Merge remote-tracking branch 'upstream/main' into DS-4410

.codecov.yml

@@ -0,0 +1,35 @@
+# DSpace configuration for Codecov.io coverage reports
+# These override the default YAML settings at
+# https://docs.codecov.io/docs/codecov-yaml#section-default-yaml
+# Can be validated via instructions at:
+# https://docs.codecov.io/docs/codecov-yaml#validate-your-repository-yaml
+
+# Tell Codecov not to send a coverage notification until (at least) 2 builds are completed
+# Since we run Unit & Integration tests in parallel, this lets Codecov know that coverage
+# needs to be merged across those builds
+codecov:
+  notify:
+    after_n_builds: 2
+
+# Settings related to code coverage analysis
+coverage:
+  status:
+    # Configuration for project-level checks. This checks how the PR changes overall coverage.
+    project:
+      default:
+        # For each PR, auto compare coverage to previous commit.
+        # Require that overall (project) coverage does NOT drop more than 0.5%
+        target: auto
+        threshold: 0.5%
+    # Configuration for patch-level checks. This checks the relative coverage of the new PR code ONLY.
+    patch:
+      default:
+         # Enable informational mode, which just provides info to reviewers & always passes
+         # https://docs.codecov.io/docs/commit-status#section-informational
+         informational: true
+
+# Turn PR comments "off". This feature adds the code coverage summary as a
+# comment on each PR. See https://docs.codecov.io/docs/pull-request-comments
+# However, this same info is available from the Codecov checks in the PR's
+# "Checks" tab in GitHub. So, the comment is unnecessary.
+comment: false

.github/pull_request_template.md

@@ -1,7 +1,7 @@
 ## References
 _Add references/links to any related issues or PRs. These may include:_
-* Related to [REST Contract](https://github.com/DSpace/Rest7Contract) or an open REST Contract PR, if any
-* Fixes [GitHub issue](https://github.com/DSpace/DSpace/issues), if any
+* Fixes #[issue-number]
+* Related to [REST Contract](https://github.com/DSpace/Rest7Contract)
 
 ## Description
 Short summary of changes (1-2 sentences).

.github/workflows/build.yml

@@ -0,0 +1,65 @@
+# DSpace 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-latest
+    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"
+    strategy:
+      # Create a matrix of two separate configurations for Unit vs Integration Tests
+      # This will ensure those tasks are run in parallel
+      matrix:
+        include:
+          # NOTE: Unit Tests include deprecated REST API v6 (as it has unit tests)
+          - type: "Unit Tests"
+            mvnflags: "-DskipUnitTests=false -Pdspace-rest"
+          # NOTE: ITs skip all code validation checks, as they are already done by Unit Test job.
+          #  - enforcer.skip     => Skip maven-enforcer-plugin rules
+          #  - checkstyle.skip   => Skip all checkstyle checks by maven-checkstyle-plugin
+          #  - license.skip      => Skip all license header checks by license-maven-plugin
+          #  - xml.skip          => Skip all XML/XSLT validation by xml-maven-plugin
+          - type: "Integration Tests"
+            mvnflags: "-DskipIntegrationTests=false -Denforcer.skip=true -Dcheckstyle.skip=true -Dlicense.skip=true -Dxml.skip=true"
+      # Do NOT exit immediately if one matrix job fails
+      # This ensures ITs continue running even if Unit Tests fail, or visa versa
+      fail-fast: false
+    # 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 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+
+      # 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-
+
+      # Run parallel Maven builds based on the above 'strategy.matrix'
+      - name: Run Maven ${{ matrix.type }}
+        env:
+          TEST_FLAGS: ${{ matrix.mvnflags }}
+        run: mvn install -B -V -P-assembly -Pcoverage-report $TEST_FLAGS
+
+      # https://github.com/codecov/codecov-action
+      - name: Upload coverage to Codecov.io
+        uses: codecov/codecov-action@v1

.github/workflows/label_merge_conflicts.yml

@@ -0,0 +1,25 @@
+# This workflow checks open PRs for merge conflicts and labels them when conflicts are found
+name: Check for merge conflicts
+
+# Run whenever the "main" branch is updated
+# NOTE: This means merge conflicts are only checked for when a PR is merged to main.
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  triage:
+    runs-on: ubuntu-latest
+    steps:
+      # See: https://github.com/mschilde/auto-label-merge-conflicts/
+      - name: Auto-label PRs with merge conflicts
+        uses: mschilde/auto-label-merge-conflicts@v2.0
+        # Add "merge conflict" label if a merge conflict is detected. Remove it when resolved.
+        # Note, the authentication token is created automatically
+        # See: https://docs.github.com/en/actions/configuring-and-managing-workflows/authenticating-with-the-github_token
+        with:
+          CONFLICT_LABEL_NAME: 'merge conflict'
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        # Ignore errors
+        continue-on-error: true

.gitignore

@@ -19,7 +19,7 @@ tags
 overlays/
 
 ## Ignore project files created by NetBeans
-nbproject/private/
+nbproject/
 build/
 nbbuild/
 dist/
@@ -41,4 +41,4 @@ nb-configuration.xml
 .DS_Store
 
 ##Ignore JRebel project configuration
-rebel.xml
+rebel.xml

.travis.yml

@@ -1,46 +0,0 @@
-language: java
-sudo: false
-dist: trusty
-
-env:
-  # Give Maven 1GB of memory to work with
-  - MAVEN_OPTS=-Xmx1024M
-
-jdk:
-  # DS-3384 Oracle JDK has DocLint enabled by default.
-  # Let's use this to catch any newly introduced DocLint issues.
-  - oraclejdk11
-
-## Should we run into any problems with oraclejdk8 on Travis, we may try the following workaround.
-## https://docs.travis-ci.com/user/languages/java#Testing-Against-Multiple-JDKs
-## https://github.com/travis-ci/travis-ci/issues/3259#issuecomment-130860338
-#addons:
-#  apt:
-#    packages:
-#      - oracle-java8-installer
-
-before_install:
-  # Remove outdated settings.xml from Travis builds. Workaround for https://github.com/travis-ci/travis-ci/issues/4629
-  - rm ~/.m2/settings.xml
-
-# Skip install stage, as we'll do it below
-install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
-
-# Build DSpace and run both Unit and Integration Tests
-script:
-  # Summary of flags used (below):
-  #     license:check           => Validate all source code license headers
-  #     -Dmaven.test.skip=false => Enable DSpace Unit Tests
-  #     -DskipITs=false         => Enable DSpace Integration Tests
-  #     -Pdspace-rest          => Enable optional dspace-rest module as part of build
-  #     -P !assembly            => Skip assembly of "dspace-installer" directory (as it can be memory intensive)
-  #     -B                      => Maven batch/non-interactive mode (recommended for CI)
-  #     -V                      => Display Maven version info before build
-  #     -Dsurefire.rerunFailingTestsCount=2 => try again for flakey tests, and keep track of/report on number of retries
-  - "mvn clean install license:check -Dmaven.test.skip=false -DskipITs=false -Pdspace-rest -P !assembly -B -V -Dsurefire.rerunFailingTestsCount=2"
-
-# After a successful build and test (see 'script'), send code coverage reports to coveralls.io
-# These code coverage reports are generated by jacoco-maven-plugin (during test process above).
-after_success:
-  # Run "verify", enabling the "coveralls" profile. This sends our reports to coveralls.io (see coveralls-maven-plugin)
-  - "cd dspace && mvn verify -P coveralls"

Dockerfile.test

@@ -51,7 +51,12 @@ RUN ant init_installation update_configs update_code update_webapps
 # Create a new tomcat image that does not retain the the build directory contents
 FROM tomcat:8-jdk11
 ENV DSPACE_INSTALL=/dspace
+ENV TOMCAT_INSTALL=/usr/local/tomcat
 COPY --from=ant_build /dspace $DSPACE_INSTALL
+# Enable the AJP connector in Tomcat's server.xml
+# NOTE: secretRequired="false" should only be used when AJP is NOT accessible from an external network. But, secretRequired="true" isn't supported by mod_proxy_ajp until Apache 2.5
+RUN sed -i '/Service name="Catalina".*/a \\n    <Connector protocol="AJP/1.3" port="8009" address="0.0.0.0" redirectPort="8443" URIEncoding="UTF-8" secretRequired="false" />' $TOMCAT_INSTALL/conf/server.xml
+# Expose Tomcat port and AJP port
 EXPOSE 8080 8009
 
 ENV JAVA_OPTS=-Xmx2000m

README.md

@@ -1,7 +1,7 @@
 
 # DSpace
 
-[![Build Status](https://travis-ci.com/DSpace/DSpace.png?branch=main)](https://travis-ci.com/DSpace/DSpace)
+[![Build Status](https://github.com/DSpace/DSpace/workflows/Build/badge.svg)](https://github.com/DSpace/DSpace/actions?query=workflow%3ABuild)
 
 [DSpace Documentation](https://wiki.lyrasis.org/display/DSDOC/) |
 [DSpace Releases](https://github.com/DSpace/DSpace/releases) |
@@ -86,37 +86,37 @@ DSpace uses GitHub to track issues:
 ### Running Tests
 
 By default, in DSpace, Unit Tests and Integration Tests are disabled. However, they are
-run automatically by [Travis CI](https://travis-ci.com/DSpace/DSpace/) for all Pull Requests and code commits.
+run automatically by [GitHub Actions](https://github.com/DSpace/DSpace/actions?query=workflow%3ABuild) for all Pull Requests and code commits.
 
