Merge tag 'dspace-9.1' into test_merge_minor

[maven-release-plugin] copy for tag dspace-9.1

.dockerignore

@@ -4,6 +4,7 @@
 */target/
 dspace/modules/*/target/
 Dockerfile.*
-dspace/src/main/docker/dspace-postgres-loadsql
+dspace/src/main/docker/dspace-postgres-pgcrypto
+dspace/src/main/docker/dspace-postgres-pgcrypto-curl
 dspace/src/main/docker/README.md
 dspace/src/main/docker-compose/

.github/dependabot.yml

@@ -11,9 +11,8 @@ updates:
   # So, only this first section can include "applies-to: security-updates"
   - package-ecosystem: "maven"
     directory: "/"
-    # Monthly dependency updates (NOTE: "schedule" doesn't apply to security updates)
     schedule:
-      interval: "monthly"
+      interval: "weekly"
       time: "02:00"
     # Allow up to 10 open PRs for dependencies
     open-pull-requests-limit: 10
@@ -134,7 +133,7 @@ updates:
     directory: "/"
     target-branch: dspace-9_x
     schedule:
-      interval: "monthly"
+      interval: "weekly"
       time: "02:00"
     # Allow up to 10 open PRs for dependencies
     open-pull-requests-limit: 10
@@ -255,7 +254,7 @@ updates:
     directory: "/"
     target-branch: dspace-8_x
     schedule:
-      interval: "monthly"
+      interval: "weekly"
       time: "02:00"
     # Allow up to 10 open PRs for dependencies
     open-pull-requests-limit: 10
@@ -376,7 +375,7 @@ updates:
     directory: "/"
     target-branch: dspace-7_x
     schedule:
-      interval: "monthly"
+      interval: "weekly"
       time: "02:00"
     # Allow up to 10 open PRs for dependencies
     open-pull-requests-limit: 10

.github/workflows/codescan.yml

@@ -47,7 +47,7 @@ jobs:
       # Initializes the CodeQL tools for scanning.
       # https://github.com/github/codeql-action
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@v3
+        uses: github/codeql-action/init@v2
         with:
           # Codescan Javascript as well since a few JS files exist in REST API's interface
           languages: java, javascript
@@ -56,8 +56,8 @@ jobs:
       # NOTE: Based on testing, this autobuild process works well for DSpace. A custom
       # DSpace build w/caching (like in build.yml) was about the same speed as autobuild.
       - name: Autobuild
-        uses: github/codeql-action/autobuild@v3
+        uses: github/codeql-action/autobuild@v2
 
       # Perform GitHub Code Scanning.
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v3
+        uses: github/codeql-action/analyze@v2

.github/workflows/docker.yml

@@ -113,19 +113,39 @@ jobs:
       REDEPLOY_SANDBOX_URL: ${{ secrets.REDEPLOY_SANDBOX_SOLR_URL }}
       REDEPLOY_DEMO_URL: ${{ secrets.REDEPLOY_DEMO_SOLR_URL }}
 
-  ########################################################
-  # Build/Push the 'dspace/dspace-postgres-loadsql' image
-  ########################################################
-  dspace-postgres-loadsql:
+  ###########################################################
+  # Build/Push the 'dspace/dspace-postgres-pgcrypto' image
+  ###########################################################
+  dspace-postgres-pgcrypto:
     # Ensure this job never runs on forked repos. It's only executed for 'dspace/dspace'
     if: github.repository == 'dspace/dspace'
     uses: ./.github/workflows/reusable-docker-build.yml
     with:
-      build_id: dspace-postgres-loadsql
-      image_name: dspace/dspace-postgres-loadsql
-      # Must build out of subdirectory to have access to install script.
+      build_id: dspace-postgres-pgcrypto-prod
+      image_name: dspace/dspace-postgres-pgcrypto
+      # Must build out of subdirectory to have access to install script for pgcrypto.
       # NOTE: this context will build the image based on the Dockerfile in the specified directory
-      dockerfile_context: ./dspace/src/main/docker/dspace-postgres-loadsql/
+      dockerfile_context: ./dspace/src/main/docker/dspace-postgres-pgcrypto/
+    secrets:
+      DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
+      DOCKER_ACCESS_TOKEN: ${{ secrets.DOCKER_ACCESS_TOKEN }}
+
+  ########################################################################
+  # Build/Push the 'dspace/dspace-postgres-pgcrypto' image (-loadsql tag)
+  ########################################################################
+  dspace-postgres-pgcrypto-loadsql:
+    # Ensure this job never runs on forked repos. It's only executed for 'dspace/dspace'
+    if: github.repository == 'dspace/dspace'
+    uses: ./.github/workflows/reusable-docker-build.yml
+    with:
+      build_id: dspace-postgres-pgcrypto-loadsql
+      image_name: dspace/dspace-postgres-pgcrypto
+      # Must build out of subdirectory to have access to install script for pgcrypto.
+      # NOTE: this context will build the image based on the Dockerfile in the specified directory
+      dockerfile_context: ./dspace/src/main/docker/dspace-postgres-pgcrypto-curl/
+      # Suffix all tags with "-loadsql". Otherwise, it uses the same
+      # tagging logic as the primary 'dspace/dspace-postgres-pgcrypto' image above.
+      tags_flavor: suffix=-loadsql
     secrets:
       DOCKER_USERNAME: ${{ secrets.DOCKER_USERNAME }}
       DOCKER_ACCESS_TOKEN: ${{ secrets.DOCKER_ACCESS_TOKEN }}
@@ -138,7 +158,7 @@ jobs:
     if: github.repository == 'dspace/dspace'
     runs-on: ubuntu-latest
     # Must run after all major images are built
-    needs: [dspace, dspace-test, dspace-cli, dspace-solr]
+    needs: [dspace, dspace-test, dspace-cli, dspace-postgres-pgcrypto, dspace-solr]
     env:
       # Override defaults dspace.server.url because backend starts at http://127.0.0.1:8080
       dspace__P__server__P__url: http://127.0.0.1:8080/server
@@ -200,19 +220,6 @@ jobs:
           result=$(wget -O- -q http://127.0.0.1:8080/server/api/core/collections)
           echo "$result"
           echo "$result" |  grep -oE "\"Dog in Yard\","
-      # Verify basic backend logging is working.
-      # 1. Access the top communities list. Verify that the "Before request" INFO statement is logged
-      # 2. Access an invalid endpoint (and ignore 404 response). Verify that a "status:404" WARN statement is logged
-      - name: Verify backend is logging properly
-        run: |
-          wget -O/dev/null -q http://127.0.0.1:8080/server/api/core/communities/search/top
-          logs=$(docker compose -f docker-compose.yml logs -n 5 dspace)
-          echo "$logs"
-          echo "$logs" | grep -o "Before request \[GET /server/api/core/communities/search/top\]"
-          wget -O/dev/null -q http://127.0.0.1:8080/server/api/does/not/exist || true
-          logs=$(docker compose -f docker-compose.yml logs -n 5 dspace)
-          echo "$logs"
-          echo "$logs" | grep -o "status:404 exception: The repository type does.not was not found"
       # Verify Handle Server can be stared and is working properly
       # 1. First generate the "[dspace]/handle-server" folder with the sitebndl.zip
       # 2. Start the Handle Server (and wait 20 seconds to let it start up)

.github/workflows/reusable-docker-build.yml

@@ -164,7 +164,7 @@ jobs:
           # Use GitHub cache to load cached Docker images and cache the results of this build
           # This decreases the number of images we need to fetch from DockerHub
           cache-from: type=gha,scope=${{ inputs.build_id }}
-          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
 
       # Export the digest of Docker build locally
       - name: Export Docker build digest
@@ -216,7 +216,7 @@ jobs:
           # Use GitHub cache to load cached Docker images and cache the results of this build
           # This decreases the number of images we need to fetch from DockerHub
           cache-from: type=gha,scope=${{ inputs.build_id }}
-          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=max
           # Export image to a local TAR file
           outputs: type=docker,dest=/tmp/${{ inputs.build_id }}.tar
 

checkstyle.xml

@@ -106,9 +106,6 @@ For more information on CheckStyle configurations below, see: http://checkstyle.
         <!-- Right braces should be on start of a new line (default value) -->
         <module name="RightCurly"/>
 
-        <!-- Enforce Java-style array declaration instead of C-style -->
-        <module name="ArrayTypeStyle"/>
-
         <!-- ##### Indentation / Whitespace requirements ##### -->
         <!-- Require 4-space indentation (default value) -->
         <module name="Indentation"/>

docker-compose.yml

@@ -65,12 +65,13 @@ services:
   # DSpace PostgreSQL database container
   dspacedb:
     container_name: dspacedb
-    # Uses the base PostgreSQL image
-    image: "docker.io/postgres:${POSTGRES_VERSION:-15}"
+    # Uses a custom Postgres image with pgcrypto installed
+    image: "${DOCKER_REGISTRY:-docker.io}/${DOCKER_OWNER:-dspace}/dspace-postgres-pgcrypto:${DSPACE_VER:-latest}"
+    build:
+      # Must build out of subdirectory to have access to install script for pgcrypto
+      context: ./dspace/src/main/docker/dspace-postgres-pgcrypto/
     environment:
       PGDATA: /pgdata
-      POSTGRES_DB: dspace
-      POSTGRES_USER: dspace
       POSTGRES_PASSWORD: dspace
     networks:
       dspacenet:

dspace-api/pom.xml

@@ -99,6 +99,20 @@
                 </executions>
             </plugin>
 
+            <plugin>
+                <groupId>org.codehaus.mojo</groupId>
+                <artifactId>build-helper-maven-plugin</artifactId>
+                <version>3.6.1</version>
+                <executions>
+                    <execution>
+                        <phase>validate</phase>
+                        <goals>
+                            <goal>maven-version</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>buildnumber-maven-plugin</artifactId>
@@ -720,7 +734,7 @@
         <dependency>
             <groupId>com.amazonaws</groupId>
             <artifactId>aws-java-sdk-s3</artifactId>
-            <version>1.12.791</version>
+            <version>1.12.785</version>
         </dependency>
 
         <!-- TODO: This may need to be replaced with the "orcid-model" artifact once this ticket is resolved:
@@ -761,7 +775,7 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.12.0</version>
+            <version>5.11.1</version>
         </dependency>
 
         <!-- Email templating -->
@@ -774,7 +788,7 @@
         <dependency>
             <groupId>org.xmlunit</groupId>
             <artifactId>xmlunit-core</artifactId>
-            <version>2.10.4</version>
+            <version>2.10.2</version>
             <scope>test</scope>
         </dependency>
 
@@ -915,7 +929,7 @@
         <dependency>
             <groupId>org.xhtmlrenderer</groupId>
             <artifactId>flying-saucer-pdf</artifactId>
-            <version>9.13.3</version>
+            <version>9.12.0</version>
             <exclusions>
                 <!-- Conflicts with Hibernate. Use version that is brought in via Hibernate -->
                 <exclusion>

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

@@ -46,7 +46,6 @@ import org.dspace.app.util.XMLUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
-import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataFieldName;
 import org.dspace.content.MetadataSchemaEnum;
@@ -54,7 +53,6 @@ import org.dspace.content.MetadataValue;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
-import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
@@ -171,10 +169,6 @@ public class StructBuilder {
                 .desc("File to receive the structure map ('-' for standard out).")
                 .hasArg().argName("output").required().build());
 
-        options.addOption(Option.builder("p").longOpt("parent")
-                .desc("Parent community or handle (optional)")
-                .hasArg().argName("parent").required(false).build());
-
         // Parse the command line.
         CommandLineParser parser = new DefaultParser();
         CommandLine line = null;
@@ -208,11 +202,6 @@ public class StructBuilder {
             outputStream = new FileOutputStream(output);
         }
 
-        String parentID = null;
-        if (line.hasOption('p')) {
-            parentID = line.getOptionValue('p');
-        }
-
         // create a context
         Context context = new Context();
 
@@ -225,30 +214,6 @@ public class StructBuilder {
             System.exit(1);
         }
 
-        // Resolve optional "parent community" ID or handle to a community
-        Community parent = null;
-        if (parentID != null) {
-            DSpaceObject dso = handleService.resolveToObject(context, parentID);
-            if (dso != null) {
-                if (dso.getType() == Constants.COMMUNITY) {
-                    parent = (Community) dso;
-                } else {
-                    System.out.println("The handle provided for the -p option does not resolve to a community. " +
-                        parentID + " is an object of type: " + Constants.typeText[dso.getType()]);
-                    System.exit(0);
-                }
-            } else {
-                // Not a handle, see if it is an ID
-                Community community = communityService.findByIdOrLegacyId(context, parentID);
-                if (community != null) {
-                    parent = community;
-                } else {
-                    System.out.println("The value provided for -p is not a valid community ID or handle: " + parentID);
-                    System.exit(0);
-                }
-            }
-        }
-
         // Export? Import?
         if (line.hasOption('x')) { // export
             exportStructure(context, outputStream);
@@ -268,7 +233,7 @@ public class StructBuilder {
             }
 
             boolean keepHandles = options.hasOption("k");
-            importStructure(context, inputStream, outputStream, parent, keepHandles);
+            importStructure(context, inputStream, outputStream, keepHandles);
 
             inputStream.close();
             outputStream.close();
@@ -285,7 +250,6 @@ public class StructBuilder {
      * @param context
      * @param input XML which describes the new communities and collections.
      * @param output input, annotated with the new objects' identifiers.
-     * @param parent Community beneath which to attach this structure
      * @param keepHandles true if Handles should be set from input.
      * @throws IOException
      * @throws ParserConfigurationException
@@ -294,7 +258,7 @@ public class StructBuilder {
      * @throws SQLException
      */
     static void importStructure(Context context, InputStream input,
-            OutputStream output, Community parent, boolean keepHandles)
+            OutputStream output, boolean keepHandles)
             throws IOException, ParserConfigurationException, SQLException,
             TransformerException, XPathExpressionException {
 
@@ -361,7 +325,7 @@ public class StructBuilder {
                                              .evaluate(document, XPathConstants.NODESET);
 
             // run the import starting with the top level communities
-            elements = handleCommunities(context, first, parent, keepHandles);
+            elements = handleCommunities(context, first, null, keepHandles);
         } catch (TransformerException ex) {
             System.err.format("Input content not understood:  %s%n", ex.getMessage());
             System.exit(1);

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

@@ -14,8 +14,6 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
 
-import org.apache.commons.cli.DefaultParser;
-import org.apache.commons.cli.DefaultParser.Builder;
 import org.apache.commons.cli.ParseException;
 import org.dspace.content.Item;
 import org.dspace.content.MetadataDSpaceCsvExportServiceImpl;
@@ -169,14 +167,4 @@ public class MetadataExportSearch extends DSpaceRunnable<MetadataExportSearchScr
         }
         return scopeObj;
     }
-
-    @Override
-    protected StepResult parse(String[] args) throws ParseException {
-        commandLine = new DefaultParser().parse(getScriptConfiguration().getOptions(), args);
-        Builder builder = new DefaultParser().builder();
-        builder.setStripLeadingAndTrailingQuotes(false);
-        commandLine = builder.build().parse(getScriptConfiguration().getOptions(), args);
-        setup();
-        return StepResult.Continue;
-    }
 }

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

@@ -495,7 +495,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
 
                 // Check it has an owning collection
                 List<String> collections = line.get("collection");
-                if (collections == null || collections.isEmpty()) {
+                if (collections == null) {
                     throw new MetadataImportException(
                         "New items must have a 'collection' assigned in the form of a handle");
                 }
@@ -1143,12 +1143,12 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
             }
 
             // look up the value and authority in solr
-            List<AuthorityValue> byValue = authorityValueService.findByValue(schema, element, qualifier, value);
+            List<AuthorityValue> byValue = authorityValueService.findByValue(c, schema, element, qualifier, value);
             AuthorityValue authorityValue = null;
             if (byValue.isEmpty()) {
                 String toGenerate = fromAuthority.generateString() + value;
                 String field = schema + "_" + element + (StringUtils.isNotBlank(qualifier) ? "_" + qualifier : "");
-                authorityValue = authorityValueService.generate(toGenerate, value, field);
+                authorityValue = authorityValueService.generate(c, toGenerate, value, field);
                 dcv.setAuthority(toGenerate);
             } else {
                 authorityValue = byValue.get(0);
@@ -1560,7 +1560,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                 ContentServiceFactory.getInstance().getMetadataFieldService();
             int i = reference.indexOf(":");
             String mfValue = reference.substring(i + 1);
-            String[] mf = reference.substring(0, i).split("\\.");
+            String mf[] = reference.substring(0, i).split("\\.");
             if (mf.length < 2) {
                 throw new MetadataImportException("Error in CSV row " + rowCount + ":\n" +
                                                       "Bad metadata field in reference: '" + reference

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

@@ -353,7 +353,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
     /**
      * Create the 'collections' file.  List handles of all Collections which
-     * contain this Item. The "owning" Collection is listed first.
+     * contain this Item.  The "owning" Collection is listed first.
      *
      * @param item list collections holding this Item.
      * @param destDir write the file here.
@@ -364,14 +364,12 @@ public class ItemExportServiceImpl implements ItemExportService {
         File outFile = new File(destDir, "collections");
         if (outFile.createNewFile()) {
             try (PrintWriter out = new PrintWriter(new FileWriter(outFile))) {
-                Collection owningCollection = item.getOwningCollection();
-                // The owning collection is null for workspace and workflow items
-                if (owningCollection != null) {
-                    out.println(owningCollection.getHandle());
-                }
+                String ownerHandle = item.getOwningCollection().getHandle();
+                out.println(ownerHandle);
                 for (Collection collection : item.getCollections()) {
-                    if (!collection.equals(owningCollection)) {
-                        out.println(collection.getHandle());
+                    String collectionHandle = collection.getHandle();
+                    if (!collectionHandle.equals(ownerHandle)) {
+                        out.println(collectionHandle);
                     }
                 }
             }

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

@@ -23,7 +23,6 @@ import java.util.UUID;
 
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.tika.Tika;
 import org.dspace.app.itemimport.factory.ItemImportServiceFactory;
@@ -335,38 +334,33 @@ public class ItemImport extends DSpaceRunnable<ItemImportScriptConfiguration> {
     protected void readZip(Context context, ItemImportService itemImportService) throws Exception {
         Optional<InputStream> optionalFileStream = Optional.empty();
         Optional<InputStream> validationFileStream = Optional.empty();
-        try {
-            if (!remoteUrl) {
-                // manage zip via upload
-                optionalFileStream = handler.getFileStream(context, zipfilename);
-                validationFileStream = handler.getFileStream(context, zipfilename);
-            } else {
-                // manage zip via remote url
-                optionalFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
-                validationFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
-            }
-
-            if (validationFileStream.isPresent()) {
-                // validate zip file
-                if (validationFileStream.isPresent()) {
-                    validateZip(validationFileStream.get());
-                }
-
-                workFile = new File(itemImportService.getTempWorkDir() + File.separator
-                        + zipfilename + "-" + context.getCurrentUser().getID());
-                FileUtils.copyInputStreamToFile(optionalFileStream.get(), workFile);
-            } else {
-                throw new IllegalArgumentException(
-                        "Error reading file, the file couldn't be found for filename: " + zipfilename);
-            }
-
-            workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
-                    + File.separator + context.getCurrentUser().getID());
-            sourcedir = itemImportService.unzip(workFile, workDir.getAbsolutePath());
-        } finally {
-            optionalFileStream.ifPresent(IOUtils::closeQuietly);
-            validationFileStream.ifPresent(IOUtils::closeQuietly);
+        if (!remoteUrl) {
+            // manage zip via upload
+            optionalFileStream = handler.getFileStream(context, zipfilename);
+            validationFileStream = handler.getFileStream(context, zipfilename);
+        } else {
+            // manage zip via remote url
+            optionalFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
+            validationFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
         }
+
+        if (validationFileStream.isPresent()) {
+            // validate zip file
+            if (validationFileStream.isPresent()) {
+                validateZip(validationFileStream.get());
+            }
+
+            workFile = new File(itemImportService.getTempWorkDir() + File.separator
+                    + zipfilename + "-" + context.getCurrentUser().getID());
+            FileUtils.copyInputStreamToFile(optionalFileStream.get(), workFile);
+        } else {
+            throw new IllegalArgumentException(
+                    "Error reading file, the file couldn't be found for filename: " + zipfilename);
+        }
+
+        workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
+                           + File.separator + context.getCurrentUser().getID());
+        sourcedir = itemImportService.unzip(workFile, workDir.getAbsolutePath());
     }
 
     /**

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

@@ -17,7 +17,6 @@ import java.util.Optional;
 import java.util.UUID;
 
 import org.apache.commons.io.FileUtils;
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.content.Collection;
@@ -112,11 +111,7 @@ public class ItemImportCLI extends ItemImport {
 
                 // validate zip file
                 InputStream validationFileStream = new FileInputStream(myZipFile);
-                try {
-                    validateZip(validationFileStream);
-                } finally {
-                    IOUtils.closeQuietly(validationFileStream);
-                }
+                validateZip(validationFileStream);
 
                 workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
                         + File.separator + context.getCurrentUser().getID());
@@ -125,28 +120,22 @@ public class ItemImportCLI extends ItemImport {
             } else {
                 // manage zip via remote url
                 Optional<InputStream> optionalFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
-                Optional<InputStream> validationFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
-                try {
-                    if (optionalFileStream.isPresent()) {
-                        // validate zip file via url
-
-                        if (validationFileStream.isPresent()) {
-                            validateZip(validationFileStream.get());
-                        }
-
-                        workFile = new File(itemImportService.getTempWorkDir() + File.separator
-                                + zipfilename + "-" + context.getCurrentUser().getID());
-                        FileUtils.copyInputStreamToFile(optionalFileStream.get(), workFile);
-                        workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
-                                + File.separator + context.getCurrentUser().getID());
-                        sourcedir = itemImportService.unzip(workFile, workDir.getAbsolutePath());
-                    } else {
-                        throw new IllegalArgumentException(
-                                "Error reading file, the file couldn't be found for filename: " + zipfilename);
+                if (optionalFileStream.isPresent()) {
+                    // validate zip file via url
+                    Optional<InputStream> validationFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
+                    if (validationFileStream.isPresent()) {
+                        validateZip(validationFileStream.get());
                     }
-                } finally {
-                    optionalFileStream.ifPresent(IOUtils::closeQuietly);
-                    validationFileStream.ifPresent(IOUtils::closeQuietly);
+
+                    workFile = new File(itemImportService.getTempWorkDir() + File.separator
+                            + zipfilename + "-" + context.getCurrentUser().getID());
+                    FileUtils.copyInputStreamToFile(optionalFileStream.get(), workFile);
+                    workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
+                                       + File.separator + context.getCurrentUser().getID());
+                    sourcedir = itemImportService.unzip(workFile, workDir.getAbsolutePath());
+                } else {
+                    throw new IllegalArgumentException(
+                            "Error reading file, the file couldn't be found for filename: " + zipfilename);
                 }
             }
         }

