Merge pull request #11396 from TexasDigitalLibrary/port_11329_to_7x

[Port dspace-7_x] Fix Hibernate syntax bugs in the CollectionDAO and BitstreamDAO

.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@v2
+        uses: github/codeql-action/init@v3
         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@v2
+        uses: github/codeql-action/autobuild@v3
 
       # Perform GitHub Code Scanning.
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@v2
+        uses: github/codeql-action/analyze@v3

.github/workflows/docker.yml

@@ -219,6 +219,19 @@ 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

@@ -165,7 +165,7 @@ 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=max
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
 
       # Export the digest of Docker build locally
       - name: Export Docker build digest
@@ -217,7 +217,7 @@ 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=max
+          cache-to: type=gha,scope=${{ inputs.build_id }},mode=min
           # Export image to a local TAR file
           outputs: type=docker,dest=/tmp/${{ inputs.build_id }}.tar
 

LICENSES_THIRD_PARTY

@@ -233,9 +233,9 @@ https://wiki.lyrasis.org/display/DSPACE/Code+Contribution+Guidelines
         * Kerby-kerb Util (org.apache.kerby:kerb-util:1.0.1 - http://directory.apache.org/kerby/kerby-kerb/kerb-util)
         * Kerby ASN1 Project (org.apache.kerby:kerby-asn1:1.0.1 - http://directory.apache.org/kerby/kerby-common/kerby-asn1)
         * Kerby PKIX Project (org.apache.kerby:kerby-pkix:1.0.1 - http://directory.apache.org/kerby/kerby-pkix)
-        * Apache Log4j 1.x Compatibility API (org.apache.logging.log4j:log4j-1.2-api:2.25.0 - https://logging.apache.org/log4j/2.x/)
-        * Apache Log4j API (org.apache.logging.log4j:log4j-api:2.25.0 - https://logging.apache.org/log4j/2.x/)
-        * Apache Log4j Core (org.apache.logging.log4j:log4j-core:2.25.0 - https://logging.apache.org/log4j/2.x/)
+        * Apache Log4j 1.x Compatibility API (org.apache.logging.log4j:log4j-1.2-api:2.25.1 - https://logging.apache.org/log4j/2.x/)
+        * Apache Log4j API (org.apache.logging.log4j:log4j-api:2.25.1 - https://logging.apache.org/log4j/2.x/)
+        * Apache Log4j Core (org.apache.logging.log4j:log4j-core:2.25.1 - https://logging.apache.org/log4j/2.x/)
         * Apache Log4j JUL Adapter (org.apache.logging.log4j:log4j-jul:2.17.2 - https://logging.apache.org/log4j/2.x/log4j-jul/)
         * Apache Log4j Layout for JSON template (org.apache.logging.log4j:log4j-layout-template-json:2.17.2 - https://logging.apache.org/log4j/2.x/log4j-layout-template-json/)
         * Apache Log4j SLF4J Binding (org.apache.logging.log4j:log4j-slf4j-impl:2.17.2 - https://logging.apache.org/log4j/2.x/log4j-slf4j-impl/)

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -99,20 +99,6 @@
                 </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>
@@ -752,7 +738,7 @@
         <dependency>
             <groupId>com.amazonaws</groupId>
             <artifactId>aws-java-sdk-s3</artifactId>
-            <version>1.12.785</version>
+            <version>1.12.791</version>
         </dependency>
 
         <dependency>
@@ -801,7 +787,7 @@
         <dependency>
             <groupId>com.opencsv</groupId>
             <artifactId>opencsv</artifactId>
-            <version>5.11.1</version>
+            <version>5.12.0</version>
         </dependency>
 
         <!-- Email templating -->
@@ -884,32 +870,32 @@
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-buffer</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
           </dependency>
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-transport</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
           </dependency>
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-transport-native-unix-common</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
            </dependency>
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-common</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
           </dependency>
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-handler</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
           </dependency>
           <dependency>
             <groupId>io.netty</groupId>
             <artifactId>netty-codec</artifactId>
-            <version>4.2.2.Final</version>
+            <version>4.2.6.Final</version>
           </dependency>
           <dependency>
             <groupId>org.apache.velocity</groupId>
@@ -919,7 +905,7 @@
           <dependency>
               <groupId>org.xmlunit</groupId>
               <artifactId>xmlunit-core</artifactId>
-              <version>2.10.2</version>
+              <version>2.10.3</version>
               <scope>test</scope>
           </dependency>
           <dependency>

dspace-api/src/main/java/org/dspace/app/bulkaccesscontrol/BulkAccessControl.java

@@ -18,6 +18,7 @@ import java.io.InputStream;
 import java.sql.SQLException;
 import java.text.DateFormat;
 import java.text.SimpleDateFormat;
+import java.time.ZoneOffset;
 import java.util.Arrays;
 import java.util.Date;
 import java.util.Iterator;
@@ -154,7 +155,7 @@ public class BulkAccessControl extends DSpaceRunnable<BulkAccessControlScriptCon
         }
 
         ObjectMapper mapper = new ObjectMapper();
-        mapper.setTimeZone(TimeZone.getTimeZone("UTC"));
+        mapper.setTimeZone(TimeZone.getTimeZone(ZoneOffset.UTC));
         BulkAccessControlInput accessControl;
         context = new Context(Context.Mode.BATCH_EDIT);
         setEPerson(context);

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

@@ -14,6 +14,8 @@ 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;
@@ -167,4 +169,14 @@ 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

@@ -494,7 +494,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
 
                 // Check it has an owning collection
                 List<String> collections = line.get("collection");
-                if (collections == null) {
+                if (collections == null || collections.isEmpty()) {
                     throw new MetadataImportException(
                         "New items must have a 'collection' assigned in the form of a handle");
                 }

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

@@ -363,12 +363,14 @@ public class ItemExportServiceImpl implements ItemExportService {
         File outFile = new File(destDir, "collections");
         if (outFile.createNewFile()) {
             try (PrintWriter out = new PrintWriter(new FileWriter(outFile))) {
-                String ownerHandle = item.getOwningCollection().getHandle();
-                out.println(ownerHandle);
+                Collection owningCollection = item.getOwningCollection();
+                // The owning collection is null for workspace and workflow items
+                if (owningCollection != null) {
+                    out.println(owningCollection.getHandle());
+                }
                 for (Collection collection : item.getCollections()) {
-                    String collectionHandle = collection.getHandle();
-                    if (!collectionHandle.equals(ownerHandle)) {
-                        out.println(collectionHandle);
+                    if (!collection.equals(owningCollection)) {
+                        out.println(collection.getHandle());
                     }
                 }
             }

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

@@ -22,6 +22,7 @@ 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;
@@ -333,6 +334,7 @@ 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);
@@ -360,6 +362,10 @@ public class ItemImport extends DSpaceRunnable<ItemImportScriptConfiguration> {
             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);
+        }
     }
 
     /**

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

@@ -17,6 +17,7 @@ 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;
@@ -111,7 +112,11 @@ public class ItemImportCLI extends ItemImport {
 
                 // validate zip file
                 InputStream validationFileStream = new FileInputStream(myZipFile);
+                try {
                     validateZip(validationFileStream);
+                } finally {
+                    IOUtils.closeQuietly(validationFileStream);
+                }
 
                 workDir = new File(itemImportService.getTempWorkDir() + File.separator + TEMP_DIR
                         + File.separator + context.getCurrentUser().getID());
@@ -120,9 +125,11 @@ 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
-                    Optional<InputStream> validationFileStream = Optional.ofNullable(new URL(zipfilename).openStream());
+
                         if (validationFileStream.isPresent()) {
                             validateZip(validationFileStream.get());
                         }
@@ -137,6 +144,10 @@ public class ItemImportCLI extends ItemImport {
                         throw new IllegalArgumentException(
                                 "Error reading file, the file couldn't be found for filename: " + zipfilename);
                     }
+                } finally {
+                    optionalFileStream.ifPresent(IOUtils::closeQuietly);
+                    validationFileStream.ifPresent(IOUtils::closeQuietly);
+                }
             }
         }
     }

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

@@ -131,7 +131,7 @@ public final class CheckerCommand {
                 collector.collect(context, info);
             }
 
-            context.uncacheEntity(bitstream);
+            context.commit();
             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), startDate),
-            criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate)
+                .lessThanOrEqualTo(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), endDate),
+            criteriaBuilder.greaterThan(mostRecentChecksumRoot.get(MostRecentChecksum_.processStartDate), startDate)
                             )
         );
         List<Order> orderList = new LinkedList<>();

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

@@ -34,35 +34,37 @@ import org.xml.sax.InputSource;
  * from {@code ${dspace.dir}/config/controlled-vocabularies/*.xml} and turns
  * them into autocompleting authorities.
  *
- * Configuration: This MUST be configured as a self-named plugin, e.g.: {@code
- * plugin.selfnamed.org.dspace.content.authority.ChoiceAuthority = \
+ * <p>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
  * }
  *
- * It AUTOMATICALLY configures a plugin instance for each XML file in the
+ * <p>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".
  *
- * 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: "::"
- * }
+ * <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>
  *
  * @author Michael B. Klein
  */
 
 public class DSpaceControlledVocabulary extends SelfNamedPlugin implements HierarchicalAuthority {
 
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(DSpaceControlledVocabulary.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
     protected static String xpathTemplate = "//node[contains(translate(@label,'ABCDEFGHIJKLMNOPQRSTUVWXYZ'," +
-        "'abcdefghijklmnopqrstuvwxyz'),'%s')]";
-    protected static String idTemplate = "//node[@id = '%s']";
-    protected static String labelTemplate = "//node[@label = '%s']";
+        "'abcdefghijklmnopqrstuvwxyz'),%s)]";
+    protected static String idTemplate = "//node[@id = %s]";
+    protected static String idTemplateQuoted = "//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 pluginNames[] = null;
@@ -106,7 +108,7 @@ 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<String>();
+            List<String> names = new ArrayList<>();
             for (String filename : xmlFiles) {
                 names.add((new File(filename)).getName().replace(".xml", ""));
             }
@@ -162,14 +164,23 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     public Choices getMatches(String text, int start, int limit, String locale) {
         init();
         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++) {
-            xpathExpression += String.format(xpathTemplate, textHierarchy[i].replaceAll("'", "&apos;").toLowerCase());
+            xpathExpressionBuilder.append(String.format(xpathTemplate, "$var" + i));
         }
+        String xpathExpression = xpathExpressionBuilder.toString();
         XPath xpath = XPathFactory.newInstance().newXPath();
-        int total = 0;
-        List<Choice> choices = new ArrayList<Choice>();
+        xpath.setXPathVariableResolver(variableName -> {
+            String varName = variableName.getLocalPart();
+            if (varName.startsWith("var")) {
+                int index = Integer.parseInt(varName.substring(3));
+                return textHierarchy[index].toLowerCase();
+            }
+            throw new IllegalArgumentException("Unexpected variable: " + varName);
+        });
+        int total;
+        List<Choice> choices;
         try {
             NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
             total = results.getLength();
@@ -185,14 +196,23 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     @Override
     public Choices getBestMatch(String text, String locale) {
         init();
-        log.debug("Getting best matches for '" + text + "'");
-        String xpathExpression = "";
+        log.debug("Getting best matches for {}'", text);
         String[] textHierarchy = text.split(hierarchyDelimiter, -1);
+        StringBuilder xpathExpressionBuilder = new StringBuilder();
         for (int i = 0; i < textHierarchy.length; i++) {
-            xpathExpression += String.format(labelTemplate, textHierarchy[i].replaceAll("'", "&apos;"));
+            xpathExpressionBuilder.append(String.format(labelTemplate, "$var" + i));
         }
+        String xpathExpression = xpathExpressionBuilder.toString();
         XPath xpath = XPathFactory.newInstance().newXPath();
-        List<Choice> choices = new ArrayList<Choice>();
+        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;
         try {
             NodeList results = (NodeList) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODESET);
             choices = getChoicesFromNodeList(results, 0, 1);
@@ -240,7 +260,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     @Override
     public Choices getChoicesByParent(String authorityName, String parentId, int start, int limit, String locale) {
         init();
-        String xpathExpression = String.format(idTemplate, parentId);
+        String xpathExpression = String.format(idTemplateQuoted, parentId);
         return getChoicesByXpath(xpathExpression, start, limit);
     }
 
@@ -264,15 +284,12 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private boolean isRootElement(Node node) {
-        if (node != null && node.getOwnerDocument().getDocumentElement().equals(node)) {
-            return true;
-        }
-        return false;
+        return node != null && node.getOwnerDocument().getDocumentElement().equals(node);
     }
 
     private Node getNode(String key) throws XPathExpressionException {
         init();
-        String xpathExpression = String.format(idTemplate, key);
+        String xpathExpression = String.format(idTemplateQuoted, key);
         Node node = getNodeFromXPath(xpathExpression);
         return node;
     }
@@ -284,7 +301,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private List<Choice> getChoicesFromNodeList(NodeList results, int start, int limit) {
-        List<Choice> choices = new ArrayList<Choice>();
+        List<Choice> choices = new ArrayList<>();
         for (int i = 0; i < results.getLength(); i++) {
             if (i < start) {
                 continue;
@@ -303,14 +320,14 @@ 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<String, String>();
+        Map<String, String> extras = new HashMap<>();
         if (StringUtils.isNotBlank(parentCurr)) {
             extras.put("parent", parentCurr);
         }
         if (StringUtils.isNotBlank(noteCurr)) {
             extras.put("note", noteCurr);
         }
-        if (childrenCurr.size() > 0) {
+        if (!childrenCurr.isEmpty()) {
             extras.put("hasChildren", "true");
         } else {
             extras.put("hasChildren", "false");
@@ -368,7 +385,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private List<String> getChildren(Node node) {
-        List<String> children = new ArrayList<String>();
+        List<String> children = new ArrayList<>();
         NodeList childNodes = node.getChildNodes();
         for (int ci = 0; ci < childNodes.getLength(); ci++) {
             Node firstChild = childNodes.item(ci);
@@ -391,7 +408,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     private boolean isSelectable(Node node) {
         Node selectableAttr = node.getAttributes().getNamedItem("selectable");
         if (null != selectableAttr) {
-            return Boolean.valueOf(selectableAttr.getNodeValue());
+            return Boolean.parseBoolean(selectableAttr.getNodeValue());
         } else { // Default is true
             return true;
         }
@@ -418,7 +435,7 @@ public class DSpaceControlledVocabulary extends SelfNamedPlugin implements Hiera
     }
 
     private Choices getChoicesByXpath(String xpathExpression, int start, int limit) {
-        List<Choice> choices = new ArrayList<Choice>();
+        List<Choice> choices = new ArrayList<>();
         XPath xpath = XPathFactory.newInstance().newXPath();
         try {
             Node parentNode = (Node) xpath.evaluate(xpathExpression, vocabulary, XPathConstants.NODE);

