[maven-release-plugin] prepare release dspace-5.11

[Prep for 5.11] Fix DSpace 5.x branch to make it releasable again.  Add Docker Compose for easier testing.

.dockerignore

@@ -0,0 +1,6 @@
+.git/
+.idea/
+.settings/
+*/target/
+dspace/modules/*/target/
+Dockerfile.*

.gitattributes

@@ -1,6 +1,12 @@
 # Auto detect text files and perform LF normalization
 * text=auto
 
+# Ensure Unix files always keep Unix line endings
+*.sh text eol=lf
+
+# Ensure Windows files always keep Windows line endings
+*.bat text eol=crlf
+
 # Standard to msysgit
 *.doc  diff=astextplain
 *.DOC  diff=astextplain

.github/workflows/build.yml

@@ -0,0 +1,84 @@
+# DSpace 5.x Continuous Integration/Build via GitHub Actions
+# Concepts borrowed from
+# https://docs.github.com/en/free-pro-team@latest/actions/guides/building-and-testing-java-with-maven
+name: Build
+
+# Run this Build for all pushes / PRs to current branch
+on: [push, pull_request]
+
+jobs:
+  tests:
+    runs-on: ubuntu-18.04
+    env:
+      # Give Maven 1GB of memory to work with
+      # Suppress all Maven "downloading" messages in Travis logs (see https://stackoverflow.com/a/35653426)
+      # This also slightly speeds builds, as there is less logging
+      MAVEN_OPTS: "-Xmx1024M -Dorg.slf4j.simpleLogger.log.org.apache.maven.cli.transfer.Slf4jMavenTransferListener=warn"
+    # These are the actual CI steps to perform per job
+    steps:
+      # https://github.com/actions/checkout
+      - name: Checkout codebase
+        uses: actions/checkout@v1
+
+      # https://github.com/actions/setup-java
+      - name: Install JDK 8
+        uses: actions/setup-java@v1
+        with:
+          java-version: 8
+
+      # https://github.com/actions/setup-ruby
+      - name: Install Ruby v2.4 (for Mirage 2)
+        uses: actions/setup-ruby@v1
+        with:
+          ruby-version: 2.4
+
+      - name: Install Node.js v6.5 (for Mirage 2)
+        shell: bash -l {0}
+        run: nvm install 6.5.0
+
+      # Install prerequisites for building Mirage2 more rapidly
+      # Includes NPM, Bower, Grunt, Ruby, Sass, Compass
+      # These versions should be kept in sync with ./dspace/modules/xml-mirage2/pom.xml
+      - name: Install Mirage 2 prerequisites
+        run: |
+          sudo npm install -g npm@3.10.8
+          npm --version
+          sudo npm install -g bower
+          sudo npm install -g grunt && sudo npm install -g grunt-cli
+          grunt --version
+          gem install sass -v 3.4.25
+          sass -v
+          gem install compass -v 1.0.1
+          compass version
+          gem env
+      # https://github.com/actions/cache
+      - name: Cache Maven dependencies
+        uses: actions/cache@v2
+        with:
+          # Cache entire ~/.m2/repository
+          path: ~/.m2/repository
+          # Cache key is hash of all pom.xml files. Therefore any changes to POMs will invalidate cache
+          key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
+          restore-keys: ${{ runner.os }}-maven-
+
+      # [Build & Unit Test] Check source code licenses and run source code Unit Tests
+      #   license:check => Validate all source code license headers
+      #   -Dmaven.test.skip=false => Enable DSpace Unit Tests
+      #   -DskipITs=false         => Enable DSpace Integration Tests
+      #   -P !assembly            => Skip normal assembly (as it can be memory intensive)
+      #   -B => Maven batch/non-interactive mode (recommended for CI)
+      #   -V => Display Maven version info before build
+      #   -Dsurefire.rerunFailingTestsCount=2 => try again for flaky tests, and keep track of/report on number of retries
+      - name: Run Maven Build & Test
+        run: mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2
+
+      # [Assemble DSpace] Ensure assembly process works (from [src]/dspace/), including Mirage 2
+      #   -Dmirage2.on=true => Build Mirage2
+      #   -Dmirage2.deps.included=false => Don't include Mirage2 build dependencies (we installed them above)
+      #   -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
+      - name: Assemble DSpace & Build Mirage 2
+        run: cd dspace && mvn package -Dmirage2.on=true -Dmirage2.deps.included=false -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2
+        env:
+          # Set GEM env variables (for Mirage 2) based on output of 'gem env' in "Install Mirage 2 prerequisites" step
+          GEM_HOME: "/home/runner/.gem/ruby/2.4.0"
+          GEM_PATH: "/home/runner/.gem/ruby/2.4.0:/opt/hostedtoolcache/Ruby/2.4.10/x64/lib/ruby/gems/2.4.0"

.gitignore

@@ -3,6 +3,7 @@ target/
 
 ## Ignore project files created by Eclipse
 .settings/
+/bin/
 .project
 .classpath
 

.travis.yml

@@ -1,45 +0,0 @@
-language: java
-
-env: 
-  # Give Maven 1GB of memory to work with
-  - MAVEN_OPTS=-Xmx1024M
-
-# Install prerequisites for building Mirage2 more rapidly
-before_install:
-  # Install latest Node.js 0.10.x & print version info
-  - nvm install 0.10
-  - node --version
-  # Install Bower
-  - npm install -g bower
-  # Install Grunt & print version info
-  - npm install -g grunt && npm install -g grunt-cli
-  - grunt --version
-  # Print ruby version info (should be installed)
-  - ruby -v
-  # Install Sass & print version info
-  - gem install sass
-  - sass -v
-  # Install Compass & print version info
-  - gem install compass
-  - compass version
-
-# Skip install stage, as we'll do it below
-install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
-
-# Two stage Build and Test
-# 1. Install & Unit Test APIs
-# 2. Assemble DSpace
-script:
-  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
-  #    (This explicitly skips building the 'dspace' assembly module, since we only want to do that ONCE.)
-  #        license:check => Validate all source code license headers
-  #        -Dmaven.test.skip=false => Enable DSpace Unit Tests
-  #        -P !dspace => SKIP full DSpace assembly (will do below)
-  #        -B => Maven batch/non-interactive mode (recommended for CI)
-  #        -V => Display Maven version info before build
-  - "mvn clean install license:check -Dmaven.test.skip=false -P !dspace -B -V"
-  # 2. [Assemble DSpace] Ensure assembly process works (from [src]/dspace/), including Mirage 2
-  #        -Dmirage2.on=true => Build Mirage2
-  #        -Dmirage2.deps.included=false => Don't include Mirage2 build dependencies (We installed them in before_install)
-  #        -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
-  - "cd dspace && mvn package -Dmirage2.on=true -Dmirage2.deps.included=false -P !assembly -B -V"

Dockerfile.cli.jdk8

@@ -0,0 +1,60 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - openjdk:8-jdk
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace-cli: dspace/dspace-cli:dspace-5_x
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-5_x-jdk8 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -P'!dspace-solr,!dspace-jspui,!dspace-xmlui,!dspace-rest,!dspace-xmlui-mirage2,!dspace-rdf,!dspace-sword,!dspace-swordv2' && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM openjdk:8-jdk as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code
+
+# Step 3 - Run jdk
+# Create a new jdk image that does not retain the the build directory contents
+FROM openjdk:8-jdk
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+
+ENV JAVA_OPTS=-Xmx1000m
+
+# This script is used to parse environment variables to configs in dspace.cfg
+# It is not executed in this Docker file, so it's up to docker-compose to call it.
+COPY dspace/src/main/docker/parse_env_to_configs.sh $DSPACE_INSTALL/bin/parse_env_to_configs.sh
+
+# Ensure all scripts are executable
+RUN chmod +x $DSPACE_INSTALL/bin/*

Dockerfile.dependencies-jdk7

@@ -0,0 +1,24 @@
+# This image will be published as dspace/dspace-dependencies:dspace-5_x-jdk7
+# The purpose of this image is to make the build for dspace/dspace run faster 
+
+# Step 1 - Run Maven Build
+FROM maven:3-jdk-7 as build
+WORKDIR /app
+
+# The Mirage2 build cannot run as root.  Setting the user to dspace.
+RUN useradd dspace \
+    && mkdir /home/dspace /app/target \
+    && chown -Rv dspace: /home/dspace /app /app/target
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Trigger the installation of all maven dependencies including the Mirage2 dependencies
+# Clean up the built artifacts in the same step to keep the docker image small
+RUN mvn package -Dmirage2.on=true && cd /app && mvn clean
+
+# Clear the contents of the /app directory so no artifacts are left when dspace:dspace is built
+USER root
+RUN rm -rf /app/*

Dockerfile.dependencies-jdk8

@@ -0,0 +1,24 @@
+# This image will be published as dspace/dspace-dependencies:dspace-5_x-jdk8
+# The purpose of this image is to make the build for dspace/dspace run faster 
+
+# Step 1 - Run Maven Build
+FROM maven:3-jdk-8 as build
+WORKDIR /app
+
+# The Mirage2 build cannot run as root.  Setting the user to dspace.
+RUN useradd dspace \
+    && mkdir /home/dspace /app/target \
+    && chown -Rv dspace: /home/dspace /app /app/target
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY dspace/src/main/docker/build.properties /app/build.properties
+
+# Trigger the installation of all maven dependencies including the Mirage2 dependencies
+# Clean up the built artifacts in the same step to keep the docker image small
+RUN mvn package -Dmirage2.on=true && mvn clean
+
+# Clear the contents of the /app directory so no artifacts are left when dspace:dspace is built
+USER root
+RUN rm -rf /app/*

Dockerfile.jdk7

@@ -0,0 +1,63 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK7 compatible
+# - tomcat:7-jre7
+# - ANT 1.9.14
+# - maven:3-jdk-7
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-5_x-jdk7
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-5_x-jdk7 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:7-jre7 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.9.14
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:7-jre7
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2

Dockerfile.jdk7-test

@@ -0,0 +1,69 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK7 compatible
+# - tomcat:7-jre7
+# - ANT 1.9.14
+# - maven:3-jdk-7
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-5_x-jdk7
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-5_x-jdk7 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:7-jre7 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.9.14
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:7-jre7
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2
+
+COPY dspace/src/main/docker/test/solr_web.xml $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml
+COPY dspace/src/main/docker/test/rest_web.xml $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml
+
+RUN sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml && \
+    sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml

Dockerfile.jdk8

@@ -0,0 +1,72 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:7-jre8
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-5_x-jdk8
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-5_x-jdk8 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:7-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:7-jre8
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2
+
+COPY dspace/src/main/docker/parse_env_to_configs.sh $DSPACE_INSTALL/bin/parse_env_to_configs.sh
+
+# Ensure all scripts are executable
+RUN chmod +x $DSPACE_INSTALL/bin/*
+
+# On startup run this command to parse environment variables to configs in dspace.cfg
+# Then start Tomcat
+CMD ["sh", "-c", "$DSPACE_INSTALL/bin/parse_env_to_configs.sh && catalina.sh run"]

Dockerfile.jdk8-test

@@ -0,0 +1,78 @@
+# This image will be published as dspace/dspace
+# See https://dspace-labs.github.io/DSpace-Docker-Images/ for usage details
+# 
+# This version is JDK8 compatible
+# - tomcat:7-jre8
+# - ANT 1.10.7
+# - maven:3-jdk-8
+# - note: 
+# - default tag for branch: dspace/dspace: dspace/dspace:dspace-5_x-jdk8
+
+# Step 1 - Run Maven Build
+FROM dspace/dspace-dependencies:dspace-5_x-jdk8 as build
+ARG TARGET_DIR=dspace-installer
+WORKDIR /app
+
+# The dspace-install directory will be written to /install
+RUN mkdir /install \
+    && chown -Rv dspace: /install
+
+USER dspace
+
+# Copy the DSpace source code into the workdir (excluding .dockerignore contents)
+ADD --chown=dspace . /app/
+COPY --chown=dspace dspace/src/main/docker/build.properties /app/build.properties
+
+# Build DSpace.  Copy the dspace-install directory to /install.  Clean up the build to keep the docker image small
+RUN mvn package -Dmirage2.on=true && \
+  mv /app/dspace/target/${TARGET_DIR}/* /install && \
+  mvn clean
+
+# Step 2 - Run Ant Deploy
+FROM tomcat:7-jre8 as ant_build
+ARG TARGET_DIR=dspace-installer
+COPY --from=build /install /dspace-src
+WORKDIR /dspace-src
+
+# Create the initial install deployment using ANT
+ENV ANT_VERSION 1.10.7
+ENV ANT_HOME /tmp/ant-$ANT_VERSION
+ENV PATH $ANT_HOME/bin:$PATH
+
+RUN mkdir $ANT_HOME && \
+    wget -qO- "https://archive.apache.org/dist/ant/binaries/apache-ant-$ANT_VERSION-bin.tar.gz" | tar -zx --strip-components=1 -C $ANT_HOME
+
+RUN ant init_installation update_configs update_code update_webapps update_solr_indexes
+
+# Step 3 - Run tomcat
+# Create a new tomcat image that does not retain the the build directory contents
+FROM tomcat:7-jre8
+ENV DSPACE_INSTALL=/dspace
+COPY --from=ant_build /dspace $DSPACE_INSTALL
+EXPOSE 8080 8009
+
+ENV JAVA_OPTS=-Xmx2000m
+
+RUN ln -s $DSPACE_INSTALL/webapps/solr    /usr/local/tomcat/webapps/solr    && \
+    ln -s $DSPACE_INSTALL/webapps/xmlui   /usr/local/tomcat/webapps/xmlui   && \
+    ln -s $DSPACE_INSTALL/webapps/jspui   /usr/local/tomcat/webapps/jspui   && \
+    ln -s $DSPACE_INSTALL/webapps/rest    /usr/local/tomcat/webapps/rest    && \
+    ln -s $DSPACE_INSTALL/webapps/oai     /usr/local/tomcat/webapps/oai     && \
+    ln -s $DSPACE_INSTALL/webapps/rdf     /usr/local/tomcat/webapps/rdf     && \
+    ln -s $DSPACE_INSTALL/webapps/sword   /usr/local/tomcat/webapps/sword   && \
+    ln -s $DSPACE_INSTALL/webapps/swordv2 /usr/local/tomcat/webapps/swordv2
+    
+COPY dspace/src/main/docker/test/solr_web.xml $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml
+COPY dspace/src/main/docker/test/rest_web.xml $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml
+
+RUN sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/solr/WEB-INF/web.xml && \
+    sed -i -e "s|\${dspace.dir}|$DSPACE_INSTALL|" $DSPACE_INSTALL/webapps/rest/WEB-INF/web.xml
+
+COPY dspace/src/main/docker/parse_env_to_configs.sh $DSPACE_INSTALL/bin/parse_env_to_configs.sh
+
+# Ensure all scripts are executable
+RUN chmod +x $DSPACE_INSTALL/bin/*
+
+# On startup run this command to parse environment variables to configs in dspace.cfg
+# Then start Tomcat
+CMD ["sh", "-c", "$DSPACE_INSTALL/bin/parse_env_to_configs.sh && catalina.sh run"]

LICENSE

@@ -1,7 +1,6 @@
-DSpace source code license:
+BSD 3-Clause License
 
-
-Copyright (c) 2002-2013, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2022, LYRASIS.  All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are
@@ -14,13 +13,12 @@ notice, this list of conditions and the following disclaimer.
 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.
+- Neither the name of the copyright holder 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
+"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,
@@ -30,11 +28,4 @@ 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.
+DAMAGE.

LICENSES_THIRD_PARTY

@@ -22,13 +22,18 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 
         * Ant-Contrib Tasks (ant-contrib:ant-contrib:1.0b3 - http://ant-contrib.sourceforge.net)
         * Code Generation Library (cglib:cglib:3.1 - http://cglib.sourceforge.net/)
+        * AWS SDK for Java - Core (com.amazonaws:aws-java-sdk-core:1.10.50 - https://aws.amazon.com/sdkforjava)
+        * AWS Java SDK for AWS KMS (com.amazonaws:aws-java-sdk-kms:1.10.50 - https://aws.amazon.com/sdkforjava)
+        * AWS Java SDK for Amazon S3 (com.amazonaws:aws-java-sdk-s3:1.10.50 - https://aws.amazon.com/sdkforjava)
         * HPPC Collections (com.carrotsearch:hppc:0.5.2 - http://labs.carrotsearch.com/hppc.html/hppc)
         * metadata-extractor (com.drewnoakes:metadata-extractor:2.6.2 - http://code.google.com/p/metadata-extractor/)
         * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.3.0 - http://wiki.fasterxml.com/JacksonHome)
-        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.1.3 - http://wiki.fasterxml.com/JacksonHome)
+        * Jackson-annotations (com.fasterxml.jackson.core:jackson-annotations:2.9.3 - http://github.com/FasterXML/jackson)
         * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
+        * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.9.3 - https://github.com/FasterXML/jackson-core)
         * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
-        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.19.0 - http://code.google.com/p/google-api-java-client/google-api-client/)
+        * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.9.3 - http://github.com/FasterXML/jackson)
+        * Google APIs Client Library for Java (com.google.api-client:google-api-client:1.19.1 - http://code.google.com/p/google-api-java-client/google-api-client/)
         * Google Analytics API v3-rev103-1.19.0 (com.google.apis:google-api-services-analytics:v3-rev103-1.19.0 - http://nexus.sonatype.org/oss-repository-hosting.html/google-api-services-analytics)
         * FindBugs-jsr305 (com.google.code.findbugs:jsr305:3.0.0 - http://findbugs.sourceforge.net/)
         * Gson (com.google.code.gson:gson:2.2.1 - http://code.google.com/p/google-gson/)
@@ -39,8 +44,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Google HTTP Client Library for Java (com.google.http-client:google-http-client:1.19.0 - http://code.google.com/p/google-http-java-client/google-http-client/)
         * Jackson 2 extensions to the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-jackson2:1.19.0 - http://code.google.com/p/google-http-java-client/google-http-client-jackson2/)
         * Google OAuth Client Library for Java (com.google.oauth-client:google-oauth-client:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client/)
-        * Java 6 (and higher) extensions to the Google OAuth Client Library for Java. (com.google.oauth-client:google-oauth-client-java6:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client-java6/)
-        * Jetty extensions to the Google OAuth Client Library for Java. (com.google.oauth-client:google-oauth-client-jetty:1.19.0 - http://code.google.com/p/google-oauth-java-client/google-oauth-client-jetty/)
         * ConcurrentLinkedHashMap (com.googlecode.concurrentlinkedhashmap:concurrentlinkedhashmap-lru:1.2 - http://code.google.com/p/concurrentlinkedhashmap)
         * FORESITE :: Object Reuse and Exchange library (com.googlecode.foresite-toolkit:foresite:0.9 - http://www.openarchives.org/ore)
         * ISO Parser (com.googlecode.mp4parser:isoparser:1.0-RC-1 - http://code.google.com/p/mp4parser/)
@@ -49,12 +52,13 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Jtwig Core Functions (com.lyncode:jtwig-functions:2.0.1 - http://www.lyncode.com/jtwig-functions)
         * Jtwig Spring (com.lyncode:jtwig-spring:2.0.1 - http://www.lyncode.com/jtwig-spring)
         * Test Support (com.lyncode:test-support:1.0.3 - http://nexus.sonatype.org/oss-repository-hosting.html/test-support)
-        * XOAI : OAI-PMH Java Toolkit (com.lyncode:xoai:3.2.9 - http://www.lyncode.com)
+        * MaxMind DB Reader (com.maxmind.db:maxmind-db:1.2.2 - http://dev.maxmind.com/)
+        * MaxMind GeoIP2 API (com.maxmind.geoip2:geoip2:2.11.0 - http://dev.maxmind.com/geoip/geoip2/web-services)
         * Spatial4J (com.spatial4j:spatial4j:0.4.1 - https://github.com/spatial4j/spatial4j)
         * Commons BeanUtils (commons-beanutils:commons-beanutils:1.8.3 - http://commons.apache.org/beanutils/)
         * Commons CLI (commons-cli:commons-cli:1.2 - http://commons.apache.org/cli/)
         * Apache Commons Codec (commons-codec:commons-codec:1.9 - http://commons.apache.org/proper/commons-codec/)
-        * Collections (commons-collections:commons-collections:3.2 - http://jakarta.apache.org/commons/collections/)
+        * Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
         * Commons Configuration (commons-configuration:commons-configuration:1.6 - http://commons.apache.org/${pom.artifactId.substring(8)}/)
         * Commons Configuration (commons-configuration:commons-configuration:1.8 - http://commons.apache.org/configuration/)
         * Commons DBCP (commons-dbcp:commons-dbcp:1.4 - http://commons.apache.org/dbcp/)
@@ -119,9 +123,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Excalibur Instrument API (org.apache.excalibur.containerkit:excalibur-instrument-api:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-instrument-modules/excalibur-instrument-api/)
         * Excalibur Logger (org.apache.excalibur.containerkit:excalibur-logger:2.2.1 - http://www.apache.org/excalibur/excalibur-containerkit/excalibur-logger/)
         * Activation (org.apache.geronimo.specs:geronimo-activation_1.0.2_spec:1.1 - http://geronimo.apache.org/geronimo-activation_1.0.2_spec)
-        * Activation 1.1 (org.apache.geronimo.specs:geronimo-activation_1.1_spec:1.0.2 - http://geronimo.apache.org/specs/geronimo-activation_1.1_spec)
-        * JavaMail 1.4 (org.apache.geronimo.specs:geronimo-javamail_1.4_spec:1.6 - http://geronimo.apache.org/maven/specs/geronimo-javamail_1.4_spec/1.6)
-        * Streaming API for XML (STAX API 1.0) (org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:1.0 - http://geronimo.apache.org/specs/geronimo-stax-api_1.0_spec)
+        * Activation 1.1 (org.apache.geronimo.specs:geronimo-activation_1.1_spec:1.1 - http://geronimo.apache.org/maven/specs/geronimo-activation_1.1_spec/1.1)
+        * JavaMail 1.4 (org.apache.geronimo.specs:geronimo-javamail_1.4_spec:1.7.1 - http://geronimo.apache.org/maven/specs/geronimo-javamail_1.4_spec/1.7.1)
         * Streaming API for XML (STAX API 1.0) (org.apache.geronimo.specs:geronimo-stax-api_1.0_spec:1.0.1 - http://geronimo.apache.org/specs/geronimo-stax-api_1.0_spec)
         * Apache Hadoop Annotations (org.apache.hadoop:hadoop-annotations:2.2.0 - no url defined)
         * Apache Hadoop Auth (org.apache.hadoop:hadoop-auth:2.2.0 - no url defined)
@@ -158,9 +161,9 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Lucene Sandbox (org.apache.lucene:lucene-sandbox:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-sandbox)
         * Lucene Spatial (org.apache.lucene:lucene-spatial:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-spatial)
         * Lucene Suggest (org.apache.lucene:lucene-suggest:4.10.2 - http://lucene.apache.org/lucene-parent/lucene-suggest)
-        * Apache FontBox (org.apache.pdfbox:fontbox:1.8.7 - http://pdfbox.apache.org/)
-        * Apache JempBox (org.apache.pdfbox:jempbox:1.8.7 - http://www.apache.org/pdfbox-parent/jempbox/)
-        * Apache PDFBox (org.apache.pdfbox:pdfbox:1.8.7 - http://www.apache.org/pdfbox-parent/pdfbox/)
+        * Apache FontBox (org.apache.pdfbox:fontbox:1.8.12 - http://pdfbox.apache.org/)
+        * Apache JempBox (org.apache.pdfbox:jempbox:1.8.12 - http://www.apache.org/pdfbox-parent/jempbox/)
+        * Apache PDFBox (org.apache.pdfbox:pdfbox:1.8.12 - http://www.apache.org/pdfbox-parent/pdfbox/)
         * Apache POI (org.apache.poi:poi:3.6 - http://poi.apache.org/)
         * Apache POI (org.apache.poi:poi-ooxml:3.6 - http://poi.apache.org/)
         * Apache POI (org.apache.poi:poi-ooxml-schemas:3.10.1 - http://poi.apache.org/)
@@ -174,8 +177,8 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Apache Tika core (org.apache.tika:tika-core:1.5 - http://tika.apache.org/)
         * Apache Tika parsers (org.apache.tika:tika-parsers:1.5 - http://tika.apache.org/)
         * Apache Tika XMP (org.apache.tika:tika-xmp:1.5 - http://tika.apache.org/)
-        * Axiom API (org.apache.ws.commons.axiom:axiom-api:1.2.10 - http://ws.apache.org/axiom/axiom-api/)
-        * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.10 - http://ws.apache.org/axiom/axiom-impl/)
+        * Axiom API (org.apache.ws.commons.axiom:axiom-api:1.2.14 - http://ws.apache.org/axiom/)
+        * Axiom Impl (org.apache.ws.commons.axiom:axiom-impl:1.2.14 - http://ws.apache.org/axiom/)
         * XmlBeans (org.apache.xmlbeans:xmlbeans:2.3.0 - http://xmlbeans.apache.org)
         * XmlBeans (org.apache.xmlbeans:xmlbeans:2.6.0 - http://xmlbeans.apache.org)
         * zookeeper (org.apache.zookeeper:zookeeper:3.4.6 - no url defined)
@@ -188,6 +191,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Data Mapper for Jackson (org.codehaus.jackson:jackson-mapper-asl:1.9.2 - http://jackson.codehaus.org)
         * Xml Compatibility extensions for Jackson (org.codehaus.jackson:jackson-xc:1.9.2 - http://jackson.codehaus.org)
         * Jettison (org.codehaus.jettison:jettison:1.1 - no url defined)
+        * Woodstox (org.codehaus.woodstox:woodstox-core-asl:4.1.4 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.0 - http://woodstox.codehaus.org)
         * Woodstox (org.codehaus.woodstox:wstx-asl:3.2.7 - http://woodstox.codehaus.org)
         * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
@@ -196,12 +200,10 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Ogg and Vorbis for Java, Core (org.gagravarr:vorbis-java-core:0.1 - https://github.com/Gagravarr/VorbisJava)
         * Apache Tika plugin for Ogg, Vorbis and FLAC (org.gagravarr:vorbis-java-tika:0.1 - https://github.com/Gagravarr/VorbisJava)
         * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
+        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
         * Jetty Server (org.mortbay.jetty:jetty:6.1.14 - http://jetty.mortbay.org/project/modules/jetty)
-        * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
         * Jetty Servlet Tester (org.mortbay.jetty:jetty-servlet-tester:6.1.14 - http://jetty.mortbay.org/project/jetty-servlet-tester)
         * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.14 - http://jetty.mortbay.org/project/jetty-util)
-        * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
-        * Servlet Specification API (org.mortbay.jetty:servlet-api:2.5-20081211 - http://jetty.mortbay.org/servlet-api)
         * Noggit (org.noggit:noggit:0.5 - http://noggit.org)
         * parboiled-core (org.parboiled:parboiled-core:1.1.6 - http://parboiled.org)
         * parboiled-java (org.parboiled:parboiled-java:1.1.6 - http://parboiled.org)
@@ -248,7 +250,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 
     BSD License:
 