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

@@ -605,7 +605,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
 
         Item item = null;
 
-        String[] mf = metaKey.split("\\.");
+        String mf[] = metaKey.split("\\.");
         if (mf.length < 2) {
             throw new Exception("Bad metadata field in reference: '" + metaKey +
                 "' (expected syntax is schema.element[.qualifier])");
@@ -913,7 +913,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
 
         // Load any additional metadata schemas
         File folder = new File(path);
-        File[] file = folder.listFiles(metadataFileFilter);
+        File file[] = folder.listFiles(metadataFileFilter);
         for (int i = 0; i < file.length; i++) {
             loadDublinCore(c, myitem, file[i].getAbsolutePath());
         }

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

@@ -97,7 +97,7 @@ public class ItemArchive {
 
             //The code to search for local schema files was copied from org.dspace.app.itemimport
             // .ItemImportServiceImpl.java
-            File[] file = dir.listFiles(new LocalSchemaFilenameFilter());
+            File file[] = dir.listFiles(new LocalSchemaFilenameFilter());
             for (int i = 0; i < file.length; i++) {
                 is = new FileInputStream(file[i]);
                 itarch.dtomList.addAll(MetadataUtilities.loadDublinCore(XMLUtils.getDocumentBuilder(), is));

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

@@ -7,7 +7,9 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.awt.image.BufferedImage;
 import java.io.InputStream;
+import javax.imageio.ImageIO;
 
 import org.dspace.content.Item;
 import org.dspace.services.ConfigurationService;
@@ -61,20 +63,27 @@ public class BrandedPreviewJPEGFilter extends MediaFilter {
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
         throws Exception {
+        // read in bitstream's image
+        BufferedImage buf = ImageIO.read(source);
+
         // get config params
         ConfigurationService configurationService
                 = DSpaceServicesFactory.getInstance().getConfigurationService();
-        int xmax = configurationService.getIntProperty("webui.preview.maxwidth");
-        int ymax = configurationService.getIntProperty("webui.preview.maxheight");
-        boolean blurring = configurationService.getBooleanProperty("webui.preview.blurring");
-        boolean hqscaling = configurationService.getBooleanProperty("webui.preview.hqscaling");
+        float xmax = (float) configurationService
+            .getIntProperty("webui.preview.maxwidth");
+        float ymax = (float) configurationService
+            .getIntProperty("webui.preview.maxheight");
+        boolean blurring = (boolean) configurationService
+            .getBooleanProperty("webui.preview.blurring");
+        boolean hqscaling = (boolean) configurationService
+            .getBooleanProperty("webui.preview.hqscaling");
         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.getThumb(
-                currentItem, source, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint, brandFont
-        );
+        return jpegFilter
+            .getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint,
+                         brandFont);
     }
 }

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

@@ -14,7 +14,7 @@ import java.io.InputStream;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 
-import org.apache.pdfbox.Loader;
+import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
 import org.apache.pdfbox.pdmodel.common.PDRectangle;
 import org.dspace.content.Bitstream;
@@ -153,8 +153,8 @@ public abstract class ImageMagickThumbnailFilter extends MediaFilter {
         // the CropBox is missing or empty because pdfbox will set it to the
         // same size as the MediaBox if it doesn't exist. Also note that we
         // only need to check the first page, since that's what we use for
-        // generating the thumbnail (PDPage uses a zero-based index).
-        PDPage pdfPage = Loader.loadPDF(f).getPage(0);
+        // generating the thumbnail (PDDocument uses a zero-based index).
+        PDPage pdfPage = PDDocument.load(f).getPage(0);
         PDRectangle pdfPageMediaBox = pdfPage.getMediaBox();
         PDRectangle pdfPageCropBox = pdfPage.getCropBox();
 

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

@@ -8,32 +8,19 @@
 package org.dspace.app.mediafilter;
 
 import java.awt.Color;
-import java.awt.Dimension;
 import java.awt.Font;
 import java.awt.Graphics2D;
 import java.awt.RenderingHints;
 import java.awt.Transparency;
-import java.awt.geom.AffineTransform;
 import java.awt.image.BufferedImage;
 import java.awt.image.BufferedImageOp;
 import java.awt.image.ConvolveOp;
 import java.awt.image.Kernel;
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
 import java.io.InputStream;
 import javax.imageio.ImageIO;
 
-import com.drew.imaging.ImageMetadataReader;
-import com.drew.imaging.ImageProcessingException;
-import com.drew.metadata.Metadata;
-import com.drew.metadata.MetadataException;
-import com.drew.metadata.exif.ExifIFD0Directory;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.Item;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -46,8 +33,6 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  * @author Jason Sherman jsherman@usao.edu
  */
 public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats {
-    private static final Logger log = LogManager.getLogger(JPEGFilter.class);
-
     @Override
     public String getFilteredName(String oldFilename) {
         return oldFilename + ".jpg";
@@ -77,115 +62,6 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         return "Generated Thumbnail";
     }
 
-    /**
-     * Gets the rotation angle from image's metadata using ImageReader.
-     * This method consumes the InputStream, so you need to be careful to don't reuse the same InputStream after
-     * computing the rotation angle.
-     *
-     * @param buf InputStream of the image file
-     * @return Rotation angle in degrees (0, 90, 180, or 270)
-     */
-    public static int getImageRotationUsingImageReader(InputStream buf) {
-        try {
-            Metadata metadata = ImageMetadataReader.readMetadata(buf);
-            ExifIFD0Directory directory = metadata.getFirstDirectoryOfType(ExifIFD0Directory.class);
-            if (directory != null && directory.containsTag(ExifIFD0Directory.TAG_ORIENTATION)) {
-                return convertRotationToDegrees(directory.getInt(ExifIFD0Directory.TAG_ORIENTATION));
-            }
-        } catch (MetadataException | ImageProcessingException | IOException e) {
-            log.error("Error reading image metadata", e);
-        }
-        return 0;
-    }
-
-    public static int convertRotationToDegrees(int valueNode) {
-        // Common orientation values:
-        // 1 = Normal (0°)
-        // 6 = Rotated 90° CW
-        // 3 = Rotated 180°
-        // 8 = Rotated 270° CW
-        switch (valueNode) {
-            case 6:
-                return 90;
-            case 3:
-                return 180;
-            case 8:
-                return 270;
-            default:
-                return 0;
-        }
-    }
-
-    /**
-     * Rotates an image by the specified angle
-     *
-     * @param image The original image
-     * @param angle The rotation angle in degrees
-     * @return Rotated image
-     */
-    public static BufferedImage rotateImage(BufferedImage image, int angle) {
-        if (angle == 0) {
-            return image;
-        }
-
-        double radians = Math.toRadians(angle);
-        double sin = Math.abs(Math.sin(radians));
-        double cos = Math.abs(Math.cos(radians));
-
-        int newWidth = (int) Math.round(image.getWidth() * cos + image.getHeight() * sin);
-        int newHeight = (int) Math.round(image.getWidth() * sin + image.getHeight() * cos);
-
-        BufferedImage rotated = new BufferedImage(newWidth, newHeight, image.getType());
-        Graphics2D g2d = rotated.createGraphics();
-        AffineTransform at = new AffineTransform();
-
-        at.translate(newWidth / 2, newHeight / 2);
-        at.rotate(radians);
-        at.translate(-image.getWidth() / 2, -image.getHeight() / 2);
-
-        g2d.setTransform(at);
-        g2d.drawImage(image, 0, 0, null);
-        g2d.dispose();
-
-        return rotated;
-    }
-
-    /**
-     * Calculates scaled dimension while maintaining aspect ratio
-     *
-     * @param imgSize  Original image dimensions
-     * @param boundary Maximum allowed dimensions
-     * @return New dimensions that fit within boundary while preserving aspect ratio
-     */
-    private Dimension getScaledDimension(Dimension imgSize, Dimension boundary) {
-
-        int originalWidth = imgSize.width;
-        int originalHeight = imgSize.height;
-        int boundWidth = boundary.width;
-        int boundHeight = boundary.height;
-        int newWidth = originalWidth;
-        int newHeight = originalHeight;
-
-
-        // First check if we need to scale width
-        if (originalWidth > boundWidth) {
-            // Scale width to fit
-            newWidth = boundWidth;
-            // Scale height to maintain aspect ratio
-            newHeight = (newWidth * originalHeight) / originalWidth;
-        }
-
-        // Then check if we need to scale even with the new height
-        if (newHeight > boundHeight) {
-            // Scale height to fit instead
-            newHeight = boundHeight;
-            newWidth = (newHeight * originalWidth) / originalHeight;
-        }
-
-        return new Dimension(newWidth, newHeight);
-    }
-
-
     /**
      * @param currentItem item
      * @param source      source input stream
@@ -196,65 +72,10 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
     @Override
     public InputStream getDestinationStream(Item currentItem, InputStream source, boolean verbose)
         throws Exception {
-        return getThumb(currentItem, source, verbose);
-    }
+        // read in bitstream's image
+        BufferedImage buf = ImageIO.read(source);
 
-    public InputStream getThumb(Item currentItem, InputStream source, boolean verbose)
-        throws Exception {
-        // get config params
-        final ConfigurationService configurationService
-            = DSpaceServicesFactory.getInstance().getConfigurationService();
-        int xmax = configurationService
-            .getIntProperty("thumbnail.maxwidth");
-        int ymax = configurationService
-            .getIntProperty("thumbnail.maxheight");
-        boolean blurring = (boolean) configurationService
-            .getBooleanProperty("thumbnail.blurring");
-        boolean hqscaling = (boolean) configurationService
-            .getBooleanProperty("thumbnail.hqscaling");
-
-        return getThumb(currentItem, source, verbose, xmax, ymax, blurring, hqscaling, 0, 0, null);
-    }
-
-    protected InputStream getThumb(
-        Item currentItem,
-        InputStream source,
-        boolean verbose,
-        int xmax,
-        int ymax,
-        boolean blurring,
-        boolean hqscaling,
-        int brandHeight,
-        int brandFontPoint,
-        String brandFont
-    ) throws Exception {
-
-        File tempFile = File.createTempFile("temp", ".tmp");
-        tempFile.deleteOnExit();
-
-        // Write to temp file
-        try (FileOutputStream fos = new FileOutputStream(tempFile)) {
-            byte[] buffer = new byte[4096];
-            int len;
-            while ((len = source.read(buffer)) != -1) {
-                fos.write(buffer, 0, len);
-            }
-        }
-
-        int rotation = 0;
-        try (FileInputStream fis = new FileInputStream(tempFile)) {
-            rotation = getImageRotationUsingImageReader(fis);
-        }
-
-        try (FileInputStream fis = new FileInputStream(tempFile)) {
-            // read in bitstream's image
-            BufferedImage buf = ImageIO.read(fis);
-
-            return getThumbDim(
-                currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, brandHeight, brandFontPoint, rotation,
-                brandFont
-            );
-        }
+        return getThumb(currentItem, buf, verbose);
     }
 
     public InputStream getThumb(Item currentItem, BufferedImage buf, boolean verbose)
@@ -262,28 +83,25 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
         // get config params
         final ConfigurationService configurationService
                 = DSpaceServicesFactory.getInstance().getConfigurationService();
-        int xmax = configurationService
+        float xmax = (float) configurationService
             .getIntProperty("thumbnail.maxwidth");
-        int ymax = configurationService
+        float ymax = (float) configurationService
             .getIntProperty("thumbnail.maxheight");
         boolean blurring = (boolean) configurationService
             .getBooleanProperty("thumbnail.blurring");
         boolean hqscaling = (boolean) configurationService
             .getBooleanProperty("thumbnail.hqscaling");
 
-        return getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, 0, 0, 0, null);
+        return getThumbDim(currentItem, buf, verbose, xmax, ymax, blurring, hqscaling, 0, 0, null);
     }
 
-    public InputStream getThumbDim(Item currentItem, BufferedImage buf, boolean verbose, int xmax, int ymax,
+    public InputStream getThumbDim(Item currentItem, BufferedImage buf, boolean verbose, float xmax, float ymax,
                                    boolean blurring, boolean hqscaling, int brandHeight, int brandFontPoint,
-                                   int rotation, String brandFont)
+                                   String brandFont)
         throws Exception {
-
-        // Rotate the image if needed
-        BufferedImage correctedImage = rotateImage(buf, rotation);
-
-        int xsize = correctedImage.getWidth();
-        int ysize = correctedImage.getHeight();
+        // now get the image dimensions
+        float xsize = (float) buf.getWidth(null);
+        float ysize = (float) buf.getHeight(null);
 
         // if verbose flag is set, print out dimensions
         // to STDOUT
@@ -291,63 +109,86 @@ public class JPEGFilter extends MediaFilter implements SelfRegisterInputFormats
             System.out.println("original size: " + xsize + "," + ysize);
         }
 
-        // Calculate new dimensions while maintaining aspect ratio
-        Dimension newDimension = getScaledDimension(
-            new Dimension(xsize, ysize),
-            new Dimension(xmax, ymax)
-        );
+        // scale by x first if needed
+        if (xsize > xmax) {
+            // calculate scaling factor so that xsize * scale = new size (max)
+            float scale_factor = xmax / xsize;
 
+            // if verbose flag is set, print out extracted text
+            // to STDOUT
+            if (verbose) {
+                System.out.println("x scale factor: " + scale_factor);
+            }
+
+            // now reduce x size
+            // and y size
+            xsize = xsize * scale_factor;
+            ysize = ysize * scale_factor;
+
+            // if verbose flag is set, print out extracted text
+            // to STDOUT
+            if (verbose) {
+                System.out.println("size after fitting to maximum width: " + xsize + "," + ysize);
+            }
+        }
+
+        // scale by y if needed
+        if (ysize > ymax) {
+            float scale_factor = ymax / ysize;
+
+            // now reduce x size
+            // and y size
+            xsize = xsize * scale_factor;
+            ysize = ysize * scale_factor;
+        }
 
         // if verbose flag is set, print details to STDOUT
         if (verbose) {
-            System.out.println("size after fitting to maximum height: " + newDimension.width + ", "
-                                   + newDimension.height);
+            System.out.println("size after fitting to maximum height: " + xsize + ", "
+                                   + ysize);
         }
 
-        xsize = newDimension.width;
-        ysize = newDimension.height;
-
         // create an image buffer for the thumbnail with the new xsize, ysize
-        BufferedImage thumbnail = new BufferedImage(xsize, ysize, BufferedImage.TYPE_INT_RGB);
+        BufferedImage thumbnail = new BufferedImage((int) xsize, (int) ysize,
+                                                    BufferedImage.TYPE_INT_RGB);
 
         // Use blurring if selected in config.
         // a little blur before scaling does wonders for keeping moire in check.
         if (blurring) {
             // send the buffered image off to get blurred.
-            correctedImage = getBlurredInstance(correctedImage);
+            buf = getBlurredInstance((BufferedImage) buf);
         }
 
         // Use high quality scaling method if selected in config.
         // this has a definite performance penalty.
         if (hqscaling) {
             // send the buffered image off to get an HQ downscale.
-            correctedImage = getScaledInstance(correctedImage, xsize, ysize,
-                                               RenderingHints.VALUE_INTERPOLATION_BICUBIC, true);
+            buf = getScaledInstance((BufferedImage) buf, (int) xsize, (int) ysize,
+                                    (Object) RenderingHints.VALUE_INTERPOLATION_BICUBIC, (boolean) true);
         }
 
         // now render the image into the thumbnail buffer
         Graphics2D g2d = thumbnail.createGraphics();
-        g2d.drawImage(correctedImage, 0, 0, xsize, ysize, null);
+        g2d.drawImage(buf, 0, 0, (int) xsize, (int) ysize, null);
 
         if (brandHeight != 0) {
             ConfigurationService configurationService
                     = DSpaceServicesFactory.getInstance().getConfigurationService();
-            Brand brand = new Brand(xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
+            Brand brand = new Brand((int) xsize, brandHeight, new Font(brandFont, Font.PLAIN, brandFontPoint), 5);
             BufferedImage brandImage = brand.create(configurationService.getProperty("webui.preview.brand"),
                                                     configurationService.getProperty("webui.preview.brand.abbrev"),
                                                     currentItem == null ? "" : "hdl:" + currentItem.getHandle());
 
-            g2d.drawImage(brandImage, 0, ysize, xsize, 20, null);
+            g2d.drawImage(brandImage, (int) 0, (int) ysize, (int) xsize, (int) 20, null);
         }
 
-
-        ByteArrayInputStream bais;
         // now create an input stream for the thumbnail buffer and return it
-        try (ByteArrayOutputStream baos = new ByteArrayOutputStream()) {
-            ImageIO.write(thumbnail, "jpeg", baos);
-            // now get the array
-            bais = new ByteArrayInputStream(baos.toByteArray());
-        }
+        ByteArrayOutputStream baos = new ByteArrayOutputStream();
+
+        ImageIO.write(thumbnail, "jpeg", baos);
+
+        // now get the array
+        ByteArrayInputStream bais = new ByteArrayInputStream(baos.toByteArray());
 
         return bais; // hope this gets written out before its garbage collected!
     }

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

@@ -11,8 +11,6 @@ import java.awt.image.BufferedImage;
 import java.io.InputStream;
 
 import org.apache.logging.log4j.Logger;
-import org.apache.pdfbox.Loader;
-import org.apache.pdfbox.io.RandomAccessReadBuffer;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.encryption.InvalidPasswordException;
 import org.apache.pdfbox.rendering.PDFRenderer;
@@ -73,7 +71,7 @@ public class PDFBoxThumbnail extends MediaFilter {
         BufferedImage buf;
 
         // Render the page image.
-        try ( PDDocument doc = Loader.loadPDF(new RandomAccessReadBuffer(source)); ) {
+        try ( PDDocument doc = PDDocument.load(source); ) {
             PDFRenderer renderer = new PDFRenderer(doc);
             buf = renderer.renderImage(0);
         } catch (InvalidPasswordException ex) {
@@ -83,7 +81,6 @@ public class PDFBoxThumbnail extends MediaFilter {
 
         // Generate thumbnail derivative and return as IO stream.
         JPEGFilter jpegFilter = new JPEGFilter();
-
         return jpegFilter.getThumb(currentItem, buf, verbose);
     }
 }

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

@@ -224,7 +224,7 @@ public class Packager {
             } else {
                 //otherwise, display list of valid packager types
                 System.out.println("\nAvailable Submission Package (SIP) types:");
-                String[] pn = pluginService
+                String pn[] = pluginService
                     .getAllPluginNames(PackageIngester.class);
                 for (int i = 0; i < pn.length; ++i) {
                     System.out.println("  " + pn[i]);
@@ -274,7 +274,7 @@ public class Packager {
             // process
             pkgParams.setRecursiveModeEnabled(true);
         }
-        String[] files = line.getArgs();
+        String files[] = line.getArgs();
         if (files.length > 0) {
             sourceFile = files[0];
         }
@@ -282,9 +282,9 @@ public class Packager {
             myPackager.submit = false;
         }
         if (line.hasOption('o')) {
-            String[] popt = line.getOptionValues('o');
+            String popt[] = line.getOptionValues('o');
             for (int i = 0; i < popt.length; ++i) {
-                String[] pair = popt[i].split("\\=", 2);
+                String pair[] = popt[i].split("\\=", 2);
                 if (pair.length == 2) {
                     pkgParams.addProperty(pair[0].trim(), pair[1].trim());
                 } else if (pair.length == 1) {
@@ -383,7 +383,7 @@ public class Packager {
             }
 
             // validate each parent arg (if any)
-            DSpaceObject[] parentObjs = null;
+            DSpaceObject parentObjs[] = null;
             if (parents != null) {
                 System.out.println("Destination parents:");
 
@@ -461,7 +461,7 @@ public class Packager {
      * @throws PackageException      if packaging error
      */
     protected void ingest(Context context, PackageIngester sip, PackageParameters pkgParams, String sourceFile,
-                          DSpaceObject[] parentObjs)
+                          DSpaceObject parentObjs[])
         throws IOException, SQLException, FileNotFoundException, AuthorizeException, CrosswalkException,
         PackageException {
         // make sure we have an input file

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

@@ -132,7 +132,7 @@ public class MetadataExposureServiceImpl implements MetadataExposureService {
                 if (key.startsWith(CONFIG_PREFIX)) {
                     if (configurationService.getBooleanProperty(key, true)) {
                         String mdField = key.substring(CONFIG_PREFIX.length());
-                        String[] segment = mdField.split("\\.", 3);
+                        String segment[] = mdField.split("\\.", 3);
 
                         // got schema.element.qualifier
                         if (segment.length == 3) {

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

@@ -113,7 +113,7 @@ public class SyndicationFeed {
         configurationService.getProperty("webui.feed.item.date", defaultDateField);
 
     // metadata field for Item description in entry:
-    private static final String[] descriptionFields =
+    private static final String descriptionFields[] =
         DSpaceServicesFactory.getInstance().getConfigurationService()
                              .getArrayProperty("webui.feed.item.description", defaultDescriptionFields);
 

