Merge branch 'main' into CST-4503-AddingNewRelationshipsInEditItem

dspace-api/pom.xml

@@ -743,7 +743,7 @@
         <dependency>
             <groupId>org.flywaydb</groupId>
             <artifactId>flyway-core</artifactId>
-            <version>6.5.5</version>
+            <version>6.5.7</version>
         </dependency>
 
         <!-- Google Analytics -->

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

@@ -81,7 +81,7 @@ public class MetadataImporter {
      * @throws SQLException                 if database error
      * @throws IOException                  if IO error
      * @throws TransformerException         if transformer error
-     * @throws ParserConfigurationException if config error
+     * @throws ParserConfigurationException if configuration error
      * @throws AuthorizeException           if authorization error
      * @throws SAXException                 if parser error
      * @throws NonUniqueMetadataException   if duplicate metadata
@@ -91,7 +91,6 @@ public class MetadataImporter {
         throws ParseException, SQLException, IOException, TransformerException,
         ParserConfigurationException, AuthorizeException, SAXException,
         NonUniqueMetadataException, RegistryImportException {
-        boolean forceUpdate = false;
 
         // create an options object and populate it
         CommandLineParser parser = new DefaultParser();
@@ -100,16 +99,14 @@ public class MetadataImporter {
         options.addOption("u", "update", false, "update an existing schema");
         CommandLine line = parser.parse(options, args);
 
-        String file = null;
         if (line.hasOption('f')) {
-            file = line.getOptionValue('f');
+            String file = line.getOptionValue('f');
+            boolean forceUpdate = line.hasOption('u');
+            loadRegistry(file, forceUpdate);
         } else {
             usage();
-            System.exit(0);
+            System.exit(1);
         }
-
-        forceUpdate = line.hasOption('u');
-        loadRegistry(file, forceUpdate);
     }
 
     /**
@@ -120,7 +117,7 @@ public class MetadataImporter {
      * @throws SQLException                 if database error
      * @throws IOException                  if IO error
      * @throws TransformerException         if transformer error
-     * @throws ParserConfigurationException if config error
+     * @throws ParserConfigurationException if configuration error
      * @throws AuthorizeException           if authorization error
      * @throws SAXException                 if parser error
      * @throws NonUniqueMetadataException   if duplicate metadata
@@ -227,7 +224,7 @@ public class MetadataImporter {
     /**
      * Process a node in the metadata registry XML file. The node must
      * be a "dc-type" node.  If the type already exists, then it
-     * will not be reimported
+     * will not be re-imported.
      *
      * @param context DSpace context object
      * @param node    the node in the DOM tree

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

@@ -24,7 +24,7 @@ import org.dspace.content.BitstreamFormat;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.w3c.dom.Document;
 import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
@@ -95,7 +95,7 @@ public class RegistryLoader {
 
             System.exit(1);
         } catch (Exception e) {
-            log.fatal(LogManager.getHeader(context, "error_loading_registries",
+            log.fatal(LogHelper.getHeader(context, "error_loading_registries",
                                            ""), e);
 
             System.err.println("Error: \n - " + e.getMessage());
@@ -135,7 +135,7 @@ public class RegistryLoader {
             loadFormat(context, n);
         }
 
-        log.info(LogManager.getHeader(context, "load_bitstream_formats",
+        log.info(LogHelper.getHeader(context, "load_bitstream_formats",
                                       "number_loaded=" + typeNodes.getLength()));
     }
 

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

@@ -138,7 +138,7 @@ public class DSpaceCSV implements Serializable {
     /**
      * Create a new instance, reading the lines in from file
      *
-     * @param inputStream the inputstream to read from
+     * @param inputStream the input stream to read from
      * @param c The DSpace Context
      * @throws Exception thrown if there is an error reading or processing the file
      */
@@ -159,7 +159,7 @@ public class DSpaceCSV implements Serializable {
                 columnCounter++;
 
                 // Remove surrounding quotes if there are any
-                if ((element.startsWith("\"")) && (element.endsWith("\""))) {
+                if (element.startsWith("\"") && element.endsWith("\"")) {
                     element = element.substring(1, element.length() - 1);
                 }
 
@@ -337,15 +337,15 @@ public class DSpaceCSV implements Serializable {
     /**
      * Set the value separator for multiple values stored in one csv value.
      *
-     * Is set in bulkedit.cfg as valueseparator
+     * Is set in {@code bulkedit.cfg} as {@code valueseparator}.
      *
-     * If not set, defaults to double pipe '||'
+     * If not set, defaults to double pipe '||'.
      */
     private void setValueSeparator() {
         // Get the value separator
         valueSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
                                               .getProperty("bulkedit.valueseparator");
-        if ((valueSeparator != null) && (!"".equals(valueSeparator.trim()))) {
+        if ((valueSeparator != null) && !valueSeparator.trim().isEmpty()) {
             valueSeparator = valueSeparator.trim();
         } else {
             valueSeparator = "||";
@@ -360,7 +360,7 @@ public class DSpaceCSV implements Serializable {
     /**
      * Set the field separator use to separate fields in the csv.
      *
-     * Is set in bulkedit.cfg as fieldseparator
+     * Is set in {@code bulkedit.cfg} as {@code fieldseparator}.
      *
      * If not set, defaults to comma ','.
      *
@@ -371,7 +371,7 @@ public class DSpaceCSV implements Serializable {
         // Get the value separator
         fieldSeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
                                               .getProperty("bulkedit.fieldseparator");
-        if ((fieldSeparator != null) && (!"".equals(fieldSeparator.trim()))) {
+        if ((fieldSeparator != null) && !fieldSeparator.trim().isEmpty()) {
             fieldSeparator = fieldSeparator.trim();
             if ("tab".equals(fieldSeparator)) {
                 fieldSeparator = "\t";
@@ -395,15 +395,15 @@ public class DSpaceCSV implements Serializable {
     /**
      * Set the authority separator for value with authority data.
      *
-     * Is set in dspace.cfg as bulkedit.authorityseparator
+     * Is set in {@code dspace.cfg} as {@code bulkedit.authorityseparator}.
      *
-     * If not set, defaults to double colon '::'
+     * If not set, defaults to double colon '::'.
      */
     private void setAuthoritySeparator() {
         // Get the value separator
         authoritySeparator = DSpaceServicesFactory.getInstance().getConfigurationService()
                                                   .getProperty("bulkedit.authorityseparator");
-        if ((authoritySeparator != null) && (!"".equals(authoritySeparator.trim()))) {
+        if ((authoritySeparator != null) && !authoritySeparator.trim().isEmpty()) {
             authoritySeparator = authoritySeparator.trim();
         } else {
             authoritySeparator = "::";
@@ -508,7 +508,7 @@ public class DSpaceCSV implements Serializable {
             int i = 0;
             for (String part : bits) {
                 int bitcounter = part.length() - part.replaceAll("\"", "").length();
-                if ((part.startsWith("\"")) && ((!part.endsWith("\"")) || ((bitcounter & 1) == 1))) {
+                if (part.startsWith("\"") && (!part.endsWith("\"") || ((bitcounter & 1) == 1))) {
                     found = true;
                     String add = bits.get(i) + fieldSeparator + bits.get(i + 1);
                     bits.remove(i);
@@ -524,7 +524,7 @@ public class DSpaceCSV implements Serializable {
         // Deal with quotes around the elements
         int i = 0;
         for (String part : bits) {
-            if ((part.startsWith("\"")) && (part.endsWith("\""))) {
+            if (part.startsWith("\"") && part.endsWith("\"")) {
                 part = part.substring(1, part.length() - 1);
                 bits.set(i, part);
             }
@@ -564,7 +564,7 @@ public class DSpaceCSV implements Serializable {
         for (String part : bits) {
             if (i > 0) {
                 // Is this a last empty item?
-                if ((last) && (i == headings.size())) {
+                if (last && (i == headings.size())) {
                     part = "";
                 }
 
@@ -577,7 +577,7 @@ public class DSpaceCSV implements Serializable {
                 csvLine.add(headings.get(i - 1), null);
                 String[] elements = part.split(escapedValueSeparator);
                 for (String element : elements) {
-                    if ((element != null) && (!"".equals(element))) {
+                    if ((element != null) && !element.isEmpty()) {
                         csvLine.add(headings.get(i - 1), element);
                     }
                 }
@@ -629,18 +629,18 @@ public class DSpaceCSV implements Serializable {
     public InputStream getInputStream() {
         StringBuilder stringBuilder = new StringBuilder();
         for (String csvLine : getCSVLinesAsStringArray()) {
-            stringBuilder.append(csvLine + "\n");
+            stringBuilder.append(csvLine).append("\n");
         }
         return IOUtils.toInputStream(stringBuilder.toString(), StandardCharsets.UTF_8);
     }
 
     /**
-     * Is it Ok to export this value? When exportAll is set to false, we don't export
+     * Is it okay to export this value? When exportAll is set to false, we don't export
      * some of the metadata elements.
      *
-     * The list can be configured via the key ignore-on-export in bulkedit.cfg
+     * The list can be configured via the key ignore-on-export in {@code bulkedit.cfg}.
      *
-     * @param md The Metadatum to examine
+     * @param md The MetadataField to examine
      * @return Whether or not it is OK to export this element
      */
     protected boolean okToExport(MetadataField md) {
@@ -649,12 +649,8 @@ public class DSpaceCSV implements Serializable {
         if (md.getQualifier() != null) {
             key += "." + md.getQualifier();
         }
-        if (ignore.get(key) != null) {
-            return false;
-        }
-
         // Must be OK, so don't ignore
-        return true;
+        return ignore.get(key) == null;
     }
 
     /**

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

@@ -25,6 +25,7 @@ import javax.annotation.Nullable;
 import org.apache.commons.cli.ParseException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
+import org.dspace.app.util.RelationshipUtils;
 import org.dspace.authority.AuthorityValue;
 import org.dspace.authority.factory.AuthorityServiceFactory;
 import org.dspace.authority.service.AuthorityValueService;
@@ -53,7 +54,7 @@ import org.dspace.content.service.RelationshipTypeService;
 import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.handle.factory.HandleServiceFactory;
@@ -640,7 +641,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
             all += part + ",";
         }
         all = all.substring(0, all.length());
-        log.debug(LogManager.getHeader(c, "metadata_import",
+        log.debug(LogHelper.getHeader(c, "metadata_import",
                                        "item_id=" + item.getID() + ",fromCSV=" + all));
 
