngines();
-        }
-
-        if (line.hasOption('p'))
-        {
-            try
-            {
-                pingSearchEngine(line.getOptionValue('p'));
-            }
-            catch (MalformedURLException me)
-            {
-                System.err
-                        .println("Bad search engine URL (include all except sitemap URL)");
-                System.exit(1);
-            }
-        }
-
-        System.exit(0);
-    }
-
-    /**
-     * Generate sitemap.org protocol and/or basic HTML sitemaps.
-     * 
-     * @param makeHTMLMap
-     *            if {@code true}, generate an HTML sitemap.
-     * @param makeSitemapOrg
-     *            if {@code true}, generate an sitemap.org sitemap.
-     * @throws SQLException
-     *             if a database error occurs.
-     * @throws IOException
-     *             if IO error occurs.
-     */
-    public static void generateSitemaps(boolean makeHTMLMap,
-            boolean makeSitemapOrg) throws SQLException, IOException
-    {
-        String sitemapStem = ConfigurationManager.getProperty("dspace.url")
-                + "/sitemap";
-        String htmlMapStem = ConfigurationManager.getProperty("dspace.url")
-                + "/htmlmap";
-        String handleURLStem = ConfigurationManager.getProperty("dspace.url")
-                + "/handle/";
-
-        File outputDir = new File(ConfigurationManager.getProperty("sitemap.dir"));
-        if (!outputDir.exists() && !outputDir.mkdir())
-        {
-            log.error("Unable to create output directory");
-        }
-        
-        AbstractGenerator html = null;
-        AbstractGenerator sitemapsOrg = null;
-
-        if (makeHTMLMap)
-        {
-            html = new HTMLSitemapGenerator(outputDir, htmlMapStem + "?map=",
-                    null);
-        }
-
-        if (makeSitemapOrg)
-        {
-            sitemapsOrg = new SitemapsOrgGenerator(outputDir, sitemapStem
-                    + "?map=", null);
-        }
-
-        Context c = new Context();
-
-        Community[] comms = Community.findAll(c);
-
-        for (int i = 0; i < comms.length; i++)
-        {
-            String url = handleURLStem + comms[i].getHandle();
-
-            if (makeHTMLMap)
-            {
-                html.addURL(url, null);
-            }
-            if (makeSitemapOrg)
-            {
-                sitemapsOrg.addURL(url, null);
-            }
-        }
-
-        Collection[] colls = Collection.findAll(c);
-
-        for (int i = 0; i < colls.length; i++)
-        {
-            String url = handleURLStem + colls[i].getHandle();
-
-            if (makeHTMLMap)
-            {
-                html.addURL(url, null);
-            }
-            if (makeSitemapOrg)
-            {
-                sitemapsOrg.addURL(url, null);
-            }
-        }
-
-        ItemIterator allItems = Item.findAll(c);
-        try
-        {
-            int itemCount = 0;
-
-            while (allItems.hasNext())
-            {
-                Item i = allItems.next();
-                String url = handleURLStem + i.getHandle();
-                Date lastMod = i.getLastModified();
-
-                if (makeHTMLMap)
-                {
-                    html.addURL(url, lastMod);
-                }
-                if (makeSitemapOrg)
-                {
-                    sitemapsOrg.addURL(url, lastMod);
-                }
-                i.decache();
-
-                itemCount++;
-            }
-
-            if (makeHTMLMap)
-            {
-                int files = html.finish();
-                log.info(LogManager.getHeader(c, "write_sitemap",
-                        "type=html,num_files=" + files + ",communities="
-                                + comms.length + ",collections=" + colls.length
-                                + ",items=" + itemCount));
-            }
-
-            if (makeSitemapOrg)
-            {
-                int files = sitemapsOrg.finish();
-                log.info(LogManager.getHeader(c, "write_sitemap",
-                        "type=html,num_files=" + files + ",communities="
-                                + comms.length + ",collections=" + colls.length
-                                + ",items=" + itemCount));
-            }
-        }
-        finally
-        {
-            if (allItems != null)
-            {
-                allItems.close();
-            }
-        }
-        
-        c.abort();
-    }
-
-    /**
-     * Ping all search engines configured in {@code dspace.cfg}.
-     * 
-     * @throws UnsupportedEncodingException
-     *             theoretically should never happen
-     */
-    public static void pingConfiguredSearchEngines()
-            throws UnsupportedEncodingException
-    {
-        String engineURLProp = ConfigurationManager
-                .getProperty("sitemap.engineurls");
-        String engineURLs[] = null;
-
-        if (engineURLProp != null)
-        {
-            engineURLs = engineURLProp.trim().split("\\s*,\\s*");
-        }
-
-        if (engineURLProp == null || engineURLs == null
-                || engineURLs.length == 0 || engineURLs[0].trim().equals(""))
-        {
-            log.warn("No search engine URLs configured to ping");
-            return;
-        }
-
-        for (int i = 0; i < engineURLs.length; i++)
-        {
-            try
-            {
-                pingSearchEngine(engineURLs[i]);
-            }
-            catch (MalformedURLException me)
-            {
-                log.warn("Bad search engine URL in configuration: "
-                        + engineURLs[i]);
-            }
-        }
-    }
-
-    /**
-     * Ping the given search engine.
-     * 
-     * @param engineURL
-     *            Search engine URL minus protocol etc, e.g.
-     *            {@code www.google.com}
-     * @throws MalformedURLException
-     *             if the passed in URL is malformed
-     * @throws UnsupportedEncodingException
-     *             theoretically should never happen
-     */
-    public static void pingSearchEngine(String engineURL)
-            throws MalformedURLException, UnsupportedEncodingException
-    {
-        // Set up HTTP proxy
-        if ((ConfigurationManager.getProperty("http.proxy.host") != null)
-                && (ConfigurationManager.getProperty("http.proxy.port") != null))
-        {
-            System.setProperty("proxySet", "true");
-            System.setProperty("proxyHost", ConfigurationManager
-                    .getProperty("http.proxy.host"));
-            System.getProperty("proxyPort", ConfigurationManager
-                    .getProperty("http.proxy.port"));
-        }
-
-        String sitemapURL = ConfigurationManager.getProperty("dspace.url")
-                + "/sitemap";
-
-        URL url = new URL(engineURL + URLEncoder.encode(sitemapURL, "UTF-8"));
-
-        try
-        {
-            HttpURLConnection connection = (HttpURLConnection) url
-                    .openConnection();
-
-            BufferedReader in = new BufferedReader(new InputStreamReader(
-                    connection.getInputStream()));
-
-            String inputLine;
-            StringBuffer resp = new StringBuffer();
-            while ((inputLine = in.readLine()) != null)
-            {
-                resp.append(inputLine).append("\n");
-            }
-            in.close();
-
-            if (connection.getResponseCode() == 200)
-            {
-                log.info("Pinged " + url.toString() + " successfully");
-            }
-            else
-            {
-                log.warn("Error response pinging " + url.toString() + ":\n"
-                        + resp);
-            }
-        }
-        catch (IOException e)
-        {
-            log.warn("Error pinging " + url.toString(), e);
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/sitemap/HTMLSitemapGenerator.java

@@ -1,114 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sitemap;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.util.Date;
-
-/**
- * Class for generating HTML "sitemaps" which contain links to various pages in
- * a DSpace site. This should improve search engine coverage of the DSpace site
- * and limit the server load caused by crawlers.
- * 
- * @author Robert Tansley
- * @author Stuart Lewis
- */
-public class HTMLSitemapGenerator extends AbstractGenerator
-{
-    /** Stem of URLs sitemaps will eventually appear at */
-    private String indexURLStem;
-
-    /** Tail of URLs sitemaps will eventually appear at */
-    private String indexURLTail;
-
-    /**
-     * Construct an HTML sitemap generator, writing files to the given
-     * directory, and with the sitemaps eventually exposed at starting with the
-     * given URL stem and tail.
-     * 
-     * @param outputDirIn
-     *            Directory to write sitemap files to
-     * @param urlStem
-     *            start of URL that sitemap files will appear at, e.g.
-     *            {@code http://dspace.myu.edu/sitemap?sitemap=}
-     * @param urlTail
-     *            end of URL that sitemap files will appear at, e.g.
-     *            {@code .html} or {@code null}
-     */
-    public HTMLSitemapGenerator(File outputDirIn, String urlStem, String urlTail)
-    {
-        super(outputDirIn);
-
-        indexURLStem = urlStem;
-        indexURLTail = (urlTail == null ? "" : urlTail);
-    }
-
-    public String getFilename(int number)
-    {
-        return "sitemap" + number + ".html";
-    }
-
-    public String getLeadingBoilerPlate()
-    {
-        return "<!DOCTYPE HTML PUBLIC \"-//W3C//DTD HTML 4.01//EN\" \"http://www.w3.org/TR/html4/strict.dtd\">\n"
-                + "<html><head><title>URL List</title></head><body><ul>";
-    }
-
-    public int getMaxSize()
-    {
-        // 50k
-        return 51200;
-    }
-
-    public int getMaxURLs()
-    {
-        return 1000;
-    }
-
-    public String getTrailingBoilerPlate()
-    {
-        return "</ul></body></html>\n";
-    }
-
-    public String getURLText(String url, Date lastMod)
-    {
-        StringBuffer urlText = new StringBuffer();
-
-        urlText.append("<li><a href=\"").append(url).append("\">").append(url)
-                .append("</a></li>\n");
-
-        return urlText.toString();
-    }
-
-    public boolean useCompression()
-    {
-        return false;
-    }
-
-    public String getIndexFilename()
-    {
-        return "sitemap_index.html";
-    }
-
-    public void writeIndex(PrintStream output, int sitemapCount)
-            throws IOException
-    {
-        output.println(getLeadingBoilerPlate());
-
-        for (int i = 0; i < sitemapCount; i++)
-        {
-            output.print("<li><a href=\"" + indexURLStem + i + indexURLTail
-                    + "\">sitemap " + i);
-            output.print("</a></li>\n");
-        }
-
-        output.println(getTrailingBoilerPlate());
-    }
-}

dspace-api/src/main/java/org/dspace/app/sitemap/SitemapsOrgGenerator.java

@@ -1,129 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sitemap;
-
-import java.io.File;
-import java.io.IOException;
-import java.io.PrintStream;
-import java.text.DateFormat;
-import java.text.SimpleDateFormat;
-import java.util.Date;
-
-/**
- * Class for generating <a href="http://sitemaps.org/">Sitemaps</a> to improve
- * search engine coverage of the DSpace site and limit the server load caused by
- * crawlers.
- * 
- * @author Robert Tansley
- * @author Stuart Lewis
- */
-public class SitemapsOrgGenerator extends AbstractGenerator
-{
-    /** Stem of URLs sitemaps will eventually appear at */
-    private String indexURLStem;
-
-    /** Tail of URLs sitemaps will eventually appear at */
-    private String indexURLTail;
-
-    /** The correct date format */
-    private DateFormat w3dtfFormat = new SimpleDateFormat(
-            "yyyy-MM-dd'T'HH:mm:ss'Z'");
-
-    /**
-     * Construct a sitemaps.org protocol sitemap generator, writing files to the
-     * given directory, and with the sitemaps eventually exposed at starting
-     * with the given URL stem and tail.
-     * 
-     * @param outputDirIn
-     *            Directory to write sitemap files to
-     * @param urlStem
-     *            start of URL that sitemap files will appear at, e.g.
-     *            {@code http://dspace.myu.edu/sitemap?sitemap=}
-     * @param urlTail
-     *            end of URL that sitemap files will appear at, e.g.
-     *            {@code .html} or {@code null}
-     */
-    public SitemapsOrgGenerator(File outputDirIn, String urlStem, String urlTail)
-    {
-        super(outputDirIn);
-
-        indexURLStem = urlStem;
-        indexURLTail = (urlTail == null ? "" : urlTail);
-    }
-
-    public String getFilename(int number)
-    {
-        return "sitemap" + number + ".xml.gz";
-    }
-
-    public String getLeadingBoilerPlate()
-    {
-        return "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
-                + "<urlset xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\">";
-    }
-
-    public int getMaxSize()
-    {
-        // 10 Mb
-        return 10485760;
-    }
-
-    public int getMaxURLs()
-    {
-        return 50000;
-    }
-
-    public String getTrailingBoilerPlate()
-    {
-        return "</urlset>";
-    }
-
-    public String getURLText(String url, Date lastMod)
-    {
-        StringBuffer urlText = new StringBuffer();
-
-        urlText.append("<url><loc>").append(url).append("</loc>");
-        if (lastMod != null)
-        {
-            urlText.append("<lastmod>").append(w3dtfFormat.format(lastMod))
-                    .append("</lastmod>");
-        }
-        urlText.append("</url>\n");
-
-        return urlText.toString();
-    }
-
-    public boolean useCompression()
-    {
-        return true;
-    }
-
-    public String getIndexFilename()
-    {
-        return "sitemap_index.xml.gz";
-    }
-
-    public void writeIndex(PrintStream output, int sitemapCount)
-            throws IOException
-    {
-        String now = w3dtfFormat.format(new Date());
-
-        output.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
-        output
-                .println("<sitemapindex xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\">");
-
-        for (int i = 0; i < sitemapCount; i++)
-        {
-            output.print("<sitemap><loc>" + indexURLStem + i + indexURLTail
-                    + "</loc>");
-            output.print("<lastmod>" + now + "</lastmod></sitemap>\n");
-        }
-
-        output.println("</sitemapindex>");
-    }
-}

dspace-api/src/main/java/org/dspace/app/statistics/CreateStatReport.java

@@ -1,392 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.GregorianCalendar;
-import java.util.Properties;
-
-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.dspace.core.Context;
-import org.dspace.core.ConfigurationManager;
-
-/**
- * This class allows the running of the DSpace statistic tools
- * 
- * Usage: java CreateStatReport -r <statistic to run>
- * Available: 	<stat-initial> <stat-general> <stat-monthly> <stat-report-initial> 
- * 				<stat-report-general> <stat-report-monthly>
- * 
- * @author Chris Yates
- *
- */
-
-public class CreateStatReport {
-
-	/**Current date and time*/
-	private static Calendar calendar = null;
-	
-	/**Reporting start date and time*/
-	private static Calendar reportStartDate = null;
-	
-	/**Path of log directory*/
-	private static String outputLogDirectory = null;
-	
-	/**Path of reporting directory*/
-	private static String outputReportDirectory = null;
-	
-	/**File suffix for log files*/
-	private static String outputSuffix = ".dat";
-	
-	/**User context*/
-	private static Context context;
-
-    /** the config file from which to configure the analyser */
-    private static String configFile = ConfigurationManager.getProperty("dspace.dir") +
-                            File.separator + "config" + File.separator +
-                            "dstat.cfg";
-
-    /*
-	 * Main method to be run from the command line executes individual statistic methods
-	 * 
-	 * Usage: java CreateStatReport -r <statistic to run> 
-	 */
-	public static void main(String[] argv) throws Exception {
-
-        // Open the statistics config file
-        FileInputStream fis = new java.io.FileInputStream(new File(configFile));
-        Properties config = new Properties();
-        config.load(fis);
-        int startMonth = 0;
-        int startYear = 2005;
-        try
-        {
-            startYear = Integer.parseInt(config.getProperty("start.year", "1").trim());
-        } catch (NumberFormatException nfe)
-        {
-            System.err.println("start.year is incorrectly set in dstat.cfg. Must be a number (e.g. 2005).");
-            System.exit(0);
-        }
-        try
-        {
-            startMonth = Integer.parseInt(config.getProperty("start.month", "2005").trim());
-        } catch (NumberFormatException nfe)
-        {
-            System.err.println("start.month is incorrectly set in dstat.cfg. Must be a number between 1 and 12.");
-            System.exit(0);
-        }
-        reportStartDate = new GregorianCalendar(startYear, startMonth - 1, 1);
-        calendar = new GregorianCalendar();
-        
-        // create context as super user
-        context = new Context();
-        context.setIgnoreAuthorization(true);
-        
-        //get paths to directories
-        outputLogDirectory = ConfigurationManager.getProperty("log.dir") + File.separator;
-        outputReportDirectory = ConfigurationManager.getProperty("report.dir") + File.separator;
-        
-        //read in command line variable to determine which statistic to run
-		CommandLineParser parser = new PosixParser();
-		Options options = new Options();
-		options.addOption("r", "report", true, "report");
-		CommandLine line = parser.parse(options, argv);
-		
-		String statAction = null;
-		
-		if(line.hasOption('r')) 
-		{
-			statAction = line.getOptionValue('r');
-		}
-		
-		if (statAction == null) {
-			usage();
-			System.exit(0);
-		}
-
-		//call appropriate statistics method
-		if(statAction.equals("stat-monthly")) {
-			statMonthly();
-		}
-		
-		if(statAction.equals("stat-general")) {
-			statGeneral();
-		}
-		
-		if(statAction.equals("stat-initial")) {
-			statInitial();
-		}
-		
-		if(statAction.equals("stat-report-general")) {
-			statReportGeneral();
-		}
-		
-		if(statAction.equals("stat-report-initial")) {
-			statReportInitial();
-		}
-		
-		if(statAction.equals("stat-report-monthly")) {
-			statReportMonthly();
-		}
-	}
-	
-	/**
-	 * This method generates a report from the first of the current month to the end of the current month.
-	 * 
-	 * @throws Exception
-	 */
-	private static void statMonthly() throws Exception {
-        
-        //Output Prefix
-        String outputPrefix = "dspace-log-monthly-";
-		
-		// set up our command line variables
-        String myLogDir = null;
-        String myFileTemplate = null;
-        String myConfigFile = null;
-        StringBuffer myOutFile = null;
-        Date myStartDate = null;
-        Date myEndDate = null;
-        boolean myLookUp = false;       
-     
-        Calendar start = new GregorianCalendar( calendar.get(Calendar.YEAR),
-        										calendar.get(Calendar.MONTH),
-        										calendar.getActualMinimum(Calendar.DAY_OF_MONTH));
-        myStartDate = start.getTime();
-        
-        Calendar end = new GregorianCalendar( calendar.get(Calendar.YEAR),
-											  calendar.get(Calendar.MONTH),
-											  calendar.getActualMaximum(Calendar.DAY_OF_MONTH));
-        myEndDate = end.getTime();
-        
-        myOutFile = new StringBuffer(outputLogDirectory);
-        myOutFile.append(outputPrefix);
-        myOutFile.append(calendar.get(Calendar.YEAR));
-        myOutFile.append("-");
-        myOutFile.append(calendar.get(Calendar.MONTH)+1);
-        myOutFile.append(outputSuffix);        
-                             
-        LogAnalyser.processLogs(context, myLogDir, myFileTemplate, myConfigFile, myOutFile.toString(), myStartDate, myEndDate, myLookUp);
-	}	
-	
-	/**
-	 * This method generates a full report based on the full log period
-	 * 
-	 * @throws Exception
-	 */
-	private static void statGeneral() throws Exception {
-		
-		//Output Prefix
-        String outputPrefix = "dspace-log-general-";
-		
-        // set up our command line variables
-        String myLogDir = null;
-        String myFileTemplate = null;
-        String myConfigFile = null;
-        StringBuffer myOutFile = null;
-        Date myStartDate = null;
-        Date myEndDate = null;
-        boolean myLookUp = false; 
-        
-        myOutFile = new StringBuffer(outputLogDirectory);
-        myOutFile.append(outputPrefix);
-        myOutFile.append(calendar.get(Calendar.YEAR));
-        myOutFile.append("-");
-        myOutFile.append(calendar.get(Calendar.MONTH)+1);
-        myOutFile.append("-");
-        myOutFile.append(calendar.get(Calendar.DAY_OF_MONTH));
-        myOutFile.append(outputSuffix); 
-		
-        LogAnalyser.processLogs(context, myLogDir, myFileTemplate, myConfigFile, myOutFile.toString(), myStartDate, myEndDate, myLookUp);
-	}
-	
-	/**
-	 * This script starts from the year and month specified below and loops each month until the current month
-	 * generating a monthly aggregation files for the DStat system.
-	 * 
-	 * @throws Exception
-	 */
-	private static void statInitial() throws Exception {
-				
-		//Output Prefix
-        String outputPrefix = "dspace-log-monthly-";
-		
-        // set up our command line variables
-        String myLogDir = null;
-        String myFileTemplate = null;
-        String myConfigFile = null;
-        StringBuffer myOutFile = null;
-        Date myStartDate = null;
-        Date myEndDate = null;
-        boolean myLookUp = false; 
-				
-		Calendar reportEndDate = new GregorianCalendar( calendar.get(Calendar.YEAR),
-				  										calendar.get(Calendar.MONTH),
-				  										calendar.getActualMaximum(Calendar.DAY_OF_MONTH));
-
-        Calendar currentMonth = (Calendar)reportStartDate.clone();
-		while(currentMonth.before(reportEndDate)) {
-									
-			Calendar start = new GregorianCalendar( currentMonth.get(Calendar.YEAR),
-													currentMonth.get(Calendar.MONTH),
-													currentMonth.getActualMinimum(Calendar.DAY_OF_MONTH));
-			myStartDate = start.getTime();
-
-			Calendar end = new GregorianCalendar( currentMonth.get(Calendar.YEAR),
-												  currentMonth.get(Calendar.MONTH),
-												  currentMonth.getActualMaximum(Calendar.DAY_OF_MONTH));
-			myEndDate = end.getTime();
-			
-			myOutFile = new StringBuffer(outputLogDirectory);
-	        myOutFile.append(outputPrefix);
-	        myOutFile.append(currentMonth.get(Calendar.YEAR));
-	        myOutFile.append("-");
-	        myOutFile.append(currentMonth.get(Calendar.MONTH)+1);
-	        myOutFile.append(outputSuffix); 
-	        	        
-	        LogAnalyser.processLogs(context, myLogDir, myFileTemplate, myConfigFile, myOutFile.toString(), myStartDate, myEndDate, myLookUp);
-	        
-			currentMonth.add(Calendar.MONTH, 1);
-		}
-	}
-	
-	/**
-	 * This method generates a full report based on the full log period
-	 * 
-	 * @throws Exception
-	 */
-	private static void statReportGeneral() throws Exception {
-		
-		//Prefix
-		String inputPrefix = "dspace-log-general-";
-		String outputPrefix = "report-general-";        
-		
-		String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
-        String myMap = null;
-		
-        myInput = new StringBuffer(outputLogDirectory);
-        myInput.append(inputPrefix);
-        myInput.append(calendar.get(Calendar.YEAR));
-        myInput.append("-");
-        myInput.append(calendar.get(Calendar.MONTH)+1);
-        myInput.append("-");
-        myInput.append(calendar.get(Calendar.DAY_OF_MONTH));
-        myInput.append(outputSuffix); 
-        
-        myOutput = new StringBuffer(outputReportDirectory);
-        myOutput.append(outputPrefix);
-        myOutput.append(calendar.get(Calendar.YEAR));
-        myOutput.append("-");
-        myOutput.append(calendar.get(Calendar.MONTH)+1);
-        myOutput.append("-");
-        myOutput.append(calendar.get(Calendar.DAY_OF_MONTH));
-        myOutput.append(".");
-        myOutput.append(myFormat);
-		
-		ReportGenerator.processReport(context, myFormat, myInput.toString(), myOutput.toString(), myMap);
-	}
-	
-	/**
-	 * This script starts from the year and month specified below and loops each month until the current month
-	 * generating monthly reports from the DStat aggregation files
-	 * 
-	 * @throws Exception
-	 */
-	private static void statReportInitial() throws Exception {
-		
-		//Prefix
-		String inputPrefix = "dspace-log-monthly-";
-		String outputPrefix = "report-";        
-		
-		String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
-        String myMap = null;
-				
-		Calendar reportEndDate = new GregorianCalendar( calendar.get(Calendar.YEAR),
-				  										calendar.get(Calendar.MONTH),
-				  										calendar.getActualMaximum(Calendar.DAY_OF_MONTH));
-		
-        Calendar currentMonth = (Calendar)reportStartDate.clone();
-
-		while(currentMonth.before(reportEndDate)) {
-			
-			myInput = new StringBuffer(outputLogDirectory);
-	        myInput.append(inputPrefix);
-	        myInput.append(currentMonth.get(Calendar.YEAR));
-	        myInput.append("-");
-	        myInput.append(currentMonth.get(Calendar.MONTH)+1);
-	        myInput.append(outputSuffix); 
-	        
-	        myOutput = new StringBuffer(outputReportDirectory);
-	        myOutput.append(outputPrefix);
-	        myOutput.append(currentMonth.get(Calendar.YEAR));
-	        myOutput.append("-");
-	        myOutput.append(currentMonth.get(Calendar.MONTH)+1);
-	        myOutput.append(".");
-	        myOutput.append(myFormat);			
-			
-			ReportGenerator.processReport(context, myFormat, myInput.toString(), myOutput.toString(), myMap);
-			
-			currentMonth.add(Calendar.MONTH, 1);
-		}	
-	}
-	
-	/**
-	 * This method generates a report from the aggregation files which have been run for the most recent month
-	 * 
-	 * @throws Exception
-	 */
-	private static void statReportMonthly() throws Exception 
-	{
-		//Prefix
-		String inputPrefix = "dspace-log-monthly-";
-		String outputPrefix = "report-";        
-		
-		String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
-        String myMap = null;
-	
-        myInput = new StringBuffer(outputLogDirectory);
-        myInput.append(inputPrefix);
-        myInput.append(calendar.get(Calendar.YEAR));
-        myInput.append("-");
-        myInput.append(calendar.get(Calendar.MONTH)+1);
-        myInput.append(outputSuffix); 
-        
-        myOutput = new StringBuffer(outputReportDirectory);
-        myOutput.append(outputPrefix);
-        myOutput.append(calendar.get(Calendar.YEAR));
-        myOutput.append("-");
-        myOutput.append(calendar.get(Calendar.MONTH)+1);
-        myOutput.append(".");
-        myOutput.append(myFormat);
-		
-        ReportGenerator.processReport(context, myFormat, myInput.toString(), myOutput.toString(), myMap);
-	}
-	
-	/*
-	 * Output the usage information
-	 */
-	private static void usage() throws Exception {
-	
-		System.out.println("Usage: java CreateStatReport -r <statistic to run>");
-		System.out.println("Available: <stat-initial> <stat-general> <stat-monthly> <stat-report-initial> <stat-report-general> <stat-report-monthly>");     
-		return;		
-	}
-}