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

@@ -535,7 +535,7 @@ public class LDAPAuthentication implements AuthenticationMethod {
                             resultDN = (sr.getName() + "," + ldap_search_context);
                         }
 
-                        String[] attlist = {ldap_email_field, ldap_givenname_field,
+                        String attlist[] = {ldap_email_field, ldap_givenname_field,
                             ldap_surname_field, ldap_phone_field, ldap_group_field};
                         Attributes atts = sr.getAttributes();
                         Attribute att;
@@ -743,7 +743,7 @@ public class LDAPAuthentication implements AuthenticationMethod {
             // groupmap contains the mapping of LDAP groups to DSpace groups
             // outer loop with the DSpace groups
             while (groupMap != null) {
-                String[] t = groupMap.split(":");
+                String t[] = groupMap.split(":");
                 String ldapSearchString = t[0];
                 String dspaceGroupName = t[1];
 

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

@@ -20,6 +20,8 @@ import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
 import org.dspace.authority.service.AuthorityValueService;
 import org.dspace.content.authority.SolrAuthority;
+import org.dspace.core.Context;
+import org.dspace.core.LogHelper;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -34,7 +36,7 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
 
     private final Logger log = org.apache.logging.log4j.LogManager.getLogger(AuthorityValueServiceImpl.class);
 
-    @Autowired
+    @Autowired(required = true)
     protected AuthorityTypes authorityTypes;
 
     protected AuthorityValueServiceImpl() {
@@ -42,7 +44,7 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
     }
 
     @Override
-    public AuthorityValue generate(String authorityKey, String content, String field) {
+    public AuthorityValue generate(Context context, String authorityKey, String content, String field) {
         AuthorityValue nextValue = null;
 
         nextValue = generateRaw(authorityKey, content, field);
@@ -53,7 +55,7 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
             if (StringUtils.isBlank(authorityKey)) {
                 // An existing metadata without authority is being indexed
                 // If there is an exact match in the index, reuse it before adding a new one.
-                List<AuthorityValue> byValue = findByExactValue(field, content);
+                List<AuthorityValue> byValue = findByExactValue(context, field, content);
                 if (byValue != null && !byValue.isEmpty()) {
                     authorityKey = byValue.get(0).getId();
                 } else {
@@ -116,70 +118,71 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
     /**
      * Item.ANY does not work here.
      *
+     * @param context     Context
      * @param authorityID authority id
      * @return AuthorityValue
      */
     @Override
-    public AuthorityValue findByUID(String authorityID) {
+    public AuthorityValue findByUID(Context context, String authorityID) {
         //Ensure that if we use the full identifier to match on
         String queryString = "id:\"" + authorityID + "\"";
-        List<AuthorityValue> findings = find(queryString);
+        List<AuthorityValue> findings = find(context, queryString);
         return findings.size() > 0 ? findings.get(0) : null;
     }
 
     @Override
-    public List<AuthorityValue> findByValue(String field, String value) {
+    public List<AuthorityValue> findByValue(Context context, String field, String value) {
         String queryString = "value:" + value + " AND field:" + field;
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
-    public AuthorityValue findByOrcidID(String orcid_id) {
+    public AuthorityValue findByOrcidID(Context context, String orcid_id) {
         String queryString = "orcid_id:" + orcid_id;
-        List<AuthorityValue> findings = find(queryString);
+        List<AuthorityValue> findings = find(context, queryString);
         return findings.size() > 0 ? findings.get(0) : null;
     }
 
     @Override
-    public List<AuthorityValue> findByExactValue(String field, String value) {
+    public List<AuthorityValue> findByExactValue(Context context, String field, String value) {
         String queryString = "value:\"" + value + "\" AND field:" + field;
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
-    public List<AuthorityValue> findByValue(String schema, String element, String qualifier,
+    public List<AuthorityValue> findByValue(Context context, String schema, String element, String qualifier,
                                             String value) {
         String field = fieldParameter(schema, element, qualifier);
-        return findByValue(field, value);
+        return findByValue(context, field, value);
     }
 
     @Override
-    public List<AuthorityValue> findByName(String schema, String element, String qualifier,
+    public List<AuthorityValue> findByName(Context context, String schema, String element, String qualifier,
                                            String name) {
         String field = fieldParameter(schema, element, qualifier);
         String queryString = "first_name:" + name + " OR last_name:" + name + " OR name_variant:" + name + " AND " +
             "field:" + field;
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
-    public List<AuthorityValue> findByAuthorityMetadata(String schema, String element,
+    public List<AuthorityValue> findByAuthorityMetadata(Context context, String schema, String element,
                                                         String qualifier, String value) {
         String field = fieldParameter(schema, element, qualifier);
         String queryString = "all_Labels:" + value + " AND field:" + field;
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
-    public List<AuthorityValue> findOrcidHolders() {
+    public List<AuthorityValue> findOrcidHolders(Context context) {
         String queryString = "orcid_id:*";
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
-    public List<AuthorityValue> findAll() {
+    public List<AuthorityValue> findAll(Context context) {
         String queryString = "*:*";
-        return find(queryString);
+        return find(context, queryString);
     }
 
     @Override
@@ -201,7 +204,7 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
         return fromAuthority;
     }
 
-    protected List<AuthorityValue> find(String queryString) {
+    protected List<AuthorityValue> find(Context context, String queryString) {
         List<AuthorityValue> findings = new ArrayList<AuthorityValue>();
         try {
             SolrQuery solrQuery = new SolrQuery();
@@ -217,7 +220,8 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
                 }
             }
         } catch (Exception e) {
-            log.error("Error while retrieving AuthorityValue from solr. query: " + queryString, e);
+            log.error(LogHelper.getHeader(context, "Error while retrieving AuthorityValue from solr",
+                                           "query: " + queryString), e);
         }
 
         return findings;

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

@@ -133,11 +133,11 @@ public class UpdateAuthorities {
         if (selectedIDs != null && !selectedIDs.isEmpty()) {
             authorities = new ArrayList<>();
             for (String selectedID : selectedIDs) {
-                AuthorityValue byUID = authorityValueService.findByUID(selectedID);
+                AuthorityValue byUID = authorityValueService.findByUID(context, selectedID);
                 authorities.add(byUID);
             }
         } else {
-            authorities = authorityValueService.findAll();
+            authorities = authorityValueService.findAll(context);
         }
 
         if (authorities != null) {

dspace-api/src/main/java/org/dspace/authority/indexer/DSpaceAuthorityIndexer.java

@@ -148,12 +148,12 @@ public class DSpaceAuthorityIndexer implements AuthorityIndexerInterface, Initia
                 !metadataAuthorityKey.startsWith(AuthorityValueService.GENERATE)) {
             // !uid.startsWith(AuthorityValueGenerator.GENERATE) is not strictly
             // necessary here but it prevents exceptions in solr
-            AuthorityValue value = authorityValueService.findByUID(metadataAuthorityKey);
+            AuthorityValue value = authorityValueService.findByUID(context, metadataAuthorityKey);
             if (value != null) {
                 return value;
             }
         }
-        return authorityValueService.generate(metadataAuthorityKey,
+        return authorityValueService.generate(context, metadataAuthorityKey,
                 metadataContent, metadataField.replaceAll("\\.", "_"));
     }
 

dspace-api/src/main/java/org/dspace/authority/service/AuthorityValueService.java

@@ -11,6 +11,7 @@ import java.util.List;
 
 import org.apache.solr.common.SolrDocument;
 import org.dspace.authority.AuthorityValue;
+import org.dspace.core.Context;
 
 /**
  * This service contains all methods for using authority values
@@ -24,125 +25,32 @@ public interface AuthorityValueService {
     public static final String SPLIT = "::";
     public static final String GENERATE = "will be generated" + SPLIT;
 
-    /**
-     * Generates an {@link AuthorityValue} based on the given parameters.
-     *
-     * @param authorityKey  the authority key to be assigned to the generated authority value
-     * @param content       the content of the generated authority value
-     * @param field         the field of the generated authority value
-     * @return the generated {@link AuthorityValue}
-     */
-    public AuthorityValue generate(String authorityKey, String content, String field);
+    public AuthorityValue generate(Context context, String authorityKey, String content, String field);
 
-    /**
-     * Updates an AuthorityValue.
-     *
-     * @param value the AuthorityValue to be updated
-     * @return the updated AuthorityValue
-     */
     public AuthorityValue update(AuthorityValue value);
 
-    /**
-     * Finds an AuthorityValue based on the provided authorityID.
-     *
-     * @param authorityID the authority ID used to search for the AuthorityValue
-     * @return the found AuthorityValue, or null if no match is found
-     */
-    public AuthorityValue findByUID(String authorityID);
+    public AuthorityValue findByUID(Context context, String authorityID);
 
-    /**
-     * Finds AuthorityValues in the given context based on field and value.
-     *
-     * @param field the field to search for AuthorityValues
-     * @param value the value to search for AuthorityValues
-     * @return a list of found AuthorityValues matching the given field and value, or an empty list if no match is found
-     */
-    public List<AuthorityValue> findByValue(String field, String value);
+    public List<AuthorityValue> findByValue(Context context, String field, String value);
 
-    /**
-     * Finds an {@link AuthorityValue} based on the provided ORCID ID.
-     *
-     * @param orcid_id the ORCID ID used to search for the AuthorityValue
-     * @return the found AuthorityValue, or null if no match is found
-     */
-    public AuthorityValue findByOrcidID(String orcid_id);
+    public AuthorityValue findByOrcidID(Context context, String orcid_id);
 
-    /**
-     * Finds {@link AuthorityValue}s based on the provided metadata schema, element, qualifier, and name.
-     *
-     * @param schema    the schema of the AuthorityValue
-     * @param element   the element of the AuthorityValue
-     * @param qualifier the qualifier of the AuthorityValue
-     * @param name      the name of the AuthorityValue
-     * @return a list of found AuthorityValues matching the given schema, element, qualifier, and name,
-     *         or an empty list if no match is found
-     */
-    public List<AuthorityValue> findByName(String schema, String element, String qualifier,
+    public List<AuthorityValue> findByName(Context context, String schema, String element, String qualifier,
                                            String name);
 
-    /**
-     * Finds {@link AuthorityValue}s based on the provided metadata schema, element, qualifier, and value.
-     *
-     * @param schema    the schema of the AuthorityValue
-     * @param element   the element of the AuthorityValue
-     * @param qualifier the qualifier of the AuthorityValue
-     * @param value     the value of the AuthorityValue
-     * @return a list of found AuthorityValues matching the given schema, element, qualifier, and value,
-     *         or an empty list if no match is found
-     */
-    public List<AuthorityValue> findByAuthorityMetadata(String schema, String element,
+    public List<AuthorityValue> findByAuthorityMetadata(Context context, String schema, String element,
                                                         String qualifier, String value);
 
-    /**
-     * Finds {@link AuthorityValue}s in the given context based on the exact field and value.
-     *
-     * @param field the field to search for AuthorityValues
-     * @param value the value to search for AuthorityValues
-     * @return a list of found AuthorityValues matching the given field and value,
-     *         or an empty list if no match is found
-     */
-    public List<AuthorityValue> findByExactValue(String field, String value);
+    public List<AuthorityValue> findByExactValue(Context context, String field, String value);
 
-    /**
-     * Finds {@link AuthorityValue}s based on the provided metadata schema, element, qualifier, and value.
-     *
-     * @param schema    the schema of the AuthorityValue
-     * @param element   the element of the AuthorityValue
-     * @param qualifier the qualifier of the AuthorityValue
-     * @param value     the value of the AuthorityValue
-     * @return a list of found AuthorityValues matching the given schema, element, qualifier, and value,
-     *         or an empty list if no match is found
-     */
-    public List<AuthorityValue> findByValue(String schema, String element, String qualifier,
+    public List<AuthorityValue> findByValue(Context context, String schema, String element, String qualifier,
                                             String value);
 
-    /**
-     * Finds AuthorityValues that are ORCID person authority values.
-     *
-     * @return a list of AuthorityValues or an empty list if no matching values are found
-     */
-    public List<AuthorityValue> findOrcidHolders();
+    public List<AuthorityValue> findOrcidHolders(Context context);
 
-    /**
-     * Retrieves all AuthorityValues from Solr.
-     *
-     * @return A list of all AuthorityValues.
-     */
-    public List<AuthorityValue> findAll();
+    public List<AuthorityValue> findAll(Context context);
 
-    /**
-     * Converts a SolrDocument into an AuthorityValue object.
-     *
-     * @param solrDocument the SolrDocument to convert
-     * @return the converted AuthorityValue object
-     */
     public AuthorityValue fromSolr(SolrDocument solrDocument);
 
-    /**
-     * Retrieves the type of authority value based on the provided metadata string.
-     *
-     * @param metadataString the metadata string used to determine the authority value type
-     * @return the {@link AuthorityValue} representing the type of authority value, or null if no match is found
-     */
     public AuthorityValue getAuthorityValueType(String metadataString);
 }

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

@@ -16,7 +16,6 @@ import java.time.LocalDate;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
-import java.util.Objects;
 import java.util.UUID;
 
 import org.apache.commons.collections4.CollectionUtils;
@@ -49,7 +48,6 @@ import org.dspace.discovery.indexobject.IndexableItem;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.GroupService;
-import org.dspace.services.ConfigurationService;
 import org.dspace.workflow.WorkflowItemService;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -86,8 +84,6 @@ public class AuthorizeServiceImpl implements AuthorizeService {
     protected WorkflowItemService workflowItemService;
     @Autowired(required = true)
     private SearchService searchService;
-    @Autowired(required = true)
-    private ConfigurationService configurationService;
 
 
     protected AuthorizeServiceImpl() {
@@ -512,26 +508,17 @@ public class AuthorizeServiceImpl implements AuthorizeService {
         return resourcePolicyService.find(c, o, actionID);
     }
 
-    @Override
-    public void inheritPolicies(Context c, DSpaceObject src, DSpaceObject dest)
-        throws SQLException, AuthorizeException {
-        inheritPolicies(c, src, dest, false);
-    }
-
     @Override
     public void inheritPolicies(Context c, DSpaceObject src,
-                                DSpaceObject dest, boolean includeCustom) throws SQLException, AuthorizeException {
+                                DSpaceObject dest) throws SQLException, AuthorizeException {
         // find all policies for the source object
         List<ResourcePolicy> policies = getPolicies(c, src);
 
-        // Only inherit non-ADMIN policies (since ADMIN policies are automatically inherited)
-        // and non-custom policies (usually applied manually?) UNLESS specified otherwise with includCustom
-        // (for example, item.addBundle() will inherit custom policies to enforce access conditions)
+        //Only inherit non-ADMIN policies (since ADMIN policies are automatically inherited)
+        //and non-custom policies as these are manually applied when appropriate
         List<ResourcePolicy> nonAdminPolicies = new ArrayList<>();
         for (ResourcePolicy rp : policies) {
-            if (rp.getAction() != Constants.ADMIN && (!StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)
-                        || (includeCustom && StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)
-                            && isNotAlreadyACustomRPOfThisTypeOnDSO(c, dest)))) {
+            if (rp.getAction() != Constants.ADMIN && !StringUtils.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)) {
                 nonAdminPolicies.add(rp);
             }
         }
@@ -957,100 +944,4 @@ public class AuthorizeServiceImpl implements AuthorizeService {
             return query + " AND ";
         }
     }
-
-    /**
-     * Add the default policies, which have not been already added to the given DSpace object
-     *
-     * @param context                   The relevant DSpace Context.
-     * @param dso                       The DSpace Object to add policies to
-     * @param defaultCollectionPolicies list of policies
-     * @throws SQLException       An exception that provides information on a database access error or other errors.
-     * @throws AuthorizeException Exception indicating the current user of the context does not have permission
-     *                            to perform a particular action.
-     */
-    @Override
-    public void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
-        List<ResourcePolicy> defaultCollectionPolicies) throws SQLException, AuthorizeException {
-        boolean appendMode = configurationService
-                .getBooleanProperty("core.authorization.installitem.inheritance-read.append-mode", false);
-        for (ResourcePolicy defaultPolicy : defaultCollectionPolicies) {
-            if (!isAnIdenticalPolicyAlreadyInPlace(context, dso, defaultPolicy.getGroup(), Constants.READ,
-                    defaultPolicy.getID()) &&
-                   (!appendMode && isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso) ||
-                    appendMode && shouldBeAppended(context, dso, defaultPolicy))) {
-                ResourcePolicy newPolicy = resourcePolicyService.clone(context, defaultPolicy);
-                newPolicy.setdSpaceObject(dso);
-                newPolicy.setAction(Constants.READ);
-                newPolicy.setRpType(ResourcePolicy.TYPE_INHERITED);
-                resourcePolicyService.update(context, newPolicy);
-            }
-        }
-    }
-
-    /**
-     * Add a list of custom policies if there are already NO custom policies in place
-     *
-     */
-    @Override
-    public void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso, List<ResourcePolicy> customPolicies)
-            throws SQLException, AuthorizeException {
-        boolean customPoliciesAlreadyInPlace =
-            findPoliciesByDSOAndType(context, dso, ResourcePolicy.TYPE_CUSTOM).size() > 0;
-        if (!customPoliciesAlreadyInPlace) {
-            addPolicies(context, customPolicies, dso);
-        }
-    }
-
-    /**
-     * Check whether or not there is already an RP on the given dso, which has actionId={@link Constants.READ} and
-     * resourceTypeId={@link ResourcePolicy.TYPE_CUSTOM}
-     *
-     * @param context DSpace context
-     * @param dso     DSpace object to check for custom read RP
-     * @return True if there is no RP on the item with custom read RP, otherwise false
-     * @throws SQLException If something goes wrong retrieving the RP on the DSO
-     */
-    private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso) throws SQLException {
-        return isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso, Constants.READ);
-    }
-
-    private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso, int action)
-            throws SQLException {
-        List<ResourcePolicy> rps = resourcePolicyService.find(context, dso, action);
-        for (ResourcePolicy rp : rps) {
-            if (rp.getRpType() != null && rp.getRpType().equals(ResourcePolicy.TYPE_CUSTOM)) {
-                return false;
-            }
-        }
-        return true;
-    }
-
-    /**
-     * Check if the provided default policy should be appended or not to the final
-     * item. If an item has at least one custom READ policy any anonymous READ
-     * policy with empty start/end date should be skipped
-     *
-     * @param context       DSpace context
-     * @param dso           DSpace object to check for custom read RP
-     * @param defaultPolicy The policy to check
-     * @return
-     * @throws SQLException If something goes wrong retrieving the RP on the DSO
-     */
-    private boolean shouldBeAppended(Context context, DSpaceObject dso, ResourcePolicy defaultPolicy)
-            throws SQLException {
-        boolean hasCustomPolicy = resourcePolicyService.find(context, dso, Constants.READ)
-                                                       .stream()
-                                                       .filter(rp -> (Objects.nonNull(rp.getRpType()) &&
-                                                            Objects.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)))
-                                                       .findFirst()
-                                                       .isPresent();
-
-        boolean isAnonymousGroup = Objects.nonNull(defaultPolicy.getGroup())
-                && StringUtils.equals(defaultPolicy.getGroup().getName(), Group.ANONYMOUS);
-
-        boolean datesAreNull = Objects.isNull(defaultPolicy.getStartDate())
-                && Objects.isNull(defaultPolicy.getEndDate());
-
-        return !(hasCustomPolicy && isAnonymousGroup && datesAreNull);
-    }
 }

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

@@ -322,19 +322,6 @@ public interface AuthorizeService {
      */
     public List<ResourcePolicy> getPoliciesActionFilterExceptRpType(Context c, DSpaceObject o, int actionID,
                                                                     String rpType) throws SQLException;
-    /**
-     * Add policies to an object to match those from a previous object
-     *
-     * @param c    context
-     * @param src  source of policies
-     * @param dest destination of inherited policies
-     * @param includeCustom whether TYPE_CUSTOM policies should be inherited
-     * @throws SQLException       if there's a database problem
-     * @throws AuthorizeException if the current user is not authorized to add these policies
-     */
-    public void inheritPolicies(Context c, DSpaceObject src, DSpaceObject dest, boolean includeCustom)
-            throws SQLException, AuthorizeException;
-
     /**
      * Add policies to an object to match those from a previous object
      *
@@ -618,10 +605,4 @@ public interface AuthorizeService {
     public void replaceAllPolicies(Context context, DSpaceObject source, DSpaceObject dest)
             throws SQLException, AuthorizeException;
 
-    public void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
-            List<ResourcePolicy> defaultCollectionPolicies) throws SQLException, AuthorizeException;
-
-    public void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso,
-            List<ResourcePolicy> defaultCollectionPolicies) throws SQLException, AuthorizeException;
-
 }

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

@@ -131,7 +131,7 @@ public final class CheckerCommand {
                 collector.collect(context, info);
             }
 
-            context.commit();
+            context.uncacheEntity(bitstream);
             bitstream = dispatcher.next();
         }
     }

dspace-api/src/main/java/org/dspace/checker/dao/impl/MostRecentChecksumDAOImpl.java

@@ -56,8 +56,8 @@ public class MostRecentChecksumDAOImpl extends AbstractHibernateDAO<MostRecentCh
         criteriaQuery.where(criteriaBuilder.and(
             criteriaBuilder.equal(mostRecentChecksumRoot.get(MostRecentChecksum_.toBeProcessed), false),
             criteriaBuilder
-                .lessThanOrEqualTo(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate),
-            criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), startDate)
+                .lessThanOrEqualTo(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), startDate),
+            criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate)
                             )
         );
         List<Order> orderList = new LinkedList<>();

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

@@ -49,7 +49,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
      * translate support-level ID to string.  MUST keep this table in sync
      * with support level definitions above.
      */
-    protected final String[] supportLevelText =
+    protected final String supportLevelText[] =
         {"UNKNOWN", "KNOWN", "SUPPORTED"};
 
 