         // Don't compare collections or actions or rowNames
@@ -677,7 +678,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                 qualifier = qualifier.substring(0, qualifier.indexOf('['));
             }
         }
-        log.debug(LogManager.getHeader(c, "metadata_import",
+        log.debug(LogHelper.getHeader(c, "metadata_import",
                                        "item_id=" + item.getID() + ",fromCSV=" + all +
                                            ",looking_for_schema=" + schema +
                                            ",looking_for_element=" + element +
@@ -697,7 +698,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
                         .getConfidence() : Choices.CF_ACCEPTED);
                 }
                 i++;
-                log.debug(LogManager.getHeader(c, "metadata_import",
+                log.debug(LogHelper.getHeader(c, "metadata_import",
                                                "item_id=" + item.getID() + ",fromCSV=" + all +
                                                    ",found=" + dcv.getValue()));
             }
@@ -748,7 +749,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
             // column "dc.contributor.author" so don't remove it
             if ((value != null) && (!"".equals(value)) && (!contains(value, fromCSV)) && fromAuthority == null) {
                 // Remove it
-                log.debug(LogManager.getHeader(c, "metadata_import",
+                log.debug(LogHelper.getHeader(c, "metadata_import",
                                                "item_id=" + item.getID() + ",fromCSV=" + all +
                                                    ",removing_schema=" + schema +
                                                    ",removing_element=" + element +
@@ -1793,36 +1794,7 @@ public class MetadataImport extends DSpaceRunnable<MetadataImportScriptConfigura
      */
     private RelationshipType matchRelationshipType(List<RelationshipType> relTypes,
                                                    String targetType, String originType, String originTypeName) {
-        RelationshipType foundRelationshipType = null;
-        if (originTypeName.split("\\.").length > 1) {
-            originTypeName = originTypeName.split("\\.")[1];
-        }
-        for (RelationshipType relationshipType : relTypes) {
-            // Is origin type leftward or righward
-            boolean isLeft = false;
-            if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType)) {
-                isLeft = true;
-            }
-            if (isLeft) {
-                // Validate typeName reference
-                if (!relationshipType.getLeftwardType().equalsIgnoreCase(originTypeName)) {
-                    continue;
-                }
-                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType) &&
-                    relationshipType.getRightType().getLabel().equalsIgnoreCase(targetType)) {
-                    foundRelationshipType = relationshipType;
-                }
-            } else {
-                if (!relationshipType.getRightwardType().equalsIgnoreCase(originTypeName)) {
-                    continue;
-                }
-                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(targetType) &&
-                    relationshipType.getRightType().getLabel().equalsIgnoreCase(originType)) {
-                    foundRelationshipType = relationshipType;
-                }
-            }
-        }
-        return foundRelationshipType;
+        return RelationshipUtils.matchRelationshipType(relTypes, targetType, originType, originTypeName);
     }
 
 }

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

@@ -13,11 +13,8 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
 
-import org.apache.commons.cli.CommandLine;
-import org.apache.commons.cli.CommandLineParser;
-import org.apache.commons.cli.DefaultParser;
-import org.apache.commons.cli.HelpFormatter;
-import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.lang3.StringUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Collection;
 import org.dspace.content.DSpaceObject;
@@ -36,221 +33,223 @@ import org.dspace.harvest.HarvestingException;
 import org.dspace.harvest.OAIHarvester;
 import org.dspace.harvest.factory.HarvestServiceFactory;
 import org.dspace.harvest.service.HarvestedCollectionService;
+import org.dspace.scripts.DSpaceRunnable;
+import org.dspace.utils.DSpace;
 
 /**
  * Test class for harvested collections.
  *
  * @author Alexey Maslov
  */
-public class Harvest {
-    private static Context context;
+public class Harvest extends DSpaceRunnable<HarvestScriptConfiguration> {
 
-    private static final HarvestedCollectionService harvestedCollectionService =
-        HarvestServiceFactory.getInstance().getHarvestedCollectionService();
-    private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
-    private static final CollectionService collectionService =
-        ContentServiceFactory.getInstance().getCollectionService();
+    private HarvestedCollectionService harvestedCollectionService;
+    protected EPersonService ePersonService;
+    private CollectionService collectionService;
 
-    public static void main(String[] argv) throws Exception {
-        // create an options object and populate it
-        CommandLineParser parser = new DefaultParser();
+    private boolean help;
+    private String command = null;
+    private String collection = null;
+    private String oaiSource = null;
+    private String oaiSetID = null;
+    private String metadataKey = null;
+    private int harvestType = 0;
 
-        Options options = new Options();
-
-        options.addOption("p", "purge", false, "delete all items in the collection");
-        options.addOption("r", "run", false, "run the standard harvest procedure");
-        options.addOption("g", "ping", false, "test the OAI server and set");
-        options.addOption("s", "setup", false, "Set the collection up for harvesting");
-        options.addOption("S", "start", false, "start the harvest loop");
-        options.addOption("R", "reset", false, "reset harvest status on all collections");
-        options.addOption("P", "purge", false, "purge all harvestable collections");
+    protected Context context;
 
 
-        options.addOption("e", "eperson", true,
-                          "eperson");
-        options.addOption("c", "collection", true,
-                          "harvesting collection (handle or id)");
-        options.addOption("t", "type", true,
-                          "type of harvesting (0 for none)");
-        options.addOption("a", "address", true,
-                          "address of the OAI-PMH server");
-        options.addOption("i", "oai_set_id", true,
-                          "id of the PMH set representing the harvested collection");
-        options.addOption("m", "metadata_format", true,
-                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
-                              "crosswalk in dspace.cfg");
+    public HarvestScriptConfiguration getScriptConfiguration() {
+        return new DSpace().getServiceManager()
+                           .getServiceByName("harvest", HarvestScriptConfiguration.class);
+    }
 
-        options.addOption("h", "help", false, "help");
+    public void setup() throws ParseException {
+        harvestedCollectionService =
+                HarvestServiceFactory.getInstance().getHarvestedCollectionService();
+        ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
+        collectionService =
+                ContentServiceFactory.getInstance().getCollectionService();
 
-        CommandLine line = parser.parse(options, argv);
+        assignCurrentUserInContext();
 
-        String command = null;
-        String eperson = null;
-        String collection = null;
-        String oaiSource = null;
-        String oaiSetID = null;
-        String metadataKey = null;
-        int harvestType = 0;
-
-        if (line.hasOption('h')) {
-            HelpFormatter myhelp = new HelpFormatter();
-            myhelp.printHelp("Harvest\n", options);
-            System.out.println("\nPING OAI server: Harvest -g -a oai_source -i oai_set_id");
-            System.out.println(
-                "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
-                    "oai_set_id -m metadata_format");
-            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out.println("START harvest scheduler: Harvest -S");
-            System.out.println("RESET all harvest status: Harvest -R");
-            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
+        help = commandLine.hasOption('h');
 
 
-            System.exit(0);
-        }
-
-        if (line.hasOption('s')) {
+        if (commandLine.hasOption('s')) {
             command = "config";
         }
-        if (line.hasOption('p')) {
+        if (commandLine.hasOption('p')) {
             command = "purge";
         }
-        if (line.hasOption('r')) {
+        if (commandLine.hasOption('r')) {
             command = "run";
         }
-        if (line.hasOption('g')) {
+        if (commandLine.hasOption('g')) {
             command = "ping";
         }
-        if (line.hasOption('S')) {
+        if (commandLine.hasOption('S')) {
             command = "start";
         }
-        if (line.hasOption('R')) {
+        if (commandLine.hasOption('R')) {
             command = "reset";
         }
-        if (line.hasOption('P')) {
+        if (commandLine.hasOption('P')) {
             command = "purgeAll";
         }
-
-
-        if (line.hasOption('e')) {
-            eperson = line.getOptionValue('e');
+        if (commandLine.hasOption('o')) {
+            command = "reimport";
         }
-        if (line.hasOption('c')) {
-            collection = line.getOptionValue('c');
+        if (commandLine.hasOption('c')) {
+            collection = commandLine.getOptionValue('c');
         }
-        if (line.hasOption('t')) {
-            harvestType = Integer.parseInt(line.getOptionValue('t'));
+        if (commandLine.hasOption('t')) {
+            harvestType = Integer.parseInt(commandLine.getOptionValue('t'));
         } else {
             harvestType = 0;
         }
-        if (line.hasOption('a')) {
-            oaiSource = line.getOptionValue('a');
+        if (commandLine.hasOption('a')) {
+            oaiSource = commandLine.getOptionValue('a');
         }
-        if (line.hasOption('i')) {
-            oaiSetID = line.getOptionValue('i');
+        if (commandLine.hasOption('i')) {
+            oaiSetID = commandLine.getOptionValue('i');
         }
-        if (line.hasOption('m')) {
-            metadataKey = line.getOptionValue('m');
+        if (commandLine.hasOption('m')) {
+            metadataKey = commandLine.getOptionValue('m');
+        }
+    }
+
+    /**
+     * This method will assign the currentUser to the {@link Context} variable which is also created in this method.
+     * The instance of the method in this class will fetch the EPersonIdentifier from this class, this identifier
+     * was given to this class upon instantiation, it'll then be used to find the {@link EPerson} associated with it
+     * and this {@link EPerson} will be set as the currentUser of the created {@link Context}
+     * @throws ParseException If something went wrong with the retrieval of the EPerson Identifier
+     */
+    protected void assignCurrentUserInContext() throws ParseException {
+        UUID currentUserUuid = this.getEpersonIdentifier();
+        try {
+            this.context = new Context(Context.Mode.BATCH_EDIT);
+            EPerson eperson = ePersonService.find(context, currentUserUuid);
+            if (eperson == null) {
+                super.handler.logError("EPerson not found: " + currentUserUuid);
+                throw new IllegalArgumentException("Unable to find a user with uuid: " + currentUserUuid);
+            }
+            this.context.setCurrentUser(eperson);
+        } catch (SQLException e) {
+            handler.handleException("Something went wrong trying to fetch eperson for uuid: " + currentUserUuid, e);
+        }
+    }
+
+    public void internalRun() throws Exception {
+        if (help) {
+            printHelp();
+            handler.logInfo("PING OAI server: Harvest -g -a oai_source -i oai_set_id");
+            handler.logInfo(
+                    "SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i " +
+                            "oai_set_id -m metadata_format");
+            handler.logInfo("RUN harvest once: Harvest -r -e eperson -c collection");
+            handler.logInfo("START harvest scheduler: Harvest -S");
+            handler.logInfo("RESET all harvest status: Harvest -R");
+            handler.logInfo("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
+            handler.logInfo("PURGE all harvestable collections: Harvest -P -e eperson");
+
+            return;
         }
 