dspace-api/src/main/java/org/dspace/app/statistics/LogLine.java

@@ -1,175 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import java.util.Date;
-
-/**
- * This class represents a single log file line and the operations that can be
- * performed on it
- *
- * The components that it represents are: Date, Level, User, Action, and additional
- * Params
- * 
- * @author  Richard Jones
- */
-public class LogLine
-{
-    /** the date of the log file line */
-    private Date date = null;
-    
-    /** the level of the log line type */
-    private String level = null;
-    
-    /** the user performing the logged action */
-    private String user = null;
-    
-    /** the action being performed */
-    private String action = null;
-    
-    /** the parameters associated with the line */
-    private String params = null;
-    
-    /**
-     * constructor to create new statistic
-     */
-    LogLine(Date date, String level, String user, String action, String params)
-    {
-        this.date = date;
-        this.level = level;
-	this.user = user;
-        this.action = action;
-        this.params = params;
-    }
-    
-    /** 
-     * get the date of the log line
-     *
-     * @return      the date of this log line
-     */
-    public Date getDate()
-    {
-        return this.date == null ? null : new Date(this.date.getTime());
-    }
-    
-    
-    /**
-     * get the level of this log line
-     *
-     * @return      the level of the log line
-     */
-    public String getLevel()
-    {
-        return this.level;
-    }
-    
-    
-    /**
-     * get the user performing the logged action
-     *
-     * @return      the user performing the logged action
-     */
-    public String getUser()
-    {
-        return this.user;
-    }
-    
-    
-    /**
-     * get the action being performed
-     *
-     * @return      the logged action
-     */
-    public String getAction()
-    {
-        return this.action;
-    }
-    
-    
-    /**
-     * get the parameters associated with the action
-     *
-     * @return      the parameters associated with the action
-     */
-    public String getParams()
-    {
-        return this.params;
-    }
-    
-    
-    /**
-     * find out if this log file line is before the given date
-     *
-     * @param   date    the date to be compared to
-     *
-     * @return          true if the line is before the given date, false if not
-     */
-    public boolean beforeDate(Date date)
-    {
-        if (date != null)
-        {
-            return (date.compareTo(this.date) >= 0);
-        }
-        return false;
-    }
-    
-    
-    /**
-     * find out if this log file line is after the given date
-     *
-     * @param   date    the date to be compared to
-     *
-     * @return          true if the line is after the given date, false if not
-     */
-    public boolean afterDate(Date date)
-    {
-        if (date != null)
-        {
-            return (date.compareTo(this.date) <= 0);
-        }
-        return false;
-    }
-    
-    
-    /**
-     * find out if the log line is of the given level.  Levels are either
-     * INFO, WARN or ERROR
-     *
-     * @param   level   the level we want to test for
-     *
-     * @return          true if the line is of the specified level, false if not
-     */
-    public boolean isLevel(String level)
-    {
-        if (this.getLevel().equals(level))
-        {
-            return true;
-        }
-        return false;
-    }
-    
-    
-    /**
-     * find out if the log line is of the given action.  Actions are not 
-     * directly constrained by the vocabulary, and any system module may define
-     * any action name for its behaviour
-     *
-     * @param   action  the action we want to test for
-     *
-     * @return          true if the line is of the specified action, false if not
-     */
-    public boolean isAction(String action)
-    {
-        if (this.getAction().equals(action))
-        {
-            return true;
-        }
-        return false;
-    }
- 
-}

dspace-api/src/main/java/org/dspace/app/statistics/Report.java

@@ -1,139 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import org.dspace.app.statistics.Statistics;
-
-import java.util.Date;
-
-/**
- * Sn interface to a generic report generating
- * class, and to provide the polymorphism necessary to allow the report
- * generator to generate any number of different formats of report
- *
- * Note: This used to be an abstract class, but has been made an interface as there wasn't
- * any logic contained within it. It's also been made public, so that you can create a Report
- * type without monkeying about in the statistics package.
- *
- * @author  Richard Jones
- */
-public interface Report
-{
-    /**
-     * output any top headers that this page needs
-     *
-     * @return      a string containing the header for the report
-     */
-    public abstract String header();
-    
-    /**
-     * output any top headers that this page needs
-     *
-     * @param   title   the title of the report, useful for email subjects or
-     *                  HTML headers
-     *
-     * @return      a string containing the header for the report
-     */
-    public abstract String header(String title);
-    
-    /**
-     * output the title in the relevant format.  This requires that the title
-     * has been set with setMainTitle()
-     *
-     * @return      a string containing the title of the report
-     */
-    public abstract String mainTitle();
-    
-    /**
-     * output the date range in the relevant format.  This requires that the
-     * date ranges have been set using setStartDate() and setEndDate()
-     *
-     * @return      a string containing date range information
-     */
-    public abstract String dateRange();
-    
-    /**
-     * output the section header in the relevant format
-     *
-     * @param   title   the title of the current section header
-     *
-     * @return      a string containing the formatted section header
-     */
-    public abstract String sectionHeader(String title);
-    
-    /**
-     * output the report block based on the passed statistics object array
-     *
-     * @param   content     a statistics object to form the basis of the displayed
-     *                      stat block
-     *
-     * @return      a string containing the formatted statistics block
-     */
-    public abstract String statBlock(Statistics content);
-    
-    /**
-     * output the floor information in the relevant format
-     *
-     * @param   floor       the floor value for the statistics block
-     *
-     * @return      a string containing the formatted floor information
-     */
-    public abstract String floorInfo(int floor);
-    
-    /**
-     * output the explanation of the stat block in the relevant format
-     *
-     * @param   explanation     the explanatory or clarification text for the stats
-     *
-     * @return      a string containing the formatted explanation
-     */
-    public abstract String blockExplanation(String explanation);
-    
-    /**
-     * output the final footers for this file
-     *
-     * @return      a string containing the report footer
-     */
-    public abstract String footer();
-    
-    /**
-     * set the main title for the report
-     *
-     * @param   name    the name of the service
-     * @param   serverName  the name of the server
-     */
-    public abstract void setMainTitle (String name, String serverName);
-    
-    /**
-     * add a statistics block to the report to the class register
-     *
-     * @param   stat    the statistics object to be added to the report
-     */
-    public abstract void addBlock(Statistics stat);
-    
-    /**
-     * render the report
-     *
-     * @return      a string containing the full content of the report
-     */
-    public abstract String render();
-    
-    /**
-     * set the starting date for the report
-     *
-     * @param   start   the start date for the report
-     */
-    public abstract void setStartDate(Date start);
-    
-    /**
-     * set the end date for the report
-     *
-     * @param   end     the end date for the report
-     */
-    public abstract void setEndDate(Date end);
-}

dspace-api/src/main/java/org/dspace/app/statistics/ReportGenerator.java

@@ -1,855 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.StringTokenizer;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-
-/**
- * This class performs the action of coordinating a usage report being
- * generated using the standard internal aggregation file format as a basis.
- * All it's configuration information must come from that file.  There is the
- * opportunity for different output format options such as HTML.
- *
- * Use the -help flag for more information
- *
- * @author  Richard Jones
- */
-public class ReportGenerator 
-{
-    // set up our class globals
-    
-    /////////////////
-    // aggregators
-    /////////////////
-    
-    /** aggregator for all actions performed in the system */
-    private static Map<String, String> actionAggregator;
-    
-    /** aggregator for all searches performed */
-    private static Map<String, String> searchAggregator;
-    
-    /** aggregator for user logins */
-    private static Map<String, String> userAggregator;
-    
-    /** aggregator for item views */
-    private static Map<String, String> itemAggregator;
-    
-    /** aggregator for current archive state statistics */
-    private static Map<String, String> archiveStats;
-    
-    
-    //////////////////
-    // statistics config data
-    //////////////////
-    
-    /** bottom limit to output for search word analysis */
-    private static int searchFloor;
-    
-    /** bottom limit to output for item view analysis */
-    private static int itemFloor;
-    
-    /** number of items from most popular to be looked up in the database */
-    private static int itemLookup;
-    
-    /** mode to use for user email display */
-    private static String userEmail;
-    
-    /** URL of the service being analysed */
-    private static String url;
-    
-    /** Name of the service being analysed */
-    private static String name;
-
-    /** average number of views per item */
-    private static int avgItemViews;
-    
-    /** name of the server being analysed */
-    private static String serverName;
-    
-    /** start date of this report */
-    private static Date startDate = null;
-    
-    /** end date of this report */
-    private static Date endDate = null;
-    
-    /** the time taken to build the aggregation file from the log */
-    private static int processTime;
-  
-    /** the number of log lines analysed */
-    private static int logLines;
-    
-    /** the number of warnings encountered */
-    private static int warnings;
-    
-    /** the list of results to be displayed in the general summary */
-    private static List<String> generalSummary;
-    
-    //////////////////
-    // regular expressions
-    //////////////////
-    
-    /** pattern that matches an unqualified aggregator property */
-    private static Pattern real = Pattern.compile("^(.+)=(.+)");
-    
-    //////////////////////////
-   // Miscellaneous variables
-   //////////////////////////
-   
-   /** process timing clock */
-   private static Calendar startTime = null;
-   
-   /** a map from log file action to human readable action */
-   private static Map<String, String> actionMap = null;
-   
-    /////////////////
-    // report generator config data
-    ////////////////
-    
-    /** the input file to build the report from */
-    private static String input = null;
-    
-   /** the log file action to human readable action map */
-   private static String map = ConfigurationManager.getProperty("dspace.dir") +
-                            File.separator + "config" + File.separator + "dstat.map";
-   
-   
-    /**
-     * main method to be run from command line.  See usage information for
-     * details as to how to use the command line flags
-     */
-    public static void main(String [] argv)
-        throws Exception, SQLException
-    {
-        // create context as super user
-        Context context = new Context();
-        context.setIgnoreAuthorization(true);
-        
-        String myFormat = null;
-        String myInput = null;
-        String myOutput = null;
-        String myMap = null;
-        
-        // read in our command line options
-        for (int i = 0; i < argv.length; i++)
-        {
-            if (argv[i].equals("-format"))
-            {
-                myFormat = argv[i+1].toLowerCase();
-            }
-            
-            if (argv[i].equals("-in"))
-            {
-                myInput = argv[i+1];
-            }
-            
-            if (argv[i].equals("-out"))
-            {
-                myOutput = argv[i+1];
-            }
-            
-            if (argv[i].equals("-map"))
-            {
-                myMap = argv[i+1];
-            }
-            
-            if (argv[i].equals("-help"))
-            {
-                usage();
-                System.exit(0);
-            }
-        }
-
-        processReport(context, myFormat, myInput, myOutput, myMap);
-    }
-    
-    /**
-     * using the pre-configuration information passed here, read in the 
-     * aggregation data and output a file containing the report in the
-     * requested format
-     *
-     * this method is retained for backwards compatibility, but delegates the actual
-     * wprk to a new method
-     *
-     * @param   context     the DSpace context in which this action is performed
-     * @param   myFormat    the desired output format (currently on HTML supported)
-     * @param   myInput     the aggregation file to be turned into a report
-     * @param   myOutput    the file into which to write the report
-     */
-    public static void processReport(Context context, String myFormat, 
-                                     String myInput, String myOutput,
-                                     String myMap)
-        throws Exception, SQLException
-    {
-        if (myMap != null)
-        {
-            map = myMap;
-        }
-
-        // create the relevant report type
-        // FIXME: at the moment we only support HTML report generation
-        Report report = null;
-        if (myFormat.equals("html"))
-        {
-            report = new HTMLReport();
-            ((HTMLReport)report).setOutput(myOutput);
-        }
-
-        if (report == null)
-        {
-            throw new IllegalStateException("Must specify a valid report format");
-        }
-
-        ReportGenerator.processReport(context, report, myInput);
-    }
-
-    /**
-     * using the pre-configuration information passed here, read in the
-     * aggregation data and output a file containing the report in the
-     * requested format
-     */
-    public static void processReport(Context context, Report report,
-                                     String myInput)
-        throws Exception, SQLException
-    {
-        startTime = new GregorianCalendar();
-             
-        /** instantiate aggregators */
-        actionAggregator = new HashMap<String, String>();
-        searchAggregator = new HashMap<String, String>();
-        userAggregator = new HashMap<String, String>();
-        itemAggregator = new HashMap<String, String>();
-        archiveStats = new HashMap<String, String>();
-        actionMap = new HashMap<String, String>();
-        
-        /** instantite lists */
-        generalSummary = new ArrayList<String>();
-                
-        // set the parameters for this analysis
-        setParameters(myInput);
-        
-        // read the input file
-        readInput(input);
-        
-        // load the log file action to human readable action map
-        readMap(map);
-        
-        report.setStartDate(startDate);
-        report.setEndDate(endDate);
-        report.setMainTitle(name, serverName);
-        
-        // define our standard variables for re-use
-        // FIXME: we probably don't need these once we've finished re-factoring
-        Iterator<String> keys = null;
-        int i = 0;
-        String explanation = null;
-        int value;
-        
-        // FIXME: All of these sections should probably be buried in their own
-        // custom methods
-        
-        Statistics overview = new Statistics();
-        
-        overview.setSectionHeader("General Overview");
-        
-        Iterator<String> summaryEntries = generalSummary.iterator();
-        while (summaryEntries.hasNext())
-        {
-            String entry = summaryEntries.next();
-            if (actionAggregator.containsKey(entry))
-            {
-                int count = Integer.parseInt(actionAggregator.get(entry));
-                overview.add(new Stat(translate(entry), count));
-            }
-        }
-        
-        report.addBlock(overview);
-        
-        // prepare the archive statistics package
-        if (archiveStats.size() > 0)
-        {
-            Statistics archiveInfo = prepareStats(archiveStats, true, false);
-            archiveInfo.setSectionHeader("Archive Information");
-            archiveInfo.setStatName("Content Type");
-            archiveInfo.setResultName("Number of items");
-        
-            report.addBlock(archiveInfo);
-        }
-        
-        
-        
-        // process the items in preparation to be displayed.  This includes sorting
-        // by view number, building the links, and getting further info where
-        // necessary
-        Statistics viewedItems = new Statistics("Item/Handle", "Number of views", itemFloor);
-        viewedItems.setSectionHeader("Items Viewed");
-        
-        Stat[] items = new Stat[itemAggregator.size()];
-        
-        keys = itemAggregator.keySet().iterator();
-        i = 0;
-        while (keys.hasNext())
-        {
-            String key = keys.next();
-            String link = url + "handle/" + key;
-            value = Integer.parseInt(itemAggregator.get(key));
-            items[i] = new Stat(key, value, link);
-            i++;
-        }
-        
-        Arrays.sort(items);
-        
-        String info = null;
-        for (i = 0; i < items.length; i++)
-        {
-            // Allow negative value to say that all items should be looked up
-            if (itemLookup < 0 || i < itemLookup)
-            {
-                info = getItemInfo(context, items[i].getKey());
-            }
-               
-            // if we get something back from the db then set it as the key,
-            // else just use the link
-            if (info != null)
-            {
-                items[i].setKey(info  + " (" + items[i].getKey() + ")");
-            }
-            else
-            {
-                items[i].setKey(items[i].getReference());
-            }
-            
-            // reset the info register
-            info = null;
-        }
-        
-        viewedItems.add(items);
-        
-        report.addBlock(viewedItems);
-        
-        // prepare a report of the full action statistics
-        Statistics fullInfo = prepareStats(actionAggregator, true, true);
-        fullInfo.setSectionHeader("All Actions Performed");
-        fullInfo.setStatName("Action");
-        fullInfo.setResultName("Number of times");
-        
-        report.addBlock(fullInfo);
-        
-        // prepare the user login statistics package
-        if (!userEmail.equals("off"))
-        {
-            Statistics userLogins = prepareStats(userAggregator, true, false);
-            userLogins.setSectionHeader("User Logins");
-            userLogins.setStatName("User");
-            userLogins.setResultName("Number of logins");
-            if (userEmail.equals("alias"))
-            {
-                explanation = "(distinct addresses)";
-                userLogins.setExplanation(explanation);
-            }
-        
-            report.addBlock(userLogins);
-        }
-
-        // prepare the search word statistics package
-        Statistics searchWords = prepareStats(searchAggregator, true, false);
-        searchWords.setSectionHeader("Words Searched");
-        searchWords.setStatName("Word");
-        searchWords.setResultName("Number of searches");
-        searchWords.setFloor(searchFloor);
-        
-        report.addBlock(searchWords);
-        
-        // FIXME: because this isn't an aggregator it can't be passed to
-        // prepareStats; should we overload this method for use with this kind
-        // of data?
-        // prepare the average item views statistics
-        if (avgItemViews > 0)
-        {
-            Statistics avg = new Statistics();
-            avg.setSectionHeader("Averaging Information");
-
-            Stat[] average = new Stat[1];
-        
-            average[0] = new Stat("Average views per item", avgItemViews);
-            avg.add(average);
-            report.addBlock(avg);
-        }
-      
-        
-        // prepare the log line level statistics
-        // FIXME: at the moment we only know about warnings, but future versions
-        // should aggregate all log line levels and display here
-        Statistics levels = new Statistics("Level", "Number of lines");
-        levels.setSectionHeader("Log Level Information");
-        
-        Stat[] level = new Stat[1];
-        level[0] = new Stat("Warnings", warnings);
-        
-        levels.add(level);
-        
-        report.addBlock(levels);
-        
-        // get the display processing time information
-        Calendar endTime = new GregorianCalendar();
-        long timeInMillis = (endTime.getTimeInMillis() - startTime.getTimeInMillis());
-        int outputProcessTime = (int) (timeInMillis / 1000);
-        
-        // prepare the processing information statistics
-        Statistics process = new Statistics("Operation", "");
-        process.setSectionHeader("Processing Information");
-        
-        Stat[] proc = new Stat[3];
-        proc[0] = new Stat("Log Processing Time", processTime);
-        proc[0].setUnits("seconds");
-        proc[1] = new Stat("Output Processing Time", outputProcessTime);
-        proc[1].setUnits("seconds");
-        proc[2] = new Stat("Log File Lines Analysed", logLines);
-        proc[2].setUnits("lines");
-        
-        process.add(proc);
-        
-        report.addBlock(process);
-
-        report.render();
-        
-        return;
-    }
-    
-    
-    /**
-     * a standard stats block preparation method for use when an aggregator
-     * has to be put out in its entirity.  This method will not be able to
-     * deal with complex cases, although it will perform sorting by value and
-     * translations as per the map file if requested
-     *
-     * @param   aggregator      the aggregator that should be converted
-     * @param   sort            should the resulting stats be sorted by value
-     * @param   translate       translate the stat name using the map file
-     *
-     * @return      a Statistics object containing all the relevant information
-     */
-    public static Statistics prepareStats(Map<String, String> aggregator, boolean sort, boolean translate)
-    {
-        Stat[] stats = new Stat[aggregator.size()];
-        if (aggregator.size() > 0)
-        {
-            int i = 0;
-            for (Map.Entry<String, String> aggregatorEntry : aggregator.entrySet())
-            {
-                String key = aggregatorEntry.getKey();
-                int value = Integer.parseInt(aggregatorEntry.getValue());
-                if (translate)
-                {
-                    stats[i] = new Stat(translate(key), value);
-                }
-                else
-                {
-                    stats[i] = new Stat(key, value);
-                }
-                i++;
-            }
-            
-            if (sort)
-            {
-                Arrays.sort(stats);
-            }
-        }
-        
-        // add the results to the statistics object
-        Statistics statistics = new Statistics();
-        statistics.add(stats);
-        
-        return statistics;
-    }
-    
-    
-    /**
-     * look the given text up in the action map table and return a translated
-     * value if one exists.  If no translation exists the original text is
-     * returned
-     *
-     * @param   text    the text to be translated
-     *
-     * @return      a string containing either the translated text or the original
-     *              text
-     */
-    public static String translate(String text)
-    {
-        if (actionMap.containsKey(text))
-        {
-            return actionMap.get(text);
-        }
-        else
-        {
-            return text;
-        }
-    }
-    
-    
-    /**
-     * read in the action map file which converts log file line actions into
-     * actions which are more understandable to humans
-     *
-     * @param   map     the map file
-     */
-    public static void readMap(String map)
-        throws IOException
-    {
-        FileReader fr = null;
-        BufferedReader br = null;
-
-        try
-        {
-            // read in the map file, printing a warning if none is found
-            String record = null;
-            try
-            {
-                fr = new FileReader(map);
-                br = new BufferedReader(fr);
-            }
-            catch (IOException e)
-            {
-                System.err.println("Failed to read map file: log file actions will be displayed without translation");
-                return;
-            }
-
-            // loop through the map file and read in the values
-            while ((record = br.readLine()) != null)
-            {
-                Matcher matchReal = real.matcher(record);
-
-                // if the line is real then read it in
-                if (matchReal.matches())
-                {
-                    actionMap.put(matchReal.group(1).trim(), matchReal.group(2).trim());
-                }
-            }
-        }
-        finally
-        {
-            if (br != null)
-            {
-                try
-                {
-                    br.close();
-                }
-                catch (IOException ioe)
-                {
-                }
-            }
-
-            if (fr != null)
-            {
-                try
-                {
-                    fr.close();
-                }
-                catch (IOException ioe)
-                {
-                }
-            }
-        }
-    }
-    
-    
-    /**
-     * set the passed parameters up as global class variables.  This has to
-     * be done in a separate method because the API permits for running from
-     * the command line with args or calling the processReport method statically
-     * from elsewhere
-     *
-     * @param   myInput     regex for log file names
-     */
-    public static void setParameters(String myInput)
-    {
-        if (myInput != null)
-        {
-            input = myInput;
-        }
-        
-        return;
-    }
-    
-    
-    /**
-     * read the input file and populate all the class globals with the contents
-     * The values that come from this file form the basis of the analysis report
-     *
-     * @param   input   the aggregator file
-     */
-    public static void readInput(String input)
-        throws IOException, ParseException
-    {
-        FileReader fr = null;
-        BufferedReader br = null;
-        
-        // read in the analysis information, throwing an error if we fail to open
-        // the given file
-        String record = null;
-        try 
-        {  
-            fr = new FileReader(input);
-            br = new BufferedReader(fr);
-        } 
-        catch (IOException e) 
-        {  
-            System.out.println("Failed to read input file: " + input);
-            return;
-        } 
-        
-        // first initialise a date format object to do our date processing
-        // if necessary
-        SimpleDateFormat sdf = new SimpleDateFormat("dd'/'MM'/'yyyy");
-
-        // FIXME: although this works, it is not very elegant
-        // loop through the aggregator file and read in the values
-        while ((record = br.readLine()) != null) 
-        {
-            // match real lines
-            Matcher matchReal = real.matcher(record);
-            
-            // pre-prepare our input strings
-            String section = null;
-            String key = null;
-            String value = null;
-            
-            // temporary string to hold the left hand side of the equation
-            String left = null;
-            
-            // match the line or skip this record
-            if (matchReal.matches())
-            {
-                // lift the values out of the matcher's result groups
-                left = matchReal.group(1).trim();
-                value = matchReal.group(2).trim();
-                
-                // now analyse the left hand side, splitting by ".", taking the
-                // first token as the section and the remainder of the string
-                // as they key if it exists
-                StringTokenizer tokens = new StringTokenizer(left, ".");
-                int numTokens = tokens.countTokens();
-                if (tokens.hasMoreTokens())
-                {
-                    section = tokens.nextToken();
-                    if (numTokens > 1)
-                    {
-                        key = left.substring(section.length() + 1);
-                    }
-                    else
-                    {
-                        key = "";
-                    }
-                }
-            }
-            else
-            {
-                continue;
-            }
-            
-            // if the line is real, then we carry on
-            // read the analysis contents in
-            if ("archive".equals(section))
-            {
-                archiveStats.put(key, value);
-            }
-            else if ("action".equals(section))
-            {
-                actionAggregator.put(key, value);
-            }
-            else if ("user".equals(section))
-            {
-                userAggregator.put(key, value);
-            }
-            else if ("search".equals(section))
-            {
-                searchAggregator.put(key, value);
-            }
-            else if ("item".equals(section))
-            {
-                itemAggregator.put(key, value);
-            }
-            else if ("user_email".equals(section))
-            {
-                userEmail = value;
-            }
-            else if ("item_floor".equals(section))
-            {
-                itemFloor = Integer.parseInt(value);
-            }
-            else if ("search_floor".equals(section))
-            {
-                searchFloor = Integer.parseInt(value);
-            }
-            else if ("host_url".equals(section))
-            {
-                url = value;
-            }
-            else if ("item_lookup".equals(section))
-            {
-                itemLookup = Integer.parseInt(value);
-            }
-            else if ("avg_item_views".equals(section))
-            {
-                try 
-                {
-                    avgItemViews = Integer.parseInt(value);
-                }
-                catch (NumberFormatException e)
-                {
-                    avgItemViews = 0;
-                }
-            }
-            else if ("server_name".equals(section))
-            {
-                serverName = value;
-            }
-            else if ("service_name".equals(section))
-            {
-                name = value;
-            }
-            else if ("start_date".equals(section))
-            {
-                startDate = sdf.parse(value);
-            }
-            else if ("end_date".equals(section))
-            {
-                endDate = sdf.parse(value);
-            }
-            else if ("analysis_process_time".equals(section))
-            {
-                processTime = Integer.parseInt(value);
-            }
-            else if ("general_summary".equals(section))
-            {
-                generalSummary.add(value);
-            }
-            else if ("log_lines".equals(section))
-            {
-                logLines = Integer.parseInt(value);
-            }
-            else if ("warnings".equals(section))
-            {
-                warnings = Integer.parseInt(value);
-            }
-        }
-
-        // close the inputs
-        br.close();
-        fr.close();
-    }
-    
-    /**
-     * get the information for the item with the given handle
-     *
-     * @param   context     the DSpace context we are operating under
-     * @param   handle      the handle of the item being looked up, in the form
-     *                      1234/567 and so forth
-     *
-     * @return      a string containing a reference (almost citation) to the
-     *              article
-     */
-    public static String getItemInfo(Context context, String handle)
-        throws SQLException
-    {
-        Item item = null;
-        
-        // ensure that the handle exists
-        try 
-        {
-            item = (Item) HandleManager.resolveToObject(context, handle);
-        } 
-        catch (Exception e)
-        {
-            return null;
-        }
-        
-        // if no handle that matches is found then also return null
-        if (item == null)
-        {
-            return null;
-        }
-        
-        // build the referece
-        // FIXME: here we have blurred the line between content and presentation
-        // and it should probably be un-blurred
-        DCValue[] title = item.getDC("title", null, Item.ANY);
-        DCValue[] author = item.getDC("contributor", "author", Item.ANY);
-        
-        StringBuffer authors = new StringBuffer();
-        if (author.length > 0)
-        {
-            authors.append("(" + author[0].value);
-        }
-        if (author.length > 1)
-        {
-            authors.append(" et al");
-        }
-        if (author.length > 0)
-        {
-           authors.append(")");
-        }
-        
-        String content = title[0].value + " " + authors.toString();
-        
-        return content;
-    }
-    
-    
-    /**
-     * output the usage information to the terminal
-     */
-    public static void usage()
-    {
-        String usage = "Usage Information:\n" +
-                        "ReportGenerator [options [parameters]]\n" +
-                        "-format [output format]\n" +
-                            "\tRequired\n" +
-                            "\tSpecify the format that you would like the output in\n" +
-                            "\tOptions:\n" +
-                            "\t\thtml\n" +
-                        "-in [aggregation file]\n" +
-                            "\tRequired\n" +
-                            "\tSpecify the aggregation data file to display\n" +
-                        "-out [output file]\n" +
-                            "\tOptional\n" +
-                            "\tSpecify the file to output the report to\n" +
-                            "\tDefault uses [dspace log directory]/report\n" +
-                        "-map [map file]\n" +
-                            "\tOptional\n" +
-                            "\tSpecify the map file to translate log file actions into human readable actions\n" +
-                            "\tDefault uses [dspace config directory]/dstat.map\n" +
-                        "-help\n" +
-                            "\tdisplay this usage information\n";
-        
-        System.out.println(usage);
-    }
-}