 * How to run both Unit Tests (via `maven-surefire-plugin`) and Integration Tests (via `maven-failsafe-plugin`):
   ```
-  mvn clean test -Dmaven.test.skip=false -DskipITs=false
+  mvn install -DskipUnitTests=false -DskipIntegrationTests=false
   ```
-* How to run just Unit Tests:
+* How to run _only_ Unit Tests:
   ```
-  mvn test -Dmaven.test.skip=false
+  mvn test -DskipUnitTests=false
   ```
 * How to run a *single* Unit Test
   ```
   # Run all tests in a specific test class
   # NOTE: failIfNoTests=false is required to skip tests in other modules
-  mvn test -Dmaven.test.skip=false -Dtest=[full.package.testClassName] -DfailIfNoTests=false
+  mvn test -DskipUnitTests=false -Dtest=[full.package.testClassName] -DfailIfNoTests=false
 
   # Run one test method in a specific test class
-  mvn test -Dmaven.test.skip=false -Dtest=[full.package.testClassName]#[testMethodName] -DfailIfNoTests=false
+  mvn test -DskipUnitTests=false -Dtest=[full.package.testClassName]#[testMethodName] -DfailIfNoTests=false
   ```
-* How to run Integration Tests (requires enabling Unit tests too)
+* How to run _only_ Integration Tests
   ```
-  mvn verify -Dmaven.test.skip=false -DskipITs=false
+  mvn install -DskipIntegrationTests=false
   ```
-* How to run a *single* Integration Test (requires enabling Unit tests too)
+* How to run a *single* Integration Test
   ```
   # Run all integration tests in a specific test class
   # NOTE: failIfNoTests=false is required to skip tests in other modules
-  mvn test -Dmaven.test.skip=false -DskipITs=false -Dtest=[full.package.testClassName] -DfailIfNoTests=false
+  mvn install -DskipIntegrationTests=false -Dit.test=[full.package.testClassName] -DfailIfNoTests=false
 
   # Run one test method in a specific test class
-  mvn test -Dmaven.test.skip=false -DskipITs=false -Dtest=[full.package.testClassName]#[testMethodName] -DfailIfNoTests=false
+  mvn install -DskipIntegrationTests=false -Dit.test=[full.package.testClassName]#[testMethodName] -DfailIfNoTests=false
   ```
 * How to run only tests of a specific DSpace module
   ```

docker-compose.yml

@@ -2,6 +2,7 @@ version: '3.7'
 networks:
   dspacenet:
 services:
+  # DSpace (backend) webapp container
   dspace:
     container_name: dspace
     image: "${DOCKER_OWNER:-dspace}/dspace:${DSPACE_VER:-dspace-7_x-test}"
@@ -15,6 +16,8 @@ services:
     ports:
     - published: 8080
       target: 8080
+    - published: 8009
+      target: 8009
     stdin_open: true
     tty: true
     volumes:
@@ -31,10 +34,12 @@ services:
       while (!</dev/tcp/dspacedb/5432) > /dev/null 2>&1; do sleep 1; done;
       /dspace/bin/dspace database migrate
       catalina.sh run
+  # DSpace database container
   dspacedb:
     container_name: dspacedb
     environment:
       PGDATA: /pgdata
+    # Uses a custom Postgres image with pgcrypto installed
     image: dspace/dspace-postgres-pgcrypto
     networks:
       dspacenet:
@@ -45,9 +50,11 @@ services:
     tty: true
     volumes:
     - pgdata:/pgdata
+  # DSpace Solr container
   dspacesolr:
     container_name: dspacesolr
-    image: dspace/dspace-solr
+    # Uses official Solr image at https://hub.docker.com/_/solr/
+    image: solr:8.7
     networks:
       dspacenet:
     ports:
@@ -55,15 +62,27 @@ services:
       target: 8983
     stdin_open: true
     tty: true
+    working_dir: /var/solr/data
     volumes:
-    - solr_authority:/opt/solr/server/solr/authority/data
-    - solr_oai:/opt/solr/server/solr/oai/data
-    - solr_search:/opt/solr/server/solr/search/data
-    - solr_statistics:/opt/solr/server/solr/statistics/data
+    # Mount our local Solr core configs so that they are available as Solr configsets on container
+    - ./dspace/solr/authority:/opt/solr/server/solr/configsets/authority
+    - ./dspace/solr/oai:/opt/solr/server/solr/configsets/oai
+    - ./dspace/solr/search:/opt/solr/server/solr/configsets/search
+    - ./dspace/solr/statistics:/opt/solr/server/solr/configsets/statistics
+    # Keep Solr data directory between reboots
+    - solr_data:/var/solr/data
+    # Initialize all DSpace Solr cores using the mounted local configsets (see above), then start Solr
+    entrypoint:
+    - /bin/bash
+    - '-c'
+    - |
+      init-var-solr
+      precreate-core authority /opt/solr/server/solr/configsets/authority
+      precreate-core oai /opt/solr/server/solr/configsets/oai
+      precreate-core search /opt/solr/server/solr/configsets/search
+      precreate-core statistics /opt/solr/server/solr/configsets/statistics
+      exec solr -f
 volumes:
   assetstore:
   pgdata:
-  solr_authority:
-  solr_oai:
-  solr_search:
-  solr_statistics:
+  solr_data:

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.0-beta4-SNAPSHOT</version>
+        <version>7.0-beta5-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -127,44 +127,82 @@
                 </executions>
             </plugin>
 
+            <!-- This plugin allows us to run a Groovy script in our Maven POM
+                 (see: https://groovy.github.io/gmaven/groovy-maven-plugin/execute.html )
+                 We are generating a OS-agnostic version (agnostic.build.dir) of
+                 the ${project.build.directory} property (full path of target dir).
+                 This is needed by the Surefire & Failsafe plugins (see below)
+                 to initialize the Unit Test environment's dspace.cfg file.
+                 Otherwise, the Unit Test Framework will not work on Windows OS.
+                 This Groovy code was mostly borrowed from:
+                 http://stackoverflow.com/questions/3872355/how-to-convert-file-separator-in-maven
+            -->
+            <plugin>
+                <groupId>org.codehaus.gmaven</groupId>
+                <artifactId>groovy-maven-plugin</artifactId>
+                <executions>
+                    <execution>
+                        <id>setproperty</id>
+                        <phase>initialize</phase>
+                        <goals>
+                            <goal>execute</goal>
+                        </goals>
+                        <configuration>
+                            <source>
+                                project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
+                                log.info("Initializing Maven property 'agnostic.build.dir' to: {}", project.properties['agnostic.build.dir']);
+                            </source>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
+
+            <plugin>
+                <groupId>com.mycila</groupId>
+                <artifactId>license-maven-plugin</artifactId>
+                <configuration>
+                    <excludes>
+                        <exclude>src/test/resources/**</exclude>
+                        <exclude>src/test/data/**</exclude>
+                        <!-- Ignore license header requirements on Flyway upgrade scripts -->
+                        <exclude>src/main/resources/org/dspace/storage/rdbms/flywayupgrade/**</exclude>
+                    </excludes>
+                </configuration>
+            </plugin>
+
         </plugins>
     </build>
 
 
     <profiles>
         <profile>
-            <id>findbugs</id>
+            <id>spotbugs</id>
             <activation>
                 <activeByDefault>false</activeByDefault>
-                <!-- property>
-                    <name>maven.test.skip</name>
-                    <value>false</value>
-                </property -->
             </activation>
             <build>
                 <plugins>
                     <plugin>
-                        <groupId>org.codehaus.mojo</groupId>
-                        <artifactId>findbugs-maven-plugin</artifactId>
+                        <groupId>com.github.spotbugs</groupId>
+                        <artifactId>spotbugs-maven-plugin</artifactId>
                     </plugin>
                 </plugins>
             </build>
         </profile>
 
-        <!-- If Unit Testing is enabled, then setup the Unit Test Environment.
-             See also the 'skiptests' profile in Parent POM. -->
+        <!-- Setup the Unit Test Environment (when -DskipUnitTests=false) -->
         <profile>
-            <id>test-environment</id>
+            <id>unit-test-environment</id>
             <activation>
                 <activeByDefault>false</activeByDefault>
                 <property>
-                    <name>maven.test.skip</name>
+                    <name>skipUnitTests</name>
                     <value>false</value>
                 </property>
             </activation>
             <build>
                 <plugins>
-                    <!-- Unit/Integration Testing setup: This plugin unzips the
+                    <!-- Unit Testing setup: This plugin unzips the
                          'testEnvironment.zip' file (created by dspace-parent POM), into
                          the 'target/testing/' folder, to essentially create a test
                          install of DSpace, against which Tests can be run. -->
@@ -184,53 +222,16 @@
                         </configuration>
                         <executions>
                             <execution>
-                                <id>setupTestEnvironment</id>
+                                <id>setupUnitTestEnvironment</id>
                                 <phase>generate-test-resources</phase>
                                 <goals>
                                     <goal>unpack</goal>
                                 </goals>
                             </execution>
-                            <execution>
-                                <id>setupIntegrationTestEnvironment</id>
-                                <phase>pre-integration-test</phase>
-                                <goals>
-                                    <goal>unpack</goal>
-                                </goals>
-                            </execution>
                         </executions>
                     </plugin>
 
-                    <!-- This plugin allows us to run a Groovy script in our Maven POM
-                         (see: http://gmaven.codehaus.org/Executing+Groovy+Code )
-                         We are generating a OS-agnostic version (agnostic.build.dir) of
-                         the ${project.build.directory} property (full path of target dir).
-                         This is needed by the Surefire & Failsafe plugins (see below)
-                         to initialize the Unit Test environment's dspace.cfg file.
-                         Otherwise, the Unit Test Framework will not work on Windows OS.
-                         This Groovy code was mostly borrowed from:
-                         http://stackoverflow.com/questions/3872355/how-to-convert-file-separator-in-maven
-                    -->
-                    <plugin>
-                        <groupId>org.codehaus.gmaven</groupId>
-                        <artifactId>groovy-maven-plugin</artifactId>
-                        <executions>
-                            <execution>
-                                <id>setproperty</id>
-                                <phase>initialize</phase>
-                                <goals>
-                                    <goal>execute</goal>
-                                </goals>
-                                <configuration>
-                                    <source>
-                                        project.properties['agnostic.build.dir'] = project.build.directory.replace(File.separator, '/');
-                                        log.info("Initializing Maven property 'agnostic.build.dir' to: {}", project.properties['agnostic.build.dir']);
-                                    </source>
-                                </configuration>
-                            </execution>
-                        </executions>
-                    </plugin>
-
-                    <!-- Run Unit Testing! This plugin just kicks off the tests (when enabled). -->
+                    <!-- Run Unit Testing! This plugin just kicks off the tests. -->
                     <plugin>
                         <artifactId>maven-surefire-plugin</artifactId>
                         <configuration>
@@ -241,11 +242,56 @@
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
+                                <solr.install.dir>${agnostic.build.dir}/testing/dspace/solr/</solr.install.dir>
                             </systemPropertyVariables>
                         </configuration>
                     </plugin>
+                </plugins>
+            </build>
+        </profile>
 
-                    <!-- Run Integration Testing! This plugin just kicks off the tests (when enabled). -->
+        <!-- Setup the Integration Test Environment (when -DskipIntegrationTests=false) -->
+        <profile>
+            <id>integration-test-environment</id>
+            <activation>
+                <activeByDefault>false</activeByDefault>
+                <property>
+                    <name>skipIntegrationTests</name>
+                    <value>false</value>
+                </property>
+            </activation>
+            <build>
+                <plugins>
+                    <!-- Integration Testing setup: This plugin unzips the
+                         'testEnvironment.zip' file (created by dspace-parent POM), into
+                         the 'target/testing/' folder, to essentially create a test
+                         install of DSpace, against which Tests can be run. -->
+                    <plugin>
+                        <artifactId>maven-dependency-plugin</artifactId>
+                        <configuration>
+                            <outputDirectory>${project.build.directory}/testing</outputDirectory>
+                            <artifactItems>
+                                <artifactItem>
+                                    <groupId>org.dspace</groupId>
+                                    <artifactId>dspace-parent</artifactId>
+                                    <version>${project.version}</version>
+                                    <type>zip</type>
+                                    <classifier>testEnvironment</classifier>
+                                </artifactItem>
+                            </artifactItems>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <id>setupIntegrationTestEnvironment</id>
+                                <phase>pre-integration-test</phase>
+                                <goals>
+                                    <goal>unpack</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+
+                    <!-- Run Integration Testing! This plugin just kicks off the tests. -->
                     <plugin>
                         <artifactId>maven-failsafe-plugin</artifactId>
                         <configuration>
@@ -255,12 +301,12 @@
                                 <dspace.dir>${agnostic.build.dir}/testing/dspace/</dspace.dir>
                                 <!-- Turn off any DSpace logging -->
                                 <dspace.log.init.disable>true</dspace.log.init.disable>
+                                <solr.install.dir>${agnostic.build.dir}/testing/dspace/solr/</solr.install.dir>
                             </systemPropertyVariables>
                         </configuration>
                     </plugin>
                 </plugins>
             </build>
-
         </profile>
     </profiles>
 
@@ -269,6 +315,13 @@
         <dependency>
             <groupId>org.hibernate</groupId>
             <artifactId>hibernate-ehcache</artifactId>
+            <exclusions>
+                <!-- Newer version pulled in via Jersey below -->
+                <exclusion>
+                    <groupId>org.javassist</groupId>
+                    <artifactId>javassist</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>org.hibernate</groupId>
@@ -279,16 +332,16 @@
             <artifactId>hibernate-validator-cdi</artifactId>
             <version>${hibernate-validator.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.hibernate.javax.persistence</groupId>
+            <artifactId>hibernate-jpa-2.1-api</artifactId>
+            <version>1.0.0.Final</version>
+        </dependency>
 
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-orm</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.glassfish</groupId>
-            <artifactId>javax.el</artifactId>
-            <version>3.0.1-b10</version>
-        </dependency>
 
         <dependency>
             <groupId>net.handle</groupId>
@@ -303,6 +356,48 @@
                     <groupId>org.ow2.asm</groupId>
                     <artifactId>asm-commons</artifactId>
                 </exclusion>
+                <!-- Newer version of Bouncycastle brought in via solr-cell -->
+                <exclusion>
+                    <groupId>org.bouncycastle</groupId>
+                    <artifactId>bcpkix-jdk15on</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.bouncycastle</groupId>
+                    <artifactId>bcprov-jdk15on</artifactId>
+                </exclusion>
+                <!-- Newer version of Jetty in our parent POM & via Solr -->
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-alpn-java-server</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-deploy</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlet</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-servlets</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-webapp</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-xml</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty.http2</groupId>
+                    <artifactId>http2-common</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty.http2</groupId>
+                    <artifactId>http2-server</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <!-- Jetty is needed to run Handle Server -->
@@ -310,10 +405,6 @@
             <groupId>org.eclipse.jetty</groupId>
             <artifactId>jetty-server</artifactId>
         </dependency>
-        <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>jargon</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>mets</artifactId>
@@ -323,6 +414,10 @@
             <artifactId>apache-jena-libs</artifactId>
             <type>pom</type>
         </dependency>
+        <dependency>
+            <groupId>commons-cli</groupId>
+            <artifactId>commons-cli</artifactId>
+        </dependency>
         <dependency>
             <groupId>commons-codec</groupId>
             <artifactId>commons-codec</artifactId>
@@ -379,10 +474,6 @@
             <groupId>org.jdom</groupId>
             <artifactId>jdom</artifactId>
         </dependency>
-        <dependency>
-            <groupId>oro</groupId>
-            <artifactId>oro</artifactId>
-        </dependency>
         <dependency>
             <groupId>org.apache.pdfbox</groupId>
             <artifactId>pdfbox</artifactId>
@@ -395,14 +486,6 @@
             <groupId>org.apache.poi</groupId>
             <artifactId>poi-scratchpad</artifactId>
         </dependency>
-        <dependency>
-            <groupId>rome</groupId>
-            <artifactId>rome</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>rome</groupId>
-            <artifactId>opensearch</artifactId>
-        </dependency>
         <dependency>
             <groupId>xalan</groupId>
             <artifactId>xalan</artifactId>
@@ -411,14 +494,6 @@
             <groupId>xerces</groupId>
             <artifactId>xercesImpl</artifactId>
         </dependency>
-        <dependency>
-            <groupId>xml-apis</groupId>
-            <artifactId>xml-apis</artifactId>
-        </dependency>
-        <dependency>
-            <groupId>javax.activation</groupId>
-            <artifactId>activation</artifactId>
-        </dependency>
         <dependency>
             <groupId>com.ibm.icu</groupId>
             <artifactId>icu4j</artifactId>
@@ -438,7 +513,7 @@
         </dependency>
         <dependency>
             <groupId>org.hamcrest</groupId>
-            <artifactId>hamcrest-core</artifactId>
+            <artifactId>hamcrest-all</artifactId>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -456,6 +531,7 @@
             <artifactId>spring-test</artifactId>
             <scope>test</scope>
         </dependency>
+        <!-- Used for RSS / ATOM syndication feeds -->
         <dependency>
             <groupId>org.rometools</groupId>
             <artifactId>rome-modules</artifactId>
@@ -479,64 +555,104 @@
 
         <dependency>
             <groupId>org.apache.solr</groupId>
-            <artifactId>solr-cell</artifactId>
+            <artifactId>solr-solrj</artifactId>
             <version>${solr.client.version}</version>
             <exclusions>
-                <!-- Newer versions provided in our parent POM -->
-                <exclusion>
-                    <groupId>org.ow2.asm</groupId>
-                    <artifactId>asm-commons</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.bouncycastle</groupId>
-                    <artifactId>bcpkix-jdk15on</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.bouncycastle</groupId>
-                    <artifactId>bcprov-jdk15on</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-xml</artifactId>
-                </exclusion>
+                <!-- Newer Jetty version brought in via Parent POM -->
                 <exclusion>
                     <groupId>org.eclipse.jetty</groupId>
                     <artifactId>jetty-http</artifactId>
                 </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-servlet</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-webapp</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-util</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-deploy</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-continuation</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-servlets</artifactId>
-                </exclusion>
                 <exclusion>
                     <groupId>org.eclipse.jetty</groupId>
                     <artifactId>jetty-io</artifactId>
                 </exclusion>
                 <exclusion>
                     <groupId>org.eclipse.jetty</groupId>
-                    <artifactId>jetty-security</artifactId>
+                    <artifactId>jetty-util</artifactId>
                 </exclusion>
             </exclusions>
         </dependency>
+        <!-- Solr Core is needed for Integration Tests (to run a MockSolrServer)     -->
+        <!-- The following Solr / Lucene dependencies also support integration tests -->
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-core</artifactId>
+            <scope>test</scope>
+            <version>${solr.client.version}</version>
+            <exclusions>
+                <!-- Newer version brought in by opencsv -->
+                <exclusion>
+                    <groupId>org.apache.commons</groupId>
+                    <artifactId>commons-text</artifactId>
+                </exclusion>
+                <!-- Newer Jetty version brought in via Parent POM -->
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-http</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-io</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-util</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-cell</artifactId>
+            <exclusions>
+                <!-- Newer version brought in by opencsv -->
+                <exclusion>
+                    <groupId>org.apache.commons</groupId>
+                    <artifactId>commons-text</artifactId>
+                </exclusion>
+                <!-- Newer Jetty version brought in via Parent POM -->
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-http</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-io</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.eclipse.jetty</groupId>
+                    <artifactId>jetty-util</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-core</artifactId>
+        </dependency>
+        <!-- Used for full-text indexing with Solr -->
+        <dependency>
+            <groupId>org.apache.tika</groupId>
+            <artifactId>tika-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-icu</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-smartcn</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.lucene</groupId>
+            <artifactId>lucene-analyzers-stempel</artifactId>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.xmlbeans</groupId>
+            <artifactId>xmlbeans</artifactId>
+        </dependency>
 
         <dependency>
             <groupId>com.maxmind.geoip2</groupId>
@@ -571,7 +687,6 @@
             <artifactId>guava</artifactId>
         </dependency>
 
-
         <dependency>
             <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
@@ -594,7 +709,7 @@
         <dependency>
             <groupId>org.flywaydb</groupId>
             <artifactId>flyway-core</artifactId>
-            <version>4.0.3</version>
+            <version>6.5.5</version>
         </dependency>
 
         <!-- Google Analytics -->
@@ -618,6 +733,7 @@
             <groupId>com.google.oauth-client</groupId>
             <artifactId>google-oauth-client</artifactId>
         </dependency>
+
         <!-- FindBugs -->
         <dependency>
             <groupId>com.google.code.findbugs</groupId>
@@ -627,6 +743,7 @@
             <groupId>com.google.code.findbugs</groupId>
             <artifactId>annotations</artifactId>
         </dependency>
+
         <dependency>
             <groupId>joda-time</groupId>
             <artifactId>joda-time</artifactId>
@@ -660,6 +777,11 @@
                     <groupId>org.apache.geronimo.specs</groupId>
                     <artifactId>*</artifactId>
                 </exclusion>
+                <!-- Exclude Woodstox, as later version provided by Solr dependencies -->
+                <exclusion>
+                    <groupId>org.codehaus.woodstox</groupId>
+                    <artifactId>woodstox-core-asl</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
         <dependency>
@@ -673,14 +795,28 @@
                     <groupId>org.apache.geronimo.specs</groupId>
                     <artifactId>*</artifactId>
                 </exclusion>
+                <!-- Exclude Woodstox, as later version provided by Solr dependencies -->
+                <exclusion>
+                    <groupId>org.codehaus.woodstox</groupId>
+                    <artifactId>woodstox-core-asl</artifactId>
+                </exclusion>
             </exclusions>
         </dependency>
 
+        <!-- Jersey / JAX-RS client (javax.ws.rs.*) dependencies needed to integrate with external sources/services -->
         <dependency>
             <groupId>org.glassfish.jersey.core</groupId>
             <artifactId>jersey-client</artifactId>
             <version>${jersey.version}</version>
         </dependency>
+        <!-- Required because Jersey no longer includes a dependency injection provider by default.
+             Needed to support PubMed API call in "PubmedImportMetadataSourceServiceImpl.GetRecord" -->
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+            <version>${jersey.version}</version>
+        </dependency>
+
         <!-- S3 -->
         <dependency>
             <groupId>com.amazonaws</groupId>
@@ -688,12 +824,30 @@
             <version>1.10.50</version>
         </dependency>
 
-        <!-- For ORCID v2 integration -->
         <dependency>
-            <groupId>org.dspace</groupId>
-            <artifactId>orcid-jaxb-api</artifactId>
-            <version>2.1.0</version>
+            <groupId>org.orcid</groupId>
+            <artifactId>orcid-model</artifactId>
+            <version>3.0.2</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>javax.validation</groupId>
+                    <artifactId>validation-api</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.jaxrs</groupId>
+                    <artifactId>jackson-jaxrs-json-provider</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.yaml</groupId>
+                    <artifactId>snakeyaml</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.javassist</groupId>
+                    <artifactId>javassist</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
+
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
@@ -704,7 +858,7 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>4.5</version>
+            <version>5.2</version>
         </dependency>
 
         <!-- Email templating -->
@@ -717,18 +871,12 @@
 
         <dependency>
             <groupId>org.xmlunit</groupId>
-            <artifactId>xmlunit-matchers</artifactId>
+            <artifactId>xmlunit-core</artifactId>
             <version>2.6.3</version>
             <scope>test</scope>
         </dependency>
 
-        <dependency>
-            <groupId>org.hibernate.javax.persistence</groupId>
-            <artifactId>hibernate-jpa-2.1-api</artifactId>
-            <version>1.0.0.Final</version>
-        </dependency>
-
-        <dependency>
+       <dependency>
             <groupId>org.apache.bcel</groupId>
             <artifactId>bcel</artifactId>
             <version>6.4.0</version>

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

@@ -14,9 +14,9 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.apache.commons.collections4.CollectionUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Community;
@@ -51,7 +51,7 @@ public class CommunityFiliator {
      */
     public static void main(String[] argv) throws Exception {
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 

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

@@ -13,10 +13,9 @@ import java.util.Locale;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang3.StringUtils;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
 import org.dspace.eperson.EPerson;
@@ -24,6 +23,8 @@ import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.eperson.service.GroupService;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * A command-line tool for creating an initial administrator for setting up a
@@ -61,7 +62,7 @@ public final class CreateAdministrator {
      */
     public static void main(String[] argv)
         throws Exception {
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = new Options();
 
         CreateAdministrator ca = new CreateAdministrator();
@@ -147,9 +148,10 @@ public final class CreateAdministrator {
                 lastName = lastName.trim();
             }
 
-            if (ConfigurationManager.getProperty("webui.supported.locales") != null) {
-                System.out.println("Select one of the following languages: " + ConfigurationManager
-                    .getProperty("webui.supported.locales"));
+            ConfigurationService cfg = DSpaceServicesFactory.getInstance().getConfigurationService();
+            if (cfg.hasProperty("webui.supported.locales")) {
+                System.out.println("Select one of the following languages: "
+                        + cfg.getProperty("webui.supported.locales"));
                 System.out.print("Language: ");
                 System.out.flush();
 

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

@@ -10,6 +10,7 @@ package org.dspace.administer;
 import java.io.BufferedWriter;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.io.Writer;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.List;
@@ -17,25 +18,28 @@ import java.util.Map;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
-import org.apache.xml.serialize.Method;
-import org.apache.xml.serialize.OutputFormat;
-import org.apache.xml.serialize.XMLSerializer;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
-import org.xml.sax.SAXException;
+import org.w3c.dom.DOMConfiguration;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.bootstrap.DOMImplementationRegistry;
+import org.w3c.dom.ls.DOMImplementationLS;
+import org.w3c.dom.ls.LSOutput;
+import org.w3c.dom.ls.LSSerializer;
 
 
 /**
  * @author Graham Triggs
  *
- * This class creates an xml document as passed in the arguments and
+ * This class creates an XML document as passed in the arguments and
  * from the metadata schemas for the repository.
  *
  * The form of the XML is as follows
@@ -61,17 +65,20 @@ public class MetadataExporter {
     private MetadataExporter() { }
 
     /**
-     * @param args commandline arguments
+     * @param args command line arguments
      * @throws ParseException          if parser error
-     * @throws SAXException            if XML parse error
      * @throws IOException             if IO error
      * @throws SQLException            if database error
      * @throws RegistryExportException if export error
+     * @throws ClassNotFoundException  if no suitable DOM implementation
+     * @throws InstantiationException  if no suitable DOM implementation
+     * @throws IllegalAccessException  if no suitable DOM implementation
      */
     public static void main(String[] args)
-        throws ParseException, SQLException, IOException, SAXException, RegistryExportException {
+        throws ParseException, SQLException, IOException, RegistryExportException,
+            ClassNotFoundException, InstantiationException, IllegalAccessException {
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = new Options();
         options.addOption("f", "file", true, "output xml file for registry");
         options.addOption("s", "schema", true, "the name of the schema to export");
@@ -95,32 +102,31 @@ public class MetadataExporter {
     }
 
     /**
-     * Save a registry to a filepath
+     * Save a registry to a file path
      *
-     * @param file   filepath
+     * @param file   file path
      * @param schema schema definition to save
      * @throws SQLException            if database error
      * @throws IOException             if IO error
-     * @throws SAXException            if XML error
      * @throws RegistryExportException if export error
+     * @throws ClassNotFoundException  if no suitable DOM implementation
+     * @throws InstantiationException  if no suitable DOM implementation
+     * @throws IllegalAccessException  if no suitable DOM implementation
      */
     public static void saveRegistry(String file, String schema)
-        throws SQLException, IOException, SAXException, RegistryExportException {
+        throws SQLException, IOException, RegistryExportException,
+            ClassNotFoundException, InstantiationException, IllegalAccessException {
         // create a context
         Context context = new Context();
         context.turnOffAuthorisationSystem();
 
-        OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
-        xmlFormat.setLineWidth(120);
-        xmlFormat.setIndent(4);
-
-        XMLSerializer xmlSerializer = new XMLSerializer(new BufferedWriter(new FileWriter(file)), xmlFormat);
-        //        XMLSerializer xmlSerializer = new XMLSerializer(System.out, xmlFormat);
-        xmlSerializer.startDocument();
-        xmlSerializer.startElement("dspace-dc-types", null);
+        // Initialize an XML document.
+        Document document = DOMImplementationRegistry.newInstance()
+                .getDOMImplementation("XML 3.0")
+                .createDocument(null, "dspace-dc-types", null);
 
         // Save the schema definition(s)
-        saveSchema(context, xmlSerializer, schema);
+        saveSchema(context, document, schema);
 
         List<MetadataField> mdFields = null;
 
@@ -139,55 +145,64 @@ public class MetadataExporter {
             mdFields = metadataFieldService.findAll(context);
         }
 
-        // Output the metadata fields
+        // Compose the metadata fields
         for (MetadataField mdField : mdFields) {
-            saveType(context, xmlSerializer, mdField);
+            saveType(context, document, mdField);
         }
 
-        xmlSerializer.endElement("dspace-dc-types");
-        xmlSerializer.endDocument();
+        // Serialize the completed document to the output file.
+        try (Writer writer = new BufferedWriter(new FileWriter(file))) {
+            DOMImplementationLS lsImplementation
+                    = (DOMImplementationLS) DOMImplementationRegistry.newInstance()
+                            .getDOMImplementation("LS");
+            LSSerializer serializer = lsImplementation.createLSSerializer();
+            DOMConfiguration configuration = serializer.getDomConfig();
+            configuration.setParameter("format-pretty-print", true);
+            LSOutput lsOutput = lsImplementation.createLSOutput();
+            lsOutput.setEncoding("UTF-8");
+            lsOutput.setCharacterStream(writer);
+            serializer.write(document, lsOutput);
+        }
 
         // abort the context, as we shouldn't have changed it!!
         context.abort();
     }
 
     /**
-     * Serialize the schema registry. If the parameter 'schema' is null or empty, save all schemas
+     * Compose the schema registry. If the parameter 'schema' is null or empty, save all schemas.
      *
      * @param context       DSpace Context
-     * @param xmlSerializer XML serializer
+     * @param document      the document being built
      * @param schema        schema (may be null to save all)
      * @throws SQLException            if database error
-     * @throws SAXException            if XML error
      * @throws RegistryExportException if export error
      */
-    public static void saveSchema(Context context, XMLSerializer xmlSerializer, String schema)
-        throws SQLException, SAXException, RegistryExportException {
+    public static void saveSchema(Context context, Document document, String schema)
+        throws SQLException, RegistryExportException {
         if (schema != null && !"".equals(schema)) {
             // Find a single named schema
             MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
 
-            saveSchema(xmlSerializer, mdSchema);
+            saveSchema(document, mdSchema);
         } else {
             // Find all schemas
             List<MetadataSchema> mdSchemas = metadataSchemaService.findAll(context);
 
             for (MetadataSchema mdSchema : mdSchemas) {
-                saveSchema(xmlSerializer, mdSchema);
+                saveSchema(document, mdSchema);
             }
         }
     }
 
     /**
-     * Serialize a single schema (namespace) registry entry
+     * Compose a single schema (namespace) registry entry
      *
-     * @param xmlSerializer XML serializer
-     * @param mdSchema      DSpace metadata schema
-     * @throws SAXException            if XML error
+     * @param document the output document being built.
+     * @param mdSchema DSpace metadata schema
      * @throws RegistryExportException if export error
      */
-    private static void saveSchema(XMLSerializer xmlSerializer, MetadataSchema mdSchema)
-        throws SAXException, RegistryExportException {
+    private static void saveSchema(Document document, MetadataSchema mdSchema)
+        throws RegistryExportException {
         // If we haven't got a schema, it's an error
         if (mdSchema == null) {
             throw new RegistryExportException("no schema to export");
@@ -206,35 +221,34 @@ public class MetadataExporter {
             return;
         }
 
-        // Output the parent tag
-        xmlSerializer.startElement("dc-schema", null);
+        Element document_element = document.getDocumentElement();
 
-        // Output the schema name
-        xmlSerializer.startElement("name", null);
-        xmlSerializer.characters(name.toCharArray(), 0, name.length());
-        xmlSerializer.endElement("name");
+        // Compose the parent tag
+        Element schema_element = document.createElement("dc-schema");
+        document_element.appendChild(schema_element);
 
-        // Output the schema namespace
-        xmlSerializer.startElement("namespace", null);
-        xmlSerializer.characters(namespace.toCharArray(), 0, namespace.length());
-        xmlSerializer.endElement("namespace");
+        // Compose the schema name
+        Element name_element = document.createElement("name");
+        schema_element.appendChild(name_element);
+        name_element.setTextContent(name);
 
-        xmlSerializer.endElement("dc-schema");
+        // Compose the schema namespace
+        Element namespace_element = document.createElement("namespace");
+        schema_element.appendChild(namespace_element);
+        namespace_element.setTextContent(namespace);
     }
 
     /**
-     * Serialize a single metadata field registry entry to xml
+     * Compose a single metadata field registry entry to XML.
      *
      * @param context       DSpace context
-     * @param xmlSerializer xml serializer
+     * @param document      the output document being built.
      * @param mdField       DSpace metadata field
-     * @throws SAXException            if XML error
      * @throws RegistryExportException if export error
      * @throws SQLException            if database error
-     * @throws IOException             if IO error
      */
-    private static void saveType(Context context, XMLSerializer xmlSerializer, MetadataField mdField)
-        throws SAXException, RegistryExportException, SQLException, IOException {
+    private static void saveType(Context context, Document document, MetadataField mdField)
+        throws RegistryExportException, SQLException {
         // If we haven't been given a field, it's an error
         if (mdField == null) {
             throw new RegistryExportException("no field to export");
@@ -251,38 +265,39 @@ public class MetadataExporter {
             throw new RegistryExportException("incomplete field information");
         }
 
-        // Output the parent tag
-        xmlSerializer.startElement("dc-type", null);
+        Element document_element = document.getDocumentElement();
 
-        // Output the schema name
-        xmlSerializer.startElement("schema", null);
-        xmlSerializer.characters(schemaName.toCharArray(), 0, schemaName.length());
-        xmlSerializer.endElement("schema");
+        // Compose the parent tag
+        Element dc_type = document.createElement("dc-type");
+        document_element.appendChild(dc_type);
 
-        // Output the element
-        xmlSerializer.startElement("element", null);
-        xmlSerializer.characters(element.toCharArray(), 0, element.length());
-        xmlSerializer.endElement("element");
+        // Compose the schema name
+        Element schema_element = document.createElement("schema");
+        dc_type.appendChild(schema_element);
+        schema_element.setTextContent(schemaName);
 
-        // Output the qualifier, if present
+        // Compose the element
+        Element element_element = document.createElement("element");
+        dc_type.appendChild(element_element);
+        element_element.setTextContent(element);
+
+        // Compose the qualifier, if present
         if (qualifier != null) {
-            xmlSerializer.startElement("qualifier", null);
-            xmlSerializer.characters(qualifier.toCharArray(), 0, qualifier.length());
-            xmlSerializer.endElement("qualifier");
+            Element qualifier_element = document.createElement("qualifier");
+            dc_type.appendChild(qualifier_element);
+            qualifier_element.setTextContent(qualifier);
         } else {
-            xmlSerializer.comment("unqualified");
+            dc_type.appendChild(document.createComment("unqualified"));
         }
 
-        // Output the scope note, if present
+        // Compose the scope note, if present
         if (scopeNote != null) {
-            xmlSerializer.startElement("scope_note", null);
-            xmlSerializer.characters(scopeNote.toCharArray(), 0, scopeNote.length());
-            xmlSerializer.endElement("scope_note");
+            Element scope_element = document.createElement("scope_note");
+            dc_type.appendChild(scope_element);
+            scope_element.setTextContent(scopeNote);
         } else {
-            xmlSerializer.comment("no scope note");
+            dc_type.appendChild(document.createComment("no scope note"));
         }
-
-        xmlSerializer.endElement("dc-type");
     }
 
     static Map<Integer, String> schemaMap = new HashMap<Integer, String>();
@@ -317,7 +332,7 @@ public class MetadataExporter {
     }
 
     /**
-     * Print the usage message to stdout
+     * Print the usage message to standard output
      */
     public static void usage() {
         String usage = "Use this class with the following options:\n" +

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

@@ -14,9 +14,9 @@ import javax.xml.transform.TransformerException;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
 import org.apache.xpath.XPathAPI;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
@@ -94,7 +94,7 @@ public class MetadataImporter {
         boolean forceUpdate = false;
 
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = new Options();
         options.addOption("f", "file", true, "source xml file for DC fields");
         options.addOption("u", "update", false, "update an existing schema");

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

@@ -7,6 +7,14 @@
  */
 package org.dspace.administer;
 
+import static org.dspace.content.service.DSpaceObjectService.MD_COPYRIGHT_TEXT;
+import static org.dspace.content.service.DSpaceObjectService.MD_INTRODUCTORY_TEXT;
+import static org.dspace.content.service.DSpaceObjectService.MD_LICENSE;
+import static org.dspace.content.service.DSpaceObjectService.MD_NAME;
+import static org.dspace.content.service.DSpaceObjectService.MD_PROVENANCE_DESCRIPTION;
+import static org.dspace.content.service.DSpaceObjectService.MD_SHORT_DESCRIPTION;
+import static org.dspace.content.service.DSpaceObjectService.MD_SIDEBAR_TEXT;
+
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -35,6 +43,7 @@ import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
+import org.dspace.content.MetadataFieldName;
 import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
@@ -88,12 +97,12 @@ public class StructBuilder {
     /**
      * A table to hold metadata for the collection being worked on.
      */
-    private static final Map<String, String> collectionMap = new HashMap<>();
+    private static final Map<String, MetadataFieldName> collectionMap = new HashMap<>();
 
     /**
      * A table to hold metadata for the community being worked on.
      */
-    private static final Map<String, String> communityMap = new HashMap<>();
+    private static final Map<String, MetadataFieldName> communityMap = new HashMap<>();
 
     protected static CommunityService communityService
             = ContentServiceFactory.getInstance().getCommunityService();
@@ -261,19 +270,19 @@ public class StructBuilder {
         }
 
         // load the mappings into the member variable hashmaps
-        communityMap.put("name", "name");
-        communityMap.put("description", "short_description");
-        communityMap.put("intro", "introductory_text");
-        communityMap.put("copyright", "copyright_text");
-        communityMap.put("sidebar", "side_bar_text");
+        communityMap.put("name", MD_NAME);
+        communityMap.put("description", MD_SHORT_DESCRIPTION);
+        communityMap.put("intro", MD_INTRODUCTORY_TEXT);
+        communityMap.put("copyright", MD_COPYRIGHT_TEXT);
+        communityMap.put("sidebar", MD_SIDEBAR_TEXT);
 
-        collectionMap.put("name", "name");
-        collectionMap.put("description", "short_description");
-        collectionMap.put("intro", "introductory_text");
-        collectionMap.put("copyright", "copyright_text");
-        collectionMap.put("sidebar", "side_bar_text");
-        collectionMap.put("license", "license");
-        collectionMap.put("provenance", "provenance_description");
+        collectionMap.put("name", MD_NAME);
+        collectionMap.put("description", MD_SHORT_DESCRIPTION);
+        collectionMap.put("intro", MD_INTRODUCTORY_TEXT);
+        collectionMap.put("copyright", MD_COPYRIGHT_TEXT);
+        collectionMap.put("sidebar", MD_SIDEBAR_TEXT);
+        collectionMap.put("license", MD_LICENSE);
+        collectionMap.put("provenance", MD_PROVENANCE_DESCRIPTION);
 
         Element[] elements = new Element[]{};
         try {
@@ -619,14 +628,16 @@ public class StructBuilder {
             }
 
             // default the short description to be an empty string
-            communityService.setMetadata(context, community, "short_description", " ");
+            communityService.setMetadataSingleValue(context, community,
+                    MD_SHORT_DESCRIPTION, null, " ");
 
             // now update the metadata
             Node tn = communities.item(i);
-            for (Map.Entry<String, String> entry : communityMap.entrySet()) {
+            for (Map.Entry<String, MetadataFieldName> entry : communityMap.entrySet()) {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
                 if (nl.getLength() == 1) {
-                    communityService.setMetadata(context, community, entry.getValue(), getStringValue(nl.item(0)));
+                    communityService.setMetadataSingleValue(context, community,
+                            entry.getValue(), null, getStringValue(nl.item(0)));
                 }
             }
 
@@ -650,30 +661,41 @@ public class StructBuilder {
             element.setAttribute("identifier", community.getHandle());
 
             Element nameElement = new Element("name");
-            nameElement.setText(communityService.getMetadata(community, "name"));
+            nameElement.setText(communityService.getMetadataFirstValue(
+                    community, CommunityService.MD_NAME, Item.ANY));
             element.addContent(nameElement);
 
-            if (communityService.getMetadata(community, "short_description") != null) {
+            String fieldValue;
+
+            fieldValue = communityService.getMetadataFirstValue(community,
+                    CommunityService.MD_SHORT_DESCRIPTION, Item.ANY);
+            if (fieldValue != null) {
                 Element descriptionElement = new Element("description");
-                descriptionElement.setText(communityService.getMetadata(community, "short_description"));
+                descriptionElement.setText(fieldValue);
                 element.addContent(descriptionElement);
             }
 
-            if (communityService.getMetadata(community, "introductory_text") != null) {
+            fieldValue = communityService.getMetadataFirstValue(community,
+                    CommunityService.MD_INTRODUCTORY_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element introElement = new Element("intro");
-                introElement.setText(communityService.getMetadata(community, "introductory_text"));