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

@@ -20,9 +20,7 @@ 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;
@@ -224,29 +222,17 @@ 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 (handle != null && baseUrl != null) {
+        if (baseUrl != null) {
             oiv.setText(baseUrl
-                            + "/bitstream/"
-                            + URLEncoder.encode(handle, "UTF-8")
-                            + "/"
-                            + sid
-                            + "/"
-                            + URLEncoder.encode(bsName, "UTF-8"));
+                + "/bitstreams/"
+                + bitstream.getID()
+                + "/download");
         } else {
             oiv.setText(URLEncoder.encode(bsName, "UTF-8"));
         }

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

@@ -152,7 +152,7 @@ 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.id not in" +
+                                  "SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit 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

@@ -12,6 +12,7 @@ import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
+import java.util.UUID;
 import javax.persistence.Query;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -19,6 +20,7 @@ import javax.persistence.criteria.Join;
 import javax.persistence.criteria.Predicate;
 import javax.persistence.criteria.Root;
 
+import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.authorize.ResourcePolicy_;
 import org.dspace.content.Collection;
@@ -40,6 +42,11 @@ 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();
     }
@@ -159,7 +166,7 @@ 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.id = " +
+        return list(createQuery(context, "SELECT DISTINCT c FROM Collection c JOIN Subscription s ON c = " +
                 "s.dSpaceObject"));
     }
 
@@ -172,14 +179,25 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
     @SuppressWarnings("unchecked")
     public List<Map.Entry<Collection, Long>> getCollectionsWithBitstreamSizesTotal(Context context)
         throws SQLException {
-        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";
+        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";
         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) {
-            returnList.add(new AbstractMap.SimpleEntry<>((Collection) o[0], (Long) o[1]));
+            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]);
+            }
         }
         return returnList;
     }

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

@@ -498,8 +498,11 @@ 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);
@@ -513,6 +516,9 @@ 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
 
@@ -520,18 +526,15 @@ 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;
     }
 

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

@@ -458,7 +458,20 @@ 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);
     }
 
+    /**
+     * Create a Query object from a CriteriaQuery
+     * @param context current Context
+     * @param criteriaQuery CriteriaQuery built via CriteriaBuilder
+     * @return corresponding Query
+     * @throws SQLException if error occurs
+     */
+    public Query createQuery(Context context, CriteriaQuery criteriaQuery) throws SQLException {
+        return this.getHibernateSession(context).createQuery(criteriaQuery);
+    }
 }

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

@@ -140,7 +140,7 @@ public class CitationDocumentServiceImpl implements CitationDocumentService, Ini
         //Load enabled collections
         String[] citationEnabledCollections = configurationService
                 .getArrayProperty("citation-page.enabled_collections");
-        citationEnabledCollectionsList = Arrays.asList(citationEnabledCollections);
+        citationEnabledCollectionsList = new ArrayList<String>(Arrays.asList(citationEnabledCollections));
 
         //Load enabled communities, and add to collection-list
         String[] citationEnabledCommunities = configurationService

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

@@ -373,7 +373,7 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport {
 
     @Override
     public String getName() {
-        return getEmail();
+        return this.getFullName();
     }
 
     String getDigestAlgorithm() {

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().length() > 0) {
+                if (e.getEmail() != null && !e.getEmail().isEmpty()) {
                     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().length() > 0) {
+                if (e.getFirstName() != null && !e.getFirstName().isEmpty()) {
                     info.put("Have 1st name", info.get("Have 1st name") + 1);
                 }
-                if (e.getLastName() != null && e.getLastName().length() > 0) {
+                if (e.getLastName() != null && !e.getLastName().isEmpty()) {
                     info.put("Have 2nd name", info.get("Have 2nd name") + 1);
                 }
-                if (e.getLanguage() != null && e.getLanguage().length() > 0) {
+                if (e.getLanguage() != null && !e.getLanguage().isEmpty()) {
                     info.put("Have lang", info.get("Have lang") + 1);
                 }
-                if (e.getNetid() != null && e.getNetid().length() > 0) {
+                if (e.getNetid() != null && !e.getNetid().isEmpty()) {
                     info.put("Have netid", info.get("Have netid") + 1);
                 }
-                if (e.getNetid() != null && e.getNetid().length() > 0) {
+                if (e.getNetid() != null && !e.getNetid().isEmpty()) {
                     info.put("Self registered", info.get("Self registered") + 1);
                 }
             }

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

@@ -105,4 +105,13 @@ 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/pubmed/service/PubmedImportMetadataSourceServiceImpl.java

@@ -55,6 +55,7 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
 
     private String urlFetch;
     private String urlSearch;
+    private String apiKey;
 
     private int attempt = 3;
 
@@ -210,6 +211,9 @@ 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>>();
@@ -286,6 +290,9 @@ 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());
@@ -316,6 +323,9 @@ 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());
@@ -388,6 +398,9 @@ 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));
@@ -428,6 +441,9 @@ 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));
@@ -457,6 +473,9 @@ 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);
@@ -532,4 +551,8 @@ public class PubmedImportMetadataSourceServiceImpl extends AbstractImportMetadat
         this.urlSearch = urlSearch;
     }
 
+    public void setApiKey(String apiKey) {
+        this.apiKey = apiKey;
+    }
+
 }

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

@@ -39,6 +39,7 @@ 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.
@@ -129,6 +130,15 @@ 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

@@ -9,6 +9,7 @@ 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;
@@ -73,12 +74,12 @@ 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.setWorkType(getWorkType(context, item));
+        work.setWorkExternalIdentifiers(getWorkExternalIds(context, item, work));
         work.setShortDescription(getShortDescription(context, item));
         work.setLanguageCode(getLanguageCode(context, item));
         work.setUrl(getUrl(context, item));
@@ -149,63 +150,71 @@ public class OrcidWorkFactory implements OrcidEntityFactory {
     }
 
     /**
-     * Creates an instance of ExternalIDs from the metadata values of the given
-     * item, using the orcid.mapping.funding.external-ids configuration.
+     * Returns a list of external work IDs constructed in the org.orcid.jaxb
+     * ExternalIDs object
      */
-    private ExternalIDs getWorkExternalIds(Context context, Item item) {
-        ExternalIDs externalIdentifiers = new ExternalIDs();
-        externalIdentifiers.getExternalIdentifier().addAll(getWorkSelfExternalIds(context, item));
-        return externalIdentifiers;
+    private ExternalIDs getWorkExternalIds(Context context, Item item, Work work) {
+        ExternalIDs externalIDs = new ExternalIDs();
+        externalIDs.getExternalIdentifier().addAll(getWorkExternalIdList(context, item, work));
+        return externalIDs;
     }
 
     /**
      * Creates a list of ExternalID, one for orcid.mapping.funding.external-ids
-     * value, taking the values from the given item.
+     * value, taking the values from the given item and work type.
      */
-    private List<ExternalID> getWorkSelfExternalIds(Context context, Item item) {
+    private List<ExternalID> getWorkExternalIdList(Context context, Item item, Work work) {
 
-        List<ExternalID> selfExternalIds = new ArrayList<ExternalID>();
+        List<ExternalID> externalIds = new ArrayList<>();
 
         Map<String, String> externalIdentifierFields = fieldMapping.getExternalIdentifierFields();
 
         if (externalIdentifierFields.containsKey(SIMPLE_HANDLE_PLACEHOLDER)) {
             String handleType = externalIdentifierFields.get(SIMPLE_HANDLE_PLACEHOLDER);
-            selfExternalIds.add(getExternalId(handleType, item.getHandle(), SELF));
+            ExternalID handle = new ExternalID();
+            handle.setType(handleType);
+            handle.setValue(item.getHandle());
+            handle.setRelationship(SELF);
+            externalIds.add(handle);
         }
 
+        // 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(this::getSelfExternalId)
-            .forEach(selfExternalIds::add);
+            .map(metadataValue -> this.getExternalId(metadataValue, workType))
+            .forEach(externalIds::add);
 
-        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);
+        return externalIds;
     }
 
     /**
      * Creates an instance of ExternalID with the given type, value and
      * relationship.
      */
-    private ExternalID getExternalId(String type, String value, Relationship 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;
+        }
         ExternalID externalID = new ExternalID();
-        externalID.setType(type);
-        externalID.setValue(value);
+        externalID.setType(identifierType);
+        externalID.setValue(metadataValue.getValue());
         externalID.setRelationship(relationship);
         return externalID;
     }
 
     /**
-     * Creates an instance of WorkType from the given item, taking the value fom the
+     * Creates an instance of WorkType from the given item, taking the value from the
      * configured metadata field (orcid.mapping.work.type).
      */
     private WorkType getWorkType(Context context, Item item) {

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

@@ -283,6 +283,8 @@ 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
      */
-    private StepResult parse(String[] args) throws ParseException {
+    protected 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

@@ -28,6 +28,7 @@ import java.text.DateFormat;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.Calendar;
 import java.util.Date;
 import java.util.EnumSet;
@@ -232,6 +233,10 @@ public class SolrLoggerServiceImpl implements SolrLoggerService, InitializingBea
             throw new RuntimeException(e);
         }
 
+        if (dspaceObject instanceof Bitstream && !isBitstreamLoggable((Bitstream) dspaceObject)) {
+            return;
+        }
+
         if (solr == null) {
             return;
         }
@@ -279,6 +284,10 @@ 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;
         }
@@ -1713,4 +1722,35 @@ 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

@@ -136,9 +136,10 @@ 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:" + hostName + ":" + item
+                append(URLEncoder.encode("oai:" + oaiPrefix + ":" + 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

@@ -423,7 +423,7 @@ public class BitstreamStorageServiceImpl implements BitstreamStorageService, Ini
             //modulo
             if ((processedCounter % batchCommitSize) == 0) {
                 log.info("Migration Commit Checkpoint: " + processedCounter);
-                context.dispatchEvents();
+                context.commit();
             }
         }
 

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

@@ -19,9 +19,11 @@ 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.
@@ -252,7 +254,10 @@ public class DSBitStoreService extends BaseBitStoreService {
         }
         File bitstreamFile = new File(bufFilename.toString());
         Path normalizedPath = bitstreamFile.toPath().normalize();
-        if (!normalizedPath.startsWith(baseDir.getAbsolutePath())) {
+        String[] allowedAssetstoreRoots = DSpaceServicesFactory.getInstance().getConfigurationService()
+                .getArrayProperty("assetstore.allowed.roots", new String[]{});
+        if (!normalizedPath.startsWith(baseDir.getAbsolutePath())
+            && !StringUtils.startsWithAny(normalizedPath.toString(), allowedAssetstoreRoots)) {
             log.error("Bitstream path outside of assetstore root requested:" +
                     "bitstream={}, path={}, assetstore={}",
                     bitstream.getID(), normalizedPath, baseDir.getAbsolutePath());

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

@@ -67,6 +67,7 @@ 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);
@@ -77,7 +78,10 @@ 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;
@@ -126,6 +130,8 @@ 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/util/DateMathParser.java

@@ -13,6 +13,7 @@ import java.time.LocalDate;
 import java.time.LocalDateTime;
 import java.time.LocalTime;
 import java.time.ZoneId;
+import java.time.ZoneOffset;
 import java.time.ZonedDateTime;
 import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeFormatterBuilder;
@@ -107,7 +108,7 @@ public class DateMathParser {
 
     private static final Logger LOG = LogManager.getLogger();
 
-    public static final TimeZone UTC = TimeZone.getTimeZone("UTC");
+    public static final TimeZone UTC = TimeZone.getTimeZone(ZoneOffset.UTC);
 
     /**
      * Default TimeZone for DateMath rounding (UTC)

dspace-api/src/main/resources/spring/spring-dspace-addon-import-services.xml

@@ -56,6 +56,7 @@
         <property name="metadataFieldMapping" ref="pubmedMetadataFieldMapping"/>
         <property name="urlFetch" value="${pubmed.url.fetch}"/>
         <property name="urlSearch" value="${pubmed.url.search}"/>
+        <property name="apiKey" value="${pubmed.apiKey}"/>
         <property name="generateQueryForItem" ref="pubmedService"></property>
         <property name="interRequestTime" value="500"/>
         <property name="supportedExtensions">

dspace-api/src/test/data/dspaceFolder/config/spring/api/workflow-actions.xml

@@ -23,7 +23,6 @@
         <property name="minimumAcceptanceScore" value="3" />
     </bean>
 
-
     <bean id="autoassignactionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.AutoAssignAction" scope="prototype"/>
     <bean id="noUserSelectionActionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.NoUserSelectionAction" scope="prototype"/>
     <bean id="assignoriginalsubmitteractionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.AssignOriginalSubmitterAction" scope="prototype"/>
@@ -46,7 +45,6 @@
         <property name="requiresUI" value="true"/>
     </bean>
 
-
     <!--Action for the select single reviewer workflow -->
     <bean id="selectrevieweraction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="selectrevieweraction"/>
@@ -66,21 +64,14 @@
         <property name="requiresUI" value="true"/>
     </bean>
 
-    <bean id="ratingreviewaction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
-        <constructor-arg type="java.lang.String" value="ratingreviewaction"/>
-        <property name="processingAction" ref="ratingreviewactionAPI" />
-        <property name="requiresUI" value="true"/>
-    </bean>
-
-    <!--Autmatic step that evaluates scores (workflow.score) and checks if they match the configured minimum for archiving -->
+    <!--Automatic step that evaluates scores (workflow.score) and checks if they match the configured minimum for archiving -->
     <bean id="evaluationaction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="evaluationaction"/>
         <property name="processingAction" ref="evaluationactionAPI" />
         <property name="requiresUI" value="false"/>
     </bean>
 