dspace-api/src/main/java/org/dspace/app/statistics/ReportTools.java

@@ -1,36 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import java.text.NumberFormat;
-
-/**
- * This class provides a number of tools that may be useful to the methods 
- * which generate the different types of report
- *
- * @author  Richard Jones
- */
-public class ReportTools
-{
-    /**
-     * method to take the given integer and produce a string to be used in
-     * the display of the report.  Basically provides an interface for a
-     * standard NumberFormat class, but without the hassle of instantiating
-     * and localising it.
-     *
-     * @param   number  the integer to be formatted
-     *
-     * @return      a string containing the formatted number
-     */
-    public static String numberFormat(int number)
-    {
-        NumberFormat nf = NumberFormat.getIntegerInstance();
-        return nf.format((double) number);
-    }
-    
-}

dspace-api/src/main/java/org/dspace/app/statistics/Stat.java

@@ -1,166 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-/**
- * This is a primitive class to represent a single statistic, which will 
- * generally be a key value pair but with the capabilities for being sorted
- *
- * Note: this class has a natural ordering that is inconsistent with equals
- *
- * @author  Richard Jones
- */
-public class Stat implements Comparable
-{
-    // FIXME: this class is functional but a bit messy, and should be neatened
-    // up and completed
-    
-    /** the key, which is effectively the text of the statistic */
-    private String key = null;
-    
-    /** the value assigned to the key, generally a count of the key */
-    private int value = 0;
-    
-    /** a reference to an external resource which relates to this statistic */
-    private String reference = null;
-    
-    /** the units that this statistic is in */
-    private String units = null;
-    
-    /**
-     * constructor to create new statistic
-     *
-     * @param   key     the key for the statistic
-     * @param   value   the value for the statistic
-     */
-    Stat(String key, int value)
-    {
-        this.key = key;
-        this.value = value;
-    }
-    
-    /**
-     * constructor to create new statistic
-     *
-     * @param   key     the key for the statistic
-     * @param   value   the value for the statistic
-     * @param   reference   the value for the external reference
-     */
-    Stat(String key, int value, String reference)
-    {
-        this.key = key;
-        this.value = value;
-        this.reference = reference;
-    }
-    
-    /**
-     * set the units of this statistic
-     *
-     * @param   unit    the units that this statistic is measured in
-     */
-    public void setUnits(String unit)
-    {
-        this.units = unit;
-    }
-    
-    /**
-     * get the unts that this statistic is measured in
-     *
-     * @return      the units this statistic is measured in
-     */
-    public String getUnits()
-    {
-        return this.units;
-    }
-    
-    /** 
-     * get the value of the statistic
-     *
-     * @return      the value of this statistic
-     */
-    public int getValue()
-    {
-        return this.value;
-    }
-    
-    
-    /**
-     * get the key (text describing) the statistic
-     *
-     * @return      the key for this statistic
-     */
-    public String getKey()
-    {
-        return this.key;
-    }
-    
-    
-    /**
-     * get the reference to related statistic information
-     *
-     * @return      the reference for this statistic
-     */
-    public String getReference()
-    {
-        return this.reference;
-    }
-    
-    
-    /**
-     * set the reference information
-     *
-     * @param   key     the key for this statistic
-     */
-    public void setKey(String key)
-    {
-        this.key = key;
-    }
-    
-    
-    /**
-     * set the reference information
-     *
-     * @param   reference   the reference for this statistic
-     */
-    public void setReference(String reference)
-    {
-        this.reference = reference;
-    }
-    
-    
-    /** 
-     * compare the current object to the given object returning -1 if o is less
-     * than the current object, 0 if they are the same, and +1 if o is greater
-     * than the current object.
-     *
-     * @param  o   the object to compare to the current one
-     *
-     * @return      +1, 0, -1 if o is less than, equal to, or greater than the
-     *              current object value.
-     */
-    public int compareTo(Object o) 
-    {
-        int objectValue = ((Stat) o).getValue();
-        
-        if (objectValue < this.getValue())
-        {
-            return -1;
-        }
-        else if (objectValue == this.getValue())
-        {
-            return 0;
-        }
-        else if (objectValue > this.getValue())
-        {
-            return 1;
-        }
-        
-        return 0;
-    }    
-    
-}

dspace-api/src/main/java/org/dspace/app/statistics/Statistics.java

@@ -1,219 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * This class provides a wrapper for a related set of statistics.  It contains
- * headers for the Stat key and value pairs for the convenience of displaying
- * them to users as, for example, HTML table headers.  It also holds the 
- * list of statistics, and can have them added to itself individually or in
- * arrays
- *
- * @author  Richard Jones
- */
-public class Statistics
-{
-    // FIXME: this class could probably do with some tidying
-    
-    /** the header for the statistics type.  Useful for outputting to user */
-    private String statName = null;
-    
-    /** the header for the results.  Useful for outputting to user */
-    private String resultName = null;
-    
-    /** a list to hold all of the stat elements that this object contains */
-    private List<Stat> stats = new ArrayList<Stat>();
-    
-    /** the floor value for this set of statistics */
-    private int floor = 0;
-    
-    /** an explanation of this statistics set */
-    private String explanation = null;
-    
-    /** the main section header for this set of statistics */
-    private String sectionHeader = null;
-    
-    /**
-     * constructor to create new set of statistics
-     */
-    Statistics()
-    {
-        // empty constructor
-    }
-    
-    /**
-     * constructor to create new statistic with relevant headers
-     *
-     * @param   statName     name of the statistic
-     * @param   resultName   name of the result
-     */
-    Statistics(String statName, String resultName)
-    {
-        this.statName = statName;
-        this.resultName = resultName;
-    }
-    
-    /**
-     * constructor to create new statistic with relevant headers
-     *
-     * @param   statName     name of the statistic
-     * @param   resultName   name of the result
-     */
-    Statistics(String statName, String resultName, int floor)
-    {
-        this.statName = statName;
-        this.resultName = resultName;
-        this.floor = floor;
-    }
-    
-    /**
-     * add an individual statistic to this object
-     *
-     * @param   stat    a statistic for this object
-     */
-    public void add(Stat stat)
-    {
-        this.stats.add(stat);
-        return;
-    }
-    
-    /**
-     * set the name of the statistic column
-     *
-     * @param   name    the name of the statistic column
-     */
-    public void setStatName(String name)
-    {
-        this.statName = name;
-    }
-    
-    /**
-     * set the name of the results column
-     *
-     * @param   name    the name of the results column
-     */
-    public void setResultName(String name)
-    {
-        this.resultName = name;
-    }
-    
-    
-    /**
-     * set the explanatory or clarification information for this block of stats
-     *
-     * @param   explanation     the explanation for this stat block
-     */
-    public void setExplanation(String explanation)
-    {
-        this.explanation = explanation;
-    }
-    
-    
-    /**
-     * get the explanation or clarification information for this block of stats
-     *
-     * @return      the explanation for this stat block
-     */
-    public String getExplanation()
-    {
-        return this.explanation;
-    }
-    
-    
-    /**
-     * set the floor value used in this stat block
-     *
-     * @param   floor   the floor value for this stat block
-     */
-    public void setFloor(int floor)
-    {
-        this.floor = floor;
-    }
-    
-    
-    /**
-     * get the floor value used in this stat block
-     *
-     * @return  the floor value for this stat block
-     */
-    public int getFloor()
-    {
-        return this.floor;
-    }
-    
-    
-    /**
-     * set the header for this particular stats block
-     *
-     * @param   header for this stats block
-     */
-    public void setSectionHeader(String header)
-    {
-        this.sectionHeader = header;
-    }
-    
-    
-    /**
-     * get the header for this particular stats block
-     *
-     * @return  the header for this stats block
-     */
-    public String getSectionHeader()
-    {
-        return this.sectionHeader;
-    }
-    
-    /**
-     * add an array of statistics to this object
-     *
-     * @param   stats   an array of statistics
-     */
-    public void add(Stat[] stats)
-    {
-        for (int i = 0; i < stats.length; i++)
-        {
-            this.stats.add(stats[i]);
-        }
-        return;
-    }
-    
-    /**
-     * get an array of statistics back from this object
-     *
-     * @return      the statistics array
-     */
-    public Stat[] getStats()
-    {
-        Stat[] myStats = new Stat[stats.size()];
-        myStats = (Stat[]) stats.toArray(myStats);
-        return myStats;
-    }
-    
-    /**
-     * get the name of the statistic
-     *
-     * @return      the name of the statistic
-     */
-    public String getStatName()
-    {
-        return statName;
-    }
-    
-    /**
-     * get the name of the result set
-     *
-     * @return      the name of the result set
-     */
-    public String getResultName()
-    {
-        return resultName;
-    }
-}

dspace-api/src/main/java/org/dspace/app/statistics/StatisticsLoader.java

@@ -1,380 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.statistics;
-
-import org.apache.commons.lang.time.DateUtils;
-import org.dspace.core.ConfigurationManager;
-
-import java.util.*;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.File;
-import java.io.FilenameFilter;
-import java.text.SimpleDateFormat;
-import java.text.ParseException;
-
-/**
- * Helper class for loading the analysis / report files from the reports directory
- */
-public class StatisticsLoader
-{
-    private static Map<String, StatsFile> monthlyAnalysis = null;
-    private static Map<String, StatsFile> monthlyReports = null;
-
-    private static StatsFile generalAnalysis = null;
-    private static StatsFile generalReport = null;
-
-    private static Date lastLoaded = null;
-    private static int fileCount   = 0;
-
-    private static Pattern analysisMonthlyPattern;
-    private static Pattern analysisGeneralPattern;
-    private static Pattern reportMonthlyPattern;
-    private static Pattern reportGeneralPattern;
-
-    private static SimpleDateFormat monthlySDF;
-    private static SimpleDateFormat generalSDF;
-
-    // one time initialisation of the regex patterns and formatters we will use
-    static
-    {
-        analysisMonthlyPattern = Pattern.compile("dspace-log-monthly-([0-9][0-9][0-9][0-9]-[0-9]+)\\.dat");
-        analysisGeneralPattern = Pattern.compile("dspace-log-general-([0-9]+-[0-9]+-[0-9]+)\\.dat");
-        reportMonthlyPattern   = Pattern.compile("report-([0-9][0-9][0-9][0-9]-[0-9]+)\\.html");
-        reportGeneralPattern   = Pattern.compile("report-general-([0-9]+-[0-9]+-[0-9]+)\\.html");
-
-        monthlySDF = new SimpleDateFormat("yyyy'-'M");
-        generalSDF = new SimpleDateFormat("yyyy'-'M'-'dd");
-    }
-
-    /**
-     * Get an array of the dates of the report files.
-     */
-    public static Date[] getMonthlyReportDates()
-    {
-        return sortDatesDescending(getDatesFromMap(monthlyReports));
-    }
-
-    /**
-     * Get an array of the dates of the analysis files.
-     */
-    public static Date[] getMonthlyAnalysisDates()
-    {
-        return sortDatesDescending(getDatesFromMap(monthlyAnalysis));
-    }
-
-    /**
-     * Convert the formatted dates that are the keys of the map into a date array.
-     * @param monthlyMap
-     */
-    protected static Date[] getDatesFromMap(Map<String, StatsFile> monthlyMap)
-    {
-        Set<String> keys = monthlyMap.keySet();
-        Date[] dates = new Date[keys.size()];
-        int i = 0;
-        for (String date : keys)
-        {
-            try
-            {
-                dates[i] = monthlySDF.parse(date);
-            }
-            catch (ParseException pe)
-            {
-            }
-
-            i++;
-        }
-
-        return dates;
-    }
-
-    /**
-     * Sort the date array in descending (reverse chronological) order.
-     * @param dates
-     * @return sorted dates.
-     */
-    protected static Date[] sortDatesDescending(Date[] dates)
-    {
-        Arrays.sort(dates, new Comparator<Date>() {
-            public int compare(Date d1, Date d2)
-            {
-                if (d1 == null && d2 == null)
-                {
-                    return 0;
-                }
-                else if (d1 == null)
-                {
-                    return -1;
-                }
-                else if (d2 == null)
-                {
-                    return 1;
-                }
-                else if (d1.before(d2))
-                {
-                    return 1;
-                }
-                else if (d2.before(d1))
-                {
-                    return -1;
-                }
-
-                return 0;
-            }
-        });
-        return dates;
-    }
-
-    /**
-     * Get the analysis file for a given date.
-     * @param date
-     */
-    public static File getAnalysisFor(String date)
-    {
-        StatisticsLoader.syncFileList();
-        StatsFile sf = (monthlyAnalysis == null ? null : monthlyAnalysis.get(date));
-        return sf == null ? null : sf.file;
-    }
-
-    /**
-     * Get the report file for a given date.
-     * @param date
-     */
-    public static File getReportFor(String date)
-    {
-        StatisticsLoader.syncFileList();
-        StatsFile sf = (monthlyReports == null ? null : monthlyReports.get(date));
-        return sf == null ? null : sf.file;
-    }
-
-    /**
-     * Get the current general analysis file.
-     */
-    public static File getGeneralAnalysis()
-    {
-        StatisticsLoader.syncFileList();
-        return generalAnalysis == null ? null : generalAnalysis.file;
-    }
-
-    /**
-     * Get the current general report file.
-     */
-    public static File getGeneralReport()
-    {
-        StatisticsLoader.syncFileList();
-        return generalReport == null ? null : generalReport.file;
-    }
-
-    /**
-     * Synchronize the cached list of analysis / report files with the reports directory
-     *
-     * We synchronize if:
-     *
-     * 1) The number of files is different (ie. files have been added or removed)
-     * 2) We haven't cached anything yet
-     * 3) The cache was last generate over an hour ago
-     */
-    private static void syncFileList()
-    {
-        // Get an array of all the analysis and report files present
-        File[] fileList = StatisticsLoader.getAnalysisAndReportFileList();
-
-        if (fileList != null && fileList.length != fileCount)
-        {
-            StatisticsLoader.loadFileList(fileList);
-        }
-        else if (lastLoaded == null)
-        {
-            StatisticsLoader.loadFileList(fileList);
-        }
-        else if (DateUtils.addHours(lastLoaded, 1).before(new Date()))
-        {
-            StatisticsLoader.loadFileList(fileList);
-        }
-    }
-
-    /**
-     * Generate the cached file list from the array of files
-     * @param fileList
-     */
-    private static synchronized void loadFileList(File[] fileList)
-    {
-        // If we haven't been passed an array of files, get one now
-        if (fileList == null || fileList.length == 0)
-        {
-            fileList = StatisticsLoader.getAnalysisAndReportFileList();
-        }
-
-        // Create new maps for the monthly analysis / reports
-        Map<String, StatsFile> newMonthlyAnalysis = new HashMap<String, StatsFile>();
-        Map<String, StatsFile> newMonthlyReports  = new HashMap<String, StatsFile>();
-
-        StatsFile newGeneralAnalysis = null;
-        StatsFile newGeneralReport = null;
-
-        if (fileList != null)
-        {
-            for (File thisFile : fileList)
-            {
-                StatsFile statsFile = null;
-
-                // If we haven't identified this file yet
-                if (statsFile == null)
-                {
-                    // See if it is a monthly analysis file
-                    statsFile = makeStatsFile(thisFile, analysisMonthlyPattern, monthlySDF);
-                    if (statsFile != null)
-                    {
-                        // If it is, add it to the map
-                        newMonthlyAnalysis.put(statsFile.dateStr, statsFile);
-                    }
-                }
-
-                // If we haven't identified this file yet
-                if (statsFile == null)
-                {
-                    // See if it is a monthly report file
-                    statsFile = makeStatsFile(thisFile, reportMonthlyPattern, monthlySDF);
-                    if (statsFile != null)
-                    {
-                        // If it is, add it to the map
-                        newMonthlyReports.put(statsFile.dateStr, statsFile);
-                    }
-                }
-
-                // If we haven't identified this file yet
-                if (statsFile == null)
-                {
-                    // See if it is a general analysis file
-                    statsFile = makeStatsFile(thisFile, analysisGeneralPattern, generalSDF);
-                    if (statsFile != null)
-                    {
-                        // If it is, ensure that we are pointing to the most recent file
-                        if (newGeneralAnalysis == null || statsFile.date.after(newGeneralAnalysis.date))
-                        {
-                            newGeneralAnalysis = statsFile;
-                        }
-                    }
-                }
-
-                // If we haven't identified this file yet
-                if (statsFile == null)
-                {
-                    // See if it is a general report file
-                    statsFile = makeStatsFile(thisFile, reportGeneralPattern, generalSDF);
-                    if (statsFile != null)
-                    {
-                        // If it is, ensure that we are pointing to the most recent file
-                        if (newGeneralReport == null || statsFile.date.after(newGeneralReport.date))
-                        {
-                            newGeneralReport = statsFile;
-                        }
-                    }
-                }
-            }
-        }
-
-        // Store the newly discovered values in the member cache
-        monthlyAnalysis = newMonthlyAnalysis;
-        monthlyReports  = newMonthlyReports;
-        generalAnalysis = newGeneralAnalysis;
-        generalReport   = newGeneralReport;
-        lastLoaded = new Date();
-    }
-
-    /**
-     * Generate a StatsFile entry for this file. The pattern and date
-     * formatters are used to identify the file as a particular type,
-     * and extract the relevant information.  If the file is not identified
-     * by the formatter provided, then we return null.
-     * @param thisFile
-     * @param thisPattern
-     * @param sdf
-     */
-    private static StatsFile makeStatsFile(File thisFile, Pattern thisPattern, SimpleDateFormat sdf)
-    {
-        Matcher matcher = thisPattern.matcher(thisFile.getName());
-        if (matcher.matches())
-        {
-            StatsFile sf = new StatsFile();
-            sf.file = thisFile;
-            sf.path = thisFile.getPath();
-            sf.dateStr = matcher.group(1).trim();
-
-            try
-            {
-                sf.date = sdf.parse(sf.dateStr);
-            }
-            catch (ParseException e)
-            {
-
-            }
-
-            return sf;
-        }
-        
-        return null;
-    }
-
-    /**
-     * Get an array of all the analysis and report files.
-     */
-    private static File[] getAnalysisAndReportFileList()
-    {
-        File reportDir = new File(ConfigurationManager.getProperty("log.dir"));
-        if (reportDir != null)
-        {
-            return reportDir.listFiles(new AnalysisAndReportFilter());
-        }
-
-        return null;
-    }
-
-    /**
-     * Simple class for holding information about an analysis/report file.
-     */
-    private static class StatsFile
-    {
-        File file;
-        String path;
-        Date date;
-        String dateStr;
-    }
-
-    /**
-     * Filter used to restrict files in the reports directory to just
-     * analysis or report types.
-     */
-    private static class AnalysisAndReportFilter implements FilenameFilter
-    {
-        public boolean accept(File dir, String name)
-        {
-            if (analysisMonthlyPattern.matcher(name).matches())
-            {
-                return true;
-            }
-
-            if (analysisGeneralPattern.matcher(name).matches())
-            {
-                return true;
-            }
-
-            if (reportMonthlyPattern.matcher(name).matches())
-            {
-                return true;
-            }
-            
-            if (reportGeneralPattern.matcher(name).matches())
-            {
-                return true;
-            }
-
-            return false;
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/statistics/package.html