-        * ASM Core (asm:asm:3.1 - http://asm.objectweb.org/asm/)
         * XMP Library for Java (com.adobe.xmp:xmpcore:5.1.2 - http://www.adobe.com/devnet/xmp.html)
         * coverity-escapers (com.coverity.security:coverity-escapers:1.1.1 - http://coverity.com/security)
         * JSONLD Java :: Core (com.github.jsonld-java:jsonld-java:0.5.0 - http://github.com/jsonld-java/jsonld-java/jsonld-java/)
@@ -265,54 +266,70 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Morfologik FSA (org.carrot2:morfologik-fsa:1.7.1 - http://morfologik.blogspot.com/morfologik-fsa/)
         * Morfologik Stemming Dictionary for Polish (org.carrot2:morfologik-polish:1.7.1 - http://morfologik.blogspot.com/morfologik-polish/)
         * Morfologik Stemming APIs (org.carrot2:morfologik-stemming:1.7.1 - http://morfologik.blogspot.com/morfologik-stemming/)
+        * Stax2 API (org.codehaus.woodstox:stax2-api:3.1.1 - http://woodstox.codehaus.org/StAX2)
         * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
-        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
-        * DSpace JSP-UI (org.dspace:dspace-jspui:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
-        * DSpace OAI-PMH (org.dspace:dspace-oai:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
-        * DSpace RDF (org.dspace:dspace-rdf:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
-        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:5.0-rc4-SNAPSHOT - http://demo.dspace.org)
-        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
-        * Apache Solr Webapp (org.dspace:dspace-solr:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
-        * DSpace SWORD (org.dspace:dspace-sword:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
-        * DSpace SWORD v2 (org.dspace:dspace-swordv2:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
-        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
+        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
+        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:5.0.7 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-api-lang)
+        * DSpace JSP-UI (org.dspace:dspace-jspui:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
+        * DSpace OAI-PMH (org.dspace:dspace-oai:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
+        * DSpace RDF (org.dspace:dspace-rdf:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
+        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:5.10-SNAPSHOT - http://demo.dspace.org)
+        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
+        * Apache Solr Webapp (org.dspace:dspace-solr:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
+        * DSpace SWORD (org.dspace:dspace-sword:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
+        * DSpace SWORD v2 (org.dspace:dspace-swordv2:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
+        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:5.10-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
+        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:5.0.7 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-xmlui-lang)
         * handle (org.dspace:handle:6.2 - no url defined)
         * jargon (org.dspace:jargon:1.4.25 - no url defined)
         * mets (org.dspace:mets:1.5.2 - no url defined)
         * oclc-harvester2 (org.dspace:oclc-harvester2:0.1.12 - no url defined)
+        * XOAI : OAI-PMH Java Toolkit (org.dspace:xoai:3.2.10 - http://nexus.sonatype.org/oss-repository-hosting.html/xoai)
         * Repackaged Cocoon Servlet Service Implementation (org.dspace.dependencies.cocoon:dspace-cocoon-servlet-service-impl:1.0.3 - http://projects.dspace.org/dspace-pom/dspace-cocoon-servlet-service-impl)
-        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
+        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:5.10-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
         * Hamcrest All (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
         * Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
         * JBibTeX (org.jbibtex:jbibtex:1.0.10 - http://www.jbibtex.org)
+        * JAXB2 Basics - Runtime (org.jvnet.jaxb2_commons:jaxb2-basics-runtime:0.9.5 - https://github.com/highsource/jaxb2-basics/jaxb2-basics-runtime)
         * ASM Core (org.ow2.asm:asm:4.1 - http://asm.objectweb.org/asm/)
         * ASM Core (org.ow2.asm:asm:4.2 - http://asm.objectweb.org/asm/)
         * ASM Analysis (org.ow2.asm:asm-analysis:4.1 - http://asm.objectweb.org/asm-analysis/)
         * ASM Commons (org.ow2.asm:asm-commons:4.1 - http://asm.objectweb.org/asm-commons/)
         * ASM Tree (org.ow2.asm:asm-tree:4.1 - http://asm.objectweb.org/asm-tree/)
         * ASM Util (org.ow2.asm:asm-util:4.1 - http://asm.objectweb.org/asm-util/)
-        * PostgreSQL JDBC Driver (postgresql:postgresql:9.1-901-1.jdbc4 - http://jdbc.postgresql.org)
         * XMLUnit for Java (xmlunit:xmlunit:1.1 - http://xmlunit.sourceforge.net/)
         * XMLUnit for Java (xmlunit:xmlunit:1.3 - http://xmlunit.sourceforge.net/)
 
     Common Development and Distribution License (CDDL):
 
-        * jersey-core (com.sun.jersey:jersey-core:1.17.1 - https://jersey.java.net/jersey-core/)
-        * jersey-json (com.sun.jersey:jersey-json:1.17.1 - https://jersey.java.net/jersey-json/)
-        * jersey-server (com.sun.jersey:jersey-server:1.17.1 - https://jersey.java.net/jersey-server/)
-        * jersey-servlet (com.sun.jersey:jersey-servlet:1.17.1 - https://jersey.java.net/jersey-servlet/)
-        * jersey-spring (com.sun.jersey.contribs:jersey-spring:1.8 - http://maven.apache.org)
+        * jersey-core (com.sun.jersey:jersey-core:1.19 - https://jersey.java.net/jersey-core/)
+        * jersey-json (com.sun.jersey:jersey-json:1.19 - https://jersey.java.net/jersey-json/)
+        * jersey-server (com.sun.jersey:jersey-server:1.19 - https://jersey.java.net/jersey-server/)
+        * jersey-servlet (com.sun.jersey:jersey-servlet:1.19 - https://jersey.java.net/jersey-servlet/)
+        * jersey-spring (com.sun.jersey.contribs:jersey-spring:1.19 - http://maven.apache.org)
         * JAXB RI (com.sun.xml.bind:jaxb-impl:2.2.3-1 - http://jaxb.java.net/)
         * JAXB Reference Implementation (com.sun.xml.bind:jaxb-impl:2.2.5 - http://jaxb.java.net/)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
         * JavaBeans Activation Framework (JAF) (javax.activation:activation:1.1 - http://java.sun.com/products/javabeans/jaf/index.jsp)
+        * javax.annotation API (javax.annotation:javax.annotation-api:1.2 - http://jcp.org/en/jsr/detail?id=250)
         * JavaMail API (javax.mail:mail:1.4 - https://glassfish.dev.java.net/javaee5/mail/)
         * Java Servlet API (javax.servlet:javax.servlet-api:3.1.0 - http://servlet-spec.java.net)
         * jsp-api (javax.servlet:jsp-api:2.0 - no url defined)
         * jstl (javax.servlet:jstl:1.1.2 - no url defined)
         * servlet-api (javax.servlet:servlet-api:2.5 - no url defined)
+        * javax.ws.rs-api (javax.ws.rs:javax.ws.rs-api:2.0.1 - http://jax-rs-spec.java.net)
+        * jsr311-api (javax.ws.rs:jsr311-api:1.1.1 - https://jsr311.dev.java.net)
         * JAXB API bundle for GlassFish V3 (javax.xml.bind:jaxb-api:2.2.2 - https://jaxb.dev.java.net/)
         * Streaming API for XML (javax.xml.stream:stax-api:1.0-2 - no url defined)
+        * HK2 API module (org.glassfish.hk2:hk2-api:2.4.0-b31 - https://hk2.java.net/hk2-api)
+        * ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:2.4.0-b31 - https://hk2.java.net/hk2-locator)
+        * HK2 Implementation Utilities (org.glassfish.hk2:hk2-utils:2.4.0-b31 - https://hk2.java.net/hk2-utils)
+        * OSGi resource locator bundle - used by various API providers that rely on META-INF/services mechanism to locate providers. (org.glassfish.hk2:osgi-resource-locator:1.0.1 - http://glassfish.org/osgi-resource-locator/)
+        * aopalliance version 1.0 repackaged as a module (org.glassfish.hk2.external:aopalliance-repackaged:2.4.0-b31 - https://hk2.java.net/external/aopalliance-repackaged)
+        * javax.inject:1 as OSGi bundle (org.glassfish.hk2.external:javax.inject:2.4.0-b31 - https://hk2.java.net/external/javax.inject)
+        * jersey-repackaged-guava (org.glassfish.jersey.bundles.repackaged:jersey-guava:2.22.1 - https://jersey.java.net/project/project/jersey-guava/)
+        * jersey-core-client (org.glassfish.jersey.core:jersey-client:2.22.1 - https://jersey.java.net/jersey-client/)
+        * jersey-core-common (org.glassfish.jersey.core:jersey-common:2.22.1 - https://jersey.java.net/jersey-common/)
         * Servlet Specification 2.5 API (org.mortbay.jetty:servlet-api-2.5:6.1.14 - http://jetty.mortbay.org/project/modules/servlet-api-2.5)
         * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
         * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
@@ -322,8 +339,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * JUnit (junit:junit:4.11 - http://junit.org)
         * AspectJ runtime (org.aspectj:aspectjrt:1.6.11 - http://www.aspectj.org)
         * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
-        * Jetty Server (org.mortbay.jetty:jetty:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/modules/jetty)
-        * Jetty Utilities (org.mortbay.jetty:jetty-util:6.1.26 - http://www.eclipse.org/jetty/jetty-parent/project/jetty-util)
         * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
         * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
 
@@ -337,7 +352,6 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Jackson-core (com.fasterxml.jackson.core:jackson-core:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
         * jackson-databind (com.fasterxml.jackson.core:jackson-databind:2.3.3 - http://wiki.fasterxml.com/JacksonHome)
         * FindBugs-Annotations (com.google.code.findbugs:annotations:3.0.0 - http://findbugs.sourceforge.net/)
-        * MaxMind GeoIP API (com.maxmind.geoip:geoip-api:1.2.11 - https://github.com/maxmind/geoip-api-java)
         * JHighlight (com.uwyn:jhighlight:1.0 - https://jhighlight.dev.java.net/)
         * JAX-RS provider for JSON content type (org.codehaus.jackson:jackson-jaxrs:1.9.2 - http://jackson.codehaus.org)
         * Xml Compatibility extensions for Jackson (org.codehaus.jackson:jackson-xc:1.9.2 - http://jackson.codehaus.org)
@@ -345,6 +359,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * DSpace TM-Extractors Dependency (org.dspace.dependencies:dspace-tm-extractors:1.0.1 - http://projects.dspace.org/dspace-pom/dspace-tm-extractors)
         * im4java (org.im4java:im4java:1.4.0 - http://sourceforge.net/projects/im4java/)
         * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
+        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
         * org.jdesktop - Swing Worker (org.jdesktop:swing-worker:1.1 - no url defined)
         * Restlet Core - API and Engine (org.restlet.jee:org.restlet:2.1.1 - http://www.restlet.org/org.restlet)
         * Restlet Extension - Servlet (org.restlet.jee:org.restlet.ext.servlet:2.1.1 - http://www.restlet.org/org.restlet.ext.servlet)
@@ -362,6 +377,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
 
         * Bouncy Castle CMS and S/MIME API (org.bouncycastle:bcmail-jdk15:1.44 - http://www.bouncycastle.org/java.html)
         * Bouncy Castle Provider (org.bouncycastle:bcprov-jdk15:1.44 - http://www.bouncycastle.org/java.html)
+        * ORCID Java API generated via JAXB (org.dspace:orcid-jaxb-api:2.1.0 - https://github.com/DSpace/orcid-jaxb-api)
         * Main (org.jmockit:jmockit:1.10 - http://www.jmockit.org)
         * OpenCloud (org.mcavallo:opencloud:0.3 - http://opencloud.mcavallo.org/)
         * Mockito (org.mockito:mockito-all:1.9.5 - http://www.mockito.org)
@@ -378,6 +394,7 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * juniversalchardet (com.googlecode.juniversalchardet:juniversalchardet:1.0.3 - http://juniversalchardet.googlecode.com/)
         * H2 Database Engine (com.h2database:h2:1.4.180 - http://www.h2database.com)
         * Javassist (org.javassist:javassist:3.16.1-GA - http://www.javassist.org/)
+        * Javassist (org.javassist:javassist:3.18.1-GA - http://www.javassist.org/)
         * Rhino (rhino:js:1.6R7 - http://www.mozilla.org/rhino/)
 
     Public Domain:
@@ -387,7 +404,10 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Reflections (org.reflections:reflections:0.9.9-RC1 - http://code.google.com/p/reflections/reflections/)
         * XZ for Java (org.tukaani:xz:1.4 - http://tukaani.org/xz/java.html)
 
-    Unknown license:
+    The JSON License:
 
-        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:5.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-api-lang)
-        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:5.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-xmlui-lang)
+        * JSON in Java (org.json:json:20180130 - https://github.com/douglascrockford/JSON-java)
+
+    The PostgreSQL License:
+
+        * PostgreSQL JDBC Driver - JDBC 4.1 (org.postgresql:postgresql:42.2.1.jre7 - https://github.com/pgjdbc/pgjdbc-parent-poms/pgjdbc-core-parent/pgjdbc-core-prevjre/postgresql)

NOTICE

@@ -1,15 +1,28 @@
+Licenses of Third-Party Libraries
+=================================
 
-Licensing Notice
+DSpace uses third-party libraries which may be distributed under
+different licenses than specified in our LICENSE file. 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 DSpace source code license, in order to
+use this software.
 
-Fedora Commons joined with the DSpace Foundation and began operating under
+Licensing Notices
+=================
+
+[July 2019] DuraSpace joined with LYRASIS (another 501(c)3 organization) in July 2019.
+LYRASIS holds the copyrights of DuraSpace.
+
+[July 2009] 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 
+[July 2007] 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

@@ -1,18 +1,16 @@
 DSpace version information can be viewed online at
- - https://wiki.duraspace.org/display/DSDOC/
+ - https://wiki.lyrasis.org/display/DSDOC/
 
 Documentation for the most recent stable release(s) may be downloaded
 or viewed online at
  - http://www.dspace.org/latest-release/
- - https://wiki.duraspace.org/display/DSDOC/
- - http://sourceforge.net/projects/dspace/files/DSpace%20Stable/
-     (select a version and read DSpace-Manual.pdf)
+ - https://wiki.lyrasis.org/display/DSDOC/
 
 Installation instructions are to be found in that documentation.
 
 In addition, a listing of all known contributors to DSpace software can be
 found online at:
-https://wiki.duraspace.org/display/DSPACE/DSpaceContributors
+https://wiki.lyrasis.org/display/DSPACE/DSpaceContributors
 
 Installation instructions for other versions may be different, so you
 are encouraged to obtain the appropriate version of the Documentation
@@ -26,20 +24,20 @@ or just:
 
  - git clone git://github.com/DSpace/DSpace.git
 
-Please refer any further problems to the dspace-tech@lists.sourceforge.net
+Please refer any further problems to the dspace-tech@googlegroups.com
 mailing list.
 
- - http://sourceforge.net/mail/?group_id=19984
+ - https://groups.google.com/d/forum/dspace-tech
 
 
-Detailed Issue Tracking for DSpace is done on our JIRA Issue Tracker
+Detailed Issue Tracking for DSpace is done in GitHub issues
 
- - https://jira.duraspace.org/browse/DS
+ - https://github.com/DSpace/DSpace/issues
 
 
 To contribute to DSpace, please see:
 
- - https://wiki.duraspace.org/display/DSPACE/How+to+Contribute+to+DSpace
+ - https://wiki.lyrasis.org/display/DSPACE/How+to+Contribute+to+DSpace
 
 
 For more details about DSpace, including a list of service providers,
@@ -47,8 +45,5 @@ places to seek help, news articles and lists of other users, please see:
 
  - http://www.dspace.org/
 
-
-DSpace source code licensing information available online at:
- - http://www.dspace.org/license/
-
-Copyright (c) 2002-2015, DuraSpace.  All rights reserved.
+DSpace source code is freely available under a standard [BSD 3-Clause license](https://opensource.org/licenses/BSD-3-Clause).
+The full license is available at http://www.dspace.org/license/

build.properties

@@ -66,14 +66,12 @@ db.password=dspace
 #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
-
-# NOTE: this configuration option is for PostgreSQL only. For Oracle, schema is equivalent
-# to user name. DSpace depends on the PostgreSQL understanding of schema. If you are using
-# Oracle, just leave this this value blank.
-
+# Schema name - if your database contains multiple schemas, you can avoid
+# problems with retrieving the definitions of duplicate object names by
+# specifying the schema name that is used for DSpace.
+# ORACLE USAGE NOTE: In Oracle, schema is equivalent to "username". This means
+# specifying a "db.schema" is often unnecessary (i.e. you can leave it blank),
+# UNLESS your Oracle DB Account (in db.username) has access to multiple schemas.
 db.schema = 
 
 # Maximum number of DB connections in pool

docker-compose-cli.yml

@@ -0,0 +1,43 @@
+#
+# 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/
+#
+
+version: "3.7"
+
+services:
+  dspace-cli:
+    image: "dspace/dspace-cli:${DSPACE_VER:-dspace-5_x}"
+    container_name: dspace-cli
+    build:
+      context: .
+      dockerfile: Dockerfile.cli.jdk8
+    environment:
+      # Env vars with double underbars in names will be replaced with periods and written to dspace.cfg
+      # The defaul values for dspace.cfg will be provided here
+      # __D__ -> -
+      # __P__ -> .
+      - dspace__P__dir=/dspace
+      - db__P__url=jdbc:postgresql://dspacedb:5432/dspace
+      - dspace__P__hostname=localhost
+      - dspace__P__baseUrl=http://localhost:8080
+      - dspace__P__name=DSpace Started with Docker Compose
+      - solr__P__server=http://dspace:8080/solr
+    volumes:
+      - assetstore:/dspace/assetstore
+    entrypoint: /dspace/bin/parse_env_to_configs.sh
+    # Any commands passed here will be forwarded to /dspace/bin/dspace by parse_env_to_configs.sh (see its code)
+    command: help
+    networks:
+      - dspacenet
+    tty: true
+    stdin_open: true
+
+volumes:
+  assetstore:
+
+networks:
+  dspacenet:

docker-compose.yml

@@ -0,0 +1,64 @@
+#
+# 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/
+#
+
+version: '3.7'
+networks:
+  dspacenet:
+services:
+  dspace:
+    container_name: dspace
+    depends_on:
+      - dspacedb
+    image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-dspace-5_x-jdk8-test}"
+    environment:
+      # Env vars with double underbars in names will be replaced with periods and written to dspace.cfg
+      # The defaul values for dspace.cfg will be provided here
+      # __D__ -> -
+      # __P__ -> .
+      - dspace__P__dir=/dspace
+      - db__P__url=jdbc:postgresql://dspacedb:5432/dspace
+      - dspace__P__hostname=localhost
+      - dspace__P__baseUrl=http://localhost:8080
+      - dspace__P__name=DSpace Started with Docker Compose
+      - solr__P__server=http://localhost:8080/solr
+    build:
+      context: .
+      dockerfile: Dockerfile.jdk8-test
+    networks:
+      dspacenet:
+    ports:
+      - published: 8080
+        target: 8080
+    stdin_open: true
+    tty: true
+    volumes:
+      - ./dspace/src/main/docker-compose/xmlui.xconf:/dspace/config/xmlui.xconf
+      - ./dspace/src/main/docker-compose/parse_configs.sh:/dspace/bin/parse_configs.sh
+      - assetstore:/dspace/assetstore
+      - solr_authority:/dspace/solr/authority/data
+      - solr_oai:/dspace/solr/oai/data
+      - solr_search:/dspace/solr/search/data
+      - solr_statistics:/dspace/solr/statistics/data
+  dspacedb:
+    container_name: dspacedb
+    environment:
+      PGDATA: /pgdata
+    image: dspace/dspace-postgres-pgcrypto
+    networks:
+      dspacenet:
+    stdin_open: true
+    tty: true
+    volumes:
+      - pgdata:/pgdata
+volumes:
+  assetstore:
+  pgdata:
+  solr_authority:
+  solr_oai:
+  solr_search:
+  solr_statistics:

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>5.0</version>
+        <version>5.11</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -209,7 +209,7 @@
                             </execution>
                         </executions>
                     </plugin>
-                    
+
                     <!-- FileWeaver plugin is in charge of initializing & "weaving" together
                          the dspace.cfg file to be used by the Unit Testing environment.
                          It weaves two files, the default 'dspace.cfg' and 'dspace.cfg.more',
@@ -528,9 +528,9 @@
             <version>1.8</version>
         </dependency>
         <dependency>
-            <groupId>com.maxmind.geoip</groupId>
-            <artifactId>geoip-api</artifactId>
-            <version>1.2.11</version>
+            <groupId>com.maxmind.geoip2</groupId>
+            <artifactId>geoip2</artifactId>
+            <version>2.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
@@ -569,10 +569,10 @@
 
 
         <dependency>
-            <groupId>postgresql</groupId>
+            <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
         </dependency>
-		
+
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
@@ -590,7 +590,7 @@
             <artifactId>im4java</artifactId>
             <version>1.4.0</version>
         </dependency>
-        
+
         <!-- Flyway DB API (flywaydb.org) is used to manage DB upgrades automatically. -->
         <dependency>
             <groupId>org.flywaydb</groupId>
@@ -603,13 +603,21 @@
             <groupId>com.google.apis</groupId>
             <artifactId>google-api-services-analytics</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.google.api-client</groupId>
+            <artifactId>google-api-client</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.http-client</groupId>
+            <artifactId>google-http-client</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.google.http-client</groupId>
             <artifactId>google-http-client-jackson2</artifactId>
         </dependency>
         <dependency>
             <groupId>com.google.oauth-client</groupId>
-            <artifactId>google-oauth-client-jetty</artifactId>
+            <artifactId>google-oauth-client</artifactId>
         </dependency>
         <!-- FindBugs -->
         <dependency>
@@ -631,6 +639,66 @@
             <version>1</version>
             <type>jar</type>
         </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-impl</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-api</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.core</groupId>
+            <artifactId>jersey-client</artifactId>
+            <version>2.22.1</version>
+        </dependency>
+        <!-- S3 -->
+        <dependency>
+            <groupId>com.amazonaws</groupId>
+            <artifactId>aws-java-sdk-s3</artifactId>
+            <version>1.10.50</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>joda-time</groupId>
+                    <artifactId>joda-time</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-databind</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <!-- S3 also wanted jackson... -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+
+        <!-- For ORCID v2 integration -->
+        <dependency>
+            <groupId>org.dspace</groupId>
+            <artifactId>orcid-jaxb-api</artifactId>
+            <version>2.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.json</groupId>
+            <artifactId>json</artifactId>
+            <version>20180130</version>
+        </dependency>
     </dependencies>
 
 </project>

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

@@ -113,8 +113,8 @@ public class CommunityFiliator
         CommunityFiliator filiator = new CommunityFiliator();
         Context c = new Context();
 
-        // ve are superuser!
-        c.setIgnoreAuthorization(true);
+        // we are superuser!
+        c.turnOffAuthorisationSystem();
 
         try
         {

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

@@ -228,7 +228,7 @@ public final class CreateAdministrator
     {
     	// Of course we aren't an administrator yet so we need to
     	// circumvent authorisation
-    	context.setIgnoreAuthorization(true);
+    	context.turnOffAuthorisationSystem();
     	
     	// Find administrator group
     	Group admins = Group.find(context, 1);

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

@@ -88,7 +88,7 @@ public class MetadataExporter
     {
         // create a context
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
 
         OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
         xmlFormat.setLineWidth(120);

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

@@ -187,7 +187,7 @@ public class DSpaceCSV implements Serializable
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while (StringUtils.isNotBlank(lineRead = input.readLine()))
+            while ((lineRead = input.readLine()) != null)
             {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line

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

@@ -1169,10 +1169,8 @@ public class MetadataImport
      */
     private static boolean isAuthorityControlledField(String md)
     {
-        int pos = md.indexOf("[");
-        String mdf = (pos > -1 ? md.substring(0, pos) : md);
-        pos = md.indexOf(":");
-        mdf = (pos > -1 ? md.substring(pos+1) : md);
+        String mdf = StringUtils.substringAfter(md, ":");
+        mdf = StringUtils.substringBefore(mdf, "[");
         return authorityControlled.contains(mdf);
     }
 

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

@@ -89,16 +89,16 @@ public class MetadataImportInvalidHeadingException extends Exception
     {
         if (type == SCHEMA)
         {
-            return "Unknown metadata schema in row " + column + ": " + badHeading;
+            return "Unknown metadata schema in column " + column + ": " + badHeading;
         } else if (type == ELEMENT)
         {
-            return "Unknown metadata element in row " + column + ": " + badHeading;
+            return "Unknown metadata element in column " + column + ": " + badHeading;
         } else if (type == MISSING)
         {
-            return "Row with missing header: Row " + column;
+            return "Row with missing header: column " + column;
         } else
         {
-            return "Bad metadata declaration in row " + column + ": " + badHeading;
+            return "Bad metadata declaration in column" + column + ": " + badHeading;
         }
     }
-}
+}

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

@@ -209,7 +209,7 @@ public class ItemExport
         }
 
         Context c = new Context();
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         if (myType == Constants.ITEM)
         {

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

@@ -284,7 +284,7 @@ public class ItemImport
             if (line.hasOption('z'))
             {
                 zip = true;
-                zipfilename = sourcedir + System.getProperty("file.separator") + line.getOptionValue('z');
+                zipfilename = line.getOptionValue('z');
             }
 
             //By default assume collections will be given on the command line
@@ -733,7 +733,7 @@ public class ItemImport
                 {
                     clist = mycollections;
                 }
-                addItem(c, mycollections, sourceDir, dircontents[i], mapOut, template);
+                addItem(c, clist, sourceDir, dircontents[i], mapOut, template);
                 System.out.println(i + " " + dircontents[i]);
                 c.clearCache();
             }
@@ -1108,6 +1108,10 @@ public class ItemImport
         {
             value = "";
         }
+        else
+        {
+        	value = value.trim();
+        }
         // //getElementData(n, "element");
         String element = getAttributeValue(n, "element");
         String qualifier = getAttributeValue(n, "qualifier"); //NodeValue();
@@ -1129,8 +1133,8 @@ public class ItemImport
         {
             qualifier = null;
         }
-
-        if (!isTest)
+        // only add metadata if it is no test and there is an real value
+        if (!isTest && !value.equals(""))
         {
             i.addMetadata(schema, element, qualifier, language, value);
         }
@@ -1999,12 +2003,14 @@ public class ItemImport
         if (destinationDir == null){
         	destinationDir = tempWorkDir;
         }
+        log.debug("Using directory " + destinationDir + " for zip extraction. (destDir arg is " + destDir +
+                ", tempWorkDir is " + tempWorkDir + ")");
 
         File tempdir = new File(destinationDir);
         if (!tempdir.isDirectory())
         {
-            log.error("'" + ConfigurationManager.getProperty("org.dspace.app.itemexport.work.dir") +
-                    "' as defined by the key 'org.dspace.app.itemexport.work.dir' in dspace.cfg " +
+            log.error("'" + ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir") +
+                    "' as defined by the key 'org.dspace.app.batchitemimport.work.dir' in dspace.cfg " +
                     "is not a valid directory");
         }
 
@@ -2012,9 +2018,15 @@ public class ItemImport
         {
             log.error("Unable to create temporary directory: " + tempdir.getAbsolutePath());
         }
-        String sourcedir = destinationDir + System.getProperty("file.separator") + zipfile.getName();
-        String zipDir = destinationDir + System.getProperty("file.separator") + zipfile.getName() + System.getProperty("file.separator");
 
+        if(!destinationDir.endsWith(System.getProperty("file.separator"))) {
+            destinationDir += System.getProperty("file.separator");
+        }
+
+        String sourcedir = destinationDir + zipfile.getName();
+        String zipDir = destinationDir + zipfile.getName() + System.getProperty("file.separator");
+
+        log.debug("zip directory to use is " + zipDir);
 
         // 3
         String sourceDirForZip = sourcedir;
@@ -2024,11 +2036,26 @@ public class ItemImport
         while (entries.hasMoreElements())
         {
             entry = entries.nextElement();
+            // Check that the true path to extract files is never outside allowed temp directories
+            // without creating any actual files on disk
+            log.debug("Inspecting entry name: " + entry.getName() + " for path traversal security");
+            File potentialExtract = new File(zipDir + entry.getName());
+            String canonicalPath = potentialExtract.getCanonicalPath();
+            log.debug("Canonical path to potential File is " + canonicalPath);
+            if(!canonicalPath.startsWith(zipDir)) {
+                log.error("Rejecting zip file: " + zipfile.getName() + " as it contains an entry that would be extracted " +
+                        "outside the temporary unzip directory: " + canonicalPath);
+                throw new IOException("Error extracting " + zipfile + ": Canonical path of zip entry: " +
+                        entry.getName() + " (" + canonicalPath + ") does not start with permissible temp " +
+                        "unzip directory (" + destinationDir + ")");
+            }
             if (entry.isDirectory())
             {
-                if (!new File(zipDir + entry.getName()).mkdir())
-                {
+                // Log error and throw IOException if a directory entry could not be created
+                File newDir = new File(zipDir + entry.getName());
+                if (!newDir.mkdirs()) {
                     log.error("Unable to create contents directory: " + zipDir + entry.getName());
+                    throw new IOException("Unable to create contents directory: " + zipDir + entry.getName());
                 }
             }
             else
@@ -2070,6 +2097,7 @@ public class ItemImport
                 byte[] buffer = new byte[1024];
                 int len;
                 InputStream in = zf.getInputStream(entry);
+                log.debug("Reading " + zipDir + entry.getName() + " into InputStream");
                 BufferedOutputStream out = new BufferedOutputStream(
                         new FileOutputStream(zipDir + entry.getName()));
                 while((len = in.read(buffer)) >= 0)
@@ -2148,7 +2176,7 @@ public class ItemImport
 					context = new Context();
 					eperson = EPerson.find(context, oldEPerson.getID());
 					context.setCurrentUser(eperson);
-					context.setIgnoreAuthorization(true);
+					context.turnOffAuthorisationSystem();
 					
 					boolean isResume = theResumeDir!=null;
 					

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

@@ -351,7 +351,7 @@ public class ItemUpdate {
 	               	
 	        context = new Context();  
 	        iu.setEPerson(context, iu.eperson);	
-	        context.setIgnoreAuthorization(true);
+	        context.turnOffAuthorisationSystem();
 	        