-
-<!--User selection actions-->
+    <!--User selection actions-->
     <bean id="claimaction" class="org.dspace.xmlworkflow.state.actions.UserSelectionActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="claimaction"/>
         <property name="processingAction" ref="claimactionAPI"/>

dspace-api/src/test/java/org/dspace/AbstractDSpaceIntegrationTest.java

@@ -12,6 +12,7 @@ import static org.junit.Assert.fail;
 import java.io.IOException;
 import java.net.URL;
 import java.sql.SQLException;
+import java.time.ZoneOffset;
 import java.util.Properties;
 import java.util.TimeZone;
 
@@ -73,8 +74,10 @@ public class AbstractDSpaceIntegrationTest {
             //Stops System.exit(0) throws exception instead of exitting
             System.setSecurityManager(new NoExitSecurityManager());
 
-            //set a standard time zone for the tests
-            TimeZone.setDefault(TimeZone.getTimeZone("Europe/Dublin"));
+            // All tests should assume UTC timezone by default (unless overridden in the test itself)
+            // This ensures that Spring doesn't attempt to change the timezone of dates that are read from the
+            // database (via Hibernate). We store all dates in the database as UTC.
+            TimeZone.setDefault(TimeZone.getTimeZone(ZoneOffset.UTC));
 
             //load the properties of the tests
             testProps = new Properties();

dspace-api/src/test/java/org/dspace/AbstractDSpaceTest.java

@@ -12,6 +12,7 @@ import static org.junit.Assert.fail;
 import java.io.IOException;
 import java.net.URL;
 import java.sql.SQLException;
+import java.time.ZoneOffset;
 import java.util.Properties;
 import java.util.TimeZone;
 
@@ -82,8 +83,10 @@ public class AbstractDSpaceTest {
     @BeforeClass
     public static void initKernel() {
         try {
-            //set a standard time zone for the tests
-            TimeZone.setDefault(TimeZone.getTimeZone("Europe/Dublin"));
+            // All tests should assume UTC timezone by default (unless overridden in the test itself)
+            // This ensures that Spring doesn't attempt to change the timezone of dates that are read from the
+            // database (via Hibernate). We store all dates in the database as UTC.
+            TimeZone.setDefault(TimeZone.getTimeZone(ZoneOffset.UTC));
 
             //load the properties of the tests
             testProps = new Properties();

dspace-api/src/test/java/org/dspace/app/bulkedit/MetadataExportSearchIT.java

@@ -251,4 +251,35 @@ public class MetadataExportSearchIT extends AbstractIntegrationTestWithDatabase
         assertNotNull(exception);
         assertEquals("nonExisting is not a valid search filter", exception.getMessage());
     }
+
+    @Test
+    public void exportMetadataSearchDoubleQuotedArgumentTest() throws Exception {
+        context.turnOffAuthorisationSystem();
+        Item quotedItem1 = ItemBuilder.createItem(context, collection)
+                .withTitle("The Special Runnable Item")
+                .withSubject("quoted-subject")
+                .build();
+        Item quotedItem2 = ItemBuilder.createItem(context, collection)
+                .withTitle("The Special Item")
+                .withSubject("quoted-subject")
+                .build();
+        context.restoreAuthSystemState();
+
+        int result = runDSpaceScript(
+                "metadata-export-search",
+                "-q", "title:\"Special Runnable\"",
+                "-n", filename);
+
+        assertEquals(0, result);
+
+        Item[] expectedResult = new Item[] {quotedItem1};
+        checkItemsPresentInFile(filename, expectedResult);
+
+        File file = new File(filename);
+        try (Reader reader = Files.newReader(file, Charset.defaultCharset());
+             CSVReader csvReader = new CSVReader(reader)) {
+            List<String[]> lines = csvReader.readAll();
+            assertEquals("Unexpected extra items in export", 2, lines.size());
+        }
+    }
 }

dspace-api/src/test/java/org/dspace/app/client/DSpaceHttpClientFactoryTest.java

@@ -17,6 +17,7 @@ import static org.mockito.Mockito.verifyNoInteractions;
 import static org.mockito.Mockito.verifyNoMoreInteractions;
 import static org.mockito.Mockito.when;
 
+import java.net.InetAddress;
 import java.util.List;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.atomic.AtomicReference;
@@ -107,7 +108,14 @@ public class DSpaceHttpClientFactoryTest {
 
     @Test
     public void testBuildWithProxyConfiguredAndHostPrefixToIgnoreSet() throws Exception {
-        setHttpProxyOnConfigurationService("local*", "www.test.com");
+        // Get hostname assigned to 127.0.0.1 (usually is "localhost", but not always)
+        InetAddress address = InetAddress.getByAddress(new byte[]{127, 0, 0, 1});
+        String hostname = address.getHostName();
+        // Take first 4 characters hostname as the prefix (e.g. "loca" in "localhost")
+        String hostnamePrefix =  hostname.substring(0, 4);
+        // Save hostname prefix to our list of hosts to ignore, followed by an asterisk.
+        // (This should result in our Proxy ignoring our localhost)
+        setHttpProxyOnConfigurationService(hostnamePrefix + "*", "www.test.com");
         CloseableHttpClient httpClient = httpClientFactory.build();
         assertThat(mockProxy.getRequestCount(), is(0));
         assertThat(mockServer.getRequestCount(), is(0));
@@ -122,7 +130,14 @@ public class DSpaceHttpClientFactoryTest {
 
     @Test
     public void testBuildWithProxyConfiguredAndHostSuffixToIgnoreSet() throws Exception {
-        setHttpProxyOnConfigurationService("www.test.com", "*host");
+        // Get hostname assigned to 127.0.0.1 (usually is "localhost", but not always)
+        InetAddress address = InetAddress.getByAddress(new byte[]{127, 0, 0, 1});
+        String hostname = address.getHostName();
+        // Take last 4 characters hostname as the suffix (e.g. "host" in "localhost")
+        String hostnameSuffix =  hostname.substring(hostname.length() - 4);
+        // Save hostname suffix to our list of hosts to ignore, preceded by an asterisk.
+        // (This should result in our Proxy ignoring our localhost)
+        setHttpProxyOnConfigurationService("www.test.com", "*" + hostnameSuffix);
         CloseableHttpClient httpClient = httpClientFactory.build();
         assertThat(mockProxy.getRequestCount(), is(0));
         assertThat(mockServer.getRequestCount(), is(0));

dspace-api/src/test/java/org/dspace/builder/ItemBuilder.java

@@ -112,6 +112,14 @@ public class ItemBuilder extends AbstractDSpaceObjectBuilder<Item> {
         return addMetadataValue(item, "dc", "identifier", "scopus", scopus);
     }
 
+    public ItemBuilder withISSN(String issn) {
+        return addMetadataValue(item, "dc", "identifier", "issn", issn);
+    }
+
+    public ItemBuilder withISBN(String isbn) {
+        return addMetadataValue(item, "dc", "identifier", "isbn", isbn);
+    }
+
     public ItemBuilder withRelationFunding(String funding) {
         return addMetadataValue(item, "dc", "relation", "funding", funding);
     }

dspace-api/src/test/java/org/dspace/checker/ChecksumCheckerIT.java

@@ -0,0 +1,193 @@
+/**
+ * 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.checker;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.junit.Assert.assertTrue;
+import static org.junit.Assert.fail;
+
+import java.sql.SQLException;
+import java.time.Instant;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.dspace.AbstractIntegrationTestWithDatabase;
+import org.dspace.builder.BitstreamBuilder;
+import org.dspace.builder.CollectionBuilder;
+import org.dspace.builder.CommunityBuilder;
+import org.dspace.builder.ItemBuilder;
+import org.dspace.checker.factory.CheckerServiceFactory;
+import org.dspace.checker.service.ChecksumHistoryService;
+import org.dspace.checker.service.MostRecentChecksumService;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+public class ChecksumCheckerIT extends AbstractIntegrationTestWithDatabase {
+    protected List<Bitstream> bitstreams;
+    protected MostRecentChecksumService checksumService =
+        CheckerServiceFactory.getInstance().getMostRecentChecksumService();
+
+    @Before
+    public void setup() throws Exception {
+        context.turnOffAuthorisationSystem();
+
+        Community parentCommunity = CommunityBuilder.createCommunity(context).build();
+        Collection collection = CollectionBuilder.createCollection(context, parentCommunity)
+            .build();
+        Item item = ItemBuilder.createItem(context, collection).withTitle("Test item")
+            .build();
+
+        int numBitstreams = 3;
+        bitstreams = new ArrayList<>();
+        for (int i = 0; i < numBitstreams; i++) {
+            String content = "Test bitstream " + i;
+            bitstreams.add(
+                BitstreamBuilder.createBitstream(
+                    context, item, IOUtils.toInputStream(content, UTF_8)
+                ).build()
+            );
+        }
+
+        context.restoreAuthSystemState();
+
+        // Call the "updateMissingBitstreams" method so that the test bitstreams
+        // already have checksums in the past when CheckerCommand runs.
+        // Otherwise, the CheckerCommand will simply update the test
+        // bitstreams without going through the BitstreamDispatcher.
+        checksumService = CheckerServiceFactory.getInstance().getMostRecentChecksumService();
+        checksumService.updateMissingBitstreams(context);
+
+        // The "updateMissingBitstreams" method updates the test bitstreams in
+        // a random order. To verify that the expected bitstreams were
+        // processed, reset the timestamps so that the bitstreams are
+        // checked in a specific order (oldest first).
+        Instant checksumInstant = Instant.ofEpochMilli(0);
+        for (Bitstream bitstream: bitstreams) {
+            MostRecentChecksum mrc = checksumService.findByBitstream(context, bitstream);
+            mrc.setProcessStartDate(Date.from(checksumInstant));
+            mrc.setProcessEndDate(Date.from(checksumInstant));
+            checksumInstant = checksumInstant.plusSeconds(10);
+        }
+        context.commit();
+    }
+
+    @After
+    public void cleanUp() throws SQLException {
+        // Need to clean up ChecksumHistory because of a referential integrity
+        // constraint violation between the most_recent_checksum table and
+        // bitstream tables
+        ChecksumHistoryService checksumHistoryService = CheckerServiceFactory.getInstance().getChecksumHistoryService();
+
+        for (Bitstream bitstream: bitstreams) {
+            checksumHistoryService.deleteByBitstream(context, bitstream);
+        }
+    }
+
+    @Test
+    public void testChecksumsRecordedWhenProcesingIsInterrupted() throws SQLException {
+        CheckerCommand checker = new CheckerCommand(context);
+
+        // The start date to use for the checker process
+        Date checkerStartDate = Date.from(Instant.now());
+
+        // Verify that all checksums are before the checker start date
+        for (Bitstream bitstream: bitstreams) {
+            MostRecentChecksum checksum = checksumService.findByBitstream(context, bitstream);
+            Date lastChecksumDate = checksum.getProcessStartDate();
+            assertTrue("lastChecksumDate (" + lastChecksumDate + ") <= checkerStartDate (" + checkerStartDate + ")",
+                lastChecksumDate.before(checkerStartDate));
+        }
+
+        // Dispatcher that throws an exception when a third bitstream is
+        // retrieved.
+        BitstreamDispatcher dispatcher = new ExpectionThrowingDispatcher(
+            context, checkerStartDate, false, 2);
+        checker.setDispatcher(dispatcher);
+
+
+        // Run the checksum checker
+        checker.setProcessStartDate(checkerStartDate);
+        try {
+            checker.process();
+            fail("SQLException should have been thrown");
+        } catch (SQLException sqle) {
+            // Rollback any pending transaction
+            context.rollback();
+        }
+
+        // Verify that the checksums of the first two bitstreams (that were
+        // processed before the exception) have been successfully recorded in
+        // the database, while the third bitstream was not updated.
+        int bitstreamCount = 0;
+        for (Bitstream bitstream: bitstreams) {
+            MostRecentChecksum checksum = checksumService.findByBitstream(context, bitstream);
+            Date lastChecksumDate = checksum.getProcessStartDate();
+
+            bitstreamCount = bitstreamCount + 1;
+            if (bitstreamCount <= 2) {
+                assertTrue("lastChecksumDate (" + lastChecksumDate + ") <= checkerStartDate (" + checkerStartDate + ")",
+                    lastChecksumDate.after(checkerStartDate));
+            } else {
+                assertTrue("lastChecksumDate (" + lastChecksumDate + ") >= checkerStartDate (" + checkerStartDate + ")",
+                    lastChecksumDate.before(checkerStartDate));
+            }
+        }
+    }
+
+    /**
+     * Subclass of SimpleDispatcher that only allows a limited number of "next"
+     * class before throwing a SQLException.
+     */
+    class ExpectionThrowingDispatcher extends SimpleDispatcher {
+        // The number of "next" calls to allow before throwing a SQLException
+        protected int maxNextCalls;
+
+        // The number of "next" method calls seen so far.
+        protected int numNextCalls = 0;
+
+        /**
+         * Constructor.
+         *
+         * @param context   Context
+         * @param startTime timestamp for beginning of checker process
+         * @param looping   indicates whether checker should loop infinitely
+         *                  through most_recent_checksum table
+         * @param maxNextCalls the number of "next" method calls to allow before
+         * throwing a SQLException.
+         */
+        public ExpectionThrowingDispatcher(Context context, Date startTime, boolean looping, int maxNextCalls) {
+            super(context, startTime, looping);
+            this.maxNextCalls = maxNextCalls;
+        }
+
+        /**
+         * Selects the next candidate bitstream.
+         *
+         * After "maxNextClass" number of calls, this method throws a
+         * SQLException.
+         *
+         * @throws SQLException if database error
+         */
+        @Override
+        public synchronized Bitstream next() throws SQLException {
+            numNextCalls = numNextCalls + 1;
+            if (numNextCalls > maxNextCalls) {
+                throw new SQLException("Max 'next' method calls exceeded");
+            }
+            return super.next();
+        }
+    }
+}

dspace-api/src/test/java/org/dspace/content/BitstreamTest.java

@@ -12,6 +12,7 @@ import static org.hamcrest.CoreMatchers.not;
 import static org.hamcrest.CoreMatchers.notNullValue;
 import static org.hamcrest.CoreMatchers.nullValue;
 import static org.hamcrest.MatcherAssert.assertThat;
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
@@ -25,6 +26,9 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
 