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

@@ -124,11 +124,13 @@ public class EntityTypeServiceImpl implements EntityTypeService {
     @Override
     public List<String> getSubmitAuthorizedTypes(Context context)
             throws SQLException, SolrServerException, IOException {
+        List<String> types = new ArrayList<>();
         StringBuilder query = null;
+        EPerson currentUser = context.getCurrentUser();
         if (!authorizeService.isAdmin(context)) {
-            EPerson currentUser = context.getCurrentUser();
+            String userId = "";
             if (currentUser != null) {
-                String userId = currentUser.getID().toString();
+                userId = currentUser.getID().toString();
                 query = new StringBuilder();
                 query.append("submit:(e").append(userId);
             }
@@ -143,10 +145,7 @@ public class EntityTypeServiceImpl implements EntityTypeService {
                 }
                 query.append(group.getID());
             }
-
-            if (query != null) {
-                query.append(")");
-            }
+            query.append(")");
         }
 
         SolrQuery sQuery = new SolrQuery("*:*");
@@ -161,8 +160,6 @@ public class EntityTypeServiceImpl implements EntityTypeService {
         sQuery.setFacetSort(FacetParams.FACET_SORT_INDEX);
         QueryResponse qResp = solrSearchCore.getSolr().query(sQuery, solrSearchCore.REQUEST_METHOD);
         FacetField facetField = qResp.getFacetField("search.entitytype");
-
-        List<String> types = new ArrayList<>();
         if (Objects.nonNull(facetField)) {
             for (Count c : facetField.getValues()) {
                 types.add(c.getName());

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

@@ -480,7 +480,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
         // now add authorization policies from owning item
         // hmm, not very "multiple-inclusion" friendly
-        authorizeService.inheritPolicies(context, item, bundle, true);
+        authorizeService.inheritPolicies(context, item, bundle);
 
         // Add the bundle to in-memory list
         item.addBundle(bundle);
@@ -1046,8 +1046,8 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
             // if come from InstallItem: remove all submission/workflow policies
             authorizeService.removeAllPoliciesByDSOAndType(context, mybundle, ResourcePolicy.TYPE_SUBMISSION);
             authorizeService.removeAllPoliciesByDSOAndType(context, mybundle, ResourcePolicy.TYPE_WORKFLOW);
-            authorizeService.addCustomPoliciesNotInPlace(context, mybundle, defaultItemPolicies);
-            authorizeService.addDefaultPoliciesNotInPlace(context, mybundle, defaultCollectionBundlePolicies);
+            addCustomPoliciesNotInPlace(context, mybundle, defaultItemPolicies);
+            addDefaultPoliciesNotInPlace(context, mybundle, defaultCollectionBundlePolicies);
 
             for (Bitstream bitstream : mybundle.getBitstreams()) {
                 // If collection has default READ policies, remove the bundle's READ policies.
@@ -1093,8 +1093,8 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         throws SQLException, AuthorizeException {
         authorizeService.removeAllPoliciesByDSOAndType(context, bitstream, ResourcePolicy.TYPE_SUBMISSION);
         authorizeService.removeAllPoliciesByDSOAndType(context, bitstream, ResourcePolicy.TYPE_WORKFLOW);
-        authorizeService.addCustomPoliciesNotInPlace(context, bitstream, defaultItemPolicies);
-        authorizeService.addDefaultPoliciesNotInPlace(context, bitstream, defaultCollectionPolicies);
+        addCustomPoliciesNotInPlace(context, bitstream, defaultItemPolicies);
+        addDefaultPoliciesNotInPlace(context, bitstream, defaultCollectionPolicies);
     }
 
     @Override
@@ -1132,7 +1132,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
             authorizeService.removeAllPoliciesByDSOAndType(context, item, ResourcePolicy.TYPE_WORKFLOW);
 
             // add default policies only if not already in place
-            authorizeService.addDefaultPoliciesNotInPlace(context, item, defaultCollectionPolicies);
+            addDefaultPoliciesNotInPlace(context, item, defaultCollectionPolicies);
         } finally {
             context.restoreAuthSystemState();
         }
@@ -1322,7 +1322,91 @@ prevent the generation of resource policy entry values with null dspace_object a
 
     */
 
+    /**
+     * Add the default policies, which have not been already added to the given DSpace object
+     *
+     * @param context                   The relevant DSpace Context.
+     * @param dso                       The DSpace Object to add policies to
+     * @param defaultCollectionPolicies list of policies
+     * @throws SQLException       An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException Exception indicating the current user of the context does not have permission
+     *                            to perform a particular action.
+     */
+    protected void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso,
+        List<ResourcePolicy> defaultCollectionPolicies) throws SQLException, AuthorizeException {
+        boolean appendMode = configurationService
+                .getBooleanProperty("core.authorization.installitem.inheritance-read.append-mode", false);
+        for (ResourcePolicy defaultPolicy : defaultCollectionPolicies) {
+            if (!authorizeService
+                .isAnIdenticalPolicyAlreadyInPlace(context, dso, defaultPolicy.getGroup(), Constants.READ,
+                    defaultPolicy.getID()) &&
+                   (!appendMode && isNotAlreadyACustomRPOfThisTypeOnDSO(context, dso) ||
+                    appendMode && shouldBeAppended(context, dso, defaultPolicy))) {
+                ResourcePolicy newPolicy = resourcePolicyService.clone(context, defaultPolicy);
+                newPolicy.setdSpaceObject(dso);
+                newPolicy.setAction(Constants.READ);
+                newPolicy.setRpType(ResourcePolicy.TYPE_INHERITED);
+                resourcePolicyService.update(context, newPolicy);
+            }
+        }
+    }
 
+    private void addCustomPoliciesNotInPlace(Context context, DSpaceObject dso, List<ResourcePolicy> customPolicies)
+            throws SQLException, AuthorizeException {
+        boolean customPoliciesAlreadyInPlace = authorizeService
+                .findPoliciesByDSOAndType(context, dso, ResourcePolicy.TYPE_CUSTOM).size() > 0;
+        if (!customPoliciesAlreadyInPlace) {
+            authorizeService.addPolicies(context, customPolicies, dso);
+        }
+    }
+
+    /**
+     * Check whether or not there is already an RP on the given dso, which has actionId={@link Constants.READ} and
+     * resourceTypeId={@link ResourcePolicy.TYPE_CUSTOM}
+     *
+     * @param context DSpace context
+     * @param dso     DSpace object to check for custom read RP
+     * @return True if there is no RP on the item with custom read RP, otherwise false
+     * @throws SQLException If something goes wrong retrieving the RP on the DSO
+     */
+    private boolean isNotAlreadyACustomRPOfThisTypeOnDSO(Context context, DSpaceObject dso) throws SQLException {
+        List<ResourcePolicy> readRPs = resourcePolicyService.find(context, dso, Constants.READ);
+        for (ResourcePolicy readRP : readRPs) {
+            if (readRP.getRpType() != null && readRP.getRpType().equals(ResourcePolicy.TYPE_CUSTOM)) {
+                return false;
+            }
+        }
+        return true;
+    }
+
+    /**
+     * Check if the provided default policy should be appended or not to the final
+     * item. If an item has at least one custom READ policy any anonymous READ
+     * policy with empty start/end date should be skipped
+     *
+     * @param context       DSpace context
+     * @param dso           DSpace object to check for custom read RP
+     * @param defaultPolicy The policy to check
+     * @return
+     * @throws SQLException If something goes wrong retrieving the RP on the DSO
+     */
+    private boolean shouldBeAppended(Context context, DSpaceObject dso, ResourcePolicy defaultPolicy)
+            throws SQLException {
+        boolean hasCustomPolicy = resourcePolicyService.find(context, dso, Constants.READ)
+                                                       .stream()
+                                                       .filter(rp -> (Objects.nonNull(rp.getRpType()) &&
+                                                            Objects.equals(rp.getRpType(), ResourcePolicy.TYPE_CUSTOM)))
+                                                       .findFirst()
+                                                       .isPresent();
+
+        boolean isAnonimousGroup = Objects.nonNull(defaultPolicy.getGroup())
+                && StringUtils.equals(defaultPolicy.getGroup().getName(), Group.ANONYMOUS);
+
+        boolean datesAreNull = Objects.isNull(defaultPolicy.getStartDate())
+                && Objects.isNull(defaultPolicy.getEndDate());
+
+        return !(hasCustomPolicy && isAnonimousGroup && datesAreNull);
+    }
 
     /**
      * Returns an iterator of Items possessing the passed metadata field, or only

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

@@ -68,7 +68,7 @@ public class Choices {
     /**
      * descriptive labels for confidence values
      */
-    private static final int[] confidenceValue = {
+    private static final int confidenceValue[] = {
         CF_UNSET,
         CF_NOVALUE,
         CF_REJECTED,
@@ -78,7 +78,7 @@ public class Choices {
         CF_UNCERTAIN,
         CF_ACCEPTED,
     };
-    private static final String[] confidenceText = {
+    private static final String confidenceText[] = {
         "UNSET",
         "NOVALUE",
         "REJECTED",
@@ -94,7 +94,7 @@ public class Choices {
     /**
      * The set of values returned by the authority
      */
-    public Choice[] values = null;
+    public Choice values[] = null;
 
     /**
      * The confidence level that applies to all values in this result set
@@ -133,9 +133,9 @@ public class Choices {
      * @param confidence confidence level
      * @param more       whether more values
      */
-    public Choices(Choice[] values, int start, int total, int confidence, boolean more) {
+    public Choices(Choice values[], int start, int total, int confidence, boolean more) {
         super();
-        this.values = ArrayUtils.clone(values);
+        this.values = (Choice[]) ArrayUtils.clone(values);
         this.start = start;
         this.total = total;
         this.confidence = confidence;
@@ -152,9 +152,9 @@ public class Choices {
      * @param more            whether more values
      * @param defaultSelected default selected value
      */
-    public Choices(Choice[] values, int start, int total, int confidence, boolean more, int defaultSelected) {
+    public Choices(Choice values[], int start, int total, int confidence, boolean more, int defaultSelected) {
         super();
-        this.values = ArrayUtils.clone(values);
+        this.values = (Choice[]) ArrayUtils.clone(values);
         this.start = start;
         this.total = total;
         this.confidence = confidence;

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

@@ -66,7 +66,7 @@ public class DCInputAuthority extends SelfNamedPlugin implements ChoiceAuthority
      * The map of the input form reader associated to use for a specific java locale
      */
     private static Map<Locale, DCInputsReader> dcis = null;
-    private static String[] pluginNames = null;
+    private static String pluginNames[] = null;
 
     public DCInputAuthority() {
         super();
@@ -87,7 +87,7 @@ public class DCInputAuthority extends SelfNamedPlugin implements ChoiceAuthority
             initPluginNames();
         }
 
-        return ArrayUtils.clone(pluginNames);
+        return (String[]) ArrayUtils.clone(pluginNames);
     }
 
     private static synchronized void initPluginNames() {
@@ -179,7 +179,7 @@ public class DCInputAuthority extends SelfNamedPlugin implements ChoiceAuthority
         String[] labelsLocale = labels.get(currentLocale.getLanguage());
         for (int i = 0; i < valuesLocale.length; ++i) {
             if (text.equalsIgnoreCase(valuesLocale[i])) {
-                Choice[] v = new Choice[1];
+                Choice v[] = new Choice[1];
                 v[0] = new Choice(String.valueOf(i), valuesLocale[i], labelsLocale[i]);
                 return new Choices(v, 0, v.length, Choices.CF_UNCERTAIN, false, 0);
             }

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

@@ -35,25 +35,23 @@ import org.xml.sax.InputSource;
  * from {@code ${dspace.dir}/config/controlled-vocabularies/*.xml} and turns
  * them into autocompleting authorities.
  *
- * <p>Configuration: This MUST be configured as a self-named plugin, e.g.: {@code
- * plugin.selfnamed.org.dspace.content.authority.ChoiceAuthority =
+ * Configuration: This MUST be configured as a self-named plugin, e.g.: {@code
+ * plugin.selfnamed.org.dspace.content.authority.ChoiceAuthority = \
  * org.dspace.content.authority.DSpaceControlledVocabulary
  * }
  *
- * <p>It AUTOMATICALLY configures a plugin instance for each XML file in the
+ * It AUTOMATICALLY configures a plugin instance for each XML file in the
  * controlled vocabularies directory. The name of the plugin is the basename of
  * the file; e.g., {@code ${dspace.dir}/config/controlled-vocabularies/nsi.xml}
  * would generate a plugin called "nsi".
  *
- * <p>Each configured plugin comes with three configuration options:
- * <ul>
- *  <li>{@code vocabulary.plugin._plugin_.hierarchy.store = <true|false>
- * # Store entire hierarchy along with selected value. Default: TRUE}</li>
- *  <li>{@code vocabulary.plugin._plugin_.hierarchy.suggest =
- * <true|false>  # Display entire hierarchy in the suggestion list.  Default: TRUE}</li>
- *  <li>{@code vocabulary.plugin._plugin_.delimiter = "<string>"
- * # Delimiter to use when building hierarchy strings. Default: "::"}</li>
- * </ul>
+ * Each configured plugin comes with three configuration options: {@code
+ * vocabulary.plugin._plugin_.hierarchy.store = <true|false>
+ * # Store entire hierarchy along with selected value. Default: TRUE
+ * vocabulary.plugin._plugin_.hierarchy.suggest =
+ * <true|false>  # Display entire hierarchy in the suggestion list.  Default: TRUE
+ * vocabulary.plugin._plugin_.delimiter = "<string>"
+ * # Delimiter to use when building hierarchy strings. Default: "::"
  * }
  *
  * @author Michael B. Klein
@@ -61,17 +59,16 @@ import org.xml.sax.InputSource;
 
 public class DSpaceControlledVocabulary extends SelfNamedPlugin implements HierarchicalAuthority {
 
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceControlledVocabulary.class);
     protected static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ'," +
-        "'abcdefghijklmnopqrstuvwxyz'),%s)]";
-    protected static String idTemplate = "//node[@id = %s]";
-    protected static String idTemplateQuoted = "//node[@id = '%s']";
-    protected static String labelTemplate = "//node[@label = %s]";
+        "'abcdefghijklmnopqrstuvwxyz'),'%s')]";
+    protected static String idTemplate = "//node[@id = '%s']";
+    protected static String labelTemplate = "//node[@label = '%s']";
     protected static String idParentTemplate = "//node[@id = '%s']/parent::isComposedBy/parent::node";
     protected static String rootTemplate = "/node";
     protected static String idAttribute = "id";
     protected static String labelAttribute = "label";
-    protected static String[] pluginNames = null;
+    protected static String pluginNames[] = null;
     protected String vocabularyName = null;
     protected InputSource vocabulary = null;
     protected Boolean suggestHierarchy = false;
@@ -97,7 +94,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
             initPluginNames();
         }
 
-        return ArrayUtils.clone(pluginNames);
+        return (String[]) ArrayUtils.clone(pluginNames);
     }
 
     private static synchronized void initPluginNames() {
@@ -113,7 +110,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
                                                            File.separator + "config" +
                                                            File.separator + "controlled-vocabularies";
             String[] xmlFiles = (new File(vocabulariesPath)).list(new xmlFilter());
-            List<String> names = new ArrayList<>();
+            List<String> names = new ArrayList<String>();
             for (String filename : xmlFiles) {
                 names.add((new File(filename)).getName().replace(".xml", ""));
             }
@@ -181,23 +178,15 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     public Choices getMatches(String text, int start, int limit, String locale) {
         init(locale);
         log.debug("Getting matches for '" + text + "'");
+        String xpathExpression = "";
         String[] textHierarchy = text.split(hierarchyDelimiter, -1);
-        StringBuilder xpathExpressionBuilder = new StringBuilder();
         for (int i = 0; i < textHierarchy.length; i++) {
-            xpathExpressionBuilder.append(String.format(xpathTemplate, "$var" + i));
+            xpathExpression +=
+                String.format(xpathTemplate, textHierarchy[i].replaceAll("'", "&apos;").toLowerCase());
         }
-        String xpathExpression = xpathExpressionBuilder.toString();
         XPath xpath = XPathFactory.newInstance().newXPath();
-        xpath.setXPathVariableResolver(variableName -> {
-            String varName = variableName.getLocalPart();
-            if (varName.startsWith("var")) {
-                int index = Integer.parseInt(varName.substring(3));
-                return textHierarchy[index].toLowerCase();
-            }
-            throw new IllegalArgumentException("Unexpected variable: " + varName);
-        });
-        int total;
-        List<Choice> choices;
+        int total = 0;
+        List<Choice> choices = new ArrayList<Choice>();
         try {
             NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
             total = results.getLength();
@@ -213,23 +202,15 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     @Override
     public Choices getBestMatch(String text, String locale) {
         init(locale);
-        log.debug("Getting best matches for {}'", text);
+        log.debug("Getting best matches for '" + text + "'");
+        String xpathExpression = "";
         String[] textHierarchy = text.split(hierarchyDelimiter, -1);
-        StringBuilder xpathExpressionBuilder = new StringBuilder();
         for (int i = 0; i < textHierarchy.length; i++) {
-            xpathExpressionBuilder.append(String.format(valueTemplate, "$var" + i));
+            xpathExpression +=
+                String.format(valueTemplate, textHierarchy[i].replaceAll("'", "&apos;"));
         }
-        String xpathExpression = xpathExpressionBuilder.toString();
         XPath xpath = XPathFactory.newInstance().newXPath();
-        xpath.setXPathVariableResolver(variableName -> {
-            String varName = variableName.getLocalPart();
-            if (varName.startsWith("var")) {
-                int index = Integer.parseInt(varName.substring(3));
-                return textHierarchy[index];
-            }
-            throw new IllegalArgumentException("Unexpected variable: " + varName);
-        });
-        List<Choice> choices;
+        List<Choice> choices = new ArrayList<Choice>();
         try {
             NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
             choices = getChoicesFromNodeList(results, 0, 1);
@@ -277,7 +258,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     @Override
     public Choices getChoicesByParent(String authorityName, String parentId, int start, int limit, String locale) {
         init(locale);
-        String xpathExpression = String.format(idTemplateQuoted, parentId);
+        String xpathExpression = String.format(idTemplate, parentId);
         return getChoicesByXpath(xpathExpression, start, limit);
     }
 
@@ -301,12 +282,15 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private boolean isRootElement(Node node) {
-        return node != null && node.getOwnerDocument().getDocumentElement().equals(node);
+        if (node != null && node.getOwnerDocument().getDocumentElement().equals(node)) {
+            return true;
+        }
+        return false;
     }
 
     private Node getNode(String key, String locale) throws XPathExpressionException {
         init(locale);
-        String xpathExpression = String.format(idTemplateQuoted, key);
+        String xpathExpression = String.format(idTemplate, key);
         Node node = getNodeFromXPath(xpathExpression);
         return node;
     }
@@ -318,7 +302,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private List<Choice> getChoicesFromNodeList(NodeList results, int start, int limit) {
-        List<Choice> choices = new ArrayList<>();
+        List<Choice> choices = new ArrayList<Choice>();
         for (int i = 0; i < results.getLength(); i++) {
             if (i < start) {
                 continue;
@@ -337,17 +321,17 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
 
     private Map<String, String> addOtherInformation(String parentCurr, String noteCurr,
             List<String> childrenCurr, String authorityCurr) {
-        Map<String, String> extras = new HashMap<>();
+        Map<String, String> extras = new HashMap<String, String>();
         if (StringUtils.isNotBlank(parentCurr)) {
             extras.put("parent", parentCurr);
         }
         if (StringUtils.isNotBlank(noteCurr)) {
             extras.put("note", noteCurr);
         }
-        if (childrenCurr.isEmpty()) {
-            extras.put("hasChildren", "false");
-        } else {
+        if (childrenCurr.size() > 0) {
             extras.put("hasChildren", "true");
+        } else {
+            extras.put("hasChildren", "false");
         }
         extras.put("id", authorityCurr);
         return extras;
@@ -402,7 +386,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private List<String> getChildren(Node node) {
-        List<String> children = new ArrayList<>();
+        List<String> children = new ArrayList<String>();
         NodeList childNodes = node.getChildNodes();
         for (int ci = 0; ci < childNodes.getLength(); ci++) {
             Node firstChild = childNodes.item(ci);
@@ -425,7 +409,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     private boolean isSelectable(Node node) {
         Node selectableAttr = node.getAttributes().getNamedItem("selectable");
         if (null != selectableAttr) {
-            return Boolean.parseBoolean(selectableAttr.getNodeValue());
+            return Boolean.valueOf(selectableAttr.getNodeValue());
         } else { // Default is true
             return true;
         }
@@ -452,7 +436,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private Choices getChoicesByXpath(String xpathExpression, int start, int limit) {
-        List<Choice> choices = new ArrayList<>();
+        List<Choice> choices = new ArrayList<Choice>();
         XPath xpath = XPathFactory.newInstance().newXPath();
         try {
             Node parentNode = (Node) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODE);

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

@@ -14,7 +14,7 @@ package org.dspace.content.authority;
 public class SampleAuthority implements ChoiceAuthority {
     private String pluginInstanceName;
 
-    protected static String[] values = {
+    protected static String values[] = {
         "sun",
         "mon",
         "tue",
@@ -24,7 +24,7 @@ public class SampleAuthority implements ChoiceAuthority {
         "sat"
     };
 
-    protected static String[] labels = {
+    protected static String labels[] = {
         "Sunday",
         "Monday",
         "Tuesday",
@@ -37,7 +37,7 @@ public class SampleAuthority implements ChoiceAuthority {
     @Override
     public Choices getMatches(String query, int start, int limit, String locale) {
         int dflt = -1;
-        Choice[] v = new Choice[values.length];
+        Choice v[] = new Choice[values.length];
         for (int i = 0; i < values.length; ++i) {
             v[i] = new Choice(String.valueOf(i), values[i], labels[i]);
             if (values[i].equalsIgnoreCase(query)) {
@@ -51,7 +51,7 @@ public class SampleAuthority implements ChoiceAuthority {
     public Choices getBestMatch(String text, String locale) {
         for (int i = 0; i < values.length; ++i) {
             if (text.equalsIgnoreCase(values[i])) {
-                Choice[] v = new Choice[1];
+                Choice v[] = new Choice[1];
                 v[0] = new Choice(String.valueOf(i), values[i], labels[i]);
                 return new Choices(v, 0, v.length, Choices.CF_UNCERTAIN, false, 0);
             }