@@ -1,50 +0,0 @@
-<!--
-
-    The contents of this file are subject to the license and copyright
-    detailed in the LICENSE and NOTICE files at the root of the source
-    tree and available online at
-
-    http://www.dspace.org/license/
-
--->
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
-<html>
-<head>
-<title>org.dspace.app.statistics package</title>
-</head>
-
-<body>
-<p>
-Defines usage event instrumentation points and provides implementations for
-testing.
-</p>
-
-<p>
-This package makes usage instrumentation (for statistics, or whatever else
-you may fancy) pluggable, while avoiding any unnecessary assumptions about how
-usage events may be transmitted, persisted, or processed.
-</p>
-
-<p>
-At appropriate points in the processing of user actions, events may be
-assembled and "fired".  What happens when an event is fired is configurable
-via the PluginManager.  One must configure a plugin for the AbstractUsageEvent
-class, defined in this package, to select an event processing implementation.
-</p>
-
-<p>
-Three "stock" implementations are provided.
-</p>
-<dl>
-	<dt>{@link org.dspace.usage.PassiveUsageEventListener PassiveUsageEventListener}</dt>
-	<dd>absorbs events without taking action, resulting in behavior identical
-		to that of DSpace before this package was added.  This is the default
-		if no plugin is configured.</dd>
-	<dt>{@link org.dspace.usage.TabFileUsageEventListener TabFileUsageEventListener}</dt>
-	<dd>writes event records to a file in Tab Separated Values format.</dd>
-	<dt>{@link org.dspace.app.statistics.UsageEventXMLLogger UsageEventXMLLogger}</dt>
-	<dd>writes event records to a file in an XML format.  Suitable mainly for
-		testing.</dd>
-</dl>
-</body>
-</html>

dspace-api/src/main/java/org/dspace/app/util/AuthorizeUtil.java

@@ -1,622 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.sql.SQLException;
-
-import org.dspace.authorize.AuthorizeConfiguration;
-import org.dspace.authorize.AuthorizeException;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.authorize.ResourcePolicy;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.Item;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-
-/**
- * This class is an addition to the AuthorizeManager that perform authorization
- * check on not CRUD (ADD, WRITE, etc.) actions.
- * 
- * @author bollini
- * 
- */
-public class AuthorizeUtil
-{
-
-    /**
-     * Is allowed manage (create, remove, edit) bitstream's policies in the
-     * current context?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param bitstream
-     *            the bitstream that the policy refer to
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             manage the bitstream's policies
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageBitstreamPolicy(Context context,
-            Bitstream bitstream) throws AuthorizeException, SQLException
-    {
-        Bundle bundle = bitstream.getBundles()[0];
-        authorizeManageBundlePolicy(context, bundle);
-    }
-
-    /**
-     * Is allowed manage (create, remove, edit) bundle's policies in the
-     * current context?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param bundle
-     *            the bundle that the policy refer to
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             manage the bundle's policies
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageBundlePolicy(Context context,
-            Bundle bundle) throws AuthorizeException, SQLException
-    {
-        Item item = bundle.getItems()[0];
-        authorizeManageItemPolicy(context, item);
-    }
-
-    /**
-     * Is allowed manage (create, remove, edit) item's policies in the
-     * current context?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param item
-     *            the item that the policy refer to
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             manage the item's policies
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageItemPolicy(Context context, Item item)
-            throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canItemAdminManagePolicies())
-        {
-            AuthorizeManager.authorizeAction(context, item, Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration.canCollectionAdminManageItemPolicies())
-        {
-            AuthorizeManager.authorizeAction(context, item
-                    .getOwningCollection(), Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration.canCommunityAdminManageItemPolicies())
-        {
-            AuthorizeManager
-                    .authorizeAction(context, item.getOwningCollection()
-                            .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage item policies");
-        }
-    }
-
-    /**
-     * Is allowed manage (create, remove, edit) collection's policies in the
-     * current context?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection that the policy refer to
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             manage the collection's policies
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageCollectionPolicy(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCollectionAdminManagePolicies())
-        {
-            AuthorizeManager.authorizeAction(context, collection,
-                    Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration
-                .canCommunityAdminManageCollectionPolicies())
-        {
-            AuthorizeManager.authorizeAction(context, collection
-                    .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage collection policies");
-        }
-    }
-
-    /**
-     * Is allowed manage (create, remove, edit) community's policies in the
-     * current context?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param community
-     *            the community that the policy refer to
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             manage the community's policies
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageCommunityPolicy(Context context,
-            Community community) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCommunityAdminManagePolicies())
-        {
-            AuthorizeManager.authorizeAction(context, community,
-                    Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage community policies");
-        }
-    }
-
-    /**
-     * Throw an AuthorizeException if the current user is not a System Admin
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @throws AuthorizeException
-     *             if the current user is not a System Admin
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void requireAdminRole(Context context)
-            throws AuthorizeException, SQLException
-    {
-        if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to perform this action");
-        }
-    }
-
-    /**
-     * Is the current user allowed to manage (add, remove, replace) the item's
-     * CC License
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param item
-     *            the item that the CC License refer to
-     * @throws AuthorizeException
-     *             if the current user is not allowed to
-     *             manage the item's CC License
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageCCLicense(Context context, Item item)
-            throws AuthorizeException, SQLException
-    {
-        try
-        {
-            AuthorizeManager.authorizeAction(context, item, Constants.ADD);
-            AuthorizeManager.authorizeAction(context, item, Constants.REMOVE);
-        }
-        catch (AuthorizeException authex)
-        {
-            if (AuthorizeConfiguration.canItemAdminManageCCLicense())
-            {
-                AuthorizeManager
-                        .authorizeAction(context, item, Constants.ADMIN);
-            }
-            else if (AuthorizeConfiguration.canCollectionAdminManageCCLicense())
-            {
-                AuthorizeManager.authorizeAction(context, item
-                        .getParentObject(), Constants.ADMIN);
-            }
-            else if (AuthorizeConfiguration.canCommunityAdminManageCCLicense())
-            {
-                AuthorizeManager.authorizeAction(context, item
-                        .getParentObject().getParentObject(), Constants.ADMIN);
-            }
-            else
-            {
-                requireAdminRole(context);
-            }
-        }
-    }
-
-    /**
-     * Is the current user allowed to manage (create, remove, edit) the
-     * collection's template item?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection
-     * @throws AuthorizeException
-     *             if the current user is not allowed to manage the collection's
-     *             template item
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageTemplateItem(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        boolean isAuthorized = collection.canEditBoolean(false);
-
-        if (!isAuthorized
-                && AuthorizeConfiguration
-                        .canCollectionAdminManageTemplateItem())
-        {
-            AuthorizeManager.authorizeAction(context, collection,
-                    Constants.ADMIN);
-        }
-        else if (!isAuthorized
-                && AuthorizeConfiguration
-                        .canCommunityAdminManageCollectionTemplateItem())
-        {
-            Community[] communities = collection.getCommunities();
-            Community parent = communities != null && communities.length > 0 ? communities[0]
-                    : null;
-            AuthorizeManager.authorizeAction(context, parent, Constants.ADMIN);
-        }
-        else if (!isAuthorized && !AuthorizeManager.isAdmin(context)) 
-        {
-            throw new AuthorizeException(
-                    "You are not authorized to create a template item for the collection");
-        }
-    }
-
-    /**
-     * Can the current user manage (create, remove, edit) the submitters group of
-     * the collection?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection
-     * @throws AuthorizeException
-     *             if the current user is not allowed to manage the collection's
-     *             submitters group
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageSubmittersGroup(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCollectionAdminManageSubmitters())
-        {
-            AuthorizeManager.authorizeAction(context, collection,
-                    Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration
-                .canCommunityAdminManageCollectionSubmitters())
-        {
-            AuthorizeManager.authorizeAction(context, collection
-                    .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage collection submitters");
-        }
-    }
-
-    /**
-     * Can the current user manage (create, remove, edit) the workflow groups of
-     * the collection?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection
-     * @throws AuthorizeException
-     *             if the current user is not allowed to manage the collection's
-     *             workflow groups
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageWorkflowsGroup(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCollectionAdminManageWorkflows())
-        {
-            AuthorizeManager.authorizeAction(context, collection,
-                    Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration
-                .canCommunityAdminManageCollectionWorkflows())
-        {
-            AuthorizeManager.authorizeAction(context, collection
-                    .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage collection workflow");
-        }
-    }
-
-    /**
-     * Can the current user create/edit the admins group of the collection?
-     * please note that the remove action need a separate check
-     * 
-     * @see #authorizeRemoveAdminGroup(Context, Collection)
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection
-     * @throws AuthorizeException
-     *             if the current user is not allowed to create/edit the
-     *             collection's admins group
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageAdminGroup(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCollectionAdminManageAdminGroup())
-        {
-            AuthorizeManager.authorizeAction(context, collection,
-                    Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration
-                .canCommunityAdminManageCollectionAdminGroup())
-        {
-            AuthorizeManager.authorizeAction(context, collection
-                    .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage collection admin");
-        }
-    }
-
-    /**
-     * Can the current user remove the admins group of the collection?
-     * please note that the create/edit actions need separate check
-     * 
-     * @see #authorizeManageAdminGroup(Context, Collection)
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param collection
-     *            the collection
-     * @throws AuthorizeException
-     *             if the current user is not allowed to remove the
-     *             collection's admins group
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeRemoveAdminGroup(Context context,
-            Collection collection) throws AuthorizeException, SQLException
-    {
-        Community[] parentCommunities = collection.getCommunities();
-        if (AuthorizeConfiguration
-                .canCommunityAdminManageCollectionAdminGroup()
-                && parentCommunities != null && parentCommunities.length > 0)
-        {
-            AuthorizeManager.authorizeAction(context, collection
-                    .getCommunities()[0], Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin can remove the admin group of a collection");
-        }
-    }
-
-    /**
-     * Can the current user create/edit the admins group of the community?
-     * please note that the remove action need a separate check
-     * 
-     * @see #authorizeRemoveAdminGroup(Context, Collection)
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param community
-     *            the community
-     * @throws AuthorizeException
-     *             if the current user is not allowed to create/edit the
-     *             community's admins group
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManageAdminGroup(Context context,
-            Community community) throws AuthorizeException, SQLException
-    {
-        if (AuthorizeConfiguration.canCommunityAdminManageAdminGroup())
-        {
-            AuthorizeManager.authorizeAction(context, community,
-                    Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin are allowed to manage community admin");
-        }
-    }
-
-    /**
-     * Can the current user remove the admins group of the community?
-     * please note that the create/edit actions need separate check
-     * 
-     * @see #authorizeManageAdminGroup(Context, Community)
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param community
-     *            the community
-     * @throws AuthorizeException
-     *             if the current user is not allowed to remove the
-     *             collection's admins group
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeRemoveAdminGroup(Context context,
-            Community community) throws SQLException, AuthorizeException
-    {
-        Community parentCommunity = community.getParentCommunity();
-        if (AuthorizeConfiguration.canCommunityAdminManageAdminGroup()
-                && parentCommunity != null)
-        {
-            AuthorizeManager.authorizeAction(context, parentCommunity,
-                    Constants.ADMIN);
-        }
-        else if (!AuthorizeManager.isAdmin(context))
-        {
-            throw new AuthorizeException(
-                    "Only system admin can remove the admin group of the community");
-        }
-    }
-
-    /**
-     * Can the current user remove or edit the supplied policy?
-     * 
-     * @param c
-     *            the DSpace Context Object
-     * @param rp
-     *            a resource policy
-     * @throws AuthorizeException
-     *             if the current context (current user) is not allowed to
-     *             remove/edit the policy
-     * @throws SQLException
-     *             if a db error occur
-     */
-    public static void authorizeManagePolicy(Context c, ResourcePolicy rp)
-            throws SQLException, AuthorizeException
-    {
-        switch (rp.getResourceType())
-        {
-        case Constants.BITSTREAM:
-            authorizeManageBitstreamPolicy(c, Bitstream.find(c, rp
-                    .getResourceID()));
-            break;
-        case Constants.BUNDLE:
-            authorizeManageBundlePolicy(c, Bundle.find(c, rp.getResourceID()));
-            break;
-
-        case Constants.ITEM:
-            authorizeManageItemPolicy(c, Item.find(c, rp.getResourceID()));
-            break;
-        case Constants.COLLECTION:
-            authorizeManageCollectionPolicy(c, Collection.find(c, rp
-                    .getResourceID()));
-            break;
-        case Constants.COMMUNITY:
-            authorizeManageCommunityPolicy(c, Community.find(c, rp
-                    .getResourceID()));
-            break;
-
-        default:
-            requireAdminRole(c);
-            break;
-        }
-    }
-
-    /**
-     * Can the current user withdraw the item?
-     * 
-     * @param context
-     *            the DSpace Context Object
-     * @param item
-     *            the item
-     * @throws SQLException
-     *             if a db error occur
-     * @throws AuthorizeException
-     *             if the current user is not allowed to perform the item
-     *             withdraw
-     */
-    public static void authorizeWithdrawItem(Context context, Item item)
-            throws SQLException, AuthorizeException
-    {
-        boolean authorized = false;
-        if (AuthorizeConfiguration.canCollectionAdminPerformItemWithdrawn())
-        {
-            authorized = AuthorizeManager.authorizeActionBoolean(context, item
-                    .getOwningCollection(), Constants.ADMIN);
-        }
-        else if (AuthorizeConfiguration.canCommunityAdminPerformItemWithdrawn())
-        {
-            authorized = AuthorizeManager
-                    .authorizeActionBoolean(context, item.getOwningCollection()
-                            .getCommunities()[0], Constants.ADMIN);
-        }
-
-        if (!authorized)
-        {
-            authorized = AuthorizeManager.authorizeActionBoolean(context, item
-                    .getOwningCollection(), Constants.REMOVE, false);
-        }
-
-        // authorized
-        if (!authorized)
-        {
-            throw new AuthorizeException(
-                    "To withdraw item must be COLLECTION_ADMIN or have REMOVE authorization on owning Collection");
-        }
-    }
-
-    /**
-    * Can the current user reinstate the item?
-    * 
-    * @param context
-    *            the DSpace Context Object
-    * @param item
-    *            the item
-    * @throws SQLException
-    *             if a db error occur
-    * @throws AuthorizeException
-    *             if the current user is not allowed to perform the item
-    *             reinstatement
-    */
-    public static void authorizeReinstateItem(Context context, Item item)
-            throws SQLException, AuthorizeException
-    {
-        Collection[] colls = item.getCollections();
-
-        for (int i = 0; i < colls.length; i++)
-        {
-            if (!AuthorizeConfiguration
-                    .canCollectionAdminPerformItemReinstatiate())
-            {
-                if (AuthorizeConfiguration
-                        .canCommunityAdminPerformItemReinstatiate()
-                        && AuthorizeManager.authorizeActionBoolean(context,
-                                colls[i].getCommunities()[0], Constants.ADMIN))
-                {
-                    // authorized
-                }
-                else
-                {
-                    AuthorizeManager.authorizeAction(context, colls[i],
-                            Constants.ADD, false);
-                }
-            }
-            else
-            {
-                AuthorizeManager.authorizeAction(context, colls[i],
-                        Constants.ADD);
-            }
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/DCInput.java

@@ -1,405 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-import org.dspace.content.MetadataSchema;
-
-/**
- * Class representing a line in an input form.
- * 
- * @author Brian S. Hughes, based on work by Jenny Toves, OCLC
- */
-public class DCInput
-{
-    /** the DC element name */
-    private String dcElement = null;
-
-    /** the DC qualifier, if any */
-    private String dcQualifier = null;
-
-    /** the DC namespace schema */
-    private String dcSchema = null;
-
-    /** a label describing input */
-    private String label = null;
-
-    /** the input type */
-    private String inputType = null;
-
-    /** is input required? */
-    private boolean required = false;
-
-    /** if required, text to display when missing */
-    private String warning = null;
-
-    /** is input repeatable? */
-    private boolean repeatable = false;
-
-    /** 'hint' text to display */
-    private String hint = null;
-
-    /** if input list-controlled, name of list */
-    private String valueListName = null;
-
-    /** if input list-controlled, the list itself */
-    private List<String> valueList = null;
-
-    /** if non-null, visibility scope restriction */
-    private String visibility = null;
-    
-    /** if non-null, readonly out of the visibility scope */
-    private String readOnly = null;
-
-    /** the name of the controlled vocabulary to use */
-    private String vocabulary = null;
-
-    /** is the entry closed to vocabulary terms? */
-    private boolean closedVocabulary = false;
-
-    /** allowed document types */
-    private List<String> typeBind = null;
-
-    /** 
-     * The scope of the input sets, this restricts hidden metadata fields from 
-     * view during workflow processing. 
-     */
-    public static final String WORKFLOW_SCOPE = "workflow";
-
-    /** 
-     * The scope of the input sets, this restricts hidden metadata fields from 
-     * view by the end user during submission. 
-     */
-    public static final String SUBMISSION_SCOPE = "submit";
-    
-    /**
-     * Class constructor for creating a DCInput object based on the contents of
-     * a HashMap
-     * 
-     * @param fieldMap
-     *            ???
-     * @param listMap
-     */
-    public DCInput(Map<String, String> fieldMap, Map<String, List<String>> listMap)
-    {
-        dcElement = fieldMap.get("dc-element");
-        dcQualifier = fieldMap.get("dc-qualifier");
-
-        // Default the schema to dublin core
-        dcSchema = fieldMap.get("dc-schema");
-        if (dcSchema == null)
-        {
-            dcSchema = MetadataSchema.DC_SCHEMA;
-        }
-
-        String repStr = fieldMap.get("repeatable");
-        repeatable = "true".equalsIgnoreCase(repStr)
-                || "yes".equalsIgnoreCase(repStr);
-        label = fieldMap.get("label");
-        inputType = fieldMap.get("input-type");
-        // these types are list-controlled
-        if ("dropdown".equals(inputType) || "qualdrop_value".equals(inputType)
-                || "list".equals(inputType))
-        {
-            valueListName = fieldMap.get("value-pairs-name");
-            valueList = listMap.get(valueListName);
-        }
-        hint = fieldMap.get("hint");
-        warning = fieldMap.get("required");
-        required = (warning != null && warning.length() > 0);
-        visibility = fieldMap.get("visibility");
-        readOnly = fieldMap.get("readonly");
-        vocabulary = fieldMap.get("vocabulary");
-        String closedVocabularyStr = fieldMap.get("closedVocabulary");
-        closedVocabulary = "true".equalsIgnoreCase(closedVocabularyStr)
-                            || "yes".equalsIgnoreCase(closedVocabularyStr);
-        
-        // parsing of the <type-bind> element (using the colon as split separator)
-        typeBind = new ArrayList<String>();
-        String typeBindDef = fieldMap.get("type-bind");
-        if(typeBindDef != null && typeBindDef.trim().length() > 0) {
-        	String[] types = typeBindDef.split(",");
-        	for(String type : types) {
-        		typeBind.add( type.trim() );
-        	}
-        }
-        
-    }
-
-    /**
-     * Is this DCInput for display in the given scope? The scope should be
-     * either "workflow" or "submit", as per the input forms definition. If the
-     * internal visibility is set to "null" then this will always return true.
-     * 
-     * @param scope
-     *            String identifying the scope that this input's visibility
-     *            should be tested for
-     * 
-     * @return whether the input should be displayed or not
-     */
-    public boolean isVisible(String scope)
-    {
-        return (visibility == null || visibility.equals(scope));
-    }
-    
-    /**
-     * Is this DCInput for display in readonly mode in the given scope? 
-     * If the scope differ from which in visibility field then we use the out attribute
-     * of the visibility element. Possible values are: hidden (default) and readonly.
-     * If the DCInput is visible in the scope then this methods must return false
-     * 
-     * @param scope
-     *            String identifying the scope that this input's readonly visibility
-     *            should be tested for
-     * 
-     * @return whether the input should be displayed in a readonly way or fully hidden
-     */
-    public boolean isReadOnly(String scope)
-    {
-        if (isVisible(scope))
-        {
-            return false;
-        }
-        else
-        {
-            return readOnly != null && readOnly.equalsIgnoreCase("readonly");
-        }
-    }
-
-
-    /**
-     * Get the repeatable flag for this row
-     * 
-     * @return the repeatable flag
-     */
-    public boolean isRepeatable()
-    {
-        return repeatable;
-    }
-
-    /**
-     * Alternate way of calling isRepeatable()
-     * 
-     * @return the repeatable flag
-     */
-    public boolean getRepeatable()
-    {
-        return isRepeatable();
-    }
-
-    /**
-     * Get the input type for this row
-     * 
-     * @return the input type
-     */
-    public String getInputType()
-    {
-        return inputType;
-    }
-
-    /**
-     * Get the DC element for this form row.
-     * 
-     * @return the DC element
-     */
-    public String getElement()
-    {
-        return dcElement;
-    }
-
-    /**
-     * Get the DC namespace prefix for this form row.
-     * 
-     * @return the DC namespace prefix
-     */
-    public String getSchema()
-    {
-        return dcSchema;
-    }
-
-    /**
-     * Get the warning string for a missing required field, formatted for an
-     * HTML table.
-     * 
-     * @return the string prompt if required field was ignored
-     */
-    public String getWarning()
-    {
-        return warning;
-    }
-
-    /**
-     * Is there a required string for this form row?
-     * 
-     * @return true if a required string is set
-     */
-    public boolean isRequired()
-    {
-        return required;
-    }
-
-    /**
-     * Get the DC qualifier for this form row.
-     * 
-     * @return the DC qualifier
-     */
-    public String getQualifier()
-    {
-        return dcQualifier;
-    }
-
-    /**
-     * Get the hint for this form row, formatted for an HTML table
-     * 
-     * @return the hints
-     */
-    public String getHints()
-    {
-        return hint;
-    }
-
-    /**
-     * Get the label for this form row.
-     * 
-     * @return the label
-     */
-    public String getLabel()
-    {
-        return label;
-    }
-
-    /**
-     * Get the name of the pairs type
-     * 
-     * @return the pairs type name
-     */
-    public String getPairsType()
-    {
-        return valueListName;
-    }
-
-    /**
-     * Get the name of the pairs type
-     * 
-     * @return the pairs type name
-     */
-    public List getPairs()
-    {
-        return valueList;
-    }
-
-    /**
-     * Get the name of the controlled vocabulary that is associated with this
-     * field
-     * 
-     * @return the name of associated the vocabulary
-     */
-    public String getVocabulary()
-    {
-        return vocabulary;
-    }
-
-    /**
-     * Set the name of the controlled vocabulary that is associated with this
-     * field
-     * 
-     * @param vocabulary
-     *            the name of the vocabulary
-     */
-    public void setVocabulary(String vocabulary)
-    {
-        this.vocabulary = vocabulary;
-    }
-
-    /**
-     * Gets the display string that corresponds to the passed storage string in
-     * a particular display-storage pair set.
-     * 
-     * @param pairTypeName
-     *            Name of display-storage pair set to search
-     * @param storedString
-     *            the string that gets stored
-     * 
-     * @return the displayed string whose selection causes storageString to be
-     *         stored, null if no match
-     */
-    public String getDisplayString(String pairTypeName, String storedString)
-    {
-        if (valueList != null && storedString != null)
-        {
-            for (int i = 0; i < valueList.size(); i += 2)
-            {
-                if (storedString.equals(valueList.get(i + 1)))
-                {
-                    return valueList.get(i);
-                }
-            }
-        }
-        return null;
-    }
-
-    /**
-     * Gets the stored string that corresponds to the passed display string in a
-     * particular display-storage pair set.
-     * 
-     * @param pairTypeName
-     *            Name of display-storage pair set to search
-     * @param displayedString
-     *            the string that gets displayed
-     * 
-     * @return the string that gets stored when displayString gets selected,
-     *         null if no match
-     */
-    public String getStoredString(String pairTypeName, String displayedString)
-    {
-        if (valueList != null && displayedString != null)
-        {
-            for (int i = 0; i < valueList.size(); i += 2)
-            {
-                if (displayedString.equals(valueList.get(i)))
-                {
-                    return valueList.get(i + 1);
-                }
-            }
-        }
-        return null;
-    }
-
-	/**
-	 * The closed attribute of the vocabulary tag for this field as set in 
-	 * input-forms.xml
-	 * 
-	 * <code> 
-	 * <field>
-	 *     .....
-	 *     <vocabulary closed="true">nsrc</vocabulary>
-	 * </field>
-	 * </code>
-	 * @return the closedVocabulary flags: true if the entry should be restricted 
-	 *         only to vocabulary terms, false otherwise
-	 */
-	public boolean isClosedVocabulary() {
-		return closedVocabulary;
-	}
-
-	/**
-	 * Decides if this field is valid for the document type
-	 * @param typeName Document type name
-	 * @return true when there is no type restriction or typeName is allowed
-	 */
-	public boolean isAllowedFor(String typeName) {
-		if(typeBind.size() == 0)
-			return true;
-		
-		return typeBind.contains(typeName);
-	}
-	
-}

dspace-api/src/main/java/org/dspace/app/util/DCInputSet.java

@@ -1,162 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Class representing all DC inputs required for a submission, organized into pages
- *
- * @author Brian S. Hughes, based on work by Jenny Toves, OCLC
- * @version $Revision$
- */
-
-public class DCInputSet
-{
-	/** name of the input set  */
-	private String formName = null; 
-	/** the inputs ordered by page and row position */
-	private DCInput[][] inputPages = null;
-	
-	/** constructor */
-	public DCInputSet(String formName, List<List<Map<String, String>>> pages, Map<String, List<String>> listMap)
-	{
-		this.formName = formName;
-		inputPages = new DCInput[pages.size()][];
-		for ( int i = 0; i < inputPages.length; i++ )
-		{
-			List<Map<String, String>> page = pages.get(i);
-			inputPages[i] = new DCInput[page.size()];
-			for ( int j = 0; j < inputPages[i].length; j++ )
-			{
-				inputPages[i][j] = new DCInput(page.get(j), listMap);
-			}
-		}
-	}
-	
-	/**
-	 * Return the name of the form that defines this input set
-	 * @return formName 	the name of the form
-	 */
-	public String getFormName()
-	{
-		return formName;
-	}
-	
-	/**
-	 * Return the number of pages in this  input set
-	 * @return number of pages
-	 */
-	public int getNumberPages()
-	{
-		return inputPages.length;
-	}
-	
-    /**
-     * Get all the rows for a page from the form definition
-     *
-     * @param  pageNum	desired page within set
-     * @param  addTitleAlternative flag to add the additional title row
-     * @param  addPublishedBefore  flag to add the additional published info
-     *
-     * @return  an array containing the page's displayable rows
-     */
-	
-	public DCInput[] getPageRows(int pageNum, boolean addTitleAlternative,
-		      					 boolean addPublishedBefore)
-	{
-		List<DCInput> filteredInputs = new ArrayList<DCInput>();
-		if ( pageNum < inputPages.length )
-		{
-			for (int i = 0; i < inputPages[pageNum].length; i++ )
-			{
-				DCInput input = inputPages[pageNum][i];
-				if (doField(input, addTitleAlternative, addPublishedBefore))
-				{
-					filteredInputs.add(input);
-				}
-			}
-		}
-
-		// Convert list into an array
-		DCInput[] inputArray = new DCInput[filteredInputs.size()];
-		return filteredInputs.toArray(inputArray);
-	}
-	
-    /**
-     * Does this set of inputs include an alternate title field?
-     *
-     * @return true if the current set has an alternate title field
-     */
-    public boolean isDefinedMultTitles()
-    {
-    	return isFieldPresent("title.alternative");
-    }
-    
-    /**
-     * Does this set of inputs include the previously published fields?
-     *
-     * @return true if the current set has all the prev. published fields
-     */
-    public boolean isDefinedPubBefore()
-    {
-    	return ( isFieldPresent("date.issued") && 
-    			 isFieldPresent("identifier.citation") &&
-				 isFieldPresent("publisher.null") );
-    }
-    
-    /**
-     * Does the current input set define the named field?
-     * Scan through every field in every page of the input set
-     *
-     * @return true if the current set has the named field
-     */
-    public boolean isFieldPresent(String fieldName)
-    {
-    	for (int i = 0; i < inputPages.length; i++)
-	    {
-    		DCInput[] pageInputs = inputPages[i];
-    		for (int row = 0; row < pageInputs.length; row++)
-    		{
-    			String fullName = pageInputs[row].getElement() + "." + 
-				              	  pageInputs[row].getQualifier();
-    			if (fullName.equals(fieldName))
-    			{
-    				return true;
-    			}
-    		}
-	    }
-    	return false;
-    }
-	
-    private static boolean doField(DCInput dcf, boolean addTitleAlternative, 
-		    					   boolean addPublishedBefore)
-    {
-    	String rowName = dcf.getElement() + "." + dcf.getQualifier();
-    	if ( rowName.equals("title.alternative") && ! addTitleAlternative )
-    	{
-    		return false;
-    	}
-    	if (rowName.equals("date.issued") && ! addPublishedBefore )
-    	{
-    		return false;
-    	}
-    	if (rowName.equals("publisher.null") && ! addPublishedBefore )
-    	{
-    		return false;
-    	}
-    	if (rowName.equals("identifier.citation") && ! addPublishedBefore )
-    	{
-    		return false;
-    	}
-
-    	return true;
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/DCInputsReader.java