@@ -148,6 +152,44 @@ public class BitstreamTest extends AbstractDSpaceObjectTest {
         assertTrue("testFindAll 2", added);
     }
 
+    @Test
+    public void testFindAllBatches() throws Exception {
+        //Adding some data for processing and cleaning this up at the end
+        context.turnOffAuthorisationSystem();
+        File f = new File(testProps.get("test.bitstream").toString());
+        List<Bitstream> inserted = new ArrayList<>();
+        for (int i = 0; i < 5; i++) {
+            Bitstream bs = bitstreamService.create(context, new FileInputStream(f));
+            inserted.add(bs);
+        }
+        context.restoreAuthSystemState();
+
+        // sorted list of all bitstreams
+        List<Bitstream> all = bitstreamService.findAll(context);
+        List<Bitstream> expected = new ArrayList<>(all);
+        expected.sort(Comparator.comparing(bs -> bs.getID().toString()));
+
+        int total = bitstreamService.countTotal(context);
+        int batchSize = 2;
+        int numberOfBatches = (int) Math.ceil((double) total / batchSize);
+
+        //collect in batches
+        List<Bitstream> collected = new ArrayList<>();
+        for (int i = 0; i < numberOfBatches; i++) {
+            Iterator<Bitstream> it = bitstreamService.findAll(context, batchSize, i * batchSize);
+            it.forEachRemaining(collected::add);
+        }
+
+        assertEquals("Batched results should match sorted findAll", expected, collected);
+
+        // Cleanup
+        context.turnOffAuthorisationSystem();
+        for (Bitstream b : inserted) {
+            bitstreamService.delete(context, b);
+        }
+        context.restoreAuthSystemState();
+    }
+
     /**
      * Test of create method, of class Bitstream.
      */

dspace-api/src/test/java/org/dspace/content/authority/DSpaceControlledVocabularyTest.java

@@ -8,6 +8,7 @@
 package org.dspace.content.authority;
 
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertNotNull;
 
 import java.io.IOException;
@@ -86,6 +87,7 @@ public class DSpaceControlledVocabularyTest extends AbstractDSpaceTest {
             CoreServiceFactory.getInstance().getPluginService().getNamedPlugin(Class.forName(PLUGIN_INTERFACE), "farm");
         assertNotNull(instance);
         Choices result = instance.getMatches(text, start, limit, locale);
+        assertNotEquals("At least one match expected", 0, result.values.length);
         assertEquals("north 40", result.values[0].value);
     }
 

dspace-api/src/test/java/org/dspace/orcid/service/OrcidEntityFactoryServiceIT.java

@@ -73,6 +73,9 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
 
     private Collection projects;
 
+    private static final String isbn = "978-0-439-02348-1";
+    private static final String issn = "1234-1234X";
+
     @Before
     public void setup() {
 
@@ -117,6 +120,7 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
             .withLanguage("en_US")
             .withType("Book")
             .withIsPartOf("Journal")
+            .withISBN(isbn)
             .withDoiIdentifier("doi-id")
             .withScopusIdentifier("scopus-id")
             .build();
@@ -149,13 +153,102 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
         assertThat(work.getExternalIdentifiers(), notNullValue());
 
         List<ExternalID> externalIds = work.getExternalIdentifiers().getExternalIdentifier();
-        assertThat(externalIds, hasSize(3));
+        assertThat(externalIds, hasSize(4));
         assertThat(externalIds, has(selfExternalId("doi", "doi-id")));
         assertThat(externalIds, has(selfExternalId("eid", "scopus-id")));
         assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+        // Book type should have SELF rel for ISBN
+        assertThat(externalIds, has(selfExternalId("isbn", isbn)));
 
     }
 
+    @Test
+    public void testJournalArticleAndISSN() {
+        context.turnOffAuthorisationSystem();
+
+        Item publication = ItemBuilder.createItem(context, publications)
+            .withTitle("Test publication")
+            .withAuthor("Walter White")
+            .withAuthor("Jesse Pinkman")
+            .withEditor("Editor")
+            .withIssueDate("2021-04-30")
+            .withDescriptionAbstract("Publication description")
+            .withLanguage("en_US")
+            .withType("Article")
+            .withIsPartOf("Journal")
+            .withISSN(issn)
+            .withDoiIdentifier("doi-id")
+            .withScopusIdentifier("scopus-id")
+            .build();
+
+        context.restoreAuthSystemState();
+
+        Activity activity = entityFactoryService.createOrcidObject(context, publication);
+        assertThat(activity, instanceOf(Work.class));
+
+        Work work = (Work) activity;
+        assertThat(work.getJournalTitle(), notNullValue());
+        assertThat(work.getJournalTitle().getContent(), is("Journal"));
+        assertThat(work.getLanguageCode(), is("en"));
+        assertThat(work.getPublicationDate(), matches(date("2021", "04", "30")));
+        assertThat(work.getShortDescription(), is("Publication description"));
+        assertThat(work.getPutCode(), nullValue());
+        assertThat(work.getWorkType(), is(WorkType.JOURNAL_ARTICLE));
+        assertThat(work.getWorkTitle(), notNullValue());
+        assertThat(work.getWorkTitle().getTitle(), notNullValue());
+        assertThat(work.getWorkTitle().getTitle().getContent(), is("Test publication"));
+        assertThat(work.getWorkContributors(), notNullValue());
+        assertThat(work.getUrl(), matches(urlEndsWith(publication.getHandle())));
+
+        List<Contributor> contributors = work.getWorkContributors().getContributor();
+        assertThat(contributors, hasSize(3));
+        assertThat(contributors, has(contributor("Walter White", AUTHOR, FIRST)));
+        assertThat(contributors, has(contributor("Editor", EDITOR, FIRST)));
+        assertThat(contributors, has(contributor("Jesse Pinkman", AUTHOR, ADDITIONAL)));
+
+        assertThat(work.getExternalIdentifiers(), notNullValue());
+
+        List<ExternalID> externalIds = work.getExternalIdentifiers().getExternalIdentifier();
+        assertThat(externalIds, hasSize(4));
+        assertThat(externalIds, has(selfExternalId("doi", "doi-id")));
+        assertThat(externalIds, has(selfExternalId("eid", "scopus-id")));
+        assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+        // journal-article should have PART_OF rel for ISSN
+        assertThat(externalIds, has(externalId("issn", issn, Relationship.PART_OF)));
+    }
+
+    @Test
+    public void testJournalWithISSN() {
+        context.turnOffAuthorisationSystem();
+
+        Item publication = ItemBuilder.createItem(context, publications)
+            .withTitle("Test journal")
+            .withEditor("Editor")
+            .withType("Journal")
+            .withISSN(issn)
+            .build();
+
+        context.restoreAuthSystemState();
+
+        Activity activity = entityFactoryService.createOrcidObject(context, publication);
+        assertThat(activity, instanceOf(Work.class));
+
+        Work work = (Work) activity;
+        assertThat(work.getWorkType(), is(WorkType.JOURNAL_ISSUE));
+        assertThat(work.getWorkTitle(), notNullValue());
+        assertThat(work.getWorkTitle().getTitle(), notNullValue());
+        assertThat(work.getWorkTitle().getTitle().getContent(), is("Test journal"));
+        assertThat(work.getUrl(), matches(urlEndsWith(publication.getHandle())));
+
+        assertThat(work.getExternalIdentifiers(), notNullValue());
+
+        List<ExternalID> externalIds = work.getExternalIdentifiers().getExternalIdentifier();
+        assertThat(externalIds, hasSize(2));
+        // journal-issue should have SELF rel for ISSN
+        assertThat(externalIds, has(selfExternalId("issn", issn)));
+        assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+    }
+
     @Test
     public void testEmptyWorkWithUnknownTypeCreation() {
 
@@ -163,6 +256,7 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
 
         Item publication = ItemBuilder.createItem(context, publications)
             .withType("TYPE")
+            .withISSN(issn)
             .build();
 
         context.restoreAuthSystemState();
@@ -183,8 +277,9 @@ public class OrcidEntityFactoryServiceIT extends AbstractIntegrationTestWithData
         assertThat(work.getExternalIdentifiers(), notNullValue());
 
         List<ExternalID> externalIds = work.getExternalIdentifiers().getExternalIdentifier();
-        assertThat(externalIds, hasSize(1));
+        assertThat(externalIds, hasSize(2));
         assertThat(externalIds, has(selfExternalId("handle", publication.getHandle())));
+        assertThat(externalIds, has(externalId("issn", issn, Relationship.PART_OF)));
     }
 
     @Test

dspace-api/src/test/java/org/dspace/statistics/export/ITIrusExportUsageEventListener.java

@@ -116,6 +116,7 @@ public class ITIrusExportUsageEventListener extends AbstractIntegrationTestWithD
         configurationService.setProperty("irus.statistics.tracker.enabled", true);
         configurationService.setProperty("irus.statistics.tracker.type-field", "dc.type");
         configurationService.setProperty("irus.statistics.tracker.type-value", "Excluded type");
+        configurationService.setProperty("oai.identifier.prefix", "localhost");
 
 
         context.turnOffAuthorisationSystem();

dspace-api/src/test/java/org/dspace/statistics/export/processor/ExportEventProcessorIT.java

@@ -62,6 +62,7 @@ public class ExportEventProcessorIT extends AbstractIntegrationTestWithDatabase
         configurationService.setProperty("irus.statistics.tracker.enabled", true);
         configurationService.setProperty("irus.statistics.tracker.type-field", "dc.type");
         configurationService.setProperty("irus.statistics.tracker.type-value", "Excluded type");
+        configurationService.setProperty("oai.identifier.prefix", "localhost");
 
         context.turnOffAuthorisationSystem();
         publication = EntityTypeBuilder.createEntityTypeBuilder(context, "Publication").build();

dspace-api/src/test/java/org/dspace/storage/bitstore/BitstreamStorageServiceImplIT.java

@@ -0,0 +1,262 @@
+/**
+ * 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.bitstore;
+
+import static java.nio.charset.StandardCharsets.UTF_8;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.equalTo;
+import static org.junit.Assert.fail;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.apache.commons.io.IOUtils;
+import org.dspace.AbstractIntegrationTestWithDatabase;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.builder.BitstreamBuilder;
+import org.dspace.builder.CollectionBuilder;
+import org.dspace.builder.CommunityBuilder;
+import org.dspace.builder.ItemBuilder;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Collection;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.BitstreamService;
+import org.dspace.core.Context;
+import org.dspace.storage.bitstore.factory.StorageServiceFactory;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+
+public class BitstreamStorageServiceImplIT extends AbstractIntegrationTestWithDatabase {
+    private BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
+    private BitstreamStorageServiceImpl bitstreamStorageService =
+        (BitstreamStorageServiceImpl) StorageServiceFactory.getInstance().getBitstreamStorageService();
+    private Collection collection;
+
+    private Map<Integer, BitStoreService> originalBitstores;
+
+    private static final Integer SOURCE_STORE = 0;
+    private static final Integer DEST_STORE = 1;
+
+    @Rule
+    public final TemporaryFolder tempStoreDir = new TemporaryFolder();
+
+    @Before
+    public void setup() throws Exception {
+
+        context.turnOffAuthorisationSystem();
+
+        parentCommunity = CommunityBuilder.createCommunity(context)
+            .build();
+
+        collection = CollectionBuilder.createCollection(context, parentCommunity)
+            .build();
+
+        originalBitstores = bitstreamStorageService.getStores();
+        Map<Integer, BitStoreService> stores = new HashMap<>();
+        DSBitStoreService sourceStore = new DSBitStoreService();
+        sourceStore.setBaseDir(tempStoreDir.newFolder("src"));
+
+        stores.put(SOURCE_STORE, sourceStore);
+        bitstreamStorageService.setStores(stores);
+
+        context.restoreAuthSystemState();
+    }
+
+    @After
+    public void cleanUp() throws IOException {
+        // Restore the bitstore storage stores
+        bitstreamStorageService.setStores(originalBitstores);
+    }
+
+    /**
+     * Test batch commit checkpointing, using the default batch commit size of 1
+     *
+     * @throws Exception if an exception occurs.
+     */
+    @Test
+    public void testDefaultBatchCommitSize() throws Exception {
+        Context context = this.context;
+
+        // Destination assetstore fails after two bitstreams have been migrated
+        DSBitStoreService destinationStore = new LimitedTempDSBitStoreService(tempStoreDir, 2);
+        Map<Integer, BitStoreService> stores = bitstreamStorageService.getStores();
+        stores.put(DEST_STORE, destinationStore);
+
+        // Create three bitstreams in the source assetstore
+        createBitstreams(context, 3);
+
+        // Three bitstreams in source assetstore at the start
+        assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(3));
+
+        // No bitstreams in destination assetstore at the start
+        assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(0));
+
+        /// Commit any pending transaction to database
+        context.commit();
+
+        // Migrate bitstreams
+        context.turnOffAuthorisationSystem();
+
+        boolean deleteOld = false;
+        Integer batchCommitSize = 1;
+        try {
+            bitstreamStorageService.migrate(
+                context, SOURCE_STORE, DEST_STORE, deleteOld,
+                batchCommitSize
+            );
+            fail("IOException should have been thrown");
+        } catch (IOException ioe) {
+            // Rollback any pending transaction
+            context.rollback();
+        }
+
+        context.restoreAuthSystemState();
+
+        // One bitstream should still be in the source assetstore, due to the
+        // interrupted migration
+        assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(1));
+
+        // Two bitstreams should have migrated to the destination assetstore
+        assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(2));
+    }
+
+    /**
+     * Test batch commit checkpointing, using the default batch commit size of 3
+     *
+     * @throws Exception if an exception occurs.
+     */
+    @Test
+    public void testBatchCommitSizeThree() throws Exception {
+        Context context = this.context;
+
+        // Destination assetstore fails after four bitstreams have been migrated
+        DSBitStoreService destinationStore = new LimitedTempDSBitStoreService(tempStoreDir, 4);
+        Map<Integer, BitStoreService> stores = bitstreamStorageService.getStores();
+        stores.put(DEST_STORE, destinationStore);
+
+        // Create five bitstreams in the source assetstore
+        createBitstreams(context, 5);
+
+        // Five bitstreams in source assetstore at the start
+        assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(5));
+
+        // No bitstreams in destination assetstore at the start
+        assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(0));
+
+        // Commit any pending transaction to database
+        context.commit();
+
+        // Migrate bitstreams
+        context.turnOffAuthorisationSystem();
+
+        boolean deleteOld = false;
+        Integer batchCommitSize = 3;
+        try {
+            bitstreamStorageService.migrate(
+                context, SOURCE_STORE, DEST_STORE, deleteOld,
+                batchCommitSize
+            );
+            fail("IOException should have been thrown");
+        } catch (IOException ioe) {
+            // Rollback any pending transaction
+            context.rollback();
+        }
+
+        context.restoreAuthSystemState();
+
+        // Since the batch commit size is 3, only three bitstreams should be
+        // marked as migrated, so there should still be two bitstreams
+        // in the source assetstore, due to the interrupted migration
+        assertThat(bitstreamService.countByStoreNumber(context, SOURCE_STORE).intValue(), equalTo(2));
+
+        // Three bitstreams should have migrated to the destination assetstore
+        assertThat(bitstreamService.countByStoreNumber(context, DEST_STORE).intValue(), equalTo(3));
+    }
+
+    private void createBitstreams(Context context, int numBitstreams)
+        throws SQLException {
+        context.turnOffAuthorisationSystem();
+        for (int i = 0; i < numBitstreams; i++) {
+            String content = "Test bitstream " + i;
+            createBitstream(content);
+        }
+        context.restoreAuthSystemState();
+        context.commit();
+    }
+
+    private Bitstream createBitstream(String content) {
+        try {
+            return BitstreamBuilder
+                .createBitstream(context, createItem(), toInputStream(content))
+                .build();
+        } catch (SQLException | AuthorizeException | IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+    private Item createItem() {
+        return ItemBuilder.createItem(context, collection)
+            .withTitle("Test item")
+            .build();
+    }
+
+
+    private InputStream toInputStream(String content) {
+        return IOUtils.toInputStream(content, UTF_8);
+    }
+
+
+    /**
+     * DSBitStoreService variation that only allows a limited number of puts
+     * to the bit store before throwing an IOException, to test the
+     * error handling of the BitstreamStorageService.migrate() method.
+     */
+    class LimitedTempDSBitStoreService extends DSBitStoreService {
+        // The number of put calls allowed before throwing an IOException
+        protected int maxPuts = Integer.MAX_VALUE;
+
+        // The number of "put" method class seen so far.
+        protected int putCallCount = 0;
+
+        /**
+         * Constructor.
+         *
+         * @param maxPuts the number of put calls to allow before throwing an
+         * IOException
+         */
+        public LimitedTempDSBitStoreService(TemporaryFolder tempStoreDir, int maxPuts) throws IOException {
+            super();
+            setBaseDir(tempStoreDir.newFolder());
+            this.maxPuts = maxPuts;
+        }
+
+        /**
+         * Store a stream of bits.
+         *
+         * After "maxPut" number of calls, this method throws an IOException.
+         * @param in The stream of bits to store
+         * @throws java.io.IOException If a problem occurs while storing the bits
+         */
+        @Override
+        public void put(Bitstream bitstream, InputStream in) throws IOException {
+            putCallCount = putCallCount + 1;
+            if (putCallCount > maxPuts) {
+                throw new IOException("Max 'put' method calls exceeded");
+            } else {
+                super.put(bitstream, in);
+            }
+        }
+    }
+}