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

@@ -46,7 +46,7 @@ public class AIPDIMCrosswalk
      */
     @Override
     public Namespace[] getNamespaces() {
-        Namespace[] result = new Namespace[1];
+        Namespace result[] = new Namespace[1];
         result[0] = XSLTCrosswalk.DIM_NS;
         return result;
     }

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

@@ -98,7 +98,7 @@ public class AIPTechMDCrosswalk implements IngestionCrosswalk, DisseminationCros
      */
     @Override
     public Namespace[] getNamespaces() {
-        Namespace[] result = new Namespace[1];
+        Namespace result[] = new Namespace[1];
         result[0] = XSLTCrosswalk.DIM_NS;
         return result;
     }

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

@@ -45,7 +45,7 @@ public class DIMDisseminationCrosswalk
 
     protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
-    private static final Namespace[] namespaces = {DIM_NS};
+    private static final Namespace namespaces[] = {DIM_NS};
 
     @Override
     public Namespace[] getNamespaces() {

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

@@ -63,7 +63,7 @@ public class METSDisseminationCrosswalk
     private static final Namespace METS_NS = Namespace
         .getNamespace("mets", "http://www.loc.gov/METS/");
 
-    private static final Namespace[] namespaces = {METS_NS, MODS_NS, XLINK_NS};
+    private static final Namespace namespaces[] = {METS_NS, MODS_NS, XLINK_NS};
 
     /**
      * URL of METS XML Schema

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

@@ -70,7 +70,7 @@ public class METSRightsCrosswalk
     private String schemaLocation =
         METSRights_NS.getURI() + " http://cosimo.stanford.edu/sdr/metsrights.xsd";
 
-    private static final Namespace[] namespaces = {METSRights_NS};
+    private static final Namespace namespaces[] = {METSRights_NS};
 
     private static final Map<Integer, String> otherTypesMapping = new HashMap<Integer, String>();
 

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

@@ -109,7 +109,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
      * Fill in the plugin alias table from DSpace configuration entries
      * for configuration files for flavors of MODS crosswalk:
      */
-    private static String[] aliases = null;
+    private static String aliases[] = null;
 
     static {
         List<String> aliasList = new ArrayList<>();
@@ -117,11 +117,11 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
         for (String key : keys) {
             aliasList.add(key.substring(CONFIG_PREFIX.length()));
         }
-        aliases = aliasList.toArray(new String[0]);
+        aliases = (String[]) aliasList.toArray(new String[aliasList.size()]);
     }
 
     public static String[] getPluginNames() {
-        return ArrayUtils.clone(aliases);
+        return (String[]) ArrayUtils.clone(aliases);
     }
 
     /**
@@ -133,7 +133,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
     private static final Namespace XLINK_NS =
         Namespace.getNamespace("xlink", "http://www.w3.org/1999/xlink");
 
-    private static final Namespace[] namespaces = {MODS_NS, XLINK_NS};
+    private static final Namespace namespaces[] = {MODS_NS, XLINK_NS};
 
     /**
      * URL of MODS XML Schema
@@ -259,7 +259,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
             while (pe.hasMoreElements()) {
                 String qdc = pe.nextElement();
                 String val = modsConfig.getProperty(qdc);
-                String[] pair = val.split("\\s+\\|\\s+", 2);
+                String pair[] = val.split("\\s+\\|\\s+", 2);
                 if (pair.length < 2) {
                     log.warn("Illegal MODS mapping in " + propsFile.toString() + ", line = " +
                                  qdc + " = " + val);

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

@@ -65,7 +65,7 @@ public class OREDisseminationCrosswalk
                                                                                      .getConfigurationService();
 
 
-    private static final Namespace[] namespaces = {ATOM_NS, ORE_NS, ORE_ATOM, RDF_NS, DCTERMS_NS, DS_NS};
+    private static final Namespace namespaces[] = {ATOM_NS, ORE_NS, ORE_ATOM, RDF_NS, DCTERMS_NS, DS_NS};
 
 
     @Override
@@ -331,14 +331,14 @@ public class OREDisseminationCrosswalk
      * @param sourceString source unescaped string
      */
     private String encodeForURL(String sourceString) {
-        Character[] lowalpha = {'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i',
+        Character lowalpha[] = {'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i',
             'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r',
             's', 't', 'u', 'v', 'w', 'x', 'y', 'z'};
-        Character[] upalpha = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
+        Character upalpha[] = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
             'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
             'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'};
-        Character[] digit = {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'};
-        Character[] mark = {'-', '_', '.', '!', '~', '*', '\'', '/', '(', ')'};
+        Character digit[] = {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'};
+        Character mark[] = {'-', '_', '.', '!', '~', '*', '\'', '/', '(', ')'};
 
         // reserved
         //Character reserved[] = {';' , '/' , '?' , ':' , '@' , '&' , '=' , '+' , '$' , ',' ,'%', '#'};

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

@@ -220,17 +220,17 @@ public class OREIngestionCrosswalk
      * @param sourceString source unescaped string
      */
     private String encodeForURL(String sourceString) {
-        Character[] lowalpha = {'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i',
+        Character lowalpha[] = {'a', 'b', 'c', 'd', 'e', 'f', 'g', 'h', 'i',
             'j', 'k', 'l', 'm', 'n', 'o', 'p', 'q', 'r',
             's', 't', 'u', 'v', 'w', 'x', 'y', 'z'};
-        Character[] upalpha = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
+        Character upalpha[] = {'A', 'B', 'C', 'D', 'E', 'F', 'G', 'H', 'I',
             'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R',
             'S', 'T', 'U', 'V', 'W', 'X', 'Y', 'Z'};
-        Character[] digit = {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'};
-        Character[] mark = {'-', '_', '.', '!', '~', '*', '\'', '(', ')'};
+        Character digit[] = {'0', '1', '2', '3', '4', '5', '6', '7', '8', '9'};
+        Character mark[] = {'-', '_', '.', '!', '~', '*', '\'', '(', ')'};
 
         // reserved
-        Character[] reserved = {';', '/', '?', ':', '@', '&', '=', '+', '$', ',', '%', '#'};
+        Character reserved[] = {';', '/', '?', ':', '@', '&', '=', '+', '$', ',', '%', '#'};
 
         Set<Character> URLcharsSet = new HashSet<Character>();
         URLcharsSet.addAll(Arrays.asList(lowalpha));

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

@@ -20,7 +20,9 @@ import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Bitstream;
 import org.dspace.content.BitstreamFormat;
+import org.dspace.content.Bundle;
 import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.content.service.BitstreamService;
@@ -56,7 +58,7 @@ public class PREMISCrosswalk
     private final String schemaLocation =
         PREMIS_NS.getURI() + " http://www.loc.gov/standards/premis/PREMIS-v1-0.xsd";
 
-    private static final Namespace[] namespaces = {PREMIS_NS};
+    private static final Namespace namespaces[] = {PREMIS_NS};
 
     protected BitstreamService bitstreamService
             = ContentServiceFactory.getInstance().getBitstreamService();
@@ -222,17 +224,29 @@ public class PREMISCrosswalk
         //  c. made-up name based on sequence ID and extension.
         String sid = String.valueOf(bitstream.getSequenceID());
         String baseUrl = configurationService.getProperty("dspace.ui.url");
+        String handle = null;
+        // get handle of parent Item of this bitstream, if there is one:
+        List<Bundle> bn = bitstream.getBundles();
+        if (bn.size() > 0) {
+            List<Item> bi = bn.get(0).getItems();
+            if (bi.size() > 0) {
+                handle = bi.get(0).getHandle();
+            }
+        }
         // get or make up name for bitstream:
         String bsName = bitstream.getName();
         if (bsName == null) {
             List<String> ext = bitstream.getFormat(context).getExtensions();
             bsName = "bitstream_" + sid + (ext.size() > 0 ? ext.get(0) : "");
         }
-        if (baseUrl != null) {
+        if (handle != null && baseUrl != null) {
             oiv.setText(baseUrl
-                + "/bitstreams/"
-                + bitstream.getID()
-                + "/download");
+                            + "/bitstream/"
+                            + URLEncoder.encode(handle, "UTF-8")
+                            + "/"
+                            + sid
+                            + "/"
+                            + URLEncoder.encode(bsName, "UTF-8"));
         } else {
             oiv.setText(URLEncoder.encode(bsName, "UTF-8"));
         }

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

@@ -109,7 +109,7 @@ public class QDCCrosswalk extends SelfNamedPlugin
     private final Map<String, String> element2qdc = new HashMap<>();
 
     // the XML namespaces from config file for this name.
-    private Namespace[] namespaces = null;
+    private Namespace namespaces[] = null;
 
     private static final Namespace DCTERMS_NS =
         Namespace.getNamespace("dcterms", "http://purl.org/dc/terms/");
@@ -139,7 +139,7 @@ public class QDCCrosswalk extends SelfNamedPlugin
      * Fill in the plugin-name table from DSpace configuration entries
      * for configuration files for flavors of QDC crosswalk:
      */
-    private static String[] aliases = null;
+    private static String aliases[] = null;
 
     static {
         initStatic();
@@ -433,7 +433,7 @@ public class QDCCrosswalk extends SelfNamedPlugin
             if ("qualifieddc".equals(me.getName())) {
                 ingest(context, dso, me.getChildren(), createMissingMetadataFields);
             } else if (element2qdc.containsKey(key)) {
-                String[] qdc = (element2qdc.get(key)).split("\\.");
+                String qdc[] = (element2qdc.get(key)).split("\\.");
 
                 MetadataField metadataField;
                 if (qdc.length == 3) {

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

@@ -73,7 +73,7 @@ public class RoleCrosswalk
      */
     @Override
     public Namespace[] getNamespaces() {
-        Namespace[] result = new Namespace[1];
+        Namespace result[] = new Namespace[1];
         result[0] = RoleDisseminator.DSROLES_NS;
         return result;
     }

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

@@ -53,10 +53,10 @@ public class SimpleDCDisseminationCrosswalk extends SelfNamedPlugin
     private static final String schemaLocation =
         DC_NS.getURI() + " " + DC_XSD;
 
-    private static final Namespace[] namespaces =
+    private static final Namespace namespaces[] =
         {DC_NS, XSI_NS};
 
-    private static final String[] aliases = {"SimpleDC", "DC"};
+    private static final String aliases[] = {"SimpleDC", "DC"};
     protected final ItemService itemService = ContentServiceFactory.getInstance().getItemService();
 
 

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

@@ -106,7 +106,7 @@ public class XSLTDisseminationCrosswalk
     protected static final ConfigurationService configurationService
             = DSpaceServicesFactory.getInstance().getConfigurationService();
 
-    private static final String[] aliases = makeAliases(DIRECTION);
+    private static final String aliases[] = makeAliases(DIRECTION);
 
     public static String[] getPluginNames() {
         return (String[]) ArrayUtils.clone(aliases);
@@ -116,7 +116,7 @@ public class XSLTDisseminationCrosswalk
     // until there's an instance, so do it in constructor.
     private String schemaLocation = null;
 
-    private Namespace[] namespaces = null;
+    private Namespace namespaces[] = null;
 
     private boolean preferList = false;
 

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

@@ -63,7 +63,7 @@ public class XSLTIngestionCrosswalk
 
     private static final String DIRECTION = "submission";
 
-    private static final String[] aliases = makeAliases(DIRECTION);
+    private static final String aliases[] = makeAliases(DIRECTION);
 
     private static final CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
     private static final CollectionService collectionService = ContentServiceFactory.getInstance()

dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java

@@ -178,7 +178,7 @@ public class BitstreamDAOImpl extends AbstractHibernateDSODAO<Bitstream> impleme
     @Override
     public int countWithNoPolicy(Context context) throws SQLException {
         Query query = createQuery(context,
-                                  "SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit not in" +
+                                  "SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit.id not in" +
                                       " (select res.dSpaceObject from ResourcePolicy res where res.resourceTypeId = " +
                                       ":typeId )");
         query.setParameter("typeId", Constants.BITSTREAM);

dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java

@@ -12,7 +12,6 @@ import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
-import java.util.UUID;
 
 import jakarta.persistence.Query;
 import jakarta.persistence.criteria.CriteriaBuilder;
@@ -20,7 +19,6 @@ import jakarta.persistence.criteria.CriteriaQuery;
 import jakarta.persistence.criteria.Join;
 import jakarta.persistence.criteria.Predicate;
 import jakarta.persistence.criteria.Root;
-import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.authorize.ResourcePolicy_;
 import org.dspace.content.Collection;
@@ -42,11 +40,6 @@ import org.dspace.eperson.Group;
  * @author kevinvandevelde at atmire.com
  */
 public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> implements CollectionDAO {
-    /**
-     * log4j logger
-     */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CollectionDAOImpl.class);
-
     protected CollectionDAOImpl() {
         super();
     }
@@ -166,7 +159,7 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
 
     @Override
     public List<Collection> findCollectionsWithSubscribers(Context context) throws SQLException {
-        return list(createQuery(context, "SELECT DISTINCT c FROM Collection c JOIN Subscription s ON c = " +
+        return list(createQuery(context, "SELECT DISTINCT c FROM Collection c JOIN Subscription s ON c.id = " +
                 "s.dSpaceObject"));
     }
 
@@ -179,25 +172,14 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
     @SuppressWarnings("unchecked")
     public List<Map.Entry<Collection, Long>> getCollectionsWithBitstreamSizesTotal(Context context)
         throws SQLException {
-        String q = "select col.id, sum(bit.sizeBytes) as totalBytes from Item i join i.collections col " +
-            "join i.bundles bun join bun.bitstreams bit group by col.id";
+        String q = "select col as collection, sum(bit.sizeBytes) as totalBytes from Item i join i.collections col " +
+            "join i.bundles bun join bun.bitstreams bit group by col";
         Query query = createQuery(context, q);
 
-        CriteriaBuilder criteriaBuilder = getCriteriaBuilder(context);
-
         List<Object[]> list = query.getResultList();
         List<Map.Entry<Collection, Long>> returnList = new ArrayList<>(list.size());
         for (Object[] o : list) {
-            CriteriaQuery<Collection> criteriaQuery = criteriaBuilder.createQuery(Collection.class);
-            Root<Collection> collectionRoot = criteriaQuery.from(Collection.class);
-            criteriaQuery.select(collectionRoot).where(criteriaBuilder.equal(collectionRoot.get("id"), (UUID) o[0]));
-            Query collectionQuery = createQuery(context, criteriaQuery);
-            Collection collection = (Collection) collectionQuery.getSingleResult();
-            if (collection != null) {
-                returnList.add(new AbstractMap.SimpleEntry<>(collection, (Long) o[1]));
-            } else {
-                log.warn("Unable to find Collection with UUID: {}", o[0]);
-            }
+            returnList.add(new AbstractMap.SimpleEntry<>((Collection) o[0], (Long) o[1]));
         }
         return returnList;
     }

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

@@ -560,7 +560,7 @@ public abstract class AbstractMETSDisseminator
             //create our metadata element (dmdSec, techMd, sourceMd, rightsMD etc.)
             MdSec mdSec = (MdSec) mdSecClass.getDeclaredConstructor().newInstance();
             mdSec.setID(gensym(mdSec.getLocalName()));
-            String[] parts = typeSpec.split(":", 2);
+            String parts[] = typeSpec.split(":", 2);
             String xwalkName;
             String metsName;
 
@@ -685,7 +685,7 @@ public abstract class AbstractMETSDisseminator
     // add either a techMd or sourceMd element to amdSec.
     // mdSecClass determines which type.
     // mdTypes[] is array of "[metsName:]PluginName" strings, maybe empty.
-    protected void addToAmdSec(AmdSec fAmdSec, String[] mdTypes, Class mdSecClass,
+    protected void addToAmdSec(AmdSec fAmdSec, String mdTypes[], Class mdSecClass,
                                Context context, DSpaceObject dso,
                                PackageParameters params,
                                MdStreamCache extraStreams)
@@ -708,10 +708,10 @@ public abstract class AbstractMETSDisseminator
             IOException, AuthorizeException, NoSuchMethodException,
             InstantiationException, IllegalAccessException, IllegalArgumentException,
             IllegalArgumentException, InvocationTargetException {
-        String[] techMdTypes = getTechMdTypes(context, dso, params);
-        String[] rightsMdTypes = getRightsMdTypes(context, dso, params);
-        String[] sourceMdTypes = getSourceMdTypes(context, dso, params);
-        String[] digiprovMdTypes = getDigiprovMdTypes(context, dso, params);
+        String techMdTypes[] = getTechMdTypes(context, dso, params);
+        String rightsMdTypes[] = getRightsMdTypes(context, dso, params);
+        String sourceMdTypes[] = getSourceMdTypes(context, dso, params);
+        String digiprovMdTypes[] = getDigiprovMdTypes(context, dso, params);
 
         // only bother if there are any sections to add
         if ((techMdTypes.length + sourceMdTypes.length +
@@ -794,10 +794,10 @@ public abstract class AbstractMETSDisseminator
         // add DMD sections
         // Each type element MAY be either just a MODS-and-crosswalk name, OR
         // a combination "MODS-name:crosswalk-name" (e.g. "DC:qDC").
-        String[] dmdTypes = getDmdTypes(context, dso, params);
+        String dmdTypes[] = getDmdTypes(context, dso, params);
 
         // record of ID of each dmdsec to make DMDID in structmap.
-        String[] dmdId = new String[dmdTypes.length];
+        String dmdId[] = new String[dmdTypes.length];
         for (int i = 0; i < dmdTypes.length; ++i) {
             MdSec dmdSec = makeMdSec(context, dso, DmdSec.class, dmdTypes[i], params, extraStreams);
             if (dmdSec != null) {
@@ -981,7 +981,7 @@ public abstract class AbstractMETSDisseminator
             // add metadata & info for Template Item, if exists
             Item templateItem = collection.getTemplateItem();
             if (templateItem != null) {
-                String[] templateDmdId = new String[dmdTypes.length];
+                String templateDmdId[] = new String[dmdTypes.length];
                 // index where we should add the first template item <dmdSec>.
                 // Index = number of <dmdSecs> already added + number of <metsHdr> = # of dmdSecs + 1
                 // (Note: in order to be a valid METS file, all dmdSecs must be before the 1st amdSec)
@@ -1239,8 +1239,8 @@ public abstract class AbstractMETSDisseminator
         try {
             // add crosswalk's namespaces and schemaLocation to this element:
             String raw = xwalk.getSchemaLocation();
-            String[] sloc = raw == null ? null : raw.split("\\s+");
-            Namespace[] ns = xwalk.getNamespaces();
+            String sloc[] = raw == null ? null : raw.split("\\s+");
+            Namespace ns[] = xwalk.getNamespaces();
             for (int i = 0; i < ns.length; ++i) {
                 String uri = ns[i].getURI();
                 if (sloc != null && sloc.length > 1 && uri.equals(sloc[0])) {

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

@@ -498,11 +498,8 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester {
                 // Finish creating the item. This actually assigns the handle,
                 // and will either install item immediately or start a workflow, based on params
                 PackageUtils.finishCreateItem(context, wsi, handle, params);
-            } else {
-                // We should have a workspace item during ingest, so this code is only here for safety.
-                // Update the object to make sure all changes are committed
-                PackageUtils.updateDSpaceObject(context, dso);
             }
+
         } else if (type == Constants.COLLECTION || type == Constants.COMMUNITY) {
             // Add logo if one is referenced from manifest
             addContainerLogo(context, dso, manifest, pkgFile, params);
@@ -516,9 +513,6 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester {
             // (this allows subclasses to do some final validation / changes as
             // necessary)
             finishObject(context, dso, params);
-
-            // Update the object to make sure all changes are committed
-            PackageUtils.updateDSpaceObject(context, dso);
         } else if (type == Constants.SITE) {
             // Do nothing by default -- Crosswalks will handle anything necessary to ingest at Site-level
 
@@ -526,15 +520,18 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester {
             // (this allows subclasses to do some final validation / changes as
             // necessary)
             finishObject(context, dso, params);
-
-            // Update the object to make sure all changes are committed
-            PackageUtils.updateDSpaceObject(context, dso);
         } else {
             throw new PackageValidationException(
                 "Unknown DSpace Object type in package, type="
                     + String.valueOf(type));
         }
 
+        // -- Step 6 --
+        // Finish things up!
+
+        // Update the object to make sure all changes are committed
+        PackageUtils.updateDSpaceObject(context, dso);
+
         return dso;
     }
 
@@ -1422,7 +1419,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester {
      * @throws AuthorizeException         if authorization error
      */
     public abstract void crosswalkObjectDmd(Context context, DSpaceObject dso,
-                                            METSManifest manifest, MdrefManager callback, Element[] dmds,
+                                            METSManifest manifest, MdrefManager callback, Element dmds[],
                                             PackageParameters params) throws CrosswalkException,
         PackageValidationException, AuthorizeException, SQLException,
         IOException;

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

@@ -109,7 +109,7 @@ public class DSpaceAIPIngester
     public void crosswalkObjectDmd(Context context, DSpaceObject dso,
                                    METSManifest manifest,
                                    MdrefManager callback,
-                                   Element[] dmds, PackageParameters params)
+                                   Element dmds[], PackageParameters params)
         throws CrosswalkException, PackageValidationException,
         AuthorizeException, SQLException, IOException {
         int found = -1;

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

@@ -138,7 +138,7 @@ public class DSpaceMETSDisseminator
 
         // XXX FIXME maybe let dmd choices be configured in DSpace config?
 