@@ -1,688 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.io.File;
-import java.util.*;
-
-import org.xml.sax.SAXException;
-import org.w3c.dom.*;
-import javax.xml.parsers.*;
-
-import org.dspace.content.MetadataSchema;
-import org.dspace.core.ConfigurationManager;
-
-/**
- * Submission form generator for DSpace. Reads and parses the installation
- * form definitions file, input-forms.xml, from the configuration directory.
- * A forms definition details the page and field layout of the metadata
- * collection pages used by the submission process. Each forms definition
- * starts with a unique name that gets associated with that form set.
- *
- * The file also specifies which collections use which form sets. At a
- * minimum, the definitions file must define a default mapping from the
- * placeholder collection #0 to the distinguished form 'default'. Any
- * collections that use a custom form set are listed paired with the name
- * of the form set they use.
- *
- * The definitions file also may contain sets of value pairs. Each value pair
- * will contain one string that the user reads, and a paired string that will
- * supply the value stored in the database if its sibling display value gets
- * selected from a choice list.
- *
- * @author  Brian S. Hughes
- * @version $Revision$
- */
-
-public class DCInputsReader
-{
-    /**
-     * The ID of the default collection. Will never be the ID of a named
-     * collection
-     */
-    public static final String DEFAULT_COLLECTION = "default";
-
-    /** Name of the form definition XML file  */
-    static final String FORM_DEF_FILE = "input-forms.xml";
-
-    /** Keyname for storing dropdown value-pair set name */
-    static final String PAIR_TYPE_NAME = "value-pairs-name";
-
-    /** The fully qualified pathname of the form definition XML file */
-    private String defsFile = ConfigurationManager.getProperty("dspace.dir")
-            + File.separator + "config" + File.separator + FORM_DEF_FILE;
-
-    /**
-     * Reference to the collections to forms map, computed from the forms
-     * definition file
-     */
-    private Map<String, String> whichForms = null;
-
-    /**
-     * Reference to the forms definitions map, computed from the forms
-     * definition file
-     */
-    private Map<String, List<List<Map<String, String>>>> formDefns  = null;
-
-    /**
-     * Reference to the value-pairs map, computed from the forms definition file
-     */
-    private Map<String, List<String>> valuePairs = null;    // Holds display/storage pairs
-    
-    /**
-     * Mini-cache of last DCInputSet requested. If submissions are not typically
-     * form-interleaved, there will be a modest win.
-     */
-    private DCInputSet lastInputSet = null;
-
-    /**
-     * Parse an XML encoded submission forms template file, and create a hashmap
-     * containing all the form information. This hashmap will contain three top
-     * level structures: a map between collections and forms, the definition for
-     * each page of each form, and lists of pairs of values that populate
-     * selection boxes.
-     */
-
-    public DCInputsReader()
-         throws DCInputsReaderException
-    {
-        buildInputs(defsFile);
-    }
-
-
-    public DCInputsReader(String fileName)
-         throws DCInputsReaderException
-    {
-        buildInputs(fileName);
-    }
-
-
-    private void buildInputs(String fileName)
-         throws DCInputsReaderException
-    {
-        whichForms = new HashMap<String, String>();
-        formDefns  = new HashMap<String, List<List<Map<String, String>>>>();
-        valuePairs = new HashMap<String, List<String>>();
-
-        String uri = "file:" + new File(fileName).getAbsolutePath();
-
-        try
-        {
-                DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
-                factory.setValidating(false);
-                factory.setIgnoringComments(true);
-                factory.setIgnoringElementContentWhitespace(true);
-                
-                DocumentBuilder db = factory.newDocumentBuilder();
-                Document doc = db.parse(uri);
-                doNodes(doc);
-                checkValues();
-        }
-        catch (FactoryConfigurationError fe)
-        {
-                throw new DCInputsReaderException("Cannot create Submission form parser",fe);
-        }
-        catch (Exception e)
-        {
-                throw new DCInputsReaderException("Error creating submission forms: "+e);
-        }
-    }
-   
-    public Iterator<String> getPairsNameIterator()
-    {
-        return valuePairs.keySet().iterator();
-    }
-
-    public List<String> getPairs(String name)
-    {
-        return valuePairs.get(name);
-    }
-
-    /**
-     * Returns the set of DC inputs used for a particular collection, or the
-     * default set if no inputs defined for the collection
-     *
-     * @param collectionHandle
-     *            collection's unique Handle
-     * @return DC input set
-     * @throws DCInputsReaderException
-     *             if no default set defined
-     */
-    public DCInputSet getInputs(String collectionHandle)
-                throws DCInputsReaderException
-    {
-        String formName = whichForms.get(collectionHandle);
-        if (formName == null)
-        {
-                formName = whichForms.get(DEFAULT_COLLECTION);
-        }
-        if (formName == null)
-        {
-                throw new DCInputsReaderException("No form designated as default");
-        }
-        // check mini-cache, and return if match
-        if ( lastInputSet != null && lastInputSet.getFormName().equals( formName ) )
-        {
-                return lastInputSet;
-        }
-        // cache miss - construct new DCInputSet
-        List<List<Map<String, String>>> pages = formDefns.get(formName);
-        if ( pages == null )
-        {
-                throw new DCInputsReaderException("Missing the " + formName  + " form");
-        }
-        lastInputSet = new DCInputSet(formName, pages, valuePairs);
-        return lastInputSet;
-    }
-    
-    /**
-     * Return the number of pages the inputs span for a desginated collection
-     * @param  collectionHandle   collection's unique Handle
-     * @return number of pages of input
-     * @throws DCInputsReaderException if no default set defined
-     */
-    public int getNumberInputPages(String collectionHandle)
-        throws DCInputsReaderException
-    {
-        return getInputs(collectionHandle).getNumberPages();
-    }
-    
-    /**
-     * Process the top level child nodes in the passed top-level node. These
-     * should correspond to the collection-form maps, the form definitions, and
-     * the display/storage word pairs.
-     */
-    private void doNodes(Node n)
-                throws SAXException, DCInputsReaderException
-    {
-        if (n == null)
-        {
-                return;
-        }
-        Node e = getElement(n);
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        boolean foundMap  = false;
-        boolean foundDefs = false;
-        for (int i = 0; i < len; i++)
-        {
-                Node nd = nl.item(i);
-                if ((nd == null) || isEmptyTextNode(nd))
-                {
-                        continue;
-                }
-                String tagName = nd.getNodeName();
-                if (tagName.equals("form-map"))
-                {
-                        processMap(nd);
-                        foundMap = true;
-                }
-                else if (tagName.equals("form-definitions"))
-                {
-                        processDefinition(nd);
-                        foundDefs = true;
-                }
-                else if (tagName.equals("form-value-pairs"))
-                {
-                        processValuePairs(nd);
-                }
-                // Ignore unknown nodes
-        }
-        if (!foundMap)
-        {
-                throw new DCInputsReaderException("No collection to form map found");
-        }
-        if (!foundDefs)
-        {
-                throw new DCInputsReaderException("No form definition found");
-        }
-    }
-
-    /**
-     * Process the form-map section of the XML file.
-     * Each element looks like:
-     *   <name-map collection-handle="hdl" form-name="name" />
-     * Extract the collection handle and form name, put name in hashmap keyed
-     * by the collection handle.
-     */
-    private void processMap(Node e)
-        throws SAXException
-    {
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-                Node nd = nl.item(i);
-                if (nd.getNodeName().equals("name-map"))
-                {
-                        String id = getAttribute(nd, "collection-handle");
-                        String value = getAttribute(nd, "form-name");
-                        String content = getValue(nd);
-                        if (id == null)
-                        {
-                                throw new SAXException("name-map element is missing collection-handle attribute");
-                        }
-                        if (value == null)
-                        {
-                                throw new SAXException("name-map element is missing form-name attribute");
-                        }
-                        if (content != null && content.length() > 0)
-                        {
-                                throw new SAXException("name-map element has content, it should be empty.");
-                        }
-                        whichForms.put(id, value);
-                }  // ignore any child node that isn't a "name-map"
-        }
-    }
-
-    /**
-     * Process the form-definitions section of the XML file. Each element is
-     * formed thusly: <form name="formname">...pages...</form> Each pages
-     * subsection is formed: <page number="#"> ...fields... </page> Each field
-     * is formed from: dc-element, dc-qualifier, label, hint, input-type name,
-     * required text, and repeatable flag.
-     */
-    private void processDefinition(Node e)
-        throws SAXException, DCInputsReaderException
-    {
-        int numForms = 0;
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-                Node nd = nl.item(i);
-                // process each form definition
-                if (nd.getNodeName().equals("form"))
-                {
-                        numForms++;
-                        String formName = getAttribute(nd, "name");
-                        if (formName == null)
-                        {
-                                throw new SAXException("form element has no name attribute");
-                        }
-                        List<List<Map<String, String>>> pages = new ArrayList<List<Map<String, String>>>(); // the form contains pages
-                        formDefns.put(formName, pages);
-                        NodeList pl = nd.getChildNodes();
-                        int lenpg = pl.getLength();
-                        for (int j = 0; j < lenpg; j++)
-                        {
-                                Node npg = pl.item(j);
-                                // process each page definition
-                                if (npg.getNodeName().equals("page"))
-                                {
-                                        String pgNum = getAttribute(npg, "number");
-                                        if (pgNum == null)
-                                        {
-                                                throw new SAXException("Form " + formName + " has no identified pages");
-                                        }
-                                        List<Map<String, String>> page = new ArrayList<Map<String, String>>();
-                                        pages.add(page);
-                                        NodeList flds = npg.getChildNodes();
-                                        int lenflds = flds.getLength();
-                                        for (int k = 0; k < lenflds; k++)
-                                        {
-                                                Node nfld = flds.item(k);
-                                                if ( nfld.getNodeName().equals("field") )
-                                                {
-                                                        // process each field definition
-                                                        Map<String, String> field = new HashMap<String, String>();
-                                                        page.add(field);
-                                                        processPageParts(formName, pgNum, nfld, field);
-
-                                                        // we omit the duplicate validation, allowing multiple fields definition for 
-                                                        // the same metadata and different visibility/type-bind
-
-                                                }
-                                        }
-                                } // ignore any child that is not a 'page'
-                        }
-                        // sanity check number of pages
-                        if (pages.size() < 1)
-                        {
-                                throw new DCInputsReaderException("Form " + formName + " has no pages");
-                        }
-                }
-        }
-        if (numForms == 0)
-        {
-                throw new DCInputsReaderException("No form definition found");
-        }
-    }
-
-    /**
-     * Process parts of a field
-     * At the end, make sure that input-types 'qualdrop_value' and
-     * 'twobox' are marked repeatable. Complain if dc-element, label,
-     * or input-type are missing.
-     */
-    private void processPageParts(String formName, String page, Node n, Map<String, String> field)
-        throws SAXException
-    {
-        NodeList nl = n.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-                Node nd = nl.item(i);
-                if ( ! isEmptyTextNode(nd) )
-                {
-                        String tagName = nd.getNodeName();
-                        String value   = getValue(nd);
-                        field.put(tagName, value);
-                        if (tagName.equals("input-type"))
-                        {
-                    if (value.equals("dropdown")
-                            || value.equals("qualdrop_value")
-                            || value.equals("list"))
-                                {
-                                        String pairTypeName = getAttribute(nd, PAIR_TYPE_NAME);
-                                        if (pairTypeName == null)
-                                        {
-                                                throw new SAXException("Form " + formName + ", field " +
-                                                                                                field.get("dc-element") +
-                                                                                                        "." + field.get("dc-qualifier") +
-                                                                                                " has no name attribute");
-                                        }
-                                        else
-                                        {
-                                                field.put(PAIR_TYPE_NAME, pairTypeName);
-                                        }
-                                }
-                        }
-                        else if (tagName.equals("vocabulary"))
-                        {
-                                String closedVocabularyString = getAttribute(nd, "closed");
-                            field.put("closedVocabulary", closedVocabularyString);
-                        }
-                }
-        }
-        String missing = null;
-        if (field.get("dc-element") == null)
-        {
-                missing = "dc-element";
-        }
-        if (field.get("label") == null)
-        {
-                missing = "label";
-        }
-        if (field.get("input-type") == null)
-        {
-                missing = "input-type";
-        }
-        if ( missing != null )
-        {
-                String msg = "Required field " + missing + " missing on page " + page + " of form " + formName;
-                throw new SAXException(msg);
-        }
-        String type = field.get("input-type");
-        if (type.equals("twobox") || type.equals("qualdrop_value"))
-        {
-                String rpt = field.get("repeatable");
-                if ((rpt == null) ||
-                                ((!rpt.equalsIgnoreCase("yes")) &&
-                                                (!rpt.equalsIgnoreCase("true"))))
-                {
-                        String msg = "The field \'"+field.get("label")+"\' must be repeatable";
-                        throw new SAXException(msg);
-                }
-        }
-    }
-
-    /**
-     * Check that this is the only field with the name dc-element.dc-qualifier
-     * If there is a duplicate, return an error message, else return null;
-     */
-    private String checkForDups(String formName, Map<String, String> field, List<List<Map<String, String>>> pages)
-    {
-        int matches = 0;
-        String err = null;
-        String schema = field.get("dc-schema");
-        String elem = field.get("dc-element");
-        String qual = field.get("dc-qualifier");
-        if ((schema == null) || (schema.equals("")))
-        {
-            schema = MetadataSchema.DC_SCHEMA;
-        }
-        String schemaTest;
-        
-        for (int i = 0; i < pages.size(); i++)
-        {
-            List<Map<String, String>> pg = pages.get(i);
-            for (int j = 0; j < pg.size(); j++)
-            {
-                Map<String, String> fld = pg.get(j);
-                if ((fld.get("dc-schema") == null) ||
-                    ((fld.get("dc-schema")).equals("")))
-                {
-                    schemaTest = MetadataSchema.DC_SCHEMA;
-                }
-                else
-                {
-                    schemaTest = fld.get("dc-schema");
-                }
-                
-                // Are the schema and element the same? If so, check the qualifier
-                if (((fld.get("dc-element")).equals(elem)) &&
-                    (schemaTest.equals(schema)))
-                {
-                    String ql = fld.get("dc-qualifier");
-                    if (qual != null)
-                    {
-                        if ((ql != null) && ql.equals(qual))
-                        {
-                            matches++;
-                        }
-                    }
-                    else if (ql == null)
-                    {
-                        matches++;
-                    }
-                }
-            }
-        }
-        if (matches > 1)
-        {
-            err = "Duplicate field " + schema + "." + elem + "." + qual + " detected in form " + formName;
-        }
-        
-        return err;
-    }
-
-
-    /**
-     * Process the form-value-pairs section of the XML file.
-     *  Each element is formed thusly:
-     *      <value-pairs name="..." dc-term="...">
-     *          <pair>
-     *            <display>displayed name-</display>
-     *            <storage>stored name</storage>
-     *          </pair>
-     * For each value-pairs element, create a new vector, and extract all
-     * the pairs contained within it. Put the display and storage values,
-     * respectively, in the next slots in the vector. Store the vector
-     * in the passed in hashmap.
-     */
-    private void processValuePairs(Node e)
-                throws SAXException
-    {
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-                Node nd = nl.item(i);
-                    String tagName = nd.getNodeName();
-
-                    // process each value-pairs set
-                    if (tagName.equals("value-pairs"))
-                    {
-                        String pairsName = getAttribute(nd, PAIR_TYPE_NAME);
-                        String dcTerm = getAttribute(nd, "dc-term");
-                        if (pairsName == null)
-                        {
-                                String errString =
-                                        "Missing name attribute for value-pairs for DC term " + dcTerm;
-                                throw new SAXException(errString);
-
-                        }
-                        List<String> pairs = new ArrayList<String>();
-                        valuePairs.put(pairsName, pairs);
-                        NodeList cl = nd.getChildNodes();
-                        int lench = cl.getLength();
-                        for (int j = 0; j < lench; j++)
-                        {
-                                Node nch = cl.item(j);
-                                String display = null;
-                                String storage = null;
-
-                                if (nch.getNodeName().equals("pair"))
-                                {
-                                        NodeList pl = nch.getChildNodes();
-                                        int plen = pl.getLength();
-                                        for (int k = 0; k < plen; k++)
-                                        {
-                                                Node vn= pl.item(k);
-                                                String vName = vn.getNodeName();
-                                                if (vName.equals("displayed-value"))
-                                                {
-                                                        display = getValue(vn);
-                                                }
-                                                else if (vName.equals("stored-value"))
-                                                {
-                                                        storage = getValue(vn);
-                                                        if (storage == null)
-                                                        {
-                                                                storage = "";
-                                                        }
-                                                } // ignore any children that aren't 'display' or 'storage'
-                                        }
-                                        pairs.add(display);
-                                        pairs.add(storage);
-                                } // ignore any children that aren't a 'pair'
-                        }
-                    } // ignore any children that aren't a 'value-pair'
-        }
-    }
-
-
-    /**
-     * Check that all referenced value-pairs are present
-     * and field is consistent
-     *
-     * Throws DCInputsReaderException if detects a missing value-pair.
-     */
-
-    private void checkValues()
-                throws DCInputsReaderException
-    {
-        // Step through every field of every page of every form
-        Iterator<String> ki = formDefns.keySet().iterator();
-        while (ki.hasNext())
-        {
-                String idName = ki.next();
-                List<List<Map<String, String>>> pages = formDefns.get(idName);
-                for (int i = 0; i < pages.size(); i++)
-                {
-                        List<Map<String, String>> page = pages.get(i);
-                        for (int j = 0; j < page.size(); j++)
-                        {
-                                Map<String, String> fld = page.get(j);
-                                // verify reference in certain input types
-                                String type = fld.get("input-type");
-                    if (type.equals("dropdown")
-                            || type.equals("qualdrop_value")
-                            || type.equals("list"))
-                                {
-                                        String pairsName = fld.get(PAIR_TYPE_NAME);
-                                        List<String> v = valuePairs.get(pairsName);
-                                        if (v == null)
-                                        {
-                                                String errString = "Cannot find value pairs for " + pairsName;
-                                                throw new DCInputsReaderException(errString);
-                                        }
-                                }
-                    
-                    			// we omit the "required" and "visibility" validation, provided this must be checked in the processing class
-                    			// only when it makes sense (if the field isn't visible means that it is not applicable, therefore it can't be required)
-
-                        }
-                }
-        }
-    }
-    
-    private Node getElement(Node nd)
-    {
-        NodeList nl = nd.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node n = nl.item(i);
-            if (n.getNodeType() == Node.ELEMENT_NODE)
-            {
-                return n;
-            }
-        }
-        return null;
-     }
-
-    private boolean isEmptyTextNode(Node nd)
-    {
-        boolean isEmpty = false;
-        if (nd.getNodeType() == Node.TEXT_NODE)
-        {
-                String text = nd.getNodeValue().trim();
-                if (text.length() == 0)
-                {
-                        isEmpty = true;
-                }
-        }
-        return isEmpty;
-    }
-
-    /**
-     * Returns the value of the node's attribute named <name>
-     */
-    private String getAttribute(Node e, String name)
-    {
-        NamedNodeMap attrs = e.getAttributes();
-        int len = attrs.getLength();
-        if (len > 0)
-        {
-                int i;
-                for (i = 0; i < len; i++)
-                {
-                        Node attr = attrs.item(i);
-                        if (name.equals(attr.getNodeName()))
-                        {
-                                return attr.getNodeValue().trim();
-                        }
-                }
-        }
-        //no such attribute
-        return null;
-    }
-
-    /**
-     * Returns the value found in the Text node (if any) in the
-     * node list that's passed in.
-     */
-    private String getValue(Node nd)
-    {
-        NodeList nl = nd.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-                Node n = nl.item(i);
-                short type = n.getNodeType();
-                if (type == Node.TEXT_NODE)
-                {
-                        return n.getNodeValue().trim();
-                }
-        }
-        // Didn't find a text node
-        return null;
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/DCInputsReaderException.java

@@ -1,56 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-/**
- * This is a superclass for exceptions representing a failure when
- * importing or exporting a package.  E.g., unacceptable package format
- * or contents.  Implementations should throw one of the more specific
- * exceptions. This class is intended for declarations and catch clauses.
- *
- * @author Larry Stone
- * @version $Revision: 3761 $
- */
-public class DCInputsReaderException extends Exception
-{
-    /**
-     * No-args constructor.
-     */
-    public DCInputsReaderException()
-    {
-        super();
-    }
-
-    /**
-     * Constructor for a given message.
-     * @param message diagnostic message.
-     */
-    public DCInputsReaderException(String message)
-    {
-        super(message);
-    }
-
-    /**
-     * Constructor for a given cause.
-     * @param cause throwable that caused this exception
-     */
-    public DCInputsReaderException(Throwable cause)
-    {
-        super(cause);
-    }
-
-    /**
-     * Constructor to create a new exception wrapping it around another exception.
-     * @param message diagnostic message.
-     * @param cause throwable that caused this exception
-     */
-    public DCInputsReaderException(String message, Throwable cause)
-    {
-        super(message, cause);
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/DSpaceContextListener.java

@@ -1,153 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import org.dspace.core.ConfigurationManager;
-import org.dspace.storage.rdbms.DatabaseManager;
-import org.apache.log4j.Logger;
-
-import javax.servlet.ServletContextListener;
-import javax.servlet.ServletContextEvent;
-
-import java.beans.Introspector;
-import java.net.URL;
-import java.net.URLConnection;
-import java.sql.Driver;
-import java.sql.DriverManager;
-import java.util.Enumeration;
-
-/**
- * Class to initialize / cleanup resources used by DSpace when the web application
- * is started or stopped
- */
-public class DSpaceContextListener implements ServletContextListener
-{
-    private static Logger log = Logger.getLogger(DSpaceContextListener.class);
-
-    /**
-     * The DSpace config parameter, this is where the path to the DSpace
-     * configuration file can be obtained
-     */
-    public static final String DSPACE_CONFIG_PARAMETER = "dspace-config";
-    
-    /**
-     * Initialize any resources required by the application
-     * @param event
-     */
-    public void contextInitialized(ServletContextEvent event)
-    {
-
-        // On Windows, URL caches can cause problems, particularly with undeployment
-        // So, here we attempt to disable them if we detect that we are running on Windows
-        try
-        {
-            String osName = System.getProperty("os.name");
-
-            if (osName != null && osName.toLowerCase().contains("windows"))
-            {
-                URL url = new URL("http://localhost/");
-                URLConnection urlConn = url.openConnection();
-                urlConn.setDefaultUseCaches(false);
-            }
-        }
-        // Any errors thrown in disabling the caches aren't significant to
-        // the normal execution of the application, so we ignore them
-        catch (RuntimeException e)
-        {
-            log.error(e.getMessage(), e);
-        }
-        catch (Exception e)
-        {
-            log.error(e.getMessage(), e);
-        }
-
-        // Paths to the various config files
-        String dspaceConfig = null;
-        
-        /**
-         * Stage 1
-         * 
-         * Locate the dspace config
-         */
-        
-        // first check the local per webapp parameter, then check the global parameter.
-        dspaceConfig = event.getServletContext().getInitParameter(DSPACE_CONFIG_PARAMETER);
-        
-        // Finally, if no config parameter found throw an error
-        if (dspaceConfig == null || "".equals(dspaceConfig))
-        {
-            throw new IllegalStateException(
-                    "\n\nDSpace has failed to initialize. This has occurred because it was unable to determine \n" +
-                    "where the dspace.cfg file is located. The path to the configuration file should be stored \n" +
-                    "in a context variable, '"+DSPACE_CONFIG_PARAMETER+"', in the global context. \n" +
-                    "No context variable was found in either location.\n\n");
-        }
-            
-        /**
-         * Stage 2
-         * 
-         * Load the dspace config. Also may load log4j configuration.
-         * (Please rely on ConfigurationManager or Log4j to configure logging)
-         * 
-         */
-        try 
-        {
-            ConfigurationManager.loadConfig(dspaceConfig);
-        }
-        catch (RuntimeException e)
-        {
-            throw e;
-        }
-        catch (Exception e)
-        {
-            throw new IllegalStateException(
-                    "\n\nDSpace has failed to initialize, during stage 2. Error while attempting to read the \n" +
-                    "DSpace configuration file (Path: '"+dspaceConfig+"'). \n" +
-                    "This has likely occurred because either the file does not exist, or it's permissions \n" +
-                    "are set incorrectly, or the path to the configuration file is incorrect. The path to \n" +
-                    "the DSpace configuration file is stored in a context variable, 'dspace-config', in \n" +
-                    "either the local servlet or global context.\n\n",e);
-        }
-
-    }
-
-    /**
-     * Clean up resources used by the application when stopped
-     * 
-     * @param event
-     */
-    public void contextDestroyed(ServletContextEvent event)
-    {
-        try
-        {
-            // Remove the database pool
-            DatabaseManager.shutdown();
-
-            // Clean out the introspector
-            Introspector.flushCaches();
-
-            // Remove any drivers registered by this classloader
-            for (Enumeration e = DriverManager.getDrivers(); e.hasMoreElements();)
-            {
-                Driver driver = (Driver) e.nextElement();
-                if (driver.getClass().getClassLoader() == getClass().getClassLoader())
-                {
-                    DriverManager.deregisterDriver(driver);
-                }
-            }
-        }
-        catch (RuntimeException e)
-        {
-            log.error("Failed to cleanup ClassLoader for webapp", e);
-        }
-        catch (Exception e)
-        {
-            log.error("Failed to cleanup ClassLoader for webapp", e);
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/DailyFileAppender.java