dspace-api/src/test/java/org/dspace/storage/bitstore/S3BitStoreServiceIT.java

@@ -26,9 +26,11 @@ import static org.junit.Assert.assertTrue;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.Paths;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
 import java.sql.SQLException;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
@@ -41,7 +43,6 @@ import com.amazonaws.services.s3.model.AmazonS3Exception;
 import com.amazonaws.services.s3.model.Bucket;
 import com.amazonaws.services.s3.model.ObjectMetadata;
 import io.findify.s3mock.S3Mock;
-import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.BooleanUtils;
 import org.dspace.AbstractIntegrationTestWithDatabase;
@@ -80,8 +81,6 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
 
     private Collection collection;
 
-    private File s3Directory;
-
     private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
 
 
@@ -89,9 +88,8 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
     public void setup() throws Exception {
 
         configurationService.setProperty("assetstore.s3.enabled", "true");
-        s3Directory = new File(System.getProperty("java.io.tmpdir"), "s3");
 
-        s3Mock = S3Mock.create(8001, s3Directory.getAbsolutePath());
+        s3Mock = new S3Mock.Builder().withPort(8001).withInMemoryBackend().build();
         s3Mock.start();
 
         amazonS3Client = createAmazonS3Client();
@@ -112,8 +110,7 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
     }
 
     @After
-    public void cleanUp() throws IOException {
-        FileUtils.deleteDirectory(s3Directory);
+    public void cleanUp() {
         s3Mock.shutdown();
     }
 
@@ -337,7 +334,7 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
         String computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         int slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
 
         path.append("2");
         computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
@@ -362,31 +359,31 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
         String computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         int slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
 
         path.append("2");
         computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
 
         path.append("3");
         computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
 
         path.append("4");
         computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
 
         path.append("56789");
         computedPath = this.s3BitStoreService.getIntermediatePath(path.toString());
         slashes = computeSlashes(path.toString());
         assertThat(computedPath, Matchers.endsWith(File.separator));
-        assertThat(computedPath.split(File.separator).length, Matchers.equalTo(slashes));
+        assertThat(countPathElements(computedPath), Matchers.equalTo(slashes));
     }
 
     @Test
@@ -465,4 +462,12 @@ public class S3BitStoreServiceIT extends AbstractIntegrationTestWithDatabase {
         return Math.min(slashes, S3BitStoreService.directoryLevels);
     }
 
+    // Count the number of elements in a Unix or Windows path.
+    // We use 'Paths' instead of splitting on slashes because these OSes use different path separators.
+    private int countPathElements(String stringPath) {
+        List<String> pathElements = new ArrayList<>();
+        Paths.get(stringPath).forEach(p -> pathElements.add(p.toString()));
+        return pathElements.size();
+    }
+
 }

dspace-iiif/pom.xml

@@ -15,7 +15,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-oai/pom.xml

@@ -8,7 +8,7 @@
     <parent>
         <artifactId>dspace-parent</artifactId>
         <groupId>org.dspace</groupId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-oai/src/main/java/org/dspace/xoai/util/ItemUtils.java

@@ -16,6 +16,7 @@ import java.util.List;
 import com.lyncode.xoai.dataprovider.xml.xoai.Element;
 import com.lyncode.xoai.dataprovider.xml.xoai.Metadata;
 import com.lyncode.xoai.util.Base64Utils;
+import org.apache.commons.text.StringEscapeUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.factory.UtilServiceFactory;
@@ -142,7 +143,7 @@ public class ItemUtils {
                     bitstream.getField().add(createValue("name", name));
                 }
                 if (oname != null) {
-                    bitstream.getField().add(createValue("originalName", name));
+                    bitstream.getField().add(createValue("originalName", oname));
                 }
                 if (description != null) {
                     bitstream.getField().add(createValue("description", description));
@@ -159,6 +160,19 @@ public class ItemUtils {
         return bundles;
     }
 
+    /**
+     * Sanitizes a string to remove characters that are invalid
+     * in XML 1.0 using the Apache Commons Text library.
+     * @param value The string to sanitize.
+     * @return A sanitized string, or null if the input was null.
+     */
+    private static String sanitize(String value) {
+        if (value == null) {
+            return null;
+        }
+        return StringEscapeUtils.escapeXml10(value);
+    }
+
     private static Element createLicenseElement(Context context, Item item)
             throws SQLException, AuthorizeException, IOException {
         Element license = create("license");
@@ -232,7 +246,7 @@ public class ItemUtils {
             valueElem = language;
         }
 
-        valueElem.getField().add(createValue("value", val.getValue()));
+        valueElem.getField().add(createValue("value", sanitize(val.getValue())));
         if (val.getAuthority() != null) {
             valueElem.getField().add(createValue("authority", val.getAuthority()));
             if (val.getConfidence() != Choices.CF_NOVALUE) {

dspace-rdf/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-rest/pom.xml

@@ -3,7 +3,7 @@
     <groupId>org.dspace</groupId>
     <artifactId>dspace-rest</artifactId>
     <packaging>war</packaging>
-    <version>7.6.4</version>
+    <version>7.6.6-SNAPSHOT</version>
     <name>DSpace (Deprecated) REST Webapp</name>
     <description>DSpace RESTful Web Services API. NOTE: this REST API is DEPRECATED.
         Please consider using the REST API in the dspace-server-webapp instead!</description>
@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-server-webapp/pom.xml

@@ -15,7 +15,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -514,7 +514,7 @@
         <dependency>
             <groupId>net.minidev</groupId>
             <artifactId>json-smart</artifactId>
-            <version>2.5.2</version>
+            <version>2.6.0</version>
         </dependency>
 
         <dependency>

dspace-server-webapp/src/main/java/org/dspace/app/rest/Application.java

@@ -9,7 +9,10 @@ package org.dspace.app.rest;
 
 import java.io.IOException;
 import java.sql.SQLException;
+import java.time.ZoneOffset;
 import java.util.List;
+import java.util.TimeZone;
+import javax.annotation.PostConstruct;
 import javax.servlet.Filter;
 
 import org.dspace.app.rest.filter.DSpaceRequestContextFilter;
@@ -262,4 +265,12 @@ public class Application extends SpringBootServletInitializer {
             }
         };
     }
+
+    @PostConstruct
+    public void setDefaultTimezone() {
+        // Set the default timezone in Spring Boot to UTC.
+        // This ensures that Spring Boot doesn't attempt to change the timezone of dates that are read from the
+        // database (via Hibernate). We store all dates in the database as UTC.
+        TimeZone.setDefault(TimeZone.getTimeZone(ZoneOffset.UTC));
+    }
 }

dspace-server-webapp/src/main/java/org/dspace/app/rest/security/OrcidLoginFilter.java

@@ -87,6 +87,7 @@ public class OrcidLoginFilter extends StatelessLoginFilter {
             String baseRediredirectUrl = configurationService.getProperty("dspace.ui.url");
             String redirectUrl = baseRediredirectUrl + "/error?status=401&code=orcid.generic-error";
             response.sendRedirect(redirectUrl); // lgtm [java/unvalidated-url-redirection]
+            this.closeOpenContext(request);
         } else {
             super.unsuccessfulAuthentication(request, response, failed);
         }

dspace-server-webapp/src/main/java/org/dspace/app/rest/security/StatelessLoginFilter.java

@@ -8,11 +8,14 @@
 package org.dspace.app.rest.security;
 
 import java.io.IOException;
+import java.sql.SQLException;
 import javax.servlet.FilterChain;
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.dspace.app.rest.utils.ContextUtil;
+import org.dspace.core.Context;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.security.authentication.AuthenticationManager;
@@ -122,6 +125,27 @@ public class StatelessLoginFilter extends AbstractAuthenticationProcessingFilter
         response.sendError(HttpServletResponse.SC_UNAUTHORIZED, "Authentication failed!");
         log.error("Authentication failed (status:{})",
                   HttpServletResponse.SC_UNAUTHORIZED, failed);
+        this.closeOpenContext(request);
+    }
+
+    /**
+     * Manually closes the open {@link Context} if one exists. We need to do this manually because
+     * {@link #continueChainBeforeSuccessfulAuthentication} is {@code false} by default, which prevents the
+     * {@link org.dspace.app.rest.filter.DSpaceRequestContextFilter} from being called. Without this call, the request
+     * would leave an open database connection.
+     *
+     * @param request The current request.
+     */
+    protected void closeOpenContext(HttpServletRequest request) {
+        if (ContextUtil.isContextAvailable(request)) {
+            try (Context context = ContextUtil.obtainContext(request)) {
+                if (context != null && context.isValid()) {
+                    context.complete();
+                }
+            } catch (SQLException e) {
+                throw new RuntimeException(e);
+            }
+        }
     }
 
 }

dspace-server-webapp/src/main/java/org/dspace/app/rest/submit/factory/impl/MetadataValueRemovePatchOperation.java

@@ -11,6 +11,8 @@ import java.sql.SQLException;
 import java.util.Arrays;
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.rest.model.MetadataValueRest;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
@@ -27,6 +29,8 @@ import org.dspace.core.Utils;
 public abstract class MetadataValueRemovePatchOperation<DSO extends DSpaceObject>
     extends RemovePatchOperation<MetadataValueRest> {
 
+    private static final Logger log = LogManager.getLogger();
+
     @Override
     protected Class<MetadataValueRest[]> getArrayClassForEvaluation() {
         return MetadataValueRest[].class;
@@ -42,7 +46,12 @@ public abstract class MetadataValueRemovePatchOperation<DSO extends DSpaceObject
         List<MetadataValue> mm = getDSpaceObjectService().getMetadata(source, metadata[0], metadata[1], metadata[2],
                                                                       Item.ANY);
         if (index != -1) {
+            if (index < mm.size()) {
                 getDSpaceObjectService().removeMetadataValues(context, source, Arrays.asList(mm.get(index)));
+            } else {
+                log.warn("value of index ({}) is out of range of the metadata value list of size {} (target: {})",
+                        index, mm.size(), target);
+            }
         } else {
             getDSpaceObjectService().clearMetadata(context, source, metadata[0], metadata[1], metadata[2], Item.ANY);
         }

dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/HttpHeadersInitializer.java

@@ -9,9 +9,11 @@ package org.dspace.app.rest.utils;
 
 import static java.util.Objects.isNull;
 import static java.util.Objects.nonNull;
-import static javax.mail.internet.MimeUtility.encodeText;
 
 import java.io.IOException;
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+import java.text.Normalizer;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.Objects;
@@ -171,9 +173,16 @@ public class HttpHeadersInitializer {
 