-
-        // Instantiate our class
-        Harvest harvester = new Harvest();
-        harvester.context = new Context(Context.Mode.BATCH_EDIT);
-
-
-        // Check our options
-        if (command == null) {
-            System.out
-                .println("Error - no parameters specified (run with -h flag for details)");
-            System.exit(1);
+        if (StringUtils.isBlank(command)) {
+            handler.logError("No parameters specified (run with -h flag for details)");
+            throw new UnsupportedOperationException("No command specified");
         } else if ("run".equals(command)) {
             // Run a single harvest cycle on a collection using saved settings.
-            if (collection == null || eperson == null) {
-                System.out
-                    .println("Error - a target collection and eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+            if (collection == null || context.getCurrentUser() == null) {
+                handler.logError("A target collection and eperson must be provided (run with -h flag for details)");
+                throw new UnsupportedOperationException("A target collection and eperson must be provided");
             }
-
-            harvester.runHarvest(collection, eperson);
+            runHarvest(context, collection);
         } else if ("start".equals(command)) {
             // start the harvest loop
             startHarvester();
         } else if ("reset".equals(command)) {
             // reset harvesting status
-            resetHarvesting();
+            resetHarvesting(context);
         } else if ("purgeAll".equals(command)) {
             // purge all collections that are set up for harvesting (obviously for testing purposes only)
-            if (eperson == null) {
-                System.out
-                    .println("Error - an eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+            if (context.getCurrentUser() == null) {
+                handler.logError("An eperson must be provided (run with -h flag for details)");
+                throw new UnsupportedOperationException("An eperson must be provided");
             }
 
             List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
             for (HarvestedCollection harvestedCollection : harvestedCollections) {
-                System.out.println(
-                    "Purging the following collections (deleting items and resetting harvest status): " +
-                        harvestedCollection
-                            .getCollection().getID().toString());
-                harvester.purgeCollection(harvestedCollection.getCollection().getID().toString(), eperson);
+                handler.logInfo(
+                        "Purging the following collections (deleting items and resetting harvest status): " +
+                                harvestedCollection
+                                        .getCollection().getID().toString());
+                purgeCollection(context, harvestedCollection.getCollection().getID().toString());
             }
             context.complete();
         } else if ("purge".equals(command)) {
             // Delete all items in a collection. Useful for testing fresh harvests.
-            if (collection == null || eperson == null) {
-                System.out
-                    .println("Error - a target collection and eperson must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+            if (collection == null || context.getCurrentUser() == null) {
+                handler.logError("A target collection and eperson must be provided (run with -h flag for details)");
+                throw new UnsupportedOperationException("A target collection and eperson must be provided");
             }
 
-            harvester.purgeCollection(collection, eperson);
+            purgeCollection(context, collection);
+            context.complete();
+
+        } else if ("reimport".equals(command)) {
+            // Delete all items in a collection. Useful for testing fresh harvests.
+            if (collection == null || context.getCurrentUser() == null) {
+                handler.logError("A target collection and eperson must be provided (run with -h flag for details)");
+                throw new UnsupportedOperationException("A target collection and eperson must be provided");
+            }
+            purgeCollection(context, collection);
+            runHarvest(context, collection);
             context.complete();
 
-            //TODO: implement this... remove all items and remember to unset "last-harvested" settings
         } else if ("config".equals(command)) {
             // Configure a collection with the three main settings
             if (collection == null) {
-                System.out.println("Error -  a target collection must be provided");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+                handler.logError("A target collection must be provided (run with -h flag for details)");
+                throw new UnsupportedOperationException("A target collection must be provided");
             }
             if (oaiSource == null || oaiSetID == null) {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+                handler.logError(
+                        "Both the OAI server address and OAI set id must be specified (run with -h flag for details)");
+                throw new UnsupportedOperationException("Both the OAI server address and OAI set id must be specified");
             }
             if (metadataKey == null) {
-                System.out
-                    .println("Error - a metadata key (commonly the prefix) must be specified for this collection");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+                handler.logError(
+                        "A metadata key (commonly the prefix) must be specified for this collection (run with -h flag" +
+                                " for details)");
+                throw new UnsupportedOperationException(
+                        "A metadata key (commonly the prefix) must be specified for this collection");
             }
 
-            harvester.configureCollection(collection, harvestType, oaiSource, oaiSetID, metadataKey);
+            configureCollection(context, collection, harvestType, oaiSource, oaiSetID, metadataKey);
         } else if ("ping".equals(command)) {
             if (oaiSource == null || oaiSetID == null) {
-                System.out.println("Error - both the OAI server address and OAI set id must be specified");
-                System.out.println(" (run with -h flag for details)");
-                System.exit(1);
+                handler.logError(
+                        "Both the OAI server address and OAI set id must be specified  (run with -h flag for details)");
+                throw new UnsupportedOperationException("Both the OAI server address and OAI set id must be specified");
             }
 
             pingResponder(oaiSource, oaiSetID, metadataKey);
         } else {
-            System.out.println("Error - your command '" + command + "' was not recoginzed properly");
-            System.out.println(" (run with -h flag for details)");
-            System.exit(1);
+            handler.logError(
+                    "Your command '" + command + "' was not recognized properly (run with -h flag for details)");
+            throw new UnsupportedOperationException("Your command '" + command + "' was not recognized properly");
         }
+
+
     }
 
     /*
      * Resolve the ID into a collection and check to see if its harvesting options are set. If so, return
      * the collection, if not, bail out.
      */
-    private Collection resolveCollection(String collectionID) {
+    private Collection resolveCollection(Context context, String collectionID) {
 
         DSpaceObject dso;
         Collection targetCollection = null;
@@ -270,14 +269,14 @@ public class Harvest {
                     }
                 } else {
                     // not a handle, try and treat it as an collection database UUID
-                    System.out.println("Looking up by UUID: " + collectionID + ", " + "in context: " + context);
+                    handler.logInfo("Looking up by UUID: " + collectionID + ", " + "in context: " + context);
                     targetCollection = collectionService.find(context, UUID.fromString(collectionID));
                 }
             }
             // was the collection valid?
             if (targetCollection == null) {
-                System.out.println("Cannot resolve " + collectionID + " to collection");
-                System.exit(1);
+                handler.logError("Cannot resolve " + collectionID + " to collection");
+                throw new UnsupportedOperationException("Cannot resolve " + collectionID + " to collection");
             }
         } catch (SQLException se) {
             se.printStackTrace();
@@ -287,12 +286,12 @@ public class Harvest {
     }
 
 
-    private void configureCollection(String collectionID, int type, String oaiSource, String oaiSetId,
+    private void configureCollection(Context context, String collectionID, int type, String oaiSource, String oaiSetId,
                                      String mdConfigId) {
-        System.out.println("Running: configure collection");
+        handler.logInfo("Running: configure collection");
 
-        Collection collection = resolveCollection(collectionID);
-        System.out.println(collection.getID());
+        Collection collection = resolveCollection(context, collectionID);
+        handler.logInfo(String.valueOf(collection.getID()));
 
         try {
             HarvestedCollection hc = harvestedCollectionService.find(context, collection);
@@ -307,9 +306,8 @@ public class Harvest {
             context.restoreAuthSystemState();
             context.complete();
         } catch (Exception e) {
-            System.out.println("Changes could not be committed");
-            e.printStackTrace();
-            System.exit(1);
+            handler.logError("Changes could not be committed");
+            handler.handleException(e);
         } finally {
             if (context != null) {
                 context.restoreAuthSystemState();
@@ -320,18 +318,15 @@ public class Harvest {
 
     /**
      * Purges a collection of all harvest-related data and settings. All items in the collection will be deleted.
+     *  @param collectionID
      *
-     * @param collectionID
-     * @param email
      */
-    private void purgeCollection(String collectionID, String email) {
-        System.out.println(
-            "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
-        Collection collection = resolveCollection(collectionID);
+    private void purgeCollection(Context context, String collectionID) {
+        handler.logInfo(
+                "Purging collection of all items and resetting last_harvested and harvest_message: " + collectionID);
+        Collection collection = resolveCollection(context, collectionID);
 
         try {
-            EPerson eperson = ePersonService.findByEmail(context, email);
-            context.setCurrentUser(eperson);
             context.turnOffAuthorisationSystem();
 
             ItemService itemService = ContentServiceFactory.getInstance().getItemService();
@@ -340,7 +335,7 @@ public class Harvest {
             while (it.hasNext()) {
                 i++;
                 Item item = it.next();
-                System.out.println("Deleting: " + item.getHandle());
+                handler.logInfo("Deleting: " + item.getHandle());
                 collectionService.removeItem(context, collection, item);
                 context.uncacheEntity(item);// Dispatch events every 50 items
                 if (i % 50 == 0) {
@@ -360,9 +355,8 @@ public class Harvest {
             context.restoreAuthSystemState();
             context.dispatchEvents();
         } catch (Exception e) {
-            System.out.println("Changes could not be committed");
-            e.printStackTrace();
-            System.exit(1);
+            handler.logError("Changes could not be committed");
+            handler.handleException(e);
         } finally {
             context.restoreAuthSystemState();
         }
@@ -372,46 +366,42 @@ public class Harvest {
     /**
      * Run a single harvest cycle on the specified collection under the authorization of the supplied EPerson
      */
-    private void runHarvest(String collectionID, String email) {
-        System.out.println("Running: a harvest cycle on " + collectionID);
+    private void runHarvest(Context context, String collectionID) {
+        handler.logInfo("Running: a harvest cycle on " + collectionID);
 