 	    	HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
 	    	if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
@@ -362,19 +362,20 @@ public class ItemUpdate {
         	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;
         }
+        finally {
+        	context.restoreAuthSystemState();
+        }
 
         if (isTest)
         {

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

@@ -11,6 +11,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.List;
+import java.util.TreeMap;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.servicemanager.DSpaceKernelImpl;
 import org.dspace.servicemanager.DSpaceKernelInit;
@@ -275,9 +276,21 @@ public class ScriptLauncher
      */
     private static void display()
     {
+        // List all command elements
         List<Element> commands = commandConfigs.getRootElement().getChildren("command");
-        System.out.println("Usage: dspace [command-name] {parameters}");
+
+        // Sort the commands by name.
+        // We cannot just use commands.sort() because it tries to remove and
+        // reinsert Elements within other Elements, and that doesn't work.
+        TreeMap<String, Element> sortedCommands = new TreeMap<>();
         for (Element command : commands)
+        {
+            sortedCommands.put(command.getChild("name").getValue(), command);
+        }
+
+        // Display the sorted list
+        System.out.println("Usage: dspace [command-name] {parameters}");
+        for (Element command : sortedCommands.values())
         {
             System.out.println(" - " + command.getChild("name").getValue() +
                                ": " + command.getChild("description").getValue());

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

@@ -7,9 +7,10 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.InputStream;
+import java.nio.file.Files;
 
 
 /**
@@ -30,9 +31,24 @@ public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter
             throws Exception
     {
 		File f = inputStreamToTempFile(source, "imthumb", ".tmp");
-    	File f2 = getThumbnailFile(f);
-		return new FileInputStream(f2);
-    }
+    	File f2 = null;
+	    try
+	    {
+		    f2 = getThumbnailFile(f);
+		    byte[] bytes = Files.readAllBytes(f2.toPath());
+		    return new ByteArrayInputStream(bytes);
+	    }
+	    finally
+	    {
+		    //noinspection ResultOfMethodCallIgnored
+		    f.delete();
+		    if (f2 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f2.delete();
+		    }
+	    }
+	}
 
 
 }

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

@@ -7,24 +7,40 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.InputStream;
+import java.nio.file.Files;
 
 public class ImageMagickPdfThumbnailFilter extends ImageMagickThumbnailFilter {
    public InputStream getDestinationStream(InputStream source)
         throws Exception
     {
 		File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
-		File f2 = getImageFile(f, 0);
-    	File f3 = getThumbnailFile(f2);
-    	return new FileInputStream(f3);
+		File f2 = null;
+	    File f3 = null;
+	    try
+	    {
+		    f2 = getImageFile(f, 0);
+		    f3 = getThumbnailFile(f2);
+		    byte[] bytes = Files.readAllBytes(f3.toPath());
+		    return new ByteArrayInputStream(bytes);
+	    }
+		finally
+	    {
+		    //noinspection ResultOfMethodCallIgnored
+		    f.delete();
+		    if (f2 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f2.delete();
+		    }
+		    if (f3 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f3.delete();
+		    }
+	    }
     }
 
-   public static final String[] PDF = {"Adobe PDF"};
-   public String[] getInputMIMETypes()
-  {
-      return PDF;
-  }
-
 }

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

@@ -23,6 +23,7 @@ import org.dspace.content.Bundle;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.im4java.core.ConvertCmd;
+import org.im4java.core.Info;
 import org.im4java.core.IM4JavaException;
 import org.im4java.core.IMOperation;
 import org.im4java.process.ProcessStarter;
@@ -34,161 +35,163 @@ import org.dspace.core.ConfigurationManager;
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  */
-public abstract class ImageMagickThumbnailFilter extends MediaFilter implements SelfRegisterInputFormats
-{
-	private static int width = 180;
-	private static int height = 120;
-	static String bitstreamDescription = "IM Thumbnail";
-	static final String defaultPattern = "Generated Thumbnail";
-	static Pattern replaceRegex = Pattern.compile(defaultPattern);
-	
-	static {
-		String pre = ImageMagickThumbnailFilter.class.getName();
-		String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
-		ProcessStarter.setGlobalSearchPath(s);
-		width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
-		height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
-		String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
-		if (description != null) {
-			bitstreamDescription = description;
-		}
-		try {
-			String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
-		    replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
-		} catch(PatternSyntaxException e) {
-			System.err.println("Invalid thumbnail replacement pattern: "+e.getMessage());
-		}
-		
-	}
-	
-	public ImageMagickThumbnailFilter() {
-	}
-	
-	
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".jpg";
-    }
+public abstract class ImageMagickThumbnailFilter extends MediaFilter {
+        private static int width = 180;
+        private static int height = 120;
+        private static boolean flatten = true;
+        static String bitstreamDescription = "IM Thumbnail";
+        static final String defaultPattern = "Generated Thumbnail";
+        static Pattern replaceRegex = Pattern.compile(defaultPattern);
+        static String cmyk_profile;
+        static String srgb_profile;
 
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "THUMBNAIL";
-    }
+        static {
+                String pre = ImageMagickThumbnailFilter.class.getName();
+                String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
+                ProcessStarter.setGlobalSearchPath(s);
+                width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
+                height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
+                flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
+                String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
+                cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
+                srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
+                if (description != null) {
+                        bitstreamDescription = description;
+                }
+                try {
+                        String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
+                        replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
+                } catch (PatternSyntaxException e) {
+                        System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
+                }
 
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "JPEG";
-    }
-
-    /**
-     * @return String bitstreamDescription
-     */
-    public String getDescription()
-    {
-        return bitstreamDescription;
-    }
-
-    public static File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
-		File f = File.createTempFile(prefix, suffix);
-		f.deleteOnExit();
-    	FileOutputStream fos = new FileOutputStream(f);
-    	
-    	byte[] buffer = new byte[1024];
-    	int len = source.read(buffer);
-    	while (len != -1) {
-    		fos.write(buffer, 0, len);
-    		len = source.read(buffer);
-    	}
-    	fos.close();
-		return f;
-    }
-    
-    public static File getThumbnailFile(File f) throws IOException, InterruptedException, IM4JavaException {
-    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-    	f2.deleteOnExit();
-    	ConvertCmd cmd = new ConvertCmd();
-		IMOperation op = new IMOperation();
-		op.addImage(f.getAbsolutePath());
-		op.thumbnail(width, height);
-		op.addImage(f2.getAbsolutePath());
-        if (MediaFilterManager.isVerbose) {
-		    System.out.println("IM Thumbnail Param: "+op);
         }
-		cmd.run(op);
-		return f2;
-    }
-    
-    public static File getImageFile(File f, int page) throws IOException, InterruptedException, IM4JavaException {
-    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-    	f2.deleteOnExit();
-    	ConvertCmd cmd = new ConvertCmd();
-		IMOperation op = new IMOperation();
-		String s = "[" + page + "]";
-		op.addImage(f.getAbsolutePath()+s);
-		op.addImage(f2.getAbsolutePath());
-        if (MediaFilterManager.isVerbose) {
-		    System.out.println("IM Image Param: "+op);
+
+        public ImageMagickThumbnailFilter() {
         }
-		cmd.run(op);
-		return f2;
-    }
-    
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-            throws Exception
-    {
-    	String nsrc = source.getName();
-    	for(Bundle b: item.getBundles("THUMBNAIL")) {
-    		for(Bitstream bit: b.getBitstreams()) {
-    			String n = bit.getName();
-    			if (n != null) {
-    				if (nsrc != null) {
-    					if (!n.startsWith(nsrc)) continue;
-    				}
-    			}
-     	    	String description = bit.getDescription();
-    	    	//If anything other than a generated thumbnail is found, halt processing
-    	    	if (description != null) {
-        	    	if (replaceRegex.matcher(description).matches()) {
-        	            if (MediaFilterManager.isVerbose) {
-        	    		    System.out.println(description + " " + nsrc + " matches pattern and is replacable.");
-        	            }
-        	    		continue;
-        	    	}
-        	    	if (description.equals(bitstreamDescription)) {
-        	            if (MediaFilterManager.isVerbose) {
-        	    		    System.out.println(bitstreamDescription + " " + nsrc + " is replacable.");
-        	            }
-        	    		continue;    	    		
-        	    	}
-    	    	}
-    			System.out.println("Custom Thumbnail exists for " + nsrc + " for item " + item.getHandle() + ".  Thumbnail will not be generated. ");
-    			return false;
-    		}
-    	}
-    	
-    	
-        return true; //assume that the thumbnail is a custom one
-    }
 
-     public String[] getInputMIMETypes()
-    {
-        return ImageIO.getReaderMIMETypes();
-    }
+        public String getFilteredName(String oldFilename) {
+                return oldFilename + ".jpg";
+        }
 
-    public String[] getInputDescriptions()
-    {
-        return null;
-    }
+        /**
+         * @return String bundle name
+         * 
+         */
+        public String getBundleName() {
+                return "THUMBNAIL";
+        }
+
+        /**
+         * @return String bitstreamformat
+         */
+        public String getFormatString() {
+                return "JPEG";
+        }
+
+        /**
+         * @return String bitstreamDescription
+         */
+        public String getDescription() {
+                return bitstreamDescription;
+        }
+
+        public static File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
+                File f = File.createTempFile(prefix, suffix);
+                f.deleteOnExit();
+                FileOutputStream fos = new FileOutputStream(f);
+
+                byte[] buffer = new byte[1024];
+                int len = source.read(buffer);
+                while (len != -1) {
+                        fos.write(buffer, 0, len);
+                        len = source.read(buffer);
+                }
+                fos.close();
+                return f;
+        }
+
+        public static File getThumbnailFile(File f) throws IOException, InterruptedException, IM4JavaException {
+                File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+                f2.deleteOnExit();
+                ConvertCmd cmd = new ConvertCmd();
+                IMOperation op = new IMOperation();
+                op.autoOrient();
+                op.addImage(f.getAbsolutePath());
+                op.thumbnail(width, height);
+                op.addImage(f2.getAbsolutePath());
+                if (MediaFilterManager.isVerbose) {
+                        System.out.println("IM Thumbnail Param: " + op);
+                }
+                cmd.run(op);
+                return f2;
+        }
+
+        public static File getImageFile(File f, int page) throws IOException, InterruptedException, IM4JavaException {
+                File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+                f2.deleteOnExit();
+                ConvertCmd cmd = new ConvertCmd();
+                IMOperation op = new IMOperation();
+                String s = "[" + page + "]";
+                op.addImage(f.getAbsolutePath() + s);
+                if (flatten) {
+                        op.flatten();
+                }
+                // PDFs using the CMYK color system can be handled specially if
+                // profiles are defined
+                if (cmyk_profile != null && srgb_profile != null) {
+                        Info imageInfo = new Info(f.getAbsolutePath() + s, true);
+                        String imageClass = imageInfo.getImageClass();
+                        if (imageClass.contains("CMYK")) {
+                                op.profile(cmyk_profile);
+                                op.profile(srgb_profile);
+                        }
+                }
+                op.addImage(f2.getAbsolutePath());
+                if (MediaFilterManager.isVerbose) {
+                        System.out.println("IM Image Param: " + op);
+                }
+                cmd.run(op);
+                return f2;
+        }
+
+        public boolean preProcessBitstream(Context c, Item item, Bitstream source) throws Exception {
+                String nsrc = source.getName();
+                for (Bundle b : item.getBundles("THUMBNAIL")) {
+                        for (Bitstream bit : b.getBitstreams()) {
+                                String n = bit.getName();
+                                if (n != null) {
+                                        if (nsrc != null) {
+                                                if (!n.startsWith(nsrc))
+                                                        continue;
+                                        }
+                                }
+                                String description = bit.getDescription();
+                                // If anything other than a generated thumbnail
+                                // is found, halt processing
+                                if (description != null) {
+                                        if (replaceRegex.matcher(description).matches()) {
+                                                if (MediaFilterManager.isVerbose) {
+                                                        System.out.println(description + " " + nsrc
+                                                                        + " matches pattern and is replacable.");
+                                                }
+                                                continue;
+                                        }
+                                        if (description.equals(bitstreamDescription)) {
+                                                if (MediaFilterManager.isVerbose) {
+                                                        System.out.println(bitstreamDescription + " " + nsrc
+                                                                        + " is replacable.");
+                                                }
+                                                continue;
+                                        }
+                                }
+                                System.out.println("Custom Thumbnail exists for " + nsrc + " for item "
+                                                + item.getHandle() + ".  Thumbnail will not be generated. ");
+                                return false;
+                        }
+                }
+
+                return true; // assume that the thumbnail is a custom one
+        }
 
-    public String[] getInputExtensions()
-    {
-        return ImageIO.getReaderFileSuffixes();
-    }
 }

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

@@ -33,7 +33,7 @@ import java.util.zip.GZIPOutputStream;
  *   }
  *   g.finish();
  * </pre>
- * 
+ *
  * @author Robert Tansley
  */
 public abstract class AbstractGenerator
@@ -59,7 +59,7 @@ public abstract class AbstractGenerator
     /**
      * 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
      */
@@ -73,7 +73,7 @@ public abstract class AbstractGenerator
 
     /**
      * Start writing a new sitemap file.
-     * 
+     *
      * @throws IOException
      *             if an error occurs creating the file
      */
@@ -97,7 +97,7 @@ public abstract class AbstractGenerator
 
     /**
      * Add the given URL to the sitemap.
-     * 
+     *
      * @param url
      *            Full URL to add
      * @param lastMod
@@ -129,7 +129,7 @@ public abstract class AbstractGenerator
 
     /**
      * Finish with the current sitemap file.
-     * 
+     *
      * @throws IOException
      *             if an error occurs writing
      */
@@ -144,15 +144,18 @@ public abstract class AbstractGenerator
      * 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();
+        if (null != currentOutput)
+        {
+            closeCurrentFile();
+        }
 
         OutputStream fo = new FileOutputStream(new File(outputDir,
                 getIndexFilename()));
@@ -165,13 +168,13 @@ public abstract class AbstractGenerator
         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
@@ -183,14 +186,14 @@ public abstract class AbstractGenerator
 
     /**
      * 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();
@@ -198,7 +201,7 @@ public abstract class AbstractGenerator
     /**
      * Return the maximum size in bytes that an individual sitemap file should
      * be.
-     * 
+     *
      * @return the size in bytes.
      */
     public abstract int getMaxSize();
@@ -206,7 +209,7 @@ public abstract class AbstractGenerator
     /**
      * Return the maximum number of URLs that an individual sitemap file should
      * contain.
-     * 
+     *
      * @return the maximum number of URLs.
      */
     public abstract int getMaxURLs();
@@ -214,7 +217,7 @@ public abstract class AbstractGenerator
     /**
      * Return whether the written sitemap files and index should be
      * GZIP-compressed.
-     * 
+     *
      * @return {@code true} if GZIP compression should be used, {@code false}
      *         otherwise.
      */
@@ -222,7 +225,7 @@ public abstract class AbstractGenerator
 
     /**
      * 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.
@@ -231,14 +234,14 @@ public abstract class AbstractGenerator
 
     /**
      * 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

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

@@ -92,7 +92,7 @@ public class CreateStatReport {
         
         // create context as super user
         context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         //get paths to directories
         outputLogDirectory = ConfigurationManager.getProperty("log.dir") + File.separator;

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

@@ -215,7 +215,7 @@ public class LogAnalyser
         
         // create context as super user
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         // set up our command line variables
         String myLogDir = null;

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

@@ -151,7 +151,7 @@ public class ReportGenerator
     {
         // create context as super user
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         String myFormat = null;
         String myInput = null;

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

@@ -7,37 +7,31 @@
  */
 package org.dspace.app.util;
 
-import java.sql.SQLException;
-
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.content.*;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
 import org.apache.log4j.Logger;
+import org.dspace.authorize.AuthorizeManager;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.Item;
+import org.dspace.content.Metadatum;
 import org.dspace.core.ConfigurationManager;
-
-import java.io.File;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.Set;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
 import org.dspace.handle.HandleManager;
-
 import org.jdom.Element;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.sql.SQLException;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * Configuration and mapping for Google Scholar output metadata
  * @author Sands Fish
@@ -125,6 +119,7 @@ public class GoogleMetadata
 
     private static final int ALL_FIELDS_IN_OPTION = 2;
 
+    private Context ourContext;
     // Load configured fields from google-metadata.properties
     static
     {
@@ -216,7 +211,11 @@ public class GoogleMetadata
         // Hold onto the item in case we need to refresh a stale parse
         this.item = item;
         itemURL = HandleManager.resolveToURL(context, item.getHandle());
+        ourContext=context;
+        EPerson currentUser = ourContext.getCurrentUser();
+        ourContext.setCurrentUser(null);
         parseItem();
+        ourContext.setCurrentUser(currentUser);
     }
 
     /**
@@ -757,16 +756,17 @@ public class GoogleMetadata
     }
 
     /**
-     * Fetch all metadata mappings
-     * 
+     * Fetch retaining the order of the values for any given key in which they
+     * where added (like authors).
+     *
      * Usage: GoogleMetadata gmd = new GoogleMetadata(item); for(Entry<String,
      * String> mapping : googlemd.getMappings()) { ... }
      * 
      * @return Iterable of metadata fields mapped to Google-formatted values
      */
-    public Set<Entry<String, String>> getMappings()
+    public Collection<Entry<String, String>> getMappings()
     {
-        return new HashSet<>(metadataMappings.entries());
+        return metadataMappings.entries();
     }
 
     /**
@@ -1041,7 +1041,6 @@ public class GoogleMetadata
 	 */
 	private Bitstream findLinkableFulltext(Item item) throws SQLException {
 		Bitstream bestSoFar = null;
-		int bitstreamCount = 0;
 		Bundle[] contentBundles = item.getBundles("ORIGINAL");
 		for (Bundle bundle : contentBundles) {
 			int primaryBitstreamId = bundle.getPrimaryBitstreamID();
@@ -1050,16 +1049,16 @@ public class GoogleMetadata
 				if (candidate.getID() == primaryBitstreamId) { // is primary -> use this one
 					if (isPublic(candidate)) {
 						return candidate;
+					}					
+				} else 
+					{
+						
+						if (bestSoFar == null && isPublic(candidate)) { //if bestSoFar is null but the candidate is not public you don't use it and try to find another
+						bestSoFar = candidate;
+						}					
 					}
-				} else if (bestSoFar == null) {
-					bestSoFar = candidate;
-				}
-				bitstreamCount++;
 			}
 		}
-		if (bitstreamCount > 1 || !isPublic(bestSoFar)) {
-			bestSoFar = null;
-		}
 
 		return bestSoFar;
 	}
@@ -1069,16 +1068,10 @@ public class GoogleMetadata
 			return false;
 		}
 		boolean result = false;
-		Context context = null;
 		try {
-			context = new Context();
-			result = AuthorizeManager.authorizeActionBoolean(context, bitstream, Constants.READ, true);
+            result = AuthorizeManager.authorizeActionBoolean(ourContext, bitstream, Constants.READ, true);
 		} catch (SQLException e) {
 			log.error("Cannot determine whether bitstream is public, assuming it isn't. bitstream_id=" + bitstream.getID(), e);
-		} finally {
-			if (context != null) {
-				context.abort();
-			}
 		}
 		return result;
 	}

dspace-api/src/main/java/org/dspace/authenticate/LDAPAuthentication.java

@@ -279,11 +279,11 @@ public class LDAPAuthentication
                         {
                             log.info(LogManager.getHeader(context,
                                     "type=ldap-login", "type=ldap_but_already_email"));
-                            context.setIgnoreAuthorization(true);
+                            context.turnOffAuthorisationSystem();
                             eperson.setNetid(netid.toLowerCase());
                             eperson.update();
                             context.commit();
-                            context.setIgnoreAuthorization(false);
+                            context.restoreAuthSystemState();
                             context.setCurrentUser(eperson);
 
                             // assign user to groups based on ldap dn
@@ -298,7 +298,7 @@ public class LDAPAuthentication
                                 // TEMPORARILY turn off authorisation
                                 try
                                 {
-                                    context.setIgnoreAuthorization(true);
+                                    context.turnOffAuthorisationSystem();
                                     eperson = EPerson.create(context);
                                     if (StringUtils.isNotEmpty(email))
                                     {
@@ -332,7 +332,7 @@ public class LDAPAuthentication
                                 }
                                 finally
                                 {
-                                    context.setIgnoreAuthorization(false);
+                                    context.restoreAuthSystemState();
                                 }
 
                                 log.info(LogManager.getHeader(context, "authenticate",
@@ -354,7 +354,7 @@ public class LDAPAuthentication
                     }
                     finally
                     {
-                        context.setIgnoreAuthorization(false);
+                        context.restoreAuthSystemState();
                     }
                 }
             }

dspace-api/src/main/java/org/dspace/authenticate/PasswordAuthentication.java

@@ -7,11 +7,7 @@
  */
 package org.dspace.authenticate;
 
-import java.sql.SQLException;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
+import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.ConfigurationManager;
@@ -20,6 +16,10 @@ import org.dspace.core.LogManager;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.sql.SQLException;
+
 /**
  * A stackable authentication method
  * based on the DSpace internal "EPerson" database.
@@ -128,7 +128,7 @@ public class PasswordAuthentication
 		// ensures they are password users
 		try
 		{
-			if (context.getCurrentUser().getPasswordHash() != null && !context.getCurrentUser().getPasswordHash().toString().equals(""))
+		if (context.getCurrentUser() != null && context.getCurrentUser().getPasswordHash()!=null && StringUtils.isNotBlank(context.getCurrentUser().getPasswordHash().toString()))
 			{
 				String groupName = ConfigurationManager.getProperty("authentication-password", "login.specialgroup");
 				if ((groupName != null) && (!groupName.trim().equals("")))
@@ -149,7 +149,7 @@ public class PasswordAuthentication
 			}
 		}
 		catch (Exception e) {
-			// The user is not a password user, so we don't need to worry about them
+            log.error(LogManager.getHeader(context,"getSpecialGroups",""),e);
 		}
 		return new int[0];
     }

dspace-api/src/main/java/org/dspace/authenticate/X509Authentication.java

@@ -612,7 +612,7 @@ public class X509Authentication implements AuthenticationMethod
                                 "from=x.509, email=" + email));
 
                         // TEMPORARILY turn off authorisation
-                        context.setIgnoreAuthorization(true);
+                        context.turnOffAuthorisationSystem();
                         eperson = EPerson.create(context);
                         eperson.setEmail(email);
                         eperson.setCanLogIn(true);
@@ -620,7 +620,7 @@ public class X509Authentication implements AuthenticationMethod
                                 eperson);
                         eperson.update();
                         context.commit();
-                        context.setIgnoreAuthorization(false);
+                        context.restoreAuthSystemState();
                         context.setCurrentUser(eperson);
                         setSpecialGroupsFlag(request, email);
                         return SUCCESS;

dspace-api/src/main/java/org/dspace/authority/SolrAuthorityInterface.java

@@ -0,0 +1,20 @@
+/**
+ * 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.authority;
+
+import java.util.List;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public interface SolrAuthorityInterface {
+
+    List<AuthorityValue> queryAuthorities(String text, int max);
+
+    AuthorityValue queryAuthorityID(String id);
+}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcid.java

@@ -1,86 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid;
-
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.Work;
-import org.dspace.authority.orcid.xml.XMLtoBio;
-import org.dspace.authority.orcid.xml.XMLtoWork;
-import org.dspace.authority.rest.RestSource;
-import org.apache.log4j.Logger;
-import org.dspace.utils.DSpace;
-import org.w3c.dom.Document;
-
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Orcid extends RestSource {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(Orcid.class);
-
-    private static Orcid orcid;
-
-    public static Orcid getOrcid() {
-        if (orcid == null) {
-            orcid = new DSpace().getServiceManager().getServiceByName("OrcidSource", Orcid.class);
-        }
-        return orcid;
-    }
-
-    private Orcid(String url) {
-        super(url);
-    }
-
-    public Bio getBio(String id) {
-        Document bioDocument = restConnector.get(id + "/orcid-bio");
-        XMLtoBio converter = new XMLtoBio();
-        Bio bio = converter.convert(bioDocument).get(0);
-        bio.setOrcid(id);
-        return bio;
-    }
-
-    public List<Work> getWorks(String id) {
-        Document document = restConnector.get(id + "/orcid-works");
-        XMLtoWork converter = new XMLtoWork();
-        return converter.convert(document);
-    }
-
-    public List<Bio> queryBio(String name, int start, int rows) {
-        Document bioDocument = restConnector.get("search/orcid-bio?q=" + URLEncoder.encode("\"" + name + "\"") + "&start=" + start + "&rows=" + rows);
-        XMLtoBio converter = new XMLtoBio();
-        return converter.convert(bioDocument);
-    }
-
-    @Override
-    public List<AuthorityValue> queryAuthorities(String text, int max) {
-        List<Bio> bios = queryBio(text, 0, max);
-        List<AuthorityValue> authorities = new ArrayList<AuthorityValue>();
-        for (Bio bio : bios) {
-            authorities.add(OrcidAuthorityValue.create(bio));
-        }
-        return authorities;
-    }
-
-    @Override
-    public AuthorityValue queryAuthorityID(String id) {
-        Bio bio = getBio(id);
-        return OrcidAuthorityValue.create(bio);
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/OrcidAuthorityValue.java

@@ -1,316 +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.authority.orcid;
-
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.AuthorityValueGenerator;
-import org.dspace.authority.PersonAuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.BioExternalIdentifier;
-import org.dspace.authority.orcid.model.BioName;
-import org.dspace.authority.orcid.model.BioResearcherUrl;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.apache.solr.common.SolrDocument;
-import org.apache.solr.common.SolrInputDocument;
-
-import java.util.*;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class OrcidAuthorityValue extends PersonAuthorityValue {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(OrcidAuthorityValue.class);
-
-    private String orcid_id;
-    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
-    private boolean update; // used in setValues(Bio bio)
-
-
-    /**
-     * Creates an instance of OrcidAuthorityValue with only uninitialized fields.
-     * This is meant to be filled in with values from an existing record.
-     * To create a brand new OrcidAuthorityValue, use create()
-     */
-    public OrcidAuthorityValue() {
-    }
-
-    public OrcidAuthorityValue(SolrDocument document) {
-        super(document);
-    }
-
-    public String getOrcid_id() {
-        return orcid_id;
-    }
-
-    public void setOrcid_id(String orcid_id) {
-        this.orcid_id = orcid_id;
-    }
-
-    public Map<String, List<String>> getOtherMetadata() {
-        return otherMetadata;
-    }
-
-    public void addOtherMetadata(String label, String data) {
-        List<String> strings = otherMetadata.get(label);
-        if (strings == null) {
-            strings = new ArrayList<String>();
-        }
-        strings.add(data);
-        otherMetadata.put(label, strings);
-    }
-
-    @Override
-    public SolrInputDocument getSolrInputDocument() {
-        SolrInputDocument doc = super.getSolrInputDocument();
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            doc.addField("orcid_id", getOrcid_id());
-        }
-
-        for (String t : otherMetadata.keySet()) {
-            List<String> data = otherMetadata.get(t);
-            for (String data_entry : data) {
-                doc.addField("label_" + t, data_entry);
-            }
-        }
-        return doc;
-    }
-
-    @Override
-    public void setValues(SolrDocument document) {
-        super.setValues(document);
-        this.orcid_id = String.valueOf(document.getFieldValue("orcid_id"));
-
-        otherMetadata = new HashMap<String, List<String>>();
-        for (String fieldName : document.getFieldNames()) {
-            String labelPrefix = "label_";
-            if (fieldName.startsWith(labelPrefix)) {
-                String label = fieldName.substring(labelPrefix.length());
-                List<String> list = new ArrayList<String>();
-                Collection<Object> fieldValues = document.getFieldValues(fieldName);
-                for (Object o : fieldValues) {
-                    list.add(String.valueOf(o));
-                }
-                otherMetadata.put(label, list);
-            }
-        }
-    }
-
-    public static OrcidAuthorityValue create() {
-        OrcidAuthorityValue orcidAuthorityValue = new OrcidAuthorityValue();
-        orcidAuthorityValue.setId(UUID.randomUUID().toString());
-        orcidAuthorityValue.updateLastModifiedDate();
-        orcidAuthorityValue.setCreationDate(new Date());
-        return orcidAuthorityValue;
-    }
-
-    /**
-     * Create an authority based on a given orcid bio
-     */
-    public static OrcidAuthorityValue create(Bio bio) {
-        OrcidAuthorityValue authority = OrcidAuthorityValue.create();
-
-        authority.setValues(bio);
-
-        return authority;
-    }
-
-    public boolean setValues(Bio bio) {
-        BioName name = bio.getName();
-
-        if (updateValue(bio.getOrcid(), getOrcid_id())) {
-            setOrcid_id(bio.getOrcid());
-        }
-
-        if (updateValue(name.getFamilyName(), getLastName())) {
-            setLastName(name.getFamilyName());
-        }
-
-        if (updateValue(name.getGivenNames(), getFirstName())) {
-            setFirstName(name.getGivenNames());
-        }
-
-        if (StringUtils.isNotBlank(name.getCreditName())) {
-            if (!getNameVariants().contains(name.getCreditName())) {
-                addNameVariant(name.getCreditName());
-                update = true;
-            }
-        }
-        for (String otherName : name.getOtherNames()) {
-            if (!getNameVariants().contains(otherName)) {
-                addNameVariant(otherName);
-                update = true;
-            }
-        }
-
-        if (updateOtherMetadata("country", bio.getCountry())) {
-            addOtherMetadata("country", bio.getCountry());
-        }
-
-        for (String keyword : bio.getKeywords()) {
-            if (updateOtherMetadata("keyword", keyword)) {
-                addOtherMetadata("keyword", keyword);
-            }
-        }
-
-        for (BioExternalIdentifier externalIdentifier : bio.getBioExternalIdentifiers()) {
-            if (updateOtherMetadata("external_identifier", externalIdentifier.toString())) {
-                addOtherMetadata("external_identifier", externalIdentifier.toString());
-            }
-        }
-
-        for (BioResearcherUrl researcherUrl : bio.getResearcherUrls()) {
-            if (updateOtherMetadata("researcher_url", researcherUrl.toString())) {
-                addOtherMetadata("researcher_url", researcherUrl.toString());
-            }
-        }
-
-        if (updateOtherMetadata("biography", bio.getBiography())) {
-            addOtherMetadata("biography", bio.getBiography());
-        }
-
-        setValue(getName());
-
-        if (update) {
-            update();
-        }
-        boolean result = update;
-        update = false;
-        return result;
-    }
-
-    private boolean updateOtherMetadata(String label, String data) {
-        List<String> strings = getOtherMetadata().get(label);
-        boolean update;
-        if (strings == null) {
-            update = StringUtils.isNotBlank(data);
-        } else {
-            update = !strings.contains(data);
-        }
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    private boolean updateValue(String incoming, String resident) {
-        boolean update = StringUtils.isNotBlank(incoming) && !incoming.equals(resident);
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    @Override
-    public Map<String, String> choiceSelectMap() {
-
-        Map<String, String> map = super.choiceSelectMap();
-
-        map.put("orcid", getOrcid_id());
-
-        return map;
-    }
-
-    public String getAuthorityType() {
-        return "orcid";
-    }
-
-    @Override
-    public String generateString() {
-        String generateString = AuthorityValueGenerator.GENERATE + getAuthorityType() + AuthorityValueGenerator.SPLIT;
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            generateString += getOrcid_id();
-        }
-        return generateString;
-    }
-
-
-    @Override
-    public AuthorityValue newInstance(String info) {
-        AuthorityValue authorityValue = null;
-        if (StringUtils.isNotBlank(info)) {
-            Orcid orcid = Orcid.getOrcid();
-            authorityValue = orcid.queryAuthorityID(info);
-        } else {
-            authorityValue = OrcidAuthorityValue.create();
-        }
-        return authorityValue;
-    }
-
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        return orcid_id != null ? orcid_id.hashCode() : 0;
-    }
-
-    public boolean hasTheSameInformationAs(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-        if (!super.hasTheSameInformationAs(o)) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        for (String key : otherMetadata.keySet()) {
-            if(otherMetadata.get(key) != null){
-                List<String> metadata = otherMetadata.get(key);
-                List<String> otherMetadata = that.otherMetadata.get(key);
-                if (otherMetadata == null) {
-                    return false;
-                } else {
-                    HashSet<String> metadataSet = new HashSet<String>(metadata);
-                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
-                    if (!metadataSet.equals(otherMetadataSet)) {
-                        return false;
-                    }
-                }
-            }else{
-                if(that.otherMetadata.get(key) != null){
-                    return false;
-                }
-            }
-        }
-
-        return true;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2.java