+                introElement.setText(fieldValue);
                 element.addContent(introElement);
             }
 
-            if (communityService.getMetadata(community, "copyright_text") != null) {
+            fieldValue = communityService.getMetadataFirstValue(community,
+                    CommunityService.MD_COPYRIGHT_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(communityService.getMetadata(community, "copyright_text"));
+                copyrightElement.setText(fieldValue);
                 element.addContent(copyrightElement);
             }
 
-            if (communityService.getMetadata(community, "side_bar_text") != null) {
+            fieldValue = communityService.getMetadataFirstValue(community,
+                    CommunityService.MD_SIDEBAR_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(communityService.getMetadata(community, "side_bar_text"));
+                sidebarElement.setText(fieldValue);
                 element.addContent(sidebarElement);
             }
 
@@ -717,14 +739,16 @@ public class StructBuilder {
             Collection collection = collectionService.create(context, parent);
 
             // default the short description to the empty string
-            collectionService.setMetadata(context, collection, "short_description", " ");
+            collectionService.setMetadataSingleValue(context, collection,
+                    MD_SHORT_DESCRIPTION, Item.ANY, " ");
 
             // import the rest of the metadata
             Node tn = collections.item(i);
-            for (Map.Entry<String, String> entry : collectionMap.entrySet()) {
+            for (Map.Entry<String, MetadataFieldName> entry : collectionMap.entrySet()) {
                 NodeList nl = XPathAPI.selectNodeList(tn, entry.getKey());
                 if (nl.getLength() == 1) {
-                    collectionService.setMetadata(context, collection, entry.getValue(), getStringValue(nl.item(0)));
+                    collectionService.setMetadataSingleValue(context, collection,
+                            entry.getValue(), null, getStringValue(nl.item(0)));
                 }
             }
 
@@ -733,42 +757,57 @@ public class StructBuilder {
             element.setAttribute("identifier", collection.getHandle());
 
             Element nameElement = new Element("name");
-            nameElement.setText(collectionService.getMetadata(collection, "name"));
+            nameElement.setText(collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_NAME, Item.ANY));
             element.addContent(nameElement);
 
-            if (collectionService.getMetadata(collection, "short_description") != null) {
+            String fieldValue;
+
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_SHORT_DESCRIPTION, Item.ANY);
+            if (fieldValue != null) {
                 Element descriptionElement = new Element("description");
-                descriptionElement.setText(collectionService.getMetadata(collection, "short_description"));
+                descriptionElement.setText(fieldValue);
                 element.addContent(descriptionElement);
             }
 
-            if (collectionService.getMetadata(collection, "introductory_text") != null) {
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_INTRODUCTORY_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element introElement = new Element("intro");
-                introElement.setText(collectionService.getMetadata(collection, "introductory_text"));
+                introElement.setText(fieldValue);
                 element.addContent(introElement);
             }
 
-            if (collectionService.getMetadata(collection, "copyright_text") != null) {
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_COPYRIGHT_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element copyrightElement = new Element("copyright");
-                copyrightElement.setText(collectionService.getMetadata(collection, "copyright_text"));
+                copyrightElement.setText(fieldValue);
                 element.addContent(copyrightElement);
             }
 
-            if (collectionService.getMetadata(collection, "side_bar_text") != null) {
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_SIDEBAR_TEXT, Item.ANY);
+            if (fieldValue != null) {
                 Element sidebarElement = new Element("sidebar");
-                sidebarElement.setText(collectionService.getMetadata(collection, "side_bar_text"));
+                sidebarElement.setText(fieldValue);
                 element.addContent(sidebarElement);
             }
 
-            if (collectionService.getMetadata(collection, "license") != null) {
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_LICENSE, Item.ANY);
+            if (fieldValue != null) {
                 Element sidebarElement = new Element("license");
-                sidebarElement.setText(collectionService.getMetadata(collection, "license"));
+                sidebarElement.setText(fieldValue);
                 element.addContent(sidebarElement);
             }
 
-            if (collectionService.getMetadata(collection, "provenance_description") != null) {
+            fieldValue = collectionService.getMetadataFirstValue(collection,
+                    CollectionService.MD_PROVENANCE_DESCRIPTION, Item.ANY);
+            if (fieldValue != null) {
                 Element sidebarElement = new Element("provenance");
-                sidebarElement.setText(collectionService.getMetadata(collection, "provenance_description"));
+                sidebarElement.setText(fieldValue);
                 element.addContent(sidebarElement);
             }
 
@@ -777,5 +816,4 @@ public class StructBuilder {
 
         return elements;
     }
-
 }

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

@@ -175,11 +175,14 @@ public class DSpaceCSV implements Serializable {
                     headings.add(element);
                 } else if (!"id".equals(element)) {
                     String authorityPrefix = "";
-                    AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
-                    if (authorityValueType != null) {
-                        String authorityType = authorityValueType.getAuthorityType();
-                        authorityPrefix = element.substring(0, authorityType.length() + 1);
-                        element = element.substring(authorityPrefix.length());
+                    if (StringUtils.startsWith(element, "[authority]")) {
+                        element = StringUtils.substringAfter(element, "[authority]");
+                        AuthorityValue authorityValueType = authorityValueService.getAuthorityValueType(element);
+                        if (authorityValueType != null) {
+                            String authorityType = authorityValueType.getAuthorityType();
+                            authorityPrefix = element.substring(0, authorityType.length() + 1);
+                            element = element.substring(authorityPrefix.length());
+                        }
                     }
 
                     // Verify that the heading is valid in the metadata registry
@@ -303,7 +306,7 @@ public class DSpaceCSV implements Serializable {
         // Specify default values
         String[] defaultValues =
             new String[] {
-                "dc.date.accessioned, dc.date.available, dc.date.updated, dc.description.provenance"
+                "dc.date.accessioned", "dc.date.available", "dc.date.updated", "dc.description.provenance"
             };
         String[] toIgnoreArray =
             DSpaceServicesFactory.getInstance()

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

@@ -10,10 +10,14 @@ package org.dspace.app.bulkedit;
 import java.sql.SQLException;
 
 import org.apache.commons.cli.ParseException;
+import org.apache.commons.lang3.StringUtils;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataDSpaceCsvExportService;
 import org.dspace.core.Context;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
+import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.scripts.DSpaceRunnable;
 import org.dspace.utils.DSpace;
 
@@ -41,8 +45,7 @@ public class MetadataExport extends DSpaceRunnable<MetadataExportScriptConfigura
     public void internalRun() throws Exception {
 
         if (help) {
-            handler.logInfo("\nfull export: metadata-export -f filename");
-            handler.logInfo("partial export: metadata-export -i handle -f filename");
+            logHelpInfo();
             printHelp();
             return;
         }
@@ -61,6 +64,11 @@ public class MetadataExport extends DSpaceRunnable<MetadataExportScriptConfigura
         context.complete();
     }
 
+    protected void logHelpInfo() {
+        handler.logInfo("\nfull export: metadata-export");
+        handler.logInfo("partial export: metadata-export -i handle");
+    }
+
     @Override
     public MetadataExportScriptConfiguration getScriptConfiguration() {
         return new DSpace().getServiceManager().getServiceByName("metadata-export",
@@ -75,17 +83,32 @@ public class MetadataExport extends DSpaceRunnable<MetadataExportScriptConfigura
             return;
         }
 
-        // Check a filename is given
-        if (!commandLine.hasOption('f')) {
-            throw new ParseException("Required parameter -f missing!");
-        }
-        filename = commandLine.getOptionValue('f');
-
-        exportAllMetadata = commandLine.hasOption('a');
-
         if (!commandLine.hasOption('i')) {
             exportAllItems = true;
         }
         handle = commandLine.getOptionValue('i');
+        filename = getFileNameForExportFile();
+
+        exportAllMetadata = commandLine.hasOption('a');
+
+    }
+
+    protected String getFileNameForExportFile() throws ParseException {
+        Context context = new Context();
+        try {
+            DSpaceObject dso = null;
+            if (StringUtils.isNotBlank(handle)) {
+                dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, handle);
+            } else {
+                dso = ContentServiceFactory.getInstance().getSiteService().findSite(context);
+            }
+            if (dso == null) {
+                throw new ParseException("A handle got given that wasn't able to be parsed to a DSpaceObject");
+            }
+            return dso.getID().toString() + ".csv";
+        } catch (SQLException e) {
+            handler.handleException("Something went wrong trying to retrieve DSO for handle: " + handle, e);
+        }
+        return null;
     }
 }

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

@@ -0,0 +1,33 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.bulkedit;
+
+import org.apache.commons.cli.ParseException;
+
+public class MetadataExportCli extends MetadataExport {
+
+    @Override
+    protected String getFileNameForExportFile() {
+        return commandLine.getOptionValue('f');
+    }
+
+    @Override
+    public void setup() throws ParseException {
+        super.setup();
+        // Check a filename is given
+        if (!commandLine.hasOption('f')) {
+            throw new ParseException("Required parameter -f missing!");
+        }
+    }
+
+    @Override
+    protected void logHelpInfo() {
+        handler.logInfo("\nfull export: metadata-export -f filename");
+        handler.logInfo("partial export: metadata-export -i handle -f filename");
+    }
+}

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

@@ -0,0 +1,26 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.bulkedit;
+
+import java.io.OutputStream;
+
+import org.apache.commons.cli.Options;
+
+public class MetadataExportCliScriptConfiguration extends MetadataExportScriptConfiguration<MetadataExportCli> {
+
+
+    @Override
+    public Options getOptions() {
+        Options options = super.getOptions();
+        options.addOption("f", "file", true, "destination where you want file written");
+        options.getOption("f").setType(OutputStream .class);
+        options.getOption("f").setRequired(true);
+        super.options = options;
+        return options;
+    }
+}

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

@@ -7,7 +7,6 @@
  */
 package org.dspace.app.bulkedit;
 
-import java.io.OutputStream;
 import java.sql.SQLException;
 
 import org.apache.commons.cli.Options;
@@ -56,9 +55,6 @@ public class MetadataExportScriptConfiguration<T extends MetadataExport> extends
 
             options.addOption("i", "id", true, "ID or handle of thing to export (item, collection, or community)");
             options.getOption("i").setType(String.class);
-            options.addOption("f", "file", true, "destination where you want file written");
-            options.getOption("f").setType(OutputStream.class);
-            options.getOption("f").setRequired(true);
             options.addOption("a", "all", false,
                               "include all metadata fields that are not normally changed (e.g. provenance)");
             options.getOption("a").setType(boolean.class);

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

@@ -51,7 +51,6 @@ import org.dspace.content.service.MetadataValueService;
 import org.dspace.content.service.RelationshipService;
 import org.dspace.content.service.RelationshipTypeService;
 import org.dspace.content.service.WorkspaceItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
@@ -61,6 +60,8 @@ import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
 import org.dspace.scripts.DSpaceRunnable;
 import org.dspace.scripts.handler.DSpaceRunnableHandler;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.dspace.utils.DSpace;
 import org.dspace.workflow.WorkflowException;
 import org.dspace.workflow.WorkflowItem;
@@ -113,14 +114,14 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
      *
      * @see #populateRefAndRowMap(DSpaceCSVLine, UUID)
      */
-    protected static HashMap<UUID, String> entityTypeMap = new HashMap<>();
+    protected HashMap<UUID, String> entityTypeMap = new HashMap<>();
 
     /**
-     * Map of UUIDs to their relations that are referenced within any import with their referers.
+     * Map of UUIDs to their relations that are referenced within any import with their referrers.
      *
      * @see #populateEntityRelationMap(String, String, String)
      */
-    protected static HashMap<String, HashMap<String, ArrayList<String>>> entityRelationMap = new HashMap<>();
+    protected HashMap<String, HashMap<String, ArrayList<String>>> entityRelationMap = new HashMap<>();
 
 
     /**
@@ -129,7 +130,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
     protected ArrayList<String> relationValidationErrors = new ArrayList<>();
 
     /**
-     * Counter of rows proccssed in a CSV.
+     * Counter of rows processed in a CSV.
      */
     protected Integer rowCount = 1;
 
@@ -158,6 +159,8 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
     protected EntityService entityService = ContentServiceFactory.getInstance().getEntityService();
     protected AuthorityValueService authorityValueService = AuthorityServiceFactory.getInstance()
                                                                                    .getAuthorityValueService();
+    protected ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
     /**
      * Create an instance of the metadata importer. Requires a context and an array of CSV lines
@@ -182,24 +185,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
         c.turnOffAuthorisationSystem();
 
         // Find the EPerson, assign to context
-        try {
-            if (commandLine.hasOption('e')) {
-                EPerson eperson;
-                String e = commandLine.getOptionValue('e');
-                if (e.indexOf('@') != -1) {
-                    eperson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(c, e);
-                } else {
-                    eperson = EPersonServiceFactory.getInstance().getEPersonService().find(c, UUID.fromString(e));
-                }
-
-                if (eperson == null) {
-                    throw new ParseException("Error, eperson cannot be found: " + e);
-                }
-                c.setCurrentUser(eperson);
-            }
-        } catch (Exception e) {
-            throw new ParseException("Unable to find DSpace user: " + e.getMessage());
-        }
+        assignCurrentUserInContext(c);
 
         if (authorityControlled == null) {
             setAuthorizedMetadataFields();
@@ -277,6 +263,18 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
 
     }
 
+    protected void assignCurrentUserInContext(Context context) throws ParseException {
+        UUID uuid = getEpersonIdentifier();
+        if (uuid != null) {
+            try {
+                EPerson ePerson = EPersonServiceFactory.getInstance().getEPersonService().find(context, uuid);
+                context.setCurrentUser(ePerson);
+            } catch (SQLException e) {
+                log.error("Something went wrong trying to fetch the eperson for uuid: " + uuid, e);
+            }
+        }
+    }
+
     /**
      * This method determines whether the changes should be applied or not. This is default set to true for the REST
      * script as we don't want to interact with the caller. This will be overwritten in the CLI script to ask for
@@ -312,9 +310,6 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
             throw new ParseException("Required parameter -f missing!");
         }
         filename = commandLine.getOptionValue('f');
-        if (!commandLine.hasOption('e')) {
-            throw new ParseException("Required parameter -e missing!");
-        }
 
         // Option to apply template to new items
         if (commandLine.hasOption('t')) {
@@ -427,7 +422,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                         // Do nothing
                     } else if ("expunge".equals(action)) {
                         // Does the configuration allow deletes?
-                        if (!ConfigurationManager.getBooleanProperty("bulkedit", "allowexpunge", false)) {
+                        if (!configurationService.getBooleanProperty("bulkedit.allowexpunge", false)) {
                             throw new MetadataImportException("'expunge' action denied by configuration");
                         }
 
@@ -1376,12 +1371,12 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
      * Set authority controlled fields
      */
     private void setAuthorizedMetadataFields() {
-        authorityControlled = new HashSet<String>();
-        Enumeration propertyNames = ConfigurationManager.getProperties().propertyNames();
+        authorityControlled = new HashSet<>();
+        Enumeration propertyNames = configurationService.getProperties().propertyNames();
         while (propertyNames.hasMoreElements()) {
             String key = ((String) propertyNames.nextElement()).trim();
             if (key.startsWith(AC_PREFIX)
-                && ConfigurationManager.getBooleanProperty(key, false)) {
+                && configurationService.getBooleanProperty(key, false)) {
                 authorityControlled.add(key.substring(AC_PREFIX.length()));
             }
         }
@@ -1411,16 +1406,16 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                         //Populate the EntityRelationMap
                         populateEntityRelationMap(uuid, key, originId.toString());
                     }
+                } else {
+                    newLine.add(key, null);
                 }
             } else {
-                if (line.get(key).size() > 1) {
+                if (line.get(key).size() > 0) {
                     for (String value : line.get(key)) {
                         newLine.add(key, value);
                     }
                 } else {
-                    if (line.get(key).size() > 0) {
-                        newLine.add(key, line.get(key).get(0));
-                    }
+                    newLine.add(key, null);
                 }
             }
         }
@@ -1525,6 +1520,9 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                 throw new MetadataImportException("Error in CSV row " + rowCount + ":\n" +
                                                       "Not a UUID or indirect entity reference: '" + reference + "'");
             }
+        }
+        if (reference.contains("::virtual::")) {
+            return UUID.fromString(StringUtils.substringBefore(reference, "::virtual::"));
         } else if (!reference.startsWith("rowName:")) { // Not a rowName ref; so it's a metadata value reference
             MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
             MetadataFieldService metadataFieldService =
@@ -1696,19 +1694,39 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                             // Add to errors if Realtionship.type cannot be derived.
                             Item originItem = null;
                             if (itemService.find(c, UUID.fromString(targetUUID)) != null) {
-                                originItem = itemService.find(c, UUID.fromString(originRefererUUID));
-                                List<MetadataValue> relTypes = itemService.
-                                                                              getMetadata(originItem, "relationship",
-                                                                                          "type", null, Item.ANY);
-                                String relTypeValue = null;
-                                if (relTypes.size() > 0) {
-                                    relTypeValue = relTypes.get(0).getValue();
+                                DSpaceCSVLine dSpaceCSVLine = this.csv.getCSVLines()
+                                                                      .get(Integer.valueOf(originRow) - 1);
+                                List<String> relTypes = dSpaceCSVLine.get("relationship.type");
+                                if (relTypes == null || relTypes.isEmpty()) {
+                                    dSpaceCSVLine.get("relationship.type[]");
+                                }
+
+                                if (relTypes != null && relTypes.size() > 0) {
+                                    String relTypeValue = relTypes.get(0);
+                                    relTypeValue = StringUtils.remove(relTypeValue, "\"").trim();
                                     originType = entityTypeService.findByEntityType(c, relTypeValue).getLabel();
                                     validateTypesByTypeByTypeName(c, targetType, originType, typeName, originRow);
                                 } else {
-                                    relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
-                                                                     "Cannot resolve Entity type for reference: "
-                                                                     + originRefererUUID);
+                                    originItem = itemService.find(c, UUID.fromString(originRefererUUID));
+                                    if (originItem != null) {
+                                        List<MetadataValue> mdv = itemService.getMetadata(originItem,
+                                                                                          "relationship",
+                                                                                          "type", null,
+                                                                                          Item.ANY);
+                                        if (!mdv.isEmpty()) {
+                                            String relTypeValue = mdv.get(0).getValue();
+                                            originType = entityTypeService.findByEntityType(c, relTypeValue).getLabel();
+                                            validateTypesByTypeByTypeName(c, targetType, originType, typeName,
+                                                                          originRow);
+                                        } else {
+                                            relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
+                                                     "Cannot resolve Entity type for reference: " + originRefererUUID);
+                                        }
+                                    } else {
+                                        relationValidationErrors.add("Error on CSV row " + originRow + ":" + "\n" +
+                                                                         "Cannot resolve Entity type for reference: "
+                                                                         + originRefererUUID);
+                                    }
                                 }
 
                             } else {
@@ -1735,11 +1753,11 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
     }
 
     /**
-     * Generates a list of potenital Relationship Types given a typeName and attempts to match the given
+     * Generates a list of potential Relationship Types given a typeName and attempts to match the given
      * targetType and originType to a Relationship Type in the list.
      *
      * @param targetType entity type of target.
-     * @param originType entity type of origin referer.
+     * @param originType entity type of origin referrer.
      * @param typeName left or right typeName of the respective Relationship.
      * @return the UUID of the item.
      */

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

@@ -10,7 +10,12 @@ package org.dspace.app.bulkedit;
 import java.io.BufferedReader;
 import java.io.IOException;
 import java.io.InputStreamReader;
+import java.util.UUID;
 
+import org.apache.commons.cli.ParseException;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.scripts.handler.DSpaceRunnableHandler;
 
 /**
@@ -30,4 +35,34 @@ public class MetadataImportCLI extends MetadataImport {
             return false;
         }
     }
+
+    @Override
+    protected void assignCurrentUserInContext(Context context) throws ParseException {
+        try {
+            if (commandLine.hasOption('e')) {
+                EPerson eperson;
+                String e = commandLine.getOptionValue('e');
+                if (e.indexOf('@') != -1) {
+                    eperson = EPersonServiceFactory.getInstance().getEPersonService().findByEmail(context, e);
+                } else {
+                    eperson = EPersonServiceFactory.getInstance().getEPersonService().find(context, UUID.fromString(e));
+                }
+
+                if (eperson == null) {
+                    throw new ParseException("Error, eperson cannot be found: " + e);
+                }
+                context.setCurrentUser(eperson);
+            }
+        } catch (Exception e) {
+            throw new ParseException("Unable to find DSpace user: " + e.getMessage());
+        }
+    }
+
+    @Override
+    public void setup() throws ParseException {
+        super.setup();
+        if (!commandLine.hasOption('e')) {
+            throw new ParseException("Required parameter -e missing!");
+        }
+    }
 }

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

@@ -7,10 +7,21 @@
  */
 package org.dspace.app.bulkedit;
 
+import org.apache.commons.cli.Options;
 import org.dspace.scripts.configuration.ScriptConfiguration;
 
 /**
  * The {@link ScriptConfiguration} for the {@link org.dspace.app.bulkedit.MetadataImportCLI} CLI script
  */
 public class MetadataImportCliScriptConfiguration extends MetadataImportScriptConfiguration<MetadataImportCLI> {
+
+    @Override
+    public Options getOptions() {
+        Options options = super.getOptions();
+        options.addOption("e", "email", true, "email address or user id of user (required if adding new items)");
+        options.getOption("e").setType(String.class);
+        options.getOption("e").setRequired(true);
+        super.options = options;
+        return options;
+    }
 }

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

@@ -57,9 +57,6 @@ public class MetadataImportScriptConfiguration<T extends MetadataImport> extends
             options.addOption("f", "file", true, "source file");
             options.getOption("f").setType(InputStream.class);
             options.getOption("f").setRequired(true);
-            options.addOption("e", "email", true, "email address or user id of user (required if adding new items)");
-            options.getOption("e").setType(String.class);
-            options.getOption("e").setRequired(true);
             options.addOption("s", "silent", false,
                               "silent operation - doesn't request confirmation of changes USE WITH CAUTION");
             options.getOption("s").setType(boolean.class);

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

@@ -17,12 +17,11 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.checker.BitstreamDispatcher;
@@ -87,7 +86,7 @@ public final class ChecksumChecker {
      */
     public static void main(String[] args) throws SQLException {
         // set up command line parser
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         CommandLine line = null;
 
         // create an options object and populate it
@@ -102,19 +101,21 @@ public final class ChecksumChecker {
         options.addOption("a", "handle", true, "Specify a handle to check");
         options.addOption("v", "verbose", false, "Report all processing");
 
-        OptionBuilder.withArgName("bitstream-ids").hasArgs().withDescription(
-            "Space separated list of bitstream ids");
-        Option useBitstreamIds = OptionBuilder.create('b');
+        Option option;
 
-        options.addOption(useBitstreamIds);
+        option = Option.builder("b")
+                .longOpt("bitstream-ids")
+                .hasArgs()
+                .desc("Space separated list of bitstream ids")
+                .build();
+        options.addOption(option);
 
-        options.addOption("p", "prune", false, "Prune configuration file");
-        options.addOption(OptionBuilder
-                              .withArgName("prune")
-                              .hasOptionalArgs(1)
-                              .withDescription(
-                                  "Prune old results (optionally using specified properties file for configuration)")
-                              .create('p'));
+        option = Option.builder("p")
+                .longOpt("prune")
+                .optionalArg(true)
+                .desc("Prune old results (optionally using specified properties file for configuration)")
+                .build();
+        options.addOption(option);
 
         try {
             line = parser.parse(options, args);

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

@@ -15,9 +15,9 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
@@ -53,7 +53,7 @@ public class Harvest {
 
     public static void main(String[] argv) throws Exception {
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 
@@ -402,11 +402,7 @@ public class Harvest {
             context.setCurrentUser(eperson);
             harvester.runHarvest();
             context.complete();
-        } catch (SQLException e) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        } catch (AuthorizeException e) {
-            throw new IllegalStateException("Failed to run harvester", e);
-        } catch (IOException e) {
+        } catch (SQLException | AuthorizeException | IOException e) {
             throw new IllegalStateException("Failed to run harvester", e);
         }
 

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

@@ -15,9 +15,9 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.dspace.app.itemexport.factory.ItemExportServiceFactory;
 import org.dspace.app.itemexport.service.ItemExportService;
 import org.dspace.content.Collection;
@@ -69,7 +69,7 @@ public class ItemExportCLITool {
      */
     public static void main(String[] argv) throws Exception {
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 

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

@@ -47,7 +47,6 @@ import org.dspace.content.MetadataValue;
 import org.dspace.content.service.BitstreamService;
 import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
@@ -57,6 +56,7 @@ import org.dspace.core.Utils;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.handle.service.HandleService;
+import org.dspace.services.ConfigurationService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -93,12 +93,14 @@ public class ItemExportServiceImpl implements ItemExportService {
     protected ItemService itemService;
     @Autowired(required = true)
     protected HandleService handleService;
+    @Autowired(required = true)
+    protected ConfigurationService configurationService;
 
 
     /**
      * log4j logger
      */
-    private Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemExportServiceImpl.class);
+    private final Logger log = org.apache.logging.log4j.LogManager.getLogger(ItemExportServiceImpl.class);
 
     protected ItemExportServiceImpl() {
 
@@ -605,7 +607,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
         // check the size of all the bitstreams against the configuration file
         // entry if it exists
-        String megaBytes = ConfigurationManager
+        String megaBytes = configurationService
             .getProperty("org.dspace.app.itemexport.max.size");
         if (megaBytes != null) {
             float maxSize = 0;
@@ -730,7 +732,7 @@ public class ItemExportServiceImpl implements ItemExportService {
     @Override
     public String getExportDownloadDirectory(EPerson ePerson)
         throws Exception {
-        String downloadDir = ConfigurationManager
+        String downloadDir = configurationService
             .getProperty("org.dspace.app.itemexport.download.dir");
         if (downloadDir == null) {
             throw new Exception(
@@ -747,7 +749,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
     @Override
     public String getExportWorkDirectory() throws Exception {
-        String exportDir = ConfigurationManager
+        String exportDir = configurationService
             .getProperty("org.dspace.app.itemexport.work.dir");
         if (exportDir == null) {
             throw new Exception(
@@ -853,7 +855,7 @@ public class ItemExportServiceImpl implements ItemExportService {
             return null;
         }
 
-        List<String> fileNames = new ArrayList<String>();
+        List<String> fileNames = new ArrayList<>();
 
         for (String fileName : downloadDir.list()) {
             if (fileName.contains("export") && fileName.endsWith(".zip")) {
@@ -870,7 +872,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
     @Override
     public void deleteOldExportArchives(EPerson eperson) throws Exception {
-        int hours = ConfigurationManager
+        int hours = configurationService
             .getIntProperty("org.dspace.app.itemexport.life.span.hours");
         Calendar now = Calendar.getInstance();
         now.setTime(new Date());
@@ -891,11 +893,11 @@ public class ItemExportServiceImpl implements ItemExportService {
 
     @Override
     public void deleteOldExportArchives() throws Exception {
-        int hours = ConfigurationManager.getIntProperty("org.dspace.app.itemexport.life.span.hours");
+        int hours = configurationService.getIntProperty("org.dspace.app.itemexport.life.span.hours");
         Calendar now = Calendar.getInstance();
         now.setTime(new Date());
         now.add(Calendar.HOUR, (-hours));
-        File downloadDir = new File(ConfigurationManager.getProperty("org.dspace.app.itemexport.download.dir"));
+        File downloadDir = new File(configurationService.getProperty("org.dspace.app.itemexport.download.dir"));
         if (downloadDir.exists()) {
             // Get a list of all the sub-directories, potentially one for each ePerson.
             File[] dirs = downloadDir.listFiles();
@@ -929,8 +931,8 @@ public class ItemExportServiceImpl implements ItemExportService {
             Locale supportedLocale = I18nUtil.getEPersonLocale(eperson);
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "export_success"));
             email.addRecipient(eperson.getEmail());
-            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/exportdownload/" + fileName);
-            email.addArgument(ConfigurationManager.getProperty("org.dspace.app.itemexport.life.span.hours"));
+            email.addArgument(configurationService.getProperty("dspace.ui.url") + "/exportdownload/" + fileName);
+            email.addArgument(configurationService.getProperty("org.dspace.app.itemexport.life.span.hours"));
 
             email.send();
         } catch (Exception e) {
@@ -947,7 +949,7 @@ public class ItemExportServiceImpl implements ItemExportService {
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "export_error"));
             email.addRecipient(eperson.getEmail());
             email.addArgument(error);
-            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/feedback");
+            email.addArgument(configurationService.getProperty("dspace.ui.url") + "/feedback");
 
             email.send();
         } catch (Exception e) {

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

@@ -8,6 +8,7 @@
 package org.dspace.app.itemimport;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -15,9 +16,9 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.dspace.app.itemimport.factory.ItemImportServiceFactory;
 import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.content.Collection;
@@ -67,7 +68,7 @@ public class ItemImportCLITool {
 
         try {
             // create an options object and populate it
-            CommandLineParser parser = new PosixParser();
+            CommandLineParser parser = new DefaultParser();
 
             Options options = new Options();
 
@@ -408,7 +409,7 @@ public class ItemImportCLITool {
                         "Deleting temporary zip directory: " + myloader.getTempWorkDirFile().getAbsolutePath());
                     myloader.cleanupZipTemp();
                 }
-            } catch (Exception ex) {
+            } catch (IOException ex) {
                 System.out.println("Unable to delete temporary zip archive location: " + myloader.getTempWorkDirFile()
                                                                                                  .getAbsolutePath());
             }

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

@@ -85,7 +85,6 @@ import org.dspace.content.service.ItemService;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.content.service.WorkspaceItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
@@ -96,6 +95,7 @@ import org.dspace.eperson.Group;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.eperson.service.GroupService;
 import org.dspace.handle.service.HandleService;
+import org.dspace.services.ConfigurationService;
 import org.dspace.utils.DSpace;
 import org.dspace.workflow.WorkflowItem;
 import org.dspace.workflow.WorkflowService;
@@ -157,8 +157,11 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
     protected WorkspaceItemService workspaceItemService;
     @Autowired(required = true)
     protected WorkflowService workflowService;
+    @Autowired(required = true)
+    protected ConfigurationService configurationService;
 
-    protected final String tempWorkDir = ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir");
+    protected final String tempWorkDir
+            = configurationService.getProperty("org.dspace.app.batchitemimport.work.dir");
 
     protected boolean isTest = false;
     protected boolean isResume = false;
@@ -217,7 +220,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
         //Determine the folder where BTE will output the results
         String outputFolder = null;
         if (workingDir == null) { //This indicates a command line import, create a random path
-            File importDir = new File(ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir"));
+            File importDir = new File(configurationService.getProperty("org.dspace.app.batchitemimport.work.dir"));
             if (!importDir.exists()) {
                 boolean success = importDir.mkdir();
                 if (!success) {
@@ -1481,7 +1484,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
 
         File tempdir = new File(destinationDir);
         if (!tempdir.isDirectory()) {
-            log.error("'" + ConfigurationManager.getProperty("org.dspace.app.itemexport.work.dir") +
+            log.error("'" + configurationService.getProperty("org.dspace.app.itemexport.work.dir") +
                           "' as defined by the key 'org.dspace.app.itemexport.work.dir' in dspace.cfg " +
                           "is not a valid directory");
         }
@@ -1506,60 +1509,54 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
                     log.error("Unable to create contents directory: " + zipDir + entry.getName());
                 }
             } else {
-                System.out.println("Extracting file: " + entry.getName());
-                log.info("Extracting file: " + entry.getName());
-
-                int index = entry.getName().lastIndexOf('/');
-                if (index == -1) {
-                    // Was it created on Windows instead?
-                    index = entry.getName().lastIndexOf('\\');
-                }
-                if (index > 0) {
-                    File dir = new File(zipDir + entry.getName().substring(0, index));
-                    if (!dir.exists() && !dir.mkdirs()) {
-                        log.error("Unable to create directory: " + dir.getAbsolutePath());
-                    }
-                    // Verify that the directory the entry is using is a subpath of zipDir (and not somewhere else!)
-                    if (!dir.toPath().normalize().startsWith(zipDir)) {
-                        throw new IOException("Bad zip entry: '" + entry.getName()
-                                                  + "' in file '" + zipfile.getAbsolutePath() + "'!"
-                                                  + " Cannot process this file.");
-                    }
-
-                    //Entries could have too many directories, and we need to adjust the sourcedir
-                    // file1.zip (SimpleArchiveFormat / item1 / contents|dublin_core|...
-                    //            SimpleArchiveFormat / item2 / contents|dublin_core|...
-                    // or
-                    // file2.zip (item1 / contents|dublin_core|...
-                    //            item2 / contents|dublin_core|...
-
-                    //regex supports either windows or *nix file paths
-                    String[] entryChunks = entry.getName().split("/|\\\\");
-                    if (entryChunks.length > 2) {
-                        if (StringUtils.equals(sourceDirForZip, sourcedir)) {
-                            sourceDirForZip = sourcedir + "/" + entryChunks[0];
-                        }
-                    }
-
-
-                }
-                byte[] buffer = new byte[1024];
-                int len;
-                File outFile = new File(zipDir + entry.getName());
-                // Verify that this file will be created in our zipDir (and not somewhere else!)
+                String entryName = entry.getName();
+                File outFile = new File(zipDir + entryName);
+                // Verify that this file will be extracted into our zipDir (and not somewhere else!)
                 if (!outFile.toPath().normalize().startsWith(zipDir)) {
-                    throw new IOException("Bad zip entry: '" + entry.getName()
+                    throw new IOException("Bad zip entry: '" + entryName
                                               + "' in file '" + zipfile.getAbsolutePath() + "'!"
                                               + " Cannot process this file.");
+                } else {
+                    System.out.println("Extracting file: " + entryName);
+                    log.info("Extracting file: " + entryName);
+
+                    int index = entryName.lastIndexOf('/');
+                    if (index == -1) {
+                        // Was it created on Windows instead?
+                        index = entryName.lastIndexOf('\\');
+                    }
+                    if (index > 0) {
+                        File dir = new File(zipDir + entryName.substring(0, index));
+                        if (!dir.exists() && !dir.mkdirs()) {
+                            log.error("Unable to create directory: " + dir.getAbsolutePath());
+                        }
+
+                        //Entries could have too many directories, and we need to adjust the sourcedir
+                        // file1.zip (SimpleArchiveFormat / item1 / contents|dublin_core|...
+                        //            SimpleArchiveFormat / item2 / contents|dublin_core|...
+                        // or
+                        // file2.zip (item1 / contents|dublin_core|...
+                        //            item2 / contents|dublin_core|...
+
+                        //regex supports either windows or *nix file paths
+                        String[] entryChunks = entryName.split("/|\\\\");
+                        if (entryChunks.length > 2) {
+                            if (StringUtils.equals(sourceDirForZip, sourcedir)) {
+                                sourceDirForZip = sourcedir + "/" + entryChunks[0];
+                            }
+                        }
+                    }
+                    byte[] buffer = new byte[1024];
+                    int len;
+                    InputStream in = zf.getInputStream(entry);
+                    BufferedOutputStream out = new BufferedOutputStream(
+                        new FileOutputStream(outFile));
+                    while ((len = in.read(buffer)) >= 0) {
+                        out.write(buffer, 0, len);
+                    }
+                    in.close();
+                    out.close();
                 }
-                InputStream in = zf.getInputStream(entry);
-                BufferedOutputStream out = new BufferedOutputStream(
-                    new FileOutputStream(outFile));
-                while ((len = in.read(buffer)) >= 0) {
-                    out.write(buffer, 0, len);
-                }
-                in.close();
-                out.close();
             }
         }
 
@@ -1652,7 +1649,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
                         }
                     }
 
-                    importDir = ConfigurationManager.getProperty(
+                    importDir = configurationService.getProperty(
                         "org.dspace.app.batchitemimport.work.dir") + File.separator + "batchuploads" + File.separator
                         + context
                         .getCurrentUser()
@@ -1810,7 +1807,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
             Email email = Email.getEmail(I18nUtil.getEmailFilename(supportedLocale, "bte_batch_import_error"));
             email.addRecipient(eperson.getEmail());
             email.addArgument(error);
-            email.addArgument(ConfigurationManager.getProperty("dspace.ui.url") + "/feedback");
+            email.addArgument(configurationService.getProperty("dspace.ui.url") + "/feedback");
 
             email.send();
         } catch (Exception e) {
@@ -1848,7 +1845,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
     @Override
     public String getImportUploadableDirectory(EPerson ePerson)
         throws Exception {
-        String uploadDir = ConfigurationManager.getProperty("org.dspace.app.batchitemimport.work.dir");
+        String uploadDir = configurationService.getProperty("org.dspace.app.batchitemimport.work.dir");
         if (uploadDir == null) {
             throw new Exception(
                 "A dspace.cfg entry for 'org.dspace.app.batchitemimport.work.dir' does not exist.");

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.app.itemupdate;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.Map;
@@ -20,22 +21,25 @@ import java.util.Map;
 public class ActionManager implements Iterable<UpdateAction> {
 
     protected Map<Class<? extends UpdateAction>, UpdateAction> registry
-        = new LinkedHashMap<Class<? extends UpdateAction>, UpdateAction>();
+        = new LinkedHashMap<>();
 
     /**
-     * Get update action
+     * Get update action.
      *
      * @param actionClass UpdateAction class
      * @return instantiation of UpdateAction class
      * @throws InstantiationException if instantiation error
      * @throws IllegalAccessException if illegal access error
+     * @throws NoSuchMethodException passed through.
+     * @throws InvocationTargetException passed through.
      */
     public UpdateAction getUpdateAction(Class<? extends UpdateAction> actionClass)
-        throws InstantiationException, IllegalAccessException {
+        throws InstantiationException, IllegalAccessException,
+            NoSuchMethodException, IllegalArgumentException, InvocationTargetException {
         UpdateAction action = registry.get(actionClass);
 
         if (action == null) {
-            action = actionClass.newInstance();
+            action = actionClass.getDeclaredConstructor().newInstance();
             registry.put(actionClass, action);
         }
 
@@ -58,7 +62,8 @@ public class ActionManager implements Iterable<UpdateAction> {
     @Override
     public Iterator<UpdateAction> iterator() {
         return new Iterator<UpdateAction>() {
-            private Iterator<Class<? extends UpdateAction>> itr = registry.keySet().iterator();
+            private final Iterator<Class<? extends UpdateAction>> itr
+                    = registry.keySet().iterator();
 
             @Override
             public boolean hasNext() {

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

@@ -24,10 +24,10 @@ import java.util.UUID;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
@@ -109,7 +109,7 @@ public class ItemUpdate {
 
     // instance variables
     protected ActionManager actionMgr = new ActionManager();
-    protected List<String> undoActionList = new ArrayList<String>();
+    protected List<String> undoActionList = new ArrayList<>();
     protected String eperson;
 
     /**
@@ -117,7 +117,7 @@ public class ItemUpdate {
      */
     public static void main(String[] argv) {
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         Options options = new Options();
 
@@ -275,7 +275,8 @@ public class ItemUpdate {
                         Class<?> cfilter = Class.forName(filterClassname);
                         pr("BitstreamFilter class to instantiate: " + cfilter.toString());
 