-        System.out.print("Initializing the harvester... ");
+        handler.logInfo("Initializing the harvester... ");
         OAIHarvester harvester = null;
         try {
-            Collection collection = resolveCollection(collectionID);
+            Collection collection = resolveCollection(context, collectionID);
             HarvestedCollection hc = harvestedCollectionService.find(context, collection);
             harvester = new OAIHarvester(context, collection, hc);
-            System.out.println("success. ");
+            handler.logInfo("Initialized the harvester successfully");
         } catch (HarvestingException hex) {
-            System.out.print("failed. ");
-            System.out.println(hex.getMessage());
+            handler.logError("Initializing the harvester failed.");
             throw new IllegalStateException("Unable to harvest", hex);
         } catch (SQLException se) {
-            System.out.print("failed. ");
-            System.out.println(se.getMessage());
+            handler.logError("Initializing the harvester failed.");
             throw new IllegalStateException("Unable to access database", se);
         }
 
         try {
             // Harvest will not work for an anonymous user
-            EPerson eperson = ePersonService.findByEmail(context, email);
-            System.out.println("Harvest started... ");
-            context.setCurrentUser(eperson);
+            handler.logInfo("Harvest started... ");
             harvester.runHarvest();
             context.complete();
         } catch (SQLException | AuthorizeException | IOException e) {
             throw new IllegalStateException("Failed to run harvester", e);
         }
 
-        System.out.println("Harvest complete. ");
+        handler.logInfo("Harvest complete. ");
     }
 
     /**
      * Resets harvest_status and harvest_start_time flags for all collections that have a row in the
      * harvested_collections table
      */
-    private static void resetHarvesting() {
-        System.out.print("Resetting harvest status flag on all collections... ");
+    private void resetHarvesting(Context context) {
+        handler.logInfo("Resetting harvest status flag on all collections... ");
 
         try {
             List<HarvestedCollection> harvestedCollections = harvestedCollectionService.findAll(context);
@@ -421,21 +411,21 @@ public class Harvest {
                 harvestedCollection.setHarvestStatus(HarvestedCollection.STATUS_READY);
                 harvestedCollectionService.update(context, harvestedCollection);
             }
-            System.out.println("success. ");
+            handler.logInfo("Reset harvest status flag successfully");
         } catch (Exception ex) {
-            System.out.println("failed. ");
-            ex.printStackTrace();
+            handler.logError("Resetting harvest status flag failed");
+            handler.handleException(ex);
         }
     }
 
     /**
      * Starts up the harvest scheduler. Terminating this process will stop the scheduler.
      */
-    private static void startHarvester() {
+    private void startHarvester() {
         try {
-            System.out.print("Starting harvest loop... ");
+            handler.logInfo("Starting harvest loop... ");
             HarvestServiceFactory.getInstance().getHarvestSchedulingService().startNewScheduler();
-            System.out.println("running. ");
+            handler.logInfo("running. ");
         } catch (Exception ex) {
             ex.printStackTrace();
         }
@@ -448,29 +438,31 @@ public class Harvest {
      * @param set            name of an item set.
      * @param metadataFormat local prefix name, or null for "dc".
      */
-    private static void pingResponder(String server, String set, String metadataFormat) {
+    private void pingResponder(String server, String set, String metadataFormat) {
         List<String> errors;
 
-        System.out.print("Testing basic PMH access:  ");
+        handler.logInfo("Testing basic PMH access:  ");
         errors = harvestedCollectionService.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", false);
+                                                               (null != metadataFormat) ? metadataFormat : "dc", false);
         if (errors.isEmpty()) {
-            System.out.println("OK");
+            handler.logInfo("OK");
         } else {
             for (String error : errors) {
-                System.err.println(error);
+                handler.logError(error);
             }
         }
 
-        System.out.print("Testing ORE support:  ");
+        handler.logInfo("Testing ORE support:  ");
         errors = harvestedCollectionService.verifyOAIharvester(server, set,
-                                                 (null != metadataFormat) ? metadataFormat : "dc", true);
+                                                               (null != metadataFormat) ? metadataFormat : "dc", true);
         if (errors.isEmpty()) {
-            System.out.println("OK");
+            handler.logInfo("OK");
         } else {
             for (String error : errors) {
-                System.err.println(error);
+                handler.logError(error);
             }
         }
     }
+
+
 }

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

@@ -0,0 +1,45 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.harvest;
+
+import java.sql.SQLException;
+
+import org.apache.commons.cli.ParseException;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+
+public class HarvestCli extends Harvest {
+
+    /**
+     * This is the overridden instance of the {@link Harvest#assignCurrentUserInContext()} method in the parent class
+     * {@link Harvest}.
+     * This is done so that the CLI version of the Script is able to retrieve its currentUser from the -e flag given
+     * with the parameters of the Script.
+     *
+     * @throws ParseException If the e flag was not given to the parameters when calling the script
+     */
+    @Override
+    protected void assignCurrentUserInContext() throws ParseException {
+        if (this.commandLine.hasOption('e')) {
+            String ePersonEmail = this.commandLine.getOptionValue('e');
+            this.context = new Context(Context.Mode.BATCH_EDIT);
+            try {
+                EPerson ePerson = ePersonService.findByEmail(this.context, ePersonEmail);
+                if (ePerson == null) {
+                    super.handler.logError("EPerson not found: " + ePersonEmail);
+                    throw new IllegalArgumentException("Unable to find a user with email: " + ePersonEmail);
+                }
+                this.context.setCurrentUser(ePerson);
+            } catch (SQLException e) {
+                throw new IllegalArgumentException("SQLException trying to find user with email: " + ePersonEmail);
+            }
+        }
+    }
+
+
+}

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

@@ -0,0 +1,22 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.harvest;
+
+import org.apache.commons.cli.Options;
+
+
+public class HarvestCliScriptConfiguration extends HarvestScriptConfiguration {
+
+    public Options getOptions() {
+        Options options = super.getOptions();
+        options.addOption("e", "eperson", true,
+                          "eperson");
+
+        return options;
+    }
+}

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

@@ -0,0 +1,79 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.harvest;
+
+import java.sql.SQLException;
+
+import org.apache.commons.cli.Options;
+import org.dspace.authorize.service.AuthorizeService;
+import org.dspace.core.Context;
+import org.dspace.scripts.configuration.ScriptConfiguration;
+import org.springframework.beans.factory.annotation.Autowired;
+
+
+public class HarvestScriptConfiguration<T extends Harvest> extends ScriptConfiguration<T> {
+    @Autowired
+    private AuthorizeService authorizeService;
+
+    private Class<T> dspaceRunnableClass;
+
+    @Override
+    public Class<T> getDspaceRunnableClass() {
+        return dspaceRunnableClass;
+    }
+
+    @Override
+    public void setDspaceRunnableClass(Class<T> dspaceRunnableClass) {
+        this.dspaceRunnableClass = dspaceRunnableClass;
+    }
+
+    public boolean isAllowedToExecute(final Context context) {
+        try {
+            return authorizeService.isAdmin(context);
+        } catch (SQLException e) {
+            throw new RuntimeException("SQLException occurred when checking if the current user is an admin", e);
+        }
+    }
+
+    public Options getOptions() {
+        Options options = new Options();
+        options.addOption("p", "purge", false, "delete all items in the collection");
+        options.getOption("p").setType(boolean.class);
+        options.addOption("r", "run", false, "run the standard harvest procedure");
+        options.getOption("r").setType(boolean.class);
+        options.addOption("g", "ping", false, "test the OAI server and set");
+        options.getOption("g").setType(boolean.class);
+        options.addOption("s", "setup", false, "Set the collection up for harvesting");
+        options.getOption("s").setType(boolean.class);
+        options.addOption("S", "start", false, "start the harvest loop");
+        options.getOption("S").setType(boolean.class);
+        options.addOption("R", "reset", false, "reset harvest status on all collections");
+        options.getOption("R").setType(boolean.class);
+        options.addOption("P", "purgeCollections", false, "purge all harvestable collections");
+        options.getOption("P").setType(boolean.class);
+        options.addOption("o", "reimport", false, "reimport all items in the collection, " +
+            "this is equivalent to -p -r, purging all items in a collection and reimporting them");
+        options.getOption("o").setType(boolean.class);
+        options.addOption("c", "collection", true,
+                          "harvesting collection (handle or id)");
+        options.addOption("t", "type", true,
+                          "type of harvesting (0 for none)");
+        options.addOption("a", "address", true,
+                          "address of the OAI-PMH server");
+        options.addOption("i", "oai_set_id", true,
+                          "id of the PMH set representing the harvested collection");
+        options.addOption("m", "metadata_format", true,
+                          "the name of the desired metadata format for harvesting, resolved to namespace and " +
+                                  "crosswalk in dspace.cfg");
+
+        options.addOption("h", "help", false, "help");
+        options.getOption("h").setType(boolean.class);
+
+        return options;
+    }
+}

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

@@ -16,6 +16,7 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.text.SimpleDateFormat;
 import java.util.ArrayList;
@@ -51,7 +52,7 @@ import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
 import org.dspace.core.I18nUtil;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.core.Utils;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.service.EPersonService;
@@ -129,7 +130,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
         while (i.hasNext()) {
             if (SUBDIR_LIMIT > 0 && ++counter == SUBDIR_LIMIT) {
-                subdir = Integer.valueOf(subDirSuffix++).toString();
+                subdir = Integer.toString(subDirSuffix++);
                 fullPath = destDirName + File.separatorChar + subdir;
                 counter = 0;
 
@@ -191,7 +192,7 @@ public class ItemExportServiceImpl implements ItemExportService {
      */
     protected void writeMetadata(Context c, Item i, File destDir, boolean migrate)
         throws Exception {
-        Set<String> schemas = new HashSet<String>();
+        Set<String> schemas = new HashSet<>();
         List<MetadataValue> dcValues = itemService.getMetadata(i, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
         for (MetadataValue metadataValue : dcValues) {
             schemas.add(metadataValue.getMetadataField().getMetadataSchema().getName());
@@ -267,7 +268,7 @@ public class ItemExportServiceImpl implements ItemExportService {
                     + Utils.addEntities(dcv.getValue()) + "</dcvalue>\n")
                     .getBytes("UTF-8");
 
-                if ((!migrate) ||
+                if (!migrate ||
                     (migrate && !(
                         ("date".equals(metadataField.getElement()) && "issued".equals(qualifier)) ||
                             ("date".equals(metadataField.getElement()) && "accessioned".equals(qualifier)) ||
@@ -292,10 +293,10 @@ public class ItemExportServiceImpl implements ItemExportService {
             }
 