@@ -0,0 +1,185 @@
+/**
+ * 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.authority.orcid;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.log4j.Logger;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.SolrAuthorityInterface;
+import org.dspace.authority.orcid.xml.XMLtoBio;
+import org.dspace.authority.rest.RESTConnector;
+import org.json.JSONObject;
+import org.orcid.jaxb.model.record_v2.Person;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ * This class contains all methods for retrieving "Person" objects calling the ORCID (version 2) endpoints.
+ * Additionally, this can also create AuthorityValues based on these returned Person objects
+ */
+public class Orcidv2 implements SolrAuthorityInterface {
+
+    private static Logger log = Logger.getLogger(Orcidv2.class);
+
+    public RESTConnector restConnector;
+    private String OAUTHUrl;
+    private String clientId;
+
+    private String clientSecret;
+
+    private String accessToken;
+
+    /**
+     *  Initialize the accessToken that is required for all subsequent calls to ORCID
+     */
+    public void init() throws IOException {
+        if (StringUtils.isNotBlank(accessToken) && StringUtils.isNotBlank(clientSecret)) {
+            String authenticationParameters = "?client_id=" + clientId + "&client_secret=" + clientSecret + "&scope=/read-public&grant_type=client_credentials";
+            HttpPost httpPost = new HttpPost(OAUTHUrl + authenticationParameters);
+            httpPost.addHeader("Accept", "application/json");
+            httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
+
+            HttpClient httpClient = HttpClientBuilder.create().build();
+            HttpResponse getResponse = httpClient.execute(httpPost);
+
+            InputStream is = getResponse.getEntity().getContent();
+            BufferedReader streamReader = new BufferedReader(new InputStreamReader(is, "UTF-8"));
+
+            JSONObject responseObject = null;
+            String inputStr;
+            while ((inputStr = streamReader.readLine()) != null && responseObject == null) {
+                if (inputStr.startsWith("{") && inputStr.endsWith("}") && inputStr.contains("access_token")) {
+                    try {
+                        responseObject = new JSONObject(inputStr);
+                    } catch (Exception e) {
+                        //Not as valid as I'd hoped, move along
+                        responseObject = null;
+                    }
+                }
+            }
+
+            if (responseObject != null && responseObject.has("access_token")) {
+                accessToken = (String) responseObject.get("access_token");
+            }
+        }
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url, String OAUTHUrl, String clientId, String clientSecret) {
+        this.restConnector = new RESTConnector(url);
+        this.OAUTHUrl = OAUTHUrl;
+        this.clientId = clientId;
+        this.clientSecret = clientSecret;
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url) {
+        this.restConnector = new RESTConnector(url);
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param text search string
+     * @return List<AuthorityValue>
+     */
+    @Override
+    public List<AuthorityValue> queryAuthorities(String text, int max) {
+        List<Person> bios = queryBio(text, max);
+        List<AuthorityValue> result = new ArrayList<>();
+        for (Person person : bios) {
+            AuthorityValue orcidAuthorityValue = Orcidv2AuthorityValue.create(person);
+            if (orcidAuthorityValue != null) {
+                result.add(orcidAuthorityValue);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Create an AuthorityValue from a Person retrieved using the given orcid identifier.
+     * @param id orcid identifier
+     * @return AuthorityValue
+     */
+    public AuthorityValue queryAuthorityID(String id) {
+        Person person = getBio(id);
+        AuthorityValue valueFromPerson = Orcidv2AuthorityValue.create(person);
+        return valueFromPerson;
+    }
+
+    /**
+     * Retrieve a Person object based on a given orcid identifier
+     * @param id orcid identifier
+     * @return Person
+     */
+    public Person getBio(String id) {
+        log.debug("getBio called with ID=" + id);
+        if(!isValid(id)){
+            return null;
+        }
+        InputStream bioDocument = restConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        Person person = converter.convertSinglePerson(bioDocument);
+        return person;
+    }
+
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param start offset to use
+     * @param rows how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int start, int rows) {
+        if (rows > 100) {
+            throw new IllegalArgumentException("The maximum number of results to retrieve cannot exceed 100.");
+        }
+
+        String searchPath = "search?q=" + URLEncoder.encode(text) + "&start=" + start + "&rows=" + rows;
+        log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
+        InputStream bioDocument = restConnector.get(searchPath, accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        List<Person> bios = converter.convert(bioDocument);
+        return bios;
+    }
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param max how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int max) {
+        return queryBio(text, 0, max);
+    }
+
+    /**
+     * Check to see if the provided text has the correct ORCID syntax.
+     * Since only searching on ORCID id is allowed, this way, we filter out any queries that would return a blank result anyway
+     */
+    private boolean isValid(String text) {
+        return StringUtils.isNotBlank(text) && text.matches(Orcidv2AuthorityValue.ORCID_ID_SYNTAX);
+    }
+}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java

@@ -0,0 +1,330 @@
+/**
+ * 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.authority.orcid;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.SolrInputDocument;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.AuthorityValueGenerator;
+import org.dspace.authority.PersonAuthorityValue;
+import org.dspace.utils.DSpace;
+import org.orcid.jaxb.model.common_v2.ExternalId;
+import org.orcid.jaxb.model.record_v2.*;
+
+import java.util.*;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public class Orcidv2AuthorityValue extends PersonAuthorityValue {
+
+    /*
+     * The ORCID identifier
+     */
+    private String orcid_id;
+
+    /*
+     * Map containing key-value pairs filled in by "setValues(Person person)".
+     * This represents all dynamic information of the object.
+     */
+    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
+
+    /**
+     * The syntax that the ORCID id needs to conform to
+     */
+    public static final String ORCID_ID_SYNTAX = "\\d{4}-\\d{4}-\\d{4}-(\\d{3}X|\\d{4})";
+
+
+    /**
+     * Creates an instance of Orcidv2AuthorityValue with only uninitialized fields.
+     * This is meant to be filled in with values from an existing record.
+     * To create a brand new Orcidv2AuthorityValue, use create()
+     */
+    public Orcidv2AuthorityValue() {
+    }
+
+    public Orcidv2AuthorityValue(SolrDocument document) {
+        super(document);
+    }
+
+
+    public String getOrcid_id() {
+        return orcid_id;
+    }
+
+    public void setOrcid_id(String orcid_id) {
+        this.orcid_id = orcid_id;
+    }
+
+    /**
+     * Create an empty authority.
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create() {
+        Orcidv2AuthorityValue orcidAuthorityValue = new Orcidv2AuthorityValue();
+        orcidAuthorityValue.setId(UUID.randomUUID().toString());
+        orcidAuthorityValue.updateLastModifiedDate();
+        orcidAuthorityValue.setCreationDate(new Date());
+        return orcidAuthorityValue;
+    }
+
+    /**
+     * Create an authority based on a given orcid bio
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create(Person person) {
+        if (person == null) {
+            return null;
+        }
+        Orcidv2AuthorityValue authority = Orcidv2AuthorityValue.create();
+
+        authority.setValues(person);
+
+        return authority;
+    }
+
+    /**
+     * Initialize this instance based on a Person object
+     * @param person Person
+     */
+    protected void setValues(Person person) {
+        NameType name = person.getName();
+
+        if (!StringUtils.equals(name.getPath(), this.getOrcid_id())) {
+            this.setOrcid_id(name.getPath());
+        }
+
+        if (!StringUtils.equals(name.getFamilyName().getValue(), this.getLastName())) {
+            this.setLastName(name.getFamilyName().getValue());
+        }
+
+        if (!StringUtils.equals(name.getGivenNames().getValue(), this.getFirstName())) {
+            this.setFirstName(name.getGivenNames().getValue());
+        }
+
+        if (name.getCreditName() != null && StringUtils.isNotBlank(name.getCreditName().getValue())) {
+            if (!this.getNameVariants().contains(name.getCreditName())) {
+                this.addNameVariant(name.getCreditName().getValue());
+            }
+        }
+
+        if (person.getKeywords() != null) {
+            for (KeywordType keyword : person.getKeywords().getKeyword()) {
+                if (this.isNewMetadata("keyword", keyword.getContent())) {
+                    this.addOtherMetadata("keyword", keyword.getContent());
+                }
+            }
+        }
+
+        ExternalIdentifiers externalIdentifiers = person.getExternalIdentifiers();
+        if (externalIdentifiers != null) {
+            for (ExternalId externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
+                if (this.isNewMetadata("external_identifier", externalIdentifier.getExternalIdValue())) {
+                    this.addOtherMetadata("external_identifier", externalIdentifier.getExternalIdValue());
+
+                }
+            }
+        }
+        if (person.getResearcherUrls() != null) {
+            for (ResearcherUrlType researcherUrl : person.getResearcherUrls().getResearcherUrl()) {
+                if (this.isNewMetadata("researcher_url", researcherUrl.getUrl().getValue())) {
+                    this.addOtherMetadata("researcher_url", researcherUrl.getUrl().getValue());
+                }
+            }
+
+        }
+        if (person.getBiography() != null) {
+            if (this.isNewMetadata("biography", person.getBiography().getContent())) {
+                this.addOtherMetadata("biography", person.getBiography().getContent());
+            }
+        }
+
+        this.setValue(this.getName());
+
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param info string info
+     * @return AuthorityValue
+     */
+    @Override
+    public AuthorityValue newInstance(String info) {
+        AuthorityValue authorityValue = null;
+        if (StringUtils.isNotBlank(info)) {
+            Orcidv2 orcid = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
+            authorityValue = orcid.queryAuthorityID(info);
+        } else {
+            authorityValue = this.create();
+        }
+        return authorityValue;
+    }
+
+    @Override
+    public void setValue(String value) {
+        super.setValue(value);
+    }
+
+    /**
+     * Check to see if the provided label / data pair is already present in the "otherMetadata" or not
+     * */
+    public boolean isNewMetadata(String label, String data) {
+        List<String> strings = getOtherMetadata().get(label);
+        boolean update;
+        if (strings == null) {
+            update = StringUtils.isNotBlank(data);
+        } else {
+            update = !strings.contains(data);
+        }
+        return update;
+    }
+
+    /**
+     * Add additional metadata to the otherMetadata map*/
+    public void addOtherMetadata(String label, String data) {
+        List<String> strings = otherMetadata.get(label);
+        if (strings == null) {
+            strings = new ArrayList<>();
+        }
+        strings.add(data);
+        otherMetadata.put(label, strings);
+    }
+
+    public Map<String, List<String>> getOtherMetadata() {
+        return otherMetadata;
+    }
+
+
+    /**
+     * Generate a solr record from this instance
+     * @return SolrInputDocument
+     */
+    @Override
+    public SolrInputDocument getSolrInputDocument() {
+        SolrInputDocument doc = super.getSolrInputDocument();
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            doc.addField("orcid_id", getOrcid_id());
+        }
+
+        for (String t : otherMetadata.keySet()) {
+            List<String> data = otherMetadata.get(t);
+            for (String data_entry : data) {
+                doc.addField("label_" + t, data_entry);
+            }
+        }
+        return doc;
+    }
+
+    /**
+     * Information that can be used the choice ui
+     * @return map
+     */
+    @Override
+    public Map<String, String> choiceSelectMap() {
+
+        Map<String, String> map = super.choiceSelectMap();
+
+        String orcid_id = getOrcid_id();
+        if (StringUtils.isNotBlank(orcid_id)) {
+            map.put("orcid", orcid_id);
+        }
+
+        return map;
+    }
+
+    @Override
+    public String getAuthorityType() {
+        return "orcid";
+    }
+
+    /**
+     * Provides a string that will allow this AuthorityType to be recognized and provides information to create a new instance to be created using public Orcidv2AuthorityValue newInstance(String info).
+     * @return see {@link org.dspace.authority.AuthorityValueGenerator#GENERATE AuthorityValueGenerator.GENERATE}
+     */
+    @Override
+    public String generateString() {
+        String generateString = AuthorityValueGenerator.GENERATE + getAuthorityType() + AuthorityValueGenerator.SPLIT;
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            generateString += getOrcid_id();
+        }
+        return generateString;
+    }
+
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        return true;
+    }
+
+    @Override
+    public int hashCode() {
+        return orcid_id != null ? orcid_id.hashCode() : 0;
+    }
+
+    /**
+     * The regular equals() only checks if both AuthorityValues describe the same authority.
+     * This method checks if the AuthorityValues have different information
+     * E.g. it is used to decide when lastModified should be updated.
+     * @param o object
+     * @return true or false
+     */
+    @Override
+    public boolean hasTheSameInformationAs(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        if (!super.hasTheSameInformationAs(o)) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        for (String key : otherMetadata.keySet()) {
+            if (otherMetadata.get(key) != null) {
+                List<String> metadata = otherMetadata.get(key);
+                List<String> otherMetadata = that.otherMetadata.get(key);
+                if (otherMetadata == null) {
+                    return false;
+                } else {
+                    HashSet<String> metadataSet = new HashSet<String>(metadata);
+                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
+                    if (!metadataSet.equals(otherMetadataSet)) {
+                        return false;
+                    }
+                }
+            } else {
+                if (that.otherMetadata.get(key) != null) {
+                    return false;
+                }
+            }
+        }
+
+        return true;
+    }
+}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Bio.java

@@ -1,113 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-package org.dspace.authority.orcid.model;
-
-import java.util.LinkedHashSet;
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Bio {
-
-    protected String orcid;
-
-    protected BioName name;
-
-    protected String country;
-
-    protected Set<String> keywords;
-
-    protected Set<BioExternalIdentifier> bioExternalIdentifiers;
-
-    protected Set<BioResearcherUrl> researcherUrls;
-
-    protected String biography;
-
-    public Bio() {
-        this.name = new BioName();
-        keywords = new LinkedHashSet<String>();
-        bioExternalIdentifiers = new LinkedHashSet<BioExternalIdentifier>();
-        researcherUrls = new LinkedHashSet<BioResearcherUrl>();
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public BioName getName() {
-        return name;
-    }
-
-    public void setName(BioName name) {
-        this.name = name;
-    }
-
-    public String getCountry() {
-        return country;
-    }
-
-    public void setCountry(String country) {
-        this.country = country;
-    }
-
-    public Set<String> getKeywords() {
-        return keywords;
-    }
-
-    public void addKeyword(String keyword) {
-        this.keywords.add(keyword);
-    }
-
-    public Set<BioExternalIdentifier> getBioExternalIdentifiers() {
-        return bioExternalIdentifiers;
-    }
-
-    public void addExternalIdentifier(BioExternalIdentifier externalReference) {
-        bioExternalIdentifiers.add(externalReference);
-    }
-
-    public Set<BioResearcherUrl> getResearcherUrls() {
-        return researcherUrls;
-    }
-
-    public void addResearcherUrl(BioResearcherUrl researcherUrl) {
-        researcherUrls.add(researcherUrl);
-    }
-
-    public String getBiography() {
-        return biography;
-    }
-
-    public void setBiography(String biography) {
-        this.biography = biography;
-    }
-
-    @Override
-    public String toString() {
-        return "Bio{" +
-                "orcid='" + orcid + '\'' +
-                ", name=" + name +
-                ", country='" + country + '\'' +
-                ", keywords=" + keywords +
-                ", bioExternalIdentifiers=" + bioExternalIdentifiers +
-                ", researcherUrls=" + researcherUrls +
-                ", biography='" + biography + '\'' +
-                '}';
-    }
-}
-

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioExternalIdentifier.java

@@ -1,109 +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.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioExternalIdentifier {
-
-
-    protected String id_orcid;
-    protected String id_common_name;
-    protected String id_reference;
-    protected String id_url;
-
-    public BioExternalIdentifier(String id_orcid, String id_common_name, String id_reference, String id_url) {
-        this.id_orcid = id_orcid;
-        this.id_common_name = id_common_name;
-        this.id_reference = id_reference;
-        this.id_url = id_url;
-    }
-
-    public String getId_orcid() {
-        return id_orcid;
-    }
-
-    public void setId_orcid(String id_orcid) {
-        this.id_orcid = id_orcid;
-    }
-
-    public String getId_common_name() {
-        return id_common_name;
-    }
-
-    public void setId_common_name(String id_common_name) {
-        this.id_common_name = id_common_name;
-    }
-
-    public String getId_reference() {
-        return id_reference;
-    }
-
-    public void setId_reference(String id_reference) {
-        this.id_reference = id_reference;
-    }
-
-    public String getId_url() {
-        return id_url;
-    }
-
-    public void setId_url(String id_url) {
-        this.id_url = id_url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioExternalIdentifier{" +
-                "id_orcid='" + id_orcid + '\'' +
-                ", id_common_name='" + id_common_name + '\'' +
-                ", id_reference='" + id_reference + '\'' +
-                ", id_url='" + id_url + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioExternalIdentifier that = (BioExternalIdentifier) o;
-
-        if (id_common_name != null ? !id_common_name.equals(that.id_common_name) : that.id_common_name != null) {
-            return false;
-        }
-        if (id_orcid != null ? !id_orcid.equals(that.id_orcid) : that.id_orcid != null) {
-            return false;
-        }
-        if (id_reference != null ? !id_reference.equals(that.id_reference) : that.id_reference != null) {
-            return false;
-        }
-        if (id_url != null ? !id_url.equals(that.id_url) : that.id_url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = id_orcid != null ? id_orcid.hashCode() : 0;
-        result = 31 * result + (id_common_name != null ? id_common_name.hashCode() : 0);
-        result = 31 * result + (id_reference != null ? id_reference.hashCode() : 0);
-        result = 31 * result + (id_url != null ? id_url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioName.java

@@ -1,115 +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.authority.orcid.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioName {
-
-    protected String givenNames;
-    protected String familyName;
-    protected String creditName;
-    protected List<String> otherNames;
-
-    BioName() {
-        otherNames = new ArrayList<String>();
-    }
-
-    BioName(String givenNames, String familyName, String creditName, List<String> otherNames) {
-        this.givenNames = givenNames;
-        this.familyName = familyName;
-        this.creditName = creditName;
-        this.otherNames = otherNames;
-    }
-
-    public String getGivenNames() {
-        return givenNames;
-    }
-
-    public void setGivenNames(String givenNames) {
-        this.givenNames = givenNames;
-    }
-
-    public String getFamilyName() {
-        return familyName;
-    }
-
-    public void setFamilyName(String familyName) {
-        this.familyName = familyName;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public List<String> getOtherNames() {
-        return otherNames;
-    }
-
-    public void setOtherNames(List<String> otherNames) {
-        this.otherNames = otherNames;
-    }
-
-    @Override
-    public String toString() {
-        return "BioName{" +
-                "givenNames='" + givenNames + '\'' +
-                ", familyName='" + familyName + '\'' +
-                ", creditName='" + creditName + '\'' +
-                ", otherNames=" + otherNames +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioName bioName = (BioName) o;
-
-        if (creditName != null ? !creditName.equals(bioName.creditName) : bioName.creditName != null) {
-            return false;
-        }
-        if (familyName != null ? !familyName.equals(bioName.familyName) : bioName.familyName != null) {
-            return false;
-        }
-        if (givenNames != null ? !givenNames.equals(bioName.givenNames) : bioName.givenNames != null) {
-            return false;
-        }
-        if (otherNames != null ? !otherNames.equals(bioName.otherNames) : bioName.otherNames != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = givenNames != null ? givenNames.hashCode() : 0;
-        result = 31 * result + (familyName != null ? familyName.hashCode() : 0);
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (otherNames != null ? otherNames.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioResearcherUrl.java

@@ -1,78 +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.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioResearcherUrl {
-
-    protected String name;
-    protected String url;
-
-    public BioResearcherUrl(String name, String url) {
-        this.name = name;
-        this.url = url;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioResearcherUrl{" +
-                "name='" + name + '\'' +
-                ", url='" + url + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioResearcherUrl that = (BioResearcherUrl) o;
-
-        if (name != null ? !name.equals(that.name) : that.name != null) {
-            return false;
-        }
-        if (url != null ? !url.equals(that.url) : that.url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = name != null ? name.hashCode() : 0;
-        result = 31 * result + (url != null ? url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Citation.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.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Citation {
-
-    private CitationType type;
-    private String citation;
-
-    public Citation(CitationType type, String citation) {
-        this.type = type;
-        this.citation = citation;
-    }
-
-    public CitationType getType() {
-        return type;
-    }
-
-    public void setType(CitationType type) {
-        this.type = type;
-    }
-
-    public String getCitation() {
-        return citation;
-    }
-
-    public void setCitation(String citation) {
-        this.citation = citation;
-    }
-
-    @Override
-    public String toString() {
-        return "Citation{" +
-                "type=" + type +
-                ", citation='" + citation + '\'' +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/CitationType.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.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum CitationType {
-
-    FORMATTED_UNSPECIFIED,
-    BIBTEX,
-    FORMATTED_APA,
-    FORMATTED_HARVARD,
-    FORMATTED_IEEE,
-    FORMATTED_MLA,
-    FORMATTED_VANCOUVER,
-    FORMATTED_CHICAGO
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Contributor.java

@@ -1,111 +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.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Contributor {
-
-    private String orcid;
-    private String creditName;
-    private String email;
-    private Set<ContributorAttribute> contributorAttributes;
-
-    public Contributor(String orcid, String creditName, String email, Set<ContributorAttribute> contributorAttributes) {
-        this.orcid = orcid;
-        this.creditName = creditName;
-        this.email = email;
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public String getEmail() {
-        return email;
-    }
-
-    public void setEmail(String email) {
-        this.email = email;
-    }
-
-    public Set<ContributorAttribute> getContributorAttributes() {
-        return contributorAttributes;
-    }
-
-    public void setContributorAttributes(Set<ContributorAttribute> contributorAttributes) {
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    @Override
-    public String toString() {
-        return "Contributor{" +
-                "orcid='" + orcid + '\'' +
-                ", creditName='" + creditName + '\'' +
-                ", email='" + email + '\'' +
-                ", contributorAttributes=" + contributorAttributes +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        Contributor that = (Contributor) o;
-
-        if (contributorAttributes != null ? !contributorAttributes.equals(that.contributorAttributes) : that.contributorAttributes != null) {
-            return false;
-        }
-        if (creditName != null ? !creditName.equals(that.creditName) : that.creditName != null) {
-            return false;
-        }
-        if (email != null ? !email.equals(that.email) : that.email != null) {
-            return false;
-        }
-        if (orcid != null ? !orcid.equals(that.orcid) : that.orcid != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = orcid != null ? orcid.hashCode() : 0;
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (email != null ? email.hashCode() : 0);
-        result = 31 * result + (contributorAttributes != null ? contributorAttributes.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttribute.java

@@ -1,79 +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.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class ContributorAttribute {
-
-    private ContributorAttributeRole role;
-    private ContributorAttributeSequence sequence;
-
-    public ContributorAttribute(ContributorAttributeRole role, ContributorAttributeSequence sequence) {
-        this.role = role;
-        this.sequence = sequence;
-    }
-
-    public ContributorAttributeRole getRole() {
-        return role;
-    }
-
-    public void setRole(ContributorAttributeRole role) {
-        this.role = role;
-    }
-
-    public ContributorAttributeSequence getSequence() {
-        return sequence;
-    }
-
-    public void setSequence(ContributorAttributeSequence sequence) {
-        this.sequence = sequence;
-    }
-
-    @Override
-    public String toString() {
-        return "ContributorAttribute{" +
-                "role=" + role +
-                ", sequence=" + sequence +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        ContributorAttribute that = (ContributorAttribute) o;
-
-        if (role != that.role) {
-            return false;
-        }
-        if (sequence != that.sequence) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = role != null ? role.hashCode() : 0;
-        result = 31 * result + (sequence != null ? sequence.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeRole.java

@@ -1,32 +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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeRole {
-
-    AUTHOR,
-    ASSIGNEE,
-    EDITOR,
-    CHAIR_OR_TRANSLATOR,
-    CO_INVESTIGATOR,
-    CO_INVENTOR,
-    GRADUATE_STUDENT,
-    OTHER_INVENTOR,
-    PRINCIPAL_INVESTIGATOR,
-    POSTDOCTORAL_RESEARCHER,
-    SUPPORT_STAFF
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeSequence.java

@@ -1,23 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeSequence {
-
-    FIRST,
-    ADDITIONAL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Work.java

@@ -1,117 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Work {
-
-    private WorkTitle workTitle;
-    private String description;
-    private Citation citation;
-    private WorkType workType;
-    private String publicationDate;
-    private WorkExternalIdentifier workExternalIdentifier;
-    private String url;
-    private Set<Contributor> contributors;
-    private String workSource;
-
-    public WorkTitle getWorkTitle() {
-        return workTitle;
-    }
-
-    public void setWorkTitle(WorkTitle workTitle) {
-        this.workTitle = workTitle;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-    public Citation getCitation() {
-        return citation;
-    }
-
-    public void setCitation(Citation citation) {
-        this.citation = citation;
-    }
-
-    public WorkType getWorkType() {
-        return workType;
-    }
-
-    public void setWorkType(WorkType workType) {
-        this.workType = workType;
-    }
-
-    public String getPublicationDate() {
-        return publicationDate;
-    }
-
-    public void setPublicationDate(String publicationDate) {
-        this.publicationDate = publicationDate;
-    }
-
-    public WorkExternalIdentifier getWorkExternalIdentifier() {
-        return workExternalIdentifier;
-    }
-
-    public void setWorkExternalIdentifier(WorkExternalIdentifier workExternalIdentifier) {
-        this.workExternalIdentifier = workExternalIdentifier;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    public Set<Contributor> getContributors() {
-        return contributors;
-    }
-
-    public void setContributors(Set<Contributor> contributors) {
-        this.contributors = contributors;
-    }
-
-    public String getWorkSource() {
-        return workSource;
-    }
-
-    public void setWorkSource(String workSource) {
-        this.workSource = workSource;
-    }
-
-    @Override
-    public String toString() {
-        return "Work{" +
-                "workTitle=" + workTitle +
-                ", description='" + description + '\'' +
-                ", citation=" + citation +
-                ", workType=" + workType +
-                ", publicationDate='" + publicationDate + '\'' +
-                ", workExternalIdentifier=" + workExternalIdentifier +
-                ", url='" + url + '\'' +
-                ", contributors=" + contributors +
-                ", workSource='" + workSource + '\'' +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifier.java