-                        filter = (BitstreamFilter) cfilter.newInstance();  //unfortunate cast, an erasure consequence
+                        filter = (BitstreamFilter) cfilter.getDeclaredConstructor()
+                                .newInstance();  //unfortunate cast, an erasure consequence
                     } catch (Exception e) {
                         pr("Error:  Failure instantiating bitstream filter class: " + filterClassname);
                         System.exit(1);

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

@@ -38,8 +38,8 @@ import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 import org.w3c.dom.NamedNodeMap;
@@ -226,7 +226,9 @@ public class MetadataUtilities {
             if (language == null) {
                 language = "en";
             } else if ("".equals(language)) {
-                language = ConfigurationManager.getProperty("default.language");
+                language = DSpaceServicesFactory.getInstance()
+                        .getConfigurationService()
+                        .getProperty("default.language");
             }
 
             DtoMetadata dtom = DtoMetadata.create(schema, element, qualifier, language, value);

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

@@ -12,7 +12,8 @@ import java.io.InputStream;
 import javax.imageio.ImageIO;
 
 import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
@@ -66,17 +67,19 @@ public class BrandedPreviewJPEGFilter extends MediaFilter {
         BufferedImage buf = ImageIO.read(source);
 
         // get config params
-        float xmax = (float) ConfigurationManager
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        float xmax = (float) configurationService
             .getIntProperty("webui.preview.maxwidth");
-        float ymax = (float) ConfigurationManager
+        float ymax = (float) configurationService
             .getIntProperty("webui.preview.maxheight");
-        boolean blurring = (boolean) ConfigurationManager
+        boolean blurring = (boolean) configurationService
             .getBooleanProperty("webui.preview.blurring");
-        boolean hqscaling = (boolean) ConfigurationManager
+        boolean hqscaling = (boolean) configurationService
             .getBooleanProperty("webui.preview.hqscaling");
-        int brandHeight = ConfigurationManager.getIntProperty("webui.preview.brand.height");
-        String brandFont = ConfigurationManager.getProperty("webui.preview.brand.font");
-        int brandFontPoint = ConfigurationManager.getIntProperty("webui.preview.brand.fontpoint");
+        int brandHeight = configurationService.getIntProperty("webui.preview.brand.height");
+        String brandFont = configurationService.getProperty("webui.preview.brand.font");
+        int brandFontPoint = configurationService.getIntProperty("webui.preview.brand.fontpoint");
 
         JPEGFilter jpegFilter = new JPEGFilter();
         return jpegFilter

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

@@ -19,8 +19,9 @@ import org.dspace.content.Bundle;
 import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.im4java.core.ConvertCmd;
 import org.im4java.core.IM4JavaException;
 import org.im4java.core.IMOperation;
@@ -33,36 +34,18 @@ import org.im4java.process.ProcessStarter;
  * no bigger than. Creates only JPEGs.
  */
 public abstract class ImageMagickThumbnailFilter extends MediaFilter {
-    protected static int width = 180;
-    protected static int height = 120;
-    private static boolean flatten = true;
-    static String bitstreamDescription = "IM Thumbnail";
-    static final String defaultPattern = "Generated Thumbnail";
-    static Pattern replaceRegex = Pattern.compile(defaultPattern);
+    private static final int DEFAULT_WIDTH = 180;
+    private static final int DEFAULT_HEIGHT = 120;
+    static final String DEFAULT_PATTERN = "Generated Thumbnail";
     protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    protected static final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
-    static String cmyk_profile;
-    static String srgb_profile;
+    protected static final String PRE = ImageMagickThumbnailFilter.class.getName();
 
     static {
-        String pre = ImageMagickThumbnailFilter.class.getName();
-        String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
+        String s = configurationService.getProperty(PRE + ".ProcessStarter");
         ProcessStarter.setGlobalSearchPath(s);
-        width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
-        height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
-        flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
-        String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
-        cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
-        srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
-        if (description != null) {
-            bitstreamDescription = description;
-        }
-        try {
-            String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
-            replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
-        } catch (PatternSyntaxException e) {
-            System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
-        }
     }
 
     public ImageMagickThumbnailFilter() {
@@ -94,7 +77,7 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
      */
     @Override
     public String getDescription() {
-        return bitstreamDescription;
+        return configurationService.getProperty(PRE + ".bitstreamDescription", "IM Thumbnail");
     }
 
     public File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
@@ -120,7 +103,8 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
         IMOperation op = new IMOperation();
         op.autoOrient();
         op.addImage(f.getAbsolutePath());
-        op.thumbnail(width, height);
+        op.thumbnail(configurationService.getIntProperty("thumbnail.maxwidth", DEFAULT_WIDTH),
+                        configurationService.getIntProperty("thumbnail.maxheight", DEFAULT_HEIGHT));
         op.addImage(f2.getAbsolutePath());
         if (verbose) {
             System.out.println("IM Thumbnail Param: " + op);
@@ -137,11 +121,14 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
         IMOperation op = new IMOperation();
         String s = "[" + page + "]";
         op.addImage(f.getAbsolutePath() + s);
-        if (flatten) {
+        if (configurationService.getBooleanProperty(PRE + ".flatten", true)) {
             op.flatten();
         }
+
         // PDFs using the CMYK color system can be handled specially if
         // profiles are defined
+        String cmyk_profile = configurationService.getProperty(PRE + ".cmyk_profile");
+        String srgb_profile = configurationService.getProperty(PRE + ".srgb_profile");
         if (cmyk_profile != null && srgb_profile != null) {
             Info imageInfo = new Info(f.getAbsolutePath() + s, true);
             String imageClass = imageInfo.getImageClass();
@@ -174,24 +161,32 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
                 String description = bit.getDescription();
                 // If anything other than a generated thumbnail
                 // is found, halt processing
+                Pattern replaceRegex;
+                try {
+                    String patt = configurationService.getProperty(PRE + ".replaceRegex", DEFAULT_PATTERN);
+                    replaceRegex = Pattern.compile(patt == null ? DEFAULT_PATTERN : patt);
+                } catch (PatternSyntaxException e) {
+                    System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
+                    throw e;
+                }
                 if (description != null) {
                     if (replaceRegex.matcher(description).matches()) {
                         if (verbose) {
-                            System.out.println(description + " " + nsrc
-                                                   + " matches pattern and is replacable.");
+                            System.out.format("%s %s matches pattern and is replacable.%n",
+                                    description, nsrc);
                         }
                         continue;
                     }
-                    if (description.equals(bitstreamDescription)) {
+                    if (description.equals(getDescription())) {
                         if (verbose) {
-                            System.out.println(bitstreamDescription + " " + nsrc
-                                                   + " is replacable.");
+                            System.out.format("%s %s is replaceable.%n",
+                                    getDescription(), nsrc);
                         }
                         continue;
                     }
                 }
-                System.out.println("Custom Thumbnail exists for " + nsrc + " for item "
-                                       + item.getHandle() + ".  Thumbnail will not be generated. ");
+                System.out.format("Custom Thumbnail exists for %s for item %s.  Thumbnail will not be generated.%n",
+                        nsrc, item.getHandle());
                 return false;
             }
         }

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

@@ -22,7 +22,8 @@ import java.io.InputStream;
 import javax.imageio.ImageIO;
 
 import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Filter image bitstreams, scaling the image to be within the bounds of
@@ -80,13 +81,15 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
     public InputStream getThumb(Item currentItem, BufferedImage buf, boolean verbose)
         throws Exception {
         // get config params
-        float xmax = (float) ConfigurationManager
+        final ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        float xmax = (float) configurationService
             .getIntProperty("thumbnail.maxwidth");
-        float ymax = (float) ConfigurationManager
+        float ymax = (float) configurationService
             .getIntProperty("thumbnail.maxheight");
-        boolean blurring = (boolean) ConfigurationManager
+        boolean blurring = (boolean) configurationService
             .getBooleanProperty("thumbnail.blurring");
-        boolean hqscaling = (boolean) ConfigurationManager
+        boolean hqscaling = (boolean) configurationService
             .getBooleanProperty("thumbnail.hqscaling");
 
         return getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, 0, 0, null);
@@ -169,9 +172,11 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);
 
         if (brandHeight != 0) {
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
             Brand brand = new Brand((int) xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
-            BufferedImage brandImage = brand.create(ConfigurationManager.getProperty("webui.preview.brand"),
-                                                    ConfigurationManager.getProperty("webui.preview.brand.abbrev"),
+            BufferedImage brandImage = brand.create(configurationService.getProperty("webui.preview.brand"),
+                                                    configurationService.getProperty("webui.preview.brand.abbrev"),
                                                     currentItem == null ? "" : "hdl:" + currentItem.getHandle());
 
             g2d.drawImage(brandImage, (int) 0, (int) ysize, (int) xsize, (int) 20, null);

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

@@ -16,12 +16,11 @@ import java.util.Map;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.MissingArgumentException;
 import org.apache.commons.cli.Option;
-import org.apache.commons.cli.OptionBuilder;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang3.ArrayUtils;
 import org.dspace.app.mediafilter.factory.MediaFilterServiceFactory;
 import org.dspace.app.mediafilter.service.MediaFilterService;
@@ -66,7 +65,7 @@ public class MediaFilterCLITool {
         System.setProperty("java.awt.headless", "true");
 
         // create an options object and populate it
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
 
         int status = 0;
 
@@ -85,26 +84,30 @@ public class MediaFilterCLITool {
         options.addOption("h", "help", false, "help");
 
         //create a "plugin" option (to specify specific MediaFilter plugins to run)
-        OptionBuilder.withLongOpt("plugins");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-            "ONLY run the specified Media Filter plugin(s)\n" +
-                "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" +
-                "Separate multiple with a comma (,)\n" +
-                "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")");
-        Option pluginOption = OptionBuilder.create('p');
-        pluginOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
+        Option pluginOption = Option.builder("p")
+                .longOpt("plugins")
+                .hasArg()
+                .hasArgs()
+                .valueSeparator(',')
+                .desc(
+                        "ONLY run the specified Media Filter plugin(s)\n" +
+                        "listed from '" + MEDIA_FILTER_PLUGINS_KEY + "' in dspace.cfg.\n" +
+                        "Separate multiple with a comma (,)\n" +
+                        "(e.g. MediaFilterManager -p \n\"Word Text Extractor\",\"PDF Text Extractor\")")
+                .build();
         options.addOption(pluginOption);
 
         //create a "skip" option (to specify communities/collections/items to skip)
-        OptionBuilder.withLongOpt("skip");
-        OptionBuilder.withValueSeparator(',');
-        OptionBuilder.withDescription(
-            "SKIP the bitstreams belonging to identifier\n" +
-                "Separate multiple identifiers with a comma (,)\n" +
-                "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)");
-        Option skipOption = OptionBuilder.create('s');
-        skipOption.setArgs(Option.UNLIMITED_VALUES); //unlimited number of args
+        Option skipOption = Option.builder("s")
+                .longOpt("skip")
+                .hasArg()
+                .hasArgs()
+                .valueSeparator(',')
+                .desc(
+                        "SKIP the bitstreams belonging to identifier\n" +
+                        "Separate multiple identifiers with a comma (,)\n" +
+                        "(e.g. MediaFilterManager -s \n 123456789/34,123456789/323)")
+                .build();
         options.addOption(skipOption);
 
         boolean isVerbose = false;
@@ -179,7 +182,7 @@ public class MediaFilterCLITool {
         mediaFilterService.setMax2Process(max2Process);
 
         //initialize an array of our enabled filters
-        List<FormatFilter> filterList = new ArrayList<FormatFilter>();
+        List<FormatFilter> filterList = new ArrayList<>();
 
         //set up each filter
         for (int i = 0; i < filterNames.length; i++) {

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

@@ -21,7 +21,8 @@ import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.encryption.InvalidPasswordException;
 import org.apache.pdfbox.text.PDFTextStripper;
 import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /*
  *
@@ -72,8 +73,10 @@ public class PDFFilter extends MediaFilter {
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
         throws Exception {
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
         try {
-            boolean useTemporaryFile = ConfigurationManager.getBooleanProperty("pdffilter.largepdfs", false);
+            boolean useTemporaryFile = configurationService.getBooleanProperty("pdffilter.largepdfs", false);
 
             // get input stream from bitstream
             // pass to filter, get string back
@@ -124,7 +127,7 @@ public class PDFFilter extends MediaFilter {
             }
         } catch (OutOfMemoryError oome) {
             log.error("Error parsing PDF document " + oome.getMessage(), oome);
-            if (!ConfigurationManager.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
+            if (!configurationService.getBooleanProperty("pdffilter.skiponmemoryexception", false)) {
                 throw oome;
             }
         }

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

@@ -17,9 +17,9 @@ import java.util.List;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.crosswalk.CrosswalkException;
@@ -175,7 +175,7 @@ public class Packager {
                               "flag can be used if you want to save (pipe) a report of all changes to a file, and " +
                               "therefore need to bypass all user interaction.");
 
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         CommandLine line = parser.parse(options, argv);
 
         String sourceFile = null;

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

@@ -19,6 +19,15 @@ import org.dspace.core.Context;
  * @author Andrea Bollini
  */
 public interface RequestItemAuthorExtractor {
-    public RequestItemAuthor getRequestItemAuthor(Context context, Item item)
-        throws SQLException;
+
+    /**
+     * Retrieve the auhtor to contact for a request copy of the give item.
+     *
+     * @param context DSpace context object
+     * @param item item to request
+     * @return An object containing name an email address to send the request to
+     *         or null if no valid email address was found.
+     * @throws SQLException if database error
+     */
+    public RequestItemAuthor getRequestItemAuthor(Context context, Item item) throws SQLException;
 }

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

@@ -10,13 +10,13 @@ package org.dspace.app.requestitem;
 import java.sql.SQLException;
 
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.Item;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.service.EPersonService;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -30,9 +30,6 @@ import org.springframework.beans.factory.annotation.Autowired;
  * @author Peter Dietz
  */
 public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
-
-    private Logger log = org.apache.logging.log4j.LogManager.getLogger(RequestItemHelpdeskStrategy.class);
-
     @Autowired(required = true)
     protected EPersonService ePersonService;
 
@@ -41,9 +38,11 @@ public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
 
     @Override
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item) throws SQLException {
-        boolean helpdeskOverridesSubmitter = ConfigurationManager
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        boolean helpdeskOverridesSubmitter = configurationService
             .getBooleanProperty("request.item.helpdesk.override", false);
-        String helpDeskEmail = ConfigurationManager.getProperty("mail.helpdesk");
+        String helpDeskEmail = configurationService.getProperty("mail.helpdesk");
 
         if (helpdeskOverridesSubmitter && StringUtils.isNotBlank(helpDeskEmail)) {
             return getHelpDeskPerson(context, helpDeskEmail);
@@ -64,18 +63,16 @@ public class RequestItemHelpdeskStrategy extends RequestItemSubmitterStrategy {
      * @throws SQLException if database error
      */
     public RequestItemAuthor getHelpDeskPerson(Context context, String helpDeskEmail) throws SQLException {
-        EPerson helpdeskEPerson = null;
-
         context.turnOffAuthorisationSystem();
-        helpdeskEPerson = ePersonService.findByEmail(context, helpDeskEmail);
+        EPerson helpdeskEPerson = ePersonService.findByEmail(context, helpDeskEmail);
         context.restoreAuthSystemState();
 
         if (helpdeskEPerson != null) {
             return new RequestItemAuthor(helpdeskEPerson);
         } else {
             String helpdeskName = I18nUtil.getMessage(
-                "org.dspace.app.requestitem.RequestItemHelpdeskStrategy.helpdeskname",
-                context);
+                    "org.dspace.app.requestitem.RequestItemHelpdeskStrategy.helpdeskname",
+                    context);
             return new RequestItemAuthor(helpdeskName, helpDeskEmail);
         }
     }

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

@@ -16,6 +16,7 @@ import org.dspace.content.MetadataValue;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -38,6 +39,7 @@ public class RequestItemMetadataStrategy extends RequestItemSubmitterStrategy {
     @Override
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item)
         throws SQLException {
+        RequestItemAuthor author = null;
         if (emailMetadata != null) {
             List<MetadataValue> vals = itemService.getMetadataByMetadataString(item, emailMetadata);
             if (vals.size() > 0) {
@@ -49,19 +51,38 @@ public class RequestItemMetadataStrategy extends RequestItemSubmitterStrategy {
                         fullname = nameVals.iterator().next().getValue();
                     }
                 }
-
                 if (StringUtils.isBlank(fullname)) {
                     fullname = I18nUtil
-                        .getMessage(
-                            "org.dspace.app.requestitem.RequestItemMetadataStrategy.unnamed",
-                            context);
+                            .getMessage(
+                                    "org.dspace.app.requestitem.RequestItemMetadataStrategy.unnamed",
+                                    context);
                 }
-                RequestItemAuthor author = new RequestItemAuthor(
-                    fullname, email);
+                author = new RequestItemAuthor(fullname, email);
                 return author;
             }
+        } else {
+            // Uses the basic strategy to look for the original submitter
+            author = super.getRequestItemAuthor(context, item);
+            // Is the author or his email  null, so get the help desk or admin name and email
+            if (null == author || null == author.getEmail()) {
+                String email = null;
+                String name = null;
+                //First get help desk name and email
+                email = DSpaceServicesFactory.getInstance()
+                        .getConfigurationService().getProperty("mail.helpdesk");
+                name = DSpaceServicesFactory.getInstance()
+                                            .getConfigurationService().getProperty("mail.helpdesk.name");
+                // If help desk mail is null get the mail and name of admin
+                if (email == null) {
+                    email = DSpaceServicesFactory.getInstance()
+                            .getConfigurationService().getProperty("mail.admin");
+                    name = DSpaceServicesFactory.getInstance()
+                            .getConfigurationService().getProperty("mail.admin.name");
+                }
+                author = new RequestItemAuthor(name, email);
+            }
         }
-        return super.getRequestItemAuthor(context, item);
+        return author;
     }
 
     public void setEmailMetadata(String emailMetadata) {

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

@@ -23,13 +23,22 @@ public class RequestItemSubmitterStrategy implements RequestItemAuthorExtractor
     public RequestItemSubmitterStrategy() {
     }
 
+    /**
+     * Returns the submitter of an Item as RequestItemAuthor or null if the
+     * Submitter is deleted.
+     *
+     * @return The submitter of the item or null if the submitter is deleted
+     * @throws SQLException if database error
+     */
     @Override
     public RequestItemAuthor getRequestItemAuthor(Context context, Item item)
         throws SQLException {
         EPerson submitter = item.getSubmitter();
-        RequestItemAuthor author = new RequestItemAuthor(
-            submitter.getFullName(), submitter.getEmail());
+        RequestItemAuthor author = null;
+        if (null != submitter) {
+            author = new RequestItemAuthor(
+                    submitter.getFullName(), submitter.getEmail());
+        }
         return author;
     }
-
 }

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

@@ -8,9 +8,7 @@
 
 /**
  * <p>SFX/OpenURL link server support.</p>
- * 
- * @see org.dspace.app.webui.jsptag.SFXLinkTag
- * @see org.dspace.app.xmlui.aspect.artifactbrowser.ItemViewer
+ *
  */
 
 package org.dspace.app.sfx;

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAJournal.java

@@ -1,49 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sherpa;
-
-/**
- * POJO representation for a SHERPA journal
- *
- * @author Andrea Bollini
- */
-public class SHERPAJournal {
-    private String title;
-
-    private String issn;
-
-    private String zetopub;
-
-    private String romeopub;
-
-    public SHERPAJournal(String title, String issn, String zetopub,
-                         String romeopub) {
-        super();
-        this.title = title;
-        this.issn = issn;
-        this.zetopub = zetopub;
-        this.romeopub = romeopub;
-    }
-
-    public String getTitle() {
-        return title;
-    }
-
-    public String getIssn() {
-        return issn;
-    }
-
-    public String getZetopub() {
-        return zetopub;
-    }
-
-    public String getRomeopub() {
-        return romeopub;
-    }
-
-}

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAPublisher.java

@@ -1,175 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sherpa;
-
-import java.util.List;
-
-/**
- * POJO representation for a SHERPA Publisher record
- *
- * @author Andrea Bollini
- */
-public class SHERPAPublisher {
-
-    private String id;
-
-    private String name;
-
-    private String alias;
-
-    private String homeurl;
-
-    private String prearchiving;
-
-    private List<String> prerestriction;
-
-    private String postarchiving;
-
-    private List<String> postrestriction;
-
-    private String pubarchiving;
-
-    private List<String> pubrestriction;
-
-    private List<String> condition;
-
-    private String paidaccessurl;
-
-    private String paidaccessname;
-
-    private String paidaccessnotes;
-
-    private List<String[]> copyright;
-
-    private String romeocolour;
-
-    private String dateadded;
-
-    private String dateupdated;
-
-    public SHERPAPublisher(String id, String name, String alias, String homeurl,
-                           String prearchiving, List<String> prerestriction,
-                           String postarchiving, List<String> postrestriction,
-                           String pubarchiving, List<String> pubrestriction,
-                           List<String> condition, String paidaccessurl,
-                           String paidaccessname, String paidaccessnotes,
-                           List<String[]> copyright, String romeocolour, String datedded,
-                           String dateupdated) {
-        this.id = id;
-
-        this.name = name;
-
-        this.alias = alias;
-
-        this.homeurl = homeurl;
-
-        this.prearchiving = prearchiving;
-
-        this.prerestriction = prerestriction;
-
-        this.postarchiving = postarchiving;
-
-        this.postrestriction = postrestriction;
-
-        this.pubarchiving = pubarchiving;
-
-        this.pubrestriction = pubrestriction;
-
-        this.condition = condition;
-
-        this.paidaccessurl = paidaccessurl;
-
-        this.paidaccessname = paidaccessname;
-
-        this.paidaccessnotes = paidaccessnotes;
-
-        this.copyright = copyright;
-
-        this.romeocolour = romeocolour;
-
-        this.dateadded = datedded;
-
-        this.dateupdated = dateupdated;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public String getAlias() {
-        return alias;
-    }
-
-    public String getHomeurl() {
-        return homeurl;
-    }
-
-    public String getPrearchiving() {
-        return prearchiving;
-    }
-
-    public List<String> getPrerestriction() {
-        return prerestriction;
-    }
-
-    public String getPostarchiving() {
-        return postarchiving;
-    }
-
-    public List<String> getPostrestriction() {
-        return postrestriction;
-    }
-
-    public String getPubarchiving() {
-        return pubarchiving;
-    }
-
-    public List<String> getPubrestriction() {
-        return pubrestriction;
-    }
-
-    public List<String> getCondition() {
-        return condition;
-    }
-
-    public String getPaidaccessurl() {
-        return paidaccessurl;
-    }
-
-    public String getPaidaccessname() {
-        return paidaccessname;
-    }
-
-    public String getPaidaccessnotes() {
-        return paidaccessnotes;
-    }
-
-    public List<String[]> getCopyright() {
-        return copyright;
-    }
-
-    public String getRomeocolour() {
-        return romeocolour;
-    }
-
-    public String getDatedded() {
-        return dateadded;
-    }
-
-    public String getDateupdated() {
-        return dateupdated;
-    }
-
-    /**
-     * Generic getter for the id
-     * @return the id value of this SHERPAPublisher
-     */
-    public String getId() {
-        return id;
-    }
-}

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAResponse.java

@@ -1,206 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.app.sherpa;
-
-import java.io.InputStream;
-import java.util.LinkedList;
-import java.util.List;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
-import org.dspace.app.util.XMLUtils;
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-
-/**
- * JAVA representation for a SHERPA API Response
- *
- * @author Andrea Bollini
- */
-public class SHERPAResponse {
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAResponse.class);
-
-    private int numHits;
-
-    private String message;
-
-    private String license;
-
-    private String licenseURL;
-
-    private String disclaimer;
-
-    private List<SHERPAJournal> journals;
-
-    private List<SHERPAPublisher> publishers;
-
-    public SHERPAResponse(InputStream xmlData) {
-        try {
-            DocumentBuilderFactory factory = DocumentBuilderFactory
-                .newInstance();
-            factory.setValidating(false);
-            factory.setIgnoringComments(true);
-            factory.setIgnoringElementContentWhitespace(true);
-            // disallow DTD parsing to ensure no XXE attacks can occur.
-            // See https://cheatsheetseries.owasp.org/cheatsheets/XML_External_Entity_Prevention_Cheat_Sheet.html
-            factory.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
-
-            DocumentBuilder db = factory.newDocumentBuilder();
-            Document inDoc = db.parse(xmlData);
-
-            Element xmlRoot = inDoc.getDocumentElement();
-            Element headersElement = XMLUtils.getSingleElement(xmlRoot,
-                                                               "header");
-            Element journalsElement = XMLUtils.getSingleElement(xmlRoot,
-                                                                "journals");
-            Element publishersElement = XMLUtils.getSingleElement(xmlRoot,
-                                                                  "publishers");
-
-            String numhitsString = XMLUtils.getElementValue(headersElement, "numhits");
-            if (StringUtils.isNotBlank(numhitsString)) {
-                numHits = Integer.parseInt(numhitsString);
-            } else {
-                numHits = 0;
-            }
-            message = XMLUtils.getElementValue(headersElement, "message");
-
-            license = XMLUtils.getElementValue(headersElement, "license");
-            licenseURL = XMLUtils.getElementValue(headersElement, "licenseurl");
-            disclaimer = XMLUtils.getElementValue(headersElement, "disclaimer");
-
-            List<Element> journalsList = XMLUtils.getElementList(
-                journalsElement, "journal");
-            List<Element> publishersList = XMLUtils.getElementList(
-                publishersElement, "publisher");
-
-            if (journalsList != null) {
-                journals = new LinkedList<SHERPAJournal>();
-                for (Element journalElement : journalsList) {
-                    journals.add(new SHERPAJournal(
-                        XMLUtils.getElementValue(journalElement, "jtitle"),
-                        XMLUtils.getElementValue(journalElement, "issn"),
-                        XMLUtils.getElementValue(journalElement, "zetopub"),
-                        XMLUtils.getElementValue(journalElement, "romeopub")));
-                }
-            }
-
-            if (publishersList != null) {
-                publishers = new LinkedList<SHERPAPublisher>();
-                for (Element publisherElement : publishersList) {
-                    Element preprintsElement = XMLUtils.getSingleElement(
-                        publisherElement, "preprints");
-                    Element preprintsRestrictionElement = XMLUtils
-                        .getSingleElement(publisherElement,
-                                          "prerestrictions");
-
-                    Element postprintsElement = XMLUtils.getSingleElement(
-                        publisherElement, "postprints");
-                    Element postprintsRestrictionElement = XMLUtils
-                        .getSingleElement(publisherElement,
-                                          "postrestrictions");
-
-                    Element pdfversionElement = XMLUtils.getSingleElement(
-                        publisherElement, "pdfversion");
-                    Element pdfversionRestrictionElement = XMLUtils
-                        .getSingleElement(publisherElement,
-                                          "pdfrestrictions");
-
-                    Element conditionsElement = XMLUtils.getSingleElement(
-                        publisherElement, "conditions");
-                    Element paidaccessElement = XMLUtils.getSingleElement(
-                        publisherElement, "paidaccess");
-
-                    Element copyrightlinksElement = XMLUtils.getSingleElement(
-                        publisherElement, "copyrightlinks");
-                    publishers
-                        .add(new SHERPAPublisher(publisherElement.getAttribute("id"), XMLUtils.getElementValue(
-                            publisherElement, "name"),
-                                                 XMLUtils.getElementValue(publisherElement,
-                                                                          "alias"), XMLUtils.getElementValue(
-                            publisherElement, "homeurl"),
-
-                                                 XMLUtils.getElementValue(preprintsElement,
-                                                                          "prearchiving"),
-                                                 XMLUtils.getElementValueList(
-                                                     preprintsRestrictionElement,
-                                                     "prerestriction"),
-
-                                                 XMLUtils.getElementValue(postprintsElement,
-                                                                          "postarchiving"),
-                                                 XMLUtils.getElementValueList(
-                                                     postprintsRestrictionElement,
-                                                     "postrestriction"),
-
-                                                 XMLUtils.getElementValue(pdfversionElement,
-                                                                          "pdfarchiving"),
-                                                 XMLUtils.getElementValueList(
-                                                     pdfversionRestrictionElement,
-                                                     "pdfrestriction"),
-
-                                                 XMLUtils
-                                                     .getElementValueList(
-                                                         conditionsElement,
-                                                         "condition"), XMLUtils
-                                                     .getElementValue(paidaccessElement,
-                                                                      "paidaccessurl"), XMLUtils
-                                                     .getElementValue(paidaccessElement,
-                                                                      "paidaccessname"), XMLUtils
-                                                     .getElementValue(paidaccessElement,
-                                                                      "paidaccessnotes"),
-                                                 XMLUtils.getElementValueArrayList(
-                                                     copyrightlinksElement,
-                                                     "copyrightlink",
-                                                     "copyrightlinktext",
-                                                     "copyrightlinkurl"), XMLUtils
-                                                     .getElementValue(publisherElement,
-                                                                      "romeocolour"), XMLUtils
-                                                     .getElementValue(publisherElement,
-                                                                      "dateadded"), XMLUtils
-                                                     .getElementValue(publisherElement,
-                                                                      "dateupdated")));
-                }
-            }
-        } catch (Exception e) {
-            log.error("Error parsing SHERPA API Response", e);
-        }
-    }
-
-    public SHERPAResponse(String message) {
-        this.message = message;
-    }
-
-    public String getMessage() {
-        return message;
-    }
-
-    public String getLicense() {
-        return license;
-    }
-
-    public String getLicenseURL() {
-        return licenseURL;
-    }
-
-    public String getDisclaimer() {
-        return disclaimer;
-    }
-
-    public List<SHERPAJournal> getJournals() {
-        return journals;
-    }
-
-    public List<SHERPAPublisher> getPublishers() {
-        return publishers;
-    }
-
-    public int getNumHits() {
-        return numHits;
-    }
-}

dspace-api/src/main/java/org/dspace/app/sherpa/SHERPAService.java

@@ -7,6 +7,13 @@
  */
 package org.dspace.app.sherpa;
 
+import java.io.IOException;
+import java.io.InputStream;
+import java.net.URI;
+import java.net.URISyntaxException;
+import java.nio.charset.StandardCharsets;
+
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpEntity;
 import org.apache.http.HttpResponse;
@@ -17,21 +24,50 @@ import org.apache.http.client.utils.URIBuilder;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.logging.log4j.Logger;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.app.sherpa.v2.SHERPAPublisherResponse;
+import org.dspace.app.sherpa.v2.SHERPAResponse;
+import org.dspace.app.sherpa.v2.SHERPAUtils;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 
+/**
+ * SHERPAService is responsible for making the HTTP call to the SHERPA v2 API
+ * for SHERPASubmitService.
+ * Note, this service is ported from DSpace 6 for the ability to search policies by ISSN
+ * There are also new DataProvider implementations provided for use as 'external sources'
+ * of journal and publisher data
+ * @see org.dspace.external.provider.impl.SHERPAv2JournalDataProvider
+ * @see org.dspace.external.provider.impl.SHERPAv2PublisherDataProvider
+ * @author Kim Shepherd
+ */
 public class SHERPAService {
     private CloseableHttpClient client = null;
 
     private int maxNumberOfTries;
     private long sleepBetweenTimeouts;
     private int timeout = 5000;
+    private String endpoint = "https://v2.sherpa.ac.uk/cgi/retrieve";
+    private String apiKey = null;
+
+    /** log4j category */
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAService.class);
+
+    @Autowired
+    ConfigurationService configurationService;
 
     /**
-     * log4j category
+     * Create a new HTTP builder with sensible defaults in constructor
      */
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAService.class);
-
     public SHERPAService() {
+        // Set configuration service
+        configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+
+        // Get endoint and API key from configuration
+        endpoint = configurationService.getProperty("sherpa.romeo.url",
+            "https://v2.sherpa.ac.uk/cgi/retrieve");
+        apiKey = configurationService.getProperty("sherpa.romeo.apikey");
+
         HttpClientBuilder builder = HttpClientBuilder.create();
         // httpclient 4.3+ doesn't appear to have any sensible defaults any more. Setting conservative defaults as
         // not to hammer the SHERPA service too much.
@@ -41,62 +77,106 @@ public class SHERPAService {
             .build();
     }
 
-
+    /**
+     * Search the SHERPA v2 API for a journal policy data using the supplied ISSN.
+     * If the API key is missing, or the HTTP response is non-OK or does not complete
+     * successfully, a simple error response will be returned.
+     * Otherwise, the response body will be passed to SHERPAResponse for parsing as JSON
+     * and the final result returned to the calling method
+     * @param query ISSN string to pass in an "issn equals" API query
+     * @return      SHERPAResponse containing an error or journal policies
+     */
     public SHERPAResponse searchByJournalISSN(String query) {
-        String endpoint = ConfigurationManager.getProperty("sherpa.romeo.url");
-        String apiKey = ConfigurationManager.getProperty("sherpa.romeo.apikey");
+        return performRequest("publication", "issn", "equals", query, 0, 1);
+    }
+
+    /**
+     * Perform an API request to the SHERPA v2 API - this could be a search or a get for any entity type
+     * but the return object here must be a SHERPAPublisherResponse not the journal-centric SHERPAResponse
+     * For more information about the type, field and predicate arguments, see the SHERPA v2 API documentation
+     * @param type          entity type eg "publisher"
+     * @param field         field eg "issn" or "title"
+     * @param predicate     predicate eg "equals" or "contains-word"
+     * @param value         the actual value to search for (eg an ISSN or partial title)
+     * @param start         start / offset of search results
+     * @param limit         maximum search results to return
+     * @return              SHERPAPublisherResponse object
+     */
+    public SHERPAPublisherResponse performPublisherRequest(String type, String field, String predicate, String value,
+                                                           int start, int limit) {
+        // API Key is *required* for v2 API calls
+        if (null == apiKey) {
+            log.error("SHERPA ROMeO API Key missing: please register for an API key and set sherpa.romeo.apikey");
+            return new SHERPAPublisherResponse("SHERPA/RoMEO configuration invalid or missing");
+        }
 
         HttpGet method = null;
-        SHERPAResponse sherpaResponse = null;
+        SHERPAPublisherResponse sherpaResponse = null;
         int numberOfTries = 0;
 
         while (numberOfTries < maxNumberOfTries && sherpaResponse == null) {
             numberOfTries++;
 
-            if (log.isDebugEnabled()) {
-                log.debug(String.format(
-                    "Trying to contact SHERPA/RoMEO - attempt %d of %d; timeout is %d; sleep between timeouts is %d",
-                    numberOfTries,
-                    maxNumberOfTries,
-                    timeout,
-                    sleepBetweenTimeouts));
-            }
+            log.debug(String.format(
+                "Trying to contact SHERPA/RoMEO - attempt %d of %d; timeout is %d; sleep between timeouts is %d",
+                numberOfTries,
+                maxNumberOfTries,
+                timeout,
+                sleepBetweenTimeouts));
 
             try {
                 Thread.sleep(sleepBetweenTimeouts);
 
-                URIBuilder uriBuilder = new URIBuilder(endpoint);
-                uriBuilder.addParameter("issn", query);
-                uriBuilder.addParameter("versions", "all");
-                if (StringUtils.isNotBlank(apiKey)) {
-                    uriBuilder.addParameter("ak", apiKey);
-                }
-
-                method = new HttpGet(uriBuilder.build());
-                method.setConfig(RequestConfig.custom()
-                                              .setConnectionRequestTimeout(timeout)
-                                              .setConnectTimeout(timeout)
-                                              .setSocketTimeout(timeout)
-                                              .build());
-                // Execute the method.
+                // Construct a default HTTP method (first result)
+                method = constructHttpGet(type, field, predicate, value, start, limit);
 
+                // Execute the method
                 HttpResponse response = client.execute(method);
                 int statusCode = response.getStatusLine().getStatusCode();
 
+                log.debug(response.getStatusLine().getStatusCode() + ": "
+                    + response.getStatusLine().getReasonPhrase());
+
                 if (statusCode != HttpStatus.SC_OK) {
-                    sherpaResponse = new SHERPAResponse("SHERPA/RoMEO return not OK status: "
-                                                            + statusCode);
+                    sherpaResponse = new SHERPAPublisherResponse("SHERPA/RoMEO return not OK status: "
+                        + statusCode);
+                    String errorBody = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+                    log.error("Error from SHERPA HTTP request: " + errorBody);
                 }
 
                 HttpEntity responseBody = response.getEntity();
 
+                // If the response body is valid, pass to SHERPAResponse for parsing as JSON
                 if (null != responseBody) {
-                    sherpaResponse = new SHERPAResponse(responseBody.getContent());
+                    log.debug("Non-null SHERPA resonse received for query of " + value);
+                    InputStream content = null;
+                    try {
+                        content = responseBody.getContent();
+                        sherpaResponse =
+                            new SHERPAPublisherResponse(content, SHERPAPublisherResponse.SHERPAFormat.JSON);
+                    } catch (IOException e) {
+                        log.error("Encountered exception while contacting SHERPA/RoMEO: " + e.getMessage(), e);
+                    } finally {
+                        if (content != null) {
+                            content.close();
+                        }
+                    }
                 } else {
-                    sherpaResponse = new SHERPAResponse("SHERPA/RoMEO returned no response");
+                    log.debug("Empty SHERPA response body for query on " + value);
+                    sherpaResponse = new SHERPAPublisherResponse("SHERPA/RoMEO returned no response");
                 }
-            } catch (Exception e) {
-                log.warn("Encountered exception while contacting SHERPA/RoMEO: " + e.getMessage(), e);
+            } catch (URISyntaxException e) {
+                String errorMessage = "Error building SHERPA v2 API URI: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAPublisherResponse(errorMessage);
+            } catch (IOException e) {
+                String errorMessage = "Encountered exception while contacting SHERPA/RoMEO: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAPublisherResponse(errorMessage);
+            }  catch (InterruptedException e) {
+                String errorMessage = "Encountered exception while sleeping thread: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAPublisherResponse(errorMessage);
             } finally {
                 if (method != null) {
                     method.releaseConnection();
@@ -105,13 +185,218 @@ public class SHERPAService {
         }
 
         if (sherpaResponse == null) {
+            log.debug("SHERPA response is still null");
+            sherpaResponse = new SHERPAPublisherResponse(
+                "Error processing the SHERPA/RoMEO answer");
+        }
+
+        // Return the final response
+        return sherpaResponse;
+    }
+
+    /**
+     * Perform an API request to the SHERPA v2 API - this could be a search or a get for any entity type
+     * For more information about the type, field and predicate arguments, see the SHERPA v2 API documentation
+     * @param type          entity type eg "publication" or "publisher"
+     * @param field         field eg "issn" or "title"
+     * @param predicate     predicate eg "equals" or "contains-word"
+     * @param value         the actual value to search for (eg an ISSN or partial title)
+     * @param start         start / offset of search results
+     * @param limit         maximum search results to return
+     * @return              SHERPAResponse object
+     */
+    public SHERPAResponse performRequest(String type, String field, String predicate, String value,
+                                         int start, int limit) {
+        // API Key is *required* for v2 API calls
+        if (null == apiKey) {
+            log.error("SHERPA ROMeO API Key missing: please register for an API key and set sherpa.romeo.apikey");
+            return new SHERPAResponse("SHERPA/RoMEO configuration invalid or missing");
+        }
+
+        HttpGet method = null;
+        SHERPAResponse sherpaResponse = null;
+        int numberOfTries = 0;
+
+        while (numberOfTries < maxNumberOfTries && sherpaResponse == null) {
+            numberOfTries++;
+
+            log.debug(String.format(
+                "Trying to contact SHERPA/RoMEO - attempt %d of %d; timeout is %d; sleep between timeouts is %d",
+                numberOfTries,
+                maxNumberOfTries,
+                timeout,
+                sleepBetweenTimeouts));
+
+            try {
+                Thread.sleep(sleepBetweenTimeouts);
+
+                // Construct a default HTTP method (first result)
+                method = constructHttpGet(type, field, predicate, value, start, limit);
+
+                // Execute the method
+                HttpResponse response = client.execute(method);
+                int statusCode = response.getStatusLine().getStatusCode();
+
+                log.debug(response.getStatusLine().getStatusCode() + ": "
+                    + response.getStatusLine().getReasonPhrase());
+
+                if (statusCode != HttpStatus.SC_OK) {
+                    sherpaResponse = new SHERPAResponse("SHERPA/RoMEO return not OK status: "