-        String[] result = null;
+        String result[] = null;
         if (params != null) {
             result = params.getProperties("dmd");
         }
@@ -163,7 +163,7 @@ public class DSpaceMETSDisseminator
     public String[] getTechMdTypes(Context context, DSpaceObject dso, PackageParameters params)
         throws SQLException, IOException, AuthorizeException {
         if (dso.getType() == Constants.BITSTREAM) {
-            String[] result = new String[1];
+            String result[] = new String[1];
             result[0] = "PREMIS";
             return result;
         } else {

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

@@ -81,7 +81,7 @@ public class DSpaceMETSIngester
     public void crosswalkObjectDmd(Context context, DSpaceObject dso,
                                    METSManifest manifest,
                                    MdrefManager callback,
-                                   Element[] dmds, PackageParameters params)
+                                   Element dmds[], PackageParameters params)
         throws CrosswalkException, PackageValidationException,
         AuthorizeException, SQLException, IOException {
         int found = -1;
@@ -185,7 +185,7 @@ public class DSpaceMETSIngester
         PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
 
         // get the MediaFilter that would create this bundle:
-        String[] mfNames = pluginService.getAllPluginNames(MediaFilter.class);
+        String mfNames[] = pluginService.getAllPluginNames(MediaFilter.class);
 
         for (int i = 0; i < mfNames.length; ++i) {
             MediaFilter mf = (MediaFilter) pluginService.getNamedPlugin(MediaFilter.class, mfNames[i]);

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

@@ -210,7 +210,7 @@ public class METSManifest {
             //  mets.xsd.dc =  http://purl.org/dc/elements/1.1/ dc.xsd
             // (filename is relative to {dspace_dir}/config/schemas/)
             String spec = configurationService.getProperty(key);
-            String[] val = spec.trim().split("\\s+");
+            String val[] = spec.trim().split("\\s+");
             if (val.length == 2) {
                 File xsd = new File(xsdPath1, val[1]);
                 if (!xsd.exists()) {
@@ -221,7 +221,7 @@ public class METSManifest {
                 } else {
                     try {
                         String u = xsd.toURI().toURL().toString();
-                        if (!result.isEmpty()) {
+                        if (result.length() > 0) {
                             result.append(" ");
                         }
                         result.append(val[0]).append(" ").append(u);
@@ -651,7 +651,7 @@ public class METSManifest {
 
                         String mimeType = mdWrap.getAttributeValue("MIMETYPE");
                         if (mimeType != null && mimeType.equalsIgnoreCase("text/xml")) {
-                            byte[] value = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
+                            byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                             Document mdd = parser.build(new ByteArrayInputStream(value));
                             List<Element> result = new ArrayList<>(1);
                             result.add(mdd.getRootElement());
@@ -719,7 +719,7 @@ public class METSManifest {
                     throw new MetadataValidationException(
                         "Invalid METS Manifest: mdWrap element with neither xmlData nor binData child.");
                 } else {
-                    byte[] value = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
+                    byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                     return new ByteArrayInputStream(value);
                 }
             } else {
@@ -950,8 +950,8 @@ public class METSManifest {
     public Element[] getDmdElements(String dmdList)
         throws MetadataValidationException {
         if (dmdList != null && !dmdList.isEmpty()) {
-            String[] dmdID = dmdList.split("\\s+");
-            Element[] result = new Element[dmdID.length];
+            String dmdID[] = dmdList.split("\\s+");
+            Element result[] = new Element[dmdID.length];
 
             for (int i = 0; i < dmdID.length; ++i) {
                 result[i] = getElementByXPath("mets:dmdSec[@ID=\"" + dmdID[i] + "\"]", false);
@@ -980,7 +980,7 @@ public class METSManifest {
             }
             return new Element[0];
         }
-        String[] amdID = amds.split("\\s+");
+        String amdID[] = amds.split("\\s+");
         List<Element> resultList = new ArrayList<>();
         for (int i = 0; i < amdID.length; ++i) {
             List rmds = getElementByXPath("mets:amdSec[@ID=\"" + amdID[i] + "\"]", false).
@@ -1167,7 +1167,7 @@ public class METSManifest {
                                     "Invalid METS Manifest: mdWrap element for streaming crosswalk without binData " +
                                         "child.");
                             } else {
-                                byte[] value = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
+                                byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                                 sxwalk.ingest(context, dso,
                                               new ByteArrayInputStream(value),
                                               mdWrap.getAttributeValue("MIMETYPE"));
@@ -1228,7 +1228,7 @@ public class METSManifest {
             log.warn("Got no bitstream ADMID, file@ID=" + fileId);
             return;
         }
-        String[] amdID = amds.split("\\s+");
+        String amdID[] = amds.split("\\s+");
         for (int i = 0; i < amdID.length; ++i) {
             Element amdSec = getElementByXPath("mets:amdSec[@ID=\"" + amdID[i] + "\"]", false);
             for (Iterator ti = amdSec.getChildren("techMD", metsNS).iterator(); ti.hasNext(); ) {
@@ -1262,7 +1262,7 @@ public class METSManifest {
             log.warn("Got no bitstream ADMID, file@ID=" + fileId);
             return;
         }
-        String[] amdID = amds.split("\\s+");
+        String amdID[] = amds.split("\\s+");
         for (int i = 0; i < amdID.length; ++i) {
             Element amdSec = getElementByXPath("mets:amdSec[@ID=\"" + amdID[i] + "\"]", false);
             for (Iterator ti = amdSec.getChildren("techMD", metsNS).iterator(); ti.hasNext(); ) {

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

@@ -19,11 +19,11 @@ import java.util.List;
 
 import org.apache.commons.lang3.ArrayUtils;
 import org.apache.logging.log4j.Logger;
-import org.apache.pdfbox.Loader;
 import org.apache.pdfbox.cos.COSDocument;
 import org.apache.pdfbox.io.MemoryUsageSetting;
-import org.apache.pdfbox.io.RandomAccessReadBuffer;
+import org.apache.pdfbox.io.RandomAccessBufferedFileInputStream;
 import org.apache.pdfbox.io.ScratchFile;
+import org.apache.pdfbox.pdfparser.PDFParser;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDDocumentInformation;
 import org.dspace.authorize.AuthorizeException;
@@ -78,10 +78,10 @@ public class PDFPackager
 
     protected static final String BITSTREAM_FORMAT_NAME = "Adobe PDF";
 
-    protected static String[] aliases = {"PDF", "Adobe PDF", "pdf", "application/pdf"};
+    protected static String aliases[] = {"PDF", "Adobe PDF", "pdf", "application/pdf"};
 
     public static String[] getPluginNames() {
-        return ArrayUtils.clone(aliases);
+        return (String[]) ArrayUtils.clone(aliases);
     }
 
     protected final BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
@@ -331,24 +331,19 @@ public class PDFPackager
         COSDocument cos = null;
 
         try {
-            PDDocument document = null;
-
+            ScratchFile scratchFile = null;
             try {
-                // Use up to 80% of JVM free memory and fall back to a temp file (unlimited size)
-                long useRAM = Runtime.getRuntime().freeMemory() * 80 / 100;
-                document = Loader.loadPDF(
-                        new RandomAccessReadBuffer(metadata),
-                        () -> new ScratchFile(MemoryUsageSetting.setupMixed(useRAM)));
+                long useRAM = Runtime.getRuntime().freeMemory() * 80 / 100; // use up to 80% of JVM free memory
+                scratchFile = new ScratchFile(
+                    MemoryUsageSetting.setupMixed(useRAM)); // then fallback to temp file (unlimited size)
             } catch (IOException ioe) {
                 log.warn("Error initializing scratch file: " + ioe.getMessage());
             }
 
-            // sanity check: loaded PDF document must not be null.
-            if (document == null) {
-                throw new MetadataValidationException("The provided stream could not be parsed into a PDF document.");
-            }
+            PDFParser parser = new PDFParser(new RandomAccessBufferedFileInputStream(metadata), scratchFile);
+            parser.parse();
+            cos = parser.getDocument();
 
-            cos = document.getDocument();
             // sanity check: PDFBox breaks on encrypted documents, so give up.
             if (cos.getEncryptionDictionary() != null) {
                 throw new MetadataValidationException("This packager cannot accept an encrypted PDF document.");

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

@@ -52,7 +52,7 @@ public class PackageParameters extends Properties {
         Enumeration pe = request.getParameterNames();
         while (pe.hasMoreElements()) {
             String name = (String) pe.nextElement();
-            String[] v = request.getParameterValues(name);
+            String v[] = request.getParameterValues(name);
             if (v.length == 0) {
                 result.setProperty(name, "");
             } else if (v.length == 1) {

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

@@ -72,7 +72,7 @@ public class PackageUtils {
     // Map of metadata elements for Communities and Collections
     // Format is alternating key/value in a straight array; use this
     // to initialize hash tables that convert to and from.
-    protected static final String[] ccMetadataMap = {
+    protected static final String ccMetadataMap[] = {
         // getMetadata()  ->  DC element.term
         "name",                    "dc.title",
         "introductory_text",       "dc.description",

dspace-api/src/main/java/org/dspace/content/service/BundleService.java

@@ -143,7 +143,7 @@ public interface BundleService extends DSpaceObjectService<Bundle>, DSpaceObject
      * @throws SQLException       when an SQL error has occurred (querying DSpace)
      * @throws AuthorizeException If the user can't make the changes
      */
-    public void setOrder(Context context, Bundle bundle, UUID[] bitstreamIds) throws AuthorizeException, SQLException;
+    public void setOrder(Context context, Bundle bundle, UUID bitstreamIds[]) throws AuthorizeException, SQLException;
 
     int countTotal(Context context) throws SQLException;
 }

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

@@ -468,9 +468,6 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
         for (Map.Entry<String, Object> entry : equals.entrySet()) {
             criteria.where(criteriaBuilder.equal(root.get(entry.getKey()), entry.getValue()));
         }
-
-        criteria.orderBy(criteriaBuilder.asc(root.get("id")));
-
         return executeCriteriaQuery(context, criteria, cacheable, maxResults, offset);
     }
 

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

@@ -192,7 +192,7 @@ public class LegacyPluginServiceImpl implements PluginService {
             classname = sequenceConfig.get(iname);
         }
 
-        Object[] result = (Object[]) Array.newInstance(interfaceClass, classname.length);
+        Object result[] = (Object[]) Array.newInstance(interfaceClass, classname.length);
         for (int i = 0; i < classname.length; ++i) {
             log.debug("Adding Sequence plugin for interface= " + iname + ", class=" + classname[i]);
             result[i] = getAnonymousPlugin(classname[i]);
@@ -277,7 +277,7 @@ public class LegacyPluginServiceImpl implements PluginService {
                 for (String classname : selfNamedVals) {
                     try {
                         Class pluginClass = Class.forName(classname, true, loader);
-                        String[] names = (String[]) pluginClass.getMethod("getPluginNames").
+                        String names[] = (String[]) pluginClass.getMethod("getPluginNames").
                             invoke(null);
                         if (names == null || names.length == 0) {
                             log.error(
@@ -302,7 +302,7 @@ public class LegacyPluginServiceImpl implements PluginService {
     }
 
     // add info for a named plugin to cache, under all its names.
-    private int installNamedConfigs(String iname, String classname, String[] names)
+    private int installNamedConfigs(String iname, String classname, String names[])
         throws ClassNotFoundException {
         int found = 0;
         for (int i = 0; i < names.length; ++i) {

dspace-api/src/main/java/org/dspace/disseminate/CitationDocumentServiceImpl.java

@@ -20,8 +20,6 @@ import java.util.Set;
 import org.apache.commons.lang3.tuple.Pair;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.apache.pdfbox.Loader;
-import org.apache.pdfbox.io.RandomAccessReadBuffer;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.apache.pdfbox.pdmodel.PDPage;
 import org.dspace.authorize.AuthorizeException;
@@ -126,7 +124,7 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
         //Load enabled collections
         String[] citationEnabledCollections = configurationService
                 .getArrayProperty("citation-page.enabled_collections");
-        citationEnabledCollectionsList = new ArrayList<String>(Arrays.asList(citationEnabledCollections));
+        citationEnabledCollectionsList = Arrays.asList(citationEnabledCollections);
 
         //Load enabled communities, and add to collection-list
         String[] citationEnabledCommunities = configurationService
@@ -266,7 +264,7 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
 
     private PDDocument loadDocumentFromDB(Context context, Bitstream bitstream) {
         try (var inputStream = bitstreamService.retrieve(context, bitstream)) {
-            return Loader.loadPDF(new RandomAccessReadBuffer(inputStream));
+            return PDDocument.load(inputStream);
         } catch (IOException | SQLException | AuthorizeException e) {
             throw new RuntimeException(e);
         }
@@ -309,4 +307,4 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
             }
         }
     }
-}
+}

dspace-api/src/main/java/org/dspace/disseminate/PdfGenerator.java

@@ -15,7 +15,6 @@ import java.io.OutputStream;
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import org.apache.pdfbox.Loader;
 import org.apache.pdfbox.pdmodel.PDDocument;
 import org.thymeleaf.TemplateEngine;
 import org.thymeleaf.context.Context;
@@ -85,7 +84,7 @@ public class PdfGenerator {
     public PDDocument generate(String html) {
         try (var out = new ByteArrayOutputStream()) {
             generate(html, out);
-            return Loader.loadPDF(out.toByteArray());
+            return PDDocument.load(out.toByteArray());
         } catch (IOException e) {
             throw new RuntimeException(e);
         }

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

@@ -79,7 +79,7 @@ public class DayTableEmbargoSetter extends DefaultEmbargoSetter {
     private Properties getTermProperties() {
         Properties termProps = new Properties();
 
-        String[] terms = DSpaceServicesFactory.getInstance().getConfigurationService()
+        String terms[] = DSpaceServicesFactory.getInstance().getConfigurationService()
                                               .getArrayProperty("embargo.terms.days");
 
         if (terms != null) {

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

@@ -79,7 +79,7 @@ public class EmbargoCLITool {
      *
      * @param argv the command line arguments given
      */
-    public static void main(String[] argv) {
+    public static void main(String argv[]) {
         int status = 0;
 
         Options options = new Options();

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

@@ -199,19 +199,19 @@ public class EmbargoServiceImpl implements EmbargoService {
 
     // return the schema part of "schema.element.qualifier" metadata field spec
     protected String getSchemaOf(String field) {
-        String[] sa = field.split("\\.", 3);
+        String sa[] = field.split("\\.", 3);
         return sa[0];
     }
 
     // return the element part of "schema.element.qualifier" metadata field spec, if any
     protected String getElementOf(String field) {
-        String[] sa = field.split("\\.", 3);
+        String sa[] = field.split("\\.", 3);
         return sa.length > 1 ? sa[1] : null;
     }
 
     // return the qualifier part of "schema.element.qualifier" metadata field spec, if any
     protected String getQualifierOf(String field) {
-        String[] sa = field.split("\\.", 3);
+        String sa[] = field.split("\\.", 3);
         return sa.length > 2 ? sa[2] : null;
     }
 

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

@@ -366,7 +366,7 @@ public class EPerson extends CacheableDSpaceObject implements DSpaceObjectLegacy
 
     @Override
     public String getName() {
-        return this.getFullName();
+        return getEmail();
     }
 
     String getDigestAlgorithm() {

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

@@ -86,7 +86,7 @@ public class EPersonCLITool {
      * @throws AuthorizeException Exception indicating the current user of the context does not have permission
      *                            to perform a particular action.
      */
-    public static void main(String[] argv)
+    public static void main(String argv[])
         throws ParseException, SQLException, AuthorizeException {
         final OptionGroup VERBS = new OptionGroup();
         VERBS.addOption(VERB_ADD);

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

@@ -45,7 +45,7 @@ public class BasicDispatcher extends Dispatcher {
         if (log.isDebugEnabled()) {
             int n = 0;
             for (Iterator i = cp.getFilters().iterator(); i.hasNext(); ++n) {
-                int[] f = (int[]) i.next();
+                int f[] = (int[]) i.next();
                 log.debug("Adding Consumer=\"" + cp.getName() + "\", instance="
                               + cp.getConsumer().toString() + ", filter["
                               + String.valueOf(n) + "]=(ObjMask="

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

@@ -110,9 +110,9 @@ public class ConsumerProfile {
 
         // Each "filter" is <objectTypes> + <eventTypes> : ...
         filters = new ArrayList<>();
-        String[] part = filterString.trim().split(":");
+        String part[] = filterString.trim().split(":");
         for (int j = 0; j < part.length; ++j) {
-            String[] fpart = part[j].split("\\+");
+            String fpart[] = part[j].split("\\+");
             if (fpart.length != 2) {
                 log.error("Bad Filter clause in consumer stanza in Configuration entry for "
                               + CONSUMER_PREFIX
@@ -120,10 +120,10 @@ public class ConsumerProfile {
                               + ".consumers: "
                               + part[j]);
             } else {
-                int[] filter = new int[2];
+                int filter[] = new int[2];
                 filter[0] = 0;
                 filter[1] = 0;
-                String[] objectNames = fpart[0].split("\\|");
+                String objectNames[] = fpart[0].split("\\|");
                 for (int k = 0; k < objectNames.length; ++k) {
                     int ot = Event.parseObjectType(objectNames[k]);
                     if (ot == 0) {
@@ -135,7 +135,7 @@ public class ConsumerProfile {
                         filter[Event.SUBJECT_MASK] |= ot;
                     }
                 }
-                String[] eventNames = fpart[1].split("\\|");
+                String eventNames[] = fpart[1].split("\\|");
                 for (int k = 0; k < eventNames.length; ++k) {
                     int et = Event.parseEventType(eventNames[k]);
                     if (et == 0) {

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

@@ -80,7 +80,7 @@ public class Event implements Serializable {
     public static final int EVENT_MASK = 1; // mask of event type
 
     // XXX NOTE: keep this up to date with any changes to event (action) types.
-    protected static final String[] eventTypeText = {"CREATE", "MODIFY",
+    protected static final String eventTypeText[] = {"CREATE", "MODIFY",
         "MODIFY_METADATA", "ADD", "REMOVE", "DELETE", "INSTALL"};
 
     /** XXX NOTE: These constants must be kept synchronized * */
@@ -590,7 +590,7 @@ public class Event implements Serializable {
     public boolean pass(List<int[]> filters) {
         boolean result = false;
 
-        for (int[] filter : filters) {
+        for (int filter[] : filters) {
             if ((subjectType & filter[SUBJECT_MASK]) != 0 && (eventType & filter[EVENT_MASK]) != 0) {
                 result = true;
             }

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

@@ -172,10 +172,10 @@ public class EventServiceImpl implements EventService {
             if (dispClass != null) {
                 try {
                     // all this to call a constructor with an argument
-                    final Class[] argTypes = {String.class};
+                    final Class argTypes[] = {String.class};
                     Constructor dc = Class.forName(dispClass).getConstructor(
                         argTypes);
-                    Object[] args = new Object[1];
+                    Object args[] = new Object[1];
                     args[0] = dispatcherName;
                     dispatcher = (Dispatcher) dc.newInstance(args);
 

dspace-api/src/main/java/org/dspace/health/Report.java

@@ -80,7 +80,7 @@ public class Report {
     // create check list
     public static LinkedHashMap<String, Check> checks() {
         LinkedHashMap<String, Check> checks = new LinkedHashMap<>();
-        String[] check_names = DSpaceServicesFactory.getInstance().getConfigurationService()
+        String check_names[] = DSpaceServicesFactory.getInstance().getConfigurationService()
                                                     .getArrayProperty("healthcheck.checks");
         PluginService pluginService = CoreServiceFactory.getInstance().getPluginService();
         for (String check_name : check_names) {

dspace-api/src/main/java/org/dspace/health/UserCheck.java

@@ -50,26 +50,26 @@ public class UserCheck extends Check {
             info.put("Self registered", 0);
 
             for (EPerson e : epersons) {
-                if (e.getEmail() != null && !e.getEmail().isEmpty()) {
+                if (e.getEmail() != null && e.getEmail().length() > 0) {
                     info.put("Have email", info.get("Have email") + 1);
                 }
                 if (e.canLogIn()) {
                     info.put("Can log in (password)",
                              info.get("Can log in (password)") + 1);
                 }
-                if (e.getFirstName() != null && !e.getFirstName().isEmpty()) {
+                if (e.getFirstName() != null && e.getFirstName().length() > 0) {
                     info.put("Have 1st name", info.get("Have 1st name") + 1);
                 }
-                if (e.getLastName() != null && !e.getLastName().isEmpty()) {
+                if (e.getLastName() != null && e.getLastName().length() > 0) {
                     info.put("Have 2nd name", info.get("Have 2nd name") + 1);
                 }
-                if (e.getLanguage() != null && !e.getLanguage().isEmpty()) {
+                if (e.getLanguage() != null && e.getLanguage().length() > 0) {
                     info.put("Have lang", info.get("Have lang") + 1);
                 }
-                if (e.getNetid() != null && !e.getNetid().isEmpty()) {
+                if (e.getNetid() != null && e.getNetid().length() > 0) {
                     info.put("Have netid", info.get("Have netid") + 1);
                 }
-                if (e.getNetid() != null && !e.getNetid().isEmpty()) {
+                if (e.getNetid() != null && e.getNetid().length() > 0) {
                     info.put("Self registered", info.get("Self registered") + 1);
                 }
             }

dspace-api/src/main/java/org/dspace/importer/external/epo/service/EpoImportMetadataSourceServiceImpl.java

@@ -29,9 +29,9 @@ import org.apache.commons.collections.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpException;
 import org.apache.http.client.utils.URIBuilder;
-import org.apache.jena.ext.xerces.impl.dv.util.Base64;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.apache.xerces.impl.dv.util.Base64;
 import org.dspace.app.util.XMLUtils;
 import org.dspace.content.Item;
 import org.dspace.importer.external.datamodel.ImportRecord;

dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadataFieldConfig.java

@@ -116,7 +116,7 @@ public class MetadataFieldConfig {
      * @param full A string representing the schema.element.qualifier triplet
      */
     public MetadataFieldConfig(String full) {
-        String[] elements = full.split("\\.");
+        String elements[] = full.split("\\.");
         if (elements.length == 2) {
             this.schema = elements[0];
             this.element = elements[1];

dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/MetadatumDTO.java

@@ -105,13 +105,4 @@ public class MetadatumDTO {
     public void setValue(String value) {
         this.value = value;
     }
-
-    /**
-     * Return string representation of MetadatumDTO
-     * @return string representation of format "[schema].[element].[qualifier]=[value]"
-     */
-    @Override
-    public String toString() {
-        return schema + "." + element + "." + qualifier + "=" + value;
-    }
 }

dspace-api/src/main/java/org/dspace/importer/external/metadatamapping/contributor/ConditionalArrayElementAttributeProcessor.java