@@ -1,348 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-
-import java.io.File;
-import java.io.IOException;
-import java.net.UnknownHostException;
-import java.text.SimpleDateFormat;
-import java.util.Calendar;
-import java.util.Date;
-
-import org.apache.commons.lang.time.DateUtils;
-import org.apache.log4j.FileAppender;
-import org.apache.log4j.helpers.LogLog;
-import org.apache.log4j.spi.LoggingEvent;
-
-/**
- * Special log appender for log4j. Adds the current date (ie. year-mon) to
- * the end of the file name, so that rolling on to the next log is simply
- * a case of starting a new one - no renaming of old logs.
- *
- * This is advisable if you are using Windows, and have multiple applications
- * (ie. dspace, dspace-oai, dspace-sword) that all want to write to the same log file,
- * as each would otherwise try to rename the old files during rollover.
- *
- * An example log4j.properties (one log per month, retains three months of logs)
- *
- * log4j.rootCategory=INFO, A1
- * log4j.appender.A1=org.dspace.app.util.DailyFileAppender
- * log4j.appender.A1.File=@@log.dir@@/dspace.log
- * log4j.appender.A1.DatePattern=yyyy-MM
- * log4j.appender.A1.MaxLogs=3
- * log4j.appender.A1.layout=org.apache.log4j.PatternLayout
- * log4j.appender.A1.layout.ConversionPattern=%d %-5p %c @ %m%n
- *
- */
-public class DailyFileAppender extends FileAppender
-{
-    /**
-     * The fixed date pattern to be used if one is not specified.
-     */
-    private static final String DATE_PATTERN = "yyyy-MM-dd";
-
-    /**
-     * The folder under which daily folders are created. This can be a absolute path
-     * or relative path also.
-     * e.g. JavaLogs/CPRILog or F:/LogFiles/CPRILog
-     */
-    private String mstrFileName;
-
-    /**
-     * Used internally and contains the name of the date derived from current system date.
-     */
-    private Date   mstrDate = new Date(System.currentTimeMillis());
-
-    /**
-     * Holds the user specified DatePattern,
-     */
-    private String mstrDatePattern = DATE_PATTERN;
-
-    private boolean mMonthOnly = false;
-
-    /**
-     * The date formatter object used for parsing the user specified DatePattern.
-     */
-    private SimpleDateFormat mobjSDF;
-
-    private boolean mWithHostName = false;
-
-    private int mMaxLogs = 0;
-
-    /**
-     * Default constructor. This is required as the appender class is dynamically
-     * loaded.
-     */
-    public DailyFileAppender()
-    {
-        super();
-    }
-
-    /* (non-Javadoc)
-     * @see org.apache.log4j.FileAppender#activateOptions()
-     */
-    public void activateOptions()
-    {
-        setFileName();
-        cleanupOldFiles();
-        super.activateOptions();
-    }
-
-/*------------------------------------------------------------------------------
- * Getters
- *----------------------------------------------------------------------------*/
-    public String getDatePattern()
-    {
-        return this.mstrDatePattern;
-    }
-
-    public String getFile()
-    {
-        return this.mstrFileName;
-    }
-
-    public boolean getWithHost()
-    {
-        return mWithHostName;
-    }
-
-    public int getMaxLogs()
-    {
-    	return mMaxLogs;
-    }
-
-/*------------------------------------------------------------------------------
- * Setters
- *----------------------------------------------------------------------------*/
-    public void setDatePattern(String pstrPattern)
-    {
-        this.mstrDatePattern = checkPattern(pstrPattern);
-        if (mstrDatePattern.contains("dd") || mstrDatePattern.contains("DD"))
-        {
-            mMonthOnly = false;
-        }
-        else
-        {
-            mMonthOnly = true;
-        }
-    }
-
-    public void setFile(String file)
-    {
-        // Trim spaces from both ends. The users probably does not want
-        // trailing spaces in file names.
-        String val = file.trim();
-        mstrFileName = val;
-     }
-
-    public void setWithHost(boolean wh)
-    {
-        mWithHostName = wh;
-    }
-
-    public void setMaxLogs(int ml)
-    {
-    	mMaxLogs = ml;
-    }
-
-/*------------------------------------------------------------------------------
- * Methods
- *----------------------------------------------------------------------------*/
-    /* (non-Javadoc)
-     * @see org.apache.log4j.WriterAppender#subAppend(org.apache.log4j.spi.LoggingEvent)
-     */
-    protected void subAppend(LoggingEvent pobjEvent)
-    {
-        Date   dtNow = new Date(System.currentTimeMillis());
-
-        boolean rollover = false;
-
-        if (mMonthOnly)
-        {
-            Calendar now = Calendar.getInstance();
-            Calendar cur = Calendar.getInstance();
-            now.setTime(dtNow);
-            cur.setTime(mstrDate);
-            rollover = !(now.get(Calendar.YEAR) == cur.get(Calendar.YEAR) && now.get(Calendar.MONTH) == cur.get(Calendar.MONTH));
-        }
-        else
-        {
-            rollover = !(DateUtils.isSameDay(dtNow, mstrDate));
-        }
-
-        if (rollover)
-        {
-            try
-            {
-                rollOver(dtNow);
-            }
-            catch (IOException IOEx)
-            {
-                LogLog.error("rollOver() failed!", IOEx);
-            }
-        }
-
-        super.subAppend(pobjEvent);
-    }
-
-/*------------------------------------------------------------------------------
- * Helpers
- *----------------------------------------------------------------------------*/
-    /**
-     * The helper function to validate the DatePattern.
-     * @param pstrPattern The DatePattern to be validated.
-     * @return The validated date pattern or defautlt DATE_PATTERN
-     */
-    private String checkPattern(String pstrPattern)
-    {
-        String strRet = null;
-        SimpleDateFormat objFmt = new SimpleDateFormat(DATE_PATTERN);
-
-        try
-        {
-            this.mobjSDF = new SimpleDateFormat(pstrPattern);
-            strRet = pstrPattern;
-        }
-        catch (NullPointerException NPExIgnore)
-        {
-            LogLog.error("Invalid DatePattern " + pstrPattern, NPExIgnore);
-            this.mobjSDF = objFmt;
-            strRet = DATE_PATTERN;
-        }
-        catch (IllegalArgumentException IlArgExIgnore)
-        {
-            LogLog.error("Invalid DatePattern " + pstrPattern, IlArgExIgnore);
-            this.mobjSDF = objFmt;
-            strRet = DATE_PATTERN;
-        }
-        finally
-        {
-            objFmt = null;
-        }
-        return strRet;
-    }
-
-    /**
-     * This function is responsible for performing the actual file rollover.
-     * @param pstrName The name of the new folder based on current system date.
-     * @throws IOException
-     */
-    private static boolean deletingFiles = false;
-    private void cleanupOldFiles()
-    {
-        // If we need to delete log files
-        if (mMaxLogs > 0 && !deletingFiles)
-        {
-			deletingFiles = true;
-
-			// Determine the final file extension with the hostname
-    		String hostFileExt = null;
-            try
-            {
-                hostFileExt = "." + java.net.InetAddress.getLocalHost().getHostName();
-            }
-            catch (UnknownHostException e)
-            {
-                LogLog.error("Unable to retrieve host name");
-            }
-
-			try
-			{
-				// Array to hold the logs we are going to keep
-				File[] logsToKeep = new File[mMaxLogs];
-
-				// Get a 'master' file handle, and the parent directory from it
-		        File logMaster = new File(mstrFileName);
-		        File logDir = logMaster.getParentFile();
-		        if (logDir.isDirectory())
-		        {
-		        	// Iterate all the files in that directory
-		        	File[] logArr = logDir.listFiles();
-		        	for (File curLog : logArr)
-		        	{
-        				LogLog.debug("Comparing '" + curLog.getAbsolutePath() + "' to '" + mstrFileName + "'");
-		        		String name = curLog.getAbsolutePath();
-
-		        		// First, see if we are not using hostname, or the log file ends with this host
-		                if (!mWithHostName || (hostFileExt != null && name.endsWith(hostFileExt)))
-		                {
-		                	// Check that the file is indeed one we want (contains the master file name)
-			        		if (name.contains(mstrFileName))
-			        		{
-			        			// Iterate through the array of logs we are keeping
-			        			for (int i = 0; curLog != null && i < logsToKeep.length; i++)
-			        			{
-			        				// Have we exhausted the 'to keep' array?
-			        				if (logsToKeep[i] == null)
-			        				{
-				        				// Empty space, retain this log file
-			        					logsToKeep[i] = curLog;
-			        					curLog = null;
-			        				}
-			        				// If the 'kept' file is older than the current one
-			        				else if (logsToKeep[i].getName().compareTo(curLog.getName()) < 0)
-			        				{
-			        					// Replace tested entry with current file
-			        					File temp = logsToKeep[i];
-			        					logsToKeep[i] = curLog;
-			        					curLog = temp;
-			        				}
-			        			}
-
-			        			// If we have a 'current' entry at this point, it's a log we don't want
-			        			if (curLog != null)
-			        			{
-			        				LogLog.debug("Deleting log " + curLog.getName());
-		        					if (curLog.delete())
-                                    {
-                                        LogLog.error("Unable to delete log file");
-                                    }
-			        			}
-			        		}
-		                }
-		        	}
-		        }
-			}
-			catch (Exception e)
-			{
-				// Don't worry about exceptions
-			}
-			finally
-			{
-				deletingFiles = false;
-			}
-        }
-    }
-
-    private void rollOver(Date dtNow) throws IOException
-    {
-        mstrDate = dtNow;
-        setFileName();
-        this.setFile(fileName, true, bufferedIO, bufferSize);
-
-        cleanupOldFiles();
-    }
-
-    private void setFileName()
-    {
-        fileName = mstrFileName + "." + mobjSDF.format(mstrDate);
-
-        if (mWithHostName)
-        {
-            try
-            {
-                fileName += "." + java.net.InetAddress.getLocalHost().getHostName();
-            }
-            catch (UnknownHostException e)
-            {
-                LogLog.error("Unable to retrieve host name");
-            }
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/MetadataExposure.java

@@ -1,158 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.Map;
-import java.util.Set;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Enumeration;
-import java.sql.SQLException;
-
-import org.apache.log4j.Logger;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.core.ConfigurationManager;
-import org.dspace.core.Context;
-
-/**
- * Static utility class to manage configuration for exposure (hiding) of
- * certain Item metadata fields.
- *
- * This class answers the question, "is the user allowed to see this
- * metadata field?"  Any external interface (UI, OAI-PMH, etc) that
- * disseminates metadata should consult it before disseminating the value
- * of a metadata field.
- *
- * Since the MetadataExposure.isHidden() method gets called in a lot of inner
- * loops, it is important to implement it efficiently, in both time and
- * memory utilization.  It computes an answer without consuming ANY memory
- * (e.g. it does not build any temporary Strings) and in close to constant
- * time by use of hash tables.  Although most sites will only hide a few
- * fields, we can't predict what the usage will be so it's better to make it
- * scalable.
- *
- * Algorithm is as follows:
- *  1. If a Context is provided and it has a user who is Administrator,
- *     always grant access (return false).
- *  2. Return true if field is on the hidden list, false otherwise.
- *
- * The internal maps are populated from DSpace Configuration at the first
- * call, in case the properties are not available in the static context.
- *
- * Configuration Properties:
- *  ## hide a single metadata field
- *  #metadata.hide.SCHEMA.ELEMENT[.QUALIFIER] = true
- *  # example: dc.type
- *  metadata.hide.dc.type = true
- *  # example: dc.description.provenance
- *  metadata.hide.dc.description.provenance = true
- *
- * @author Larry Stone
- * @version $Revision: 3734 $
- */
-public class MetadataExposure
-{
-    private static Logger log = Logger.getLogger(MetadataExposure.class);
-
-    private static Map<String,Set<String>> hiddenElementSets = null;
-    private static Map<String,Map<String,Set<String>>> hiddenElementMaps = null;
-
-    private static final String CONFIG_PREFIX = "metadata.hide.";
-
-    public static boolean isHidden(Context context, String schema, String element, String qualifier)
-        throws SQLException
-    {
-        // the administrator's override
-        if (context != null && AuthorizeManager.isAdmin(context))
-        {
-            return false;
-        }
-
-        // for schema.element, just check schema->elementSet
-        if (!isInitialized())
-        {
-            init();
-        }
-
-        if (qualifier == null)
-        {
-            Set<String> elts = hiddenElementSets.get(schema);
-            return elts == null ? false : elts.contains(element);
-        }
-
-        // for schema.element.qualifier, just schema->eltMap->qualSet
-        else
-        {
-            Map<String,Set<String>> elts = hiddenElementMaps.get(schema);
-            if (elts == null)
-            {
-                return false;
-            }
-            Set<String> quals = elts.get(element);
-            return quals == null ? false : quals.contains(qualifier);
-        }
-    }
-
-    private static boolean isInitialized()
-    {
-        return hiddenElementSets != null;
-    }
-
-    // load maps from configuration unless it's already done.
-    private static synchronized void init()
-    {
-        if (!isInitialized())
-        {
-            hiddenElementSets = new HashMap<String,Set<String>>();
-            hiddenElementMaps = new HashMap<String,Map<String,Set<String>>>();
-
-            Enumeration pne = ConfigurationManager.propertyNames();
-            while (pne.hasMoreElements())
-            {
-                String key = (String)pne.nextElement();
-                if (key.startsWith(CONFIG_PREFIX))
-                {
-                    String mdField = key.substring(CONFIG_PREFIX.length());
-                    String segment[] = mdField.split("\\.", 3);
-
-                    // got schema.element.qualifier
-                    if (segment.length == 3)
-                    {
-                        Map<String,Set<String>> eltMap = hiddenElementMaps.get(segment[0]);
-                        if (eltMap == null)
-                        {
-                            eltMap = new HashMap<String,Set<String>>();
-                            hiddenElementMaps.put(segment[0], eltMap);
-                        }
-                        if (!eltMap.containsKey(segment[1]))
-                        {
-                            eltMap.put(segment[1], new HashSet<String>());
-                        }
-                        eltMap.get(segment[1]).add(segment[2]);
-                    }
-
-                    // got schema.element
-                    else if (segment.length == 2)
-                    {
-                        if (!hiddenElementSets.containsKey(segment[0]))
-                        {
-                            hiddenElementSets.put(segment[0], new HashSet<String>());
-                        }
-                        hiddenElementSets.get(segment[0]).add(segment[1]);
-                    }
-
-                    // oops..
-                    else
-                    {
-                        log.warn("Bad format in hidden metadata directive, field=\""+mdField+"\", config property="+key);
-                    }
-                }
-            }
-        }
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/OpenSearch.java

@@ -1,349 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.handle.HandleManager;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.net.URLEncoder;
-import java.io.UnsupportedEncodingException;
-import java.sql.SQLException;
-
-import org.w3c.dom.Document;
-
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.output.DOMOutputter;
-import org.jdom.output.XMLOutputter;
-
-import org.apache.log4j.Logger;
-
-import org.dspace.content.DSpaceObject;
-import org.dspace.core.ConfigurationManager;
-
-import com.sun.syndication.feed.module.opensearch.OpenSearchModule;
-import com.sun.syndication.feed.module.opensearch.entity.OSQuery;
-import com.sun.syndication.feed.module.opensearch.impl.OpenSearchModuleImpl;
-import com.sun.syndication.io.FeedException;
-
-/**
- * Utility Class with static methods for producing OpenSearch-compliant search results,
- * and the OpenSearch description document.
- * <p>
- * OpenSearch is a specification for describing and advertising search-engines
- * and their result formats. Commonly, RSS and Atom formats are used, which
- * the current implementation supports, as is HTML (used directly in browsers).
- * NB: this is baseline OpenSearch, no extensions currently supported.
- * </p>
- * <p>
- * The value of the "scope" parameter should either be absent (which means no
- * scope restriction), or the handle of a community or collection.
- * </p>
- * 
- * @author Richard Rodgers
- *
- */
-public class OpenSearch
-{
-    private static final Logger log = Logger.getLogger(OpenSearch.class);
-
-    // are open search queries enabled?
-    private static boolean enabled = false;
-    // supported results formats
-    private static List<String> formats = null;
-    // Namespaces used
-    private static final String osNs = "http://a9.com/-/spec/opensearch/1.1/";
-
-    // base search UI URL
-    private static String uiUrl = null;
-    // base search service URL
-    private static String svcUrl = null;
-    
-    static
-    {
-    	enabled = ConfigurationManager.getBooleanProperty("websvc.opensearch.enable");
-        svcUrl = ConfigurationManager.getProperty("dspace.url") + "/" +
-                 ConfigurationManager.getProperty("websvc.opensearch.svccontext");
-        uiUrl = ConfigurationManager.getProperty("dspace.url") + "/" +
-                ConfigurationManager.getProperty("websvc.opensearch.uicontext");
-
-    	// read rest of config info if enabled
-    	formats = new ArrayList<String>();
-    	if (enabled)
-    	{
-    		String fmtsStr = ConfigurationManager.getProperty("websvc.opensearch.formats");
-    		if ( fmtsStr != null )
-    		{
-    			for (String fmt : fmtsStr.split(","))
-    			{
-    				formats.add(fmt);
-    			}
-    		}
-    	}
-        }
-    
-    /**
-     * Returns list of supported formats
-     * 
-     * @return list of format names - 'rss', 'atom' or 'html'
-     */
-    public static List<String> getFormats()
-    {
-    	return formats;
-    }
-    
-    /**
-     * Returns a mime-type associated with passed format
-     * 
-     * @param format the results document format (rss, atom, html)
-     * @return content-type mime-type
-     */
-    public static String getContentType(String format)
-    {
-    	return "html".equals(format) ? "text/html" : 
-    									"application/" + format + "+xml; charset=UTF-8";
-    }
-    
-    /**
-     * Returns the OpenSearch service document appropriate for given scope
-     * 
-     * @param scope - null for entire repository, or handle or community or collection
-     * @return document the service document
-     * @throws IOException
-     */
-    public static Document getDescriptionDoc(String scope) throws IOException
-    {
-    	return jDomToW3(getServiceDocument(scope));
-    }
-    
-    /**
-     * Returns OpenSearch Servic Document as a string
-     * 
-     * @param scope - null for entire repository, or handle or community or collection
-     * @return service document as a string
-     */
-    public static String getDescription(String scope)
-    {
-    	return new XMLOutputter().outputString(getServiceDocument(scope));
-    }
-    
-    /**
-     * Returns a formatted set of search results as a string
-     * 
-     * @param format results format - html, rss or atom
-     * @param query - the search query
-     * @param totalResults - the hit count
-     * @param start - start result index
-     * @param pageSize - page size
-     * @param scope - search scope, null or community/collection handle
-     * @param results the retreived DSpace objects satisfying search
-     * @param labels labels to apply - format specific
-     * @return formatted search results
-     * @throws IOException
-     */
-    public static String getResultsString(String format, String query, int totalResults, int start, int pageSize,
-    		                          	  DSpaceObject scope, DSpaceObject[] results,
-    		                          	  Map<String, String> labels) throws IOException
-    {
-        try
-        {
-            return getResults(format, query, totalResults, start, pageSize, scope, results, labels).outputString();
-        }
-        catch (FeedException e)
-        {
-            log.error(e.toString(), e);
-            	throw new IOException("Unable to generate feed", e);
-        }
-    }
-    
-    /**
-     * Returns a formatted set of search results as a document
-     * 
-     * @param format results format - html, rss or atom
-     * @param query - the search query
-     * @param totalResults - the hit count
-     * @param start - start result index
-     * @param pageSize - page size
-     * @param scope - search scope, null or community/collection handle
-     * @param results the retreived DSpace objects satisfying search
-     * @param labels labels to apply - format specific
-     * @return formatted search results
-     * @throws IOException
-     */
-    public static Document getResultsDoc(String format, String query, int totalResults, int start, int pageSize,
-    		                          DSpaceObject scope, DSpaceObject[] results, Map<String, String> labels)
-                                      throws IOException
-    {
-        try
-        {
-            return getResults(format, query, totalResults, start, pageSize, scope, results, labels).outputW3CDom();
-        }
-        catch (FeedException e)
-        {
-            log.error(e.toString(), e);
-            throw new IOException("Unable to generate feed", e);
-        }
-    }
-
-    private static SyndicationFeed getResults(String format, String query, int totalResults, int start, int pageSize,
-                                          DSpaceObject scope, DSpaceObject[] results, Map<String, String> labels)
-    {
-        // Encode results in requested format
-        if ("rss".equals(format))
-        {
-            format = "rss_2.0";
-        }
-        else if ("atom".equals(format))
-        {
-            format = "atom_1.0";
-        }
-    	
-        SyndicationFeed feed = new SyndicationFeed(labels.get(SyndicationFeed.MSG_UITYPE));
-        feed.populate(null, scope, results, labels);
-        feed.setType(format);
-        feed.addModule(openSearchMarkup(query, totalResults, start, pageSize));
-    	return feed;
-	}
-    
-    /*
-     * Generates the OpenSearch elements which are added to the RSS or Atom feeds as foreign markup
-     * wrapped in a module
-     * 
-     * @param query the search query
-     * @param qRes the search results
-     * @return module
-     */
-    private static OpenSearchModule openSearchMarkup(String query, int totalResults, int start, int pageSize)
-    {
-    	OpenSearchModule osMod = new OpenSearchModuleImpl();
-    	osMod.setTotalResults(totalResults);
-    	osMod.setStartIndex(start);
-    	osMod.setItemsPerPage(pageSize);
-    	OSQuery osq = new OSQuery();
-    	osq.setRole("request");
-        try
-        {
-            osq.setSearchTerms(URLEncoder.encode(query, "UTF-8"));
-        }
-        catch(UnsupportedEncodingException e)
-        {
-            log.error(e);
-        }
-        osq.setStartPage(1 + (start / pageSize));
-        osMod.addQuery(osq);
-        return osMod;
-    }
-    
-    /**
-     * Returns as a document the OpenSearch service document
-     * 
-     * @param scope - null for the entire repository, or a collection/community handle
-     * @return Service Document
-     */
-    private static org.jdom.Document getServiceDocument(String scope)
-    {
-    	Namespace ns = Namespace.getNamespace(osNs);
-        Element root = new Element("OpenSearchDescription", ns);
-        root.addContent(new Element("ShortName", ns).setText(ConfigurationManager.getProperty("websvc.opensearch.shortname")));
-        root.addContent(new Element("LongName", ns).setText(ConfigurationManager.getProperty("websvc.opensearch.longname")));
-        root.addContent(new Element("Description", ns).setText(ConfigurationManager.getProperty("websvc.opensearch.description")));
-        root.addContent(new Element("InputEncoding", ns).setText("UTF-8"));
-        root.addContent(new Element("OutputEncoding", ns).setText("UTF-8"));
-        // optional elements
-        String sample = ConfigurationManager.getProperty("websvc.opensearch.samplequery");
-        if (sample != null && sample.length() > 0)
-        {
-        	Element sq = new Element("Query", ns).setAttribute("role", "example");
-        	root.addContent(sq.setAttribute("searchTerms", sample));
-        }
-        String tags = ConfigurationManager.getProperty("websvc.opensearch.tags");
-        if (tags != null && tags.length() > 0)
-        {
-        	root.addContent(new Element("Tags", ns).setText(tags));
-        }
-        String contact = ConfigurationManager.getProperty("mail.admin");
-        if (contact != null && contact.length() > 0)
-        {
-        	root.addContent(new Element("Contact", ns).setText(contact));
-        }
-        String faviconUrl = ConfigurationManager.getProperty("websvc.opensearch.faviconurl");
-        if (faviconUrl != null && faviconUrl.length() > 0)
-        {
-        	String dim = String.valueOf(16);
-        	String type = faviconUrl.endsWith("ico") ? "image/vnd.microsoft.icon" : "image/png";
-        	Element fav = new Element("Image", ns).setAttribute("height", dim).setAttribute("width", dim).
-        	                setAttribute("type", type).setText(faviconUrl);
-        	root.addContent(fav);
-        }
-        // service URLs
-        for (String format : formats)
-        {
-        	Element url = new Element("Url", ns).setAttribute("type", getContentType(format));
-        	StringBuffer template = new StringBuffer();
-        	if ("html".equals(format))
-        	{
-        		template.append(uiUrl);
-        	}
-        	else
-        	{
-        		template.append(svcUrl);
-        	}
-            template.append("?query={searchTerms}");
-        	if(! "html".equals(format))
-        	{
-               	template.append("&start={startIndex?}&rpp={count?}&format=");
-               	template.append(format);
-        	}
-        	if (scope != null)
-        	{
-        		template.append("&scope=");
-        		template.append(scope);
-        	}
-        	url.setAttribute("template", template.toString());
-        	root.addContent(url);
-        }
-        return new org.jdom.Document(root);
-    }
-    
-    /**
-     * Converts a JDOM document to a W3C one
-     * @param jdomDoc
-     * @return W3C Document object
-     * @throws IOException
-     */
-    private static Document jDomToW3(org.jdom.Document jdomDoc) throws IOException
-    {
-        DOMOutputter domOut = new DOMOutputter();
-        try
-        {
-        	return domOut.output(jdomDoc);
-        }
-        catch(JDOMException jde)
-        {
-        	throw new IOException("JDOM output exception", jde);
-        }
-    }
-
-    public static DSpaceObject resolveScope(Context context, String scope) throws SQLException
-    {
-        if(scope == null || "".equals(scope))
-            return null;
-
-        DSpaceObject dso = HandleManager.resolveToObject(context, scope);
-        if(dso == null || dso.getType() == Constants.ITEM)
-            throw new IllegalArgumentException("Scope handle "+scope+" should point to a valid Community or Collection");
-        return dso;
-    }
-
-}