+                        + statusCode);
+                    String errorBody = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
+                    log.error("Error from SHERPA HTTP request: " + errorBody);
+                }
+
+                HttpEntity responseBody = response.getEntity();
+
+                // If the response body is valid, pass to SHERPAResponse for parsing as JSON
+                if (null != responseBody) {
+                    log.debug("Non-null SHERPA resonse received for query of " + value);
+                    InputStream content = null;
+                    try {
+                        content = responseBody.getContent();
+                        sherpaResponse = new SHERPAResponse(content, SHERPAResponse.SHERPAFormat.JSON);
+                    } catch (IOException e) {
+                        log.error("Encountered exception while contacting SHERPA/RoMEO: " + e.getMessage(), e);
+                    } finally {
+                        if (content != null) {
+                            content.close();
+                        }
+                    }
+                } else {
+                    log.debug("Empty SHERPA response body for query on " + value);
+                    sherpaResponse = new SHERPAResponse("SHERPA/RoMEO returned no response");
+                }
+            } catch (URISyntaxException e) {
+                String errorMessage = "Error building SHERPA v2 API URI: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAResponse(errorMessage);
+            } catch (IOException e) {
+                String errorMessage = "Encountered exception while contacting SHERPA/RoMEO: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAResponse(errorMessage);
+            }  catch (InterruptedException e) {
+                String errorMessage = "Encountered exception while sleeping thread: " + e.getMessage();
+                log.error(errorMessage, e);
+                sherpaResponse = new SHERPAResponse(errorMessage);
+            } finally {
+                if (method != null) {
+                    method.releaseConnection();
+                }
+            }
+        }
+
+        if (sherpaResponse == null) {
+            log.debug("SHERPA response is still null");
             sherpaResponse = new SHERPAResponse(
                 "Error processing the SHERPA/RoMEO answer");
         }
 
+        // Return the final response
         return sherpaResponse;
     }
 
+    /**
+     * Construct HTTP GET object for a "field,predicate,value" query with default start, limit
+     * eg. "title","contains-word","Lancet" or "issn","equals","1234-1234"
+     * @param field the field (issn, title, etc)
+     * @param predicate the predicate (contains-word, equals, etc - see API docs)
+     * @param value the query value itself
+     * @return HttpGet method which can then be executed by the client
+     * @throws URISyntaxException if the URL build fails
+     */
+    public HttpGet constructHttpGet(String type, String field, String predicate, String value)
+        throws URISyntaxException {
+        return constructHttpGet(type, field, predicate, value, 0, 1);
+    }
+
+    /**
+     * Construct HTTP GET object for a "field,predicate,value" query
+     * eg. "title","contains-word","Lancet" or "issn","equals","1234-1234"
+     * @param field the field (issn, title, etc)
+     * @param predicate the predicate (contains-word, equals, etc - see API docs)
+     * @param value the query value itself
+     * @param start row offset
+     * @param limit number of results to return
+     * @return HttpGet object to be executed by the client
+     * @throws URISyntaxException
+     */
+    public HttpGet constructHttpGet(String type, String field, String predicate, String value, int start, int limit)
+        throws URISyntaxException {
+        // Sanitise query string (strip some characters) field, predicate and value
+        if (null == type) {
+            type = "publication";
+        }
+        field = SHERPAUtils.sanitiseQuery(field);
+        predicate = SHERPAUtils.sanitiseQuery(predicate);
+        value = SHERPAUtils.sanitiseQuery(value);
+        type = SHERPAUtils.sanitiseQuery(type);
+
+        // Build URL based on search query
+        URIBuilder uriBuilder = new URIBuilder(endpoint);
+        uriBuilder.addParameter("item-type", type);
+        uriBuilder.addParameter("filter", "[[\"" + field + "\",\"" + predicate + "\",\"" + value + "\"]]");
+        uriBuilder.addParameter("format", "Json");
+        // Set optional start (offset) and limit parameters
+        if (start >= 0) {
+            uriBuilder.addParameter("offset", String.valueOf(start));
+        }
+        if (limit > 0) {
+            uriBuilder.addParameter("limit", String.valueOf(limit));
+        }
+        if (StringUtils.isNotBlank(apiKey)) {
+            uriBuilder.addParameter("api-key", apiKey);
+        }
+
+        log.debug("SHERPA API URL: " + uriBuilder.toString());
+
+        // Create HTTP GET object
+        HttpGet method = new HttpGet(uriBuilder.build());
+
+        // Set connection parameters
+        int timeout = 5000;
+        method.setConfig(RequestConfig.custom()
+            .setConnectionRequestTimeout(timeout)
+            .setConnectTimeout(timeout)
+            .setSocketTimeout(timeout)
+            .build());
+
+        return method;
+    }
+
+    /**
+     * Prepare the API query for execution by the HTTP client
+     * @param query     ISSN query string
+     * @param endpoint  API endpoint (base URL)
+     * @param apiKey    API key parameter
+     * @return          URI object
+     * @throws URISyntaxException
+     */
+    public URI prepareQuery(String query, String endpoint, String apiKey) throws URISyntaxException {
+        // Sanitise query string
+        query = SHERPAUtils.sanitiseQuery(query);
+
+        // Instantiate URI builder
+        URIBuilder uriBuilder = new URIBuilder(endpoint);
+
+        // Build URI parameters from supplied values
+        uriBuilder.addParameter("item-type", "publication");
+
+        // Log warning if no query is supplied
+        if (null == query) {
+            log.warn("No ISSN supplied as query string for SHERPA service search");
+        }
+        uriBuilder.addParameter("filter", "[[\"issn\",\"equals\",\"" + query + "\"]]");
+        uriBuilder.addParameter("format", "Json");
+        if (StringUtils.isNotBlank(apiKey)) {
+            uriBuilder.addParameter("api-key", apiKey);
+        }
+        log.debug("Would search SHERPA endpoint with " + uriBuilder.toString());
+
+        // Return final built URI
+        return uriBuilder.build();
+    }
+
     public void setMaxNumberOfTries(int maxNumberOfTries) {
         this.maxNumberOfTries = maxNumberOfTries;
     }

dspace-api/src/main/java/org/dspace/app/sherpa/submit/SHERPASubmitService.java

@@ -7,49 +7,111 @@
  */
 package org.dspace.app.sherpa.submit;
 
+import java.util.Iterator;
 import java.util.LinkedHashSet;
+import java.util.LinkedList;
 import java.util.List;
 import java.util.Set;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
-import org.dspace.app.sherpa.SHERPAResponse;
 import org.dspace.app.sherpa.SHERPAService;
+import org.dspace.app.sherpa.v2.SHERPAResponse;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 
+/**
+ * SHERPASubmitService is
+ * @see
+ * @author Kim Shepherd
+ */
 public class SHERPASubmitService {
-    private SHERPAService sherpaService;
 
-    private SHERPASubmitConfigurationService configuration;
+    /**
+     * Spring beans for configuration and API service
+     */
+    protected SHERPAService sherpaService;
+    protected SHERPASubmitConfigurationService configuration;
 
     /**
      * log4j logger
      */
     private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPASubmitService.class);
 
+    /**
+     * Setter for configuration (from Spring)
+     * @see "dspace-dspace-addon-sherpa-configuration-services.xml"
+     * @param configuration
+     */
     public void setConfiguration(SHERPASubmitConfigurationService configuration) {
         this.configuration = configuration;
     }
 
+    /**
+     * Setter for SHERPA service, reponsible for actual HTTP API calls
+     * @see "dspace-dspace-addon-sherpa-configuration-services.xml"
+     * @param sherpaService
+     */
     public void setSherpaService(SHERPAService sherpaService) {
         this.sherpaService = sherpaService;
     }
 
-    public SHERPAResponse searchRelatedJournals(Context context, Item item) {
+    /**
+     * Search SHERPA for journal policies matching the ISSNs in the item.
+     * Rather than a 'search' query for any/all ISSNs, the v2 API requires a separate
+     * query for each ISSN found in the item. The ISSNs are extracted using the configured
+     * issnItemExtractor(s) in the SHERPA spring configuration.
+     * The ISSNs are not validated with a regular expression or other rules - any values
+     * extracted will be included in API queries.
+     * @see "dspace-dspace-addon-sherpa-configuration-services.xml"
+     * @param context   DSpace context
+     * @param item      DSpace item containing ISSNs to be checked
+     * @return          SHERPA v2 API response (policy data)
+     */
+    public List<SHERPAResponse> searchRelatedJournals(Context context, Item item) {
         Set<String> issns = getISSNs(context, item);
         if (issns == null || issns.size() == 0) {
             return null;
         } else {
-            return sherpaService.searchByJournalISSN(StringUtils.join(issns, ","));
+            // SHERPA v2 API no longer supports "OR'd" ISSN search, perform individual searches instead
+            Iterator<String> issnIterator = issns.iterator();
+            List<SHERPAResponse> responses = new LinkedList<>();
+            while (issnIterator.hasNext()) {
+                String issn = issnIterator.next();
+                SHERPAResponse response = sherpaService.searchByJournalISSN(issn);
+                if (response.isError()) {
+                    // Continue with loop
+                    log.warn("Failed to look up SHERPA ROMeO result for ISSN: " + issn
+                        + ": " + response.getMessage());
+                }
+                // Store this response, even if it has an error (useful for UI reporting)
+                responses.add(response);
+            }
+            if (responses.isEmpty()) {
+                responses.add(new SHERPAResponse("SHERPA ROMeO lookup failed"));
+            }
+            return responses;
         }
     }
 
+    /**
+     * Search SHERPA for journal policies matching the passed ISSN.
+     * The ISSN are not validated with a regular expression or other rules - any String
+     * passed to this method will be considered an ISSN for the purposes of an API query
+     * @param issn  ISSN string
+     * @return      SHERPA v2 API response object (policy data)
+     */
     public SHERPAResponse searchRelatedJournalsByISSN(String issn) {
         return sherpaService.searchByJournalISSN(issn);
     }
 
+    /**
+     * Using the configured itemIssnExtractors from SHERPA configuration, extract
+     * ISSNs from item metadata or authority values
+     * @param context   DSpace context
+     * @param item      Item containing metadata / authority values
+     * @return          Set of ISSN strings
+     */
     public Set<String> getISSNs(Context context, Item item) {
         Set<String> issns = new LinkedHashSet<String>();
         if (configuration.getIssnItemExtractors() == null) {
@@ -68,6 +130,13 @@ public class SHERPASubmitService {
         return issns;
     }
 
+    /**
+     * Simple boolean test that runs the getISSNs extraction method
+     * to determine whether an item has any ISSNs at all
+     * @param context   DSpace context
+     * @param item      Item to test
+     * @return          boolean indicating presence of >=1 ISSNs
+     */
     public boolean hasISSNs(Context context, Item item) {
         Set<String> issns = getISSNs(context, item);
         if (issns == null || issns.size() == 0) {

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAJournal.java

@@ -0,0 +1,111 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+import java.util.List;
+
+/**
+ * Plain java representation of a SHERPA Journal object, based on SHERPA API v2 responses.
+ *
+ * In a SHERPA search for journal deposit policies, this is generally structured
+ * as a list in the SHERPAResponse object.
+ * Each journal contains a list of publisher data and list of publishing policies as well as basic metadata
+ * about the journal such as ISSNs, titles, whether it appears in DOAJ, primary publisher, etc.
+ * @see SHERPAResponse
+ * @see org.dspace.external.provider.impl.SHERPAv2JournalDataProvider
+ *
+ * @author Kim Shepherd
+ */
+public class SHERPAJournal {
+
+    private List<String> titles;
+    private String url;
+    private List<String> issns;
+    private String romeoPub;
+    private String zetoPub;
+    private SHERPAPublisher publisher;
+    private List<SHERPAPublisher> publishers;
+    private List<SHERPAPublisherPolicy> policies;
+    private Boolean inDOAJ;
+
+    public SHERPAJournal() {
+
+    }
+
+    public List<String> getTitles() {
+        return titles;
+    }
+
+    public void setTitles(List<String> titles) {
+        this.titles = titles;
+    }
+
+    public String getUrl() {
+        return url;
+    }
+
+    public void setUrl(String url) {
+        this.url = url;
+    }
+
+    public List<String> getIssns() {
+        return issns;
+    }
+
+    public void setIssns(List<String> issns) {
+        this.issns = issns;
+    }
+
+    public String getRomeoPub() {
+        return romeoPub;
+    }
+
+    public void setRomeoPub(String romeoPub) {
+        this.romeoPub = romeoPub;
+    }
+
+    public String getZetoPub() {
+        return zetoPub;
+    }
+
+    public void setZetoPub(String zetoPub) {
+        this.zetoPub = zetoPub;
+    }
+
+    public SHERPAPublisher getPublisher() {
+        return publisher;
+    }
+
+    public void setPublisher(SHERPAPublisher publisher) {
+        this.publisher = publisher;
+    }
+
+    public List<SHERPAPublisher> getPublishers() {
+        return publishers;
+    }
+
+    public void setPublishers(List<SHERPAPublisher> publishers) {
+        this.publishers = publishers;
+    }
+
+    public List<SHERPAPublisherPolicy> getPolicies() {
+        return policies;
+    }
+
+    public void setPolicies(List<SHERPAPublisherPolicy> policies) {
+        this.policies = policies;
+    }
+
+    public Boolean getInDOAJ() {
+        return inDOAJ;
+    }
+
+    public void setInDOAJ(Boolean inDOAJ) {
+        this.inDOAJ = inDOAJ;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAPermittedVersion.java

@@ -0,0 +1,118 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+import java.util.List;
+
+/**
+ * Plain java representation of a SHERPA Permitted Version object, based on SHERPA API v2 responses.
+ *
+ * In a SHERPA search for journal deposit policies, this data is contained within a publisher policy.
+ * Each permitted version is for a particular article version (eg. submitted, accepted, published) and contains
+ *
+ * A list of general conditions / terms for deposit of this version of work
+ * A list of allowed locations (eg. institutional repository, personal homepage, non-commercial repository)
+ * A list of prerequisite conditions for deposit (eg. attribution, linking to published version)
+ * A list of required licences for the deposited work (eg. CC-BY-NC)
+ * Embargo requirements, if any
+ *
+ * This class also has some helper data for labels, which can be used with i18n when displaying policy information
+ *
+ * @see SHERPAPublisherPolicy
+ */
+public class SHERPAPermittedVersion {
+
+    // Version (submitted, accepted, published)
+    private String articleVersion;
+
+    // Version label
+    private String articleVersionLabel;
+
+    // Option number
+    private int option;
+
+    // General conditions
+    private List<String> conditions;
+    // Prerequisites (eg. if required by funder)
+    private List<String> prerequisites;
+    // Allowed locations
+    private List<String> locations;
+    // Required license(s)
+    private List<String> licenses;
+    // Embargo
+    private SHERPAEmbargo embargo;
+
+    protected class SHERPAEmbargo {
+        String units;
+        int amount;
+    }
+
+    public String getArticleVersion() {
+        return articleVersion;
+    }
+
+    public void setArticleVersion(String articleVersion) {
+        this.articleVersion = articleVersion;
+    }
+
+    public List<String> getConditions() {
+        return conditions;
+    }
+
+    public void setConditions(List<String> conditions) {
+        this.conditions = conditions;
+    }
+
+    public List<String> getPrerequisites() {
+        return prerequisites;
+    }
+
+    public void setPrerequisites(List<String> prerequisites) {
+        this.prerequisites = prerequisites;
+    }
+
+    public List<String> getLocations() {
+        return locations;
+    }
+
+    public void setLocations(List<String> locations) {
+        this.locations = locations;
+    }
+
+    public List<String> getLicenses() {
+        return licenses;
+    }
+
+    public void setLicenses(List<String> licenses) {
+        this.licenses = licenses;
+    }
+
+    public SHERPAEmbargo getEmbargo() {
+        return embargo;
+    }
+
+    public void setEmbargo(SHERPAEmbargo embargo) {
+        this.embargo = embargo;
+    }
+
+    public int getOption() {
+        return option;
+    }
+
+    public void setOption(int option) {
+        this.option = option;
+    }
+
+    public String getArticleVersionLabel() {
+        return articleVersionLabel;
+    }
+
+    public void setArticleVersionLabel(String articleVersionLabel) {
+        this.articleVersionLabel = articleVersionLabel;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAPublisher.java

@@ -0,0 +1,100 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+/**
+ * Plain java representation of a SHERPA Publisher object, based on SHERPA API v2 responses.
+ *
+ * In a search for SHERPA journal deposit policy, this publisher object will appear in a list of publishers
+ * from the journal object, and as a single publisher member for the primary/current publisher of the journal.
+ * In a search for SHERPA publisher information, this object will appear in a list of publishers from the main
+ * SHERPA Publisher Response object
+ *
+ * @see SHERPAJournal
+ * @see SHERPAPublisherResponse
+ */
+public class SHERPAPublisher {
+    private String name = null;
+    private String relationshipType;
+    private String country;
+    private String uri = null;
+    private String identifier = null;
+    private int publicationCount;
+
+    // this is not technically in the same place in SHERPA data model but it makes more sense to apply it here
+    // is it is treated as a 'special case' - just for printing links to paid OA access policies
+    private String paidAccessDescription;
+    private String paidAccessUrl;
+
+    public SHERPAPublisher() {
+    }
+
+    public String getName() {
+        return name;
+    }
+
+    public void setName(String name) {
+        this.name = name;
+    }
+
+    public String getRelationshipType() {
+        return relationshipType;
+    }
+
+    public void setRelationshipType(String relationshipType) {
+        this.relationshipType = relationshipType;
+    }
+
+    public String getCountry() {
+        return country;
+    }
+
+    public void setCountry(String country) {
+        this.country = country;
+    }
+
+    public String getUri() {
+        return uri;
+    }
+
+    public void setUri(String uri) {
+        this.uri = uri;
+    }
+
+    public int getPublicationCount() {
+        return publicationCount;
+    }
+
+    public void setPublicationCount(int publicationCount) {
+        this.publicationCount = publicationCount;
+    }
+
+    public String getPaidAccessDescription() {
+        return paidAccessDescription;
+    }
+
+    public void setPaidAccessDescription(String paidAccessDescription) {
+        this.paidAccessDescription = paidAccessDescription;
+    }
+
+    public String getPaidAccessUrl() {
+        return paidAccessUrl;
+    }
+
+    public void setPaidAccessUrl(String paidAccessUrl) {
+        this.paidAccessUrl = paidAccessUrl;
+    }
+
+    public String getIdentifier() {
+        return identifier;
+    }
+
+    public void setIdentifier(String identifier) {
+        this.identifier = identifier;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAPublisherPolicy.java

@@ -0,0 +1,128 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+import java.util.List;
+import java.util.Map;
+
+/**
+ * Plain java representation of a SHERPA Publisher Policy object, based on SHERPA API v2 responses.
+ *
+ * In a SHERPA search for deposit policies, each journal contains one or more publisher policies
+ * Each publisher policies contains a list of different article versions (eg. submitted, accepted, published)
+ * which hold the data about what can be done with each version.
+ * This class also holds copyright URLs and other policy URLs, as well as some helper information for display
+ * of overall policies in UI (as per legacy SHERPA data)
+ *
+ * @see SHERPAJournal
+ * @see SHERPAPermittedVersion
+ */
+public class SHERPAPublisherPolicy {
+
+    private int id;
+    private boolean openAccessPermitted;
+    private String uri;
+    private String internalMoniker;
+    private List<SHERPAPermittedVersion> permittedVersions;
+    private Map<String, String> urls;
+    private boolean openAccessProhibited;
+    private int publicationCount;
+
+    // The legacy "can" / "cannot" indicators
+    private String preArchiving = "cannot";
+    private String postArchiving = "cannot";
+    private String pubArchiving = "cannot";
+
+    public int getId() {
+        return id;
+    }
+
+    public void setId(int id) {
+        this.id = id;
+    }
+
+    public boolean isOpenAccessPermitted() {
+        return openAccessPermitted;
+    }
+
+    public void setOpenAccessPermitted(boolean openAccessPermitted) {
+        this.openAccessPermitted = openAccessPermitted;
+    }
+
+    public String getUri() {
+        return uri;
+    }
+
+    public void setUri(String uri) {
+        this.uri = uri;
+    }
+
+    public String getInternalMoniker() {
+        return internalMoniker;
+    }
+
+    public void setInternalMoniker(String internalMoniker) {
+        this.internalMoniker = internalMoniker;
+    }
+
+    public List<SHERPAPermittedVersion> getPermittedVersions() {
+        return permittedVersions;
+    }
+
+    public void setPermittedVersions(List<SHERPAPermittedVersion> permittedVersions) {
+        this.permittedVersions = permittedVersions;
+    }
+
+    public Map<String, String> getUrls() {
+        return urls;
+    }
+
+    public void setUrls(Map<String, String> urls) {
+        this.urls = urls;
+    }
+
+    public boolean isOpenAccessProhibited() {
+        return openAccessProhibited;
+    }
+
+    public void setOpenAccessProhibited(boolean openAccessProhibited) {
+        this.openAccessProhibited = openAccessProhibited;
+    }
+
+    public int getPublicationCount() {
+        return publicationCount;
+    }
+
+    public void setPublicationCount(int publicationCount) {
+        this.publicationCount = publicationCount;
+    }
+
+    public String getPreArchiving() {
+        return preArchiving;
+    }
+
+    public void setPreArchiving(String preArchiving) {
+        this.preArchiving = preArchiving;
+    }
+
+    public String getPostArchiving() {
+        return postArchiving;
+    }
+
+    public void setPostArchiving(String postArchiving) {
+        this.postArchiving = postArchiving;
+    }
+
+    public String getPubArchiving() {
+        return pubArchiving;
+    }
+
+    public void setPubArchiving(String pubArchiving) {
+        this.pubArchiving = pubArchiving;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAPublisherResponse.java

@@ -0,0 +1,223 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.LinkedList;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
+import org.json.JSONTokener;
+
+/**
+ * Model class for the SHERPAv2 API (JSON) response for a publisher search
+ * The structure and approached used is quite different to the simple v1 API used previously
+ *
+ * @see SHERPAPublisher
+ *
+ * @author Kim Shepherd
+ * 
+ */
+public class SHERPAPublisherResponse {
+    // Is this response to be treated as an error?
+    private boolean error;
+
+    // Error message
+    private String message;
+
+    // Parsed system metadata from search results
+    private SHERPASystemMetadata metadata;
+
+    // List of parsed publisher results
+    private List<SHERPAPublisher> publishers;
+
+    // Internal Sherpa ID
+    private int id;
+
+    // SHERPA URI (the human page version of this API response)
+    private String uri;
+
+    // Format enum - currently only JSON is supported
+    public enum SHERPAFormat {
+        JSON, XML
+    };
+
+    private static Logger log = Logger.getLogger(SHERPAPublisherResponse.class);
+
+    /**
+     * Parse SHERPA v2 API for a given format
+     * @param input - input stream from the HTTP response content
+     * @param format - requested format
+     * @throws IOException
+     */
+    public SHERPAPublisherResponse(InputStream input, SHERPAFormat format) throws IOException {
+        if (format == SHERPAFormat.JSON) {
+            parseJSON(input);
+        }
+    }
+
+    /**
+     * Parse the SHERPA v2 API JSON and construct simple list of publisher objects
+     * This method does not return a value, but rather populates the metadata and publishers objects
+     * with data parsed from the JSON.
+     * @param jsonData - the JSON input stream from the API result response body
+     */
+    private void parseJSON(InputStream jsonData) throws IOException {
+        InputStreamReader streamReader = new InputStreamReader(jsonData);
+        JSONTokener jsonTokener = new JSONTokener(streamReader);
+        JSONObject httpResponse;
+        try {
+            httpResponse = new JSONObject(jsonTokener);
+            if (httpResponse.has("items")) {
+                JSONArray items = httpResponse.getJSONArray("items");
+
+                // items array in this context is publisher results - parsing is more simple than
+                // parsing the full journal / policy responses
+                if (items.length() > 0) {
+                    metadata = new SHERPASystemMetadata();
+                    this.publishers = new LinkedList<>();
+                    // Iterate search result items
+                    for (int itemIndex = 0; itemIndex < items.length(); itemIndex++) {
+                        SHERPAPublisher sherpaPublisher = new SHERPAPublisher();
+
+                        JSONObject item = items.getJSONObject(0);
+
+                        // Parse system metadata (per-item / result information)
+                        if (item.has("system_metadata")) {
+                            JSONObject systemMetadata = item.getJSONObject("system_metadata");
+                            metadata = parseSystemMetadata(systemMetadata);
+                            if (metadata.getId() >= 0) {
+                                // Set publisher identifier to be the internal SHERPA ID
+                                // eg. '30' (Elsevier)
+                                sherpaPublisher.setIdentifier(String.valueOf(metadata.getId()));
+                            }
+                        }
+
+                        // Set publisher name
+                        sherpaPublisher.setName(parsePublisherName(item));
+
+                        // Set publisher URL
+                        sherpaPublisher.setUri(parsePublisherURL(item));
+
+                        this.publishers.add(sherpaPublisher);
+                    }
+
+                } else {
+                    error = true;
+                    message = "No results found";
+                }
+            } else {
+                error = true;
+                message = "No results found";
+            }
+
+        } catch (JSONException e) {
+            log.error("Failed to parse SHERPA response", e);
+            error = true;
+        } finally {
+            streamReader.close();
+        }
+    }
+
+    /**
+     * Parse system metadata and return populated SHERPASystemMetadata object
+     * @param systemMetadata
+     */
+    private SHERPASystemMetadata parseSystemMetadata(JSONObject systemMetadata) {
+
+        SHERPASystemMetadata metadata = new SHERPASystemMetadata();
+
+        if (systemMetadata.has("uri")) {
+            this.uri = systemMetadata.getString("uri");
+            metadata.setUri(this.uri);
+        } else {
+            log.error("SHERPA URI missing for API response item");
+        }
+        if (systemMetadata.has("id")) {
+            this.id = systemMetadata.getInt("id");
+            metadata.setId(this.id);
+        } else {
+            log.error("SHERPA internal ID missing for API response item");
+        }
+        // Get date created and added - DSpace expects this in the publisher object, though
+        if (systemMetadata.has("date_created")) {
+            metadata.setDateCreated(systemMetadata.getString("date_created"));
+        }
+        if (systemMetadata.has("date_modified")) {
+            metadata.setDateModified(systemMetadata.getString("date_modified"));
+        }
+
+        return metadata;
+    }
+
+    /**
+     * Parse publisher array and return the first name string found
+     * @param publisher - array of publisher JSON data
+     * @return first publisher name found (trimmed String)
+     */
+    private String parsePublisherName(JSONObject publisher) {
+        String name = null;
+        if (publisher.has("name")) {
+            JSONArray publisherNames = publisher.getJSONArray("name");
+            if (publisherNames.length() > 0) {
+                JSONObject publisherName = publisherNames.getJSONObject(0);
+                if (publisherName.has("name")) {
+                    name = publisherName.getString("name").trim();
+                }
+            }
+        }
+        return name;
+    }
+
+
+    /**
+     * Parse publisher URL from the json data
+     * @param publisher - publisher object (from JSON array)
+     * @return publisher URL as string
+     */
+    private String parsePublisherURL(JSONObject publisher) {
+        if (publisher.has("url")) {
+            return publisher.getString("url");
+        }
+        return null;
+    }
+
+    /**
+     * Create new response object to be handled as an error
+     * @param message - the message to render in logs or error pages
+     */
+    public SHERPAPublisherResponse(String message) {
+        this.message = message;
+        this.error = true;
+    }
+
+    public boolean isError() {
+        return error;
+    }
+
+    public String getMessage() {
+        return message;
+    }
+
+    public void setMessage(String message) {
+        this.message = message;
+    }
+
+    public SHERPASystemMetadata getMetadata() {
+        return metadata;
+    }
+
+    public List<SHERPAPublisher> getPublishers() {
+        return publishers;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAResponse.java

@@ -0,0 +1,557 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+
+import org.apache.log4j.Logger;
+import org.dspace.core.I18nUtil;
+import org.json.JSONArray;
+import org.json.JSONException;
+import org.json.JSONObject;
+import org.json.JSONTokener;
+
+/**
+ * Model class for the SHERPAv2 API (JSON) response for a publication (journal) search
+ * The structure and approached used is quite different to the simple v1 API used previously
+ * The structure is based on journal data, which in turn contains data about publishers and policies
+ *
+ * @see SHERPAJournal
+ * 
+ * @author Kim Shepherd
+ * 
+ */
+public class SHERPAResponse {
+    // Is this response to be treated as an error?
+    private boolean error;
+
+    // Error message
+    private String message;
+
+    // Parsed system metadata from search results
+    private SHERPASystemMetadata metadata;
+
+    // List of parsed journal results
+    private List<SHERPAJournal> journals;
+
+    // Internal Sherpa ID
+    private int id;
+
+    // SHERPA URI (the human page version of this API response)
+    private String uri;
+
+    // Format enum - currently only JSON is supported
+    public enum SHERPAFormat {
+        JSON, XML
+    };
+
+    private static Logger log = Logger.getLogger(SHERPAResponse.class);
+
+    /**
+     * Parse SHERPA v2 API for a given format
+     * @param input - input stream from the HTTP response content
+     * @param format - requested format
+     * @throws IOException
+     */
+    public SHERPAResponse(InputStream input, SHERPAFormat format) throws IOException {
+        if (format == SHERPAFormat.JSON) {
+            parseJSON(input);
+        }
+    }
+
+    /**
+     * Parse the SHERPA v2 API JSON and construct Romeo policy data for display
+     * This method does not return a value, but rather populates the metadata and journals objects
+     * with data parsed from the JSON.
+     * @param jsonData - the JSON input stream from the API result response body
+     */
+    private void parseJSON(InputStream jsonData) throws IOException {
+        InputStreamReader streamReader = new InputStreamReader(jsonData);
+        JSONTokener jsonTokener = new JSONTokener(streamReader);
+        JSONObject httpResponse;
+        try {
+            httpResponse = new JSONObject(jsonTokener);
+            if (httpResponse.has("items")) {
+                JSONArray items = httpResponse.getJSONArray("items");
+
+                // items array is search results, *not* journals or publishers - they are listed for each item
+                // - however, we only ever want one result since we're passing an "equals ISSN" query
+                if (items.length() > 0) {
+                    metadata = new SHERPASystemMetadata();
+                    this.journals = new LinkedList<>();
+                    // Iterate search result items
+                    for (int itemIndex = 0; itemIndex < items.length(); itemIndex++) {
+                        List<SHERPAPublisher> sherpaPublishers = new LinkedList<>();
+                        List<SHERPAPublisherPolicy> policies = new ArrayList<>();
+                        SHERPAPublisher sherpaPublisher = new SHERPAPublisher();
+                        SHERPAJournal sherpaJournal = new SHERPAJournal();
+
+                        JSONObject item = items.getJSONObject(0);
+
+                        // Parse system metadata (per-item / result information)
+                        if (item.has("system_metadata")) {
+                            JSONObject systemMetadata = item.getJSONObject("system_metadata");
+                            metadata = parseSystemMetadata(systemMetadata);
+                        }
+
+                        // Parse "publisher policy"
+                        // note - most of the information that was previously under 'publisher' is now under here
+                        if (item.has("publisher_policy")) {
+
+                            // Parse main publisher policies node
+                            JSONArray publisherPolicies = item.getJSONArray("publisher_policy");
+                            for (int i = 0; i < publisherPolicies.length(); i++) {
+
+                                JSONObject policy = publisherPolicies.getJSONObject(i);
+
+                                // Special case - quickly check the policy for the 'paid access' option
+                                // and continue if found, then parse the rest of the policy
+                                String moniker = null;
+                                if (policy.has("internal_moniker")) {
+                                    moniker = policy.getString("internal_moniker");
+                                }
+                                // This seems to be usually policy(ies) for the journal proper
+                                // and then an "Open access option" which contains some of the info
+                                // that the 'paidaccess' node in the old API used to contain
+                                // Look for: internal_moniker = "Open access option"
+                                // Check if this is OA options (Paid Access) or not
+                                if ("Open access option".equalsIgnoreCase(moniker)) {
+                                    log.debug("This is the Open access options policy - a special case");
+                                    if (policy.has("urls")) {
+                                        JSONArray urls = policy.getJSONArray("urls");
+                                        for (int u = 0; u < urls.length(); u++) {
+                                            JSONObject url = urls.getJSONObject(u);
+                                            if (url.has("description") &&
+                                                "Open Access".equalsIgnoreCase(url.getString("description"))) {
+                                                log.debug("Found OA paid access url: " + url.getString("url"));
+                                                sherpaPublisher.setPaidAccessDescription(url.getString("description"));
+                                                sherpaPublisher.setPaidAccessUrl(url.getString("url"));
+                                                break;
+                                            }
+                                        }
+                                    }
+                                    // Continue the loop here - this "policy" is a bit different and we
+                                    // don't want to add irrelevant conditions to the policy
+                                    continue;
+                                }
+
+                                // Parse the main publisher policy object and add to the list
+                                SHERPAPublisherPolicy sherpaPublisherPolicy = parsePublisherPolicy(policy);
+                                policies.add(sherpaPublisherPolicy);
+                            }
+
+                            // set publisher name - note we're only looking for the first name here
+                            // as per previous functionality (for simple display)
+                            if (item.has("publishers")) {
+                                JSONArray publishers = item.getJSONArray("publishers");
+                                if (publishers.length() > 0) {
+                                    JSONObject publisherElement = publishers.getJSONObject(0);
+                                    if (publisherElement.has("publisher")) {
+                                        JSONObject publisher = publisherElement.getJSONObject("publisher");
+                                        sherpaPublisher.setName(parsePublisherName(publisher));
+                                        sherpaPublisher.setUri(parsePublisherURL(publisher));
+                                    }
+                                }
+                            }
+
+                            // Parse journal data
+                            sherpaJournal = parseJournal(item, sherpaPublisher.getName());
+                        }
+
+                        sherpaPublishers.add(sherpaPublisher);
+                        sherpaJournal.setPublisher(sherpaPublisher);
+                        sherpaJournal.setPublishers(sherpaPublishers);
+                        sherpaJournal.setPolicies(policies);
+                        this.journals.add(sherpaJournal);
+                    }
+
+                } else {
+                    error = true;
+                    message = "No results found";
+                }
+            } else {
+                error = true;
+                message = "No results found";
+            }
+
+        } catch (JSONException e) {
+            log.error("Failed to parse SHERPA response", e);
+            error = true;
+        } finally {
+            streamReader.close();
+        }
+    }
+
+    /**
+     * Parse system metadata and return populated SHERPASystemMetadata object
+     * @param systemMetadata
+     */
+    private SHERPASystemMetadata parseSystemMetadata(JSONObject systemMetadata) {
+
+        SHERPASystemMetadata metadata = new SHERPASystemMetadata();
+
+        if (systemMetadata.has("uri")) {
+            this.uri = systemMetadata.getString("uri");
+            metadata.setUri(this.uri);
+        } else {
+            log.error("SHERPA URI missing for API response item");
+        }
+        if (systemMetadata.has("id")) {
+            this.id = systemMetadata.getInt("id");
+            metadata.setId(this.id);
+        } else {
+            log.error("SHERPA internal ID missing for API response item");
+        }
+        // Get date created and added - DSpace expects this in the publisher object, though
+        if (systemMetadata.has("date_created")) {
+            metadata.setDateCreated(systemMetadata.getString("date_created"));
+        }
+        if (systemMetadata.has("date_modified")) {
+            metadata.setDateModified(systemMetadata.getString("date_modified"));
+        }
+        // Is this item publicly visible?
+        if (systemMetadata.has("publicly_visible")) {
+            metadata.setPubliclyVisible ("yes".equals(systemMetadata
+                .getString("publicly_visible")));
+        }
+        // Is this item listed in the DOAJ?
+        if (systemMetadata.has("listed_in_doaj")) {
+            metadata.setPubliclyVisible ("yes".equals(systemMetadata
+                .getString("listed_in_doaj")));
+        }
+
+        return metadata;
+    }
+
+    /**
+     * Parse journal JSON data and return populated bean
+     * This method also takes publisherName as a string to help construct some
+     * legacy labels
+     * @param item - the main result item JSON (which is the closest thing to an actual 'journal')
+     * @param publisherName - the parsed publisher name
+     * @return
+     */
+    private SHERPAJournal parseJournal(JSONObject item, String publisherName) {
+
+        SHERPAJournal sherpaJournal = new SHERPAJournal();
+
+        // set journal title
+        if (item.has("title")) {
+            JSONArray titles = item.getJSONArray("title");
+            if (titles.length() > 0) {
+                List<String> titleList = new ArrayList<>();
+                for (int t = 0; t < titles.length(); t++) {
+                    JSONObject title = titles.getJSONObject(t);
+                    if (title.has("title")) {
+                        titleList.add(title.getString("title").trim());
+                    }
+                }
+                sherpaJournal.setTitles(titleList);
+                if (titleList.size() > 0) {
+                    // Faking this a bit based on what I'd seen - not in the API v2 data
+                    sherpaJournal.setRomeoPub(publisherName + ": "
+                        + titleList.get(0));
+                    sherpaJournal.setZetoPub(publisherName + ": "
+                        + titleList.get(0));
+                    log.debug("Found journal title: " + titleList.get(0));
+                }
+            }
+        }
+
+        // Journal URL
+        if (item.has("url")) {
+            sherpaJournal.setUrl(item.getString("url"));
+        }
+
+        // set ISSNs
+        if (item.has("issns")) {
+            JSONArray issns = item.getJSONArray("issns");
+            // just get first - DSpace data model only allows for one
+            List<String> issnList = new ArrayList<>();
+            for (int ii = 0; ii < issns.length(); ii++) {
+                JSONObject issn = issns.getJSONObject(ii);
+                issnList.add(issn.getString("issn").trim());
+            }
+            sherpaJournal.setIssns(issnList);
+        }
+
+        // Is the item in DOAJ?
+        if (item.has("listed_in_doaj")) {
+            sherpaJournal.setInDOAJ(("yes".equals(item.getString("listed_in_doaj"))));
+        }
+
+        return sherpaJournal;
+    }
+
+    /**
+     * Parse a publisher_policy JSON data and return a populated bean
+     * @param policy - each publisher policy node in the JSON array
+     * @return populated SHERPAPublisherPolicy object
+     */
+    private SHERPAPublisherPolicy parsePublisherPolicy(JSONObject policy) {
+
+        SHERPAPublisherPolicy sherpaPublisherPolicy = new SHERPAPublisherPolicy();
+
+        // Get and set monikers
+        String moniker = null;
+        if (policy.has("internal_moniker")) {
+            moniker = policy.getString("internal_moniker");
+            sherpaPublisherPolicy.setInternalMoniker(moniker);
+        }
+
+        // URLs (used to be Copyright Links)
+        if (policy.has("urls")) {
+            JSONArray urls = policy.getJSONArray("urls");
+            Map<String, String> copyrightLinks = new TreeMap<>();
+            for (int u = 0; u < urls.length(); u++) {
+                JSONObject url = urls.getJSONObject(u);
+                if (url.has("description") && url.has("url")) {
+                    log.debug("Setting copyright URL: " + url.getString("url"));
+                    copyrightLinks.put(url.getString("url"), url.getString("description"));
+                }
+            }
+            sherpaPublisherPolicy.setUrls(copyrightLinks);
+        }
+
+        // Permitted OA options
+        int submittedOption = 0;
+        int acceptedOption = 0;
+        int publishedOption = 0;
+        int currentOption = 0;
+        if (policy.has("permitted_oa")) {
+            List<String> allowed = new ArrayList<>();
+            JSONArray permittedOA = policy.getJSONArray("permitted_oa");
+            List<SHERPAPermittedVersion> permittedVersions = new ArrayList<>();
+
+            // Iterate each permitted OA version / option. The permitted_oa node is also known as a 'pathway' --
+            // essentially "a way to get a work into a repository". Each pathway could refer to one article version
+            // like a pre-print, or multiple versions might have the same acceptable locations and conditions.
+            // As described below, where multiple versions are referenced in a single permitted_oa pathway, they will
+            // be split out and treated separately. This keeps processing simple, especially later in display or
+            // compliance checking when it is preferred to group / indicate rules by the article version
+            for (int p = 0; p < permittedOA.length(); p++) {
+                JSONObject permitted = permittedOA.getJSONObject(p);
+                // Although it adds redundancy, we will treat each 'article version' within
+                // the permitted_oa ("pathway") node as a separate version altogether to keep the rest of our display
+                // handled nicely. This was confirmed as an appropriate approach by JISC
+                if (permitted.has("article_version")) {
+                    JSONArray versions = permitted.getJSONArray("article_version");
+                    for (int v = 0; v < versions.length(); v++) {
+                        // Parse this permitted_oa node but specifically looking for the article_version 'v'
+                        SHERPAPermittedVersion permittedVersion = parsePermittedVersion(permitted, v);
+
+                        // To determine which option # we are, inspect article versions and set
+                        allowed.add(permittedVersion.getArticleVersion());
+                        if ("submitted".equals(permittedVersion.getArticleVersion())) {
+                            submittedOption++;
+                            currentOption = submittedOption;
+                        } else if ("accepted".equals(permittedVersion.getArticleVersion())) {
+                            acceptedOption++;
+                            currentOption = acceptedOption;
+                        } else if ("published".equals(permittedVersion.getArticleVersion())) {
+                            publishedOption++;
+                            currentOption = publishedOption;
+                        }
+                        permittedVersion.setOption(currentOption);
+                        permittedVersions.add(permittedVersion);
+                    }
+                }
+
+                // Populate the old indicators into the publisher policy object
+                if (allowed.contains("submitted")) {
+                    sherpaPublisherPolicy.setPreArchiving("can");
+                }
+                if (allowed.contains("accepted")) {
+                    sherpaPublisherPolicy.setPostArchiving("can");
+                }
+                if (allowed.contains("published")) {
+                    sherpaPublisherPolicy.setPubArchiving("can");
+                }
+
+            }
+            sherpaPublisherPolicy.setPermittedVersions(permittedVersions);
+        }
+
+        return sherpaPublisherPolicy;
+    }
+
+    /**
+     * Parse permitted version JSON and populate new bean from the data
+     * @param permitted - each 'permitted_oa' node in the JSON array
+     * @return populated SHERPAPermittedVersion object
+     */
+    private SHERPAPermittedVersion parsePermittedVersion(JSONObject permitted, int index) {
+
+        SHERPAPermittedVersion permittedVersion = new SHERPAPermittedVersion();
+
+        // Get the article version, which is ultimately used for the ticks / crosses
+        // in the UI display. My assumptions around translation:
+        // submitted = preprint
+        // accepted = postprint
+        // published = pdfversion
+        // These strings can be used to construct i18n messages.
+        String articleVersion = "unknown";
+        String versionLabel = "Unknown";
+
+        // Each 'permitted OA' can actually refer to multiple versions
+        if (permitted.has("article_version")) {
+            JSONArray versions = permitted.getJSONArray("article_version");
+
+            // Get one particular article version to return as a PermittedVersion. The outer loop calling this
+            // is iterating all permitted_oa and permitted_oa->article_version array members
+            articleVersion = versions.getString(index);
+            permittedVersion.setArticleVersion(articleVersion);
+            log.debug("Added allowed version: " + articleVersion + " to list");
+        }
+
+        // Add labels for this particular article version
+        if ("submitted".equals(articleVersion)) {
+            versionLabel = I18nUtil.getMessage("jsp.sherpa.submitted-version-label");