@@ -1,127 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.importer.external.metadatamapping.contributor;
-
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-
-import com.fasterxml.jackson.core.JsonProcessingException;
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
-/**
- * This Processor extracts values from a JSON array, but only when a condition
- * on another attribute is met. For example, to extract all values of
- * /names/value where /names/types contains "ror_display".
- *
- * Configurable via:
- *   pathToArray: e.g., /names
- *   elementAttribute: e.g., /value
- *   filterAttribute: e.g., /types
- *   requiredValueInFilter: e.g., ror_display
- *
- * Supports filtering when the filter attribute is either a JSON array or a single string.
- *
- * Example JSON:
- * {
- *   "items": [{
- *     "names": [
- *       { "types": ["label", "ror_display"], "value": "Instituto Federal do Piauí" },
- *       { "types": ["acronym"], "value": "IFPI" }
- *     ]
- *   }]
- * }
- * This processor can extract "Instituto Federal do Piauí" using proper configuration.
- *
- * Author: Jesiel (based on Mykhaylo Boychuk’s original processor)
- */
-public class ConditionalArrayElementAttributeProcessor implements JsonPathMetadataProcessor {
-
-    private static final Logger log = LogManager.getLogger();
-
-    private String pathToArray;
-    private String elementAttribute;
-    private String filterAttribute;
-    private String requiredValueInFilter;
-
-    @Override
-    public Collection<String> processMetadata(String json) {
-        JsonNode rootNode = convertStringJsonToJsonNode(json);
-        Collection<String> results = new ArrayList<>();
-
-        if (rootNode == null) {
-            return results;
-        }
-
-        Iterator<JsonNode> array = rootNode.at(pathToArray).iterator();
-        while (array.hasNext()) {
-            JsonNode element = array.next();
-            JsonNode filterNode = element.at(filterAttribute);
-
-            boolean match = false;
-
-            if (filterNode.isArray()) {
-                for (JsonNode filterValue : filterNode) {
-                    if (requiredValueInFilter.equalsIgnoreCase(filterValue.textValue())) {
-                        match = true;
-                        break;
-                    }
-                }
-            } else if (filterNode.isTextual()) {
-                if (requiredValueInFilter.equalsIgnoreCase(filterNode.textValue())) {
-                    match = true;
-                }
-            }
-
-            if (match) {
-                JsonNode valueNode = element.at(elementAttribute);
-                if (valueNode.isTextual()) {
-                    results.add(valueNode.textValue());
-                } else if (valueNode.isArray()) {
-                    for (JsonNode item : valueNode) {
-                        if (item.isTextual() && StringUtils.isNotBlank(item.textValue())) {
-                            results.add(item.textValue());
-                        }
-                    }
-                }
-            }
-        }
-
-        return results;
-    }
-
-    private JsonNode convertStringJsonToJsonNode(String json) {
-        ObjectMapper mapper = new ObjectMapper();
-        try {
-            return mapper.readTree(json);
-        } catch (JsonProcessingException e) {
-            log.error("Unable to process JSON response.", e);
-            return null;
-        }
-    }
-
-    public void setPathToArray(String pathToArray) {
-        this.pathToArray = pathToArray;
-    }
-
-    public void setElementAttribute(String elementAttribute) {
-        this.elementAttribute = elementAttribute;
-    }
-
-    public void setFilterAttribute(String filterAttribute) {
-        this.filterAttribute = filterAttribute;
-    }
-
-    public void setRequiredValueInFilter(String requiredValueInFilter) {
-        this.requiredValueInFilter = requiredValueInFilter;
-    }
-}

dspace-api/src/main/java/org/dspace/importer/external/pubmed/service/PubmedImportMetadataSourceServiceImpl.java

@@ -56,7 +56,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
 
     private String urlFetch;
     private String urlSearch;
-    private String apiKey;
 
     private int attempt = 3;
 
@@ -212,9 +211,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         @Override
         public Integer call() throws Exception {
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder.addParameter("api_key", apiKey);
-            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("term", query.getParameterAsClass("query", String.class));
             Map<String, Map<String, String>> params = new HashMap<String, Map<String,String>>();
@@ -291,9 +287,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             List<ImportRecord> records = new LinkedList<ImportRecord>();
 
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder.addParameter("api_key", apiKey);
-            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("retstart", start.toString());
             uriBuilder.addParameter("retmax", count.toString());
@@ -324,9 +317,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             String webEnv = getSingleElementValue(response, "WebEnv");
 
             URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder2.addParameter("api_key", apiKey);
-            }
             uriBuilder2.addParameter("db", "pubmed");
             uriBuilder2.addParameter("retstart", start.toString());
             uriBuilder2.addParameter("retmax", count.toString());
@@ -399,9 +389,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         public ImportRecord call() throws Exception {
 
             URIBuilder uriBuilder = new URIBuilder(urlFetch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder.addParameter("api_key", apiKey);
-            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("retmode", "xml");
             uriBuilder.addParameter("id", query.getParameterAsClass("id", String.class));
@@ -442,9 +429,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         public Collection<ImportRecord> call() throws Exception {
 
             URIBuilder uriBuilder = new URIBuilder(urlSearch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder.addParameter("api_key", apiKey);
-            }
             uriBuilder.addParameter("db", "pubmed");
             uriBuilder.addParameter("usehistory", "y");
             uriBuilder.addParameter("term", query.getParameterAsClass("term", String.class));
@@ -474,9 +458,6 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
             String queryKey = getSingleElementValue(response, "QueryKey");
 
             URIBuilder uriBuilder2 = new URIBuilder(urlFetch);
-            if (StringUtils.isNotBlank(apiKey)) {
-                uriBuilder.addParameter("api_key", apiKey);
-            }
             uriBuilder2.addParameter("db", "pubmed");
             uriBuilder2.addParameter("retmode", "xml");
             uriBuilder2.addParameter("WebEnv", webEnv);
@@ -552,8 +533,4 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         this.urlSearch = urlSearch;
     }
 
-    public void setApiKey(String apiKey) {
-        this.apiKey = apiKey;
-    }
-
 }

dspace-api/src/main/java/org/dspace/importer/external/ror/service/RorImportMetadataSourceServiceImpl.java

@@ -46,7 +46,7 @@ public class RorImportMetadataSourceServiceImpl extends AbstractImportMetadataSo
 
     private String url;
 
-    private int timeout = 5000;
+    private int timeout = 1000;
 
     @Autowired
     private LiveImportClient liveImportClient;

dspace-api/src/main/java/org/dspace/orcid/model/OrcidWorkFieldMapping.java

@@ -39,7 +39,6 @@ public class OrcidWorkFieldMapping {
      * The metadata fields related to the work external identifiers.
      */
     private Map<String, String> externalIdentifierFields = new HashMap<>();
-    private Map<String, List<String>> externalIdentifierPartOfMap = new HashMap<>();
 
     /**
      * The metadata field related to the work publication date.
@@ -130,15 +129,6 @@ public class OrcidWorkFieldMapping {
         this.externalIdentifierFields = parseConfigurations(externalIdentifierFields);
     }
 
-    public Map<String, List<String>> getExternalIdentifierPartOfMap() {
-        return this.externalIdentifierPartOfMap;
-    }
-
-    public void setExternalIdentifierPartOfMap(
-            HashMap<String, List<String>> externalIdentifierPartOfMap) {
-        this.externalIdentifierPartOfMap = externalIdentifierPartOfMap;
-    }
-
     public String getPublicationDateField() {
         return publicationDateField;
     }

dspace-api/src/main/java/org/dspace/orcid/model/factory/impl/OrcidWorkFactory.java

@@ -9,7 +9,6 @@ package org.dspace.orcid.model.factory.impl;
 
 import static org.apache.commons.lang3.StringUtils.isBlank;
 import static org.apache.commons.lang3.StringUtils.isNotBlank;
-import static org.orcid.jaxb.model.common.Relationship.PART_OF;
 import static org.orcid.jaxb.model.common.Relationship.SELF;
 
 import java.util.ArrayList;
@@ -74,12 +73,12 @@ public class OrcidWorkFactory implements OrcidEntityFactory {
     @Override
     public Activity createOrcidObject(Context context, Item item) {
         Work work = new Work();
-        work.setWorkType(getWorkType(context, item));
         work.setJournalTitle(getJournalTitle(context, item));
         work.setWorkContributors(getWorkContributors(context, item));
         work.setWorkTitle(getWorkTitle(context, item));
         work.setPublicationDate(getPublicationDate(context, item));
-        work.setWorkExternalIdentifiers(getWorkExternalIds(context, item, work));
+        work.setWorkExternalIdentifiers(getWorkExternalIds(context, item));
+        work.setWorkType(getWorkType(context, item));
         work.setShortDescription(getShortDescription(context, item));
         work.setLanguageCode(getLanguageCode(context, item));
         work.setUrl(getUrl(context, item));
@@ -150,65 +149,57 @@ public class OrcidWorkFactory implements OrcidEntityFactory {
     }
 
     /**
-     * Returns a list of external work IDs constructed in the org.orcid.jaxb
-     * ExternalIDs object
+     * Creates an instance of ExternalIDs from the metadata values of the given
+     * item, using the orcid.mapping.funding.external-ids configuration.
      */
-    private ExternalIDs getWorkExternalIds(Context context, Item item, Work work) {
-        ExternalIDs externalIDs = new ExternalIDs();
-        externalIDs.getExternalIdentifier().addAll(getWorkExternalIdList(context, item, work));
-        return externalIDs;
+    private ExternalIDs getWorkExternalIds(Context context, Item item) {
+        ExternalIDs externalIdentifiers = new ExternalIDs();
+        externalIdentifiers.getExternalIdentifier().addAll(getWorkSelfExternalIds(context, item));
+        return externalIdentifiers;
     }
 
     /**
      * Creates a list of ExternalID, one for orcid.mapping.funding.external-ids
-     * value, taking the values from the given item and work type.
+     * value, taking the values from the given item.
      */
-    private List<ExternalID> getWorkExternalIdList(Context context, Item item, Work work) {
+    private List<ExternalID> getWorkSelfExternalIds(Context context, Item item) {
 
-        List<ExternalID> externalIds = new ArrayList<>();
+        List<ExternalID> selfExternalIds = new ArrayList<>();
 
         Map<String, String> externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
 
         if (externalIdentifierFields.containsKey(SIMPLE_HANDLE_PLACEHOLDER)) {
             String handleType = externalIdentifierFields.get(SIMPLE_HANDLE_PLACEHOLDER);
-            ExternalID handle = new ExternalID();
-            handle.setType(handleType);
-            handle.setValue(item.getHandle());
-            handle.setRelationship(SELF);
-            externalIds.add(handle);
+            selfExternalIds.add(getExternalId(handleType, item.getHandle(), SELF));
         }
 
-        // Resolve work type, used to determine identifier relationship type
-        // For version / funding relationships, we might want to use more complex
-        // business rules than just "work and id type"
-        final String workType = (work != null && work.getWorkType() != null) ?
-            work.getWorkType().value() : WorkType.OTHER.value();
         getMetadataValues(context, item, externalIdentifierFields.keySet()).stream()
-            .map(metadataValue -> this.getExternalId(metadataValue, workType))
-            .forEach(externalIds::add);
+            .map(this::getSelfExternalId)
+            .forEach(selfExternalIds::add);
 
-        return externalIds;
+        return selfExternalIds;
+    }
+
+    /**
+     * Creates an instance of ExternalID taking the value from the given
+     * metadataValue. The type of the ExternalID is calculated using the
+     * orcid.mapping.funding.external-ids configuration. The relationship of the
+     * ExternalID is SELF.
+     */
+    private ExternalID getSelfExternalId(MetadataValue metadataValue) {
+        Map<String, String> externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
+        String metadataField = metadataValue.getMetadataField().toString('.');
+        return getExternalId(externalIdentifierFields.get(metadataField), metadataValue.getValue(), SELF);
     }
 
     /**
      * Creates an instance of ExternalID with the given type, value and
      * relationship.
      */
-    private ExternalID getExternalId(MetadataValue metadataValue, String workType) {
-        Map<String, String> externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
-        Map<String, List<String>> externalIdentifierPartOfMap = fieldMapping.getExternalIdentifierPartOfMap();
-        String metadataField = metadataValue.getMetadataField().toString('.');
-        String identifierType = externalIdentifierFields.get(metadataField);
-        // Default relationship type is SELF, configuration can
-        // override to PART_OF based on identifier and work type
-        Relationship relationship = SELF;
-        if (externalIdentifierPartOfMap.containsKey(identifierType)
-                && externalIdentifierPartOfMap.get(identifierType).contains(workType)) {
-            relationship = PART_OF;
-        }
+    private ExternalID getExternalId(String type, String value, Relationship relationship) {
         ExternalID externalID = new ExternalID();
-        externalID.setType(identifierType);
-        externalID.setValue(metadataValue.getValue());
+        externalID.setType(type);
+        externalID.setValue(value);
         externalID.setRelationship(relationship);
         return externalID;
     }

dspace-api/src/main/java/org/dspace/profile/ResearcherProfileServiceImpl.java

@@ -283,8 +283,6 @@ public class ResearcherProfileServiceImpl implements ResearcherProfileService {
         itemService.addMetadata(context, item, "dc", "title", null, null, fullName);
         itemService.addMetadata(context, item, "person", "email", null, null, ePerson.getEmail());
         itemService.addMetadata(context, item, "dspace", "object", "owner", null, fullName, id, CF_ACCEPTED);
-        itemService.addMetadata(context, item, "person", "familyName", null, null, ePerson.getLastName());
-        itemService.addMetadata(context, item, "person", "givenName", null, null, ePerson.getFirstName());
 
         item = installItemService.installItem(context, workspaceItem);
 

dspace-api/src/main/java/org/dspace/scripts/DSpaceRunnable.java

@@ -117,7 +117,7 @@ public abstract class DSpaceRunnable<T extends ScriptConfiguration> implements R
      * @param args              The primitive array of Strings representing the parameters
      * @throws ParseException   If something goes wrong
      */
-    protected StepResult parse(String[] args) throws ParseException {
+    private StepResult parse(String[] args) throws ParseException {
         commandLine = new DefaultParser().parse(getScriptConfiguration().getOptions(), args);
         setup();
         return StepResult.Continue;

dspace-api/src/main/java/org/dspace/statistics/SolrLoggerServiceImpl.java

@@ -34,7 +34,6 @@ import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
 import java.time.temporal.ChronoUnit;
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.HashSet;
@@ -232,10 +231,6 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             throw new RuntimeException(e);
         }
 
-        if (dspaceObject instanceof Bitstream && !isBitstreamLoggable((Bitstream) dspaceObject)) {
-            return;
-        }
-
         if (solr == null) {
             return;
         }
@@ -283,10 +278,6 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
     @Override
     public void postView(DSpaceObject dspaceObject,
                          String ip, String userAgent, String xforwardedfor, EPerson currentUser, String referrer) {
-        if (dspaceObject instanceof Bitstream && !isBitstreamLoggable((Bitstream) dspaceObject)) {
-            return;
-        }
-
         if (solr == null) {
             return;
         }
@@ -1626,35 +1617,4 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
 
         throw new UnknownHostException("unknown ip format");
     }
-
-    /**
-     * Checks if a given Bitstream's bundles are configured to be logged in Solr statistics.
-     *
-     * @param bitstream The bitstream to check.
-     * @return {@code true} if the bitstream event should be logged, {@code false} otherwise.
-     */
-    private boolean isBitstreamLoggable(Bitstream bitstream) {
-        String[] allowedBundles = configurationService
-            .getArrayProperty("solr-statistics.query.filter.bundles");
-        if (allowedBundles == null || allowedBundles.length == 0) {
-            return true;
-        }
-        List<String> allowedBundlesList = Arrays.asList(allowedBundles);
-        try {
-            List<Bundle> actualBundles = bitstream.getBundles();
-            if (actualBundles.isEmpty()) {
-                return true;
-            }
-            for (Bundle bundle : actualBundles) {
-                if (allowedBundlesList.contains(bundle.getName())) {
-                    return true;
-                }
-            }
-        } catch (SQLException e) {
-            log.error("Error checking bitstream bundles for logging statistics for bitstream {}",
-                bitstream.getID(), e);
-            return true;
-        }
-        return false;
-    }
 }

dspace-api/src/main/java/org/dspace/statistics/export/processor/ExportEventProcessor.java

@@ -137,10 +137,9 @@ public abstract class ExportEventProcessor {
             .append(URLEncoder.encode(clientUA, UTF_8));
 
         String hostName = Utils.getHostName(configurationService.getProperty("dspace.ui.url"));
-        String oaiPrefix = configurationService.getProperty("oai.identifier.prefix");
 
         data.append("&").append(URLEncoder.encode("rft.artnum", UTF_8)).append("=").
-                append(URLEncoder.encode("oai:" + oaiPrefix + ":" + item
+                append(URLEncoder.encode("oai:" + hostName + ":" + item
                         .getHandle(), UTF_8));
         data.append("&").append(URLEncoder.encode("rfr_dat", UTF_8)).append("=")
             .append(URLEncoder.encode(referer, UTF_8));

dspace-api/src/main/java/org/dspace/storage/bitstore/BitstreamStorageServiceImpl.java

@@ -429,7 +429,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
             //modulo
             if ((processedCounter % batchCommitSize) == 0) {
                 log.info("Migration Commit Checkpoint: " + processedCounter);
-                context.commit();
+                context.dispatchEvents();
             }
         }
 

dspace-api/src/main/java/org/dspace/storage/bitstore/DSBitStoreService.java

@@ -19,11 +19,9 @@ import java.security.NoSuchAlgorithmException;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.dspace.content.Bitstream;
 import org.dspace.core.Utils;
-import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Native DSpace (or "Directory Scatter" if you prefer) asset store.
@@ -254,10 +252,7 @@ public class DSBitStoreService extends BaseBitStoreService {
         }
         File bitstreamFile = new File(bufFilename.toString());
         Path normalizedPath = bitstreamFile.toPath().normalize();
-        String[] allowedAssetstoreRoots = DSpaceServicesFactory.getInstance().getConfigurationService()
-                .getArrayProperty("assetstore.allowed.roots", new String[]{});
-        if (!normalizedPath.startsWith(baseDir.getAbsolutePath())
-            && !StringUtils.startsWithAny(normalizedPath.toString(), allowedAssetstoreRoots)) {
+        if (!normalizedPath.startsWith(baseDir.getAbsolutePath())) {
             log.error("Bitstream path outside of assetstore root requested:" +
                     "bitstream={}, path={}, assetstore={}",
                     bitstream.getID(), normalizedPath, baseDir.getAbsolutePath());

dspace-api/src/main/java/org/dspace/storage/rdbms/DatabaseUtils.java

@@ -123,6 +123,16 @@ public class DatabaseUtils {
 
                         // Print basic database connection information
                         printDBInfo(connection);
+
+                        // Print any database warnings/errors found (if any)
+                        boolean issueFound = printDBIssues(connection);
+
+                        // If issues found, exit with an error status (even if connection succeeded).
+                        if (issueFound) {
+                            System.exit(1);
+                        } else {
+                            System.exit(0);
+                        }
                     } catch (SQLException sqle) {
                         System.err.println("\nError running 'test': ");
                         System.err.println(" - " + sqle);
@@ -160,6 +170,16 @@ public class DatabaseUtils {
                                                        "migrate'.");
                             }
                         }
+
+                        // Print any database warnings/errors found (if any)
+                        boolean issueFound = printDBIssues(connection);
+
+                        // If issues found, exit with an error status
+                        if (issueFound) {
+                            System.exit(1);
+                        } else {
+                            System.exit(0);
+                        }
                     } catch (SQLException e) {
                         System.err.println("Info exception:");
                         e.printStackTrace(System.err);
@@ -315,6 +335,31 @@ public class DatabaseUtils {
                     }
 
                     try (Connection connection = dataSource.getConnection()) {
+                        String dbType = getDbType(connection);
+
+                        // Not all Postgres user accounts will be able to run a 'clean',
+                        // as only 'superuser' accounts can remove the 'pgcrypto' extension.
+                        if (dbType.equals(DBMS_POSTGRES)) {
+                            // Check if database user has permissions suitable to run a clean
+                            if (!PostgresUtils.checkCleanPermissions(connection)) {
+                                String username = connection.getMetaData().getUserName();
+                                // Exit immediately, providing a descriptive error message
+                                System.out.println(
+                                    "\nERROR: The database user '" + username + "' does not have sufficient " +
+                                        "privileges to run a 'database clean' (via Flyway).");
+                                System.out.println(
+                                    "\nIn order to run a 'clean', the database user MUST have 'superuser' privileges");
+                                System.out.println(
+                                    "OR the '" + PostgresUtils.PGCRYPTO + "' extension must be installed in a " +
+                                        "separate schema (see documentation).");
+                                System.out.println(
+                                    "\nOptionally, you could also manually remove the '" + PostgresUtils.PGCRYPTO +
+                                        "' extension first (DROP EXTENSION " + PostgresUtils.PGCRYPTO +
+                                        " CASCADE;), then rerun the 'clean'");
+                                System.exit(1);
+                            }
+                        }
+
                         BufferedReader input = new BufferedReader(new InputStreamReader(System.in,
                                                                                         StandardCharsets.UTF_8));
 