         // distposition may be null here if contentType is null
         if (!isNullOrEmpty(disposition)) {
-            httpHeaders.put(CONTENT_DISPOSITION, Collections.singletonList(String.format(CONTENT_DISPOSITION_FORMAT,
+            String fallbackAsciiName = createFallbackAsciiName(this.fileName);
+            String encodedUtf8Name = createEncodedUtf8Name(this.fileName);
+
+            String headerValue = String.format(
+                "%s; filename=\"%s\"; filename*=UTF-8''%s",
                 disposition,
-                                                                                         encodeText(fileName))));
+                fallbackAsciiName,
+                encodedUtf8Name
+            );
+            httpHeaders.put(CONTENT_DISPOSITION, Collections.singletonList(headerValue));
         }
         log.debug("Content-Disposition : {}", disposition);
 
@@ -261,4 +270,41 @@ public class HttpHeadersInitializer {
         return Arrays.binarySearch(matchValues, toMatch) > -1 || Arrays.binarySearch(matchValues, "*") > -1;
     }
 
+    /**
+     * Creates a safe ASCII-only fallback filename by removing diacritics (accents)
+     * and replacing any remaining non-ASCII characters.
+     * E.g., "ä-ö-é.pdf" becomes "a-o-e.pdf".
+     * @param originalFilename The original filename.
+     * @return A string containing only ASCII characters.
+     */
+    private String createFallbackAsciiName(String originalFilename) {
+        if (originalFilename == null) {
+            return "";
+        }
+        String normalized = Normalizer.normalize(originalFilename, Normalizer.Form.NFD);
+        String withoutAccents = normalized.replaceAll("\\p{InCombiningDiacriticalMarks}+", "");
+        return withoutAccents.replaceAll("[^\\x00-\\x7F]", "");
+    }
+
+    /**
+     * Creates a percent-encoded UTF-8 filename according to RFC 5987.
+     * This is for the `filename*` parameter.
+     * E.g., "ä ö é.pdf" becomes "%C3%A4%20%C3%B6%20%C3%A9.pdf".
+     * @param originalFilename The original filename.
+     * @return A percent-encoded string.
+     */
+    private String createEncodedUtf8Name(String originalFilename) {
+        if (originalFilename == null) {
+            return "";
+        }
+        try {
+            String encoded = URLEncoder.encode(originalFilename, StandardCharsets.UTF_8.toString());
+            return encoded.replace("+", "%20");
+        } catch (java.io.UnsupportedEncodingException e) {
+            // Fallback to a simple ASCII name if encoding fails.
+            log.error("UTF-8 encoding not supported, which should not happen.", e);
+            return createFallbackAsciiName(originalFilename);
+        }
+    }
+
 }

dspace-server-webapp/src/main/java/org/dspace/app/rest/utils/UsageReportUtils.java

@@ -27,6 +27,7 @@ import org.dspace.content.Site;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.handle.service.HandleService;
+import org.dspace.services.ConfigurationService;
 import org.dspace.statistics.Dataset;
 import org.dspace.statistics.content.DatasetDSpaceObjectGenerator;
 import org.dspace.statistics.content.DatasetTimeGenerator;
@@ -46,6 +47,9 @@ import org.springframework.stereotype.Component;
 @Component
 public class UsageReportUtils {
 
+    @Autowired
+    private ConfigurationService configurationService;
+
     @Autowired
     private HandleService handleService;
 
@@ -135,13 +139,14 @@ public class UsageReportUtils {
      */
     private UsageReportRest resolveGlobalUsageReport(Context context)
         throws SQLException, IOException, ParseException, SolrServerException {
+        int topItemsLimit = configurationService.getIntProperty("usage-statistics.topItemsLimit", 10);
+
         StatisticsListing statListing = new StatisticsListing(
             new StatisticsDataVisits());
 
-        // Adding a new generator for our top 10 items without a name length delimiter
+        // Adding a new generator for our top n items without a name length delimiter
         DatasetDSpaceObjectGenerator dsoAxis = new DatasetDSpaceObjectGenerator();
-        // TODO make max nr of top items (views wise)? Must be set
-        dsoAxis.addDsoChild(Constants.ITEM, 10, false, -1);
+        dsoAxis.addDsoChild(Constants.ITEM, topItemsLimit, false, -1);
         statListing.addDatasetGenerator(dsoAxis);
 
         Dataset dataset = statListing.getDataset(context, 1);
@@ -182,7 +187,7 @@ public class UsageReportUtils {
         UsageReportPointDsoTotalVisitsRest totalVisitPoint = new UsageReportPointDsoTotalVisitsRest();
         totalVisitPoint.setType(StringUtils.substringAfterLast(dso.getClass().getName().toLowerCase(), "."));
         totalVisitPoint.setId(dso.getID().toString());
-        if (dataset.getColLabels().size() > 0) {
+        if (!dataset.getColLabels().isEmpty()) {
             totalVisitPoint.setLabel(dso.getName());
             totalVisitPoint.addValue("views", Integer.valueOf(dataset.getMatrix()[0][0]));
         } else {
@@ -205,10 +210,14 @@ public class UsageReportUtils {
      */
     private UsageReportRest resolveTotalVisitsPerMonth(Context context, DSpaceObject dso)
         throws SQLException, IOException, ParseException, SolrServerException {
+        String startDateInterval =
+            configurationService.getProperty("usage-statistics.startDateInterval", "-6");
+        String endDateInterval =
+            configurationService.getProperty("usage-statistics.endDateInterval", "+1");
+
         StatisticsTable statisticsTable = new StatisticsTable(new StatisticsDataVisits(dso));
         DatasetTimeGenerator timeAxis = new DatasetTimeGenerator();
-        // TODO month start and end as request para?
-        timeAxis.setDateInterval("month", "-6", "+1");
+        timeAxis.setDateInterval("month", startDateInterval, endDateInterval);
         statisticsTable.addDatasetGenerator(timeAxis);
         DatasetDSpaceObjectGenerator dsoAxis = new DatasetDSpaceObjectGenerator();
         dsoAxis.addDsoChild(dso.getType(), 10, false, -1);
@@ -275,7 +284,10 @@ public class UsageReportUtils {
      */
     private UsageReportRest resolveTopCountries(Context context, DSpaceObject dso)
         throws SQLException, IOException, ParseException, SolrServerException {
-        Dataset dataset = this.getTypeStatsDataset(context, dso, "countryCode", 1);
+        int topCountriesLimit =
+            configurationService.getIntProperty("usage-statistics.topCountriesLimit", 100);
+
+        Dataset dataset = this.getTypeStatsDataset(context, dso, "countryCode", topCountriesLimit, 1);
 
         UsageReportRest usageReportRest = new UsageReportRest();
         for (int i = 0; i < dataset.getColLabels().size(); i++) {
@@ -299,7 +311,10 @@ public class UsageReportUtils {
      */
     private UsageReportRest resolveTopCities(Context context, DSpaceObject dso)
         throws SQLException, IOException, ParseException, SolrServerException {
-        Dataset dataset = this.getTypeStatsDataset(context, dso, "city", 1);
+        int topCitiesLimit =
+            configurationService.getIntProperty("usage-statistics.topCitiesLimit", 100);
+
+        Dataset dataset = this.getTypeStatsDataset(context, dso, "city", topCitiesLimit, 1);
 
         UsageReportRest usageReportRest = new UsageReportRest();
         for (int i = 0; i < dataset.getColLabels().size(); i++) {
@@ -339,16 +354,17 @@ public class UsageReportUtils {
      * @param dso            DSO we want the stats dataset of
      * @param typeAxisString String of the type we want on the axis of the dataset (corresponds to solr field),
      *                       examples: countryCode, city
+     * @param typeAxisMax    Maximum amount of results to return in the dataset
      * @param facetMinCount  Minimum amount of results on a facet data point for it to be added to dataset
      * @return Stats dataset with the given type on the axis, of the given DSO and with given facetMinCount
      */
-    private Dataset getTypeStatsDataset(Context context, DSpaceObject dso, String typeAxisString, int facetMinCount)
+    private Dataset getTypeStatsDataset(Context context, DSpaceObject dso, String typeAxisString, int typeAxisMax,
+                                        int facetMinCount)
         throws SQLException, IOException, ParseException, SolrServerException {
         StatisticsListing statListing = new StatisticsListing(new StatisticsDataVisits(dso));
         DatasetTypeGenerator typeAxis = new DatasetTypeGenerator();
         typeAxis.setType(typeAxisString);
-        // TODO make max nr of top countries/cities a request para? Must be set
-        typeAxis.setMax(100);
+        typeAxis.setMax(typeAxisMax);
         statListing.addDatasetGenerator(typeAxis);
         return statListing.getDataset(context, facetMinCount);
     }

dspace-server-webapp/src/test/java/org/dspace/app/rest/AbstractLiveImportIntegrationTest.java

@@ -16,12 +16,12 @@ import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.http.ProtocolVersion;
 import org.apache.http.StatusLine;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.entity.BasicHttpEntity;
-import org.apache.tools.ant.filters.StringInputStream;
 import org.dspace.app.rest.test.AbstractControllerIntegrationTest;
 import org.dspace.importer.external.datamodel.ImportRecord;
 import org.dspace.importer.external.metadatamapping.MetadatumDTO;
@@ -43,7 +43,8 @@ public class AbstractLiveImportIntegrationTest extends AbstractControllerIntegra
     private void checkMetadataValue(List<MetadatumDTO> list, List<MetadatumDTO> list2) {
         assertEquals(list.size(), list2.size());
         for (int i = 0; i < list.size(); i++) {
-            assertTrue(sameMetadatum(list.get(i), list2.get(i)));
+            assertTrue("'" + list.get(i).toString() + "' should be equal to '" + list2.get(i).toString() + "'",
+                       sameMetadatum(list.get(i), list2.get(i)));
         }
     }
 
@@ -70,7 +71,7 @@ public class AbstractLiveImportIntegrationTest extends AbstractControllerIntegra
             throws UnsupportedEncodingException {
         BasicHttpEntity basicHttpEntity = new BasicHttpEntity();
         basicHttpEntity.setChunked(true);
-        basicHttpEntity.setContent(new StringInputStream(xmlExample));
+        basicHttpEntity.setContent(IOUtils.toInputStream(xmlExample));
 
         CloseableHttpResponse response = mock(CloseableHttpResponse.class);
         when(response.getStatusLine()).thenReturn(statusLine(statusCode, reason));

dspace-server-webapp/src/test/java/org/dspace/app/rest/BitstreamRestControllerIT.java

@@ -8,7 +8,6 @@
 package org.dspace.app.rest;
 
 import static java.util.UUID.randomUUID;
-import static javax.mail.internet.MimeUtility.encodeText;
 import static org.apache.commons.codec.CharEncoding.UTF_8;
 import static org.apache.commons.collections.CollectionUtils.isEmpty;
 import static org.apache.commons.io.IOUtils.toInputStream;
@@ -347,7 +346,11 @@ public class BitstreamRestControllerIT extends AbstractControllerIntegrationTest
         //2. A public item with a bitstream
 
         String bitstreamContent = "0123456789";
-        String bitstreamName = "ภาษาไทย";
+        String bitstreamName = "ภาษาไทย-com-acentuação.pdf";
+        String expectedAscii = "-com-acentuacao.pdf";
+        String expectedUtf8Encoded =
+        "%E0%B8%A0%E0%B8%B2%E0%B8%A9%E0%B8%B2%E0%B9%84%E0%B8%97%E0%B8%A2-"
+        + "com-acentua%C3%A7%C3%A3o.pdf";
 
         try (InputStream is = IOUtils.toInputStream(bitstreamContent, CharEncoding.UTF_8)) {
 
@@ -371,7 +374,9 @@ public class BitstreamRestControllerIT extends AbstractControllerIntegrationTest
             //We expect the content disposition to have the encoded bitstream name
             .andExpect(header().string(
                 "Content-Disposition",
-                "attachment;filename=\"" + encodeText(bitstreamName) + "\""
+                String.format("attachment; filename=\"%s\"; filename*=UTF-8''%s",
+                              expectedAscii,
+                              expectedUtf8Encoded)
             ));
     }
 

dspace-server-webapp/src/test/java/org/dspace/app/rest/ResearcherProfileRestRepositoryIT.java

@@ -143,6 +143,7 @@ public class ResearcherProfileRestRepositoryIT extends AbstractControllerIntegra
 
         user = EPersonBuilder.createEPerson(context)
             .withEmail("user@example.com")
+            .withNameInMetadata("Example", "User")
             .withPassword(password)
             .build();
 
@@ -322,7 +323,7 @@ public class ResearcherProfileRestRepositoryIT extends AbstractControllerIntegra
     public void testCreateAndReturn() throws Exception {
 
         String id = user.getID().toString();
-        String name = user.getName();
+        String name = user.getFullName();
 
         String authToken = getAuthToken(user.getEmail(), password);
 
@@ -341,6 +342,8 @@ public class ResearcherProfileRestRepositoryIT extends AbstractControllerIntegra
             .andExpect(status().isOk())
             .andExpect(jsonPath("$.type", is("item")))
             .andExpect(jsonPath("$.metadata", matchMetadata("dspace.object.owner", name, id, 0)))
+            .andExpect(jsonPath("$.metadata", matchMetadata("person.givenName", user.getFirstName(), 0)))
+            .andExpect(jsonPath("$.metadata", matchMetadata("person.familyName", user.getLastName(), 0)))
             .andExpect(jsonPath("$.metadata", matchMetadata("dspace.entity.type", "Person", 0)));
 
         getClient(authToken).perform(get("/api/eperson/profiles/{id}/eperson", id))
@@ -390,7 +393,7 @@ public class ResearcherProfileRestRepositoryIT extends AbstractControllerIntegra
     public void testCreateAndReturnWithAdmin() throws Exception {
 
         String id = user.getID().toString();
-        String name = user.getName();
+        String name = user.getFullName();
 
         configurationService.setProperty("researcher-profile.collection.uuid", null);
 