             // When migrating, only keep date.issued if it is different to date.accessioned
-            if ((migrate) &&
+            if (migrate &&
                 (dateIssued != null) &&
                 (dateAccessioned != null) &&
-                (!dateIssued.equals(dateAccessioned))) {
+                !dateIssued.equals(dateAccessioned)) {
                 utf8 = ("  <dcvalue element=\"date\" "
                     + "qualifier=\"issued\">"
                     + Utils.addEntities(dateIssued) + "</dcvalue>\n")
@@ -330,7 +331,7 @@ public class ItemExportServiceImpl implements ItemExportService {
         File outFile = new File(destDir, filename);
 
         if (outFile.createNewFile()) {
-            PrintWriter out = new PrintWriter(new FileWriter(outFile));
+            PrintWriter out = new PrintWriter(new FileWriter(outFile, StandardCharsets.UTF_8));
 
             out.println(i.getHandle());
 
@@ -360,7 +361,7 @@ public class ItemExportServiceImpl implements ItemExportService {
         File outFile = new File(destDir, "contents");
 
         if (outFile.createNewFile()) {
-            PrintWriter out = new PrintWriter(new FileWriter(outFile));
+            PrintWriter out = new PrintWriter(new FileWriter(outFile, StandardCharsets.UTF_8));
 
             List<Bundle> bundles = i.getBundles();
 
@@ -474,7 +475,7 @@ public class ItemExportServiceImpl implements ItemExportService {
     public void createDownloadableExport(DSpaceObject dso,
                                          Context context, boolean migrate) throws Exception {
         EPerson eperson = context.getCurrentUser();
-        ArrayList<DSpaceObject> list = new ArrayList<DSpaceObject>(1);
+        ArrayList<DSpaceObject> list = new ArrayList<>(1);
         list.add(dso);
         processDownloadableExport(list, context, eperson == null ? null
             : eperson.getEmail(), migrate);
@@ -491,7 +492,7 @@ public class ItemExportServiceImpl implements ItemExportService {
     @Override
     public void createDownloadableExport(DSpaceObject dso,
                                          Context context, String additionalEmail, boolean migrate) throws Exception {
-        ArrayList<DSpaceObject> list = new ArrayList<DSpaceObject>(1);
+        ArrayList<DSpaceObject> list = new ArrayList<>(1);
         list.add(dso);
         processDownloadableExport(list, context, additionalEmail, migrate);
     }
@@ -652,7 +653,7 @@ public class ItemExportServiceImpl implements ItemExportService {
                         while (iter.hasNext()) {
                             String keyName = iter.next();
                             List<UUID> uuids = itemsMap.get(keyName);
-                            List<Item> items = new ArrayList<Item>();
+                            List<Item> items = new ArrayList<>();
                             for (UUID uuid : uuids) {
                                 items.add(itemService.find(context, uuid));
                             }
@@ -876,7 +877,7 @@ public class ItemExportServiceImpl implements ItemExportService {
             .getIntProperty("org.dspace.app.itemexport.life.span.hours");
         Calendar now = Calendar.getInstance();
         now.setTime(new Date());
-        now.add(Calendar.HOUR, (-hours));
+        now.add(Calendar.HOUR, -hours);
         File downloadDir = new File(getExportDownloadDirectory(eperson));
         if (downloadDir.exists()) {
             File[] files = downloadDir.listFiles();
@@ -896,7 +897,7 @@ public class ItemExportServiceImpl implements ItemExportService {
         int hours = configurationService.getIntProperty("org.dspace.app.itemexport.life.span.hours");
         Calendar now = Calendar.getInstance();
         now.setTime(new Date());
-        now.add(Calendar.HOUR, (-hours));
+        now.add(Calendar.HOUR, -hours);
         File downloadDir = new File(configurationService.getProperty("org.dspace.app.itemexport.download.dir"));
         if (downloadDir.exists()) {
             // Get a list of all the sub-directories, potentially one for each ePerson.
@@ -936,7 +937,7 @@ public class ItemExportServiceImpl implements ItemExportService {
 
             email.send();
         } catch (Exception e) {
-            log.warn(LogManager.getHeader(context, "emailSuccessMessage", "cannot notify user of export"), e);
+            log.warn(LogHelper.getHeader(context, "emailSuccessMessage", "cannot notify user of export"), e);
         }
     }
 

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

@@ -296,29 +296,36 @@ public class ItemImportCLITool {
 
                 // validate each collection arg to see if it's a real collection
                 for (int i = 0; i < collections.length; i++) {
-                    // is the ID a handle?
-                    if (collections[i].indexOf('/') != -1) {
-                        // string has a / so it must be a handle - try and resolve
-                        // it
-                        mycollections.add((Collection) handleService
-                            .resolveToObject(c, collections[i]));
 
-                        // resolved, now make sure it's a collection
-                        if ((mycollections.get(i) == null)
-                            || (mycollections.get(i).getType() != Constants.COLLECTION)) {
-                            mycollections.set(i, null);
+                    Collection resolved = null;
+
+                    if (collections[i] != null) {
+
+                        // is the ID a handle?
+                        if (collections[i].indexOf('/') != -1) {
+                            // string has a / so it must be a handle - try and resolve
+                            // it
+                            resolved = ((Collection) handleService
+                                .resolveToObject(c, collections[i]));
+
+                        } else {
+                            // not a handle, try and treat it as an integer collection database ID
+                            resolved = collectionService.find(c, UUID.fromString(collections[i]));
+
                         }
-                    } else if (collections[i] != null) {
-                        // not a handle, try and treat it as an integer collection database ID
-                        mycollections.set(i, collectionService.find(c, UUID.fromString(collections[i])));
+
                     }
 
                     // was the collection valid?
-                    if (mycollections.get(i) == null) {
+                    if ((resolved == null)
+                            || (resolved.getType() != Constants.COLLECTION)) {
                         throw new IllegalArgumentException("Cannot resolve "
                                                                + collections[i] + " to collection");
                     }
 
+                    // add resolved collection to list
+                    mycollections.add(resolved);
+
                     // print progress info
                     String owningPrefix = "";
 
@@ -327,7 +334,7 @@ public class ItemImportCLITool {
                     }
 
                     System.out.println(owningPrefix + " Collection: "
-                                           + mycollections.get(i).getName());
+                                           + resolved.getName());
                 }
             } // end of validating collections
 

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

@@ -55,6 +55,7 @@ import org.apache.logging.log4j.Logger;
 import org.apache.xpath.XPathAPI;
 import org.dspace.app.itemimport.service.ItemImportService;
 import org.dspace.app.util.LocalSchemaFilenameFilter;
+import org.dspace.app.util.RelationshipUtils;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.authorize.service.AuthorizeService;
@@ -68,6 +69,9 @@ import org.dspace.content.Item;
 import org.dspace.content.MetadataField;
 import org.dspace.content.MetadataSchema;
 import org.dspace.content.MetadataSchemaEnum;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.Relationship;
+import org.dspace.content.RelationshipType;
 import org.dspace.content.WorkspaceItem;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.content.service.BitstreamService;
@@ -77,12 +81,15 @@ import org.dspace.content.service.InstallItemService;
 import org.dspace.content.service.ItemService;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
+import org.dspace.content.service.MetadataValueService;
+import org.dspace.content.service.RelationshipService;
+import org.dspace.content.service.RelationshipTypeService;
 import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.Email;
 import org.dspace.core.I18nUtil;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.EPersonService;
@@ -151,6 +158,12 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
     protected WorkflowService workflowService;
     @Autowired(required = true)
     protected ConfigurationService configurationService;
+    @Autowired(required = true)
+    protected RelationshipService relationshipService;
+    @Autowired(required = true)
+    protected RelationshipTypeService relationshipTypeService;
+    @Autowired(required = true)
+    protected MetadataValueService metadataValueService;
 
     protected String tempWorkDir;
 
@@ -160,6 +173,9 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
     protected boolean useWorkflowSendEmail = false;
     protected boolean isQuiet = false;
 
+    //remember which folder item was imported from
+    Map<String, Item> itemFolderMap = null;
+
     @Override
     public void afterPropertiesSet() throws Exception {
         tempWorkDir = configurationService.getProperty("org.dspace.app.batchitemimport.work.dir");
@@ -211,10 +227,13 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
         // create the mapfile
         File outFile = null;
         PrintWriter mapOut = null;
+
         try {
             Map<String, String> skipItems = new HashMap<>(); // set of items to skip if in 'resume'
             // mode
 
+            itemFolderMap = new HashMap<>();
+
             System.out.println("Adding items from directory: " + sourceDir);
             log.debug("Adding items from directory: " + sourceDir);
             System.out.println("Generating mapfile: " + mapFile);
@@ -255,6 +274,12 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
             for (int i = 0; i < dircontents.length; i++) {
                 if (skipItems.containsKey(dircontents[i])) {
                     System.out.println("Skipping import of " + dircontents[i]);
+
+                    //we still need the item in the map for relationship linking
+                    String skippedHandle = skipItems.get(dircontents[i]);
+                    Item skippedItem = (Item) handleService.resolveToObject(c, skippedHandle);
+                    itemFolderMap.put(dircontents[i], skippedItem);
+
                 } else {
                     List<Collection> clist;
                     if (directoryFileCollections) {
@@ -274,12 +299,19 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
                     } else {
                         clist = mycollections;
                     }
+
                     Item item = addItem(c, clist, sourceDir, dircontents[i], mapOut, template);
+
+                    itemFolderMap.put(dircontents[i], item);
+
                     c.uncacheEntity(item);
                     System.out.println(i + " " + dircontents[i]);
                 }
             }
 
+            //now that all items are imported, iterate again to link relationships
+            addRelationships(c, sourceDir);
+
         } finally {
             if (mapOut != null) {
                 mapOut.flush();
@@ -288,6 +320,276 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
         }
     }
 