@@ -1,71 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkExternalIdentifier {
-
-    private WorkExternalIdentifierType workExternalIdentifierType;
-    private String workExternalIdenfitierID;
-
-    public WorkExternalIdentifier(WorkExternalIdentifierType workExternalIdentifierType, String workExternalIdenfitierID) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-        this.workExternalIdenfitierID = workExternalIdenfitierID;
-    }
-
-    public WorkExternalIdentifierType getWorkExternalIdentifierType() {
-        return workExternalIdentifierType;
-    }
-
-    public void setWorkExternalIdentifierType(WorkExternalIdentifierType workExternalIdentifierType) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-    }
-
-    @Override
-    public String toString() {
-        return "WorkExternalIdentifier{" +
-                "workExternalIdentifierType=" + workExternalIdentifierType +
-                ", workExternalIdenfitierID='" + workExternalIdenfitierID + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        WorkExternalIdentifier that = (WorkExternalIdentifier) o;
-
-        if (workExternalIdenfitierID != null ? !workExternalIdenfitierID.equals(that.workExternalIdenfitierID) : that.workExternalIdenfitierID != null) {
-            return false;
-        }
-        if (workExternalIdentifierType != that.workExternalIdentifierType) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = workExternalIdentifierType != null ? workExternalIdentifierType.hashCode() : 0;
-        result = 31 * result + (workExternalIdenfitierID != null ? workExternalIdenfitierID.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifierType.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.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkExternalIdentifierType {
-
-//    OTHER_ID,
-    ARXIV,
-    ASIN,
-    ASIN_TLD,
-    BIBCODE,
-    DOI,
-    EID,
-    ISBN,
-    ISSN,
-    JFM,
-    JSTOR,
-    LCCN,
-    MR,
-    OCLC,
-    OL,
-    OSTI,
-    PMC,
-    PMID,
-    RFC,
-    SSRN,
-    ZBL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkTitle.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.authority.orcid.model;
-
-import java.util.Map;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkTitle {
-
-    private String title;
-    private String subtitle;
-    private Map<String, String> translatedTitles;
-
-    public WorkTitle(String title, String subtitle, Map<String, String> translatedTitles) {
-        this.title = title;
-        this.subtitle = subtitle;
-        this.translatedTitles = translatedTitles;
-    }
-
-    public String getTitle() {
-        return title;
-    }
-
-    public void setTitle(String title) {
-        this.title = title;
-    }
-
-    public String getSubtitle() {
-        return subtitle;
-    }
-
-    public void setSubtitle(String subtitle) {
-        this.subtitle = subtitle;
-    }
-
-    public String getTranslatedTitles(String languageCode) {
-        return translatedTitles.get(languageCode);
-    }
-
-    public void setTranslatedTitle(String languageCode, String translatedTitle) {
-        translatedTitles.put(languageCode, translatedTitle);
-    }
-
-    @Override
-    public String toString() {
-        return "WorkTitle{" +
-                "title='" + title + '\'' +
-                ", subtitle='" + subtitle + '\'' +
-                ", translatedTitles=" + translatedTitles +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkType.java

@@ -1,57 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118795
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkType {
-
-    BOOK,
-    BOOK_CHAPTER,
-    BOOK_REVIEW,
-    DICTIONARY_ENTRY,
-    DISSERTATION,
-    ENCYCLOPEDIA_ARTICLE,
-    EDITED_BOOK,
-    JOURNAL_ARTICLE,
-    JOURNAL_ISSUE,
-    MAGAZINE_ARTICLE,
-    MANUAL,
-    ONLINE_RESOURCE,
-    NEWSLETTER_ARTICLE,
-    NEWSPAPER_ARTICLE,
-    REPORT,
-    RESEARCH_TOOL,
-    SUPERVISED_STUDENT_PUBLICATION,
-    TEST,
-    TRANSLATION,
-    WEBSITE,
-    CONFERENCE_ABSTRACT,
-    CONFERENCE_PAPER,
-    CONFERENCE_POSTER,
-    DISCLOSURE,
-    LICENSE,
-    PATENT,
-    REGISTERED_COPYRIGHT,
-    ARTISTIC_PERFORMANCE,
-    DATA_SET,
-    INVENTION,
-    LECTURE_SPEECH,
-    RESEARCH_TECHNIQUE,
-    SPIN_OFF_COMPANY,
-    STANDARDS_AND_POLICY,
-    TECHNICAL_STANDARD,
-    OTHER
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/xml/Converter.java

@@ -8,7 +8,13 @@
 package org.dspace.authority.orcid.xml;
 
 import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+import java.io.InputStream;
+import java.net.URISyntaxException;
 
 /**
  *
@@ -24,11 +30,15 @@ public abstract class Converter<T> {
      */
     private static Logger log = Logger.getLogger(Converter.class);
 
+    public abstract T convert(InputStream document);
 
-    protected void processError(Document xml) {
-        String errorMessage = XMLErrors.getErrorMessage(xml);
-        log.error("The orcid-message reports an error: " + errorMessage);
+    protected Object unmarshall(InputStream input, Class<?> type) throws SAXException, URISyntaxException {
+        try {
+            JAXBContext context = JAXBContext.newInstance(type);
+            Unmarshaller unmarshaller = context.createUnmarshaller();
+            return unmarshaller.unmarshal(input);
+        } catch (JAXBException e) {
+            throw new RuntimeException("Unable to unmarshall orcid message" + e);
+        }
     }
-
-    public abstract T convert(Document document);
 }

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLErrors.java

@@ -1,73 +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.authority.orcid.xml;
-
-import org.dspace.authority.util.XMLUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-
-import javax.xml.xpath.XPathExpressionException;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class XMLErrors {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(XMLErrors.class);
-
-    private static final String ERROR_DESC = "/orcid-message/error-desc";
-
-    /**
-     * Evaluates whether a given xml document contains errors or not.
-     *
-     * @param xml The given xml document
-     * @return true if the given xml document is null
-     * or if it contains errors
-     */
-    public static boolean check(Document xml) {
-
-        if (xml == null) {
-            return true;
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent == null;
-    }
-
-    public static String getErrorMessage(Document xml) {
-
-        if (xml == null) {
-            return "Did not receive an XML document.";
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent;
-    }
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoBio.java

@@ -7,23 +7,22 @@
  */
 package org.dspace.authority.orcid.xml;
 
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.BioExternalIdentifier;
-import org.dspace.authority.orcid.model.BioName;
-import org.dspace.authority.orcid.model.BioResearcherUrl;
-import org.dspace.authority.util.XMLUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
 
-import javax.xml.xpath.XPathExpressionException;
+import org.apache.log4j.Logger;
+import org.dspace.authority.orcid.Orcidv2;
+import org.dspace.utils.DSpace;
+import org.orcid.jaxb.model.common_v2.OrcidId;
+import org.orcid.jaxb.model.record_v2.Person;
+import org.orcid.jaxb.model.search_v2.Result;
+import org.orcid.jaxb.model.search_v2.Search;
+import org.xml.sax.SAXException;
+
+import java.io.InputStream;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 
 /**
- *
  * @author Antoine Snyers (antoine at atmire.com)
  * @author Kevin Van de Velde (kevin at atmire dot com)
  * @author Ben Bosman (ben at atmire dot com)
@@ -36,216 +35,39 @@ public class XMLtoBio extends Converter {
      */
     private static Logger log = Logger.getLogger(XMLtoBio.class);
 
-    /**
-     * orcid-message XPATHs
-     */
-
-    protected String ORCID_BIO = "//orcid-bio";
-
-//    protected String ORCID = "parent::*/orcid";
-    protected String ORCID = "parent::*/orcid-identifier/path";
-
-    protected String PERSONAL_DETAILS = "personal-details";
-    protected String GIVEN_NAMES = PERSONAL_DETAILS + "/given-names";
-    protected String FAMILY_NAME = PERSONAL_DETAILS + "/family-name";
-    protected String CREDIT_NAME = PERSONAL_DETAILS + "/credit-name";
-    protected String OTHER_NAMES = PERSONAL_DETAILS + "/other-names";
-    protected String OTHER_NAME = OTHER_NAMES + "/other-name";
-
-    protected String CONTACT_DETAILS = "contact-details";
-    protected String COUNTRY = CONTACT_DETAILS + "/address/country";
-
-    protected String KEYWORDS = "keywords";
-    protected String KEYWORD = KEYWORDS + "/keyword";
-
-    protected String EXTERNAL_IDENTIFIERS = "external-identifiers";
-    protected String EXTERNAL_IDENTIFIER = EXTERNAL_IDENTIFIERS + "/external-identifier";
-    protected String EXTERNAL_ID_ORCID = "external-id-orcid";
-    protected String EXTERNAL_ID_COMMNON_NAME = "external-id-common-name";
-    protected String EXTERNAL_ID_REFERENCE = "external-id-reference";
-    protected String EXTERNAL_ID_URL = "external-id-url";
-
-    protected String RESEARCHER_URLS = "researcher-urls";
-    protected String RESEARCHER_URL = "researcher-urls/researcher-url";
-    protected String URL_NAME = "url-name";
-    protected String URL = "url";
-
-    protected String BIOGRAPHY = ORCID_BIO + "/biography";
-
-    protected String AFFILIATIONS = ORCID_BIO + "/affiliation";
-
-    /**
-     * Regex
-     */
-
-    protected String ORCID_NOT_FOUND = "ORCID [\\d-]* not found";
-
-
-    public List<Bio> convert(Document xml) {
-        List<Bio> result = new ArrayList<Bio>();
-
-        if (XMLErrors.check(xml)) {
-
-            try {
-                Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, ORCID_BIO);
-                while (iterator.hasNext()) {
-                    Bio bio = convertBio(iterator.next());
-                    result.add(bio);
-                }
-            } catch (XPathExpressionException e) {
-                log.error("Error in xpath syntax", e);
-            }
-        } else {
-            processError(xml);
-        }
-
-        return result;
-    }
-
-    private Bio convertBio(Node node) {
-        Bio bio = new Bio();
-
-        setOrcid(node,bio);
-        setPersonalDetails(node, bio);
-        setContactDetails(node, bio);
-        setKeywords(node, bio);
-        setExternalIdentifiers(node, bio);
-        setResearcherUrls(node, bio);
-        setBiography(node, bio);
-
-        return bio;
-    }
-
-    protected void processError(Document xml)  {
-        String errorMessage = XMLErrors.getErrorMessage(xml);
-
-        if(errorMessage.matches(ORCID_NOT_FOUND))
-        {
-            // do something?
-        }
-
-        log.error("The orcid-message reports an error: " + errorMessage);
-    }
-
-
-    private void setOrcid(Node node, Bio bio) {
+    @Override
+    public List<Person> convert(InputStream xml) {
+        List<Person> bios= new ArrayList<>();
         try {
-            String orcid = XMLUtils.getTextContent(node, ORCID);
-            bio.setOrcid(orcid);
-        } catch (XPathExpressionException e) {
-            log.debug("Error in finding the biography in bio xml.", e);
-        }
-    }
+            Orcidv2 connector = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
 
-    protected void setBiography(Node xml, Bio bio) {
-        try {
-            String biography = XMLUtils.getTextContent(xml, BIOGRAPHY);
-            bio.setBiography(biography);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the biography in bio xml.", e);
-        }
-    }
-
-    protected void setResearcherUrls(Node xml, Bio bio) {
-        try {
-            NodeList researcher_urls = XMLUtils.getNodeList(xml, RESEARCHER_URL);
-            if (researcher_urls != null) {
-                for (int i = 0; i < researcher_urls.getLength(); i++) {
-                    Node researcher_url = researcher_urls.item(i);
-                    if (researcher_url.getNodeType() != Node.TEXT_NODE) {
-                        String url_name = XMLUtils.getTextContent(researcher_url, URL_NAME);
-                        String url = XMLUtils.getTextContent(researcher_url, URL);
-                        BioResearcherUrl researcherUrl = new BioResearcherUrl(url_name, url);
-                        bio.addResearcherUrl(researcherUrl);
+            Search search = (Search) unmarshall(xml, Search.class);
+            for(Result result : search.getResult()){
+                OrcidId orcidIdentifier = result.getOrcidIdentifier();
+                if(orcidIdentifier!=null){
+                    log.debug("Found OrcidId=" + orcidIdentifier.toString());
+                    String orcid = orcidIdentifier.getUriPath();
+                    Person bio = connector.getBio(orcid);
+                    if(bio!=null){
+                        bios.add(bio);
                     }
                 }
             }
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the researcher url in bio xml.", e);
+        } catch (SAXException | URISyntaxException e) {
+            log.error(e);
         }
+        return bios;
     }
 
-    protected void setExternalIdentifiers(Node xml, Bio bio) {
+    public Person convertSinglePerson(InputStream xml) {
+        Person person = null;
         try {
-
-            Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, EXTERNAL_IDENTIFIER);
-            while (iterator.hasNext()) {
-                Node external_identifier = iterator.next();
-                String id_orcid = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_ORCID);
-                String id_common_name = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_COMMNON_NAME);
-                String id_reference = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_REFERENCE);
-                String id_url = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_URL);
-                BioExternalIdentifier externalIdentifier = new BioExternalIdentifier(id_orcid, id_common_name, id_reference, id_url);
-                bio.addExternalIdentifier(externalIdentifier);
-            }
-
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the external identifier in bio xml.", e);
-        }
-    }
-
-    protected void setKeywords(Node xml, Bio bio) {
-        try {
-            NodeList keywords = XMLUtils.getNodeList(xml, KEYWORD);
-            if (keywords != null) {
-                for (int i = 0; i < keywords.getLength(); i++) {
-                    String keyword = keywords.item(i).getTextContent();
-                    String[] split = keyword.split(",");
-                    for (String k : split) {
-                        bio.addKeyword(k.trim());
-                    }
-                }
-            }
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the keywords in bio xml.", e);
-        }
-    }
-
-    protected void setContactDetails(Node xml, Bio bio) {
-        try {
-            String country = XMLUtils.getTextContent(xml, COUNTRY);
-            bio.setCountry(country);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the country in bio xml.", e);
-        }
-    }
-
-    protected void setPersonalDetails(Node xml, Bio bio) {
-        BioName name = bio.getName();
-
-        try {
-            String givenNames = XMLUtils.getTextContent(xml, GIVEN_NAMES);
-            name.setGivenNames(givenNames);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the given names in bio xml.", e);
-        }
-
-        try {
-            String familyName = XMLUtils.getTextContent(xml, FAMILY_NAME);
-            name.setFamilyName(familyName);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the family name in bio xml.", e);
-        }
-
-        try {
-            String creditName = XMLUtils.getTextContent(xml, CREDIT_NAME);
-            name.setCreditName(creditName);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the credit name in bio xml.", e);
-        }
-
-        try {
-
-            Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, OTHER_NAME);
-            while (iterator.hasNext()) {
-                Node otherName = iterator.next();
-                String textContent = otherName.getTextContent();
-                name.getOtherNames().add(textContent.trim());
-            }
-
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the other names in bio xml.", e);
+            person = (Person) unmarshall(xml, Person.class);
+            return person;
+        } catch (SAXException | URISyntaxException e) {
+            log.error(e);
         }
+        return null;
     }
 
 }

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoWork.java

@@ -1,239 +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.authority.orcid.xml;
-
-import org.dspace.authority.orcid.model.*;
-import org.dspace.authority.util.*;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import javax.xml.xpath.XPathExpressionException;
-import java.util.*;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class XMLtoWork extends Converter {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(XMLtoWork.class);
-
-    /**
-     * orcid-message XPATHs
-     */
-
-    protected String ORCID_WORKS = "//orcid-works";
-    protected String ORCID_WORK = ORCID_WORKS + "/orcid-work";
-
-    protected String WORK_TITLE = "work-title";
-    protected String TITLE = WORK_TITLE + "/title";
-    protected String SUBTITLE = WORK_TITLE + "/subtitle";
-    protected String TRANSLATED_TITLES = WORK_TITLE + "/translated-title";
-    protected String TRANSLATED_TITLES_LANGUAGE = "@language-code";
-
-    protected String SHORT_DESCRIPTION = "short-description";
-
-    protected String WORK_CITATION = "work-citation";
-    protected String CITATION_TYPE = WORK_CITATION + "/work-citation-type";
-    protected String CITATION = WORK_CITATION + "/citation";
-
-    protected String WORK_TYPE = "work-type";
-
-    protected String PUBLICATION_DATE = "publication-date";
-    protected String YEAR = PUBLICATION_DATE + "/year";
-    protected String MONTH = PUBLICATION_DATE + "/month";
-    protected String DAY = PUBLICATION_DATE + "/day";
-
-    protected String WORK_EXTERNAL_IDENTIFIERS = "work-external-identifiers";
-    protected String WORK_EXTERNAL_IDENTIFIER = WORK_EXTERNAL_IDENTIFIERS + "/work-external-identifier";
-    protected String WORK_EXTERNAL_IDENTIFIER_TYPE = "work-external-identifier-type";
-    protected String WORK_EXTERNAL_IDENTIFIER_ID = "work-external-identifier-id";
-
-    protected String URL = "url";
-
-    protected String WORK_CONTRIBUTOR = "work-contributors";
-    protected String CONTRIBUTOR = WORK_CONTRIBUTOR+"/contributor";
-    protected String CONTRIBUTOR_ORCID = "contributor-orcid";
-    protected String CREDIT_NAME = "credit-name";
-    protected String CONTRIBUTOR_EMAIL = "contributor-email";
-    protected String CONTRIBUTOR_ATTRIBUTES = "contributor-attributes";
-    protected String CONTRIBUTOR_SEQUENCE = "contributor-sequence";
-    protected String CONTRIBUTOR_ROLE = "contributor-role";
-
-    protected String WORK_SOURCE = "work-source";
-
-
-    public List<Work> convert(Document document) {
-        List<Work> result = new ArrayList<Work>();
-
-        if (XMLErrors.check(document)) {
-
-            try {
-                Iterator<Node> iterator = XMLUtils.getNodeListIterator(document, ORCID_WORK);
-                while (iterator.hasNext()) {
-                    Work work = convertWork(iterator.next());
-                    result.add(work);
-                }
-            } catch (XPathExpressionException e) {
-                log.error("Error in xpath syntax", e);
-            }
-        } else {
-            processError(document);
-        }
-
-        return result;
-    }
-
-    protected Work convertWork(Node node) throws XPathExpressionException {
-        Work work = new Work();
-        setTitle(node, work);
-        setDescription(node, work);
-        setCitation(node, work);
-        setWorkType(node, work);
-        setPublicationDate(node, work);
-        setExternalIdentifiers(node, work);
-        setUrl(node, work);
-        setContributors(node, work);
-        setWorkSource(node, work);
-
-        return work;
-    }
-
-    protected void setWorkSource(Node node, Work work) throws XPathExpressionException {
-        String workSource = XMLUtils.getTextContent(node, WORK_SOURCE);
-        work.setWorkSource(workSource);
-    }
-
-    protected void setContributors(Node node, Work work) throws XPathExpressionException {
-
-        Set<Contributor> contributors = new HashSet<Contributor>();
-
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, CONTRIBUTOR);
-        while (iterator.hasNext()) {
-            Node nextContributorNode = iterator.next();
-            String orcid = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_ORCID);
-            String creditName = XMLUtils.getTextContent(nextContributorNode, CREDIT_NAME);
-            String email = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_EMAIL);
-
-            Set<ContributorAttribute> contributorAttributes = new HashSet<ContributorAttribute>();
-            NodeList attributeNodes = XMLUtils.getNodeList(nextContributorNode, CONTRIBUTOR_ATTRIBUTES);
-            Iterator<Node> attributesIterator = XMLUtils.getNodeListIterator(attributeNodes);
-            while (attributesIterator.hasNext()) {
-                Node nextAttribute = attributesIterator.next();
-
-                String roleText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_ROLE);
-                ContributorAttributeRole role = EnumUtils.lookup(ContributorAttributeRole.class, roleText);
-
-                String sequenceText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_SEQUENCE);
-                ContributorAttributeSequence sequence = EnumUtils.lookup(ContributorAttributeSequence.class, sequenceText);
-
-                ContributorAttribute attribute = new ContributorAttribute(role, sequence);
-                contributorAttributes.add(attribute);
-            }
-
-            Contributor contributor = new Contributor(orcid, creditName, email, contributorAttributes);
-            contributors.add(contributor);
-        }
-
-        work.setContributors(contributors);
-    }
-
-    protected void setUrl(Node node, Work work) throws XPathExpressionException {
-        String url = XMLUtils.getTextContent(node, URL);
-        work.setUrl(url);
-    }
-
-    protected void setExternalIdentifiers(Node node, Work work) throws XPathExpressionException {
-
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, WORK_EXTERNAL_IDENTIFIER);
-        while (iterator.hasNext()) {
-            Node work_external_identifier = iterator.next();
-            String typeText = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_TYPE);
-
-            WorkExternalIdentifierType type = EnumUtils.lookup(WorkExternalIdentifierType.class, typeText);
-
-            String id = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_ID);
-
-            WorkExternalIdentifier externalID = new WorkExternalIdentifier(type, id);
-            work.setWorkExternalIdentifier(externalID);
-        }
-    }
-
-    protected void setPublicationDate(Node node, Work work) throws XPathExpressionException {
-
-        String year = XMLUtils.getTextContent(node, YEAR);
-        String month = XMLUtils.getTextContent(node, MONTH);
-        String day = XMLUtils.getTextContent(node, DAY);
-
-        String publicationDate = year;
-        if (StringUtils.isNotBlank(month)) {
-            publicationDate += "-" + month;
-            if (StringUtils.isNotBlank(day)) {
-                publicationDate += "-" + day;
-            }
-        }
-
-        work.setPublicationDate(publicationDate);
-    }
-
-    protected void setWorkType(Node node, Work work) throws XPathExpressionException {
-
-        String workTypeText = XMLUtils.getTextContent(node, WORK_TYPE);
-        WorkType workType = EnumUtils.lookup(WorkType.class, workTypeText);
-
-        work.setWorkType(workType);
-    }
-
-    protected void setCitation(Node node, Work work) throws XPathExpressionException {
-
-        String typeText = XMLUtils.getTextContent(node, CITATION_TYPE);
-        CitationType type = EnumUtils.lookup(CitationType.class, typeText);
-
-        String citationtext = XMLUtils.getTextContent(node, CITATION);
-
-        Citation citation = new Citation(type, citationtext);
-        work.setCitation(citation);
-    }
-
-    protected void setDescription(Node node, Work work) throws XPathExpressionException {
-
-        String description = null;
-        description = XMLUtils.getTextContent(node, SHORT_DESCRIPTION);
-        work.setDescription(description);
-    }
-
-    protected void setTitle(Node node, Work work) throws XPathExpressionException {
-
-        String title = XMLUtils.getTextContent(node, TITLE);
-
-        String subtitle = XMLUtils.getTextContent(node, SUBTITLE);
-
-        Map<String, String> translatedTitles = new HashMap<String, String>();
-        NodeList nodeList = XMLUtils.getNodeList(node, TRANSLATED_TITLES);
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(nodeList);
-        while (iterator.hasNext()) {
-            Node languageNode = iterator.next();
-            String language = XMLUtils.getTextContent(languageNode, TRANSLATED_TITLES_LANGUAGE);
-            String translated_title = XMLUtils.getTextContent(languageNode, ".");
-            translatedTitles.put(language, translated_title);
-        }
-
-        WorkTitle workTitle = new WorkTitle(title, subtitle, translatedTitles);
-        work.setWorkTitle(workTitle);
-    }
-
-}

dspace-api/src/main/java/org/dspace/authority/rest/RESTConnector.java

@@ -7,13 +7,12 @@
  */
 package org.dspace.authority.rest;
 
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.dspace.authority.util.XMLUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
 
 import java.io.InputStream;
 import java.util.Scanner;
@@ -38,26 +37,28 @@ public class RESTConnector {
         this.url = url;
     }
 
-    public Document get(String path) {
-        Document document = null;
+    public InputStream get(String path, String accessToken) {
 
         InputStream result = null;
         path = trimSlashes(path);
 
         String fullPath = url + '/' + path;
         HttpGet httpGet = new HttpGet(fullPath);
+        if(StringUtils.isNotBlank(accessToken)){
+            httpGet.addHeader("Content-Type", "application/vnd.orcid+xml");
+            httpGet.addHeader("Authorization","Bearer "+accessToken);
+        }
         try {
             HttpClient httpClient = HttpClientBuilder.create().build();
             HttpResponse getResponse = httpClient.execute(httpGet);
             //do not close this httpClient
             result = getResponse.getEntity().getContent();
-            document = XMLUtils.convertStreamToXML(result);
 
         } catch (Exception e) {
             getGotError(e, fullPath);
         }
 
-        return document;
+        return result;
     }
 
     protected void getGotError(Exception e, String fullPath) {

dspace-api/src/main/java/org/dspace/authority/rest/RestSource.java

@@ -7,9 +7,7 @@
  */
 package org.dspace.authority.rest;
 
-import org.dspace.authority.AuthorityValue;
-
-import java.util.List;
+import org.dspace.authority.SolrAuthorityInterface;
 
 /**
  *
@@ -18,21 +16,11 @@ import java.util.List;
  * @author Ben Bosman (ben at atmire dot com)
  * @author Mark Diggory (markd at atmire dot com)
  */
-public abstract class RestSource {
+public abstract class RestSource implements SolrAuthorityInterface {
 
     protected RESTConnector restConnector;
 
     public RestSource(String url) {
         this.restConnector = new RESTConnector(url);
     }
-
-    /**
-     * TODO
-     * com.atmire.org.dspace.authority.rest.RestSource#queryAuthorities -> add field, so the source can decide whether to query /users or something else.
-     * -> implement subclasses
-     * -> implement usages
-     */
-    public abstract List<AuthorityValue> queryAuthorities(String text, int max);
-
-    public abstract AuthorityValue queryAuthorityID(String id);
 }

dspace-api/src/main/java/org/dspace/authorize/AuthorizeManager.java

@@ -20,6 +20,7 @@ import org.dspace.eperson.Group;
 import org.dspace.storage.rdbms.DatabaseManager;
 import org.dspace.storage.rdbms.TableRow;
 import org.dspace.storage.rdbms.TableRowIterator;
+import org.dspace.workflow.WorkflowItem;
 
 /**
  * AuthorizeManager handles all authorization checks for DSpace. For better
@@ -295,8 +296,43 @@ public class AuthorizeManager
             }
         }
 
+        // In case the dso is an bundle or bitstream we must ignore custom 
+        // policies if it does not belong to at least one installed item (see 
+        // DS-2614).
+        // In case the dso is an item and a corresponding workspace or workflow
+        // item exist, we have to ignore custom policies (see DS-2614).
+        boolean ignoreCustomPolicies = false;
+        if (o instanceof Bitstream)
+        {
+            Bitstream b = (Bitstream) o;
+
+            // Ensure that this is not a collection or community logo
+            DSpaceObject parent = b.getParentObject();
+            if (!(parent instanceof Collection) && !(parent instanceof Community))
+            {
+                ignoreCustomPolicies = !isAnyItemInstalled(c, b.getBundles());
+            }
+        }
+        if (o instanceof Bundle)
+        {
+            ignoreCustomPolicies = !isAnyItemInstalled(c, new Bundle[] {(Bundle) o});
+        }
+        if (o instanceof Item)
+        {
+            if (WorkspaceItem.findByItem(c, (Item) o) != null ||
+                    WorkflowItem.findByItem(c, (Item) o) != null)
+            {
+                ignoreCustomPolicies = true;
+            }
+        }
+        
         for (ResourcePolicy rp : getPoliciesActionFilter(c, o, action))
         {
+            if (ignoreCustomPolicies 
+                    && ResourcePolicy.TYPE_CUSTOM.equals(rp.getRpType()))
+            {
+                continue;
+            }
             // check policies for date validity
             if (rp.isDateValid())
             {
@@ -306,7 +342,7 @@ public class AuthorizeManager
                 }
 
                 if ((rp.getGroupID() != -1)
-                        && (Group.isMember(c, rp.getGroupID())))
+                        && (Group.isMember(c, e, rp.getGroupID())))
                 {
                     // group was set, and eperson is a member
                     // of that group
@@ -318,7 +354,26 @@ public class AuthorizeManager
         // default authorization is denial
         return false;
     }
-
+    
+    // check whether any bundle belongs to any item that passed submission 
+    // and workflow process
+    protected static boolean isAnyItemInstalled(Context ctx, Bundle[] bundles)
+            throws SQLException
+    {
+        for (Bundle bundle : bundles)
+        {
+            for (Item item : bundle.getItems())
+            {
+                if (WorkspaceItem.findByItem(ctx, item) == null
+                        && WorkflowItem.findByItem(ctx, item) == null)
+                {
+                    return true;
+                }
+            }
+        }
+        return false;
+    }
+    
     ///////////////////////////////////////////////
     // admin check methods
     ///////////////////////////////////////////////
@@ -480,7 +535,9 @@ public class AuthorizeManager
 
         rp.update();
 