dspace-api/src/main/java/org/dspace/app/util/SubmissionConfig.java

@@ -1,172 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.io.Serializable;
-
-import org.apache.log4j.Logger;
-
-/**
- * Class representing a single Item Submission config definition, organized into
- * steps. This class represents the structure of a single 'submission-process'
- * node in the item-submission.xml configuration file.
- *
- * Note: Implements Serializable as it will be saved to the current session during submission.
- * Please ensure that nothing is added to this class that isn't also serializable
- * 
- * @see org.dspace.app.util.SubmissionConfigReader
- * @see org.dspace.app.util.SubmissionStepConfig
- * 
- * @author Tim Donohue, based on DCInputSet by Brian S. Hughes
- * @version $Revision$
- */
-
-public class SubmissionConfig implements Serializable
-{
-    /** name of the item submission process */
-    private String submissionName = null;
-
-    /** the configuration classes for the steps in this submission process */
-    private SubmissionStepConfig[] submissionSteps = null;
-
-    /** whether or not this submission process is being used in a workflow * */
-    private boolean isWorkflow = false;
-
-    /** log4j logger */
-    private static Logger log = Logger.getLogger(SubmissionConfig.class);
-
-    /**
-     * Constructs a new Submission Configuration object, based on the XML
-     * configuration file (item-submission.xml)
-     * 
-     * @param submissionName
-     *            the submission process name
-     * @param steps
-     *            the vector listing of step information to build
-     *            SubmissionStepConfig objects for this submission process
-     * @param isWorkflowProcess
-     *            whether this submission process is being used in a workflow or
-     *            not. If it is a workflow process this may limit the steps that
-     *            are available for editing.
-     */
-    public SubmissionConfig(String submissionName, List<Map<String, String>> steps,
-            boolean isWorkflowProcess)
-    {
-        this.submissionName = submissionName;
-        this.isWorkflow = isWorkflowProcess;
-
-        // initialize a vector of SubmissionStepConfig objects
-        List<SubmissionStepConfig> stepConfigs = new ArrayList<SubmissionStepConfig>();
-
-        // loop through our steps, and create SubmissionStepConfig objects
-        for (int stepNum = 0; stepNum < steps.size(); stepNum++)
-        {
-            Map<String, String> stepInfo = steps.get(stepNum);
-            SubmissionStepConfig step = new SubmissionStepConfig(stepInfo);
-
-            // Only add this step to the process if either:
-            // (a) this is not a workflow process OR
-            // (b) this is a workflow process, and this step is editable in a
-            // workflow
-            if ((!this.isWorkflow)
-                    || ((this.isWorkflow) && step.isWorkflowEditable()))
-            {
-                // set the number of the step (starts at 0) and add it
-                step.setStepNumber(stepConfigs.size());
-                stepConfigs.add(step);
-
-                log.debug("Added step '" + step.getProcessingClassName()
-                        + "' as step #" + step.getStepNumber()
-                        + " of submission process " + submissionName);
-
-            }
-        }
-
-        // get steps as an array of Strings
-        submissionSteps = stepConfigs
-                .toArray(new SubmissionStepConfig[stepConfigs.size()]);
-    }
-
-    /**
-     * Return the name of the item submission process definition
-     * 
-     * @return the name of the submission process
-     */
-    public String getSubmissionName()
-    {
-        return submissionName;
-    }
-
-    /**
-     * Return the number of steps in this submission process
-     * 
-     * @return number of steps
-     */
-    public int getNumberOfSteps()
-    {
-        return submissionSteps.length;
-    }
-
-    /**
-     * Return whether or not this submission process is being used in a
-     * workflow!
-     * 
-     * @return true, if it's a workflow process. false, otherwise.
-     */
-    public boolean isWorkflow()
-    {
-        return isWorkflow;
-    }
-
-    /**
-     * Retrieve a particular Step configuration in this Item Submission Process
-     * configuration. The first step is numbered "0" (although step #0 is the
-     * implied "select collection" step).
-     * <p>
-     * If you want to retrieve the step after the "select collection" step, you
-     * should retrieve step #1.
-     * 
-     * If the specified step isn't found, null is returned.
-     * 
-     * @param stepNum
-     *            desired step to retrieve
-     * 
-     * @return the SubmissionStepConfig object for the step
-     */
-
-    public SubmissionStepConfig getStep(int stepNum)
-    {
-        if ((stepNum > submissionSteps.length - 1) || (stepNum < 0))
-        {
-            return null;
-        }
-        else
-        {
-            return submissionSteps[stepNum];
-        }
-    }
-
-    /**
-     * Returns whether or not there are more steps which follow the specified
-     * "stepNum". For example, if you specify stepNum=4, then this method checks
-     * to see if there is a Step #5. The first step is numbered "0".
-     * 
-     * @param stepNum
-     *            the current step.
-     * 
-     * @return true, if a step at "stepNum+1" exists. false, otherwise.
-     */
-
-    public boolean hasMoreSteps(int stepNum)
-    {
-        return (getStep(stepNum + 1) != null);
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/SubmissionConfigReader.java

@@ -1,653 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.io.File;
-import java.util.*;
-import javax.servlet.ServletException;
-import org.xml.sax.SAXException;
-import org.w3c.dom.*;
-import javax.xml.parsers.*;
-
-import org.apache.log4j.Logger;
-
-import org.dspace.core.ConfigurationManager;
-
-/**
- * Item Submission configuration generator for DSpace. Reads and parses the
- * installed submission process configuration file, item-submission.xml, from
- * the configuration directory. This submission process definition details the
- * ordering of the steps (and number of steps) that occur during the Item
- * Submission Process. There may be multiple Item Submission processes defined,
- * where each definition is assigned a unique name.
- * 
- * The file also specifies which collections use which Item Submission process.
- * At a minimum, the definitions file must define a default mapping from the
- * placeholder collection # to the distinguished submission process 'default'.
- * Any collections that use a custom submission process are listed paired with
- * the name of the item submission process they use.
- * 
- * @see org.dspace.app.util.SubmissionConfig
- * @see org.dspace.app.util.SubmissionStepConfig
- * 
- * @author Tim Donohue based on DCInputsReader by Brian S. Hughes
- * @version $Revision$
- */
-
-public class SubmissionConfigReader
-{
-    /**
-     * The ID of the default collection. Will never be the ID of a named
-     * collection
-     */
-    public static final String DEFAULT_COLLECTION = "default";
-
-    /** Prefix of the item submission definition XML file */
-    static final String SUBMIT_DEF_FILE_PREFIX = "item-submission";
-    
-    /** Suffix of the item submission definition XML file */
-    static final String SUBMIT_DEF_FILE_SUFFIX = ".xml";
-
-    /** log4j logger */
-    private static Logger log = Logger.getLogger(SubmissionConfigReader.class);
-
-	/** The fully qualified pathname of the directory containing the Item Submission Configuration file */
-    private String configDir = ConfigurationManager.getProperty("dspace.dir")
-            + File.separator + "config" + File.separator;
-            
-    /**
-     * Hashmap which stores which submission process configuration is used by
-     * which collection, computed from the item submission config file
-     * (specifically, the 'submission-map' tag)
-     */
-    private Map<String, String> collectionToSubmissionConfig = null;
-
-    /**
-     * Reference to the global submission step definitions defined in the
-     * "step-definitions" section
-     */
-    private Map<String, Map<String, String>> stepDefns = null;
-
-    /**
-     * Reference to the item submission definitions defined in the
-     * "submission-definitions" section
-     */
-    private Map<String, List<Map<String, String>>> submitDefns = null;
-
-    /**
-     * Mini-cache of last SubmissionConfig object requested (so that we don't
-     * always reload from scratch)
-     */
-    private SubmissionConfig lastSubmissionConfig = null;
-
-    /**
-     * Load Submission Configuration from the
-     * item-submission.xml configuration file 
-     */
-    public SubmissionConfigReader() throws ServletException
-    {
-        buildInputs(configDir + SUBMIT_DEF_FILE_PREFIX + SUBMIT_DEF_FILE_SUFFIX);
-    }
-
-    /**
-     * Parse an XML encoded item submission configuration file.
-     * <P>
-     * Creates two main hashmaps:
-     * <ul>
-     * <li>Hashmap of Collection to Submission definition mappings -
-     * defines which Submission process a particular collection uses
-     * <li>Hashmap of all Submission definitions.  List of all valid
-     * Submision Processes by name.
-     * </ul>
-     */
-    private void buildInputs(String fileName) throws ServletException
-    {
-        collectionToSubmissionConfig = new HashMap<String, String>();
-        submitDefns = new HashMap<String, List<Map<String, String>>>();
-
-        String uri = "file:" + new File(fileName).getAbsolutePath();
-
-        try
-        {
-            DocumentBuilderFactory factory = DocumentBuilderFactory
-                    .newInstance();
-            factory.setValidating(false);
-            factory.setIgnoringComments(true);
-            factory.setIgnoringElementContentWhitespace(true);
-
-            DocumentBuilder db = factory.newDocumentBuilder();
-            Document doc = db.parse(uri);
-            doNodes(doc);
-        }
-        catch (FactoryConfigurationError fe)
-        {
-            throw new ServletException(
-                    "Cannot create Item Submission Configuration parser", fe);
-        }
-        catch (Exception e)
-        {
-            throw new ServletException(
-                    "Error creating Item Submission Configuration: " + e);
-        }
-    }
-
-    /**
-     * Returns the Item Submission process config used for a particular
-     * collection, or the default if none is defined for the collection
-     * 
-     * @param collectionHandle
-     *            collection's unique Handle
-     * @param isWorkflow
-     *            whether or not we are loading the submission process for a
-     *            workflow
-     * @return the SubmissionConfig representing the item submission config
-     * 
-     * @throws ServletException
-     *             if no default submission process configuration defined
-     */
-    public SubmissionConfig getSubmissionConfig(String collectionHandle,
-            boolean isWorkflow) throws ServletException
-    {
-        // get the name of the submission process config for this collection
-        String submitName = collectionToSubmissionConfig
-                .get(collectionHandle);
-        if (submitName == null)
-        {
-            submitName = collectionToSubmissionConfig
-                    .get(DEFAULT_COLLECTION);
-        }
-        if (submitName == null)
-        {
-            throw new ServletException(
-                    "No item submission process configuration designated as 'default' in 'submission-map' section of 'item-submission.xml'.");
-        }
-
-        log.debug("Loading submission process config named '" + submitName
-                + "'");
-
-        // check mini-cache, and return if match
-        if (lastSubmissionConfig != null
-                && lastSubmissionConfig.getSubmissionName().equals(submitName)
-                && lastSubmissionConfig.isWorkflow() == isWorkflow)
-        {
-            log.debug("Found submission process config '" + submitName
-                    + "' in cache.");
-
-            return lastSubmissionConfig;
-        }
-
-        // cache miss - construct new SubmissionConfig
-        List<Map<String, String>> steps = submitDefns.get(submitName);
-
-        if (steps == null)
-        {
-            throw new ServletException(
-                    "Missing the Item Submission process config '" + submitName
-                            + "' (or unable to load) from 'item-submission.xml'.");
-        }
-
-        log.debug("Submission process config '" + submitName
-                + "' not in cache. Reloading from scratch.");
-
-        lastSubmissionConfig = new SubmissionConfig(submitName, steps,
-                isWorkflow);
-
-        log.debug("Submission process config has "
-                + lastSubmissionConfig.getNumberOfSteps() + " steps listed.");
-
-        return lastSubmissionConfig;
-    }
-
-    /**
-     * Returns a particular global step definition based on its ID.
-     * <P>
-     * Global step definitions are those defined in the <step-definitions>
-     * section of the configuration file.
-     * 
-     * @param stepID
-     *            step's identifier
-     * 
-     * @return the SubmissionStepConfig representing the step
-     * 
-     * @throws ServletException
-     *             if no default submission process configuration defined
-     */
-    public SubmissionStepConfig getStepConfig(String stepID)
-            throws ServletException
-    {
-        // We should already have the step definitions loaded
-        if (stepDefns != null)
-        {
-            // retreive step info
-            Map<String, String> stepInfo = stepDefns.get(stepID);
-
-            if (stepInfo != null)
-            {
-                return new SubmissionStepConfig(stepInfo);
-            }
-        }
-
-        return null;
-    }
-
-    /**
-     * Process the top level child nodes in the passed top-level node. These
-     * should correspond to the collection-form maps, the form definitions, and
-     * the display/storage word pairs.
-     */
-    private void doNodes(Node n) throws SAXException, ServletException
-    {
-        if (n == null)
-        {
-            return;
-        }
-        Node e = getElement(n);
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        boolean foundMap = false;
-        boolean foundStepDefs = false;
-        boolean foundSubmitDefs = false;
-        for (int i = 0; i < len; i++)
-        {
-            Node nd = nl.item(i);
-            if ((nd == null) || isEmptyTextNode(nd))
-            {
-                continue;
-            }
-            String tagName = nd.getNodeName();
-            if (tagName.equals("submission-map"))
-            {
-                processMap(nd);
-                foundMap = true;
-            }
-            else if (tagName.equals("step-definitions"))
-            {
-                processStepDefinition(nd);
-                foundStepDefs = true;
-            }
-            else if (tagName.equals("submission-definitions"))
-            {
-                processSubmissionDefinition(nd);
-                foundSubmitDefs = true;
-            }
-            // Ignore unknown nodes
-        }
-        if (!foundMap)
-        {
-            throw new ServletException(
-                    "No collection to item submission map ('submission-map') found in 'item-submission.xml'");
-        }
-        if (!foundStepDefs)
-        {
-            throw new ServletException("No 'step-definitions' section found in 'item-submission.xml'");
-        }
-        if (!foundSubmitDefs)
-        {
-            throw new ServletException(
-                    "No 'submission-definitions' section found in 'item-submission.xml'");
-        }
-    }
-
-    /**
-     * Process the submission-map section of the XML file. Each element looks
-     * like: <name-map collection-handle="hdl" submission-name="name" /> Extract
-     * the collection handle and item submission name, put name in hashmap keyed
-     * by the collection handle.
-     */
-    private void processMap(Node e) throws SAXException
-    {
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node nd = nl.item(i);
-            if (nd.getNodeName().equals("name-map"))
-            {
-                String id = getAttribute(nd, "collection-handle");
-                String value = getAttribute(nd, "submission-name");
-                String content = getValue(nd);
-                if (id == null)
-                {
-                    throw new SAXException(
-                            "name-map element is missing collection-handle attribute in 'item-submission.xml'");
-                }
-                if (value == null)
-                {
-                    throw new SAXException(
-                            "name-map element is missing submission-name attribute in 'item-submission.xml'");
-                }
-                if (content != null && content.length() > 0)
-                {
-                    throw new SAXException(
-                            "name-map element has content in 'item-submission.xml', it should be empty.");
-                }
-                collectionToSubmissionConfig.put(id, value);
-            } // ignore any child node that isn't a "name-map"
-        }
-    }
-
-    /**
-     * Process the "step-definition" section of the XML file. Each element is
-     * formed thusly: <step id="unique-id"> ...step_fields... </step> The valid
-     * step_fields are: heading, processing-servlet.
-     * <P>
-     * Extract the step information (from the step_fields) and place in a
-     * HashMap whose key is the step's unique id.
-     */
-    private void processStepDefinition(Node e) throws SAXException,
-            ServletException
-    {
-        stepDefns = new HashMap<String, Map<String, String>>();
-
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node nd = nl.item(i);
-            // process each step definition
-            if (nd.getNodeName().equals("step"))
-            {
-                String stepID = getAttribute(nd, "id");
-                if (stepID == null)
-                {
-                    throw new SAXException(
-                            "step element has no 'id' attribute in 'item-submission.xml', which is required in the 'step-definitions' section");
-                }
-                else if (stepDefns.containsKey(stepID))
-                {
-                    throw new SAXException(
-                            "There are two step elements with the id '" + stepID + "' in 'item-submission.xml'");
-                }
-
-                Map<String, String> stepInfo = processStepChildNodes("step-definition", nd);
-
-                stepDefns.put(stepID, stepInfo);
-            } // ignore any child that is not a 'step'
-        }
-
-        // Sanity check number of step definitions
-        if (stepDefns.size() < 1)
-        {
-            throw new ServletException(
-                    "step-definition section has no steps! A step with id='collection' is required in 'item-submission.xml'!");
-        }
-
-        // Sanity check to see that the required "collection" step is defined
-        if (!stepDefns.containsKey(SubmissionStepConfig.SELECT_COLLECTION_STEP))
-        {
-            throw new ServletException(
-                    "The step-definition section is REQUIRED to have a step with id='"
-                            + SubmissionStepConfig.SELECT_COLLECTION_STEP
-                            + "' in 'item-submission.xml'!  This step is used to ensure that a new item submission is assigned to a collection.");
-        }
-
-        // Sanity check to see that the required "complete" step is defined
-        if (!stepDefns.containsKey(SubmissionStepConfig.COMPLETE_STEP))
-        {
-            throw new ServletException(
-                    "The step-definition section is REQUIRED to have a step with id='"
-                            + SubmissionStepConfig.COMPLETE_STEP
-                            + "' in 'item-submission.xml'!  This step is used to perform all processing necessary at the completion of the submission (e.g. starting workflow).");
-        }
-    }
-
-    /**
-     * Process the "submission-definition" section of the XML file. Each element
-     * is formed thusly: <submission-process name="submitName">...steps...</submit-process>
-     * Each step subsection is formed: <step> ...step_fields... </step> (with
-     * optional "id" attribute, to reference a step from the <step-definition>
-     * section). The valid step_fields are: heading, class-name.
-     * <P>
-     * Extract the submission-process name and steps and place in a HashMap
-     * whose key is the submission-process's unique name.
-     */
-    private void processSubmissionDefinition(Node e) throws SAXException,
-            ServletException
-    {
-        int numSubmitProcesses = 0;
-        List<String> submitNames = new ArrayList<String>();
-
-        // find all child nodes of the 'submission-definition' node and loop
-        // through
-        NodeList nl = e.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node nd = nl.item(i);
-
-            // process each 'submission-process' node
-            if (nd.getNodeName().equals("submission-process"))
-            {
-                numSubmitProcesses++;
-                String submitName = getAttribute(nd, "name");
-                if (submitName == null)
-                {
-                    throw new SAXException(
-                            "'submission-process' element has no 'name' attribute in 'item-submission.xml'");
-                }
-                else if (submitNames.contains(submitName))
-                {
-                    throw new SAXException(
-                            "There are two 'submission-process' elements with the name '"
-                                    + submitName + "' in 'item-submission.xml'.");
-                }
-                submitNames.add(submitName);
-
-                // the 'submission-process' definition contains steps
-                List<Map<String, String>> steps = new ArrayList<Map<String, String>>();
-                submitDefns.put(submitName, steps);
-
-                // loop through all the 'step' nodes of the 'submission-process'
-                NodeList pl = nd.getChildNodes();
-                int lenStep = pl.getLength();
-                for (int j = 0; j < lenStep; j++)
-                {
-                    Node nStep = pl.item(j);
-
-                    // process each 'step' definition
-                    if (nStep.getNodeName().equals("step"))
-                    {
-                        // check for an 'id' attribute
-                        String stepID = getAttribute(nStep, "id");
-
-                        Map<String, String> stepInfo;
-
-                        // if this step has an id, load its information from the
-                        // step-definition section
-                        if ((stepID != null) && (stepID.length() > 0))
-                        {
-                            if (stepDefns.containsKey(stepID))
-                            {
-                                // load the step information from the
-                                // step-definition
-                                stepInfo = stepDefns.get(stepID);
-                            }
-                            else
-                            {
-                                throw new SAXException(
-                                        "The Submission process config named "
-                                                + submitName
-                                                + " contains a step with id="
-                                                + stepID
-                                                + ".  There is no step with this 'id' defined in the 'step-definition' section of 'item-submission.xml'.");
-                            }
-
-                            // Ignore all children of a step element with an
-                            // "id"
-                        }
-                        else
-                        {
-                            // get information about step from its children
-                            // nodes
-                            stepInfo = processStepChildNodes(
-                                    "submission-process", nStep);
-                        }
-
-                        steps.add(stepInfo);
-
-                    } // ignore any child that is not a 'step'
-                }
-
-                // sanity check number of steps
-                if (steps.size() < 1)
-                {
-                    throw new ServletException(
-                            "Item Submission process config named "
-                                    + submitName + " has no steps defined in 'item-submission.xml'");
-                }
-
-                // ALL Item Submission processes MUST BEGIN with selecting a
-                // Collection. So, automatically insert in the "collection" step
-                // (from the 'step-definition' section)
-                // Note: we already did a sanity check that this "collection"
-                // step exists.
-                steps.add(0, stepDefns
-                        .get(SubmissionStepConfig.SELECT_COLLECTION_STEP));
-
-                // ALL Item Submission processes MUST END with the
-                // "Complete" processing step.
-                // So, automatically append in the "complete" step
-                // (from the 'step-definition' section)
-                // Note: we already did a sanity check that this "complete"
-                // step exists.
-                steps.add(stepDefns
-                        .get(SubmissionStepConfig.COMPLETE_STEP));
-
-            }
-        }
-        if (numSubmitProcesses == 0)
-        {
-            throw new ServletException(
-                    "No 'submission-process' elements/definitions found in 'item-submission.xml'");
-        }
-    }
-
-    /**
-     * Process the children of the "step" tag of the XML file. Returns a HashMap
-     * of all the fields under that "step" tag, where the key is the field name,
-     * and the value is the field value.
-     * 
-     */
-    private Map<String, String> processStepChildNodes(String configSection, Node nStep)
-            throws SAXException, ServletException
-    {
-        // initialize the HashMap of step Info
-        Map<String, String> stepInfo = new HashMap<String, String>();
-
-        NodeList flds = nStep.getChildNodes();
-        int lenflds = flds.getLength();
-        for (int k = 0; k < lenflds; k++)
-        {
-            // process each child node of a <step> tag
-            Node nfld = flds.item(k);
-
-            if (!isEmptyTextNode(nfld))
-            {
-                String tagName = nfld.getNodeName();
-                String value = getValue(nfld);
-                stepInfo.put(tagName, value);
-            }
-        }// end for each field
-
-        // check for ID attribute & save to step info
-        String stepID = getAttribute(nStep, "id");
-        if (stepID != null && stepID.length() > 0)
-        {
-            stepInfo.put("id", stepID);
-        }
-
-        // look for REQUIRED 'step' information
-        String missing = null;
-        if (stepInfo.get("processing-class") == null)
-        {
-            missing = "'processing-class'";
-        }
-        if (missing != null)
-        {
-            String msg = "Required field " + missing
-                    + " missing in a 'step' in the " + configSection
-                    + " of the item submission configuration file ('item-submission.xml')";
-            throw new SAXException(msg);
-        }
-
-        return stepInfo;
-    }
-
-    private Node getElement(Node nd)
-    {
-        NodeList nl = nd.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node n = nl.item(i);
-            if (n.getNodeType() == Node.ELEMENT_NODE)
-            {
-                return n;
-            }
-        }
-        return null;
-    }
-
-    private boolean isEmptyTextNode(Node nd)
-    {
-        boolean isEmpty = false;
-        if (nd.getNodeType() == Node.TEXT_NODE)
-        {
-            String text = nd.getNodeValue().trim();
-            if (text.length() == 0)
-            {
-                isEmpty = true;
-            }
-        }
-        return isEmpty;
-    }
-
-    /**
-     * Returns the value of the node's attribute named <name>
-     */
-    private String getAttribute(Node e, String name)
-    {
-        NamedNodeMap attrs = e.getAttributes();
-        int len = attrs.getLength();
-        if (len > 0)
-        {
-            int i;
-            for (i = 0; i < len; i++)
-            {
-                Node attr = attrs.item(i);
-                if (name.equals(attr.getNodeName()))
-                {
-                    return attr.getNodeValue().trim();
-                }
-            }
-        }
-        // no such attribute
-        return null;
-    }
-
-    /**
-     * Returns the value found in the Text node (if any) in the node list that's
-     * passed in.
-     */
-    private String getValue(Node nd)
-    {
-        NodeList nl = nd.getChildNodes();
-        int len = nl.getLength();
-        for (int i = 0; i < len; i++)
-        {
-            Node n = nl.item(i);
-            short type = n.getNodeType();
-            if (type == Node.TEXT_NODE)
-            {
-                return n.getNodeValue().trim();
-            }
-        }
-        // Didn't find a text node
-        return null;
-    }
-}