+        } else if ("accepted".equals(articleVersion)) {
+            versionLabel = I18nUtil.getMessage("jsp.sherpa.accepted-version-label");
+        } else if ("published".equals(articleVersion)) {
+            versionLabel = I18nUtil.getMessage("jsp.sherpa.published-version-label");
+        }
+        // Set the article version label based on the i18n text set above
+        permittedVersion.setArticleVersionLabel(versionLabel);
+
+        // These are now child arrays, in old API they were explicit like
+        // "preprint restrictions", etc., and just contained text rather than data
+        if (permitted.has("conditions")) {
+            List<String> conditionList = new ArrayList<>();
+            JSONArray conditions = permitted.getJSONArray("conditions");
+            for (int c = 0; c < conditions.length(); c++) {
+                conditionList.add(conditions.getString(c).trim());
+            }
+            permittedVersion.setConditions(conditionList);
+        }
+
+        // Any prerequisites for this option (eg required by funder)
+        List<String> prerequisites = new ArrayList<>();
+        if (permitted.has("prerequisites")) {
+            JSONObject prereqs = permitted.getJSONObject("prerequisites");
+            if (prereqs.has("prerequisites_phrases")) {
+                JSONArray phrases = prereqs.getJSONArray("prerequisites_phrases");
+                for (int pp = 0; pp < phrases.length(); pp++) {
+                    JSONObject phrase = phrases.getJSONObject(pp);
+                    if (phrase.has("phrase")) {
+                        prerequisites.add(phrase.getString("phrase").trim());
+                    }
+                }
+            }
+        }
+        permittedVersion.setPrerequisites(prerequisites);
+
+        // Locations where this version / option may be archived
+        List<String> sherpaLocations = new ArrayList<>();
+        if (permitted.has("location")) {
+            JSONObject locations = permitted.getJSONObject("location");
+            if (locations.has("location_phrases")) {
+                JSONArray locationPhrases = locations.getJSONArray("location_phrases");
+                if (locationPhrases.length() > 0) {
+                    for (int l = 0; l < locationPhrases.length(); l++) {
+                        JSONObject locationPhrase = locationPhrases.getJSONObject(l);
+                        if (locationPhrase.has("phrase")) {
+                            sherpaLocations.add(locationPhrase.getString("phrase").trim());
+                        }
+                    }
+                }
+            }
+        }
+        permittedVersion.setLocations(sherpaLocations);
+
+        List<String> sherpaLicenses = new ArrayList<>();
+        // required licences
+        if (permitted.has("license")) {
+            JSONArray licences = permitted.getJSONArray("license");
+            for (int l = 0; l < licences.length(); l++) {
+                JSONObject licence = licences.getJSONObject(l);
+                if (licence.has("license_phrases")) {
+                    JSONArray phrases = licence.getJSONArray("license_phrases");
+                    for (int ll = 0; ll < phrases.length(); ll++) {
+                        JSONObject phrase = phrases.getJSONObject(ll);
+                        if (phrase.has("phrase")) {
+                            sherpaLicenses.add(phrase.getString("phrase").trim());
+                        }
+                    }
+                }
+            }
+        }
+        permittedVersion.setLicenses(sherpaLicenses);
+
+        return permittedVersion;
+    }
+
+    /**
+     * Parse publisher array and return the first name string found
+     * @param publisher - array of publisher JSON data
+     * @return first publisher name found (trimmed String)
+     */
+    private String parsePublisherName(JSONObject publisher) {
+        String name = null;
+        if (publisher.has("name")) {
+            JSONArray publisherNames = publisher.getJSONArray("name");
+            if (publisherNames.length() > 0) {
+                JSONObject publisherName = publisherNames.getJSONObject(0);
+                if (publisherName.has("name")) {
+                    name = publisherName.getString("name").trim();
+                }
+            }
+        }
+        return name;
+    }
+
+
+    /**
+     * Parse publisher URL from the json data
+     * @param publisher - publisher object (from JSON array)
+     * @return publisher URL as string
+     */
+    private String parsePublisherURL(JSONObject publisher) {
+        if (publisher.has("url")) {
+            return publisher.getString("url");
+        }
+        return null;
+    }
+
+    /**
+     * Create new response object to be handled as an error
+     * @param message - the message to render in logs or error pages
+     */
+    public SHERPAResponse(String message) {
+        this.message = message;
+        this.error = true;
+    }
+
+    public boolean isError() {
+        return error;
+    }
+
+    public String getMessage() {
+        return message;
+    }
+
+    public void setMessage(String message) {
+        this.message = message;
+    }
+
+    public List<SHERPAJournal> getJournals() {
+        return journals;
+    }
+
+    public SHERPASystemMetadata getMetadata() {
+        return metadata;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPASystemMetadata.java

@@ -0,0 +1,80 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+/**
+ * Plain java representation of a SHERPA System Metadata object, based on SHERPA API v2 responses.
+ *
+ * This data is included in both journal deposit policy and publisher searches and contains basic metadata
+ * about the SHERPA record and API response, eg. creation and modification dates, internal IDs, permissions, etc.
+ *
+ * @see SHERPAResponse
+ * @see SHERPAPublisherResponse
+ *
+ * @author Kim Shepherd
+ */
+public class SHERPASystemMetadata {
+
+    private int id;
+    private String uri;
+    private String dateCreated;
+    private String dateModified;
+    private boolean isPubliclyVisible = false;
+    private boolean inDOAJ = false;
+
+    public SHERPASystemMetadata() {
+    }
+
+    public int getId() {
+        return id;
+    }
+
+    public void setId(int id) {
+        this.id = id;
+    }
+
+    public String getUri() {
+        return uri;
+    }
+
+    public void setUri(String uri) {
+        this.uri = uri;
+    }
+
+    public String getDateCreated() {
+        return dateCreated;
+    }
+
+    public void setDateCreated(String dateCreated) {
+        this.dateCreated = dateCreated;
+    }
+
+    public String getDateModified() {
+        return dateModified;
+    }
+
+    public void setDateModified(String dateModified) {
+        this.dateModified = dateModified;
+    }
+
+    public boolean isPubliclyVisible() {
+        return isPubliclyVisible;
+    }
+
+    public void setPubliclyVisible(boolean publiclyVisible) {
+        isPubliclyVisible = publiclyVisible;
+    }
+
+    public boolean isInDOAJ() {
+        return inDOAJ;
+    }
+
+    public void setInDOAJ(boolean inDOAJ) {
+        this.inDOAJ = inDOAJ;
+    }
+}

dspace-api/src/main/java/org/dspace/app/sherpa/v2/SHERPAUtils.java

@@ -0,0 +1,38 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.sherpa.v2;
+
+/**
+ * SHERPA v2 API query handling utility methods (static). Used by external data providers and SHERPA service.
+ *
+ * @author Kim Shepherd
+ */
+public final class SHERPAUtils {
+
+    // Private constructor (since this is a Utility class)
+    private SHERPAUtils() {}
+
+    /**
+     * Sanitise a SHERPA v2 API query for some special JSON characters to help with parsing at remote end
+     * Strip all these characters: "'{};
+     * The URI builder used in the provider and service classes will perform URL encoding. This string
+     * is the raw query submitted to the provider or service.
+     * @param query query string
+     * @return safe query string
+     */
+    public static String sanitiseQuery(String query) {
+        String safe = query;
+        try {
+            safe = query.replaceAll("['{}\";]", "");
+        } catch (NullPointerException e) {
+            safe = "";
+        }
+        return safe;
+    }
+
+}

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

@@ -23,10 +23,12 @@ import java.util.List;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
+import org.apache.commons.collections4.CollectionUtils;
+import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
@@ -39,6 +41,11 @@ import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
+import org.dspace.discovery.DiscoverQuery;
+import org.dspace.discovery.DiscoverResult;
+import org.dspace.discovery.SearchService;
+import org.dspace.discovery.SearchServiceException;
+import org.dspace.discovery.SearchUtils;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
@@ -52,7 +59,7 @@ public class GenerateSitemaps {
     /**
      * Logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(GenerateSitemaps.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(GenerateSitemaps.class);
 
     private static final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     private static final CollectionService collectionService =
@@ -60,6 +67,7 @@ public class GenerateSitemaps {
     private static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
     private static final ConfigurationService configurationService =
         DSpaceServicesFactory.getInstance().getConfigurationService();
+    private static final SearchService searchService = SearchUtils.getSearchService();
 
     /**
      * Default constructor
@@ -69,7 +77,7 @@ public class GenerateSitemaps {
     public static void main(String[] args) throws Exception {
         final String usage = GenerateSitemaps.class.getCanonicalName();
 
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         HelpFormatter hf = new HelpFormatter();
 
         Options options = new Options();
@@ -84,6 +92,9 @@ public class GenerateSitemaps {
         options
             .addOption("p", "ping", true,
                        "ping specified search engine URL");
+        options
+            .addOption("d", "delete", false,
+                "delete sitemaps dir and its contents");
 
         CommandLine line = null;
 
@@ -105,10 +116,9 @@ public class GenerateSitemaps {
         }
 
         /*
-         * Sanity check -- if no sitemap generation or pinging to do, print
-         * usage
+         * Sanity check -- if no sitemap generation or pinging to do, or deletion, print usage
          */
-        if (line.getArgs().length != 0 || line.hasOption('b')
+        if (line.getArgs().length != 0 || line.hasOption('d') || line.hasOption('b')
             && line.hasOption('s') && !line.hasOption('g')
             && !line.hasOption('m') && !line.hasOption('y')
             && !line.hasOption('p')) {
@@ -123,6 +133,10 @@ public class GenerateSitemaps {
             generateSitemaps(!line.hasOption('b'), !line.hasOption('s'));
         }
 
+        if (line.hasOption('d')) {
+            deleteSitemaps();
+        }
+
         if (line.hasOption('a')) {
             pingConfiguredSearchEngines();
         }
@@ -140,6 +154,29 @@ public class GenerateSitemaps {
         System.exit(0);
     }
 
+    /**
+     * Runs generate-sitemaps without any params for the scheduler (task-scheduler.xml).
+     *
+     * @throws SQLException if a database error occurs.
+     * @throws IOException  if IO error occurs.
+     */
+    public static void generateSitemapsScheduled() throws IOException, SQLException {
+        generateSitemaps(true, true);
+    }
+
+    /**
+     * Delete the sitemaps directory and its contents if it exists
+     * @throws IOException  if IO error occurs
+     */
+    public static void deleteSitemaps() throws IOException {
+        File outputDir = new File(configurationService.getProperty("sitemap.dir"));
+        if (!outputDir.exists() && !outputDir.isDirectory()) {
+            log.error("Unable to delete sitemaps directory, doesn't exist or isn't a directort");
+        } else {
+            FileUtils.deleteDirectory(outputDir);
+        }
+    }
+
     /**
      * Generate sitemap.org protocol and/or basic HTML sitemaps.
      *
@@ -150,14 +187,9 @@ public class GenerateSitemaps {
      * @throws IOException  if IO error
      *                      if IO error occurs.
      */
-    public static void generateSitemaps(boolean makeHTMLMap,
-                                        boolean makeSitemapOrg) throws SQLException, IOException {
-        String sitemapStem = configurationService.getProperty("dspace.ui.url")
-            + "/sitemap";
-        String htmlMapStem = configurationService.getProperty("dspace.ui.url")
-            + "/htmlmap";
-        String handleURLStem = configurationService.getProperty("dspace.ui.url")
-            + "/handle/";
+    public static void generateSitemaps(boolean makeHTMLMap, boolean makeSitemapOrg) throws SQLException, IOException {
+        String uiURLStem = configurationService.getProperty("dspace.ui.url");
+        String sitemapStem = uiURLStem + "/sitemap";
 
         File outputDir = new File(configurationService.getProperty("sitemap.dir"));
         if (!outputDir.exists() && !outputDir.mkdir()) {
@@ -168,13 +200,11 @@ public class GenerateSitemaps {
         AbstractGenerator sitemapsOrg = null;
 
         if (makeHTMLMap) {
-            html = new HTMLSitemapGenerator(outputDir, htmlMapStem + "?map=",
-                                            null);
+            html = new HTMLSitemapGenerator(outputDir, sitemapStem, ".html");
         }
 
         if (makeSitemapOrg) {
-            sitemapsOrg = new SitemapsOrgGenerator(outputDir, sitemapStem
-                + "?map=", null);
+            sitemapsOrg = new SitemapsOrgGenerator(outputDir, sitemapStem, ".xml");
         }
 
         Context c = new Context(Context.Mode.READ_ONLY);
@@ -182,7 +212,7 @@ public class GenerateSitemaps {
         List<Community> comms = communityService.findAll(c);
 
         for (Community comm : comms) {
-            String url = handleURLStem + comm.getHandle();
+            String url = uiURLStem + "/communities/" + comm.getID();
 
             if (makeHTMLMap) {
                 html.addURL(url, null);
@@ -197,7 +227,7 @@ public class GenerateSitemaps {
         List<Collection> colls = collectionService.findAll(c);
 
         for (Collection coll : colls) {
-            String url = handleURLStem + coll.getHandle();
+            String url = uiURLStem + "/collections/" + coll.getID();
 
             if (makeHTMLMap) {
                 html.addURL(url, null);
@@ -214,14 +244,37 @@ public class GenerateSitemaps {
 
         while (allItems.hasNext()) {
             Item i = allItems.next();
-            String url = handleURLStem + i.getHandle();
-            Date lastMod = i.getLastModified();
 
-            if (makeHTMLMap) {
-                html.addURL(url, lastMod);
-            }
-            if (makeSitemapOrg) {
-                sitemapsOrg.addURL(url, lastMod);
+            DiscoverQuery entityQuery = new DiscoverQuery();
+            entityQuery.setQuery("search.uniqueid:\"Item-" + i.getID() + "\" and entityType:*");
+            entityQuery.addSearchField("entityType");
+
+            try {
+                DiscoverResult discoverResult = searchService.search(c, entityQuery);
+
+                String url;
+                if (CollectionUtils.isNotEmpty(discoverResult.getIndexableObjects())
+                    && CollectionUtils.isNotEmpty(discoverResult.getSearchDocument(
+                        discoverResult.getIndexableObjects().get(0)).get(0).getSearchFieldValues("entityType"))
+                    && StringUtils.isNotBlank(discoverResult.getSearchDocument(
+                        discoverResult.getIndexableObjects().get(0)).get(0).getSearchFieldValues("entityType").get(0))
+                ) {
+                    url = uiURLStem + "/entities/" + StringUtils.lowerCase(discoverResult.getSearchDocument(
+                            discoverResult.getIndexableObjects().get(0))
+                        .get(0).getSearchFieldValues("entityType").get(0)) + "/" + i.getID();
+                } else {
+                    url = uiURLStem + "/items/" + i.getID();
+                }
+                Date lastMod = i.getLastModified();
+
+                if (makeHTMLMap) {
+                    html.addURL(url, lastMod);
+                }
+                if (makeSitemapOrg) {
+                    sitemapsOrg.addURL(url, lastMod);
+                }
+            } catch (SearchServiceException e) {
+                log.error("Failed getting entitytype through solr for item " + i.getID() + ": " + e.getMessage());
             }
 
             c.uncacheEntity(i);

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

@@ -59,7 +59,7 @@ public class SitemapsOrgGenerator extends AbstractGenerator {
 
     @Override
     public String getFilename(int number) {
-        return "sitemap" + number + ".xml.gz";
+        return "sitemap" + number + ".xml";
     }
 
     @Override
@@ -100,12 +100,12 @@ public class SitemapsOrgGenerator extends AbstractGenerator {
 
     @Override
     public boolean useCompression() {
-        return true;
+        return false;
     }
 
     @Override
     public String getIndexFilename() {
-        return "sitemap_index.xml.gz";
+        return "sitemap_index.xml";
     }
 
     @Override

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

@@ -16,10 +16,11 @@ import java.util.Properties;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.Options;
-import org.apache.commons.cli.PosixParser;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * This class allows the running of the DSpace statistic tools
@@ -56,7 +57,7 @@ public class CreateStatReport {
     /**
      * File suffix for log files
      */
-    private static String outputSuffix = ".dat";
+    private static final String outputSuffix = ".dat";
 
     /**
      * User context
@@ -66,9 +67,6 @@ public class CreateStatReport {
     /**
      * the config file from which to configure the analyser
      */
-    private static String configFile = ConfigurationManager.getProperty("dspace.dir") +
-        File.separator + "config" + File.separator +
-        "dstat.cfg";
 
     /**
      * Default constructor
@@ -81,8 +79,12 @@ public class CreateStatReport {
      * Usage: java CreateStatReport -r <statistic to run>
      */
     public static void main(String[] argv) throws Exception {
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
 
         // Open the statistics config file
+        final String configFile = configurationService.getProperty("dspace.dir")
+                + File.separator + "config" + File.separator + "dstat.cfg";
         FileInputStream fis = new java.io.FileInputStream(new File(configFile));
         Properties config = new Properties();
         config.load(fis);
@@ -108,11 +110,11 @@ public class CreateStatReport {
         context.turnOffAuthorisationSystem();
 
         //get paths to directories
-        outputLogDirectory = ConfigurationManager.getProperty("log.report.dir") + File.separator;
-        outputReportDirectory = ConfigurationManager.getProperty("report.dir") + File.separator;
+        outputLogDirectory = configurationService.getProperty("log.report.dir") + File.separator;
+        outputReportDirectory = configurationService.getProperty("report.dir") + File.separator;
 
         //read in command line variable to determine which statistic to run
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = new Options();
         options.addOption("r", "report", true, "report");
         CommandLine line = parser.parse(options, argv);
@@ -405,6 +407,5 @@ public class CreateStatReport {
         System.out.println(
             "Available: <stat-initial> <stat-general> <stat-monthly> <stat-report-initial> <stat-report-general> " +
                 "<stat-report-monthly>");
-        return;
     }
 }

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

@@ -20,7 +20,8 @@ import java.util.List;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * This class provides HTML reports for the ReportGenerator class
@@ -34,7 +35,7 @@ public class HTMLReport implements Report {
     /**
      * a list of the statistic blocks being managed by this class
      */
-    private List<Statistics> blocks = new ArrayList<Statistics>();
+    private final List<Statistics> blocks = new ArrayList<>();
 
     /**
      * the title for the page
@@ -59,16 +60,23 @@ public class HTMLReport implements Report {
     /**
      * the output file to which to write aggregation data
      */
-    private String output = ConfigurationManager.getProperty("dspace.dir") +
-        File.separator + "log" + File.separator + "report";
+    private String output;
 
     /**
-     * constructor for HTML reporting
+     * Output file path is set to {@code ${dspace.dir}/log/report}.
      */
     public HTMLReport() {
-        // empty constructor
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        output = configurationService.getProperty("dspace.dir")
+                + File.separator + "log" + File.separator + "report";
     }
 
+    /**
+     * Set a non-default output file path.
+     *
+     * @param newOutput new path to the report.
+     */
     public void setOutput(String newOutput) {
         if (newOutput != null) {
             output = newOutput;
@@ -82,7 +90,7 @@ public class HTMLReport implements Report {
      */
     @Override
     public String render() {
-        StringBuffer frag = new StringBuffer();
+        StringBuilder frag = new StringBuilder();
 
         // get the page headings
         frag.append(header(pageTitle));
@@ -140,7 +148,7 @@ public class HTMLReport implements Report {
      * @return an HTML string providing internal page navigation
      */
     public String navigation() {
-        StringBuffer frag = new StringBuffer();
+        StringBuilder frag = new StringBuilder();
 
         frag.append("<div class=\"reportNavigation\">");
         frag.append("<a href=\"#general_overview\">General Overview</a>");
@@ -173,7 +181,6 @@ public class HTMLReport implements Report {
     @Override
     public void addBlock(Statistics stat) {
         blocks.add(stat);
-        return;
     }
 
 
@@ -207,7 +214,7 @@ public class HTMLReport implements Report {
      */
     @Override
     public String dateRange() {
-        StringBuffer frag = new StringBuffer();
+        StringBuilder frag = new StringBuilder();
         DateFormat df = DateFormat.getDateInstance();
 
         frag.append("<div class=\"reportDate\">");
@@ -255,7 +262,6 @@ public class HTMLReport implements Report {
         if (pageTitle == null) {
             pageTitle = mainTitle;
         }
-        return;
     }
 
 
@@ -280,7 +286,7 @@ public class HTMLReport implements Report {
         // FIXME: this need to be figured out to integrate nicely into the
         // whole JSTL thing, but for the moment it's just going to deliver
         // some styles
-        StringBuffer frag = new StringBuffer();
+        StringBuilder frag = new StringBuilder();
 
         frag.append("<style type=\"text/css\">\n");
         frag.append("body { font-family: Arial, Helvetica, sans-serif }");
@@ -334,7 +340,7 @@ public class HTMLReport implements Report {
      */
     @Override
     public String statBlock(Statistics content) {
-        StringBuffer frag = new StringBuffer();
+        StringBuilder frag = new StringBuilder();
         Stat[] stats = content.getStats();
 
         // start the table
@@ -345,14 +351,14 @@ public class HTMLReport implements Report {
             frag.append("\t<tr>\n");
             frag.append("\t\t<th>\n");
             if (content.getStatName() != null) {
-                frag.append("\t\t\t" + content.getStatName() + "\n");
+                frag.append("\t\t\t").append(content.getStatName()).append("\n");
             } else {
                 frag.append("\t\t\t&nbsp;\n");
             }
             frag.append("\t\t</th>\n");
             frag.append("\t\t<th>\n");
             if (content.getResultName() != null) {
-                frag.append("\t\t\t" + content.getResultName() + "\n");
+                frag.append("\t\t\t").append(content.getResultName()).append("\n");
             } else {
                 frag.append("\t\t\t&nbsp;\n");
             }
@@ -370,10 +376,10 @@ public class HTMLReport implements Report {
                 style = "reportEvenRow";
             }
 
-            frag.append("\t<tr class=\"" + style + "\">\n\t\t<td>\n");
+            frag.append("\t<tr class=\"").append(style).append("\">\n\t\t<td>\n");
             frag.append("\t\t\t");
             if (stats[i].getReference() != null) {
-                frag.append("<a href=\"" + stats[i].getReference() + "\" ");
+                frag.append("<a href=\"").append(stats[i].getReference()).append("\" ");
                 frag.append("target=\"_blank\">");
             }
             frag.append(this.clean(stats[i].getKey()));
@@ -405,9 +411,9 @@ public class HTMLReport implements Report {
     @Override
     public String floorInfo(int floor) {
         if (floor > 0) {
-            StringBuffer frag = new StringBuffer();
+            StringBuilder frag = new StringBuilder();
             frag.append("<div class=\"reportFloor\">");
-            frag.append("(more than " + ReportTools.numberFormat(floor) + " times)");
+            frag.append("(more than ").append(ReportTools.numberFormat(floor)).append(" times)");
             frag.append("</div>\n");
             return frag.toString();
         } else {
@@ -419,12 +425,12 @@ public class HTMLReport implements Report {
      * output the explanation of the report block in HTML format
      *
      * @param explanation some text explaining the coming report block
-     * @return a string containing an explanaton HTML formatted
+     * @return a string containing an explanation HTML formatted
      */
     @Override
     public String blockExplanation(String explanation) {
         if (explanation != null) {
-            StringBuffer frag = new StringBuffer();
+            StringBuilder frag = new StringBuilder();
             frag.append("<div class=\"reportExplanation\">");
             frag.append(explanation);
             frag.append("</div>\n\n");

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

@@ -30,13 +30,14 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringUtils;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.dspace.core.Utils;
 import org.dspace.discovery.DiscoverQuery;
 import org.dspace.discovery.SearchServiceException;
 import org.dspace.discovery.SearchUtils;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * This class performs all the actual analysis of a given set of DSpace log
@@ -268,7 +269,7 @@ public class LogAnalyser {
     /**
      * the log directory to be analysed
      */
-    private static String logDir = ConfigurationManager.getProperty("log.report.dir");
+    private static String logDir;
 
     /**
      * the regex to describe the file name format
@@ -276,16 +277,14 @@ public class LogAnalyser {
     private static String fileTemplate = "dspace\\.log.*";
 
     /**
-     * the config file from which to configure the analyser
+     * the configuration file from which to configure the analyser
      */
-    private static String configFile = ConfigurationManager.getProperty("dspace.dir") +
-        File.separator + "config" + File.separator +
-        "dstat.cfg";
+    private static String configFile;
 
     /**
      * the output file to which to write aggregation data
      */
-    private static String outFile = ConfigurationManager.getProperty("log.report.dir") + File.separator + "dstat.dat";
+    private static String outFile;
 
     /**
      * the starting date of the report
@@ -582,9 +581,11 @@ public class LogAnalyser {
         }
 
         // now do the host name and url lookup
-        hostName = Utils.getHostName(ConfigurationManager.getProperty("dspace.ui.url"));
-        name = ConfigurationManager.getProperty("dspace.name").trim();
-        url = ConfigurationManager.getProperty("dspace.ui.url").trim();
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        hostName = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
+        name = configurationService.getProperty("dspace.name").trim();
+        url = configurationService.getProperty("dspace.ui.url").trim();
         if ((url != null) && (!url.endsWith("/"))) {
             url = url + "/";
         }
@@ -622,8 +623,13 @@ public class LogAnalyser {
                                      String myConfigFile, String myOutFile,
                                      Date myStartDate, Date myEndDate,
                                      boolean myLookUp) {
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+
         if (myLogDir != null) {
             logDir = myLogDir;
+        } else {
+            logDir = configurationService.getProperty("log.report.dir");
         }
 
         if (myFileTemplate != null) {
@@ -632,6 +638,9 @@ public class LogAnalyser {
 
         if (myConfigFile != null) {
             configFile = myConfigFile;
+        } else {
+            configFile = configurationService.getProperty("dspace.dir")
+                    + File.separator + "config" + File.separator + "dstat.cfg";
         }
 
         if (myStartDate != null) {
@@ -644,9 +653,9 @@ public class LogAnalyser {
 
         if (myOutFile != null) {
             outFile = myOutFile;
+        } else {
+            outFile = configurationService.getProperty("log.report.dir") + File.separator + "dstat.dat";
         }
-
-        return;
     }
 
 
@@ -657,7 +666,7 @@ public class LogAnalyser {
      */
     public static String createOutput() {
         // start a string buffer to hold the final output
-        StringBuffer summary = new StringBuffer();
+        StringBuilder summary = new StringBuilder();
 
         // define an iterator that will be used to go over the hashmap keys
         Iterator<String> keys = null;
@@ -820,7 +829,7 @@ public class LogAnalyser {
      */
     public static void setRegex(String fileTemplate) {
         // build the exclude characters regular expression
-        StringBuffer charRegEx = new StringBuffer();
+        StringBuilder charRegEx = new StringBuilder();
         charRegEx.append("[");
         for (int i = 0; i < excludeChars.size(); i++) {
             charRegEx.append("\\").append(excludeChars.get(i));
@@ -864,7 +873,7 @@ public class LogAnalyser {
         logRegex = Pattern.compile(fileTemplate);
 
         // set up the pattern for matching any of the query types
-        StringBuffer typeRXString = new StringBuffer();
+        StringBuilder typeRXString = new StringBuilder();
         typeRXString.append("(");
         for (int i = 0; i < excludeTypes.size(); i++) {
             if (i > 0) {
@@ -876,7 +885,7 @@ public class LogAnalyser {
         typeRX = Pattern.compile(typeRXString.toString());
 
         // set up the pattern for matching any of the words to exclude
-        StringBuffer wordRXString = new StringBuffer();
+        StringBuilder wordRXString = new StringBuilder();
         wordRXString.append("(");
         for (int i = 0; i < excludeWords.size(); i++) {
             if (i > 0) {
@@ -890,8 +899,6 @@ public class LogAnalyser {
         }
         wordRXString.append(")");
         wordRX = Pattern.compile(wordRXString.toString());
-
-        return;
     }
 
     /**
@@ -920,18 +927,18 @@ public class LogAnalyser {
      */
     public static void readConfig(String configFile) throws IOException {
         //instantiate aggregators
-        actionAggregator = new HashMap<String, Integer>();
-        searchAggregator = new HashMap<String, Integer>();
-        userAggregator = new HashMap<String, Integer>();
-        itemAggregator = new HashMap<String, Integer>();
-        archiveStats = new HashMap<String, Integer>();
+        actionAggregator = new HashMap<>();
+        searchAggregator = new HashMap<>();
+        userAggregator = new HashMap<>();
+        itemAggregator = new HashMap<>();
+        archiveStats = new HashMap<>();
 
         //instantiate lists
-        generalSummary = new ArrayList<String>();
-        excludeWords = new ArrayList<String>();
-        excludeTypes = new ArrayList<String>();
-        excludeChars = new ArrayList<String>();
-        itemTypes = new ArrayList<String>();
+        generalSummary = new ArrayList<>();
+        excludeWords = new ArrayList<>();
+        excludeTypes = new ArrayList<>();
+        excludeChars = new ArrayList<>();
+        itemTypes = new ArrayList<>();
 
         // prepare our standard file readers and buffered readers
         FileReader fr = null;
@@ -1002,8 +1009,6 @@ public class LogAnalyser {
         // close the inputs
         br.close();
         fr.close();
-
-        return;
     }
 
     /**

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

@@ -32,10 +32,11 @@ import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
 import org.dspace.handle.service.HandleService;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * This class performs the action of coordinating a usage report being
@@ -161,7 +162,7 @@ public class ReportGenerator {
     /**
      * pattern that matches an unqualified aggregator property
      */
-    private static Pattern real = Pattern.compile("^(.+)=(.+)");
+    private static final Pattern real = Pattern.compile("^(.+)=(.+)");
 
     //////////////////////////
     // Miscellaneous variables
@@ -189,11 +190,12 @@ public class ReportGenerator {
     /**
      * the log file action to human readable action map
      */
-    private static String map = ConfigurationManager.getProperty("dspace.dir") +
-        File.separator + "config" + File.separator + "dstat.map";
+    private static String map;
 
     private static final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
     private static final HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
+    private static final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
     /**
      * Default constructor
@@ -268,6 +270,9 @@ public class ReportGenerator {
         throws Exception, SQLException {
         if (myMap != null) {
             map = myMap;
+        } else {
+            map = configurationService.getProperty("dspace.dir")
+                    + File.separator + "config" + File.separator + "dstat.map";
         }
 
         // create the relevant report type
@@ -302,15 +307,15 @@ public class ReportGenerator {
         startTime = new GregorianCalendar();
 
         /** instantiate aggregators */
-        actionAggregator = new HashMap<String, String>();
-        searchAggregator = new HashMap<String, String>();
-        userAggregator = new HashMap<String, String>();
-        itemAggregator = new HashMap<String, String>();
-        archiveStats = new HashMap<String, String>();
-        actionMap = new HashMap<String, String>();
+        actionAggregator = new HashMap<>();
+        searchAggregator = new HashMap<>();
+        userAggregator = new HashMap<>();
+        itemAggregator = new HashMap<>();
+        archiveStats = new HashMap<>();
+        actionMap = new HashMap<>();
 
-        /** instantite lists */
-        generalSummary = new ArrayList<String>();
+        /** instantiate lists */
+        generalSummary = new ArrayList<>();
 
         // set the parameters for this analysis
         setParameters(myInput);
@@ -486,8 +491,6 @@ public class ReportGenerator {
         report.addBlock(process);
 
         report.render();
-
-        return;
     }
 
 
@@ -612,8 +615,6 @@ public class ReportGenerator {
         if (myInput != null) {
             input = myInput;
         }
-
-        return;
     }
 
 
@@ -768,9 +769,9 @@ public class ReportGenerator {
         List<MetadataValue> author = itemService
             .getMetadata(item, MetadataSchemaEnum.DC.getName(), "contributor", "author", Item.ANY);
 
-        StringBuffer authors = new StringBuffer();
+        StringBuilder authors = new StringBuilder();
         if (author.size() > 0) {
-            authors.append("(" + author.get(0).getValue());
+            authors.append("(").append(author.get(0).getValue());
         }
         if (author.size() > 1) {
             authors.append(" et al");

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

@@ -22,7 +22,8 @@ import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.time.DateUtils;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Helper class for loading the analysis / report files from the reports directory
@@ -219,8 +220,8 @@ public class StatisticsLoader {
         }
 
         // Create new maps for the monthly analysis / reports
-        Map<String, StatsFile> newMonthlyAnalysis = new HashMap<String, StatsFile>();
-        Map<String, StatsFile> newMonthlyReports = new HashMap<String, StatsFile>();
+        Map<String, StatsFile> newMonthlyAnalysis = new HashMap<>();
+        Map<String, StatsFile> newMonthlyReports = new HashMap<>();
 
         StatsFile newGeneralAnalysis = null;
         StatsFile newGeneralReport = null;
@@ -320,7 +321,9 @@ public class StatisticsLoader {
      * @return array of files
      */
     private static File[] getAnalysisAndReportFileList() {
-        File reportDir = new File(ConfigurationManager.getProperty("log.report.dir"));
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        File reportDir = new File(configurationService.getProperty("log.report.dir"));
         if (reportDir != null) {
             return reportDir.listFiles(new AnalysisAndReportFilter());
         }

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

@@ -14,8 +14,9 @@ import java.util.Date;
 
 import org.dspace.app.util.factory.UtilServiceFactory;
 import org.dspace.app.util.service.WebAppService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -57,7 +58,9 @@ abstract public class AbstractDSpaceWebapp
 
         started = new Date();
 
-        url = ConfigurationManager.getProperty("dspace.ui.url");
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        url = configurationService.getProperty("dspace.ui.url");
         if (null == url) {
             throw new IllegalStateException("dspace.ui.url is undefined");
         }

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

@@ -16,8 +16,9 @@ import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CommunityService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Utility class for lists of collections.
@@ -55,8 +56,11 @@ public class CollectionDropDown {
      * @return Full path to the collection (truncated)
      * @throws SQLException if database error
      */
-    public static String collectionPath(Context context, Collection col, int maxchars) throws SQLException {
-        String separator = ConfigurationManager.getProperty("subcommunity.separator");
+    public static String collectionPath(Context context, Collection col, int maxchars)
+            throws SQLException {
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        String separator = configurationService.getProperty("subcommunity.separator");
         if (separator == null) {
             separator = " > ";
         }

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

@@ -12,6 +12,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
+import javax.annotation.Nullable;
 
 import org.apache.commons.lang3.StringUtils;
 import org.dspace.content.MetadataSchemaEnum;
@@ -144,6 +145,7 @@ public class DCInput {
     private String relationshipType = null;
     private String searchConfiguration = null;
     private String filter;
+    private List<String> externalSources;
 
     /**
      * The scope of the input sets, this restricts hidden metadata fields from
@@ -225,6 +227,15 @@ public class DCInput {
         relationshipType = fieldMap.get("relationship-type");
         searchConfiguration = fieldMap.get("search-configuration");
         filter = fieldMap.get("filter");
+        externalSources = new ArrayList<>();
+        String externalSourcesDef = fieldMap.get("externalsources");
+        if (StringUtils.isNotBlank(externalSourcesDef)) {
+            String[] sources = StringUtils.split(externalSourcesDef, ",");
+            for (String source: sources) {
+                externalSources.add(StringUtils.trim(source));
+            }
+        }
+
     }
 
     /**
@@ -291,7 +302,7 @@ public class DCInput {
      *
      * @return the input type
      */
-    public String getInputType() {
+    public @Nullable String getInputType() {
         return inputType;
     }
 
@@ -521,6 +532,10 @@ public class DCInput {
         return filter;
     }
 
+    public List<String> getExternalSources() {
+        return externalSources;
+    }
+
     public boolean isQualdropValue() {
         if ("qualdrop_value".equals(getInputType())) {
             return true;

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

@@ -10,6 +10,7 @@ package org.dspace.app.util;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.core.Utils;
 /**
  * Class representing all DC inputs required for a submission, organized into pages
@@ -109,7 +110,7 @@ public class DCInputSet {
             for (int j = 0; j < inputs[i].length; j++) {
                 DCInput field = inputs[i][j];
                 // If this is a "qualdrop_value" field, then the full field name is the field + dropdown qualifier
-                if (field.getInputType().equals("qualdrop_value")) {
+                if (StringUtils.equals(field.getInputType(), "qualdrop_value")) {
                     List<String> pairs = field.getPairs();
                     for (int k = 0; k < pairs.size(); k += 2) {
                         String qualifier = pairs.get(k + 1);

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.app.util;
 
+import java.lang.reflect.InvocationTargetException;
 import javax.servlet.ServletContextEvent;
 import javax.servlet.ServletContextListener;
 
@@ -27,13 +28,11 @@ public class DSpaceWebappListener implements ServletContextListener {
 
         try {
             Class webappClass = Class.forName("org.dspace.utils.DSpaceWebapp");
-            webApp = (AbstractDSpaceWebapp) webappClass.newInstance();
+            webApp = (AbstractDSpaceWebapp) webappClass.getDeclaredConstructor().newInstance();
             webApp.register();
-        } catch (ClassNotFoundException ex) {
-            event.getServletContext().log("Can't create webapp MBean:  " + ex.getMessage());
-        } catch (InstantiationException ex) {
-            event.getServletContext().log("Can't create webapp MBean:  " + ex.getMessage());
-        } catch (IllegalAccessException ex) {
+        } catch (ClassNotFoundException | InstantiationException
+                | IllegalAccessException | IllegalArgumentException
+                | NoSuchMethodException | InvocationTargetException ex) {
             event.getServletContext().log("Can't create webapp MBean:  " + ex.getMessage());
         }
     }

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

@@ -22,7 +22,7 @@ public interface DSpaceWebappMXBean {
     public boolean isUI();
 
     /**
-     * What kind of webapp?  XMLUI, OAI, etc.
+     * What kind of webapp? Server, etc.
      *
      * @return kind of webapp
      */

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

@@ -26,6 +26,7 @@ import java.util.Properties;
 
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.factory.AuthorizeServiceFactory;
 import org.dspace.content.Bitstream;
@@ -36,10 +37,11 @@ import org.dspace.content.MetadataSchema;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.jdom.Element;
 
 /**
@@ -51,7 +53,7 @@ import org.jdom.Element;
 @SuppressWarnings("deprecation")
 public class GoogleMetadata {
 
-    private final static Logger log = org.apache.logging.log4j.LogManager.getLogger(GoogleMetadata.class);
+    private final static Logger log = LogManager.getLogger(GoogleMetadata.class);
 
     protected static final String GOOGLE_PREFIX = "google.";
 
@@ -62,7 +64,7 @@ public class GoogleMetadata {
     protected String itemURL;
 
     // Configuration keys and fields
-    protected static Map<String, String> googleScholarSettings = new HashMap<String, String>();
+    protected static Map<String, String> googleScholarSettings = new HashMap<>();
 
     // Google field names (e.g. citation_fieldname) and formatted metadata
     // values
@@ -132,35 +134,39 @@ public class GoogleMetadata {
 
     private static GoogleBitstreamComparator googleBitstreamComparator = null;
 
-    // Load configured fields from google-metadata.properties
-    static {
+    private final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
-        File loadedFile = null;
-        URL url = null;
-        InputStream is = null;
-
-        String googleConfigFile = ConfigurationManager
+    /**
+     * Load configured fields from google-metadata.properties.
+     */
+    private void loadGoogleScholarSettings()
+            throws MalformedURLException, IOException {
+        String googleConfigFile = configurationService
             .getProperty("google-metadata.config");
-        log.info("Using [" + googleConfigFile
-                     + "] for Google Metadata configuration");
+        log.info("Using [{}] for Google Metadata configuration", googleConfigFile);
 
-        loadedFile = new File(googleConfigFile);
+        File loadedFile = new File(googleConfigFile);
+        URL url;
         try {
-            url = loadedFile.toURL();
+            url = loadedFile.toURI().toURL();
 
         } catch (MalformedURLException mux) {
-            log.error("Can't find Google Metadata configuration file: "
-                          + googleConfigFile, mux);
+            log.error("Can't find Google Metadata configuration file: {}",
+                          googleConfigFile, mux);
+            throw mux;
         }
 
         Properties properties = new Properties();
+        InputStream is;
         try {
             is = url.openStream();
             properties.load(is);
 
         } catch (IOException iox) {
-            log.error("Could not read Google Metadata configuration file: "
-                          + googleConfigFile, iox);
+            log.error("Could not read Google Metadata configuration file: {}",
+                          googleConfigFile, iox);
+            throw iox;
         }
 
         Enumeration propertyNames = properties.propertyNames();
@@ -180,19 +186,21 @@ public class GoogleMetadata {
             }
         }
 
-        if (log.isDebugEnabled()) {
-            logConfiguration();
-        }
+        logConfiguration();
     }
 
     /**
      * Dump Metadata field mapping to log
      */
     public static void logConfiguration() {
+        if (!log.isDebugEnabled()) {
+            return;
+        }
+
         log.debug("Google Metadata Configuration Mapping:");
 
         for (String name : googleScholarSettings.keySet()) {
-            log.debug("  " + name + " => " + googleScholarSettings.get(name));
+            log.debug("  {} => {}", name, googleScholarSettings.get(name));
         }
     }
 
@@ -202,9 +210,14 @@ public class GoogleMetadata {
      *
      * @param context context
      * @param item    The item being viewed to extract metadata from
-     * @throws SQLException if database error
+     * @throws SQLException if database error.
+     * @throws java.io.IOException passed through.
      */
-    public GoogleMetadata(Context context, Item item) throws SQLException {
+    public GoogleMetadata(Context context, Item item)
+            throws SQLException, IOException {
+        if (googleScholarSettings.isEmpty()) {
+            loadGoogleScholarSettings();
+        }
 
         // Hold onto the item in case we need to refresh a stale parse
         this.item = item;
@@ -336,7 +349,7 @@ public class GoogleMetadata {
             int optionMatches = 0;
             String[] components;
             List<MetadataValue> values;
-            ArrayList<MetadataValue> resolvedFields = new ArrayList<MetadataValue>();
+            ArrayList<MetadataValue> resolvedFields = new ArrayList<>();
 
             for (String field : optionFields) {
 
@@ -399,8 +412,8 @@ public class GoogleMetadata {
      */
     protected ArrayList<ArrayList<String>> parseOptions(String configFilter) {
 
-        ArrayList<String> options = new ArrayList<String>();
-        ArrayList<ArrayList<String>> parsedOptions = new ArrayList<ArrayList<String>>();
+        ArrayList<String> options = new ArrayList<>();
+        ArrayList<ArrayList<String>> parsedOptions = new ArrayList<>();
 
         if (null == configFilter || configFilter.equals("")) {
             return null;
@@ -414,7 +427,7 @@ public class GoogleMetadata {
                 options.add(option.trim());
             }
         } else {
-            options = new ArrayList<String>();
+            options = new ArrayList<>();
             options.add(configFilter);
         }
 
@@ -426,12 +439,12 @@ public class GoogleMetadata {
         for (String option : options) {
 
             ArrayList<String> fields;
-            parsedFields = new ArrayList<String>();
+            parsedFields = new ArrayList<>();
 
             if (option.contains(",")) {
                 fields = parseFields(option);
             } else {
-                fields = new ArrayList<String>();
+                fields = new ArrayList<>();
                 fields.add(option);
             }
 
@@ -472,7 +485,7 @@ public class GoogleMetadata {
      */
     protected ArrayList<String> parseFields(String configString) {
 
-        ArrayList<String> fields = new ArrayList<String>();
+        ArrayList<String> fields = new ArrayList<>();
 
         for (String field : configString.split("\\,")) {
             fields.add(field.trim());
@@ -523,7 +536,7 @@ public class GoogleMetadata {
             List<MetadataValue> allMD = itemService.getMetadata(item, components[0], components[1],
                                                                 components[2], Item.ANY);
 
-            ArrayList<String> expandedDC = new ArrayList<String>();
+            ArrayList<String> expandedDC = new ArrayList<>();
             for (MetadataValue v : allMD) {
 
                 // De-dup multiple occurrences of field names in item
@@ -558,7 +571,7 @@ public class GoogleMetadata {
         MetadataSchema metadataSchema = v.getMetadataField().getMetadataSchema();
         name.append(metadataSchema.getName()).append(".").append(metadataField.getElement());
         if (null != metadataField.getQualifier()) {
-            name.append("." + metadataField.getQualifier());