+        c.turnOffAuthorisationSystem();
         o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -534,8 +591,10 @@ public class AuthorizeManager
         rp.setRpType(type);
 
         rp.update();
-
+        
+        c.turnOffAuthorisationSystem();
         o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -799,7 +858,9 @@ public class AuthorizeManager
             drp.update();
         }
 
+        c.turnOffAuthorisationSystem();
         dest.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -815,12 +876,14 @@ public class AuthorizeManager
     public static void removeAllPolicies(Context c, DSpaceObject o)
             throws SQLException
     {
-        o.updateLastModified();
-
         // FIXME: authorization check?
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? ",
                 o.getType(), o.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -837,7 +900,7 @@ public class AuthorizeManager
             throws SQLException
     {
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
-                + "resource_type_id= ? AND resource_id= ? AND rptype <> ? ",
+                + "resource_type_id= ? AND resource_id= ? AND (rptype <> ? OR rptype IS NULL)",
                 o.getType(), o.getID(), type);
     }
 
@@ -861,6 +924,29 @@ public class AuthorizeManager
                 + "resource_type_id= ? AND resource_id= ? AND rptype=? ",
                 o.getType(), o.getID(), type);
     }
+    
+	/**
+	 * Change all the policies related to the action (fromPolicy) of the
+	 * specified object to the new action (toPolicy)
+	 * 
+	 * @param context
+	 * @param dso
+	 *            the dspace object
+	 * @param fromAction
+	 *            the action to change
+	 * @param toAction
+	 *            the new action to set
+	 * @throws SQLException
+	 * @throws AuthorizeException
+	 */
+	public static void switchPoliciesAction(Context context, DSpaceObject dso, int fromAction, int toAction)
+			throws SQLException, AuthorizeException {
+		List<ResourcePolicy> rps = getPoliciesActionFilter(context, dso, fromAction);
+		for (ResourcePolicy rp : rps) {
+			rp.setAction(toAction);
+			rp.update();
+		}
+	}
 
     /**
      * Remove all policies from an object that match a given action. FIXME
@@ -879,7 +965,6 @@ public class AuthorizeManager
     public static void removePoliciesActionFilter(Context context,
                                                   DSpaceObject dso, int actionID) throws SQLException
     {
-        dso.updateLastModified();
         if (actionID == -1)
         {
             // remove all policies from object
@@ -891,6 +976,10 @@ public class AuthorizeManager
                             "resource_id= ? AND action_id= ? ",
                     dso.getType(), dso.getID(), actionID);
         }
+        
+        context.turnOffAuthorisationSystem();
+        dso.updateLastModified();
+        context.restoreAuthSystemState();
     }
 
     /**
@@ -927,11 +1016,13 @@ public class AuthorizeManager
     public static void removeGroupPolicies(Context c, DSpaceObject o, Group g)
             throws SQLException
     {
-        o.updateLastModified();
-
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? AND epersongroup_id= ? ",
                 o.getType(), o.getID(), g.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -950,10 +1041,13 @@ public class AuthorizeManager
     public static void removeEPersonPolicies(Context c, DSpaceObject o, EPerson e)
             throws SQLException
     {
-        o.updateLastModified();
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? AND eperson_id= ? ",
                 o.getType(), o.getID(), e.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**

dspace-api/src/main/java/org/dspace/authorize/FixDefaultPolicies.java

@@ -36,7 +36,7 @@ public class FixDefaultPolicies
         Context c = new Context();
 
         // turn off authorization
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         //////////////////////
         // carnage begins here

dspace-api/src/main/java/org/dspace/authorize/PolicySet.java

@@ -63,7 +63,7 @@ public class PolicySet
         Context c = new Context();
 
         // turn off authorization
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         //////////////////////
         // carnage begins here

dspace-api/src/main/java/org/dspace/browse/BrowserScope.java

@@ -354,7 +354,7 @@ public class BrowserScope
      */
     public void setResultsPerPage(int resultsPerPage)
     {
-        if (resultsPerPage > -1 || browseIndex.isTagCloudEnabled())
+        if (resultsPerPage > -1 || (browseIndex != null && browseIndex.isTagCloudEnabled()))
         {
             this.resultsPerPage = resultsPerPage;
         }

dspace-api/src/main/java/org/dspace/browse/SolrBrowseDAO.java

@@ -32,6 +32,8 @@ import org.dspace.utils.DSpace;
  * 
  * @author Andrea Bollini (CILEA)
  * @author Adán Román Ruiz at arvo.es (bugfix)
+ * @author Panagiotis Koutsourakis (National Documentation Centre) (bugfix)
+ * @author Kostas Stamatis (National Documentation Centre) (bugfix)
  * 
  */
 public class SolrBrowseDAO implements BrowseDAO
@@ -336,6 +338,22 @@ public class SolrBrowseDAO implements BrowseDAO
         addStatusFilter(query);
         query.setMaxResults(0);
         query.addFilterQueries("search.resourcetype:" + Constants.ITEM);
+
+        // We need to take into account the fact that we may be in a subset of the items
+        if (authority != null)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_authority_filter}"
+                    + authority);
+        }
+        else if (this.value != null && !valuePartial)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_value_filter}" + this.value);
+        }
+        else if (valuePartial)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_partial}" + this.value);
+        }
+
         if (isAscending)
         {
             query.setQuery("bi_"+column + "_sort" + ": [* TO \"" + value + "\"}");
@@ -343,6 +361,7 @@ public class SolrBrowseDAO implements BrowseDAO
         else
         {
             query.setQuery("bi_" + column + "_sort" + ": {\"" + value + "\" TO *]");
+	        query.addFilterQueries("-(bi_" + column + "_sort" + ":" + value + "*)");
         }
 	    boolean includeUnDiscoverable = itemsWithdrawn || !itemsDiscoverable;
         DiscoverResult resp = null;

dspace-api/src/main/java/org/dspace/content/Collection.java

@@ -28,6 +28,7 @@ import org.dspace.workflow.WorkflowItem;
 import org.dspace.xmlworkflow.storedcomponents.CollectionRole;
 import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 
+import java.io.Serializable;
 import java.io.IOException;
 import java.io.InputStream;
 import java.sql.PreparedStatement;
@@ -47,7 +48,6 @@ import java.util.*;
  * effect.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 public class Collection extends DSpaceObject
 {
@@ -294,31 +294,48 @@ public class Collection extends DSpaceObject
      * @return the collections in the system
      * @throws SQLException
      */
-    public static Collection[] findAll(Context context) throws SQLException {
+    public static Collection[] findAll(Context context) throws SQLException
+    {
         TableRowIterator tri = null;
-        try {
-            String query = "SELECT c.* FROM collection c " +
-                    "LEFT JOIN metadatavalue m on (m.resource_id = c.collection_id and m.resource_type_id = ? and m.metadata_field_id = ?) ";
-            if(DatabaseManager.isOracle()){
-                query += " ORDER BY cast(m.text_value as varchar2(128))";
-            }else{
-                query += " ORDER BY m.text_value";
-            }
+        List<Collection> collections = null;
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer query = new StringBuffer(
+            "SELECT c.*" +
+            "FROM collection c " +
+            "LEFT JOIN metadatavalue m ON (" +
+              "m.resource_id = c.collection_id AND " +
+              "m.resource_type_id = ? AND " +
+              "m.metadata_field_id = ?" +
+            ")"
+        );
 
-            tri = DatabaseManager.query(context,
-                    query,
-                    Constants.COLLECTION,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(), "title", null).getFieldID()
-            );
-        } catch (SQLException e) {
-            log.error("Find all Collections - ",e);
-            throw e;
+        if (DatabaseManager.isOracle())
+        {
+            query.append(" ORDER BY cast(m.text_value as varchar2(128))");
+        }
+        else
+        {
+            query.append(" ORDER BY m.text_value");
         }
 
-        List<Collection> collections = new ArrayList<Collection>();
+        params.add(Constants.COLLECTION);
+        params.add(
+          MetadataField.findByElement(
+            context,
+            MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(),
+            "title",
+            null
+          ).getFieldID()
+        );
 
         try
         {
+            tri = DatabaseManager.query(
+              context, query.toString(), params.toArray()
+            );
+
+            collections = new ArrayList<Collection>();
+
             while (tri.hasNext())
             {
                 TableRow row = tri.next();
@@ -337,6 +354,11 @@ public class Collection extends DSpaceObject
                 }
             }
         }
+        catch (SQLException e)
+        {
+            log.error("Find all Collections - ", e);
+            throw e;
+        }
         finally
         {
             // close the TableRowIterator to free up resources
@@ -363,31 +385,47 @@ public class Collection extends DSpaceObject
     public static Collection[] findAll(Context context, Integer limit, Integer offset) throws SQLException
     {
         TableRowIterator tri = null;
-        try{
-            String query = "SELECT c.* FROM collection c " +
-                    "LEFT JOIN metadatavalue m on (m.resource_id = c.collection_id and m.resource_type_id = ? and m.metadata_field_id = ?) ";
+        List<Collection> collections = null;
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer query = new StringBuffer(
+            "SELECT c.*" +
+            "FROM collection c " +
+            "LEFT JOIN metadatavalue m ON (" +
+              "m.resource_id = c.collection_id AND " +
+              "m.resource_type_id = ? AND " +
+              "m.metadata_field_id = ?" +
+            ")"
+        );
 
-            if(DatabaseManager.isOracle()){
-                query += " ORDER BY cast(m.text_value as varchar2(128))";
-            }else{
-                query += " ORDER BY m.text_value";
-            }
-            query += " limit ? offset ?";
-            tri = DatabaseManager.query(context,
-                    query,
-                    Constants.COLLECTION,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(), "title", null).getFieldID(),
-                    limit,
-                    offset
-            );
-        } catch (SQLException e) {
-            log.error("Find all Collections offset/limit - ",e);
-            throw e;
+        if (DatabaseManager.isOracle())
+        {
+            query.append(" ORDER BY cast(m.text_value as varchar2(128))");
         }
-        List<Collection> collections = new ArrayList<Collection>();
+        else
+        {
+            query.append(" ORDER BY m.text_value");
+        }
+
+        params.add(Constants.COLLECTION);
+        params.add(
+          MetadataField.findByElement(
+            context,
+            MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(),
+            "title",
+            null
+          ).getFieldID()
+        );
+
+        DatabaseManager.applyOffsetAndLimit(query, params, offset, limit);
 
         try
         {
+            tri = DatabaseManager.query(
+              context, query.toString(), params.toArray()
+            );
+
+            collections = new ArrayList<Collection>();
+
             while (tri.hasNext())
             {
                 TableRow row = tri.next();
@@ -406,6 +444,11 @@ public class Collection extends DSpaceObject
                 }
             }
         }
+        catch (SQLException e)
+        {
+            log.error("Find all Collections offset/limit - ", e);
+            throw e;
+        }
         finally
         {
             // close the TableRowIterator to free up resources
@@ -450,13 +493,20 @@ public class Collection extends DSpaceObject
      */
     public ItemIterator getItems(Integer limit, Integer offset) throws SQLException
     {
-        String myQuery = "SELECT item.* FROM item, collection2item WHERE "
-                + "item.item_id=collection2item.item_id AND "
-                + "collection2item.collection_id= ? "
-                + "AND item.in_archive='1' limit ? offset ?";
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer myQuery = new StringBuffer(
+            "SELECT item.* " + 
+            "FROM item, collection2item " + 
+            "WHERE item.item_id = collection2item.item_id " +
+              "AND collection2item.collection_id = ? " +
+              "AND item.in_archive = '1'"
+        );
 
-        TableRowIterator rows = DatabaseManager.queryTable(ourContext, "item",
-                myQuery,getID(), limit, offset);
+        params.add(getID());
+        DatabaseManager.applyOffsetAndLimit(myQuery, params, offset, limit);
+
+        TableRowIterator rows = DatabaseManager.query(ourContext,
+                myQuery.toString(), params.toArray());
 
         return new ItemIterator(ourContext, rows);
     }
@@ -679,8 +729,6 @@ public class Collection extends DSpaceObject
             g.setName("COLLECTION_" + getID() + "_WORKFLOW_STEP_" + step);
             g.update();
             setWorkflowGroup(step, g);
-
-            AuthorizeManager.addPolicy(ourContext, this, Constants.ADD, g);
         }
 
         return workflowGroup[step - 1];
@@ -689,26 +737,82 @@ public class Collection extends DSpaceObject
     /**
      * Set the workflow group corresponding to a particular workflow step.
      * <code>null</code> can be passed in if there should be no associated
-     * group for that workflow step; any existing group is NOT deleted.
+     * group for that workflow step.  Any existing group is NOT deleted.
      *
      * @param step
      *            the workflow step (1-3)
-     * @param g
+     * @param newGroup
      *            the new workflow group, or <code>null</code>
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException passed through.
      */
-    public void setWorkflowGroup(int step, Group g)
+    public void setWorkflowGroup(int step, Group newGroup)
+            throws SQLException, AuthorizeException
     {
-        workflowGroup[step - 1] = g;
-
-        if (g == null)
+        Group oldGroup = getWorkflowGroup(step);
+        String stepColumn;
+        int action;
+        switch(step)
         {
-            collectionRow.setColumnNull("workflow_step_" + step);
+        case 1:
+            action = Constants.WORKFLOW_STEP_1;
+            stepColumn = "workflow_step_1";
+            break;
+        case 2:
+            action = Constants.WORKFLOW_STEP_2;
+            stepColumn = "workflow_step_2";
+            break;
+        case 3:
+            action = Constants.WORKFLOW_STEP_3;
+            stepColumn = "workflow_step_3";
+            break;
+        default:
+            throw new IllegalArgumentException("Illegal step count:  " + step);
         }
+        workflowGroup[step-1] = newGroup;
+        if (newGroup != null)
+            collectionRow.setColumn(stepColumn, newGroup.getID());
         else
-        {
-            collectionRow.setColumn("workflow_step_" + step, g.getID());
-        }
+            collectionRow.setColumnNull(stepColumn);
         modified = true;
+
+        // Deal with permissions.
+        try {
+            ourContext.turnOffAuthorisationSystem();
+            // remove the policies for the old group
+            if (oldGroup != null)
+            {
+                List<ResourcePolicy> oldPolicies = AuthorizeManager
+                        .getPoliciesActionFilter(ourContext, this, action);
+                int oldGroupID = oldGroup.getID();
+                for (ResourcePolicy rp : oldPolicies)
+                {
+                    if (rp.getGroupID() == oldGroupID)
+                        rp.delete();
+                }
+
+                oldPolicies = AuthorizeManager
+                        .getPoliciesActionFilter(ourContext, this, Constants.ADD);
+                for (ResourcePolicy rp : oldPolicies)
+                {
+                    if ((rp.getGroupID() == oldGroupID)
+                            && ResourcePolicy.TYPE_WORKFLOW.equals(rp.getRpType()))
+                        rp.delete();
+                }
+           }
+
+            // New group can be null to delete workflow step.
+            // We need to grant permissions if new group is not null.
+            if (newGroup != null)
+            {
+                AuthorizeManager.addPolicy(ourContext, this, action, newGroup,
+                        ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(ourContext, this, Constants.ADD, newGroup,
+                        ResourcePolicy.TYPE_WORKFLOW);
+            }
+        } finally {
+            ourContext.restoreAuthSystemState();
+        }
     }
 
     /**
@@ -1513,7 +1617,7 @@ public class Collection extends DSpaceObject
 
     public static Collection[] findAuthorizedOptimized(Context context, int actionID) throws java.sql.SQLException
     {
-        if(! ConfigurationManager.getBooleanProperty("org.dspace.content.Collection.findAuthorizedPerformanceOptimize", true)) {
+        if(! ConfigurationManager.getBooleanProperty("org.dspace.content.Collection.findAuthorizedPerformanceOptimize", false)) {
             // Fallback to legacy query if config says so. The rationale could be that a site found a bug.
             return findAuthorized(context, null, actionID);
         }

dspace-api/src/main/java/org/dspace/content/Community.java

@@ -280,7 +280,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(context);
 
                 // First check the cache
                 Community fromCache = (Community) context.fromCache(
@@ -350,7 +350,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(context);
 
                 // First check the cache
                 Community fromCache = (Community) context.fromCache(
@@ -683,7 +683,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Collection fromCache = (Collection) ourContext.fromCache(
@@ -757,7 +757,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Community fromCache = (Community) ourContext.fromCache(
@@ -812,7 +812,7 @@ public class Community extends DSpaceObject
         {
             if (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Community fromCache = (Community) ourContext.fromCache(

dspace-api/src/main/java/org/dspace/content/InstallItem.java

@@ -60,6 +60,8 @@ public class InstallItem
             IOException, AuthorizeException
     {
         Item item = is.getItem();
+        Collection collection = is.getCollection();
+        
         IdentifierService identifierService = new DSpace().getSingletonService(IdentifierService.class);
         try {
             if(suppliedHandle == null)
@@ -74,7 +76,15 @@ public class InstallItem
 
         populateMetadata(c, item);
 
-        return finishItem(c, item, is);
+        // Finish up / archive the item
+        item = finishItem(c, item, is);
+        
+        // As this is a BRAND NEW item, as a final step we need to remove the
+        // submitter item policies created during deposit and replace them with
+        // the default policies from the collection.
+        item.inheritCollectionDefaultPolicies(collection);
+        
+        return item;
     }
 
     /**
@@ -205,8 +215,18 @@ public class InstallItem
         item.addDC("description", "provenance", "en", provDescription);
     }
 
-    // final housekeeping when adding new Item to archive
-    // common between installing and "restoring" items.
+    /**
+     * Final housekeeping when adding a new Item into the archive.
+     * This method is used by *both* installItem() and restoreItem(),
+     * so all actions here will be run for a newly added item or a restored item.
+     *
+     * @param c DSpace Context
+     * @param item Item in question
+     * @param is InProgressSubmission object
+     * @return final "archived" Item
+     * @throws SQLException if database error
+     * @throws AuthorizeException if authorization error
+     */
     private static Item finishItem(Context c, Item item, InProgressSubmission is)
         throws SQLException, IOException, AuthorizeException
     {
@@ -229,10 +249,6 @@ public class InstallItem
         // remove in-progress submission
         is.deleteWrapper();
 
-        // remove the item's policies and replace them with
-        // the defaults from the collection
-        item.inheritCollectionDefaultPolicies(is.getCollection());
-
         // set embargo lift date and take away read access if indicated.
         EmbargoManager.setEmbargo(c, item);
 

dspace-api/src/main/java/org/dspace/content/Item.java

@@ -24,14 +24,15 @@ import org.dspace.authorize.AuthorizeManager;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.browse.BrowseException;
 import org.dspace.browse.IndexBrowse;
+import org.dspace.content.authority.ChoiceAuthorityManager;
+import org.dspace.content.authority.Choices;
+import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
-import org.dspace.content.authority.Choices;
-import org.dspace.content.authority.ChoiceAuthorityManager;
-import org.dspace.event.Event;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
+import org.dspace.event.Event;
 import org.dspace.handle.HandleManager;
 import org.dspace.identifier.IdentifierException;
 import org.dspace.identifier.IdentifierService;
@@ -40,6 +41,8 @@ import org.dspace.storage.rdbms.TableRow;
 import org.dspace.storage.rdbms.TableRowIterator;
 import org.dspace.utils.DSpace;
 import org.dspace.versioning.VersioningService;
+import org.dspace.workflow.WorkflowItem;
+import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 
 /**
  * Class representing an item in DSpace.
@@ -263,7 +266,7 @@ public class Item extends DSpaceObject
         }
 
         String query = "SELECT item.* FROM metadatavalue,item WHERE item.in_archive='1' " +
-                "AND item.item_id = metadatavalue.item_id AND metadata_field_id = ?";
+                "AND item.item_id = metadatavalue.resource_id AND metadatavalue.resource_type_id=2 AND metadata_field_id = ?";
         TableRowIterator rows = null;
         if (Item.ANY.equals(authority)) {
             rows = DatabaseManager.queryTable(context, "item", query, mdf.getFieldID());
@@ -1158,8 +1161,14 @@ public class Item extends DSpaceObject
         ourContext.addEvent(new Event(Event.MODIFY, Constants.ITEM, getID(), 
                 "WITHDRAW", getIdentifiers(ourContext)));
 
-        // remove all authorization policies, saving the custom ones
-        AuthorizeManager.removeAllPoliciesByDSOAndTypeNotEqualsTo(ourContext, this, ResourcePolicy.TYPE_CUSTOM);
+        // switch all READ authorization policies to WITHDRAWN_READ
+		AuthorizeManager.switchPoliciesAction(ourContext, this, Constants.READ, Constants.WITHDRAWN_READ);
+		for (Bundle bnd : this.getBundles()) {
+			AuthorizeManager.switchPoliciesAction(ourContext, bnd, Constants.READ, Constants.WITHDRAWN_READ);
+			for (Bitstream bs : bnd.getBitstreams()) {
+				AuthorizeManager.switchPoliciesAction(ourContext, bs, Constants.READ, Constants.WITHDRAWN_READ);
+			}
+		}
 
         // Write log
         log.info(LogManager.getHeader(ourContext, "withdraw_item", "user="
@@ -1217,16 +1226,28 @@ public class Item extends DSpaceObject
         ourContext.addEvent(new Event(Event.MODIFY, Constants.ITEM, getID(), 
                 "REINSTATE", getIdentifiers(ourContext)));
 
-        // authorization policies
-        if (colls.length > 0)
-        {
-            // FIXME: not multiple inclusion friendly - just apply access
-            // policies from first collection
-            // remove the item's policies and replace them with
-            // the defaults from the collection
-            inheritCollectionDefaultPolicies(colls[0]);
+        // restore all WITHDRAWN_READ authorization policies back to READ
+        for (Bundle bnd : this.getBundles()) {
+			AuthorizeManager.switchPoliciesAction(ourContext, bnd, Constants.WITHDRAWN_READ, Constants.READ);
+			for (Bitstream bs : bnd.getBitstreams()) {
+				AuthorizeManager.switchPoliciesAction(ourContext, bs, Constants.WITHDRAWN_READ, Constants.READ);
+			}
+		}
+        
+        // check if the item was withdrawn before the fix DS-3097
+        if (AuthorizeManager.getPoliciesActionFilter(ourContext, this, Constants.WITHDRAWN_READ).size() != 0) {
+        	AuthorizeManager.switchPoliciesAction(ourContext, this, Constants.WITHDRAWN_READ, Constants.READ);
         }
-
+        else {
+	        // authorization policies
+	        if (colls.length > 0)
+	        {
+	            // remove the item's policies and replace them with
+	            // the defaults from the collection
+	        	adjustItemPolicies(getOwningCollection());
+	        }
+        }
+        
         // Write log
         log.info(LogManager.getHeader(ourContext, "reinstate_item", "user="
                 + e.getEmail() + ",item_id=" + getID()));
@@ -1254,9 +1275,6 @@ public class Item extends DSpaceObject
         log.info(LogManager.getHeader(ourContext, "delete_item", "item_id="
                 + getID()));
 
-        // Remove from cache
-        ourContext.removeCached(this, getID());
-
         // Remove from browse indices, if appropriate
         /** XXX FIXME
          ** Although all other Browse index updates are managed through
@@ -1303,6 +1321,8 @@ public class Item extends DSpaceObject
         // remove version attached to the item
         removeVersion();
 
+        // Remove from cache
+        ourContext.removeCached(this, getID());
 
         // Finally remove item row
         DatabaseManager.delete(ourContext, itemRow);
@@ -1750,7 +1770,12 @@ public class Item extends DSpaceObject
         // is this collection not yet created, and an item template is created
         if (getOwningCollection() == null)
         {
-            return true;
+        	if (!isInProgressSubmission()) {
+        		return true;
+        	}
+        	else {
+        		return false;
+        	}
         }
 
         // is this person an COLLECTION_EDITOR for the owning collection?
@@ -1762,6 +1787,20 @@ public class Item extends DSpaceObject
         return false;
     }
     
+    /**
+     * Check if the item is an inprogress submission
+     * @param context
+     * @param item
+     * @return <code>true</code> if the item is an inprogress submission, i.e. a WorkspaceItem or WorkflowItem
+     * @throws SQLException
+     */
+    public boolean isInProgressSubmission() throws SQLException {
+		return WorkspaceItem.findByItem(ourContext, this) != null ||
+				((ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow")
+						&& XmlWorkflowItem.findByItem(ourContext, this) != null)
+						|| WorkflowItem.findByItem(ourContext, this) != null);
+    }
+    
     public String getName()
     {
         return getMetadataFirstValue(MetadataSchema.DC_SCHEMA, "title", null, Item.ANY);

dspace-api/src/main/java/org/dspace/content/WorkspaceItem.java

@@ -81,6 +81,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            ID of the workspace item
      * 
      * @return the workspace item, or null if the ID is invalid.
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem find(Context context, int id)
             throws SQLException
@@ -131,6 +132,9 @@ public class WorkspaceItem implements InProgressSubmission
      *            of the collection's template item
      * 
      * @return the newly created workspace item
+     * @throws org.dspace.authorize.AuthorizeException passed through.
+     * @throws java.sql.SQLException passed through.
+     * @throws java.io.IOException passed through.
      */
     public static WorkspaceItem create(Context c, Collection coll,
             boolean template) throws AuthorizeException, SQLException,
@@ -140,98 +144,49 @@ public class WorkspaceItem implements InProgressSubmission
         AuthorizeManager.authorizeAction(c, coll, Constants.ADD);
 
         // Create an item
-        Item i = Item.create(c);
-        i.setSubmitter(c.getCurrentUser());
+        Item item = Item.create(c);
+        item.setSubmitter(c.getCurrentUser());
 
-        // Now create the policies for the submitter and workflow
-        // users to modify item and contents
+        // Now create the policies for the submitter to modify item and contents.
         // contents = bitstreams, bundles
         // FIXME: icky hardcoded workflow steps
         Group step1group = coll.getWorkflowGroup(1);
         Group step2group = coll.getWorkflowGroup(2);
         Group step3group = coll.getWorkflowGroup(3);
 
-        EPerson e = c.getCurrentUser();
+        EPerson submitter = c.getCurrentUser();
 
-        // read permission
-        AuthorizeManager.addPolicy(c, i, Constants.READ, e, ResourcePolicy.TYPE_SUBMISSION);
+        // Add policies for the submitter
+        AuthorizeManager.addPolicy(c, item, Constants.READ, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.WRITE, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.ADD, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.REMOVE, submitter, ResourcePolicy.TYPE_SUBMISSION);
 
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
+        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow"))
+        {
+            // Add policies for the workflow step administrative groups
             if (step1group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step1group, ResourcePolicy.TYPE_WORKFLOW);
             }
 
             if (step2group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step2group, ResourcePolicy.TYPE_WORKFLOW);
             }
 
             if (step3group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-
-        // write permission
-        AuthorizeManager.addPolicy(c, i, Constants.WRITE, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-        // add permission
-        AuthorizeManager.addPolicy(c, i, Constants.ADD, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-        // remove contents permission
-        AuthorizeManager.addPolicy(c, i, Constants.REMOVE, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step3group, ResourcePolicy.TYPE_WORKFLOW);
             }
         }
 
@@ -244,22 +199,22 @@ public class WorkspaceItem implements InProgressSubmission
 
             for (int n = 0; n < md.length; n++)
             {
-                i.addMetadata(md[n].schema, md[n].element, md[n].qualifier, md[n].language,
+                item.addMetadata(md[n].schema, md[n].element, md[n].qualifier, md[n].language,
                         md[n].value);
             }
         }
 
-        i.update();
+        item.update();
 
         // Create the workspace item row
         TableRow row = DatabaseManager.row("workspaceitem");
 
-        row.setColumn("item_id", i.getID());
+        row.setColumn("item_id", item.getID());
         row.setColumn("collection_id", coll.getID());
 
         log.info(LogManager.getHeader(c, "create_workspace_item",
                 "workspace_item_id=" + row.getIntColumn("workspace_item_id")
-                        + "item_id=" + i.getID() + "collection_id="
+                        + "item_id=" + item.getID() + "collection_id="
                         + coll.getID()));
 