@@ -411,6 +414,8 @@ public class ResearcherProfileRestRepositoryIT extends AbstractControllerIntegra
         getClient(authToken).perform(get("/api/eperson/profiles/{id}/item", id))
             .andExpect(status().isOk())
             .andExpect(jsonPath("$.type", is("item")))
+            .andExpect(jsonPath("$.metadata", matchMetadata("person.givenName", user.getFirstName(), 0)))
+            .andExpect(jsonPath("$.metadata", matchMetadata("person.familyName", user.getLastName(), 0)))
             .andExpect(jsonPath("$.metadata", matchMetadata("dspace.object.owner", name, id, 0)))
             .andExpect(jsonPath("$.metadata", matchMetadata("dspace.entity.type", "Person", 0)));
 

dspace-server-webapp/src/test/java/org/dspace/app/rest/test/WebappLoggingIT.java

@@ -0,0 +1,101 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.rest.test;
+
+import static org.junit.Assert.assertTrue;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.core.Appender;
+import org.apache.logging.log4j.core.LogEvent;
+import org.apache.logging.log4j.core.LoggerContext;
+import org.apache.logging.log4j.core.appender.AbstractAppender;
+import org.apache.logging.log4j.core.config.Configuration;
+import org.apache.logging.log4j.core.config.LoggerConfig;
+import org.apache.logging.log4j.core.config.Property;
+import org.apache.logging.log4j.core.layout.PatternLayout;
+import org.junit.After;
+import org.junit.Test;
+
+/**
+ * Test basic log4j logging functionality, extending AbstractControllerIntegrationTest
+ * purely to make sure we are testing the *web application* and not just the kernel
+ * as that is where logging has broken in the past.
+ *
+ * @author Kim Shepherd
+ */
+public class WebappLoggingIT extends AbstractControllerIntegrationTest {
+
+    private static final Logger logger = LogManager.getLogger(WebappLoggingIT.class);
+    private static final String APPENDER_NAME = "DSpaceTestAppender";
+
+    static class InMemoryAppender extends AbstractAppender {
+        private final List<String> messages = new ArrayList<>();
+
+        protected InMemoryAppender(String name) {
+            super(
+                name,
+                null,
+                PatternLayout.newBuilder().withPattern("%m").build(),
+                false,
+                Property.EMPTY_ARRAY
+            );
+            start();
+        }
+
+        @Override
+        public void append(LogEvent event) {
+            messages.add(event.getMessage().getFormattedMessage());
+        }
+
+        public List<String> getMessages() {
+            return messages;
+        }
+    }
+
+    @Test
+    public void testLogging() throws Exception {
+        LoggerContext context = (LoggerContext) LogManager.getContext(false);
+        Configuration config = context.getConfiguration();
+
+        InMemoryAppender appender = new InMemoryAppender(APPENDER_NAME);
+        config.addAppender(appender);
+
+        LoggerConfig testLoggerConfig = new LoggerConfig(logger.getName(), Level.INFO, false);
+        testLoggerConfig.addAppender(appender, null, null);
+        config.addLogger(logger.getName(), testLoggerConfig);
+        context.updateLoggers();
+
+        logger.info("DSPACE TEST LOG ENTRY");
+
+        List<String> messages = appender.getMessages();
+        assertTrue(messages.stream().anyMatch(msg -> msg.contains("DSPACE TEST LOG ENTRY")));
+    }
+
+    @After
+    public void cleanupAppender() {
+        LoggerContext context = (LoggerContext) LogManager.getContext(false);
+        Configuration config = context.getConfiguration();
+
+        config.removeLogger(logger.getName());
+
+        Appender appender = config.getAppender(APPENDER_NAME);
+        if (appender != null) {
+            appender.stop();
+            config.getAppenders().remove(APPENDER_NAME);
+        }
+
+        context.updateLoggers();
+}
+
+}
+

dspace-server-webapp/src/test/java/org/dspace/app/sword/Swordv1IT.java

@@ -10,16 +10,30 @@ package org.dspace.app.sword;
 
 import static org.hamcrest.CoreMatchers.containsString;
 import static org.hamcrest.CoreMatchers.equalTo;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertThat;
 
+import java.nio.file.Path;
+import java.util.List;
+
 import org.dspace.app.rest.test.AbstractWebClientIntegrationTest;
+import org.dspace.builder.CollectionBuilder;
+import org.dspace.builder.CommunityBuilder;
+import org.dspace.content.Collection;
 import org.dspace.services.ConfigurationService;
+import org.hamcrest.MatcherAssert;
 import org.junit.Assume;
 import org.junit.Before;
-import org.junit.Ignore;
 import org.junit.Test;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.io.FileSystemResource;
+import org.springframework.http.ContentDisposition;
+import org.springframework.http.HttpEntity;
+import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.RequestEntity;
 import org.springframework.http.ResponseEntity;
 import org.springframework.test.context.TestPropertySource;
 
@@ -45,6 +59,9 @@ public class Swordv1IT extends AbstractWebClientIntegrationTest {
     private final String DEPOSIT_PATH = "/sword/deposit";
     private final String MEDIA_LINK_PATH = "/sword/media-link";
 
+    // ATOM Content type returned by SWORDv1
+    private final String ATOM_CONTENT_TYPE = "application/atom+xml;charset=UTF-8";
+
     @Before
     public void onlyRunIfConfigExists() {
         // These integration tests REQUIRE that SWORDWebConfig is found/available (as this class deploys SWORD)
@@ -93,10 +110,76 @@ public class Swordv1IT extends AbstractWebClientIntegrationTest {
     }
 
     @Test
-    @Ignore
     public void depositTest() throws Exception {
-        // TODO: Actually test a full deposit via SWORD.
-        // Currently, we are just ensuring the /deposit endpoint exists (see above) and isn't throwing a 404
+        context.turnOffAuthorisationSystem();
+        // Create a top level community and one Collection
+        parentCommunity = CommunityBuilder.createCommunity(context)
+                                          .withName("Parent Community")
+                                          .build();
+        // Make sure our Collection allows the "eperson" user to submit into it
+        Collection collection = CollectionBuilder.createCollection(context, parentCommunity)
+                                                 .withName("Test SWORDv1 Collection")
+                                                 .withSubmitterGroup(eperson)
+                                                 .build();
+        // Above changes MUST be committed to the database for SWORDv2 to see them.
+        context.commit();
+        context.restoreAuthSystemState();
+
+        // Specify zip file
+        // NOTE: We are using the same "example.zip" as SWORDv2IT because that same ZIP is valid for both v1 and v2
+        FileSystemResource zipFile = new FileSystemResource(Path.of("src", "test", "resources", "org",
+                                                                    "dspace", "app", "sword2", "example.zip"));
+
+        // Add required headers
+        HttpHeaders headers = new HttpHeaders();
+        headers.setContentType(MediaType.valueOf("application/zip"));
+        headers.setContentDisposition(ContentDisposition.attachment().filename("example.zip").build());
+        headers.set("X-Packaging", "http://purl.org/net/sword-types/METSDSpaceSIP");
+        headers.setAccept(List.of(MediaType.APPLICATION_ATOM_XML));
+
+        //----
+        // STEP 1: Verify upload/submit via SWORDv1 works
+        //----
+        // Send POST to upload Zip file via SWORD
+        ResponseEntity<String> response = postResponseAsString(DEPOSIT_PATH + "/" + collection.getHandle(),
+                                                               eperson.getEmail(), password,
+                                                               new HttpEntity<>(zipFile.getInputStream().readAllBytes(),
+                                                                                headers));
+
+        // Expect a 201 CREATED response with ATOM content returned
+        assertEquals(HttpStatus.CREATED, response.getStatusCode());
+        assertEquals(ATOM_CONTENT_TYPE, response.getHeaders().getContentType().toString());
+
+        // MUST return a "Location" header which is the "/sword/media-link/*" URI of the zip file bitstream within
+        // the created item (e.g. /sword/media-link/[handle-prefix]/[handle-suffix]/bitstream/[uuid])
+        assertNotNull(response.getHeaders().getLocation());
+        String mediaLink = response.getHeaders().getLocation().toString();
+
+        // Body should include the SWORD version in generator tag
+        MatcherAssert.assertThat(response.getBody(),
+                                 containsString("<atom:generator uri=\"http://www.dspace.org/ns/sword/1.3.1\"" +
+                                                    " version=\"1.3\"/>"));
+        // Verify Item title also is returned in the body
+        MatcherAssert.assertThat(response.getBody(), containsString("Attempts to detect retrotransposition"));
+
+        //----
+        // STEP 2: Verify /media-link access works
+        //----
+        // Media-Link URI should work when requested by the EPerson who did the deposit
+        HttpHeaders authHeaders = new HttpHeaders();
+        authHeaders.setBasicAuth(eperson.getEmail(), password);
+        RequestEntity request = RequestEntity.get(mediaLink)
+                                             .accept(MediaType.valueOf("application/atom+xml"))
+                                             .headers(authHeaders)
+                                             .build();
+        response = responseAsString(request);
+
+        // Expect a 200 response with ATOM feed content returned
+        assertEquals(HttpStatus.OK, response.getStatusCode());
+        assertEquals(ATOM_CONTENT_TYPE, response.getHeaders().getContentType().toString());
+        // Body should include a link to the zip bitstream in the newly created Item
+        // This just verifies "example.zip" exists in the body.
+        MatcherAssert.assertThat(response.getBody(), containsString("example.zip"));
     }
 
     @Test
@@ -105,13 +188,8 @@ public class Swordv1IT extends AbstractWebClientIntegrationTest {
         ResponseEntity<String> response = getResponseAsString(MEDIA_LINK_PATH);
         // Expect a 401 response code
         assertThat(response.getStatusCode(), equalTo(HttpStatus.UNAUTHORIZED));
-    }
 
-    @Test
-    @Ignore
-    public void mediaLinkTest() throws Exception {
-        // TODO: Actually test a /media-link request.
-        // Currently, we are just ensuring the /media-link endpoint exists (see above) and isn't throwing a 404
+        //NOTE: An authorized /media-link test is performed in depositTest() above.
     }
 }
 

dspace-services/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
     </parent>
 
     <properties>

dspace-sword/pom.xml

@@ -15,7 +15,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-swordv2/pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace/config/crosswalks/orcid/mapConverter-dspace-to-orcid-publication-type.properties

@@ -4,20 +4,21 @@ Article = journal-article
 Book = book
 Book\ chapter = book-chapter
 Dataset = data-set
-Learning\ Object = other
-Image = other
-Image,\ 3-D = other
-Map = other
-Musical\ Score = other
+Learning\ Object = learning-object
+Image = image
+Image,\ 3-D = image
+Journal = journal-issue
+Map = cartographic-material
+Musical\ Score = musical-composition
 Plan\ or\ blueprint = other
 Preprint = preprint
 Presentation = other
-Recording,\ acoustical = other
-Recording,\ musical = other
-Recording,\ oral = other
+Recording,\ acoustical = sound
+Recording,\ musical = sound
+Recording,\ oral = sound
 Software = software
-Technical\ Report = other
-Thesis = other
-Video = other
+Technical\ Report = report
+Thesis = dissertation-thesis
+Video = moving-image
 Working\ Paper = working-paper
 Other = other

dspace/config/modules/assetstore.cfg

@@ -18,6 +18,9 @@ assetstore.dir = ${dspace.dir}/assetstore
 # `bitstore.xml` configuration.
 assetstore.index.primary = 0
 
+#if the assetstore path is symbolic link, use this configuration to allow that path.
+#assetstore.allowed.roots = /data/assetstore
+
 #---------------------------------------------------------------#
 #-------------- Amazon S3 Specific Configurations --------------#
 #---------------------------------------------------------------#

dspace/config/modules/external-providers.cfg

@@ -45,6 +45,9 @@ epo.searchUrl = https://ops.epo.org/rest-services/published-data/search
 #################################################################
 #----------------------   PubMed   -----------------------------#
 #---------------------------------------------------------------#
+# If apiKey is set then it's used, if not set or blank then it's not
+# Max amount of requests per ip per second with apiKey is 10; without 3
+pubmed.apiKey =
 pubmed.url.search = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi
 pubmed.url.fetch = https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi
 #################################################################

dspace/config/modules/orcid.cfg

@@ -1,4 +1,3 @@
-
 #------------------------------------------------------------------#
 #--------------------ORCID GENERIC CONFIGURATIONS------------------#
 #------------------------------------------------------------------#
@@ -58,12 +57,18 @@ orcid.mapping.work.contributors = dc.contributor.editor::editor
 
 ##orcid.mapping.work.external-ids syntax is <metadatafield>::<type> or $simple-handle::<type>
 ##The full list of available external identifiers is available here https://pub.orcid.org/v3.0/identifiers
+# The identifiers need to have a relationship of SELF, PART_OF, VERSION_OF or FUNDED_BY.
+# The default for most identifiers is SELF. The default for identifiers more commonly
+# associated with 'parent' publciations (ISSN, ISBN) is PART_OF.
+# See the map in `orcid-services.xml`
+# VERSION_OF and FUNDED_BY are not currently implemented.
 orcid.mapping.work.external-ids = dc.identifier.doi::doi
 orcid.mapping.work.external-ids = dc.identifier.scopus::eid
 orcid.mapping.work.external-ids = dc.identifier.pmid::pmid
 orcid.mapping.work.external-ids = $simple-handle::handle
 orcid.mapping.work.external-ids = dc.identifier.isi::wosuid
 orcid.mapping.work.external-ids = dc.identifier.issn::issn
+orcid.mapping.work.external-ids = dc.identifier.isbn::isbn
 
 ### Funding mapping ###
 orcid.mapping.funding.title = dc.title
@@ -141,6 +146,9 @@ orcid.bulk-synchronization.max-attempts = 5
 #--------------------ORCID EXTERNAL DATA MAPPING-------------------#
 #------------------------------------------------------------------#
 