+            name.append(".").append(metadataField.getQualifier());
         }
 
         return name.toString();
@@ -687,7 +700,7 @@ public class GoogleMetadata {
      * @return List of elements
      */
     public List<Element> disseminateList() {
-        List<Element> metas = new ArrayList<Element>();
+        List<Element> metas = new ArrayList<>();
 
         for (Entry<String, String> m : getMappings()) {
             Element e = new Element("meta");
@@ -889,7 +902,7 @@ public class GoogleMetadata {
             Bitstream bitstream = findLinkableFulltext(item);
             if (bitstream != null) {
                 StringBuilder path = new StringBuilder();
-                path.append(ConfigurationManager.getProperty("dspace.ui.url"));
+                path.append(configurationService.getProperty("dspace.ui.url"));
 
                 if (item.getHandle() != null) {
                     path.append("/bitstream/");
@@ -1075,7 +1088,7 @@ public class GoogleMetadata {
         // FIXME: Shouldn't have to parse identifiers for every identification.
 
         ArrayList<ArrayList<String>> options = parseOptions(dConfig);
-        HashMap<String, ArrayList<String>> mdPairs = new HashMap<String, ArrayList<String>>();
+        HashMap<String, ArrayList<String>> mdPairs = new HashMap<>();
 
         // Parse field/value pairs from field identifier string
         for (ArrayList<String> option : options) {
@@ -1092,7 +1105,7 @@ public class GoogleMetadata {
                     }
                 } else {
                     // Otherwise, add it as the first occurrence of this field
-                    ArrayList<String> newField = new ArrayList<String>();
+                    ArrayList<String> newField = new ArrayList<>();
                     newField.add(parsedPair[1].trim());
                     mdPairs.put(parsedPair[0].trim(), newField);
 
@@ -1113,7 +1126,7 @@ public class GoogleMetadata {
 
         // Check resolved/present metadata fields against configured values
         ArrayList<MetadataValue> presentMD = resolveMetadataFields(sb.toString());
-        if (null != presentMD && presentMD.size() != 0) {
+        if (null != presentMD && !presentMD.isEmpty()) {
             for (MetadataValue v : presentMD) {
                 String fieldName = buildFieldName(v);
                 if (mdPairs.containsKey(fieldName)) {

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

@@ -18,10 +18,10 @@ import javax.xml.parsers.ParserConfigurationException;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -48,9 +48,9 @@ public class InitializeEntities {
 
     private final static Logger log = LogManager.getLogger();
 
-    private RelationshipTypeService relationshipTypeService;
-    private RelationshipService relationshipService;
-    private EntityTypeService entityTypeService;
+    private final RelationshipTypeService relationshipTypeService;
+    private final RelationshipService relationshipService;
+    private final EntityTypeService entityTypeService;
 
 
     private InitializeEntities() {
@@ -62,14 +62,14 @@ public class InitializeEntities {
     /**
      * The main method for this script
      *
-     * @param argv  The commandline arguments given with this command
+     * @param argv  The command line arguments given with this command
      * @throws SQLException         If something goes wrong with the database
      * @throws AuthorizeException   If something goes wrong with permissions
      * @throws ParseException       If something goes wrong with the parsing
      */
     public static void main(String[] argv) throws SQLException, AuthorizeException, ParseException {
         InitializeEntities initializeEntities = new InitializeEntities();
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = createCommandLineOptions();
         CommandLine line = parser.parse(options,argv);
         String fileLocation = getFileLocationFromCommandLine(line);

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

@@ -377,7 +377,7 @@ public class SubmissionConfigReader {
         for (int i = 0; i < len; i++) {
             Node nd = nl.item(i);
             // process each step definition
-            if (nd.getNodeName().equals("step")) {
+            if (StringUtils.equalsIgnoreCase(nd.getNodeName(), "step-definition")) {
                 String stepID = getAttribute(nd, "id");
                 if (stepID == null) {
                     throw new SAXException(

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

@@ -8,6 +8,7 @@
 package org.dspace.app.util;
 
 import java.io.IOException;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Date;
 import java.util.List;
@@ -49,7 +50,6 @@ import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.discovery.IndexableObject;
 import org.dspace.discovery.indexobject.IndexableCollection;
@@ -102,7 +102,7 @@ public class SyndicationFeed {
         };
     protected String defaultExternalMedia = "dc.source.uri";
 
-    private final ConfigurationService configurationService =
+    private static final ConfigurationService configurationService =
         DSpaceServicesFactory.getInstance().getConfigurationService();
 
     // metadata field for Item title in entry:
@@ -196,18 +196,19 @@ public class SyndicationFeed {
 
         // dso is null for the whole site, or a search without scope
         if (dso == null) {
-            defaultTitle = ConfigurationManager.getProperty("dspace.name");
+            defaultTitle = configurationService.getProperty("dspace.name");
             feed.setDescription(localize(labels, MSG_FEED_DESCRIPTION));
             objectURL = resolveURL(request, null);
-            logoURL = ConfigurationManager.getProperty("webui.feed.logo.url");
+            logoURL = configurationService.getProperty("webui.feed.logo.url");
         } else {
             Bitstream logo = null;
             if (dso instanceof IndexableCollection) {
                 Collection col = ((IndexableCollection) dso).getIndexedObject();
                 defaultTitle = col.getName();
-                feed.setDescription(collectionService.getMetadata(col, "short_description"));
+                feed.setDescription(collectionService.getMetadataFirstValue(col,
+                        CollectionService.MD_SHORT_DESCRIPTION, Item.ANY));
                 logo = col.getLogo();
-                String cols = ConfigurationManager.getProperty("webui.feed.podcast.collections");
+                String cols = configurationService.getProperty("webui.feed.podcast.collections");
                 if (cols != null && cols.length() > 1 && cols.contains(col.getHandle())) {
                     podcastFeed = true;
                 }
@@ -215,9 +216,10 @@ public class SyndicationFeed {
             } else if (dso instanceof IndexableCommunity) {
                 Community comm = ((IndexableCommunity) dso).getIndexedObject();
                 defaultTitle = comm.getName();
-                feed.setDescription(communityService.getMetadata(comm, "short_description"));
+                feed.setDescription(communityService.getMetadataFirstValue(comm,
+                        CommunityService.MD_SHORT_DESCRIPTION, Item.ANY));
                 logo = comm.getLogo();
-                String comms = ConfigurationManager.getProperty("webui.feed.podcast.communities");
+                String comms = configurationService.getProperty("webui.feed.podcast.communities");
                 if (comms != null && comms.length() > 1 && comms.contains(comm.getHandle())) {
                     podcastFeed = true;
                 }
@@ -251,7 +253,7 @@ public class SyndicationFeed {
 
         // add entries for items
         if (items != null) {
-            List<SyndEntry> entries = new ArrayList<SyndEntry>();
+            List<SyndEntry> entries = new ArrayList<>();
             for (IndexableObject idxObj : items) {
                 if (!(idxObj instanceof IndexableItem)) {
                     continue;
@@ -277,7 +279,7 @@ public class SyndicationFeed {
                 // date of last change to Item
                 entry.setUpdatedDate(item.getLastModified());
 
-                StringBuffer db = new StringBuffer();
+                StringBuilder db = new StringBuilder();
                 for (String df : descriptionFields) {
                     // Special Case: "(date)" in field name means render as date
                     boolean isDate = df.indexOf("(date)") > 0;
@@ -313,7 +315,7 @@ public class SyndicationFeed {
                 // This gets the authors into an ATOM feed
                 List<MetadataValue> authors = itemService.getMetadataByMetadataString(item, authorField);
                 if (authors.size() > 0) {
-                    List<SyndPerson> creators = new ArrayList<SyndPerson>();
+                    List<SyndPerson> creators = new ArrayList<>();
                     for (MetadataValue author : authors) {
                         SyndPerson sp = new SyndPersonImpl();
                         sp.setName(author.getValue());
@@ -329,7 +331,7 @@ public class SyndicationFeed {
                     if (dcCreatorField != null) {
                         List<MetadataValue> dcAuthors = itemService.getMetadataByMetadataString(item, dcCreatorField);
                         if (dcAuthors.size() > 0) {
-                            List<String> creators = new ArrayList<String>();
+                            List<String> creators = new ArrayList<>();
                             for (MetadataValue author : dcAuthors) {
                                 creators.add(author.getValue());
                             }
@@ -345,7 +347,7 @@ public class SyndicationFeed {
                     if (dcDescriptionField != null) {
                         List<MetadataValue> v = itemService.getMetadataByMetadataString(item, dcDescriptionField);
                         if (v.size() > 0) {
-                            StringBuffer descs = new StringBuffer();
+                            StringBuilder descs = new StringBuilder();
                             for (MetadataValue d : v) {
                                 if (descs.length() > 0) {
                                     descs.append("\n\n");
@@ -374,8 +376,6 @@ public class SyndicationFeed {
                                     enc.setLength(bit.getSizeBytes());
                                     enc.setUrl(urlOfBitstream(request, bit));
                                     enclosures.add(enc);
-                                } else {
-                                    continue;
                                 }
                             }
                         }
@@ -395,7 +395,7 @@ public class SyndicationFeed {
                             }
                         }
 
-                    } catch (Exception e) {
+                    } catch (SQLException e) {
                         System.out.println(e.getMessage());
                     }
                     entry.setEnclosures(enclosures);
@@ -501,7 +501,7 @@ public class SyndicationFeed {
 
     // utility to get config property with default value when not set.
     protected static String getDefaultedConfiguration(String key, String dfl) {
-        String result = ConfigurationManager.getProperty(key);
+        String result = configurationService.getProperty(key);
         return (result == null) ? dfl : result;
     }
 
@@ -531,14 +531,14 @@ public class SyndicationFeed {
         if (dso == null) {
             if (baseURL == null) {
                 if (request == null) {
-                    baseURL = ConfigurationManager.getProperty("dspace.ui.url");
+                    baseURL = configurationService.getProperty("dspace.ui.url");
                 } else {
-                    baseURL = ConfigurationManager.getProperty("dspace.ui.url");
+                    baseURL = configurationService.getProperty("dspace.ui.url");
                     baseURL += request.getContextPath();
                 }
             }
             return baseURL;
-        } else if (ConfigurationManager.getBooleanProperty("webui.feed.localresolve")) {
+        } else if (configurationService.getBooleanProperty("webui.feed.localresolve")) {
             // return a link to handle in repository
             return resolveURL(request, null) + "/handle/" + dso.getHandle();
         } else {

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

@@ -15,9 +15,9 @@ import java.util.List;
 
 import org.apache.http.HttpResponse;
 import org.apache.http.HttpStatus;
-import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpHead;
-import org.apache.http.impl.client.DefaultHttpClient;
+import org.apache.http.impl.client.CloseableHttpClient;
+import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.dao.WebAppDAO;
 import org.dspace.app.util.service.WebAppService;
@@ -76,13 +76,13 @@ public class WebAppServiceImpl implements WebAppService {
 
             for (WebApp app : webApps) {
                 method = new HttpHead(app.getUrl());
-                HttpClient client = new DefaultHttpClient();
-                HttpResponse response = client.execute(method);
-                int status = response.getStatusLine().getStatusCode();
+                int status;
+                try (CloseableHttpClient client = HttpClientBuilder.create().build()) {
+                    HttpResponse response = client.execute(method);
+                    status = response.getStatusLine().getStatusCode();
+                }
                 if (status != HttpStatus.SC_OK) {
-                    delete(context, app
-
-                    );
+                    delete(context, app);
                     continue;
                 }
 

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

@@ -7,6 +7,8 @@
  */
 package org.dspace.authenticate;
 
+import static org.dspace.eperson.service.EPersonService.MD_PHONE;
+
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.Arrays;
@@ -33,7 +35,6 @@ import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.dspace.eperson.EPerson;
@@ -41,19 +42,28 @@ import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
 import org.dspace.eperson.service.GroupService;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * This combined LDAP authentication method supersedes both the 'LDAPAuthentication'
  * and the 'LDAPHierarchicalAuthentication' methods. It's capable of both:
- * - authenticaton  against a flat LDAP tree where all users are in the same unit
- * (if search.user or search.password is not set)
- * - authentication against structured hierarchical LDAP trees of users.
+ * <ul>
+ *   <li>authentication against a flat LDAP tree where all users are in the same unit
+ *       (if {@code search.user} or {@code search.password} is not set)</li>
+ *   <li>authentication against structured hierarchical LDAP trees of users.</li>
+ * </ul>
  * An initial bind is required using a user name and password in order to
  * search the tree and find the DN of the user. A second bind is then required to
  * check the credentials of the user by binding directly to their DN.
  *
- * @author Stuart Lewis, Chris Yates, Alex Barbieri, Flavio Botelho, Reuben Pasquini, Samuel Ottenhoff, Ivan Masár
- * @version $Revision$
+ * @author Stuart Lewis
+ * @author Chris Yates
+ * @author Alex Barbieri
+ * @author Flavio Botelho
+ * @author Reuben Pasquini
+ * @author Samuel Ottenhoff
+ * @author Ivan Masár
  */
 public class LDAPAuthentication
     implements AuthenticationMethod {
@@ -61,13 +71,17 @@ public class LDAPAuthentication
     /**
      * log4j category
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
-
-    protected AuthenticationService authenticationService = AuthenticateServiceFactory.getInstance()
-                                                                                      .getAuthenticationService();
-    protected EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    protected GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
+    private static final Logger log
+            = org.apache.logging.log4j.LogManager.getLogger(LDAPAuthentication.class);
 
+    protected AuthenticationService authenticationService
+            = AuthenticateServiceFactory.getInstance().getAuthenticationService();
+    protected EPersonService ePersonService
+            = EPersonServiceFactory.getInstance().getEPersonService();
+    protected GroupService groupService
+            = EPersonServiceFactory.getInstance().getGroupService();
+    protected ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
     /**
      * Let a real auth method return true if it wants.
@@ -80,7 +94,7 @@ public class LDAPAuthentication
                                    String username)
         throws SQLException {
         // Looks to see if autoregister is set or not
-        return ConfigurationManager.getBooleanProperty("authentication-ldap", "autoregister");
+        return configurationService.getBooleanProperty("authentication-ldap.autoregister");
     }
 
     /**
@@ -128,7 +142,7 @@ public class LDAPAuthentication
         // ensures they are LDAP users
         try {
             if (!context.getCurrentUser().getNetid().equals("")) {
-                String groupName = ConfigurationManager.getProperty("authentication-ldap", "login.specialgroup");
+                String groupName = configurationService.getProperty("authentication-ldap.login.specialgroup");
                 if ((groupName != null) && (!groupName.trim().equals(""))) {
                     Group ldapGroup = groupService.findByName(context, groupName);
                     if (ldapGroup == null) {
@@ -142,7 +156,7 @@ public class LDAPAuthentication
                     }
                 }
             }
-        } catch (Exception npe) {
+        } catch (SQLException ex) {
             // The user is not an LDAP user, so we don't need to worry about them
         }
         return Collections.EMPTY_LIST;
@@ -205,11 +219,11 @@ public class LDAPAuthentication
         SpeakerToLDAP ldap = new SpeakerToLDAP(log);
 
         // Get the DN of the user
-        boolean anonymousSearch = ConfigurationManager.getBooleanProperty("authentication-ldap", "search.anonymous");
-        String adminUser = ConfigurationManager.getProperty("authentication-ldap", "search.user");
-        String adminPassword = ConfigurationManager.getProperty("authentication-ldap", "search.password");
-        String objectContext = ConfigurationManager.getProperty("authentication-ldap", "object_context");
-        String idField = ConfigurationManager.getProperty("authentication-ldap", "id_field");
+        boolean anonymousSearch = configurationService.getBooleanProperty("authentication-ldap.search.anonymous");
+        String adminUser = configurationService.getProperty("authentication-ldap.search.user");
+        String adminPassword = configurationService.getProperty("authentication-ldap.search.password");
+        String objectContext = configurationService.getProperty("authentication-ldap.object_context");
+        String idField = configurationService.getProperty("authentication-ldap.id_field");
         String dn = "";
 
         // If adminUser is blank and anonymous search is not allowed, then we can't search so construct the DN
@@ -263,9 +277,8 @@ public class LDAPAuthentication
                 if (StringUtils.isEmpty(email)) {
                     // If no email, check if we have a "netid_email_domain". If so, append it to the netid to create
                     // email
-                    if (StringUtils
-                        .isNotEmpty(ConfigurationManager.getProperty("authentication-ldap", "netid_email_domain"))) {
-                        email = netid + ConfigurationManager.getProperty("authentication-ldap", "netid_email_domain");
+                    if (configurationService.hasProperty("authentication-ldap.netid_email_domain")) {
+                        email = netid + configurationService.getProperty("authentication-ldap.netid_email_domain");
                     } else {
                         // We don't have a valid email address. We'll default it to 'netid' but log a warning
                         log.warn(LogManager.getHeader(context, "autoregister",
@@ -310,7 +323,8 @@ public class LDAPAuthentication
                                         eperson.setLastName(context, ldap.ldapSurname);
                                     }
                                     if (StringUtils.isNotEmpty(ldap.ldapPhone)) {
-                                        ePersonService.setMetadata(context, eperson, "phone", ldap.ldapPhone);
+                                        ePersonService.setMetadataSingleValue(context, eperson,
+                                                MD_PHONE, ldap.ldapPhone, null);
                                     }
                                     eperson.setNetid(netid.toLowerCase());
                                     eperson.setCanLogIn(true);
@@ -365,21 +379,34 @@ public class LDAPAuthentication
         /**
          * LDAP settings
          */
-        String ldap_provider_url = ConfigurationManager.getProperty("authentication-ldap", "provider_url");
-        String ldap_id_field = ConfigurationManager.getProperty("authentication-ldap", "id_field");
-        String ldap_search_context = ConfigurationManager.getProperty("authentication-ldap", "search_context");
-        String ldap_search_scope = ConfigurationManager.getProperty("authentication-ldap", "search_scope");
+        final String ldap_provider_url;
+        final String ldap_id_field;
+        final String ldap_search_context;
+        final String ldap_search_scope;
 
-        String ldap_email_field = ConfigurationManager.getProperty("authentication-ldap", "email_field");
-        String ldap_givenname_field = ConfigurationManager.getProperty("authentication-ldap", "givenname_field");
-        String ldap_surname_field = ConfigurationManager.getProperty("authentication-ldap", "surname_field");
-        String ldap_phone_field = ConfigurationManager.getProperty("authentication-ldap", "phone_field");
-        String ldap_group_field = ConfigurationManager.getProperty("authentication-ldap", "login.groupmap.attribute");
+        final String ldap_email_field;
+        final String ldap_givenname_field;
+        final String ldap_surname_field;
+        final String ldap_phone_field;
+        final String ldap_group_field;
 
-        boolean useTLS = ConfigurationManager.getBooleanProperty("authentication-ldap", "starttls", false);
+        final boolean useTLS;
 
         SpeakerToLDAP(Logger thelog) {
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
             log = thelog;
+
+            ldap_provider_url = configurationService.getProperty("authentication-ldap.provider_url");
+            ldap_id_field = configurationService.getProperty("authentication-ldap.id_field");
+            ldap_search_context = configurationService.getProperty("authentication-ldap.search_context");
+            ldap_search_scope = configurationService.getProperty("authentication-ldap.search_scope");
+            ldap_email_field = configurationService.getProperty("authentication-ldap.email_field");
+            ldap_givenname_field = configurationService.getProperty("authentication-ldap.givenname_field");
+            ldap_surname_field = configurationService.getProperty("authentication-ldap.surname_field");
+            ldap_phone_field = configurationService.getProperty("authentication-ldap.phone_field");
+            ldap_group_field = configurationService.getProperty("authentication-ldap.login.groupmap.attribute");
+            useTLS = configurationService.getBooleanProperty("authentication-ldap.starttls", false);
         }
 
         protected String getDNOfUser(String adminUser, String adminPassword, Context context, String netid) {
@@ -399,7 +426,8 @@ public class LDAPAuthentication
             }
 
             // Set up environment for creating initial context
-            Hashtable<String, String> env = new Hashtable<String, String>();
+            @SuppressWarnings("UseOfObsoleteCollectionType")
+            Hashtable<String, String> env = new Hashtable<>();
             env.put(javax.naming.Context.INITIAL_CONTEXT_FACTORY, "com.sun.jndi.ldap.LdapCtxFactory");
             env.put(javax.naming.Context.PROVIDER_URL, ldap_provider_url);
 
@@ -447,7 +475,7 @@ public class LDAPAuthentication
                     SearchControls ctrls = new SearchControls();
                     ctrls.setSearchScope(ldap_search_scope_value);
 
-                    String searchName = "";
+                    String searchName;
                     if (useTLS) {
                         searchName = ldap_search_context;
                     } else {
@@ -555,7 +583,8 @@ public class LDAPAuthentication
 
 
                 // Set up environment for creating initial context
-                Hashtable<String, String> env = new Hashtable<String, String>();
+                @SuppressWarnings("UseOfObsoleteCollectionType")
+                Hashtable<String, String> env = new Hashtable<>();
                 env.put(javax.naming.Context.INITIAL_CONTEXT_FACTORY,
                         "com.sun.jndi.ldap.LdapCtxFactory");
                 env.put(javax.naming.Context.PROVIDER_URL, ldap_provider_url);
@@ -652,7 +681,7 @@ public class LDAPAuthentication
         if (StringUtils.isNotBlank(dn)) {
             System.out.println("dn:" + dn);
             int i = 1;
-            String groupMap = ConfigurationManager.getProperty("authentication-ldap", "login.groupmap." + i);
+            String groupMap = configurationService.getProperty("authentication-ldap", "login.groupmap." + i);
 
             boolean cmp;
 
@@ -692,7 +721,7 @@ public class LDAPAuthentication
                     }
                 }
 
-                groupMap = ConfigurationManager.getProperty("authentication-ldap", "login.groupmap." + ++i);
+                groupMap = configurationService.getProperty("authentication-ldap", "login.groupmap." + ++i);
             }
         }
     }

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

@@ -24,11 +24,14 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.MetadataField;
+import org.dspace.content.MetadataFieldName;
 import org.dspace.content.MetadataSchema;
+import org.dspace.content.MetadataSchemaEnum;
 import org.dspace.content.NonUniqueMetadataException;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.MetadataFieldService;
@@ -65,13 +68,12 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  * @author <a href="mailto:bliong@melcoe.mq.edu.au">Bruc Liong, MELCOE</a>
  * @author <a href="mailto:kli@melcoe.mq.edu.au">Xiang Kevin Li, MELCOE</a>
  * @author <a href="http://www.scottphillips.com">Scott Phillips</a>
- * @version $Revision$
  */
 public class ShibAuthentication implements AuthenticationMethod {
     /**
      * log4j category
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(ShibAuthentication.class);
+    private static final Logger log = LogManager.getLogger(ShibAuthentication.class);
 
     /**
      * Additional metadata mappings
@@ -843,25 +845,24 @@ public class ShibAuthentication implements AuthenticationMethod {
 
             // Truncate values
             if (value == null) {
-                log.warn(
-                    "Unable to update the eperson's '" + field + "' metadata because the header '" + header + "' does" +
-                        " not exist.");
+                log.warn("Unable to update the eperson's '{}' metadata"
+                        + " because the header '{}' does not exist.", field, header);
                 continue;
             } else if ("phone".equals(field) && value.length() > PHONE_MAX_SIZE) {
-                log.warn(
-                    "Truncating eperson phone metadata because it is longer than " + PHONE_MAX_SIZE + ": '" + value +
-                        "'");
+                log.warn("Truncating eperson phone metadata because it is longer than {}: '{}'",
+                        PHONE_MAX_SIZE, value);
                 value = value.substring(0, PHONE_MAX_SIZE);
             } else if (value.length() > METADATA_MAX_SIZE) {
-                log.warn(
-                    "Truncating eperson " + field + " metadata because it is longer than " + METADATA_MAX_SIZE + ": " +
-                        "'" + value + "'");
+                log.warn("Truncating eperson {} metadata because it is longer than {}: '{}'",
+                        field, METADATA_MAX_SIZE, value);
                 value = value.substring(0, METADATA_MAX_SIZE);
             }
 
-            ePersonService.setMetadata(context, eperson, field, value);
-            log.debug(
-                "Updated the eperson's '" + field + "' metadata using header: '" + header + "' = '" + value + "'.");
+            String[] nameParts = MetadataFieldName.parse(field);
+            ePersonService.setMetadataSingleValue(context, eperson,
+                    nameParts[0], nameParts[1], nameParts[2], value, null);
+            log.debug("Updated the eperson's '{}' metadata using header: '{}' = '{}'.",
+                    field, header, value);
         }
         ePersonService.update(context, eperson);
         context.dispatchEvents();
@@ -889,10 +890,8 @@ public class ShibAuthentication implements AuthenticationMethod {
     protected int swordCompatibility(Context context, String username, String password, HttpServletRequest request)
         throws SQLException {
 
-        EPerson eperson = null;
-
         log.debug("Shibboleth Sword compatibility activated.");
-        eperson = ePersonService.findByEmail(context, username.toLowerCase());
+        EPerson eperson = ePersonService.findByEmail(context, username.toLowerCase());
 
         if (eperson == null) {
             // lookup failed.
@@ -951,7 +950,7 @@ public class ShibAuthentication implements AuthenticationMethod {
         }
 
 
-        HashMap<String, String> map = new HashMap<String, String>();
+        HashMap<String, String> map = new HashMap<>();
 
         String[] mappingString = configurationService.getArrayProperty("authentication-shibboleth.eperson.metadata");
         boolean autoCreate = configurationService
@@ -990,19 +989,19 @@ public class ShibAuthentication implements AuthenticationMethod {
 
             if (valid) {
                 // The eperson field is fine, we can use it.
-                log.debug("Loading additional eperson metadata mapping for: '" + header + "' = '" + name + "'");
+                log.debug("Loading additional eperson metadata mapping for: '{}' = '{}'",
+                        header, name);
                 map.put(header, name);
             } else {
                 // The field doesn't exist, and we can't use it.
-                log.error(
-                    "Skipping the additional eperson metadata mapping for: '" + header + "' = '" + name + "' because " +
-                        "the field is not supported by the current configuration.");
+                log.error("Skipping the additional eperson metadata mapping for: '{}' = '{}'"
+                        + " because the field is not supported by the current configuration.",
+                        header, name);
             }
         } // foreach metadataStringList
 
 
         metadataHeaderMap = map;
-        return;
     }
 
     /**
@@ -1020,12 +1019,8 @@ public class ShibAuthentication implements AuthenticationMethod {
             return false;
         }
 
-        // The phone is a predefined field
-        if ("phone".equals(metadataName)) {
-            return true;
-        }
-
-        MetadataField metadataField = metadataFieldService.findByElement(context, "eperson", metadataName, null);
+        MetadataField metadataField = metadataFieldService.findByElement(context,
+                MetadataSchemaEnum.EPERSON.getName(), metadataName, null);
         return metadataField != null;
     }
 
@@ -1063,10 +1058,7 @@ public class ShibAuthentication implements AuthenticationMethod {
         try {
             context.turnOffAuthorisationSystem();
             metadataField = metadataFieldService.create(context, epersonSchema, metadataName, null, null);
-        } catch (AuthorizeException e) {
-            log.error(e.getMessage(), e);
-            return false;
-        } catch (NonUniqueMetadataException e) {
+        } catch (AuthorizeException | NonUniqueMetadataException e) {
             log.error(e.getMessage(), e);
             return false;
         } finally {
@@ -1211,7 +1203,7 @@ public class ShibAuthentication implements AuthenticationMethod {
         // Shibboleth attributes are separated by semicolons (and semicolons are
         // escaped with a backslash). So here we will scan through the string and
         // split on any unescaped semicolons.
-        List<String> valueList = new ArrayList<String>();
+        List<String> valueList = new ArrayList<>();
         int idx = 0;
         do {
             idx = values.indexOf(';', idx);

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

@@ -12,6 +12,7 @@ import java.net.MalformedURLException;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.apache.solr.client.solrj.SolrClient;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -21,7 +22,8 @@ import org.apache.solr.client.solrj.response.FacetField;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrInputDocument;
 import org.dspace.authority.indexer.AuthorityIndexingService;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * @author Antoine Snyers (antoine at atmire.com)
@@ -31,7 +33,7 @@ import org.dspace.core.ConfigurationManager;
  */
 public class AuthoritySolrServiceImpl implements AuthorityIndexingService, AuthoritySearchService {
 
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthoritySolrServiceImpl.class);
+    private static final Logger log = LogManager.getLogger(AuthoritySolrServiceImpl.class);
 
     protected AuthoritySolrServiceImpl() {
 
@@ -46,7 +48,9 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
             throws MalformedURLException, SolrServerException, IOException {
         if (solr == null) {
 
-            String solrService = ConfigurationManager.getProperty("solr.authority.server");
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
+            String solrService = configurationService.getProperty("solr.authority.server");
 
             log.debug("Solr authority URL: " + solrService);
 
@@ -153,7 +157,7 @@ public class AuthoritySolrServiceImpl implements AuthorityIndexingService, Autho
 
         QueryResponse response = getSolr().query(solrQuery);
 
-        List<String> results = new ArrayList<String>();
+        List<String> results = new ArrayList<>();
         FacetField facetField = response.getFacetField("field");
         if (facetField != null) {
             List<FacetField.Count> values = facetField.getValues();

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

@@ -7,20 +7,22 @@
  */
 package org.dspace.authority;
 
+import java.lang.reflect.InvocationTargetException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 /**
  * This class contains a list of active authority types.
  * It can be used to created a new instance of a specific type.
- * However if you need to make a new instance to store it in solr, you need to use AuthorityValueGenerator.
- * To create an instance from a solr record, use AuthorityValue#fromSolr(SolrDocument).
+ * However if you need to make a new instance to store it in Solr, you need to use {@link AuthorityValueGenerator}.
+ * To create an instance from a Solr record, use {@link AuthorityValue#fromSolr(SolrDocument)}.
  *
- * This class is instantiated in spring and accessed by a static method in AuthorityValue.
+ * This class is instantiated in Spring and accessed by a static method in AuthorityValue.
  *
  * @author Antoine Snyers (antoine at atmire.com)
  * @author Kevin Van de Velde (kevin at atmire dot com)
@@ -32,11 +34,11 @@ public class AuthorityTypes {
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityTypes.class);
+    private static final Logger log = LogManager.getLogger(AuthorityTypes.class);
 
-    protected List<AuthorityValue> types = new ArrayList<AuthorityValue>();
+    protected List<AuthorityValue> types = new ArrayList<>();
 
-    protected Map<String, AuthorityValue> fieldDefaults = new HashMap<String, AuthorityValue>();
+    protected Map<String, AuthorityValue> fieldDefaults = new HashMap<>();
 
 
     public List<AuthorityValue> getTypes() {
@@ -60,10 +62,10 @@ public class AuthorityTypes {
         for (AuthorityValue authorityValue : types) {
             if (authorityValue.getAuthorityType().equals(type)) {
                 try {
-                    result = authorityValue.getClass().newInstance();
-                } catch (InstantiationException e) {
-                    log.error("Error", e);
-                } catch (IllegalAccessException e) {
+                    result = authorityValue.getClass().getDeclaredConstructor().newInstance();
+                } catch (InstantiationException | IllegalAccessException
+                        | NoSuchMethodException | SecurityException
+                        | IllegalArgumentException | InvocationTargetException e) {
                     log.error("Error", e);
                 }
             }

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

@@ -8,6 +8,7 @@
 package org.dspace.authority;
 
 import java.io.PrintWriter;
+import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -15,19 +16,22 @@ import java.util.List;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
+import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * @author Antoine Snyers (antoine at atmire.com)
@@ -40,21 +44,23 @@ public class UpdateAuthorities {
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(UpdateAuthorities.class);
+    private static final Logger log = LogManager.getLogger(UpdateAuthorities.class);
 
     protected PrintWriter print = null;
 
-    private Context context;
+    private final Context context;
     private List<String> selectedIDs;
 
     protected final ItemService itemService;
     protected final AuthorityValueService authorityValueService;
+    protected final ConfigurationService configurationService;
 
     public UpdateAuthorities(Context context) {
         print = new PrintWriter(System.out);
         this.context = context;
         this.authorityValueService = AuthorityServiceFactory.getInstance().getAuthorityValueService();
         this.itemService = ContentServiceFactory.getInstance().getItemService();
+        this.configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
     }
 
     public static void main(String[] args) throws ParseException {
@@ -78,7 +84,7 @@ public class UpdateAuthorities {
     }
 
     protected static int processArgs(String[] args, UpdateAuthorities UpdateAuthorities) throws ParseException {
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         Options options = createCommandLineOptions();
         CommandLine line = parser.parse(options, args);
 
@@ -102,7 +108,7 @@ public class UpdateAuthorities {
     }
 
     private void setSelectedIDs(String b) {
-        this.selectedIDs = new ArrayList<String>();
+        this.selectedIDs = new ArrayList<>();
         String[] orcids = b.split(",");
         for (String orcid : orcids) {
             this.selectedIDs.add(orcid.trim());
@@ -125,7 +131,7 @@ public class UpdateAuthorities {
         List<AuthorityValue> authorities;
 
         if (selectedIDs != null && !selectedIDs.isEmpty()) {
-            authorities = new ArrayList<AuthorityValue>();
+            authorities = new ArrayList<>();
             for (String selectedID : selectedIDs) {
                 AuthorityValue byUID = authorityValueService.findByUID(context, selectedID);
                 authorities.add(byUID);
@@ -149,7 +155,7 @@ public class UpdateAuthorities {
     protected void followUp(AuthorityValue authority) {
         print.println("Updated: " + authority.getValue() + " - " + authority.getId());
 
-        boolean updateItems = ConfigurationManager.getBooleanProperty("solrauthority", "auto-update-items");
+        boolean updateItems = configurationService.getBooleanProperty("solrauthority.auto-update-items");
         if (updateItems) {
             updateItems(authority);
         }
@@ -169,7 +175,7 @@ public class UpdateAuthorities {
                     print.println("Updated item with handle " + next.getHandle());
                 }
             }
-        } catch (Exception e) {
+        } catch (SQLException | AuthorizeException e) {
             log.error("Error updating item", e);
             print.println("Error updating item. " + Arrays.toString(e.getStackTrace()));
         }

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

@@ -460,7 +460,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
                                                                        groupService.allMemberGroups(c, e),
                                                                        Constants.ADMIN, Constants.COLLECTION);
 
-            if (CollectionUtils.isNotEmpty(policies)) {
+            if (CollectionUtils.isNotEmpty(policies) || isCommunityAdmin(c, e)) {
                 return true;
             }
         }
@@ -614,6 +614,12 @@ public class AuthorizeServiceImpl implements AuthorizeService {
         resourcePolicyService.removeDsoEPersonPolicies(c, o, e);
     }
 
+    @Override
+    public void removeAllEPersonPolicies(Context c, EPerson e)
+        throws SQLException, AuthorizeException {
+        resourcePolicyService.removeAllEPersonPolicies(c, e);
+    }
+
     @Override
     public List<Group> getAuthorizedGroups(Context c, DSpaceObject o,
                                            int actionID) throws java.sql.SQLException {

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

@@ -114,6 +114,11 @@ public class ResourcePolicyServiceImpl implements ResourcePolicyService {
         return resourcePolicyDAO.findByEPersonGroupTypeIdAction(c, e, groups, action, type_id);
     }
 
+    @Override
+    public List<ResourcePolicy> find(Context context, EPerson ePerson) throws SQLException {
+        return resourcePolicyDAO.findByEPerson(context, ePerson);
+    }
+
     @Override
     public List<ResourcePolicy> findByTypeGroupActionExceptId(Context context, DSpaceObject dso, Group group,
                                                               int action, int notPolicyID)
@@ -246,6 +251,11 @@ public class ResourcePolicyServiceImpl implements ResourcePolicyService {
 
     }
 
+    @Override
+    public void removeAllEPersonPolicies(Context context, EPerson ePerson) throws SQLException, AuthorizeException {
+        resourcePolicyDAO.deleteByEPerson(context, ePerson);
+    }
+
     @Override
     public void removeGroupPolicies(Context c, Group group) throws SQLException {
         resourcePolicyDAO.deleteByGroup(c, group);

dspace-api/src/main/java/org/dspace/authorize/dao/ResourcePolicyDAO.java

@@ -33,6 +33,8 @@ public interface ResourcePolicyDAO extends GenericDAO<ResourcePolicy> {
     public List<ResourcePolicy> findByDsoAndType(Context context, DSpaceObject dSpaceObject, String type)
         throws SQLException;
 
+    public List<ResourcePolicy> findByEPerson(Context context, EPerson ePerson) throws SQLException;
+
     public List<ResourcePolicy> findByGroup(Context context, Group group) throws SQLException;
 
     public List<ResourcePolicy> findByDSoAndAction(Context context, DSpaceObject dso, int actionId) throws SQLException;
@@ -66,6 +68,15 @@ public interface ResourcePolicyDAO extends GenericDAO<ResourcePolicy> {
 
     public void deleteByDsoEPersonPolicies(Context context, DSpaceObject dso, EPerson ePerson) throws SQLException;
 
+    /**
+     * Deletes all policies that belong to an EPerson
+     *
+     * @param context       DSpace context object
+     * @param ePerson       ePerson whose policies to delete
+     * @throws SQLException if database error
+     */
+    public void deleteByEPerson(Context context, EPerson ePerson) throws SQLException;
+
     public void deleteByDsoAndTypeNotEqualsTo(Context c, DSpaceObject o, String type) throws SQLException;
 
     /**
@@ -101,7 +112,7 @@ public interface ResourcePolicyDAO extends GenericDAO<ResourcePolicy> {
      * @return               total resource policies of the ePerson
      * @throws SQLException  if database error
      */
-    public int countByEPerson(Context context, EPerson eperson) throws SQLException;
+    public int countByEPerson(Context context, EPerson ePerson) throws SQLException;
 
     /**
      * Return a paginated list of policies related to a resourceUuid belong to an ePerson

dspace-api/src/main/java/org/dspace/authorize/dao/impl/ResourcePolicyDAOImpl.java

@@ -63,6 +63,16 @@ public class ResourcePolicyDAOImpl extends AbstractHibernateDAO<ResourcePolicy>
         return list(context, criteriaQuery, false, ResourcePolicy.class, -1, -1);
     }
 
+    @Override
+    public List<ResourcePolicy> findByEPerson(Context context, EPerson ePerson) throws SQLException {
+        CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
+        CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, ResourcePolicy.class);
+        Root<ResourcePolicy> resourcePolicyRoot = criteriaQuery.from(ResourcePolicy.class);
+        criteriaQuery.select(resourcePolicyRoot);
+        criteriaQuery.where(criteriaBuilder.equal(resourcePolicyRoot.get(ResourcePolicy_.eperson), ePerson));
+        return list(context, criteriaQuery, false, ResourcePolicy.class, -1, -1);
+    }
+
     @Override
     public List<ResourcePolicy> findByGroup(Context context, Group group) throws SQLException {
         CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
@@ -194,6 +204,15 @@ public class ResourcePolicyDAOImpl extends AbstractHibernateDAO<ResourcePolicy>
 
     }
 
+    @Override
+    public void deleteByEPerson(Context context, EPerson ePerson) throws SQLException {
+        String queryString = "delete from ResourcePolicy where eperson= :eperson";
+        Query query = createQuery(context, queryString);
+        query.setParameter("eperson", ePerson);
+        query.executeUpdate();
+
+    }
+
     @Override
     public void deleteByDsoAndTypeNotEqualsTo(Context context, DSpaceObject dso, String type) throws SQLException {
 
@@ -247,10 +266,10 @@ public class ResourcePolicyDAOImpl extends AbstractHibernateDAO<ResourcePolicy>
     }
 
     @Override
-    public int countByEPerson(Context context, EPerson eperson) throws SQLException {
+    public int countByEPerson(Context context, EPerson ePerson) throws SQLException {
         Query query = createQuery(context,
                 "SELECT count(*) FROM " + ResourcePolicy.class.getSimpleName() + " WHERE eperson_id = (:epersonUuid) ");
-        query.setParameter("epersonUuid", eperson.getID());
+        query.setParameter("epersonUuid", ePerson.getID());
         return count(query);
     }
 

dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java

@@ -449,6 +449,16 @@ public interface AuthorizeService {
      */
     public void removeEPersonPolicies(Context c, DSpaceObject o, EPerson e) throws SQLException, AuthorizeException;
 
+    /**
+     * Removes all policies from an eperson that belong to an EPerson.
+     *
+     * @param c current context
+     * @param e the eperson
+     * @throws SQLException if there's a database problem
+     * @throws AuthorizeException if authorization error
+     */
+    public void removeAllEPersonPolicies(Context c, EPerson e) throws SQLException, AuthorizeException;
+
     /**
      * Returns all groups authorized to perform an action on an object. Returns
      * empty array if no matches.

dspace-api/src/main/java/org/dspace/authorize/service/ResourcePolicyService.java

@@ -39,6 +39,16 @@ public interface ResourcePolicyService extends DSpaceCRUDService<ResourcePolicy>
 
     public List<ResourcePolicy> find(Context context, Group group) throws SQLException;
 
+    /**
+     * Retrieve a list of ResourcePolicies by EPerson
+     *
+     * @param c         context
+     * @param ePerson   the EPerson for which to look up the resource policies
+     * @return a list of ResourcePolicies for the provided EPerson
+     * @throws SQLException if there's a database problem
+     */
+    public List<ResourcePolicy> find(Context c, EPerson ePerson) throws SQLException;
+
     public List<ResourcePolicy> find(Context c, EPerson e, List<Group> groups, int action, int type_id)
         throws SQLException;
 
@@ -72,6 +82,16 @@ public interface ResourcePolicyService extends DSpaceCRUDService<ResourcePolicy>
     public void removeDsoEPersonPolicies(Context context, DSpaceObject dso, EPerson ePerson)
         throws SQLException, AuthorizeException;
 
+    /**
+     *  Removes all ResourcePolicies related to an EPerson
+     *
+     * @param context   context
+     * @param ePerson   the EPerson for which the ResourcePolicies will be deleted
+     * @throws SQLException if there's a database problem
+     * @throws AuthorizeException when the current user is not authorized
+     */
+    public void removeAllEPersonPolicies(Context context, EPerson ePerson) throws SQLException, AuthorizeException;
+
     public void removeGroupPolicies(Context c, Group group) throws SQLException;
 
     public void removeDsoAndTypeNotEqualsToPolicies(Context c, DSpaceObject o, String type)

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

@@ -7,8 +7,11 @@
  */
 package org.dspace.browse;
 
-import org.dspace.core.ConfigurationManager;
+import java.lang.reflect.InvocationTargetException;
+
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Factory class to generate DAOs based on the configuration
@@ -33,16 +36,21 @@ public class BrowseDAOFactory {
      */
     public static BrowseDAO getInstance(Context context)
         throws BrowseException {
-        String className = ConfigurationManager.getProperty("browseDAO.class");
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        String className = configurationService.getProperty("browseDAO.class");
         if (className == null) {
             // SOLR implementation is the default since DSpace 4.0
             return new SolrBrowseDAO(context);
         }
         try {
             return (BrowseDAO) Class
-                .forName(ConfigurationManager.getProperty("browseDAO.class"))
+                .forName(configurationService.getProperty("browseDAO.class"))
                 .getConstructor(Context.class).newInstance(context);
-        } catch (Exception e) {
+        } catch (ClassNotFoundException | IllegalAccessException
+                | IllegalArgumentException | InstantiationException
+                | NoSuchMethodException | SecurityException |