         DatabaseManager.insert(c, row);
@@ -280,6 +235,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the eperson
      * 
      * @return the corresponding workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findByEPerson(Context context, EPerson ep)
             throws SQLException
@@ -332,6 +288,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the collection
      * 
      * @return the corresponding workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findByCollection(Context context, Collection c)
             throws SQLException
@@ -384,6 +341,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the item
      *
      * @return workflow item corresponding to the item, or null
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem findByItem(Context context, Item i)
             throws SQLException
@@ -408,6 +366,7 @@ public class WorkspaceItem implements InProgressSubmission
      * @param   context     the context object
      *
      * @return      all workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findAll(Context context)
         throws SQLException
@@ -505,6 +464,8 @@ public class WorkspaceItem implements InProgressSubmission
 
     /**
      * Update the workspace item, including the unarchived item.
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException passed through.
      */
     public void update() throws SQLException, AuthorizeException
     {
@@ -554,6 +515,10 @@ public class WorkspaceItem implements InProgressSubmission
      * Delete the workspace item. The entry in workspaceitem, the unarchived
      * item and its contents are all removed (multiple inclusion
      * notwithstanding.)
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException
+     *          if not original submitter or an administrator.
+     * @throws java.io.IOException passed through.
      */
     public void deleteAll() throws SQLException, AuthorizeException,
             IOException

dspace-api/src/main/java/org/dspace/content/authority/SolrAuthority.java

@@ -7,9 +7,6 @@
  */
 package org.dspace.content.authority;
 
-import org.dspace.authority.AuthoritySearchService;
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.rest.RestSource;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -17,6 +14,9 @@ import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.params.CommonParams;
+import org.dspace.authority.AuthoritySearchService;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.SolrAuthorityInterface;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.utils.DSpace;
 
@@ -35,7 +35,7 @@ import java.util.Map;
 public class SolrAuthority implements ChoiceAuthority {
 
     private static final Logger log = Logger.getLogger(SolrAuthority.class);
-    private RestSource source = new DSpace().getServiceManager().getServiceByName("AuthoritySource", RestSource.class);
+    protected SolrAuthorityInterface source = new DSpace().getServiceManager().getServiceByName("AuthoritySource", SolrAuthorityInterface.class);
     private boolean externalResults = false;
 
     public Choices getMatches(String field, String text, int collection, int start, int limit, String locale, boolean bestMatch) {

dspace-api/src/main/java/org/dspace/content/crosswalk/ContextAwareDisseminationCrosswalk.java

@@ -0,0 +1,44 @@
+/**
+ * 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.content.crosswalk;
+
+import org.dspace.core.Context;
+
+import java.sql.SQLException;
+
+/**
+ * Created by jonas - jonas@atmire.com on 21/04/17.
+ * Implementation of the {@link DisseminationCrosswalk} interface that enables the ability to set a Context manually
+ */
+public abstract class ContextAwareDisseminationCrosswalk  implements DisseminationCrosswalk{
+
+    private Context context;
+    private boolean contextCreatedInternally = false;
+
+    public void setContext(Context context){
+        this.context = context;
+    }
+    public Context getContext() throws SQLException {
+        if(context == null|| !context.isValid()){
+            context=new Context();
+            contextCreatedInternally = true;
+        }
+        return context;
+    }
+
+    public void handleContextCleanup() throws SQLException {
+        if(contextCreatedInternally){
+            context.complete();
+        }else{
+            context.commit();
+        }
+    }
+
+
+}

dspace-api/src/main/java/org/dspace/content/crosswalk/CreativeCommonsTextStreamDisseminationCrosswalk.java

@@ -27,7 +27,10 @@ import org.dspace.license.CreativeCommons;
  *
  * @author  Larry Stone
  * @version $Revision: 1.0 $
+ * 
+ * @deprecated to make uniforme JSPUI and XMLUI approach the bitstream with the license in the textual format it is no longer stored see https://jira.duraspace.org/browse/DS-2604 
  */
+@Deprecated
 public class CreativeCommonsTextStreamDisseminationCrosswalk
     implements StreamDisseminationCrosswalk
 {

dspace-api/src/main/java/org/dspace/content/crosswalk/DisseminationCrosswalk.java

@@ -7,15 +7,15 @@
  */
 package org.dspace.content.crosswalk;
 
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.List;
-
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
 import org.jdom.Element;
 import org.jdom.Namespace;
 
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.List;
+
 /**
  * Dissemination Crosswalk plugin -- translate DSpace native
  * metadata into an external XML format.
@@ -107,6 +107,9 @@ public interface DisseminationCrosswalk
      * Execute crosswalk, returning one XML root element as
      * a JDOM <code>Element</code> object.
      * This is typically the root element of a document.
+     * Note that, if the implementing class is of type "{@link org.dspace.content.crosswalk.ContextAwareDisseminationCrosswalk}"
+     * and a context is present in the method call, you should set the context before calling this method. -> "{@link org.dspace.content.crosswalk.ContextAwareDisseminationCrosswalk#setContext(org.dspace.core.Context)}"
+     * The implementing class should then use the  "{@link ContextAwareDisseminationCrosswalk#getContext()}" and  "{@link ContextAwareDisseminationCrosswalk#handleContextCleanup()}" to retrieve and commit/complete the context respectively
      * <p>
      *
      * @param dso the  DSpace Object whose metadata to export.

dspace-api/src/main/java/org/dspace/content/crosswalk/METSRightsCrosswalk.java

@@ -7,17 +7,6 @@
  */
 package org.dspace.content.crosswalk;
 
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Date;
-
-import java.text.SimpleDateFormat;
-import java.util.logging.Level;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
@@ -33,6 +22,12 @@ import org.dspace.eperson.Group;
 import org.jdom.Element;
 import org.jdom.Namespace;
 
+import java.io.IOException;
+import java.sql.SQLException;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 /**
  * METSRights Ingestion & Dissemination Crosswalk
  * <p>
@@ -51,7 +46,7 @@ import org.jdom.Namespace;
  * @author Tim Donohue
  * @version $Revision: 2108 $
  */
-public class METSRightsCrosswalk 
+public class METSRightsCrosswalk extends ContextAwareDisseminationCrosswalk
     implements IngestionCrosswalk, DisseminationCrosswalk
 {
     /** log4j category */
@@ -120,14 +115,14 @@ public class METSRightsCrosswalk
      * METSRights PermissionTypes.
      *
      * @param dso DSpace Object
+     * @param context Context Object
      * @return XML Element corresponding to the new <RightsDeclarationMD> translation
      * @throws CrosswalkException
      * @throws IOException
      * @throws SQLException
      * @throws AuthorizeException
      */
-    @Override
-    public Element disseminateElement(DSpaceObject dso)
+    public Element disseminateElement(Context context,DSpaceObject dso)
         throws CrosswalkException,
                IOException, SQLException, AuthorizeException
     {
@@ -156,7 +151,6 @@ public class METSRightsCrosswalk
         // what those rights are -- too many types of content can be stored in DSpace
 
         //Get all policies on this DSpace Object
-        Context context = new Context();
         List<ResourcePolicy> policies = AuthorizeManager.getPolicies(context, dso);
 
         //For each DSpace policy
@@ -282,9 +276,31 @@ public class METSRightsCrosswalk
            
         }//end for each policy
 
-        context.complete();
         return rightsMD;
     }
+    /**
+     * Actually Disseminate into METSRights schema.  This method locates all DSpace
+     * policies (permissions) for the provided object, and translates them into
+     * METSRights PermissionTypes.
+     *
+     * @param dso DSpace Object
+     * @return XML Element corresponding to the new <RightsDeclarationMD> translation
+     * @throws CrosswalkException
+     * @throws IOException
+     * @throws SQLException
+     * @throws AuthorizeException
+     * @deprecated Do not use this method, please opt for "{@link #disseminateElement(Context context, DSpaceObject dso)}" instead, as this does not internally need to create a new Context
+     */
+    @Override
+    @Deprecated
+    public Element disseminateElement(DSpaceObject dso)
+            throws CrosswalkException,
+            IOException, SQLException, AuthorizeException {
+        Context context = getContext();
+        Element element = disseminateElement(context, dso);
+        handleContextCleanup();
+        return element;
+    }
 
     @Override
     public List<Element> disseminateList(DSpaceObject dso)
@@ -435,134 +451,81 @@ public class METSRightsCrosswalk
     public void ingest(Context context, DSpaceObject dso, List<Element> ml)
         throws CrosswalkException, IOException, SQLException, AuthorizeException
     {
-        // we cannot crosswalk METSRights to a SITE object
+        // SITE objects are not supported by the METSRightsCrosswalk
         if (dso.getType() == Constants.SITE)
         {
             throw new CrosswalkObjectNotSupported("Wrong target object type, METSRightsCrosswalk cannot crosswalk a SITE object.");
         }
 
-        //First, clear all existing Policies on this DSpace Object
-        // as we don't want them to conflict with policies we will be adding
-        if(!ml.isEmpty())
+        // If we're fed the top-level <RightsDeclarationMD> wrapper element, recurse into its guts.
+        // What we need to analyze are the <Context> elements underneath it.
+        if(!ml.isEmpty() && ml.get(0).getName().equals("RightsDeclarationMD"))
         {
-            AuthorizeManager.removeAllPolicies(context, dso);
+            ingest(context, dso, ml.get(0).getChildren());
         }
-
-        // Loop through each Element in the List
-        List<ResourcePolicy> policies = new ArrayList<ResourcePolicy>();
-        for (Element element : ml)
+        else
         {
-            // if we're fed a <RightsDeclarationMD> wrapper object, recurse on its guts:
-            if (element.getName().equals("RightsDeclarationMD"))
+            // Loop through each <Context> Element in the passed in List, creating a ResourcePolicy for each
+            List<ResourcePolicy> policies = new ArrayList<>();
+            for (Element element : ml)
             {
-                ingest(context, dso, element.getChildren());
-            }
-            // "Context" section (where permissions are stored)
-            else if (element.getName().equals("Context"))
-            {
-                //get what class of context this is
-                String contextClass = element.getAttributeValue("CONTEXTCLASS");
-
-                if ((element.getAttributeValue("start-date") != null)
-                       || (element.getAttributeValue("end-date") != null)
-                       || (element.getAttributeValue("rpName") != null))
-                {                 
-                    SimpleDateFormat sdf = new SimpleDateFormat( "yyyy-MM-dd" );
-                    try {
-                        ResourcePolicy rp = ResourcePolicy.create(context);
-                        if (element.getAttributeValue("CONTEXTCLASS").equalsIgnoreCase("GENERAL PUBLIC")) {
-                            Group anonGroup = Group.find(context, 0);
-                            rp.setGroup(anonGroup);
-                        }
-                        else
-                        {
-                            if (element.getAttributeValue("CONTEXTCLASS").equalsIgnoreCase("REPOSITORY MGR")) {
-                                Group adminGroup = Group.find(context, 1);
-                                rp.setGroup(adminGroup);
-                            }
-                        }
-                        if (element.getAttributeValue("rpName") != null)
-                        {
-                            rp.setRpName(element.getAttributeValue("rpName"));
-                        }
-                        try {
-                            if (element.getAttributeValue("start-date") != null)
-                            {
-                                rp.setStartDate(sdf.parse(element.getAttributeValue("start-date")));
-                            }
-                            if (element.getAttributeValue("end-date") != null)
-                            {
-                                rp.setEndDate(sdf.parse(element.getAttributeValue("end-date")));
-                            }
-                        }catch (ParseException ex) {
-                            java.util.logging.Logger.getLogger(METSRightsCrosswalk.class.getName()).log(Level.SEVERE, null, ex);
-                        }
-
-                        List<Element> le = new ArrayList<Element>(element.getChildren());
-                        for (Element el : le)
-                        {
-                            if ((el.getAttributeValue("DISCOVER").equalsIgnoreCase("true")) 
-                                    && (el.getAttributeValue("DISPLAY").equalsIgnoreCase("true")))
-                            {
-                                if (el.getAttributeValue("DELETE").equalsIgnoreCase("false"))
-                                {
-                                    if (el.getAttributeValue("MODIFY").equalsIgnoreCase("false"))
-                                    {
-                                        rp.setAction(Constants.READ);
-                                    }
-                                    else
-                                    {
-                                        rp.setAction(Constants.WRITE);
-                                    }
-                                }
-                                else
-                                {
-                                    if (el.getAttributeValue("MODIFY").equalsIgnoreCase("true"))
-                                    {
-                                        rp.setAction(Constants.DELETE);
-                                        if ((el.getAttributeValue("COPY").equalsIgnoreCase("true"))
-                                                &&(el.getAttributeValue("DUPLICATE").equalsIgnoreCase("true"))
-                                                &&(el.getAttributeValue("PRINT").equalsIgnoreCase("true")))
-                                        {
-                                            rp.setAction(Constants.ADMIN);
-                                        }
-                                    }
-                                }
-                            }
-                        }
-                        policies.add(rp);
-                    } catch (NullPointerException ex) {
-                        java.util.logging.Logger.getLogger(METSRightsCrosswalk.class.getName()).log(Level.SEVERE, null, ex);
-                    }
-                    assignPermissions(context, dso, policies);
-                }
-                else
+                // Must be a "Context" section (where permissions are stored)
+                if (element.getName().equals("Context"))
                 {
-                    //also get reference to the <Permissions> element
+                    //get what class of context this is
+                    String contextClass = element.getAttributeValue("CONTEXTCLASS");
+
+                    ResourcePolicy rp = ResourcePolicy.create(context);
+                    SimpleDateFormat sdf = new SimpleDateFormat( "yyyy-MM-dd" );
+
+                    // get reference to the <Permissions> element
+                    // Note: we are assuming here that there will only ever be ONE <Permissions>
+                    //  element. Currently there are no known use cases for multiple.
                     Element permsElement = element.getChild("Permissions", METSRights_NS);
+                    if(permsElement == null) {
+                            log.error("No <Permissions> element was found. Skipping this <Context> element.");
+                            continue;
+                    }
+
+                    if (element.getAttributeValue("rpName") != null)
+                    {
+                        rp.setRpName(element.getAttributeValue("rpName"));
+                    }
+                    try {
+                        if (element.getAttributeValue("start-date") != null)
+                        {
+                            rp.setStartDate(sdf.parse(element.getAttributeValue("start-date")));
+                        }
+                        if (element.getAttributeValue("end-date") != null)
+                        {
+                            rp.setEndDate(sdf.parse(element.getAttributeValue("end-date")));
+                        }
+                    }catch (ParseException ex) {
+                        log.error("Failed to parse embargo date. The date needs to be in the format 'yyyy-MM-dd'.", ex);
+                    }
 
                     //Check if this permission pertains to Anonymous users
                     if(ANONYMOUS_CONTEXTCLASS.equals(contextClass))
                     {
                         //get DSpace Anonymous group, ID=0
-                        Group anonGroup = Group.find(context, 0);
+                        Group anonGroup = Group.find(context, Group.ANONYMOUS_ID);
                         if(anonGroup==null)
                         {
                             throw new CrosswalkInternalException("The DSpace database has not been properly initialized.  The Anonymous Group is missing from the database.");
                         }
 
-                        assignPermissions(context, dso, anonGroup, permsElement);
+                        rp.setGroup(anonGroup);
                     } // else if this permission declaration pertains to Administrators
                     else if(ADMIN_CONTEXTCLASS.equals(contextClass))
                     {
                         //get DSpace Administrator group, ID=1
-                        Group adminGroup = Group.find(context, 1);
+                        Group adminGroup = Group.find(context, Group.ADMIN_ID);
                         if(adminGroup==null)
                         {
                             throw new CrosswalkInternalException("The DSpace database has not been properly initialized.  The Administrator Group is missing from the database.");
                         }
 
-                        assignPermissions(context, dso, adminGroup, permsElement);
+                        rp.setGroup(adminGroup);
                     } // else if this permission pertains to another DSpace group
                     else if(GROUP_CONTEXTCLASS.equals(contextClass))
                     {
@@ -591,8 +554,8 @@ public class METSRightsCrosswalk
                                         + "Please restore this group using the SITE AIP, or recreate it.");
                             }
 
-                            //assign permissions to group on this object
-                            assignPermissions(context, dso, group, permsElement);
+                            //assign group to policy
+                            rp.setGroup(group);
                         }
                         catch(PackageException pe)
                         {
@@ -600,7 +563,7 @@ public class METSRightsCrosswalk
                             //We'll just wrap it as a CrosswalkException and throw it upwards
                             throw new CrosswalkException(pe);
                         }
-                    }//end if Group
+                    }// else if this permission pertains to a DSpace person
                     else if(PERSON_CONTEXTCLASS.equals(contextClass))
                     {
                         //we need to find the person it pertains to
@@ -629,89 +592,26 @@ public class METSRightsCrosswalk
                                     + "Please restore this Person object using the SITE AIP, or recreate it.");
                         }
 
-                        //assign permissions to person on this object
-                        assignPermissions(context, dso, person, permsElement);
+                        //assign person to the policy
+                        rp.setEPerson(person);
                     }//end if Person
-                    else
+                    else {
                         log.error("Unrecognized CONTEXTCLASS:  " + contextClass);
-                }
-            } //end if "Context" element
-        }//end while loop
-    }
+                    }
 
+                    //set permissions on policy add to list of policies
+                    rp.setAction(parsePermissions(permsElement));
+                    policies.add(rp);
+                } //end if "Context" element
+            }//end for loop
 
-    /**
-     * Parses the 'permsElement' (corresponding to a <code>Permissions</code>
-     * element), and assigns those permissions to the specified Group
-     * on the specified DSpace Object.
-     *
-     * @param context DSpace context object
-     * @param dso The DSpace Object
-     * @param group The DSpace Group
-     * @param permsElement The METSRights <code>Permissions</code> element
-     */
-private void assignPermissions(Context context, DSpaceObject dso, List<ResourcePolicy> policies)
-        throws SQLException, AuthorizeException
-    {
-        AuthorizeManager.removeAllPolicies(context, dso);
-        if (policies == null){
-            throw new AuthorizeException("Policies are null");
-        }
-        else{
+            // Finally, we need to remove any existing policies from the current object,
+            // and replace them with the policies provided via METSRights. NOTE:
+            // if the list of policies provided by METSRights is an empty list, then
+            // the final object will have no policies attached.
+            AuthorizeManager.removeAllPolicies(context, dso);
             AuthorizeManager.addPolicies(context, policies, dso);
-        }
-    }
-
-    private void assignPermissions(Context context, DSpaceObject dso, Group group, Element permsElement)
-            throws SQLException, AuthorizeException
-    {
-        //first, parse our permissions to determine which action we are allowing in DSpace
-        int actionID = parsePermissions(permsElement);
-
-        //If action ID is less than base READ permissions (value=0),
-        // then something must've gone wrong in the parsing
-        if(actionID < Constants.READ)
-        {
-            log.warn("Unable to properly restore all access permissions on object ("
-                        + "type=" + Constants.typeText[dso.getType()] + ", "
-                        + "handle=" + dso.getHandle() + ", "
-                        + "ID=" + dso.getID()
-                        + ") for group '" + group.getName() + "'.");
-        }
-
-        //Otherwise, add the appropriate group policy for this object
-        AuthorizeManager.addPolicy(context, dso, actionID, group);
-    }
-
-     /**
-     * Parses the 'permsElement' (corresponding to a <code>Permissions</code>
-     * element), and assigns those permissions to the specified EPerson
-     * on the specified DSpace Object.
-     *
-     * @param context DSpace context object
-     * @param dso The DSpace Object
-     * @param person The DSpace EPerson
-     * @param permsElement The METSRights <code>Permissions</code> element
-     */
-    private void assignPermissions(Context context, DSpaceObject dso, EPerson person, Element permsElement)
-            throws SQLException, AuthorizeException
-    {
-        //first, parse our permissions to determine which action we are allowing in DSpace
-        int actionID = parsePermissions(permsElement);
-
-        //If action ID is less than base READ permissions (value=0),
-        // then something must've gone wrong in the parsing
-        if(actionID < Constants.READ)
-        {
-            log.warn("Unable to properly restore all access permissions on object ("
-                        + "type=" + Constants.typeText[dso.getType()] + ", "
-                        + "handle=" + dso.getHandle() + ", "
-                        + "ID=" + dso.getID()
-                        + ") for person '" + person.getEmail() + "'.");
-        }
-
-        //Otherwise, add the appropriate EPerson policy for this object
-        AuthorizeManager.addPolicy(context, dso, actionID, person);
+        } // end else
     }
 
     /**
@@ -784,4 +684,5 @@ private void assignPermissions(Context context, DSpaceObject dso, List<ResourceP
         // return -1 to signify failure (as 0 = READ permissions)
         return -1;
     }
+
 }

dspace-api/src/main/java/org/dspace/content/packager/AbstractMETSIngester.java

@@ -21,15 +21,7 @@ import java.util.zip.ZipFile;
 
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
-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.DSpaceObject;
-import org.dspace.content.FormatIdentifier;
-import org.dspace.content.Item;
-import org.dspace.content.WorkspaceItem;
+import org.dspace.content.*;
 import org.dspace.content.crosswalk.CrosswalkException;
 import org.dspace.content.crosswalk.MetadataValidationException;
 import org.dspace.core.ConfigurationManager;
@@ -37,6 +29,8 @@ import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.dspace.handle.HandleManager;
+import org.dspace.workflow.WorkflowItem;
+import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 import org.jdom.Element;
 
 /**
@@ -324,18 +318,18 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
         }
         else
         {
-            ZipFile zip = new ZipFile(pkgFile);
+            try(ZipFile zip = new ZipFile(pkgFile))
+            {
+                // Retrieve the manifest file entry (named mets.xml)
+                ZipEntry manifestEntry = zip.getEntry(METSManifest.MANIFEST_FILE);
 
-            // Retrieve the manifest file entry (named mets.xml)
-            ZipEntry manifestEntry = zip.getEntry(METSManifest.MANIFEST_FILE);
-
-            // parse the manifest and sanity-check it.
-            manifest = METSManifest.create(zip.getInputStream(manifestEntry),
-                    validate, getConfigurationName());
-
-            // close the Zip file for now
-            // (we'll extract the other files from zip when we need them)
-            zip.close();
+                if(manifestEntry!=null)
+                {
+                    // parse the manifest and sanity-check it.
+                    manifest = METSManifest.create(zip.getInputStream(manifestEntry),
+                        validate, getConfigurationName());
+                }
+            }
         }
 
         // return our parsed out METS manifest
@@ -660,8 +654,24 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             addBitstreams(context, item, manifest, pkgFile, params, callback);
 
             // have subclass manage license since it may be extra package file.
-            addLicense(context, item, license, (Collection) dso
-                    .getParentObject(), params);
+            Collection owningCollection = (Collection) dso.getParentObject();
+            if(owningCollection == null)
+            {
+                //We are probably dealing with an item that isn't archived yet
+                InProgressSubmission inProgressSubmission = WorkspaceItem.findByItem(context, item);
+                if(inProgressSubmission == null)
+                {
+                    if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow"))
+                    {
+                        inProgressSubmission = XmlWorkflowItem.findByItem(context, item);
+                    }else{
+                        inProgressSubmission = WorkflowItem.findByItem(context, item);
+                    }
+                }
+                owningCollection = inProgressSubmission.getCollection();
+            }
+
+            addLicense(context, item, license, owningCollection, params);
 
             // FIXME ?
             // should set lastModifiedTime e.g. when ingesting AIP.

dspace-api/src/main/java/org/dspace/core/Constants.java

@@ -127,6 +127,8 @@ public class Constants
      */
     public static final int ADMIN = 11;
     
+    public static final int WITHDRAWN_READ = 12;
+    
     /** Position of front page news item -- top box */
     public static final int NEWS_TOP = 0;
 
@@ -139,7 +141,7 @@ public class Constants
     public static final String[] actionText = { "READ", "WRITE",
             "OBSOLETE (DELETE)", "ADD", "REMOVE", "WORKFLOW_STEP_1",
             "WORKFLOW_STEP_2", "WORKFLOW_STEP_3", "WORKFLOW_ABORT",
-            "DEFAULT_BITSTREAM_READ", "DEFAULT_ITEM_READ", "ADMIN" };
+            "DEFAULT_BITSTREAM_READ", "DEFAULT_ITEM_READ", "ADMIN", "WITHDRAWN_READ" };
 
     /**
      * generating constants for the relevance array dynamically is simple: just
@@ -175,7 +177,9 @@ public class Constants
             0, // 8 - WORKFLOW_ABORT
             RCOLLECTION, // 9 - DEFAULT_BITSTREAM_READ
             RCOLLECTION, // 10 - DEFAULT_ITEM_READ
-            RITEM | RCOLLECTION | RCOMMUNITY // 11 - ADMIN
+            RITEM | RCOLLECTION | RCOMMUNITY, // 11 - ADMIN
+            RBITSTREAM | RBUNDLE | RITEM // 12 - WITHDRAWN_READ
+
     };
 
     public static final String DEFAULT_ENCODING = "UTF-8";

dspace-api/src/main/java/org/dspace/core/Email.java

@@ -474,8 +474,18 @@ public class Email
         System.out.println(" - To: " + to);
         System.out.println(" - Subject: " + subject);
         System.out.println(" - Server: " + server);
+        boolean disabled = ConfigurationManager.getBooleanProperty("mail.server.disabled", false);
         try
         {
+            if( disabled)
+            {
+                System.err.println("\nError sending email:");
+                System.err.println(" - Error: cannot test email because mail.server.disabled is set to true");
+                System.err.println("\nPlease see the DSpace documentation for assistance.\n");
+                System.err.println("\n");
+                System.exit(1);
+                return;
+            }
             e.send();
         }
         catch (MessagingException me)

dspace-api/src/main/java/org/dspace/core/NewsManager.java

@@ -16,6 +16,9 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+
+import org.dspace.core.service.NewsService;
+import org.dspace.utils.DSpace;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -39,6 +42,10 @@ public class NewsManager
      */
     public static String readNewsFile(String newsFile)
     {
+    	NewsService newsService = new DSpace().getSingletonService(NewsService.class);
+    	if (!newsService.validate(newsFile)) {
+    		throw new IllegalArgumentException("The file "+ newsFile + " is not a valid news file");
+    	}
         String fileName = getNewsFilePath();
 
         fileName += newsFile;
@@ -81,6 +88,10 @@ public class NewsManager
      */
     public static String writeNewsFile(String newsFile, String news)
     {
+    	NewsService newsService = new DSpace().getSingletonService(NewsService.class);
+    	if (!newsService.validate(newsFile)) {
+    		throw new IllegalArgumentException("The file "+ newsFile + " is not a valid news file");
+    	}
         String fileName = getNewsFilePath();
 
         fileName += newsFile;

dspace-api/src/main/java/org/dspace/core/NewsServiceImpl.java

@@ -0,0 +1,29 @@
+/**
+ * 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.core;
+
+import java.util.List;
+
+import org.dspace.core.service.NewsService;
+
+public class NewsServiceImpl implements NewsService {
+	private List<String> acceptableFilenames;
+	
+	public void setAcceptableFilenames(List<String> acceptableFilenames) {
+		this.acceptableFilenames = acceptableFilenames;
+	}
+	
+	@Override
+	public boolean validate(String newsName) {
+		if (acceptableFilenames != null) {
+			return acceptableFilenames.contains(newsName);
+		}
+		return false;
+	}
+
+}

dspace-api/src/main/java/org/dspace/core/service/NewsService.java

@@ -0,0 +1,12 @@
+/**
+ * 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.core.service;
+
+public interface NewsService {
+	boolean validate(String newsName);
+}

dspace-api/src/main/java/org/dspace/curate/CurationCli.java

@@ -164,7 +164,7 @@ public class CurationCli
         }
         else
         {
-            c.setIgnoreAuthorization(true);
+            c.turnOffAuthorisationSystem();
         }
 