+# Note - the below mapping is for ORCID->DSpace imports, not for
+# DSpace->ORCID exports (see orcid.mapping.work.*)
+
 ### Work (Publication) external-data.mapping ###
 orcid.external-data.mapping.publication.title = dc.title
 

dspace/config/modules/usage-statistics.cfg

@@ -61,3 +61,20 @@ usage-statistics.shardedByYear = false
 
 # Only anonymize statistics records older than this threshold (expressed in days)
 #anonymize_statistics.time_threshold = 90
+
+# Maximum number of items to display in the usage statistics report for an entire repository
+usage-statistics.topItemsLimit = 10
+
+# Number of months to begin retrieving usage statistics for total visits per month of a DSpace object
+# For example, -6 means include the previous six months
+usage-statistics.startDateInterval = -6
+
+# Number of months to end retrieving usage statistics for total visits per month of a DSpace object
+# For example, +1 means include the current month
+usage-statistics.endDateInterval = +1
+
+# Maximum number of countries to display in the usage statistics reports
+usage-statistics.topCountriesLimit = 100
+
+# Maximum number of cities to display in the usage statistics reports
+usage-statistics.topCitiesLimit = 100

dspace/config/spring/api/orcid-services.xml

@@ -55,6 +55,27 @@
 	<bean id="orcidWorkFactoryFieldMapping" class="org.dspace.orcid.model.OrcidWorkFieldMapping" >
 		<property name="contributorFields" value="${orcid.mapping.work.contributors}" />
 		<property name="externalIdentifierFields" value="${orcid.mapping.work.external-ids}" />
+            <property name="externalIdentifierPartOfMap">
+                <map>
+                    <entry key="issn">
+                        <list>
+                            <value>journal-article</value>
+                            <value>magazine-article</value>
+                            <value>newspaper-article</value>
+                            <value>data-set</value>
+                            <value>learning-object</value>
+                            <value>other</value>
+                        </list>
+                    </entry>
+                    <entry key="isbn">
+                        <list>
+                            <value>book-chapter</value>
+                            <value>book-review</value>
+                            <value>other</value>
+                        </list>
+                    </entry>
+                </map>
+            </property>
             <property name="publicationDateField" value="${orcid.mapping.work.publication-date}" />
             <property name="titleField" value="${orcid.mapping.work.title}" />
             <property name="journalTitleField" value="${orcid.mapping.work.journal-title}" />

dspace/config/spring/api/workflow-actions.xml

@@ -21,7 +21,6 @@
         <property name="minimumAcceptanceScore" value="3" />
     </bean>
 
-
     <bean id="autoassignactionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.AutoAssignAction" scope="prototype"/>
     <bean id="noUserSelectionActionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.NoUserSelectionAction" scope="prototype"/>
     <bean id="assignoriginalsubmitteractionAPI" class="org.dspace.xmlworkflow.state.actions.userassignment.AssignOriginalSubmitterAction" scope="prototype"/>
@@ -44,7 +43,6 @@
         <property name="requiresUI" value="true"/>
     </bean>
 
-
     <!--Action for the select single reviewer workflow -->
     <bean id="selectrevieweraction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="selectrevieweraction"/>
@@ -64,21 +62,14 @@
         <property name="requiresUI" value="true"/>
     </bean>
 
-    <bean id="ratingreviewaction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
-        <constructor-arg type="java.lang.String" value="ratingreviewaction"/>
-        <property name="processingAction" ref="ratingreviewactionAPI" />
-        <property name="requiresUI" value="true"/>
-    </bean>
-
-    <!--Autmatic step that evaluates scores (workflow.score) and checks if they match the configured minimum for archiving -->
+    <!--Automatic step that evaluates scores (workflow.score) and checks if they match the configured minimum for archiving -->
     <bean id="evaluationaction" class="org.dspace.xmlworkflow.state.actions.WorkflowActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="evaluationaction"/>
         <property name="processingAction" ref="evaluationactionAPI" />
         <property name="requiresUI" value="false"/>
     </bean>
 
-
-<!--User selection actions-->
+    <!--User selection actions-->
     <bean id="claimaction" class="org.dspace.xmlworkflow.state.actions.UserSelectionActionConfig" scope="prototype">
         <constructor-arg type="java.lang.String" value="claimaction"/>
         <property name="processingAction" ref="claimactionAPI"/>

dspace/modules/additions/pom.xml

@@ -17,7 +17,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>7.6.4</version>
+      <version>7.6.6-SNAPSHOT</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/modules/pom.xml

@@ -11,7 +11,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>../../pom.xml</relativePath>
     </parent>
 

dspace/modules/rest/pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>modules</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace/modules/server/pom.xml

@@ -13,7 +13,7 @@ just adding new jar in the classloader</description>
     <parent>
         <artifactId>modules</artifactId>
         <groupId>org.dspace</groupId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace/pom.xml

@@ -16,7 +16,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>7.6.4</version>
+        <version>7.6.6-SNAPSHOT</version>
         <relativePath>../pom.xml</relativePath>
     </parent>
 

dspace/solr/search/conf/schema.xml

@@ -324,7 +324,7 @@
     <dynamicField name="*_mlt" type="text" indexed="true" stored="true" multiValued="true" omitNorms="true" termVectors="true" termPositions="true" termOffsets="true"/>
 
     <!--Date matching-->
-    <dynamicField name="*.year" type="sint" indexed="true" stored="true" multiValued="true" omitNorms="true" />
+    <dynamicField name="*_year" type="sint" indexed="true" stored="true" multiValued="true" omitNorms="true" />
     <dynamicField name="*_dt" type="date" indexed="true" stored="true" multiValued="false" omitNorms="true"  docValues="true"/>
 
     <!--Used for matching on all other fields -->

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.dspace</groupId>
     <artifactId>dspace-parent</artifactId>
     <packaging>pom</packaging>
-    <version>7.6.4</version>
+    <version>7.6.6-SNAPSHOT</version>
     <name>DSpace Parent Project</name>
     <description>
    	DSpace open source software is a turnkey institutional repository application.
@@ -27,18 +27,18 @@
         <postgresql.driver.version>42.7.7</postgresql.driver.version>
         <solr.client.version>8.11.4</solr.client.version>
 
-        <ehcache.version>3.10.8</ehcache.version>
+        <ehcache.version>3.11.1</ehcache.version>
         <errorprone.version>2.31.0</errorprone.version>
         <!-- NOTE: when updating jackson.version, also sync jackson-databind.version below -->
-        <jackson.version>2.19.1</jackson.version>
-        <jackson-databind.version>2.19.1</jackson-databind.version>
+        <jackson.version>2.19.2</jackson.version>
+        <jackson-databind.version>2.19.2</jackson-databind.version>
         <javax-annotation.version>1.3.2</javax-annotation.version>
         <jaxb-api.version>2.3.1</jaxb-api.version>
         <jaxb-runtime.version>2.3.9</jaxb-runtime.version>
         <jcache-version>1.1.1</jcache-version>
         <!-- NOTE: Jetty needed for Solr, Handle Server & tests -->
-        <jetty.version>9.4.57.v20241219</jetty.version>
-        <log4j.version>2.25.0</log4j.version>
+        <jetty.version>9.4.58.v20250814</jetty.version>
+        <log4j.version>2.25.1</log4j.version>
         <pdfbox-version>2.0.34</pdfbox-version>
         <rome.version>1.19.0</rome.version>
         <slf4j.version>1.7.36</slf4j.version>
@@ -89,7 +89,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-enforcer-plugin</artifactId>
-                    <version>3.5.0</version>
+                    <version>3.6.1</version>
                     <executions>
                         <execution>
                             <id>enforce-java</id>
@@ -295,7 +295,7 @@
                 <plugin>
                     <groupId>com.github.spotbugs</groupId>
                     <artifactId>spotbugs-maven-plugin</artifactId>
-                    <version>4.9.3.0</version>
+                    <version>4.9.4.2</version>
                     <configuration>
                         <effort>Max</effort>
                         <threshold>Low</threshold>
@@ -305,7 +305,7 @@
                         <dependency>
                             <groupId>com.github.spotbugs</groupId>
                             <artifactId>spotbugs</artifactId>
-                            <version>4.9.3</version>
+                            <version>4.9.4</version>
                         </dependency>
                     </dependencies>
                     <executions>
@@ -363,7 +363,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-javadoc-plugin</artifactId>
-                    <version>3.11.2</version>
+                    <version>3.11.3</version>
                     <configuration>
                         <!-- Never fail a build based on Javadoc errors -->
                         <failOnError>false</failOnError>
@@ -515,10 +515,10 @@
     </build>
 
     <profiles>
-        <!-- Allow for passing extra memory to Unit/Integration tests.
-             By default this gives unit tests 1GB of memory max (when tests are enabled),
-             unless tweaked on commandline (e.g. "-Dtest.argLine=-Xmx512m"). Since
-             m-surefire-p and m-failsafe-p both fork a new JVM for testing, they ignores MAVEN_OPTS. -->
+        <!-- Profile which sets our default system properties for all Unit/Integration tests.
+             By default, this sets UTF-8 encoding for all tests and gives tests 1GB of memory max.
+             Both m-surefire-p and m-failsafe-p are unable to use MAVEN_OPTS because they fork a new JVM for testing.
+             These default settings may be overridden via the commandline (e.g. "-Dtest.argLine=-Xmx512m"). -->
         <profile>
             <id>test-argLine</id>
             <activation>
@@ -527,7 +527,7 @@
                 </property>
             </activation>
             <properties>
-                <test.argLine>-Xmx1024m</test.argLine>
+                <test.argLine>-Xmx1024m -Dfile.encoding=UTF-8</test.argLine>
             </properties>
         </profile>
 
@@ -680,7 +680,7 @@
                     <plugin>
                         <groupId>org.codehaus.mojo</groupId>
                         <artifactId>license-maven-plugin</artifactId>
-                        <version>2.5.0</version>
+                        <version>2.6.0</version>
                         <!-- This plugin only needs to be run on the Parent POM
                              as it aggregates results from all child POMs. -->
                         <inherited>false</inherited>
@@ -875,14 +875,14 @@
                    <dependency>
                        <groupId>org.dspace</groupId>
                        <artifactId>dspace-rest</artifactId>
-                       <version>7.6.4</version>
+                       <version>7.6.6-SNAPSHOT</version>
                        <type>jar</type>
                        <classifier>classes</classifier>
                    </dependency>
                    <dependency>
                        <groupId>org.dspace</groupId>
                        <artifactId>dspace-rest</artifactId>
-                       <version>7.6.4</version>
+                       <version>7.6.6-SNAPSHOT</version>
                        <type>war</type>
                    </dependency>
                </dependencies>
@@ -1031,69 +1031,69 @@
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-api</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-api</artifactId>
                 <type>test-jar</type>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
                 <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>org.dspace.modules</groupId>
                 <artifactId>additions</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
 
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-sword</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-swordv2</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-oai</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-services</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-server-webapp</artifactId>
                 <type>test-jar</type>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
                 <scope>test</scope>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-rdf</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-iiif</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-server-webapp</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
                 <type>jar</type>
                 <classifier>classes</classifier>
             </dependency>
             <dependency>
                 <groupId>org.dspace</groupId>
                 <artifactId>dspace-server-webapp</artifactId>
-                <version>7.6.4</version>
+                <version>7.6.6-SNAPSHOT</version>
                 <type>war</type>
             </dependency>
             <!-- DSpace API Localization Packages -->
@@ -1324,7 +1324,7 @@
             <dependency>
                 <groupId>org.apache.james</groupId>
                 <artifactId>apache-mime4j-core</artifactId>
-                <version>0.8.12</version>
+                <version>0.8.13</version>
             </dependency>
             <!-- Tika and solr-core disagree on versions of ASM -->
             <dependency>
@@ -1473,12 +1473,12 @@
             <dependency>
                 <groupId>commons-cli</groupId>
                 <artifactId>commons-cli</artifactId>
-                <version>1.9.0</version>
+                <version>1.10.0</version>
             </dependency>
             <dependency>
                 <groupId>commons-codec</groupId>
                 <artifactId>commons-codec</artifactId>
-                <version>1.18.0</version>
+                <version>1.19.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.commons</groupId>
@@ -1498,12 +1498,12 @@
             <dependency>
                 <groupId>commons-io</groupId>
                 <artifactId>commons-io</artifactId>
-                <version>2.19.0</version>
+                <version>2.20.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-lang3</artifactId>
-                <version>3.17.0</version>
+                <version>3.18.0</version>
             </dependency>
             <!-- NOTE: We don't use commons-logging or commons-compress directly,
                  but many dependencies rely on them. Only here specified to avoid dependency convergence issues. -->
@@ -1515,7 +1515,7 @@
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-compress</artifactId>
-                <version>1.27.1</version>
+                <version>1.28.0</version>
             </dependency>
             <dependency>
                 <groupId>org.apache.commons</groupId>
@@ -1525,12 +1525,12 @@
             <dependency>
                 <groupId>org.apache.commons</groupId>
                 <artifactId>commons-text</artifactId>
-                <version>1.13.1</version>
+                <version>1.14.0</version>
             </dependency>
             <dependency>
                 <groupId>commons-validator</groupId>
                 <artifactId>commons-validator</artifactId>
-                <version>1.9.0</version>
+                <version>1.10.0</version>
             </dependency>
             <dependency>
                 <groupId>joda-time</groupId>
@@ -1701,7 +1701,7 @@
             <dependency>
                 <groupId>com.google.http-client</groupId>
                 <artifactId>google-http-client</artifactId>
-                <version>1.47.0</version>
+                <version>1.47.1</version>
                 <exclusions>
                     <exclusion>
                         <groupId>com.google.errorprone</groupId>
@@ -1718,12 +1718,12 @@
             <dependency>
                 <groupId>io.grpc</groupId>
                 <artifactId>grpc-context</artifactId>
-                <version>1.73.0</version>
+                <version>1.75.0</version>
             </dependency>
             <dependency>
                 <groupId>com.google.http-client</groupId>
                 <artifactId>google-http-client-jackson2</artifactId>
-                <version>1.47.0</version>
+                <version>1.47.1</version>
                 <exclusions>
                     <exclusion>
                         <artifactId>jackson-core</artifactId>
@@ -1745,7 +1745,7 @@
             <dependency>
                 <groupId>com.google.http-client</groupId>
                 <artifactId>google-http-client-gson</artifactId>
-                <version>1.47.0</version>
+                <version>1.47.1</version>
             </dependency>
             <dependency>
                 <groupId>com.squareup.okhttp3</groupId>
@@ -1939,7 +1939,7 @@
         <connection>scm:git:git@github.com:DSpace/DSpace.git</connection>
         <developerConnection>scm:git:git@github.com:DSpace/DSpace.git</developerConnection>
         <url>https://github.com/DSpace/DSpace</url>
-        <tag>dspace-7.6.4</tag>
+        <tag>dspace-7_x</tag>
     </scm>
 
     <repositories>