+     /**
+      * Add relationships from a 'relationships' manifest file.
+      * 
+      * @param c Context
+      * @param sourceDir The parent import source directory
+      * @throws Exception
+      */
+    protected void addRelationships(Context c, String sourceDir) throws Exception {
+
+        for (Map.Entry<String, Item> itemEntry : itemFolderMap.entrySet()) {
+
+            String folderName = itemEntry.getKey();
+            String path = sourceDir + File.separatorChar + folderName;
+            Item item = itemEntry.getValue();
+
+            //look for a 'relationship' manifest
+            Map<String, List<String>> relationships = processRelationshipFile(path, "relationships");
+            if (!relationships.isEmpty()) {
+
+                for (Map.Entry<String, List<String>> relEntry : relationships.entrySet()) {
+
+                    String relationshipType = relEntry.getKey();
+                    List<String> identifierList = relEntry.getValue();
+
+                    for (String itemIdentifier : identifierList) {
+
+                        if (isTest) {
+                            System.out.println("\tAdding relationship (type: " + relationshipType +
+                                ") from " + folderName + " to " + itemIdentifier);
+                            continue;
+                        }
+
+                        //find referenced item
+                        Item relationItem = resolveRelatedItem(c, itemIdentifier);
+                        if (null == relationItem) {
+                            throw new Exception("Could not find item for " + itemIdentifier);
+                        }
+
+                        //get entity type of entity and item
+                        String itemEntityType = getEntityType(item);
+                        String relatedEntityType = getEntityType(relationItem);
+
+                        //find matching relationship type
+                        List<RelationshipType> relTypes = relationshipTypeService.findByLeftwardOrRightwardTypeName(
+                            c, relationshipType);
+                        RelationshipType foundRelationshipType = RelationshipUtils.matchRelationshipType(
+                            relTypes, relatedEntityType, itemEntityType, relationshipType);
+
+                        if (foundRelationshipType == null) {
+                            throw new Exception("No Relationship type found for:\n" +
+                                "Target type: " + relatedEntityType + "\n" +
+                                "Origin referer type: " + itemEntityType + "\n" +
+                                "with typeName: " + relationshipType
+                            );
+                        }
+
+                        boolean left = false;
+                        if (foundRelationshipType.getLeftwardType().equalsIgnoreCase(relationshipType)) {
+                            left = true;
+                        }
+
+                        // Placeholder items for relation placing
+                        Item leftItem = null;
+                        Item rightItem = null;
+                        if (left) {
+                            leftItem = item;
+                            rightItem = relationItem;
+                        } else {
+                            leftItem = relationItem;
+                            rightItem = item;
+                        }
+
+                        // Create the relationship
+                        int leftPlace = relationshipService.findNextLeftPlaceByLeftItem(c, leftItem);
+                        int rightPlace = relationshipService.findNextRightPlaceByRightItem(c, rightItem);
+                        Relationship persistedRelationship = relationshipService.create(
+                            c, leftItem, rightItem, foundRelationshipType, leftPlace, rightPlace);
+                        // relationshipService.update(c, persistedRelationship);
+
+                        System.out.println("\tAdded relationship (type: " + relationshipType + ") from " +
+                            leftItem.getHandle() + " to " + rightItem.getHandle());
+
+                    }
+
+                }
+
+            }
+
+        }
+
+    }
+
+    /**
+     * Get the item's entity type from meta.
+     * 
+     * @param item
+     * @return
+     */
+    protected String getEntityType(Item item) throws Exception {
+        return itemService.getMetadata(item, "dspace", "entity", "type", Item.ANY).get(0).getValue();
+    }
+
+    /**
+     * Read the relationship manifest file.
+     * 
+     * Each line in the file contains a relationship type id and an item identifier in the following format:
+     * 
+     * relation.<relation_key> <handle|uuid|folderName:import_item_folder|schema.element[.qualifier]:value>
+     * 
+     * The input_item_folder should refer the folder name of another item in this import batch.
+     * 
+     * @param path The main import folder path.
+     * @param filename The name of the manifest file to check ('relationships')
+     * @return Map of found relationships
+     * @throws Exception
+     */
+    protected Map<String, List<String>> processRelationshipFile(String path, String filename) throws Exception {
+
+        File file = new File(path + File.separatorChar + filename);
+        Map<String, List<String>> result = new HashMap<>();
+
+        if (file.exists()) {
+
+            System.out.println("\tProcessing relationships file: " + filename);
+
+            BufferedReader br = null;
+            try {
+                br = new BufferedReader(new FileReader(file));
+                String line = null;
+                while ((line = br.readLine()) != null) {
+                    line = line.trim();
+                    if ("".equals(line)) {
+                        continue;
+                    }
+
+                    String relationshipType = null;
+                    String itemIdentifier = null;
+
+                    StringTokenizer st = new StringTokenizer(line);
+
+                    if (st.hasMoreTokens()) {
+                        relationshipType = st.nextToken();
+                        if (relationshipType.split("\\.").length > 1) {
+                            relationshipType = relationshipType.split("\\.")[1];
+                        }
+                    } else {
+                        throw new Exception("Bad mapfile line:\n" + line);
+                    }
+
+                    if (st.hasMoreTokens()) {
+                        itemIdentifier = st.nextToken("").trim();
+                    } else {
+                        throw new Exception("Bad mapfile line:\n" + line);
+                    }
+
+                    if (!result.containsKey(relationshipType)) {
+                        result.put(relationshipType, new ArrayList<>());
+                    }
+
+                    result.get(relationshipType).add(itemIdentifier);
+
+                }
+
+            } catch (FileNotFoundException e) {
+                System.out.println("\tNo relationships file found.");
+            } finally {
+                if (br != null) {
+                    try {
+                        br.close();
+                    } catch (IOException e) {
+                        System.out.println("Non-critical problem releasing resources.");
+                    }
+                }
+            }
+
+        }
+
+        return result;
+    }
+
+     /**
+      * Resolve an item identifier referred to in the relationships manifest file.
+      *
+      * The import item map will be checked first to see if the identifier refers to an item folder
+      * that was just imported. Next it will try to find the item by handle or UUID, or by a unique
+      * meta value.
+      * 
+      * @param c Context
+      * @param itemIdentifier The identifier string found in the import manifest (handle, uuid, or import subfolder)
+      * @return Item if found, or null.
+      * @throws Exception
+      */
+    protected Item resolveRelatedItem(Context c, String itemIdentifier) throws Exception {
+
+        if (itemIdentifier.contains(":")) {
+
+            if (itemIdentifier.startsWith("folderName:") || itemIdentifier.startsWith("rowName:")) {
+                //identifier refers to a folder name in this import
+                int i = itemIdentifier.indexOf(":");
+                String folderName = itemIdentifier.substring(i + 1);
+                if (itemFolderMap.containsKey(folderName)) {
+                    return itemFolderMap.get(folderName);
+                }
+
+            } else {
+
+                //lookup by meta value
+                int i = itemIdentifier.indexOf(":");
+                String metaKey = itemIdentifier.substring(0, i);
+                String metaValue = itemIdentifier.substring(i + 1);
+                return findItemByMetaValue(c, metaKey, metaValue);
+
+            }
+
+        } else if (itemIdentifier.indexOf('/') != -1) {
+            //resolve by handle
+            return (Item) handleService.resolveToObject(c, itemIdentifier);
+
+        } else {
+            //try to resolve by UUID
+            return itemService.findByIdOrLegacyId(c, itemIdentifier);
+        }
+
+        return null;
+
+    }
+
+    /**
+     * Lookup an item by a (unique) meta value.
+     * 
+     * @param metaKey
+     * @param metaValue
+     * @return Item
+     * @throws Exception if single item not found.
+     */
+    protected Item findItemByMetaValue(Context c, String metaKey, String metaValue) throws Exception {
+
+        Item item = null;
+
+        String mf[] = metaKey.split("\\.");
+        if (mf.length < 2) {
+            throw new Exception("Bad metadata field in reference: '" + metaKey +
+                "' (expected syntax is schema.element[.qualifier])");
+        }
+        String schema = mf[0];
+        String element = mf[1];
+        String qualifier = mf.length == 2 ? null : mf[2];
+        try {
+            MetadataField mfo = metadataFieldService.findByElement(c, schema, element, qualifier);
+            Iterator<MetadataValue> mdv = metadataValueService.findByFieldAndValue(c, mfo, metaValue);
+            if (mdv.hasNext()) {
+                MetadataValue mdvVal = mdv.next();
+                UUID uuid = mdvVal.getDSpaceObject().getID();
+                if (mdv.hasNext()) {
+                    throw new Exception("Ambiguous reference; multiple matches in db: " + metaKey);
+                }
+                item = itemService.find(c, uuid);
+            }
+        } catch (SQLException e) {
+            throw new Exception("Error looking up item by metadata reference: " + metaKey, e);
+        }
+
+        if (item == null) {
+            throw new Exception("Item not found by metadata reference: " + metaKey);
+        }
+
+        return item;
+
+    }
+
     @Override
     public void replaceItems(Context c, List<Collection> mycollections,
                              String sourceDir, String mapFile, boolean template) throws Exception {
@@ -1689,7 +1991,7 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
 
             email.send();
         } catch (Exception e) {
-            log.warn(LogManager.getHeader(context, "emailSuccessMessage", "cannot notify user of import"), e);
+            log.warn(LogHelper.getHeader(context, "emailSuccessMessage", "cannot notify user of import"), e);
         }
     }
 
@@ -1823,4 +2125,5 @@ public class ItemImportServiceImpl implements ItemImportService, InitializingBea
     public void setQuiet(boolean isQuiet) {
         this.isQuiet = isQuiet;
     }
+
 }

dspace-api/src/main/java/org/dspace/app/itemmarking/ItemMarkingAvailabilityBitstreamStrategy.java

@@ -11,6 +11,8 @@ import java.io.UnsupportedEncodingException;
 import java.sql.SQLException;
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.Util;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
@@ -34,8 +36,9 @@ public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtr
     @Autowired(required = true)
     protected ItemService itemService;
 
-    public ItemMarkingAvailabilityBitstreamStrategy() {
+    private static final Logger LOG = LogManager.getLogger();
 
+    public ItemMarkingAvailabilityBitstreamStrategy() {
     }
 
     @Override
@@ -43,14 +46,14 @@ public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtr
         throws SQLException {
 
         List<Bundle> bundles = itemService.getBundles(item, "ORIGINAL");
-        if (bundles.size() == 0) {
+        if (bundles.isEmpty()) {
             ItemMarkingInfo markInfo = new ItemMarkingInfo();
             markInfo.setImageName(nonAvailableImageName);
 
             return markInfo;
         } else {
             Bundle originalBundle = bundles.iterator().next();
-            if (originalBundle.getBitstreams().size() == 0) {
+            if (originalBundle.getBitstreams().isEmpty()) {
                 ItemMarkingInfo markInfo = new ItemMarkingInfo();
                 markInfo.setImageName(nonAvailableImageName);
 