@@ -323,6 +368,11 @@ public class DatabaseUtils {
                             .println("\nWARNING: ALL DATA AND TABLES IN YOUR DATABASE WILL BE PERMANENTLY DELETED.\n");
                         System.out.println("There is NO turning back from this action. Backup your DB before " +
                                                "continuing.");
+                        if (dbType.equals(DBMS_POSTGRES)) {
+                            System.out.println(
+                                "\nPOSTGRES WARNING: the '" + PostgresUtils.PGCRYPTO + "' extension will be dropped " +
+                                "if it is in the same schema as the DSpace database.\n");
+                        }
                         System.out.print("Do you want to PERMANENTLY DELETE everything from your database? [y/n]: ");
                         String choiceString = input.readLine();
                         input.close();
@@ -426,10 +476,108 @@ public class DatabaseUtils {
             "Database Software: " + meta.getDatabaseProductName() + " version " + meta.getDatabaseProductVersion());
         System.out.println("Database Driver: " + meta.getDriverName() + " version " + meta.getDriverVersion());
 
+        // For Postgres, report whether pgcrypto is installed
+        // (If it isn't, we'll also write out warnings...see below)
+        if (dbType.equals(DBMS_POSTGRES)) {
+            boolean pgcryptoUpToDate = PostgresUtils.isPgcryptoUpToDate();
+            Double pgcryptoVersion = PostgresUtils.getPgcryptoInstalledVersion(connection);
+            System.out.println(
+                "PostgreSQL '" + PostgresUtils.PGCRYPTO + "' extension installed/up-to-date? " + pgcryptoUpToDate + "" +
+                    " " + ((pgcryptoVersion != null) ? "(version=" + pgcryptoVersion + ")" : "(not installed)"));
+        }
         // Finally, print out our version of Flyway
         System.out.println("FlywayDB Version: " + VersionPrinter.getVersion());
     }
 
+    /**
+     * Print any warnings about current database setup to System.err (if any).
+     * This is utilized by both the 'test' and 'info' commandline options.
+     *
+     * @param connection current database connection
+     * @return boolean true if database issues found, false otherwise
+     * @throws SQLException if database error occurs
+     */
+    private static boolean printDBIssues(Connection connection) throws SQLException {
+        boolean issueFound = false;
+
+        // Get the DB Type
+        String dbType = getDbType(connection);
+
+        // For PostgreSQL databases, we need to check for the 'pgcrypto' extension.
+        // If it is NOT properly installed, we'll need to warn the user, as DSpace will be unable to proceed.
+        if (dbType.equals(DBMS_POSTGRES)) {
+            // Get version of pgcrypto available in this postgres instance
+            Double pgcryptoAvailable = PostgresUtils.getPgcryptoAvailableVersion(connection);
+
+            // Generic requirements message
+            String requirementsMsg = "\n** DSpace REQUIRES PostgreSQL >= " + PostgresUtils.POSTGRES_VERSION + " AND "
+                + PostgresUtils.PGCRYPTO + " extension >= " + PostgresUtils.PGCRYPTO_VERSION + " **\n";
+
+            // Check if installed in PostgreSQL & a supported version
+            if (pgcryptoAvailable != null && pgcryptoAvailable.compareTo(PostgresUtils.PGCRYPTO_VERSION) >= 0) {
+                // We now know it's available in this Postgres. Let's see if it is installed in this database.
+                Double pgcryptoInstalled = PostgresUtils.getPgcryptoInstalledVersion(connection);
+
+                // Check if installed in database, but outdated version
+                if (pgcryptoInstalled != null && pgcryptoInstalled.compareTo(PostgresUtils.PGCRYPTO_VERSION) < 0) {
+                    System.out.println(
+                        "\nWARNING: Required PostgreSQL '" + PostgresUtils.PGCRYPTO + "' extension is OUTDATED " +
+                            "(installed version=" + pgcryptoInstalled + ", available version = " + pgcryptoAvailable
+                            + ").");
+                    System.out.println(requirementsMsg);
+                    System.out.println(
+                        "To update it, please connect to your DSpace database as a 'superuser' and manually run the " +
+                            "following command: ");
+                    System.out.println(
+                        "\n  ALTER EXTENSION " + PostgresUtils.PGCRYPTO + " UPDATE TO '" + pgcryptoAvailable + "';\n");
+                    issueFound = true;
+                } else if (pgcryptoInstalled == null) {
+                    // If it's not installed in database
+
+                    System.out.println(
+                        "\nWARNING: Required PostgreSQL '" + PostgresUtils.PGCRYPTO + "' extension is NOT INSTALLED " +
+                            "on this database.");
+                    System.out.println(requirementsMsg);
+                    System.out.println(
+                        "To install it, please connect to your DSpace database as a 'superuser' and manually run the " +
+                            "following command: ");
+                    System.out.println("\n  CREATE EXTENSION " + PostgresUtils.PGCRYPTO + ";\n");
+                    issueFound = true;
+                }
+            } else if (pgcryptoAvailable != null && pgcryptoAvailable.compareTo(PostgresUtils.PGCRYPTO_VERSION) < 0) {
+                // If installed in Postgres, but an unsupported version
+
+                System.out.println(
+                    "\nWARNING: UNSUPPORTED version of PostgreSQL '" + PostgresUtils.PGCRYPTO + "' extension found " +
+                        "(version=" + pgcryptoAvailable + ").");
+                System.out.println(requirementsMsg);
+                System.out.println(
+                    "Make sure you are running a supported version of PostgreSQL, and then install " + PostgresUtils
+                        .PGCRYPTO + " version >= " + PostgresUtils.PGCRYPTO_VERSION);
+                System.out.println(
+                    "The '" + PostgresUtils.PGCRYPTO + "' extension is often provided in the 'postgresql-contrib' " +
+                        "package for your operating system.");
+                issueFound = true;
+            } else if (pgcryptoAvailable == null) {
+                // If it's not installed in Postgres
+
+                System.out.println(
+                    "\nWARNING: PostgreSQL '" + PostgresUtils.PGCRYPTO + "' extension is NOT AVAILABLE. Please " +
+                        "install it into this PostgreSQL instance.");
+                System.out.println(requirementsMsg);
+                System.out.println(
+                    "The '" + PostgresUtils.PGCRYPTO + "' extension is often provided in the 'postgresql-contrib' " +
+                        "package for your operating system.");
+                System.out.println(
+                    "Once the extension is installed globally, please connect to your DSpace database as a " +
+                        "'superuser' and manually run the following command: ");
+                System.out.println("\n  CREATE EXTENSION " + PostgresUtils.PGCRYPTO + ";\n");
+                issueFound = true;
+            }
+        }
+        return issueFound;
+    }
+
     /**
      * Setup/Initialize the Flyway Configuration to run against our DSpace database
      * and point at our migration scripts.

dspace-api/src/main/java/org/dspace/storage/rdbms/PostgreSQLCryptoChecker.java

@@ -0,0 +1,149 @@
+/**
+ * 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.storage.rdbms;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+import java.sql.Statement;
+
+import org.apache.logging.log4j.Logger;
+import org.flywaydb.core.api.FlywayException;
+import org.flywaydb.core.api.callback.Callback;
+import org.flywaydb.core.api.callback.Context;
+import org.flywaydb.core.api.callback.Event;
+
+/**
+ * This is a FlywayCallback class which automatically verifies that "pgcrypto"
+ * is at the proper version before running any database migrations.
+ * <P>
+ * When running PostgreSQL, pgcrypto is REQUIRED by DSpace as it allows UUIDs
+ * to be generated.
+ * <P>
+ * During a database "clean", this also de-registers "pgcrypto" proir to the
+ * full database clean.
+ *
+ * @author Tim Donohue
+ */
+public class PostgreSQLCryptoChecker implements Callback {
+    private Logger log = org.apache.logging.log4j.LogManager.getLogger(PostgreSQLCryptoChecker.class);
+
+    /**
+     * Check for pgcrypto (if needed). Throws an exception if pgcrypto is
+     * not installed or needs an upgrade.
+     *
+     * @param connection database connection
+     */
+    public void checkPgCrypto(Connection connection) {
+        String dbType;
+        try {
+            dbType = DatabaseUtils.getDbType(connection);
+        } catch (SQLException se) {
+            throw new FlywayException("Unable to determine database type.", se);
+        }
+
+        // ONLY Check if this is a PostgreSQL database
+        if (dbType != null && dbType.equals(DatabaseUtils.DBMS_POSTGRES)) {
+            // If this is a PostgreSQL database, then a supported version
+            // of the 'pgcrypto' extension MUST be installed to continue.
+
+            // Check if pgcrypto is both installed & a supported version
+            if (!PostgresUtils.isPgcryptoUpToDate()) {
+                throw new FlywayException(
+                    "This PostgreSQL Database is INCOMPATIBLE with DSpace. The upgrade will NOT proceed. " +
+                        "A supported version (>=" + PostgresUtils.PGCRYPTO_VERSION + ") of the '" + PostgresUtils
+                        .PGCRYPTO + "' extension must be installed! " +
+                        "Please run 'dspace database info' for additional info/tips.");
+            }
+        }
+    }
+
+    /**
+     * Remove pgcrypto (if necessary).
+     * <P>
+     * The pgcrypto extension MUST be removed before a clean or else errors occur.
+     * This method checks if it needs to be removed and, if so, removes it.
+     *
+     * @param connection database connection
+     */
+    public void removePgCrypto(Connection connection) {
+        try {
+            String dbType = DatabaseUtils.getDbType(connection);
+
+            // ONLY remove if this is a PostgreSQL database
+            if (dbType != null && dbType.equals(DatabaseUtils.DBMS_POSTGRES)) {
+                // Get current schema
+                String schema = DatabaseUtils.getSchemaName(connection);
+
+                // Check if pgcrypto is in this schema
+                // If so, it MUST be removed before a 'clean'
+                if (PostgresUtils.isPgcryptoInSchema(schema)) {
+                    // remove the extension
+                    try (Statement statement = connection.createStatement()) {
+                        // WARNING: ONLY superusers can remove pgcrypto. However, at this point,
+                        // we have already verified user acct permissions via PostgresUtils.checkCleanPermissions()
+                        // (which is called prior to a 'clean' being triggered).
+                        statement.execute("DROP EXTENSION " + PostgresUtils.PGCRYPTO + " CASCADE");
+                    }
+                }
+            }
+        } catch (SQLException e) {
+            throw new FlywayException("Failed to check for and/or remove '" + PostgresUtils.PGCRYPTO + "' extension",
+                                      e);
+        }
+    }
+
+    /**
+     * The callback name, Flyway will use this to sort the callbacks alphabetically before executing them
+     * @return The callback name
+     */
+    @Override
+    public String getCallbackName() {
+        // Return class name only (not prepended by package)
+        return PostgreSQLCryptoChecker.class.getSimpleName();
+    }
+
+    /**
+     * Events supported by this callback.
+     * @param event Flyway event
+     * @param context Flyway context
+     * @return true if BEFORE_BASELINE, BEFORE_MIGRATE or BEFORE_CLEAN
+     */
+    @Override
+    public boolean supports(Event event, Context context) {
+        return event.equals(Event.BEFORE_BASELINE) || event.equals(Event.BEFORE_MIGRATE) ||
+            event.equals(Event.BEFORE_CLEAN);
+    }
+
+    /**
+     * Whether event can be handled in a transaction or whether it must be handle outside of transaction.
+     * @param event Flyway event
+     * @param context Flyway context
+     * @return true
+     */
+    @Override
+    public boolean canHandleInTransaction(Event event, Context context) {
+        return true;
+    }
+
+    /**
+     * What to run when the callback is triggered.
+     * @param event Flyway event
+     * @param context Flyway context
+     */
+    @Override
+    public void handle(Event event, Context context) {
+        // If, before initializing or migrating database, check for pgcrypto
+        // Else, before Cleaning database, remove pgcrypto (if exists)
+        if (event.equals(Event.BEFORE_BASELINE) || event.equals(Event.BEFORE_MIGRATE)) {
+            checkPgCrypto(context.getConnection());
+        } else if (event.equals(Event.BEFORE_CLEAN)) {
+            removePgCrypto(context.getConnection());
+        }
+
+    }
+}

dspace-api/src/main/java/org/dspace/storage/rdbms/PostgresUtils.java

@@ -0,0 +1,218 @@
+/**
+ * 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.storage.rdbms;
+
+import static org.dspace.storage.rdbms.DatabaseUtils.getSchemaName;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import javax.sql.DataSource;
+
+import org.flywaydb.core.api.FlywayException;
+
+/**
+ * Database utility class specific to Postgres.
+ * This class contains tools and methods which are useful in determining
+ * the status of a PostgreSQL database backend.  It's a companion class
+ * to DatabaseUtils, but PostgreSQL specific.
+ *
+ * @author Tim Donohue
+ */
+public class PostgresUtils {
+    // PostgreSQL pgcrypto extension name, and required versions of Postgres & pgcrypto
+    public static final String PGCRYPTO = "pgcrypto";
+    public static final Double PGCRYPTO_VERSION = 1.1;
+    public static final Double POSTGRES_VERSION = 9.4;
+
+    /**
+     * Default constructor
+     */
+    private PostgresUtils() { }
+
+    /**
+     * Get version of pgcrypto extension available. The extension is "available"
+     * if it's been installed via operating system tools/packages. It also
+     * MUST be installed in the DSpace database (see getPgcryptoInstalled()).
+     * <P>
+     * The pgcrypto extension is required for Postgres databases
+     *
+     * @param connection database connection
+     * @return version number or null if not available
+     */
+    protected static Double getPgcryptoAvailableVersion(Connection connection) {
+        Double version = null;
+
+        String checkPgCryptoAvailable = "SELECT default_version AS version FROM pg_available_extensions WHERE name=?";
+
+        // Run the query to obtain the version of 'pgcrypto' available
+        try (PreparedStatement statement = connection.prepareStatement(checkPgCryptoAvailable)) {
+            statement.setString(1, PGCRYPTO);
+            try (ResultSet results = statement.executeQuery()) {
+                if (results.next()) {
+                    version = results.getDouble("version");
+                }
+            }
+        } catch (SQLException e) {
+            throw new FlywayException("Unable to determine whether 'pgcrypto' extension is available.", e);
+        }
+
+        return version;
+    }
+
+    /**
+     * Get version of pgcrypto extension installed in the DSpace database.
+     * <P>
+     * The pgcrypto extension is required for Postgres databases to support
+     * UUIDs.
+     *
+     * @param connection database connection
+     * @return version number or null if not installed
+     */
+    protected static Double getPgcryptoInstalledVersion(Connection connection) {
+        Double version = null;
+
+        String checkPgCryptoInstalled = "SELECT extversion AS version FROM pg_extension WHERE extname=?";
+
+        // Run the query to obtain the version of 'pgcrypto' installed on this database
+        try (PreparedStatement statement = connection.prepareStatement(checkPgCryptoInstalled)) {
+            statement.setString(1, PGCRYPTO);
+            try (ResultSet results = statement.executeQuery()) {
+                if (results.next()) {
+                    version = results.getDouble("version");
+                }
+            }
+        } catch (SQLException e) {
+            throw new FlywayException("Unable to determine whether 'pgcrypto' extension is installed.", e);
+        }
+
+        return version;
+    }
+
+    /**
+     * Check if the pgcrypto extension is BOTH installed AND up-to-date.
+     * <P>
+     * This requirement is only needed for PostgreSQL databases.
+     * It doesn't matter what schema pgcrypto is installed in, as long as it exists.
+     *
+     * @return true if everything is installed and up-to-date. False otherwise.
+     */
+    public static boolean isPgcryptoUpToDate() {
+        // Get our configured dataSource
+        DataSource dataSource = DatabaseUtils.getDataSource();
+
+        try (Connection connection = dataSource.getConnection()) {
+            Double pgcryptoInstalled = getPgcryptoInstalledVersion(connection);
+
+            // Check if installed & up-to-date in this DSpace database
+            if (pgcryptoInstalled != null && pgcryptoInstalled.compareTo(PGCRYPTO_VERSION) >= 0) {
+                return true;
+            }
+
+            return false;
+        } catch (SQLException e) {
+            throw new FlywayException("Unable to determine whether 'pgcrypto' extension is up-to-date.", e);
+        }
+    }
+
+    /**
+     * Check if the pgcrypto extension is installed into a particular schema
+     * <P>
+     * This allows us to check if pgcrypto needs to be REMOVED prior to running
+     * a 'clean' on this database. If pgcrypto is in the same schema as the
+     * dspace database, a 'clean' will require removing pgcrypto FIRST.
+     *
+     * @param schema name of schema
+     * @return true if pgcrypto is in this schema. False otherwise.
+     */
+    public static boolean isPgcryptoInSchema(String schema) {
+        // Get our configured dataSource
+        DataSource dataSource = DatabaseUtils.getDataSource();
+
+        try (Connection connection = dataSource.getConnection()) {
+            // Check if pgcrypto is installed in the current database schema.
+            String pgcryptoInstalledInSchema = "SELECT extversion FROM pg_extension,pg_namespace " +
+                "WHERE pg_extension.extnamespace=pg_namespace.oid " +
+                "AND extname=? " +
+                "AND nspname=?;";
+            Double pgcryptoVersion = null;
+            try (PreparedStatement statement = connection.prepareStatement(pgcryptoInstalledInSchema)) {
+                statement.setString(1, PGCRYPTO);
+                statement.setString(2, schema);
+                try (ResultSet results = statement.executeQuery()) {
+                    if (results.next()) {
+                        pgcryptoVersion = results.getDouble("extversion");
+                    }
+                }
+            }
+
+            // If a pgcrypto version returns, it's installed in this schema
+            if (pgcryptoVersion != null) {
+                return true;
+            } else {
+                return false;
+            }
+        } catch (SQLException e) {
+            throw new FlywayException(
+                "Unable to determine whether 'pgcrypto' extension is installed in schema '" + schema + "'.", e);
+        }
+    }
+
+
+    /**
+     * Check if the current user has permissions to run a clean on existing
+     * database.
+     * <P>
+     * Mostly this just checks if you need to remove pgcrypto, and if so,
+     * whether you have permissions to do so.
+     *
+     * @param connection database connection
+     * @return true if permissions valid, false otherwise
+     */
+    protected static boolean checkCleanPermissions(Connection connection) {
+        try {
+            // get username of our db user
+            String username = connection.getMetaData().getUserName();
+
+            // Check their permissions. Are they a 'superuser'?
+            String checkSuperuser = "SELECT rolsuper FROM pg_roles WHERE rolname=?;";
+            boolean superuser = false;
+            try (PreparedStatement statement = connection.prepareStatement(checkSuperuser)) {
+                statement.setString(1, username);
+                try (ResultSet results = statement.executeQuery()) {
+                    if (results.next()) {
+                        superuser = results.getBoolean("rolsuper");
+                    }
+                }
+            } catch (SQLException e) {
+                throw new FlywayException("Unable to determine if user '" + username + "' is a superuser.", e);
+            }
+
+            // If user is a superuser, then "clean" can be run successfully
+            if (superuser) {
+                return true;
+            } else {
+                // Otherwise, we'll need to see which schema 'pgcrypto' is installed in
+
+                // Get current schema name
+                String schema = getSchemaName(connection);
+
+                // If pgcrypto is installed in this schema, then superuser privileges are needed to remove it
+                if (isPgcryptoInSchema(schema)) {
+                    return false;
+                } else {
+                    // otherwise, a 'clean' can be run by anyone
+                    return true;
+                }
+            }
+        } catch (SQLException e) {
+            throw new FlywayException("Unable to determine if DB user has 'clean' privileges.", e);
+        }
+    }
+}

dspace-api/src/main/java/org/dspace/subscriptions/SubscriptionEmailNotificationServiceImpl.java

@@ -67,7 +67,6 @@ public class SubscriptionEmailNotificationServiceImpl implements SubscriptionEma
     public void perform(Context context, DSpaceRunnableHandler handler, String subscriptionType, String frequency) {
         List<IndexableObject> communityItems = new ArrayList<>();
         List<IndexableObject> collectionsItems = new ArrayList<>();
-        EPerson currentEperson = context.getCurrentUser();
         try {
             List<Subscription> subscriptions =
                                findAllSubscriptionsBySubscriptionTypeAndFrequency(context, subscriptionType, frequency);
@@ -78,10 +77,7 @@ public class SubscriptionEmailNotificationServiceImpl implements SubscriptionEma
                 for (Subscription subscription : subscriptions) {
                     DSpaceObject dSpaceObject = subscription.getDSpaceObject();
                     EPerson ePerson = subscription.getEPerson();
-                    // Set the current user to the subscribed eperson because the Solr query checks
-                    // the permissions of the current user in the ANONYMOUS group.
-                    // If there is no user (i.e., `current user = null`), it will send an email with no new items.
-                    context.setCurrentUser(ePerson);
+
                     if (!authorizeService.authorizeActionBoolean(context, ePerson, dSpaceObject, READ, true)) {
                         iterator++;
                         continue;
@@ -130,8 +126,6 @@ public class SubscriptionEmailNotificationServiceImpl implements SubscriptionEma
             handler.handleException(e);
             context.abort();
         }
-        // Reset the current user because it was changed to subscriber eperson
-        context.setCurrentUser(currentEperson);
     }
 
     @SuppressWarnings("rawtypes")

dspace-api/src/main/java/org/dspace/testing/PubMedToImport.java

@@ -58,7 +58,7 @@ public class PubMedToImport {
      */
     private PubMedToImport() { }
 
-    public static void main(String[] args) {
+    public static void main(String args[]) {
         Options options = new Options();
 
         options.addOption(new Option("s", "source", true, "Source xml"));

dspace-api/src/main/java/org/dspace/util/SolrImportExport.java

@@ -556,7 +556,7 @@ public class SolrImportExport {
             YearMonth monthStartDate;
             String monthStart = monthFacet.getValue();
             try {
-                monthStartDate = YearMonth.parse(monthStart, DateTimeFormatter.ISO_OFFSET_DATE_TIME);
+                monthStartDate = YearMonth.parse(monthStart);
             } catch (DateTimeParseException e) {
                 throw new SolrImportExportException("Could not read start of month batch as date: " + monthStart, e);
             }