dspace-api/src/main/java/org/dspace/app/util/SubmissionInfo.java

@@ -1,703 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.servlet.ServletException;
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpSession;
-
-import org.apache.log4j.Logger;
-import org.dspace.content.Bitstream;
-import org.dspace.content.Bundle;
-import org.dspace.content.InProgressSubmission;
-
-import org.dspace.submit.AbstractProcessingStep;
-import org.dspace.workflow.WorkflowItem;
-import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
-
-/**
- * Information about an item being editing with the submission UI
- * 
- * @author Robert Tansley
- * @version $Revision$
- */
-public class SubmissionInfo extends HashMap
-{
-    /** log4j logger */
-    private static Logger log = Logger.getLogger(SubmissionInfo.class);
-    
-    /** The item which is being submitted */
-    private InProgressSubmission submissionItem = null;
-
-    /**
-    * The Submission process config, which holds all info about the submission
-    * process that this item is going through (including all steps, etc)
-    */
-    private SubmissionConfig submissionConfig = null;
-    
-    /**
-    * Handle of the collection where this item is being submitted
-    */
-    private String collectionHandle = null;
-    
-    /***************************************************************************
-    * Holds all information used to build the Progress Bar in a key,value set.
-    * Keys are the number of the step, followed by the number of the page
-    * within the step (e.g. "2.1" = The first page of Step 2) (e.g. "5.2" = The
-    * second page of Step 5) Values are the Headings to display for each step
-    * (e.g. "Describe")
-    **************************************************************************/
-    private Map<String, String> progressBar = null;
-    
-    /** The element or element_qualifier to show more input boxes for */
-    private String moreBoxesFor;
-
-    /** The element or element_qualifier to scroll to initially using anchor */
-    private String jumpToField;
-
-    /** If non-empty, form-relative indices of missing fields */
-    private List<String> missingFields;
-
-    /** Specific bundle we're dealing with */
-    private Bundle bundle;
-
-    /** Specific bitstream we're dealing with */
-    private Bitstream bitstream;
-    
-    /** Reader for submission process configuration file * */
-    private static SubmissionConfigReader submissionConfigReader;
-    
-    /**
-     * Default Constructor - PRIVATE
-     * <p>
-     * Create a SubmissionInfo object
-     * using the load() method!
-     * 
-     */
-    private SubmissionInfo()
-    {
-    }
-
-    /**
-     * Loads all known submission information based on the given in progress
-     * submission and request object.
-     * <P>
-     * If subItem is null, then just loads the default submission information
-     * for a new submission.
-     * 
-     * @param request
-     *            The HTTP Servlet Request object          
-     * @param subItem
-     *            The in-progress submission we are loading information for
-     * 
-     * @return a SubmissionInfo object
-     * 
-     * @throws ServletException
-     *             if an error occurs
-     */
-    public static SubmissionInfo load(HttpServletRequest request, InProgressSubmission subItem) throws ServletException
-    {
-        boolean forceReload = false;
-    	SubmissionInfo subInfo = new SubmissionInfo();
-        
-        // load SubmissionConfigReader only the first time
-        // or if we're using a different UI now.
-        if (submissionConfigReader == null)
-        {
-            submissionConfigReader = new SubmissionConfigReader();
-            forceReload=true;
-        }
-
-        // save the item which is going through the submission process
-        subInfo.setSubmissionItem(subItem);
-
-        // Only if the submission item is created can we set its collection
-        String collectionHandle = SubmissionConfigReader.DEFAULT_COLLECTION;
-        if (subItem != null)
-        {
-            collectionHandle = subItem.getCollection().getHandle();
-        }
-
-        // save this collection handle to this submission info object
-        subInfo.setCollectionHandle(collectionHandle);
-
-        // load Submission Process config for this item's collection
-        // (Note: this also loads the Progress Bar info, since it is
-        // dependent on the Submission config)
-        loadSubmissionConfig(request, subInfo, forceReload);
-
-        return subInfo;
-    }
-
-    /**
-     * Is this submission in the workflow process?
-     * 
-     * @return true if the current submission is in the workflow process
-     */
-    public boolean isInWorkflow()
-    {
-        return ((this.submissionItem != null) && (this.submissionItem instanceof WorkflowItem || this.submissionItem instanceof XmlWorkflowItem));
-    }
-
-    /**
-     * Return the current in progress submission
-     * 
-     * @return the InProgressSubmission object representing the current
-     *         submission
-     */
-    public InProgressSubmission getSubmissionItem()
-    {
-        return this.submissionItem;
-    }
-
-    /**
-     * Updates the current in progress submission item
-     * 
-     * @param subItem
-     *            the new InProgressSubmission object
-     */
-    public void setSubmissionItem(InProgressSubmission subItem)
-    {
-        this.submissionItem = subItem;
-    }
-
-    /**
-     * Return the current submission process config (which includes all steps
-     * which need to be completed for the submission to be successful)
-     * 
-     * @return the SubmissionConfig object, which contains info on all the steps
-     *         in the current submission process
-     */
-    public SubmissionConfig getSubmissionConfig()
-    {
-        return this.submissionConfig;
-    }
-
-    /**
-     * Causes the SubmissionConfig to be completely reloaded from the XML
-     * configuration file (item-submission.xml).
-     * <P>
-     * Note: This also reloads the progress bar info, since the progress bar
-     * depends entirely on the submission process (and its steps).
-     * 
-     * @param request
-     *            The HTTP Servlet Request object
-     * 
-     * @throws ServletException
-     *             if an error occurs
-     */
-    public void reloadSubmissionConfig(HttpServletRequest request)
-            throws ServletException
-    {
-        // Only if the submission item is created can we set its collection
-        String collectionHandle = SubmissionConfigReader.DEFAULT_COLLECTION;
-        if (this.submissionItem != null)
-        {
-            collectionHandle = submissionItem.getCollection().getHandle();
-        }
-        this.setCollectionHandle(collectionHandle);
-
-        // force a reload of the submission process configuration
-        loadSubmissionConfig(request, this, true);
-    }
-
-    /**
-     * Returns a particular global step definition based on its ID.
-     * <P>
-     * Global step definitions are those defined in the <step-definitions>
-     * section of the configuration file.
-     * 
-     * @param stepID
-     *            step's identifier
-     * 
-     * @return the SubmissionStepConfig representing the step
-     * 
-     * @throws ServletException
-     *             if no default submission process configuration defined
-     */
-    public SubmissionStepConfig getStepConfig(String stepID)
-            throws ServletException
-    {
-        return submissionConfigReader.getStepConfig(stepID);
-    }
-
-    
-    /**
-     * Return text information suitable for logging.
-     * <p>
-     * This method is used by several of the Step classes
-     * to log major events during the submission process (e.g. when
-     * license agreement was accepted, when item was submitted, 
-     * when it was available in DSpace, etc.)
-     * 
-     * @return the type and ID of the submission, bundle and/or bitstream for
-     *         logging
-     */
-    public String getSubmissionLogInfo()
-    {
-        String info = "";
-
-        if (isInWorkflow())
-        {
-            info = info + "workflow_id=" + getSubmissionItem().getID();
-        }
-        else
-        {
-            info = info + "workspace_item_id" + getSubmissionItem().getID();
-        }
-
-        if (getBundle() != null)
-        {
-            info = info + ",bundle_id=" + getBundle().getID();
-        }
-
-        if (getBitstream() != null)
-        {
-            info = info + ",bitstream_id=" + getBitstream().getID();
-        }
-
-        return info;
-    }
-    
-    /**
-     * Gets the handle of the collection to which this item is being submitted
-     * 
-     * @return the collection handle
-     */
-    public String getCollectionHandle()
-    {
-        return this.collectionHandle;
-    }
-
-    /**
-     * Sets the handle of the collection to which this item is being submitted
-     * 
-     * @param handle
-     *            the new collection handle
-     */
-    public void setCollectionHandle(String handle)
-    {
-        this.collectionHandle = handle;
-    }
-
-    /**
-     * Return the information used to build the progress bar (this includes all
-     * the steps in this submission, as well as the ordering and names of the
-     * steps).
-     * <p>
-     * Returns a Hashmap, with the following specifics:
-     * <p>
-     * Keys are the number of the step, followed by the number of the page
-     * within the step
-     * <p>
-     * (e.g. "2.1" = The first page of Step 2)
-     * <p>
-     * (e.g. "5.2" = The second page of Step 5)
-     * <P>
-     * Values are the Headings to display for each step (e.g. "Describe")
-     * 
-     * @return a Hashmap of Progress Bar information.
-     */
-    public Map<String, String> getProgressBarInfo()
-    {
-        return this.progressBar;
-    }
-
-    /**
-     * Return the current bitstream we're working with (This is used during
-     * upload processes, or user interfaces that are dealing with bitstreams)
-     * 
-     * @return the Bitstream object for the bitstream
-     */
-    public Bitstream getBitstream()
-    {
-        return this.bitstream;
-    }
-
-    /**
-     * Sets the current bitstream we're working with (This is used during upload
-     * processes, or user interfaces that are dealing with bitstreams)
-     * 
-     * @param bits
-     *            the bitstream
-     */
-    public void setBitstream(Bitstream bits)
-    {
-        this.bitstream = bits;
-    }
-
-    /**
-     * Return the current bundle we're working with (This is used during upload
-     * processes, or user interfaces that are dealing with bundles/bitstreams)
-     * 
-     * @return the Bundle object for the bundle
-     */
-    public Bundle getBundle()
-    {
-        return this.bundle;
-    }
-
-    /**
-     * Sets the current bundle we're working with (This is used during upload
-     * processes, or user interfaces that are dealing with bundles/bitstreams)
-     * 
-     * @param bund
-     *            the bundle
-     */
-    public void setBundle(Bundle bund)
-    {
-        this.bundle = bund;
-    }
-
-    /**
-     * Return form related indices of the required fields which were not filled
-     * out by the user.
-     * 
-     * @return a List of empty fields which are required
-     */
-    public List<String> getMissingFields()
-    {
-        return this.missingFields;
-    }
-
-    /**
-     * Sets the form related indices of the required fields which were not
-     * filled out by the user.
-     * 
-     * @param missing
-     *            the List of empty fields which are required
-     */
-    public void setMissingFields(List<String> missing)
-    {
-        this.missingFields = missing;
-    }
-
-    /**
-     * Return metadata field which user has requested more input boxes be
-     * displayed (by pressing "Add More" on one of the "Describe" pages)
-     * 
-     * @return the String name of the field element
-     */
-    public String getMoreBoxesFor()
-    {
-        return this.moreBoxesFor;
-    }
-
-    /**
-     * Sets the metadata field which user has requested more input boxes be
-     * displayed (by pressing "Add More" on one of the "Describe" pages)
-     * 
-     * @param fieldname
-     *            the name of the field element on the page
-     */
-    public void setMoreBoxesFor(String fieldname)
-    {
-        this.moreBoxesFor = fieldname;
-    }
-
-    /**
-     * Return metadata field which JSP should "jump to" (i.e. set focus on) when
-     * the JSP next loads. This is used during the Describe step.
-     * 
-     * @return the String name of the field element
-     */
-    public String getJumpToField()
-    {
-        return this.jumpToField;
-    }
-
-    /**
-     * Sets metadata field which JSP should "jump to" (i.e. set focus on) when
-     * the JSP next loads. This is used during the Describe step.
-     * 
-     * @param fieldname
-     *            the name of the field on the page
-     */
-    public void setJumpToField(String fieldname)
-    {
-        this.jumpToField = fieldname;
-    }
-
-    /**
-     * Load necessary information to build the Progress Bar for the Item
-     * Submission Progress.
-     * 
-     * This information is returned in the form of a HashMap (which is then
-     * stored as a part of the SubmissionInfo). The HashMap takes the following
-     * form:
-     * 
-     * Keys - the number of the step, followed by the number of the page within
-     * the step (e.g. "2.1" = The first page of Step 2) (e.g. "5.2" = The second
-     * page of Step 5)
-     * 
-     * Values - the headings to display for each step (e.g. "Describe",
-     * "Verify")
-     * 
-     * @param request
-     *            The HTTP Servlet Request object
-     * @param subInfo
-     *            the SubmissionInfo object we are loading into
-     * @param forceReload
-     *            If true, this method reloads from scratch (and overwrites
-     *            cached progress bar info)
-     * 
-     */
-    private static void loadProgressBar(HttpServletRequest request,
-            SubmissionInfo subInfo, boolean forceReload)
-    {
-        Map<String, String> progressBarInfo = null;
-
-        log.debug("Loading Progress Bar Info");
-
-        if (!forceReload)
-        {
-            // first, attempt to load from cache
-            progressBarInfo = loadProgressBarFromCache(request
-                    .getSession());
-        }
-
-        if (progressBarInfo != null && log.isDebugEnabled())
-        {
-            log.debug("Found Progress Bar Info in cache: "
-                    + progressBarInfo.size()
-                    + " pages to display in progress bar");
-        }
-        // if unable to load from cache, must load from scratch
-        else
-        {
-            progressBarInfo = new LinkedHashMap<String, String>();
-
-            // loop through all steps
-            for (int i = 0; i < subInfo.submissionConfig.getNumberOfSteps(); i++)
-            {
-                // get the current step info
-                SubmissionStepConfig currentStep = subInfo.submissionConfig
-                        .getStep(i);
-                String stepNumber = Integer.toString(currentStep
-                        .getStepNumber());
-                String stepHeading = currentStep.getHeading();
-
-                // as long as this step is visible, include it in
-                // the Progress Bar
-                if (currentStep.isVisible())
-                {
-                    // default to just one page in this step
-                    int numPages = 1;
-
-                    try
-                    {
-                        // load the processing class for this step
-                        ClassLoader loader = subInfo.getClass()
-                                .getClassLoader();
-                        Class<AbstractProcessingStep> stepClass = (Class<AbstractProcessingStep>)loader.loadClass(currentStep.getProcessingClassName());
-
-                        // call the "getNumberOfPages()" method of the class
-                        // to get it's number of pages
-                        AbstractProcessingStep step = stepClass.newInstance();
-
-                        // get number of pages from servlet
-                        numPages = step.getNumberOfPages(request, subInfo);
-                    }
-                    catch (Exception e)
-                    {
-                        log.error(
-                                "Error loading progress bar information from Step Class '"
-                                        + currentStep.getProcessingClassName()
-                                        + "' Error:", e);
-                    }
-
-                    // save each of the step's pages to the progress bar
-                    for (int j = 1; j <= numPages; j++)
-                    {
-                        String pageNumber = Integer.toString(j);
-
-                        // store ("stepNumber.pageNumber", Heading) for each
-                        // page in the step
-                        progressBarInfo.put(stepNumber + "." + pageNumber,
-                                stepHeading);
-                    }// end for each page
-                }
-            }// end for each step
-
-            log.debug("Loaded Progress Bar Info from scratch: "
-                    + progressBarInfo.size()
-                    + " pages to display in progress bar");
-
-            // cache this new progress bar
-            saveProgressBarToCache(request.getSession(), progressBarInfo);
-        }// end if null
-
-        // save progressBarInfo to submission Info
-        subInfo.progressBar = progressBarInfo;
-    }
-
-    /**
-     * Saves all progress bar information into session cache. This saves us from
-     * having to reload this same progress bar over and over again.
-     * 
-     * @param session
-     *            The HTTP Session object
-     * @param progressBarInfo
-     *            The progress bar info to cache
-     * 
-     */
-    private static void saveProgressBarToCache(HttpSession session,
-            Map<String, String> progressBarInfo)
-    {
-        // cache progress bar info to Session
-        session.setAttribute("submission.progressbar", progressBarInfo);
-    }
-
-    /**
-     * Attempts to retrieve progress bar information (for a particular
-     * collection) from session cache.
-     * 
-     * If the progress bar info cannot be found, returns null
-     * 
-     * @param session
-     *            The HTTP Session object
-     * 
-     * @return progressBarInfo HashMap (if found), or null (if not)
-     * 
-     */
-    private static Map<String, String> loadProgressBarFromCache(HttpSession session)
-    {
-        return (Map<String, String>) session.getAttribute("submission.progressbar");
-    }
-
-    /**
-     * Loads SubmissionConfig object for the given submission info object. If a
-     * SubmissionConfig object cannot be loaded, a Servlet Error is thrown.
-     * <p>
-     * This method just loads this SubmissionConfig object internally, so that
-     * it is available via a call to "getSubmissionConfig()"
-     * 
-     * @param request
-     *            The HTTP Servlet Request object
-     * @param subInfo
-     *            the SubmissionInfo object we are loading into
-     * @param forceReload
-     *            If true, this method reloads from scratch (and overwrites
-     *            cached SubmissionConfig)
-     * 
-     */
-    private static void loadSubmissionConfig(HttpServletRequest request,
-            SubmissionInfo subInfo, boolean forceReload)
-            throws ServletException
-    {
-
-        log.debug("Loading Submission Config information");
-
-        if (!forceReload)
-        {
-            // first, try to load from cache
-            subInfo.submissionConfig = loadSubmissionConfigFromCache(request
-                    .getSession(), subInfo.getCollectionHandle(), subInfo
-                    .isInWorkflow());
-        }
-
-        if (subInfo.submissionConfig == null || forceReload)
-        {
-            // reload the proper Submission process config
-            // (by reading the XML config file)
-            subInfo.submissionConfig = submissionConfigReader
-                    .getSubmissionConfig(subInfo.getCollectionHandle(), subInfo
-                            .isInWorkflow());
-
-            // cache this new submission process configuration
-            saveSubmissionConfigToCache(request.getSession(),
-                    subInfo.submissionConfig, subInfo.getCollectionHandle(),
-                    subInfo.isInWorkflow());
-
-            // also must force reload Progress Bar info,
-            // since it's based on the Submission config
-            loadProgressBar(request, subInfo, true);
-        }
-        else
-        {
-            log.debug("Found Submission Config in session cache!");
-
-            // try and reload progress bar from cache
-            loadProgressBar(request, subInfo, false);
-        }
-    }
-
-    /**
-     * Saves SubmissionConfig object into session cache. This saves us from
-     * having to reload this object during every "Step".
-     * 
-     * @param session
-     *            The HTTP Session object
-     * @param subConfig
-     *            The SubmissionConfig to cache
-     * @param collectionHandle
-     *            The Collection handle this SubmissionConfig corresponds to
-     * @param isWorkflow
-     *            Whether this SubmissionConfig corresponds to a workflow
-     * 
-     * 
-     */
-    private static void saveSubmissionConfigToCache(HttpSession session,
-            SubmissionConfig subConfig, String collectionHandle,
-            boolean isWorkflow)
-    {
-        // cache the submission process config
-        // and the collection it corresponds to
-        session.setAttribute("submission.config", subConfig);
-        session.setAttribute("submission.config.collection", collectionHandle);
-        session.setAttribute("submission.config.isWorkflow", Boolean.valueOf(
-                isWorkflow));
-    }
-
-    /**
-     * Loads SubmissionConfig object from session cache for the given
-     * Collection. If a SubmissionConfig object cannot be found, null is
-     * returned.
-     * 
-     * @param session
-     *            The HTTP Session object
-     * @param collectionHandle
-     *            The Collection handle of the SubmissionConfig to load
-     * @param isWorkflow
-     *            whether or not we loading the Submission process for a
-     *            workflow item
-     * 
-     * @return The cached SubmissionConfig for this collection
-     */
-    private static SubmissionConfig loadSubmissionConfigFromCache(
-            HttpSession session, String collectionHandle, boolean isWorkflow)
-    {
-        // attempt to load submission process config
-        // from cache for the current collection
-        String cachedHandle = (String) session
-                .getAttribute("submission.config.collection");
-
-        Boolean cachedIsWorkflow = (Boolean) session
-                .getAttribute("submission.config.isWorkflow");
-
-        // only load from cache if the collection handle and
-        // workflow item status both match!
-        if (collectionHandle.equals(cachedHandle)
-                && isWorkflow == cachedIsWorkflow.booleanValue())
-
-        {
-            return (SubmissionConfig) session.getAttribute("submission.config");
-        }
-        else
-        {
-            return null;
-        }
-    }
-    
-}
-

dspace-api/src/main/java/org/dspace/app/util/SubmissionStepConfig.java

@@ -1,220 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.util;
-
-import java.util.Map;
-import java.io.Serializable;
-
-/**
- * Class representing configuration for a single step within an Item Submission
- * Process. In other words, this is a single step in the SubmissionConfig class.
- * This class represents the structure of a single 'step' node in the
- * item-submission.xml configuration file.
- *
- * Note: Implements Serializable as it will be saved to the current session during submission.
- * Please ensure that nothing is added to this class that isn't also serializable
- * 
- * @see org.dspace.app.util.SubmissionConfigReader
- * @see org.dspace.app.util.SubmissionConfig
- * 
- * @author Tim Donohue
- * @version $Revision$
- */
-public class SubmissionStepConfig implements Serializable
-{
-    /*
-     * The identifier for the Select Collection step
-     */
-    public static final String SELECT_COLLECTION_STEP = "collection";
-
-    /*
-     * The identifier for the Completion step
-     */
-    public static final String COMPLETE_STEP = "complete";
-
-    /**
-     * the id for this step ('id' only exists if this step is defined in the
-     * <step-definitions> section)
-     */
-    private String id = null;
-
-    /** the heading for this step */
-    private String heading = null;
-
-    /** the name of the java processing class for this step */
-    private String processingClassName = null;
-   
-    /** whether or not this step is editable during workflow (default=true) */
-    private boolean workflowEditable = true;
-
-    /** 
-     * The full name of the JSP-UI binding class for this step. This field is
-     * ONLY used by the JSP-UI.
-     **/
-    private String jspBindingClassName = null;
-
-    /**
-     * The full name of the Manakin XML-UI Transformer class which will generate
-     * the necessary DRI for displaying this class in Manakin. This field is
-     * ONLY used by the Manakin XML-UI.
-     */
-    private String xmlBindingClassName = null;
-
-    /** The number of this step in the current SubmissionConfig */
-    private int number = -1;
-
-    /**
-     * Class constructor for creating an empty SubmissionStepConfig object
-     */
-    public SubmissionStepConfig()
-    {
-    }
-
-    /**
-     * Class constructor for creating a SubmissionStepConfig object based on the
-     * contents of a HashMap initialized by the SubmissionConfig object.
-     * 
-     * @param stepMap
-     *            the HashMap containing all required information about this
-     *            step
-     */
-    public SubmissionStepConfig(Map<String, String> stepMap)
-    {
-        id = stepMap.get("id");
-        heading = stepMap.get("heading");
-        processingClassName = stepMap.get("processing-class");
-        jspBindingClassName = stepMap.get("jspui-binding");
-        xmlBindingClassName = stepMap.get("xmlui-binding");
-
-        String wfEditString = stepMap.get("workflow-editable");
-        if (wfEditString != null && wfEditString.length() > 0)
-        {
-            workflowEditable = Boolean.parseBoolean(wfEditString);
-        }
-    }
-
-    /**
-     * Get the ID for this step. An ID is only defined if the step exists in the
-     * <step-definitions> section. This ID field is used to reference special
-     * steps (like the required step with id="collection")
-     * 
-     * @return the step ID
-     */
-    public String getId()
-    {
-        return id;
-    }
-
-    /**
-     * Get the heading for this step. This can either be a property from
-     * Messages.properties, or the actual heading text. If this "heading"
-     * contains a period(.) it is assumed to reference Messages.properties.
-     * 
-     * @return the heading
-     */
-    public String getHeading()
-    {
-        return heading;
-    }
-
-    /**
-     * Get the class which handles all processing for this step.
-     * <p>
-     * This class must extend the org.dspace.submit.AbstractProcessingStep class,
-     * and provide processing for BOTH the JSP-UI and XML-UI
-     * 
-     * @return the class's full class path (e.g.
-     *         "org.dspace.submit.step.MySampleStep")
-     */
-    public String getProcessingClassName()
-    {
-        return processingClassName;
-    }
-
-    /**
-     * Retrieve the full class name of the Manakin Transformer which will
-     * generate this step's DRI, for display in Manakin XML-UI.
-     * <P>
-     * This class must extend the
-     * org.dspace.app.xmlui.aspect.submission.StepTransformer class.
-     * <P>
-     * This property is only used by the Manakin XML-UI, and therefore is not
-     * relevant if you are using the JSP-UI.
-     * 
-     * @return the full java class name of the Transformer to use for this step
-     */
-    public String getXMLUIClassName()
-    {
-        return xmlBindingClassName;
-    }
-    
-    /**
-     * Retrieve the full class name of the JSP-UI "binding" class which will
-     * initialize and call the necessary JSPs for display in the JSP-UI
-     * <P>
-     * This class must extend the
-     * org.dspace.app.webui.submit.JSPStep class.
-     * <P>
-     * This property is only used by the JSP-UI, and therefore is not
-     * relevant if you are using the XML-UI (aka. Manakin).
-     * 
-     * @return the full java class name of the JSPStep to use for this step
-     */
-    public String getJSPUIClassName()
-    {
-        return jspBindingClassName;
-    }
-
-    /**
-     * Get the number of this step in the current Submission process config.
-     * Step numbers start with #0 (although step #0 is ALWAYS the special
-     * "select collection" step)
-     * 
-     * @return the number of this step in the current SubmissionConfig
-     */
-    public int getStepNumber()
-    {
-        return number;
-    }
-
-    /**
-     * Sets the number of this step in the current Submission process config.
-     * Step numbers start with #0 (although step #0 is ALWAYS the special
-     * "select collection" step)
-     * 
-     * @param stepNum
-     *            the step number.
-     */
-    protected void setStepNumber(int stepNum)
-    {
-        this.number = stepNum;
-    }
-
-    /**
-     * Whether or not this step is editable during workflow processing. If
-     * "true", then this step will appear in the "Edit Metadata" stage of the
-     * workflow process.
-     * 
-     * @return if step is editable in a workflow process
-     */
-    public boolean isWorkflowEditable()
-    {
-        return workflowEditable;
-    }
-
-    /**
-     * Whether or not this step is visible within the Progress Bar. A step is
-     * only visible if it has been assigned a Heading, otherwise it's invisible
-     * 
-     * @return if step is visible within the progress bar
-     */
-    public boolean isVisible()
-    {
-        return ((heading != null) && (heading.length() > 0));
-    }
-}