@@ -72,8 +75,7 @@ public class ItemMarkingAvailabilityBitstreamStrategy implements ItemMarkingExtr
                 try {
                     bsLink = bsLink + Util.encodeBitstreamName(bitstream.getName(), Constants.DEFAULT_ENCODING);
                 } catch (UnsupportedEncodingException e) {
-
-                    e.printStackTrace();
+                    LOG.warn("DSpace uses an unsupported encoding", e);
                 }
 
                 signInfo.setLink(bsLink);

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

@@ -105,6 +105,7 @@ public class ContentsEntry {
         return new ContentsEntry(arp[0], arp[1], actionId, groupName, arp[3]);
     }
 
+    @Override
     public String toString() {
         StringBuilder sb = new StringBuilder(filename);
         if (bundlename != null) {

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

@@ -120,6 +120,7 @@ class DtoMetadata {
         return true;
     }
 
+    @Override
     public String toString() {
         String s = "\tSchema: " + schema + " Element: " + element;
         if (qualifier != null) {

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

@@ -17,6 +17,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
 import java.io.PrintWriter;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -55,7 +56,7 @@ public class ItemArchive {
     protected Transformer transformer = null;
 
     protected List<DtoMetadata> dtomList = null;
-    protected List<DtoMetadata> undoDtomList = new ArrayList<DtoMetadata>();
+    protected List<DtoMetadata> undoDtomList = new ArrayList<>();
 
     protected List<UUID> undoAddContents = new ArrayList<>(); // for undo of add
 
@@ -325,7 +326,7 @@ public class ItemArchive {
                 PrintWriter pw = null;
                 try {
                     File f = new File(dir, ItemUpdate.DELETE_CONTENTS_FILE);
-                    pw = new PrintWriter(new BufferedWriter(new FileWriter(f)));
+                    pw = new PrintWriter(new BufferedWriter(new FileWriter(f, StandardCharsets.UTF_8)));
                     for (UUID i : undoAddContents) {
                         pw.println(i);
                     }

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

@@ -9,6 +9,7 @@ package org.dspace.app.mediafilter;
 
 import java.io.ByteArrayInputStream;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import javax.swing.text.Document;
 import javax.swing.text.html.HTMLEditorKit;
 
@@ -36,7 +37,7 @@ public class HTMLFilter extends MediaFilter {
     }
 
     /**
-     * @return String bitstreamformat
+     * @return String bitstream format
      */
     @Override
     public String getFormatString() {
@@ -73,9 +74,9 @@ public class HTMLFilter extends MediaFilter {
         String extractedText = doc.getText(0, doc.getLength());
 
         // generate an input stream with the extracted text
-        byte[] textBytes = extractedText.getBytes();
+        byte[] textBytes = extractedText.getBytes(StandardCharsets.UTF_8);
         ByteArrayInputStream bais = new ByteArrayInputStream(textBytes);
 
-        return bais; // will this work? or will the byte array be out of scope?
+        return bais;
     }
 }

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

@@ -10,6 +10,7 @@ package org.dspace.app.mediafilter;
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 
 import org.apache.poi.POITextExtractor;
 import org.apache.poi.extractor.ExtractorFactory;
@@ -66,6 +67,6 @@ public class PoiWordFilter
         }
 
         // return the extracted text as a stream.
-        return new ByteArrayInputStream(text.getBytes());
+        return new ByteArrayInputStream(text.getBytes(StandardCharsets.UTF_8));
     }
 }

dspace-api/src/main/java/org/dspace/app/requestitem/dao/impl/RequestItemDAOImpl.java

@@ -37,7 +37,7 @@ public class RequestItemDAOImpl extends AbstractHibernateDAO<RequestItem> implem
         Root<RequestItem> requestItemRoot = criteriaQuery.from(RequestItem.class);
         criteriaQuery.select(requestItemRoot);
         criteriaQuery.where(criteriaBuilder.equal(requestItemRoot.get(RequestItem_.token), token));
-        return uniqueResult(context, criteriaQuery, false, RequestItem.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, RequestItem.class);
     }
 
 

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

@@ -73,6 +73,7 @@ public class SHERPAService {
     /**
      * Complete initialization of the Bean.
      */
+    @SuppressWarnings("unused")
     @PostConstruct
     private void init() {
         // Get endoint and API key from configuration

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

@@ -18,7 +18,7 @@ import org.dspace.app.sherpa.SHERPAService;
 import org.dspace.app.sherpa.v2.SHERPAResponse;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 
 /**
  * SHERPASubmitService is
@@ -115,7 +115,7 @@ public class SHERPASubmitService {
     public Set<String> getISSNs(Context context, Item item) {
         Set<String> issns = new LinkedHashSet<String>();
         if (configuration.getIssnItemExtractors() == null) {
-            log.warn(LogManager.getHeader(context, "searchRelatedJournals",
+            log.warn(LogHelper.getHeader(context, "searchRelatedJournals",
                                           "no issnItemExtractors defined"));
             return null;
         }

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

@@ -13,15 +13,18 @@ import java.util.List;
  * Plain java representation of a SHERPA Permitted Version object, based on SHERPA API v2 responses.
  *
  * In a SHERPA search for journal deposit policies, this data is contained within a publisher policy.
- * Each permitted version is for a particular article version (eg. submitted, accepted, published) and contains
+ * Each permitted version is for a particular article version (e.g. submitted, accepted, published) and contains:
  *
- * A list of general conditions / terms for deposit of this version of work
- * A list of allowed locations (eg. institutional repository, personal homepage, non-commercial repository)
- * A list of prerequisite conditions for deposit (eg. attribution, linking to published version)
- * A list of required licences for the deposited work (eg. CC-BY-NC)
- * Embargo requirements, if any
+ * <ul>
+ *   <li>A list of general conditions / terms for deposit of this version of work</li>
+ *   <li>A list of allowed locations (e.g. institutional repository, personal homepage, non-commercial repository)</li>
+ *   <li>A list of prerequisite conditions for deposit (e.g. attribution, linking to published version)</li>
+ *   <li>A list of required licenses for the deposited work (e.g. CC-BY-NC)</li>
+ *   <li>Embargo requirements, if any</li>
+ * </ul>
  *
- * This class also has some helper data for labels, which can be used with i18n when displaying policy information
+ * This class also has some helper data for labels, which can be used with i18n
+ * when displaying policy information.
  *
  * @see SHERPAPublisherPolicy
  */
@@ -44,7 +47,7 @@ public class SHERPAPermittedVersion {
     // Embargo
     private SHERPAEmbargo embargo;
 
-    protected class SHERPAEmbargo {
+    protected static class SHERPAEmbargo {
         String units;
         int amount;
     }

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

@@ -10,7 +10,8 @@ package org.dspace.app.sherpa.v2;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
-import java.util.LinkedList;
+import java.nio.charset.StandardCharsets;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
@@ -74,7 +75,7 @@ public class SHERPAPublisherResponse {
      * @param jsonData - the JSON input stream from the API result response body
      */
     private void parseJSON(InputStream jsonData) throws IOException {
-        InputStreamReader streamReader = new InputStreamReader(jsonData);
+        InputStreamReader streamReader = new InputStreamReader(jsonData, StandardCharsets.UTF_8);
         JSONTokener jsonTokener = new JSONTokener(streamReader);
         JSONObject httpResponse;
         try {
@@ -86,7 +87,7 @@ public class SHERPAPublisherResponse {
                 // parsing the full journal / policy responses
                 if (items.length() > 0) {
                     metadata = new SHERPASystemMetadata();
-                    this.publishers = new LinkedList<>();
+                    this.publishers = new ArrayList<>();
                     // Iterate search result items
                     for (int itemIndex = 0; itemIndex < items.length(); itemIndex++) {
                         SHERPAPublisher sherpaPublisher = new SHERPAPublisher();

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

@@ -10,8 +10,8 @@ package org.dspace.app.sherpa.v2;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.TreeMap;
@@ -78,7 +78,7 @@ public class SHERPAResponse {
      * @param jsonData - the JSON input stream from the API result response body
      */
     private void parseJSON(InputStream jsonData) throws IOException {
-        InputStreamReader streamReader = new InputStreamReader(jsonData);
+        InputStreamReader streamReader = new InputStreamReader(jsonData, StandardCharsets.UTF_8);
         JSONTokener jsonTokener = new JSONTokener(streamReader);
         JSONObject httpResponse;
         try {
@@ -90,10 +90,10 @@ public class SHERPAResponse {
                 // - however, we only ever want one result since we're passing an "equals ISSN" query
                 if (items.length() > 0) {
                     metadata = new SHERPASystemMetadata();
-                    this.journals = new LinkedList<>();
+                    this.journals = new ArrayList<>();
                     // Iterate search result items
                     for (int itemIndex = 0; itemIndex < items.length(); itemIndex++) {
-                        List<SHERPAPublisher> sherpaPublishers = new LinkedList<>();
+                        List<SHERPAPublisher> sherpaPublishers = new ArrayList<>();
                         List<SHERPAPublisherPolicy> policies = new ArrayList<>();
                         SHERPAPublisher sherpaPublisher = new SHERPAPublisher();
                         SHERPAJournal sherpaJournal = new SHERPAJournal();
@@ -289,7 +289,7 @@ public class SHERPAResponse {
 
         // Is the item in DOAJ?
         if (item.has("listed_in_doaj")) {
-            sherpaJournal.setInDOAJ(("yes".equals(item.getString("listed_in_doaj"))));
+            sherpaJournal.setInDOAJ("yes".equals(item.getString("listed_in_doaj")));
         }
 
         return sherpaJournal;
@@ -403,7 +403,6 @@ public class SHERPAResponse {
         // published = pdfversion
         // These strings can be used to construct i18n messages.
         String articleVersion = "unknown";
-        String versionLabel = "Unknown";
 
         // Each 'permitted OA' can actually refer to multiple versions
         if (permitted.has("article_version")) {