+                InvocationTargetException e) {
             throw new BrowseException("The configuration for browseDAO is invalid: " + className, e);
         }
     }

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

@@ -13,7 +13,8 @@ import java.util.StringTokenizer;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.dspace.sort.SortException;
 import org.dspace.sort.SortOption;
 
@@ -414,6 +415,7 @@ public final class BrowseIndex {
      * @return the name of the table
      * @deprecated 1.5
      */
+    @Deprecated
     public static String getTableName(int number, boolean isCommunity, boolean isCollection, boolean isDistinct,
                                       boolean isMap) {
         return BrowseIndex.getTableName(makeTableBaseName(number), isCommunity, isCollection, isDistinct, isMap);
@@ -462,6 +464,7 @@ public final class BrowseIndex {
      * @return the name of the table
      * @deprecated 1.5
      */
+    @Deprecated
     public String getTableName(boolean isCommunity, boolean isCollection, boolean isDistinct, boolean isMap) {
         if (isDistinct || isMap) {
             return BrowseIndex.getTableName(number, isCommunity, isCollection, isDistinct, isMap);
@@ -482,6 +485,7 @@ public final class BrowseIndex {
      * @return the name of the table
      * @deprecated 1.5
      */
+    @Deprecated
     public String getTableName(boolean isCommunity, boolean isCollection) {
         return getTableName(isCommunity, isCollection, false, false);
     }
@@ -514,6 +518,7 @@ public final class BrowseIndex {
      * @return table name
      * @deprecated 1.5
      */
+    @Deprecated
     public String getTableName(boolean isDistinct, boolean isCommunity, boolean isCollection) {
         return getTableName(isCommunity, isCollection, isDistinct, false);
     }
@@ -649,6 +654,7 @@ public final class BrowseIndex {
      * @throws BrowseException if browse error
      * @deprecated
      */
+    @Deprecated
     public static String[] tables()
         throws BrowseException {
         BrowseIndex[] bis = getBrowseIndices();
@@ -670,13 +676,14 @@ public final class BrowseIndex {
         throws BrowseException {
         int idx = 1;
         String definition;
-        ArrayList<BrowseIndex> browseIndices = new ArrayList<BrowseIndex>();
+        ArrayList<BrowseIndex> browseIndices = new ArrayList<>();
 
-        while (((definition = ConfigurationManager.getProperty("webui.browse.index." + idx))) != null) {
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        while (((definition = configurationService.getProperty("webui.browse.index." + idx))) != null) {
             BrowseIndex bi = new BrowseIndex(definition, idx);
-            bi.displayFrequencies = Boolean.valueOf(ConfigurationManager
-                                                        .getBooleanProperty("webui.browse.metadata.show-freq."
-                                                                                + idx, true));
+            bi.displayFrequencies = configurationService
+                    .getBooleanProperty("webui.browse.metadata.show-freq." + idx, true);
 
             browseIndices.add(bi);
             idx++;
@@ -804,8 +811,8 @@ public final class BrowseIndex {
      * @return true or false
      */
     public boolean isTagCloudEnabled() {
-
-        return ConfigurationManager.getBooleanProperty("webui.browse.index.tagcloud." + number);
-
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        return configurationService.getBooleanProperty("webui.browse.index.tagcloud." + number);
     }
 }

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

@@ -475,6 +475,7 @@ public class BrowseInfo {
      * @return an empty array of Item.
      * @deprecated
      */
+    @Deprecated
     public Item[] getItemResults() {
         return new Item[0];
     }

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

@@ -10,7 +10,8 @@ package org.dspace.browse;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Class to represent the configuration of the cross-linking between browse
@@ -23,7 +24,7 @@ public class CrossLinks {
     /**
      * a map of the desired links
      */
-    private Map<String, String> links = new HashMap<String, String>();
+    private Map<String, String> links = new HashMap<>();
 
     /**
      * Construct a new object which will obtain the configuration for itself.
@@ -35,7 +36,9 @@ public class CrossLinks {
         int i = 1;
         while (true) {
             String field = "webui.browse.link." + i;
-            String config = ConfigurationManager.getProperty(field);
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
+            String config = configurationService.getProperty(field);
             if (config == null) {
                 break;
             }

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

@@ -7,8 +7,11 @@
  */
 package org.dspace.browse;
 
-import org.dspace.core.ConfigurationManager;
+import java.lang.reflect.InvocationTargetException;
+
 import org.dspace.core.Context;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Factory class to allow us to load the correct DAO for registering
@@ -38,16 +41,22 @@ public class ItemCountDAOFactory {
         /** Log4j logger */
         ItemCountDAO dao = null;
 
-        String className = ConfigurationManager.getProperty("ItemCountDAO.class");
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        String className = configurationService.getProperty("ItemCountDAO.class");
 
         // SOLR implementation is the default since DSpace 4.0
         if (className == null) {
             dao = new ItemCountDAOSolr();
         } else {
             try {
-                dao = (ItemCountDAO) Class
-                    .forName(className.trim()).newInstance();
-            } catch (Exception e) {
+                dao = (ItemCountDAO) Class.forName(className.trim())
+                        .getDeclaredConstructor()
+                        .newInstance();
+            } catch (ClassNotFoundException | IllegalAccessException
+                    | InstantiationException | NoSuchMethodException
+                    | SecurityException | IllegalArgumentException
+                    | InvocationTargetException e) {
                 throw new ItemCountException("The configuration for ItemCountDAO is invalid: " + className, e);
             }
         }

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

@@ -12,8 +12,10 @@ import java.util.Locale;
 import com.ibm.icu.text.CollationElementIterator;
 import com.ibm.icu.text.Collator;
 import com.ibm.icu.text.RuleBasedCollator;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.dspace.core.ConfigurationManager;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 import org.dspace.text.filter.TextFilter;
 
 /**
@@ -32,7 +34,7 @@ import org.dspace.text.filter.TextFilter;
  * @author Graham Triggs
  */
 public class LocaleOrderingFilter implements TextFilter {
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(LocaleOrderingFilter.class);
+    private static final Logger log = LogManager.getLogger(LocaleOrderingFilter.class);
 
     /**
      * Uses a Locale dependent Collator to generate a sort string
@@ -47,7 +49,7 @@ public class LocaleOrderingFilter implements TextFilter {
         // Have we got a collator?
         if (collator != null) {
             int element;
-            StringBuffer buf = new StringBuffer();
+            StringBuilder buf = new StringBuilder();
 
             // Iterate through the elements of the collator
             CollationElementIterator iter = collator.getCollationElementIterator(str);
@@ -107,7 +109,9 @@ public class LocaleOrderingFilter implements TextFilter {
         Locale theLocale = null;
 
         // Get a Locale configuration from the dspace.cfg
-        String locale = ConfigurationManager.getProperty("webui.browse.sort.locale");
+        ConfigurationService configurationService
+                = DSpaceServicesFactory.getInstance().getConfigurationService();
+        String locale = configurationService.getProperty("webui.browse.sort.locale");
 
         if (locale != null) {
             // Attempt to create Locale for the configured value

dspace-api/src/main/java/org/dspace/checker/DailyReportEmailer.java

@@ -17,17 +17,19 @@ import javax.mail.MessagingException;
 
 import org.apache.commons.cli.CommandLine;
 import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.DefaultParser;
 import org.apache.commons.cli.HelpFormatter;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.apache.commons.cli.PosixParser;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.SimpleReporterService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
 import org.dspace.core.Utils;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * <p>
@@ -44,7 +46,7 @@ public class DailyReportEmailer {
     /**
      * log4j logger.
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DailyReportEmailer.class);
+    private static final Logger log = LogManager.getLogger(DailyReportEmailer.class);
 
     /**
      * Default constructor.
@@ -63,14 +65,16 @@ public class DailyReportEmailer {
     public void sendReport(File attachment, int numberOfBitstreams)
         throws IOException, javax.mail.MessagingException {
         if (numberOfBitstreams > 0) {
-            String hostname = Utils.getHostName(ConfigurationManager.getProperty("dspace.ui.url"));
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
+            String hostname = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
             Email email = new Email();
-            email.setSubject(
-                "Checksum checker Report - " + numberOfBitstreams + " Bitstreams found with POSSIBLE issues on " +
-                    hostname);
+            email.setSubject(String.format(
+                "Checksum checker Report - %d Bitstreams found with POSSIBLE issues on %s",
+                    numberOfBitstreams, hostname));
             email.setContent("Checker Report", "report is attached ...");
             email.addAttachment(attachment, "checksum_checker_report.txt");
-            email.addRecipient(ConfigurationManager.getProperty("mail.admin"));
+            email.addRecipient(configurationService.getProperty("mail.admin"));
             email.send();
         }
     }
@@ -98,7 +102,7 @@ public class DailyReportEmailer {
      */
     public static void main(String[] args) {
         // set up command line parser
-        CommandLineParser parser = new PosixParser();
+        CommandLineParser parser = new DefaultParser();
         CommandLine line = null;
 
         // create an options object and populate it
@@ -164,7 +168,9 @@ public class DailyReportEmailer {
             int numBitstreams = 0;
 
             // create a temporary file in the log directory
-            String dirLocation = ConfigurationManager.getProperty("log.report.dir");
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
+            String dirLocation = configurationService.getProperty("log.report.dir");
             File directory = new File(dirLocation);
 
             if (directory.exists() && directory.isDirectory()) {
@@ -247,7 +253,7 @@ public class DailyReportEmailer {
             if (writer != null) {
                 try {
                     writer.close();
-                } catch (Exception e) {
+                } catch (IOException e) {
                     log.fatal("Could not close writer", e);
                 }
             }

dspace-api/src/main/java/org/dspace/checker/ResultsPruner.java

@@ -19,12 +19,14 @@ import java.util.Properties;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.checker.factory.CheckerServiceFactory;
 import org.dspace.checker.service.ChecksumHistoryService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.Utils;
+import org.dspace.services.ConfigurationService;
+import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Manages the deletion of results from the checksum history. It uses the
@@ -40,7 +42,7 @@ public final class ResultsPruner {
     /**
      * Default logger.
      */
-    private static final Logger LOG = org.apache.logging.log4j.LogManager.getLogger(ResultsPruner.class);
+    private static final Logger LOG = LogManager.getLogger(ResultsPruner.class);
 
     /**
      * Factory method for the default results pruner configuration using
@@ -51,12 +53,13 @@ public final class ResultsPruner {
      */
     public static ResultsPruner getDefaultPruner(Context context) {
         try {
-            return getPruner(context, ConfigurationManager.getProperties());
+            ConfigurationService configurationService
+                    = DSpaceServicesFactory.getInstance().getConfigurationService();
+            return getPruner(context, configurationService.getProperties());
         } catch (FileNotFoundException e) {
             throw new IllegalStateException(
                 "VeryExceptionalException - config file not there! ", e);
         }
-
     }
 
 

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

@@ -7,11 +7,14 @@
  */
 package org.dspace.content;
 
+import static org.dspace.content.service.DSpaceObjectService.MD_LICENSE;
+
 import java.sql.SQLException;
 import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import javax.annotation.Nonnull;
 import javax.persistence.Cacheable;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -46,7 +49,6 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * effect.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 @Entity
 @Table(name = "collection")
@@ -87,23 +89,11 @@ public class Collection extends DSpaceObject implements DSpaceObjectLegacySuppor
         joinColumns = {@JoinColumn(name = "collection_id")},
         inverseJoinColumns = {@JoinColumn(name = "community_id")}
     )
-    private Set<Community> communities = new HashSet<>();
+    private final Set<Community> communities = new HashSet<>();
 
     @Transient
     private transient CollectionService collectionService;
 
-    // Keys for accessing Collection metadata
-    @Transient
-    public static final String COPYRIGHT_TEXT = "copyright_text";
-    @Transient
-    public static final String INTRODUCTORY_TEXT = "introductory_text";
-    @Transient
-    public static final String SHORT_DESCRIPTION = "short_description";
-    @Transient
-    public static final String SIDEBAR_TEXT = "side_bar_text";
-    @Transient
-    public static final String PROVENANCE_TEXT = "provenance_description";
-
     /**
      * Protected constructor, create object using:
      * {@link org.dspace.content.service.CollectionService#create(Context, Community)}
@@ -207,10 +197,17 @@ public class Collection extends DSpaceObject implements DSpaceObjectLegacySuppor
      * Get the license that users must grant before submitting to this
      * collection.
      *
-     * @return the license for this collection
+     * @return the license for this collection. Never null.
      */
+    @Nonnull
     public String getLicenseCollection() {
-        return getCollectionService().getMetadata(this, "license");
+        String license = getCollectionService()
+                .getMetadataFirstValue(this, CollectionService.MD_LICENSE, Item.ANY);
+        if (null == license) {
+            return "";
+        } else {
+            return license;
+        }
     }
 
     /**
@@ -222,7 +219,7 @@ public class Collection extends DSpaceObject implements DSpaceObjectLegacySuppor
      * @throws SQLException if database error
      */
     public void setLicense(Context context, String license) throws SQLException {
-        getCollectionService().setMetadata(context, this, "license", license);
+        getCollectionService().setMetadataSingleValue(context, this, MD_LICENSE, Item.ANY, license);
     }
 
     /**

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

@@ -36,7 +36,6 @@ import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
 import org.dspace.content.service.WorkspaceItemService;
-import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
@@ -55,9 +54,11 @@ import org.dspace.eperson.service.SubscribeService;
 import org.dspace.event.Event;
 import org.dspace.harvest.HarvestedCollection;
 import org.dspace.harvest.service.HarvestedCollectionService;
+import org.dspace.identifier.IdentifierException;
+import org.dspace.identifier.service.IdentifierService;
+import org.dspace.services.ConfigurationService;
 import org.dspace.workflow.factory.WorkflowServiceFactory;
 import org.dspace.xmlworkflow.WorkflowConfigurationException;
-import org.dspace.xmlworkflow.XmlWorkflowFactoryImpl;
 import org.dspace.xmlworkflow.factory.XmlWorkflowFactory;
 import org.dspace.xmlworkflow.state.Workflow;
 import org.dspace.xmlworkflow.storedcomponents.CollectionRole;
@@ -93,6 +94,8 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     protected CommunityService communityService;
     @Autowired(required = true)
     protected GroupService groupService;
+    @Autowired(required = true)
+    protected IdentifierService identifierService;
 
     @Autowired(required = true)
     protected LicenseService licenseService;
@@ -112,6 +115,9 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     @Autowired(required = true)
     protected SearchService searchService;
 
+    @Autowired(required = true)
+    protected ConfigurationService configurationService;
+
     protected CollectionServiceImpl() {
         super();
     }
@@ -132,13 +138,6 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         //Add our newly created collection to our community, authorization checks occur in THIS method
         communityService.addCollection(context, community, newCollection);
 
-        //Update our community so we have a collection identifier
-        if (handle == null) {
-            handleService.createHandle(context, newCollection);
-        } else {
-            handleService.createHandle(context, newCollection, handle);
-        }
-
         // create the default authorization policy for collections
         // of 'anonymous' READ
         Group anonymousGroup = groupService.findByName(context, Group.ANONYMOUS);
@@ -151,6 +150,18 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         authorizeService
             .createResourcePolicy(context, newCollection, anonymousGroup, null, Constants.DEFAULT_BITSTREAM_READ, null);
 
+        collectionDAO.save(context, newCollection);
+
+        //Update our collection so we have a collection identifier
+        try {
+            if (handle == null) {
+                identifierService.register(context, newCollection);
+            } else {
+                identifierService.register(context, newCollection, handle);
+            }
+        } catch (IllegalStateException | IdentifierException ex) {
+            throw new IllegalStateException(ex);
+        }
 
         context.addEvent(new Event(Event.CREATE, Constants.COLLECTION,
                                    newCollection.getID(), newCollection.getHandle(),
@@ -160,7 +171,6 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
                                       "collection_id=" + newCollection.getID())
                      + ",handle=" + newCollection.getHandle());
 
-        collectionDAO.save(context, newCollection);
         return newCollection;
     }
 
@@ -190,7 +200,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
     @Override
     public List<Collection> findAuthorizedOptimized(Context context, int actionID) throws SQLException {
-        if (!ConfigurationManager
+        if (!configurationService
             .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);
@@ -291,9 +301,10 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     }
 
     @Override
-    public void setMetadata(Context context, Collection collection, String field, String value)
-        throws MissingResourceException, SQLException {
-        if ((field.trim()).equals("name") && (value == null || value.trim().equals(""))) {
+    public void setMetadataSingleValue(Context context, Collection collection,
+            MetadataFieldName field, String language, String value)
+            throws MissingResourceException, SQLException {
+        if (field.equals(MD_NAME) && (value == null || value.trim().equals(""))) {
             try {
                 value = I18nUtil.getMessage("org.dspace.workflow.WorkflowManager.untitled");
             } catch (MissingResourceException e) {
@@ -301,21 +312,19 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
             }
         }
 
-        String[] MDValue = getMDValueByLegacyField(field);
-
         /*
          * Set metadata field to null if null
          * and trim strings to eliminate excess
          * whitespace.
          */
         if (value == null) {
-            clearMetadata(context, collection, MDValue[0], MDValue[1], MDValue[2], Item.ANY);
+            clearMetadata(context, collection, field.SCHEMA, field.ELEMENT, field.QUALIFIER, Item.ANY);
             collection.setMetadataModified();
         } else {
-            setMetadataSingleValue(context, collection, MDValue[0], MDValue[1], MDValue[2], null, value);
+            super.setMetadataSingleValue(context, collection, field, null, value);
         }
 
-        collection.addDetails(field);
+        collection.addDetails(field.toString());
     }
 
     @Override
@@ -387,7 +396,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
             log.error(LogManager.getHeader(context, "setWorkflowGroup",
                     "collection_id=" + collection.getID() + " " + e.getMessage()), e);
         }
-        if (!StringUtils.equals(XmlWorkflowFactoryImpl.LEGACY_WORKFLOW_NAME, workflow.getID())) {
+        if (!StringUtils.equals(workflowFactory.getDefaultWorkflow().getID(), workflow.getID())) {
             throw new IllegalArgumentException(
                     "setWorkflowGroup can be used only on collection with the default basic dspace workflow. "
                     + "Instead, the collection: "
@@ -455,22 +464,6 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         }
     }
 
-    /**
-     * Get the value of a metadata field
-     *
-     * @param collection which collection to operate on
-     * @param field      the name of the metadata field to get
-     * @return the value of the metadata field
-     * @throws IllegalArgumentException if the requested metadata field doesn't exist
-     */
-    @Override
-    @Deprecated
-    public String getMetadata(Collection collection, String field) {
-        String[] MDValue = getMDValueByLegacyField(field);
-        String value = getMetadataFirstValue(collection, MDValue[0], MDValue[1], MDValue[2], Item.ANY);
-        return value == null ? "" : value;
-    }
-
     @Override
     public Group createSubmitters(Context context, Collection collection) throws SQLException, AuthorizeException {
         // Check authorisation - Must be an Admin to create Submitters Group
@@ -551,7 +544,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
     @Override
     public String getLicense(Collection collection) {
-        String license = getMetadata(collection, "license");
+        String license = getMetadataFirstValue(collection, CollectionService.MD_LICENSE, Item.ANY);
 
         if (license == null || license.trim().equals("")) {
             // Fallback to site-wide default
@@ -923,7 +916,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     public List<Collection> findCollectionsWithSubmit(String q, Context context, Community community,
         int offset, int limit) throws SQLException, SearchServiceException {
 
-        List<Collection> collections = new ArrayList<Collection>();
+        List<Collection> collections = new ArrayList<>();
         DiscoverQuery discoverQuery = new DiscoverQuery();
         discoverQuery.setDSpaceObjectFilter(IndexableCollection.TYPE);
         discoverQuery.setStart(offset);

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

@@ -63,13 +63,13 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
         joinColumns = {@JoinColumn(name = "parent_comm_id")},
         inverseJoinColumns = {@JoinColumn(name = "child_comm_id")}
     )
-    private Set<Community> subCommunities = new HashSet<>();
+    private final Set<Community> subCommunities = new HashSet<>();
 
     @ManyToMany(fetch = FetchType.LAZY, mappedBy = "subCommunities")
-    private Set<Community> parentCommunities = new HashSet<>();
+    private final Set<Community> parentCommunities = new HashSet<>();
 
     @ManyToMany(fetch = FetchType.LAZY, mappedBy = "communities", cascade = {CascadeType.PERSIST})
-    private Set<Collection> collections = new HashSet<>();
+    private final Set<Collection> collections = new HashSet<>();
 
     @OneToOne
     @JoinColumn(name = "admin")
@@ -83,12 +83,6 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
     @JoinColumn(name = "logo_bitstream_id")
     private Bitstream logo = null;
 
-    // Keys for accessing Community metadata
-    public static final String COPYRIGHT_TEXT = "copyright_text";
-    public static final String INTRODUCTORY_TEXT = "introductory_text";
-    public static final String SHORT_DESCRIPTION = "short_description";
-    public static final String SIDEBAR_TEXT = "side_bar_text";
-
     @Transient
     protected transient CommunityService communityService;
 

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

@@ -37,6 +37,8 @@ import org.dspace.core.LogManager;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.GroupService;
 import org.dspace.event.Event;
+import org.dspace.identifier.IdentifierException;
+import org.dspace.identifier.service.IdentifierService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -51,7 +53,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
     /**
      * log4j category
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CommunityServiceImpl.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(CommunityServiceImpl.class);
 
     @Autowired(required = true)
     protected CommunityDAO communityDAO;
@@ -69,6 +71,8 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
     protected BitstreamService bitstreamService;
     @Autowired(required = true)
     protected SiteService siteService;
+    @Autowired(required = true)
+    protected IdentifierService identifierService;
 
     protected CommunityServiceImpl() {
         super();
@@ -90,17 +94,6 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
         Community newCommunity = communityDAO.create(context, new Community());
 
-        try {
-            if (handle == null) {
-                handleService.createHandle(context, newCommunity);
-            } else {
-                handleService.createHandle(context, newCommunity, handle);
-            }
-        } catch (IllegalStateException ie) {
-            //If an IllegalStateException is thrown, then an existing object is already using this handle
-            throw ie;
-        }
-
         if (parent != null) {
             parent.addSubCommunity(newCommunity);
             newCommunity.addParentCommunity(parent);
@@ -115,14 +108,24 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
         communityDAO.save(context, newCommunity);
 
+        try {
+            if (handle == null) {
+                identifierService.register(context, newCommunity);
+            } else {
+                identifierService.register(context, newCommunity, handle);
+            }
+        }  catch (IllegalStateException | IdentifierException ex) {
+            throw new IllegalStateException(ex);
+        }
+
         context.addEvent(new Event(Event.CREATE, Constants.COMMUNITY, newCommunity.getID(), newCommunity.getHandle(),
-                                   getIdentifiers(context, newCommunity)));
+                getIdentifiers(context, newCommunity)));
 
         // if creating a top-level Community, simulate an ADD event at the Site.
         if (parent == null) {
             context.addEvent(new Event(Event.ADD, Constants.SITE, siteService.findSite(context).getID(),
-                                       Constants.COMMUNITY, newCommunity.getID(), newCommunity.getHandle(),
-                                       getIdentifiers(context, newCommunity)));
+                    Constants.COMMUNITY, newCommunity.getID(), newCommunity.getHandle(),
+                    getIdentifiers(context, newCommunity)));
         }
 
         log.info(LogManager.getHeader(context, "create_community",
@@ -175,17 +178,10 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
     }
 
     @Override
-    public String getMetadata(Community community, String field) {
-        String[] MDValue = getMDValueByLegacyField(field);
-        String value = getMetadataFirstValue(community, MDValue[0], MDValue[1], MDValue[2], Item.ANY);
-        return value == null ? "" : value;
-    }
-
-    @Override
-    public void setMetadata(Context context, Community community, String field, String value)
-        throws MissingResourceException, SQLException {
-        if ((field.trim()).equals("name")
-            && (value == null || value.trim().equals(""))) {
+    public void setMetadataSingleValue(Context context, Community community,
+            MetadataFieldName field, String language, String value)
+            throws MissingResourceException, SQLException {
+        if (field.equals(MD_NAME) && (value == null || value.trim().equals(""))) {
             try {
                 value = I18nUtil.getMessage("org.dspace.workflow.WorkflowManager.untitled");
             } catch (MissingResourceException e) {
@@ -193,19 +189,19 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
             }
         }
 
-        String[] MDValue = getMDValueByLegacyField(field);
-
         /*
          * Set metadata field to null if null
          * and trim strings to eliminate excess
          * whitespace.
          */
         if (value == null) {
-            clearMetadata(context, community, MDValue[0], MDValue[1], MDValue[2], Item.ANY);
+            clearMetadata(context, community, field.SCHEMA, field.ELEMENT, field.QUALIFIER, Item.ANY);
+            community.setMetadataModified();
         } else {
-            setMetadataSingleValue(context, community, MDValue[0], MDValue[1], MDValue[2], null, value);
+            super.setMetadataSingleValue(context, community, field, null, value);
         }
-        community.addDetails(field);
+
+        community.addDetails(field.toString());
     }
 
     @Override
@@ -310,7 +306,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
     @Override
     public List<Community> getAllParents(Context context, Community community) throws SQLException {
-        List<Community> parentList = new ArrayList<Community>();
+        List<Community> parentList = new ArrayList<>();
         Community parent = (Community) getParentObject(context, community);
         while (parent != null) {
             parentList.add(parent);
@@ -332,7 +328,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
     @Override
     public List<Collection> getAllCollections(Context context, Community community) throws SQLException {
-        List<Collection> collectionList = new ArrayList<Collection>();
+        List<Collection> collectionList = new ArrayList<>();
         List<Community> subCommunities = community.getSubcommunities();
         for (Community subCommunity : subCommunities) {
             addCollectionList(subCommunity, collectionList);
@@ -629,6 +625,10 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
             case Constants.DELETE:
                 if (AuthorizeConfiguration.canCommunityAdminPerformSubelementDeletion()) {
                     adminObject = getParentObject(context, community);
+                    if (adminObject == null) {
+                        //top-level community, has to be admin of the current community
+                        adminObject = community;
+                    }
                 }
                 break;
             case Constants.ADD:

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

@@ -131,7 +131,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     @Override
     public List<MetadataValue> getMetadata(T dso, String schema, String element, String qualifier, String lang) {
         // Build up list of matching values
-        List<MetadataValue> values = new ArrayList<MetadataValue>();
+        List<MetadataValue> values = new ArrayList<>();
         for (MetadataValue dcv : dso.getMetadata()) {
             if (match(schema, element, qualifier, lang, dcv)) {
                 values.add(dcv);
@@ -207,8 +207,8 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     }
 
     @Override
-    public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang,
-                            List<String> values) throws SQLException {
+    public List<MetadataValue> addMetadata(Context context, T dso, String schema, String element, String qualifier,
+                            String lang, List<String> values) throws SQLException {
         MetadataField metadataField = metadataFieldService.findByElement(context, schema, element, qualifier);
         if (metadataField == null) {
             throw new SQLException(
@@ -216,12 +216,12 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                     "exist!");
         }
 
-        addMetadata(context, dso, metadataField, lang, values);
+        return addMetadata(context, dso, metadataField, lang, values);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang,
-                            List<String> values, List<String> authorities, List<Integer> confidences)
+    public List<MetadataValue> addMetadata(Context context, T dso, String schema, String element, String qualifier,
+                               String lang, List<String> values, List<String> authorities, List<Integer> confidences)
         throws SQLException {
         // We will not verify that they are valid entries in the registry
         // until update() is called.
@@ -231,15 +231,16 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                 "bad_dublin_core schema=" + schema + "." + element + "." + qualifier + ". Metadata field does not " +
                     "exist!");
         }
-        addMetadata(context, dso, metadataField, lang, values, authorities, confidences);
+        return addMetadata(context, dso, metadataField, lang, values, authorities, confidences);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String lang, List<String> values,
-                            List<String> authorities, List<Integer> confidences)
+    public List<MetadataValue> addMetadata(Context context, T dso, MetadataField metadataField, String lang,
+                                           List<String> values, List<String> authorities, List<Integer> confidences)
         throws SQLException {
         boolean authorityControlled = metadataAuthorityService.isAuthorityControlled(metadataField);
         boolean authorityRequired = metadataAuthorityService.isAuthorityRequired(metadataField);
+        List<MetadataValue> newMetadata = new ArrayList<>(values.size());
         // We will not verify that they are valid entries in the registry
         // until update() is called.
         for (int i = 0; i < values.size(); i++) {
@@ -250,6 +251,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                 }
             }
             MetadataValue metadataValue = metadataValueService.create(context, dso, metadataField);
+            newMetadata.add(metadataValue);
             //Set place to list length of all metadatavalues for the given schema.element.qualifier combination.
             // Subtract one to adhere to the 0 as first element rule
             metadataValue.setPlace(
@@ -296,7 +298,6 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                     }
                 }
                 metadataValue.setValue(String.valueOf(dcvalue));
-                ;
             } else {
                 metadataValue.setValue(null);
             }
@@ -304,37 +305,39 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
 //            metadataValueService.update(context, metadataValue);
             dso.addDetails(metadataField.toString());
         }
+        return newMetadata;
     }
 
     @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value,
-                            String authority, int confidence) throws SQLException {
-        addMetadata(context, dso, metadataField, language, Arrays.asList(value), Arrays.asList(authority),
-                    Arrays.asList(confidence));
+    public MetadataValue addMetadata(Context context, T dso, MetadataField metadataField, String language,
+                            String value, String authority, int confidence) throws SQLException {
+        return addMetadata(context, dso, metadataField, language, Arrays.asList(value), Arrays.asList(authority),
+                    Arrays.asList(confidence)).get(0);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang,
-                            String value) throws SQLException {
-        addMetadata(context, dso, schema, element, qualifier, lang, Arrays.asList(value));
+    public MetadataValue addMetadata(Context context, T dso, String schema, String element, String qualifier,
+                             String lang, String value) throws SQLException {
+        return addMetadata(context, dso, schema, element, qualifier, lang, Arrays.asList(value)).get(0);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String language, String value)
+    public MetadataValue addMetadata(Context context, T dso, MetadataField metadataField, String language, String value)
         throws SQLException {
-        addMetadata(context, dso, metadataField, language, Arrays.asList(value));
+        return addMetadata(context, dso, metadataField, language, Arrays.asList(value)).get(0);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, MetadataField metadataField, String language, List<String> values)
+    public List<MetadataValue> addMetadata(Context context, T dso, MetadataField metadataField, String language,
+                                           List<String> values)
         throws SQLException {
         if (metadataField != null) {
             String fieldKey = metadataAuthorityService
                 .makeFieldKey(metadataField.getMetadataSchema().getName(), metadataField.getElement(),
                               metadataField.getQualifier());
             if (metadataAuthorityService.isAuthorityControlled(fieldKey)) {
-                List<String> authorities = new ArrayList<String>();
-                List<Integer> confidences = new ArrayList<Integer>();
+                List<String> authorities = new ArrayList<>();
+                List<Integer> confidences = new ArrayList<>();
                 for (int i = 0; i < values.size(); ++i) {
                     if (dso instanceof Item) {
                         getAuthoritiesAndConfidences(fieldKey, ((Item) dso).getOwningCollection(), values, authorities,
@@ -343,18 +346,19 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                         getAuthoritiesAndConfidences(fieldKey, null, values, authorities, confidences, i);
                     }
                 }
-                addMetadata(context, dso, metadataField, language, values, authorities, confidences);
+                return addMetadata(context, dso, metadataField, language, values, authorities, confidences);
             } else {
-                addMetadata(context, dso, metadataField, language, values, null, null);
+                return addMetadata(context, dso, metadataField, language, values, null, null);
             }
         }
+        return new ArrayList<>(0);
     }
 
     @Override
-    public void addMetadata(Context context, T dso, String schema, String element, String qualifier, String lang,
-                            String value, String authority, int confidence) throws SQLException {
-        addMetadata(context, dso, schema, element, qualifier, lang, Arrays.asList(value), Arrays.asList(authority),
-                    Arrays.asList(confidence));
+    public MetadataValue addMetadata(Context context, T dso, String schema, String element, String qualifier,
+                            String lang, String value, String authority, int confidence) throws SQLException {
+        return addMetadata(context, dso, schema, element, qualifier, lang, Arrays.asList(value),
+                Arrays.asList(authority), Arrays.asList(confidence)).get(0);
     }
 
     @Override
@@ -405,6 +409,24 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
         return null;
     }
 
+    /**
+     * Retrieve first metadata field value
+     *
+     * @param dso       The DSpaceObject which we ask for metadata.
+     * @param field     {schema, element, qualifier} for the desired field.
+     * @param language  the language to match, or <code>Item.ANY</code>
+     * @return the first metadata field value
+     */
+    @Override
+    public String getMetadataFirstValue(T dso, MetadataFieldName field, String language) {
+        List<MetadataValue> metadataValues
+                = getMetadata(dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER, language);
+        if (CollectionUtils.isNotEmpty(metadataValues)) {
+            return metadataValues.get(0).getValue();
+        }
+        return null;
+    }
+
     /**
      * Set first metadata field value
      *
@@ -420,6 +442,21 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
         }
     }
 
+    @Override
+    public void setMetadataSingleValue(Context context, T dso, MetadataFieldName field,
+            String language, String value)
+            throws SQLException {
+        if (value != null) {
+            clearMetadata(context, dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER,
+                    language);
+
+            String newValueLanguage = (Item.ANY.equals(language)) ? null : language;
+            addMetadata(context, dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER,
+                    newValueLanguage, value);
+            dso.setMetadataModified();
+        }
+    }
+
     /**
      * Utility method for pattern-matching metadata elements.  This
      * method will return <code>true</code> if the given schema,
@@ -569,6 +606,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
             //RelationshipMetadataValue instance.
             //This is done to ensure that the order is correct.
             metadataValues.sort(new Comparator<MetadataValue>() {
+                @Override
                 public int compare(MetadataValue o1, MetadataValue o2) {
                     int compare = o1.getPlace() - o2.getPlace();
                     if (compare == 0) {
@@ -660,33 +698,35 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     @Override
     public void addAndShiftRightMetadata(Context context, T dso, String schema, String element, String qualifier,
                                          String lang, String value, String authority, int confidence, int index)
-        throws SQLException {
+            throws SQLException {
 
         List<MetadataValue> list = getMetadata(dso, schema, element, qualifier);
 
-        clearMetadata(context, dso, schema, element, qualifier, Item.ANY);
-
         int idx = 0;
+        int place = 0;
         boolean last = true;
         for (MetadataValue rr : list) {
             if (idx == index) {
-                addMetadata(context, dso, schema, element, qualifier,
-                            lang, value, authority, confidence);
+                MetadataValue newMetadata = addMetadata(context, dso, schema, element, qualifier,
+                        lang, value, authority, confidence);
+
+                moveSingleMetadataValue(context, dso, place, newMetadata);
+                place++;
                 last = false;
             }
-            addMetadata(context, dso, schema, element, qualifier,
-                        rr.getLanguage(), rr.getValue(), rr.getAuthority(), rr.getConfidence());
+            moveSingleMetadataValue(context, dso, place, rr);
+            place++;
             idx++;
         }
         if (last) {
             addMetadata(context, dso, schema, element, qualifier,
-                        lang, value, authority, confidence);
+                    lang, value, authority, confidence);
         }
     }
 
     @Override
     public void moveMetadata(Context context, T dso, String schema, String element, String qualifier, int from, int to)
-        throws SQLException, IllegalArgumentException {
+            throws SQLException, IllegalArgumentException {
 
         if (from == to) {
             throw new IllegalArgumentException("The \"from\" location MUST be different from \"to\" location");
@@ -701,8 +741,6 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                         "\n Idx from:" + from + " Idx to: " + to);
         }
 
-        clearMetadata(context, dso, schema, element, qualifier, Item.ANY);
-
         int idx = 0;
         MetadataValue moved = null;
         for (MetadataValue md : list) {
@@ -714,49 +752,51 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
         }
 
         idx = 0;
+        int place = 0;
         boolean last = true;
         for (MetadataValue rr : list) {
             if (idx == to && to < from) {
-                addMetadata(context, dso, schema, element, qualifier, moved.getLanguage(), moved.getValue(),
-                            moved.getAuthority(), moved.getConfidence());
+                moveSingleMetadataValue(context, dso, place, moved);
+                place++;
                 last = false;
             }
             if (idx != from) {
-                addMetadata(context, dso, schema, element, qualifier, rr.getLanguage(), rr.getValue(),
-                            rr.getAuthority(), rr.getConfidence());
+                moveSingleMetadataValue(context, dso, place, rr);
+                place++;
             }
             if (idx == to && to > from) {
-                addMetadata(context, dso, schema, element, qualifier, moved.getLanguage(), moved.getValue(),
-                            moved.getAuthority(), moved.getConfidence());
+                moveSingleMetadataValue(context, dso, place, moved);
+                place++;
                 last = false;
             }
             idx++;
         }
         if (last) {
-            addMetadata(context, dso, schema, element, qualifier, moved.getLanguage(), moved.getValue(),
-                        moved.getAuthority(), moved.getConfidence());
+            moveSingleMetadataValue(context, dso, place, moved);
         }
     }
 
+    /**
+     * Supports moving metadata by updating the place of the metadata value.
+     *
+     * @param context current DSpace session.
+     * @param dso     unused.
+     * @param place   ordinal position of the value in the list of that field's values.
+     * @param rr      the value to be placed.
+     */
+    protected void moveSingleMetadataValue(Context context, T dso, int place, MetadataValue rr) {
+        //just move the metadata
+        rr.setPlace(place);
+    }
+
     @Override
     public void replaceMetadata(Context context, T dso, String schema, String element, String qualifier, String lang,
                                 String value, String authority, int confidence, int index) throws SQLException {
 
         List<MetadataValue> list = getMetadata(dso, schema, element, qualifier);
 
-        clearMetadata(context, dso, schema, element, qualifier, Item.ANY);
-
-        int idx = 0;
-        for (MetadataValue rr : list) {
-            if (idx == index) {
-                addMetadata(context, dso, schema, element, qualifier,
-                            lang, value, authority, confidence);
-            } else {
-                addMetadata(context, dso, schema, element, qualifier,
-                            rr.getLanguage(), rr.getValue(), rr.getAuthority(), rr.getConfidence());
-            }
-            idx++;
-        }
+        removeMetadataValues(context, dso, Arrays.asList(list.get(index)));
+        addAndShiftRightMetadata(context, dso, schema, element, qualifier, lang, value, authority, confidence, index);
     }
 
     @Override

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.content;
 
+import java.util.Objects;
 import javax.persistence.Column;
 import javax.persistence.Entity;
 import javax.persistence.GeneratedValue;
@@ -15,6 +16,8 @@ import javax.persistence.Id;
 import javax.persistence.SequenceGenerator;
 import javax.persistence.Table;
 
+import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.lang3.builder.HashCodeBuilder;
 import org.dspace.core.ReloadableEntity;
 
 /**
@@ -45,7 +48,8 @@ public class EntityType implements ReloadableEntity<Integer> {
 
     /**
      * The standard setter for the ID of this EntityType
-     * @param id    The ID that this EntityType's ID will be set to
+     *
+     * @param id The ID that this EntityType's ID will be set to
      */
     public void setId(Integer id) {
         this.id = id;
@@ -53,7 +57,8 @@ public class EntityType implements ReloadableEntity<Integer> {
 
     /**
      * The standard getter for the label of this EntityType
-     * @return  The label for this EntityType
+     *
+     * @return The label for this EntityType
      */
     public String getLabel() {
         return label;
@@ -61,6 +66,7 @@ public class EntityType implements ReloadableEntity<Integer> {
 
     /**
      * The standard setter for the label of this EntityType
+     *
      * @param label The label that this EntityType's label will be set to
      */
     public void setLabel(String label) {
@@ -69,9 +75,40 @@ public class EntityType implements ReloadableEntity<Integer> {
 
     /**
      * The standard getter for the ID of this EntityType
-     * @return  The ID for this EntityType
+     *
+     * @return The ID for this EntityType
      */
     public Integer getID() {
         return id;
     }
+
+    /**
+     * Determines whether two entity types are equal based on the id and the label
+     * @param obj   object to be compared
+     * @return
+     */
+    public boolean equals(Object obj) {
+        if (!(obj instanceof EntityType)) {
+            return false;
+        }
+        EntityType entityType = (EntityType) obj;
+
+        if (!Objects.equals(this.getID(), entityType.getID())) {
+            return false;
+        }
+
+        if (!StringUtils.equals(this.getLabel(), entityType.getLabel())) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * Returns a hash code value for the object.
+     * @return  hash code value
+     */
+    @Override
+    public int hashCode() {
+        return new HashCodeBuilder().append(getID()).toHashCode();
+    }
 }