         Curator curator = new Curator();

dspace-api/src/main/java/org/dspace/curate/TaskResolver.java

@@ -29,36 +29,50 @@ import org.dspace.core.PluginManager;
 /**
  * TaskResolver takes a logical name of a curation task and attempts to deliver 
  * a suitable implementation object. Supported implementation types include:
- * (1) Classpath-local Java classes configured and loaded via PluginManager.
- * (2) Local script-based tasks, viz. coded in any scripting language whose
+ * <ol>
+ *  <li> Classpath-local Java classes configured and loaded via PluginManager</li>.
+ *  <li> Local script-based tasks, viz. coded in any scripting language whose
  * runtimes are accessible via the JSR-223 scripting API. This really amounts
- * to the family of dynamic JVM languages: JRuby, Jython, Groovy, Javascript, etc
- * Note that the requisite jars and other resources for these languages must be
- * installed in the DSpace instance for them to be used here.
+ * to the family of dynamic JVM languages: JRuby, Jython, Groovy, Javascript, etc.</li>
+ * </ol>
+ * <p>
+ * Note that the requisite jars and other resources for these languages must
+ * be installed in the DSpace instance for them to be used here.
  * Further work may involve remote URL-loadable code, etc. 
  * 
+ * <p>
  * Scripted tasks are managed in a directory configured with the
- * dspace/config/modules/curate.cfg property "script.dir". A catalog of
- * scripted tasks named 'task.catalog" is kept in this directory.
+ * {@code dspace/config/modules/curate.cfg} property "script.dir".
+ * A catalog of
+ * scripted tasks named "task.catalog" is kept in this directory.
  * Each task has a 'descriptor' property with value syntax:
- * <engine>|<relFilePath>|<implClassCtor>
+ * <br/>
+ * {@code <engine>|<relFilePath>|<implClassCtor>}
+ *
+ * <p>
  * An example property:
- * 
- * linkchecker = ruby|rubytask.rb|LinkChecker.new
- * 
+ * <br/>
+ * {@code linkchecker = ruby|rubytask.rb|LinkChecker.new}
+ *
+ * <p>
  * This descriptor means that a 'ruby' script engine will be created,
- * a script file named 'rubytask.rb' in the directory <script.dir> will be
- * loaded and the resolver will expect an evaluation of 'LinkChecker.new' will 
- * provide a correct implementation object.
- * 
+ * a script file named 'rubytask.rb' in the directory {@code <script.dir>}
+ * will be
+ * loaded and the resolver will expect an evaluation of 'LinkChecker.new'
+ * will provide a correct implementation object.
+ *
+ * <p>
  * Script files may embed their descriptors to facilitate deployment.
- * To accomplish this, a script must include the descriptor string with syntax:
- * $td=<descriptor> somewhere on a comment line. for example:
- * 
- * # My descriptor $td=ruby|rubytask.rb|LinkChecker.new
- * 
- * For portability, the <relFilePath> component may be omitted in this context.
- * Thus, $td=ruby||LinkChecker.new will be expanded to a descriptor
+ * To accomplish this, a script must include the descriptor string with
+ * syntax {@code $td=<descriptor>} somewhere on a comment line. For example:
+ *
+ * <p>
+ * {@code # My descriptor $td=ruby|rubytask.rb|LinkChecker.new}
+ *
+ * <p>
+ * For portability, the {@code <relFilePath>} component may be omitted in
+ * this context.
+ * Thus, {@code $td=ruby||LinkChecker.new} will be expanded to a descriptor
  * with the name of the embedding file.
  * 
  * @author richardrodgers

dspace-api/src/main/java/org/dspace/discovery/DiscoverQuery.java

@@ -218,10 +218,20 @@ public class DiscoverQuery {
         this.facetOffset = facetOffset;
     }
 
+    /**
+     * Sets the fields which you want Discovery to return in the search results.
+     * It is HIGHLY recommended to limit the fields returned, as by default
+     * some backends (like Solr) will return everything.
+     * @param field field to add to the list of fields returned
+     */
     public void addSearchField(String field){
         this.searchFields.add(field);
     }
 
+    /**
+     * Get list of fields which Discovery will return in the search results
+     * @return List of field names
+     */
     public List<String> getSearchFields() {
         return searchFields;
     }

dspace-api/src/main/java/org/dspace/discovery/IndexClient.java

@@ -39,7 +39,7 @@ public class IndexClient {
     public static void main(String[] args) throws SQLException, IOException, SearchServiceException {
 
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
 
         String usage = "org.dspace.discovery.IndexClient [-cbhf[r <item handle>]] or nothing to update/clean an existing index.";
         Options options = new Options();

dspace-api/src/main/java/org/dspace/discovery/SearchService.java

@@ -113,4 +113,11 @@ public interface SearchService {
      * @return the indexed field
      */
     String toSortFieldIndex(String metadataField, String type);
+
+    /**
+     * Utility method to escape any special characters in a user's query
+     * @param query
+     * @return query with any special characters escaped
+     */
+    String escapeQueryChars(String query);
 }

dspace-api/src/main/java/org/dspace/discovery/SolrServiceImpl.java

@@ -119,6 +119,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     private static final Logger log = Logger.getLogger(SolrServiceImpl.class);
 
     protected static final String LAST_INDEXED_FIELD = "SolrIndexer.lastIndexed";
+    protected static final String HANDLE_FIELD = "handle";
+    protected static final String RESOURCE_TYPE_FIELD = "search.resourcetype";
+    protected static final String RESOURCE_ID_FIELD = "search.resourceid";
 
     public static final String FILTER_SEPARATOR = "\n|||\n";
 
@@ -149,9 +152,11 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
                     solr.setBaseURL(solrService);
                     solr.setUseMultiPartPost(true);
+                    // Dummy/test query to search for Item (type=2) of ID=1
                     SolrQuery solrQuery = new SolrQuery()
-                            .setQuery("search.resourcetype:2 AND search.resourceid:1");
-
+                            .setQuery(RESOURCE_TYPE_FIELD + ":2 AND " + RESOURCE_ID_FIELD + ":1");
+                    // Only return obj identifier fields in result doc
+                    solrQuery.setFields(RESOURCE_TYPE_FIELD, RESOURCE_ID_FIELD);
                     solr.query(solrQuery);
 
                     // As long as Solr initialized, check with DatabaseUtils to see
@@ -323,7 +328,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
         try {
             if(getSolr() != null){
-                getSolr().deleteByQuery("handle:\"" + handle + "\"");
+                getSolr().deleteByQuery(HANDLE_FIELD + ":\"" + handle + "\"");
                 if(commit)
                 {
                     getSolr().commit();
@@ -462,37 +467,49 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             }
             if (force)
             {
-                getSolr().deleteByQuery("search.resourcetype:[2 TO 4]");
+                getSolr().deleteByQuery(RESOURCE_TYPE_FIELD + ":[2 TO 4]");
             } else {
                 SolrQuery query = new SolrQuery();
-                query.setQuery("search.resourcetype:[2 TO 4]");
-                QueryResponse rsp = getSolr().query(query);
-                SolrDocumentList docs = rsp.getResults();
+                // Query for all indexed Items, Collections and Communities,
+                // returning just their handle
+                query.setFields(HANDLE_FIELD);
+                query.addSort(HANDLE_FIELD, SolrQuery.ORDER.asc);
+                query.setQuery(RESOURCE_TYPE_FIELD + ":[2 TO 4]");
 
-                Iterator iter = docs.iterator();
-                while (iter.hasNext())
-                {
+                // Get the total amount of results
+                QueryResponse totalResponse = getSolr().query(query);
+                long total = totalResponse.getResults().getNumFound();
 
-                 SolrDocument doc = (SolrDocument) iter.next();
+                int start = 0;
+                int batch = 100;
 
-                String handle = (String) doc.getFieldValue("handle");
+                query.setRows(batch);
+                while (start < total) {
+                    query.setStart(start);
+                    QueryResponse rsp = getSolr().query(query);
+                    SolrDocumentList docs = rsp.getResults();
 
-                DSpaceObject o = HandleManager.resolveToObject(context, handle);
+                    for (SolrDocument doc : docs) {
+                        String handle = (String) doc.getFieldValue(HANDLE_FIELD);
 
-                if (o == null)
-                {
-                    log.info("Deleting: " + handle);
-                    /*
-                          * Use IndexWriter to delete, its easier to manage
-                          * write.lock
-                          */
-                    unIndexContent(context, handle);
-                } else {
-                    context.removeCached(o, o.getID());
-                    log.debug("Keeping: " + handle);
+                        DSpaceObject o = HandleManager.resolveToObject(context, handle);
+
+                        if (o == null) {
+                            log.info("Deleting: " + handle);
+                            /*
+                             * Use IndexWriter to delete, its easier to manage
+                             * write.lock
+                             */
+                            unIndexContent(context, handle);
+                        } else {
+                            context.removeCached(o, o.getID());
+                            log.debug("Keeping: " + handle);
+                        }
+                    }
+
+                    start += batch;
                 }
             }
-            }
         } catch(Exception e)
         {
 
@@ -616,7 +633,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         boolean inIndex = false;
 
         SolrQuery query = new SolrQuery();
-        query.setQuery("handle:" + handle);
+        query.setQuery(HANDLE_FIELD + ":" + handle);
+        // Specify that we ONLY want the LAST_INDEXED_FIELD returned in the field list (fl)
+        query.setFields(LAST_INDEXED_FIELD);
         QueryResponse rsp;
 
         try {
@@ -1444,9 +1463,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         // New fields to weaken the dependence on handles, and allow for faster
         // list display
 		doc.addField("search.uniqueid", type+"-"+id);
-        doc.addField("search.resourcetype", Integer.toString(type));
+        doc.addField(RESOURCE_TYPE_FIELD, Integer.toString(type));
 
-        doc.addField("search.resourceid", Integer.toString(id));
+        doc.addField(RESOURCE_ID_FIELD, Integer.toString(id));
 
         // want to be able to search for handle, so use keyword
         // (not tokenized, but it is indexed)
@@ -1454,7 +1473,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             // want to be able to search for handle, so use keyword
             // (not tokenized, but it is indexed)
-            doc.addField("handle", handle);
+            doc.addField(HANDLE_FIELD, handle);
         }
 
         if (locations != null)
@@ -1584,7 +1603,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 discoveryQuery.addFilterQueries("location:l" + dso.getID());
             } else if (dso instanceof Item)
             {
-                discoveryQuery.addFilterQueries("handle:" + dso.getHandle());
+                discoveryQuery.addFilterQueries(HANDLE_FIELD + ":" + dso.getHandle());
             }
         }
         return search(context, discoveryQuery, includeUnDiscoverable);
@@ -1620,6 +1639,18 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 		}
 
         solrQuery.setQuery(query);
+
+        // Add any search fields to our query. This is the limited list
+        // of fields that will be returned in the solr result
+        for(String fieldName : discoveryQuery.getSearchFields())
+        {
+            solrQuery.addField(fieldName);
+        }
+        // Also ensure a few key obj identifier fields are returned with every query
+        solrQuery.addField(HANDLE_FIELD);
+        solrQuery.addField(RESOURCE_TYPE_FIELD);
+        solrQuery.addField(RESOURCE_ID_FIELD);
+
         if(discoveryQuery.isSpellCheck())
         {
             solrQuery.setParam(SpellingParams.SPELLCHECK_Q, query);
@@ -1640,7 +1671,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         }
         if(discoveryQuery.getDSpaceObjectFilter() != -1)
         {
-            solrQuery.addFilterQuery("search.resourcetype:" + discoveryQuery.getDSpaceObjectFilter());
+            solrQuery.addFilterQuery(RESOURCE_TYPE_FIELD + ":" + discoveryQuery.getDSpaceObjectFilter());
         }
 
         for (int i = 0; i < discoveryQuery.getFieldPresentQueries().size(); i++)
@@ -1753,7 +1784,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 query.addFilterQueries("location:l" + dso.getID());
             } else if (dso instanceof Item)
             {
-                query.addFilterQueries("handle:" + dso.getHandle());
+                query.addFilterQueries(HANDLE_FIELD + ":" + dso.getHandle());
             }
         }
         return searchJSON(context, query, jsonIdentifier);
@@ -1807,7 +1838,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 {
                     result.addDSpaceObject(dso);
                 } else {
-                    log.error(LogManager.getHeader(context, "Error while retrieving DSpace object from discovery index", "Handle: " + doc.getFirstValue("handle")));
+                    log.error(LogManager.getHeader(context, "Error while retrieving DSpace object from discovery index", "Handle: " + doc.getFirstValue(HANDLE_FIELD)));
                     continue;
                 }
 
@@ -1926,9 +1957,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     protected static DSpaceObject findDSpaceObject(Context context, SolrDocument doc) throws SQLException {
 
-        Integer type = (Integer) doc.getFirstValue("search.resourcetype");
-        Integer id = (Integer) doc.getFirstValue("search.resourceid");
-        String handle = (String) doc.getFirstValue("handle");
+        Integer type = (Integer) doc.getFirstValue(RESOURCE_TYPE_FIELD);
+        Integer id = (Integer) doc.getFirstValue(RESOURCE_ID_FIELD);
+        String handle = (String) doc.getFirstValue(HANDLE_FIELD);
 
         if (type != null && id != null)
         {
@@ -1981,7 +2012,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             SolrQuery solrQuery = new SolrQuery();
             solrQuery.setQuery(query);
-            solrQuery.setFields("search.resourceid", "search.resourcetype");
+            //Only return obj identifier fields in result doc
+            solrQuery.setFields(RESOURCE_ID_FIELD, RESOURCE_TYPE_FIELD);
             solrQuery.setStart(offset);
             solrQuery.setRows(max);
             if (orderfield != null)
@@ -2001,7 +2033,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             {
                 SolrDocument doc = (SolrDocument) iter.next();
 
-                DSpaceObject o = DSpaceObject.find(context, (Integer) doc.getFirstValue("search.resourcetype"), (Integer) doc.getFirstValue("search.resourceid"));
+                DSpaceObject o = DSpaceObject.find(context, (Integer) doc.getFirstValue(RESOURCE_TYPE_FIELD), (Integer) doc.getFirstValue(RESOURCE_ID_FIELD));
 
                 if (o != null)
                 {
@@ -2089,7 +2121,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         try{
             SolrQuery solrQuery = new SolrQuery();
             //Set the query to handle since this is unique
-            solrQuery.setQuery("handle: " + item.getHandle());
+            solrQuery.setQuery(HANDLE_FIELD + ": " + item.getHandle());
+            //Only return obj identifier fields in result doc
+            solrQuery.setFields(HANDLE_FIELD, RESOURCE_TYPE_FIELD, RESOURCE_ID_FIELD);
             //Add the more like this parameters !
             solrQuery.setParam(MoreLikeThisParams.MLT, true);
             //Add a comma separated list of the similar fields
@@ -2320,4 +2354,13 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 			throw new SearchServiceException(e.getMessage(), e);
 		}
 	}
+
+    @Override
+    public String escapeQueryChars(String query) {
+        // Use Solr's built in query escape tool
+        // WARNING: You should only escape characters from user entered queries,
+        // otherwise you may accidentally BREAK field-based queries (which often
+        // rely on special characters to separate the field from the query value)
+        return ClientUtils.escapeQueryChars(query);
+    }
 }

dspace-api/src/main/java/org/dspace/embargo/EmbargoManager.java

@@ -91,10 +91,9 @@ public class EmbargoManager
              }
         }
         String slift = myLift.toString();
-        boolean ignoreAuth = context.ignoreAuthorization();
         try
         {
-            context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();
             item.clearMetadata(lift_schema, lift_element, lift_qualifier, Item.ANY);
             item.addMetadata(lift_schema, lift_element, lift_qualifier, null, slift);
             log.info("Set embargo on Item "+item.getHandle()+", expires on: "+slift);
@@ -105,7 +104,7 @@ public class EmbargoManager
         }
         finally
         {
-            context.setIgnoreAuthorization(ignoreAuth);
+            context.restoreAuthSystemState();
         }
     }
 
@@ -267,7 +266,7 @@ public class EmbargoManager
         try
         {
             context = new Context();
-            context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();
             Date now = new Date();
              
             // scan items under embargo

dspace-api/src/main/java/org/dspace/eperson/EPerson.java

@@ -499,7 +499,7 @@ public class EPerson extends DSpaceObject
             break;
 
         case LANGUAGE:
-            s = "m_text_value";
+            s = "m.text_value";
             t = "language";
             break;
         case NETID:
@@ -507,23 +507,26 @@ public class EPerson extends DSpaceObject
             break;
 
         default:
-            s = "m_text_value";
+            s = "m.text_value";
             t = "lastname";
         }
 
         // NOTE: The use of 's' in the order by clause can not cause an SQL
         // injection because the string is derived from constant values above.
-        TableRowIterator rows = DatabaseManager.query(context, "SELECT * FROM eperson e ORDER BY ?",s);
+        TableRowIterator rows;
         if(!t.equals("")) {
             rows = DatabaseManager.query(context,
                     "SELECT * FROM eperson e " +
-                            "LEFT JOIN metadatavalue m on (m.resource_id = e.eperson_id and m.resource_type_id = ? and m.metadata_field_id = ?) " +
-                            "ORDER BY ?",
+                    "LEFT JOIN metadatavalue m on (m.resource_id = e.eperson_id and m.resource_type_id = ? and m.metadata_field_id = ?) " +
+                    "ORDER BY " + s,
                     Constants.EPERSON,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), t, null).getFieldID(),
-                    s
+                    MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), t, null).getFieldID()
             );
         }
+        else {
+        	rows =  DatabaseManager.query(context, "SELECT * FROM eperson e ORDER BY " + s);
+        }
+        
 
 
 

dspace-api/src/main/java/org/dspace/eperson/Group.java

@@ -358,9 +358,9 @@ public class Group extends DSpaceObject
     }
 
     /**
-     * fast check to see if an eperson is a member called with eperson id, does
-     * database lookup without instantiating all of the epeople objects and is
-     * thus a static method
+     * fast check to see if the current EPerson is a member of a Group.  Does
+     * database lookup without instantiating all of the EPerson objects and is
+     * thus a static method.
      * 
      * @param c
      *            context
@@ -380,6 +380,29 @@ public class Group extends DSpaceObject
         return epersonInGroup(c, groupid, currentuser);
     }
 
+    /**
+     * Fast check to see if a given EPerson is a member of a Group.
+     * Does database lookup without instantiating all of the EPerson objects and
+     * is thus a static method.
+     *
+     * @param c current DSpace context.
+     * @param eperson candidate to test for membership.
+     * @param groupid group whose membership is to be tested.
+     * @return true if {@link eperson} is a member of Group {@link groupid}.
+     * @throws SQLException passed through
+     */
+    public static boolean isMember(Context c, EPerson eperson, int groupid)
+            throws SQLException
+    {
+        // Every EPerson is a member of Anonymous
+        if (groupid == 0)
+        {
+            return true;
+        }
+
+        return epersonInGroup(c, groupid, eperson);
+    }
+
     /**
      * Get all of the groups that an eperson is a member of.
      * 

dspace-api/src/main/java/org/dspace/event/EventManager.java

@@ -284,14 +284,23 @@ public class EventManager
         {
             Context ctx = new Context();
 
-            for (Iterator ci = ((Dispatcher) dispatcher).getConsumers()
-                    .iterator(); ci.hasNext();)
-            {
-                ConsumerProfile cp = (ConsumerProfile) ci.next();
-                if (cp != null)
+            try {
+
+                for (Iterator ci = ((Dispatcher) dispatcher).getConsumers()
+                        .iterator(); ci.hasNext();)
                 {
-                    cp.getConsumer().finish(ctx);
+                    ConsumerProfile cp = (ConsumerProfile) ci.next();
+                    if (cp != null)
+                    {
+                        cp.getConsumer().finish(ctx);
+                    }
                 }
+
+                ctx.complete();
+
+            } catch (Exception e) {
+                ctx.abort();
+                throw e;
             }
             return;
 

dspace-api/src/main/java/org/dspace/handle/UpdateHandlePrefix.java

@@ -9,89 +9,167 @@ package org.dspace.handle;
 
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
-
+import java.sql.SQLException;
+import org.apache.log4j.Logger;
 import org.dspace.core.Context;
 import org.dspace.storage.rdbms.DatabaseManager;
 import org.dspace.storage.rdbms.TableRow;
-import org.dspace.search.DSIndexer;
-import org.dspace.browse.IndexBrowse;
+import org.dspace.discovery.IndexClient;
 
 /**
  * A script to update the handle values in the database. This is typically used
- * when moving from a test machine (handle = 123456789) to a production service.
+ * when moving from a test machine (handle = 123456789) to a production service
+ * or when make a test clone from production service.
  *
  * @author Stuart Lewis
+ * @author Ivo Prajer (Czech Technical University in Prague)
  */
 public class UpdateHandlePrefix
 {
+
+    private static final Logger log = Logger.getLogger(UpdateHandlePrefix.class);
+
+    /**
+     * When invoked as a command-line tool, updates handle prefix
+     *
+     * @param args the command-line arguments, none used
+     * @throws java.lang.Exception
+     *
+     */
     public static void main(String[] args) throws Exception
     {
-        // There should be two paramters
+        // There should be two parameters
         if (args.length < 2)
         {
             System.out.println("\nUsage: update-handle-prefix <old handle> <new handle>\n");
+            System.exit(1);
         }
         else
         {
-            // Confirm with the user that this is what they want to do
             String oldH = args[0];
             String newH = args[1];
 
-            BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+            // Get info about changes
+            System.out.println("\nGetting information about handles from database...");
             Context context = new Context();
-            System.out.println("If you continue, all handles in your repository with prefix " +
-                                oldH + " will be updated to have handle prefix " + newH + "\n");
-            String sql = "SELECT count(*) as count FROM handle " +
+            String sql = "SELECT count(*) as count " +
+                         "FROM handle " +
                          "WHERE handle LIKE '" + oldH + "%'";
             TableRow row = DatabaseManager.querySingle(context, sql, new Object[] {});
             long count = row.getLongColumn("count");
-            System.out.println(count + " items will be updated.\n");
-            System.out.print("Have you taken a backup, and are you ready to continue? [y/n]: ");
-            String choiceString = input.readLine();
 
-            if (choiceString.equalsIgnoreCase("y"))
+            if (count > 0)
             {
-                // Make the changes
-                System.out.print("Updating handle table... ");
-                sql = "update handle set handle = '" + newH + "' || '/' || handle_id " +
-                      "where handle like '" + oldH + "/%'";
-                int updated = DatabaseManager.updateQuery(context, sql, new Object[] {});
-                System.out.println(updated + " items updated");
+                // Print info text about changes
+                System.out.println(
+                  "In your repository will be updated " + count + " handle" +
+                  ((count > 1) ? "s" : "") + " to new prefix " + newH +
+                  " from original " + oldH + "!\n"
+                );
 
-                System.out.print("Updating metadatavalues table... ");
-                sql = "UPDATE metadatavalue SET text_value= (SELECT 'http://hdl.handle.net/' || " +
-                      "handle FROM handle WHERE handle.resource_id=item_id AND " +
-                      "handle.resource_type_id=2) WHERE  text_value LIKE 'http://hdl.handle.net/%';";
-                updated = DatabaseManager.updateQuery(context, sql, new Object[] {});
-                System.out.println(updated + " metadata values updated");
+                // Confirm with the user that this is what they want to do
+                System.out.print(
+                  "Servlet container (e.g. Apache Tomcat, Jetty, Caucho Resin) must be running.\n" +
+                  "If it is necessary, please make a backup of the database.\n" +
+                  "Are you ready to continue? [y/n]: "
+                );
+                BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+                String choiceString = input.readLine();
 
-                // Commit the changes
-                context.complete();
-
-                System.out.print("Re-creating browse and search indexes... ");                
-
-                // Reinitialise the browse system
-                IndexBrowse.main(new String[] {"-i"});
-
-                // Reinitialise the browse system
-                try
+                if (choiceString.equalsIgnoreCase("y"))
                 {
-                    DSIndexer.main(new String[0]);
-                }
-                catch (Exception e)
-                {
-                    // Not a lot we can do
-                    System.out.println("Error re-indexing:");
-                    e.printStackTrace();
-                    System.out.println("\nPlease manually run [dspace]/bin/index-all");
-                }
+                    try {
+                        log.info("Updating handle prefix from " + oldH + " to " + newH);
 
-                // All done
-                System.out.println("\nHandles successfully updated.");
+                        // Make the changes
+                        System.out.print("\nUpdating handle table... ");
+                        sql = "UPDATE handle " +
+                              "SET handle = '" + newH + "' || '/' || handle_id " +
+                              "WHERE handle like '" + oldH + "/%'";
+                        int updHdl = DatabaseManager.updateQuery(context, sql, new Object[] {});
+                        System.out.println(
+                          updHdl + " item" + ((updHdl > 1) ? "s" : "") + " updated"
+                        );
+
+                        System.out.print("Updating metadatavalues table... ");
+                        sql = "UPDATE metadatavalue " +
+                              "SET text_value = " +
+                                "(" +
+                                  "SELECT 'http://hdl.handle.net/' || handle " +
+                                  "FROM handle " +
+                                  "WHERE handle.resource_id = metadatavalue.resource_id " +
+                                    "AND handle.resource_type_id = 2" +
+                                ") " +
+                              "WHERE text_value LIKE 'http://hdl.handle.net/" + oldH + "/%'" +
+                                "AND EXISTS " +
+                                  "(" +
+                                    "SELECT 1 " +
+                                    "FROM handle " + 
+                                    "WHERE handle.resource_id = metadatavalue.resource_id " +
+                                      "AND handle.resource_type_id = 2" +
+                                  ")";
+                        int updMeta = DatabaseManager.updateQuery(context, sql, new Object[] {});
+                        System.out.println(
+                          updMeta + " metadata value" + ((updMeta > 1) ? "s" : "") + " updated"
+                        );
+
+                        // Commit the changes
+                        context.complete();
+
+                        log.info(
+                          "Done with updating handle prefix. " +
+                          "It was changed " + updHdl + " handle" + ((updHdl > 1) ? "s" : "") +
+                          " and " + updMeta + " metadata record" + ((updMeta > 1) ? "s" : "")
+                        );
+
+                    }
+                    catch (SQLException sqle)
+                    {
+                        if ((context != null) && (context.isValid()))
+                        {
+                            context.abort();
+                            context = null;
+                        }
+                        System.out.println("\nError during SQL operations.");
+                        throw sqle;
+                    }
+
+                    System.out.println("Handles successfully updated in database.\n");
+                    System.out.println("Re-creating browse and search indexes...");
+
+                    try
+                    {
+                        // Reinitialise the search and browse system
+                        IndexClient.main(new String[] {"-b"});
+                        System.out.println("Browse and search indexes are ready now.");
+                        // All done
+                        System.out.println("\nAll done successfully. Please check the DSpace logs!\n");
+                    }
+                    catch (Exception e)
+                    {
+                        // Not a lot we can do
+                        System.out.println("Error during re-indexing.");
+                        System.out.println(
+                          "\n\nAutomatic re-indexing failed. Please perform it manually.\n" +
+                          "You should run one of the following commands:\n\n" +
+                          "  [dspace]/bin/dspace index-discovery -b\n\n" +
+                          "If you are using Solr for browse (this is the default setting).\n" +
+                          "When launching this command, your servlet container must be running.\n\n" +
+                          "  [dspace]/bin/dspace index-lucene-init\n\n" +
+                          "If you enabled Lucene for search.\n" +
+                          "When launching this command, your servlet container must be shutdown.\n"
+                        );
+                        throw e;
+                    }
+                }
+                else
+                {
+                    System.out.println("No changes have been made to your data.\n");
+                }
             }
             else
             {
-                System.out.println("No changes have been made to your data.");
+                System.out.println("Nothing to do! All handles are up-to-date.\n");
             }
         }
     }

dspace-api/src/main/java/org/dspace/identifier/DOIIdentifierProvider.java

@@ -10,7 +10,6 @@ package org.dspace.identifier;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Metadatum;
@@ -68,12 +67,12 @@ public class DOIIdentifierProvider
     public static final String DOI_QUALIFIER = "uri";
     
     public static final Integer TO_BE_REGISTERED = 1;
-    public static final Integer TO_BE_RESERVERED = 2;
+    public static final Integer TO_BE_RESERVED = 2;
     public static final Integer IS_REGISTERED = 3;
     public static final Integer IS_RESERVED = 4;
-    public static final Integer UPDATE_RESERVERED = 5;
+    public static final Integer UPDATE_RESERVED = 5;
     public static final Integer UPDATE_REGISTERED = 6;
-    public static final Integer UPDATE_BEFORE_REGISTERATION = 7;
+    public static final Integer UPDATE_BEFORE_REGISTRATION = 7;
     public static final Integer TO_BE_DELETED = 8;
     public static final Integer DELETED = 9;
     
@@ -251,7 +250,7 @@ public class DOIIdentifierProvider
             return;
         } 
                 
-        doiRow.setColumn("status", TO_BE_RESERVERED);
+        doiRow.setColumn("status", TO_BE_RESERVED);
         try
         {
             DatabaseManager.update(context, doiRow);
@@ -353,11 +352,11 @@ public class DOIIdentifierProvider
         }
         else if (TO_BE_REGISTERED == doiRow.getIntColumn("status")) 
         {
-            doiRow.setColumn("status", UPDATE_BEFORE_REGISTERATION);
+            doiRow.setColumn("status", UPDATE_BEFORE_REGISTRATION);
         }
         else if (IS_RESERVED == doiRow.getIntColumn("status")) 
         {
-            doiRow.setColumn("status", UPDATE_RESERVERED);
+            doiRow.setColumn("status", UPDATE_RESERVED);
         }
         else
         {
@@ -416,11 +415,11 @@ public class DOIIdentifierProvider
         {
             doiRow.setColumn("status", IS_REGISTERED);
         }
-        else if (UPDATE_BEFORE_REGISTERATION == doiRow.getIntColumn("status")) 
+        else if (UPDATE_BEFORE_REGISTRATION == doiRow.getIntColumn("status"))
         {
             doiRow.setColumn("status", TO_BE_REGISTERED);
         }
-        else if (UPDATE_RESERVERED == doiRow.getIntColumn("status")) 
+        else if (UPDATE_RESERVED == doiRow.getIntColumn("status"))
         {
             doiRow.setColumn("status", IS_RESERVED);
         }