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

@@ -40,7 +40,7 @@ import org.dspace.content.service.CollectionService;
 import org.dspace.content.service.CommunityService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.discovery.DiscoverQuery;
 import org.dspace.discovery.DiscoverResult;
 import org.dspace.discovery.SearchService;
@@ -284,7 +284,7 @@ public class GenerateSitemaps {
 
         if (makeHTMLMap) {
             int files = html.finish();
-            log.info(LogManager.getHeader(c, "write_sitemap",
+            log.info(LogHelper.getHeader(c, "write_sitemap",
                                           "type=html,num_files=" + files + ",communities="
                                               + comms.size() + ",collections=" + colls.size()
                                               + ",items=" + itemCount));
@@ -292,7 +292,7 @@ public class GenerateSitemaps {
 
         if (makeSitemapOrg) {
             int files = sitemapsOrg.finish();
-            log.info(LogManager.getHeader(c, "write_sitemap",
+            log.info(LogHelper.getHeader(c, "write_sitemap",
                                           "type=html,num_files=" + files + ",communities="
                                               + comms.size() + ",collections=" + colls.size()
                                               + ",items=" + itemCount));

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

@@ -86,7 +86,7 @@ public class SitemapsOrgGenerator extends AbstractGenerator {
 
     @Override
     public String getURLText(String url, Date lastMod) {
-        StringBuffer urlText = new StringBuffer();
+        StringBuilder urlText = new StringBuilder();
 
         urlText.append("<url><loc>").append(url).append("</loc>");
         if (lastMod != null) {

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

@@ -64,10 +64,6 @@ public class CreateStatReport {
      */
     private static Context context;
 
-    /**
-     * the config file from which to configure the analyser
-     */
-
     /**
      * Default constructor
      */
@@ -170,22 +166,19 @@ public class CreateStatReport {
         String myLogDir = null;
         String myFileTemplate = null;
         String myConfigFile = null;
-        StringBuffer myOutFile = null;
-        Date myStartDate = null;
-        Date myEndDate = null;
         boolean myLookUp = false;
 
         Calendar start = new GregorianCalendar(calendar.get(Calendar.YEAR),
                                                calendar.get(Calendar.MONTH),
                                                calendar.getActualMinimum(Calendar.DAY_OF_MONTH));
-        myStartDate = start.getTime();
+        Date myStartDate = start.getTime();
 
         Calendar end = new GregorianCalendar(calendar.get(Calendar.YEAR),
                                              calendar.get(Calendar.MONTH),
                                              calendar.getActualMaximum(Calendar.DAY_OF_MONTH));
-        myEndDate = end.getTime();
+        Date myEndDate = end.getTime();
 
-        myOutFile = new StringBuffer(outputLogDirectory);
+        StringBuilder myOutFile = new StringBuilder(outputLogDirectory);
         myOutFile.append(outputPrefix);
         myOutFile.append(calendar.get(Calendar.YEAR));
         myOutFile.append("-");
@@ -211,12 +204,11 @@ public class CreateStatReport {
         String myLogDir = null;
         String myFileTemplate = null;
         String myConfigFile = null;
-        StringBuffer myOutFile = null;
         Date myStartDate = null;
         Date myEndDate = null;
         boolean myLookUp = false;
 
-        myOutFile = new StringBuffer(outputLogDirectory);
+        StringBuilder myOutFile = new StringBuilder(outputLogDirectory);
         myOutFile.append(outputPrefix);
         myOutFile.append(calendar.get(Calendar.YEAR));
         myOutFile.append("-");
@@ -245,9 +237,6 @@ public class CreateStatReport {
         String myLogDir = null;
         String myFileTemplate = null;
         String myConfigFile = null;
-        StringBuffer myOutFile = null;
-        Date myStartDate = null;
-        Date myEndDate = null;
         boolean myLookUp = false;
 
         Calendar reportEndDate = new GregorianCalendar(calendar.get(Calendar.YEAR),
@@ -260,14 +249,14 @@ public class CreateStatReport {
             Calendar start = new GregorianCalendar(currentMonth.get(Calendar.YEAR),
                                                    currentMonth.get(Calendar.MONTH),
                                                    currentMonth.getActualMinimum(Calendar.DAY_OF_MONTH));
-            myStartDate = start.getTime();
+            Date myStartDate = start.getTime();
 
             Calendar end = new GregorianCalendar(currentMonth.get(Calendar.YEAR),
                                                  currentMonth.get(Calendar.MONTH),
                                                  currentMonth.getActualMaximum(Calendar.DAY_OF_MONTH));
-            myEndDate = end.getTime();
+            Date myEndDate = end.getTime();
 
-            myOutFile = new StringBuffer(outputLogDirectory);
+            StringBuilder myOutFile = new StringBuilder(outputLogDirectory);
             myOutFile.append(outputPrefix);
             myOutFile.append(currentMonth.get(Calendar.YEAR));
             myOutFile.append("-");
@@ -293,11 +282,9 @@ public class CreateStatReport {
         String outputPrefix = "report-general-";
 
         String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
         String myMap = null;
 
-        myInput = new StringBuffer(outputLogDirectory);
+        StringBuilder myInput = new StringBuilder(outputLogDirectory);
         myInput.append(inputPrefix);
         myInput.append(calendar.get(Calendar.YEAR));
         myInput.append("-");
@@ -306,7 +293,7 @@ public class CreateStatReport {
         myInput.append(calendar.get(Calendar.DAY_OF_MONTH));
         myInput.append(outputSuffix);
 
-        myOutput = new StringBuffer(outputReportDirectory);
+        StringBuilder myOutput = new StringBuilder(outputReportDirectory);
         myOutput.append(outputPrefix);
         myOutput.append(calendar.get(Calendar.YEAR));
         myOutput.append("-");
@@ -332,8 +319,6 @@ public class CreateStatReport {
         String outputPrefix = "report-";
 
         String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
         String myMap = null;
 
         Calendar reportEndDate = new GregorianCalendar(calendar.get(Calendar.YEAR),
@@ -344,14 +329,14 @@ public class CreateStatReport {
 
         while (currentMonth.before(reportEndDate)) {
 
-            myInput = new StringBuffer(outputLogDirectory);
+            StringBuilder myInput = new StringBuilder(outputLogDirectory);
             myInput.append(inputPrefix);
             myInput.append(currentMonth.get(Calendar.YEAR));
             myInput.append("-");
             myInput.append(currentMonth.get(Calendar.MONTH) + 1);
             myInput.append(outputSuffix);
 
-            myOutput = new StringBuffer(outputReportDirectory);
+            StringBuilder myOutput = new StringBuilder(outputReportDirectory);
             myOutput.append(outputPrefix);
             myOutput.append(currentMonth.get(Calendar.YEAR));
             myOutput.append("-");
@@ -376,18 +361,16 @@ public class CreateStatReport {
         String outputPrefix = "report-";
 
         String myFormat = "html";
-        StringBuffer myInput = null;
-        StringBuffer myOutput = null;
         String myMap = null;
 
-        myInput = new StringBuffer(outputLogDirectory);
+        StringBuilder myInput = new StringBuilder(outputLogDirectory);
         myInput.append(inputPrefix);
         myInput.append(calendar.get(Calendar.YEAR));
         myInput.append("-");
         myInput.append(calendar.get(Calendar.MONTH) + 1);
         myInput.append(outputSuffix);
 
-        myOutput = new StringBuffer(outputReportDirectory);
+        StringBuilder myOutput = new StringBuilder(outputReportDirectory);
         myOutput.append(outputPrefix);
         myOutput.append(calendar.get(Calendar.YEAR));
         myOutput.append("-");

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

@@ -31,7 +31,7 @@ import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringUtils;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.core.Utils;
 import org.dspace.discovery.DiscoverQuery;
 import org.dspace.discovery.SearchServiceException;
@@ -1144,17 +1144,17 @@ public class LogAnalyser {
         if (match.matches()) {
             // set up a new log line object
             LogLine logLine = new LogLine(parseDate(match.group(1).trim()),
-                                          LogManager.unescapeLogField(match.group(2)).trim(),
-                                          LogManager.unescapeLogField(match.group(3)).trim(),
-                                          LogManager.unescapeLogField(match.group(4)).trim(),
-                                          LogManager.unescapeLogField(match.group(5)).trim());
+                                          LogHelper.unescapeLogField(match.group(2)).trim(),
+                                          LogHelper.unescapeLogField(match.group(3)).trim(),
+                                          LogHelper.unescapeLogField(match.group(4)).trim(),
+                                          LogHelper.unescapeLogField(match.group(5)).trim());
 
             return logLine;
         } else {
             match = validBase.matcher(line);
             if (match.matches()) {
                 LogLine logLine = new LogLine(parseDate(match.group(1).trim()),
-                                              LogManager.unescapeLogField(match.group(2)).trim(),
+                                              LogHelper.unescapeLogField(match.group(2)).trim(),
                                               null,
                                               null,
                                               null

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

@@ -10,8 +10,6 @@ package org.dspace.app.util;
 import java.io.File;
 import java.io.IOException;
 import java.sql.SQLException;
-import java.util.LinkedList;
-import java.util.List;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -30,7 +28,6 @@ import org.dspace.content.EntityType;
 import org.dspace.content.RelationshipType;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.EntityTypeService;
-import org.dspace.content.service.RelationshipService;
 import org.dspace.content.service.RelationshipTypeService;
 import org.dspace.core.Context;
 import org.w3c.dom.Document;
@@ -40,22 +37,20 @@ import org.w3c.dom.NodeList;
 import org.xml.sax.SAXException;
 
 /**
- * This script is used to initialize the database with a set of relationshiptypes that are written
+ * This script is used to initialize the database with a set of relationship types that are written
  * in an xml file that is given to this script.
- * This XML file needs to have a proper XML structure and needs to define the variables of the RelationshipType object
+ * This XML file needs to have a proper XML structure and needs to define the variables of the RelationshipType object.
  */
 public class InitializeEntities {
 
     private final static Logger log = LogManager.getLogger();
 
     private final RelationshipTypeService relationshipTypeService;
-    private final RelationshipService relationshipService;
     private final EntityTypeService entityTypeService;
 
 
     private InitializeEntities() {
         relationshipTypeService = ContentServiceFactory.getInstance().getRelationshipTypeService();
-        relationshipService = ContentServiceFactory.getInstance().getRelationshipService();
         entityTypeService = ContentServiceFactory.getInstance().getEntityTypeService();
     }
 
@@ -111,14 +106,12 @@ public class InitializeEntities {
         try {
             File fXmlFile = new File(fileLocation);
             DocumentBuilderFactory dbFactory = DocumentBuilderFactory.newInstance();
-            DocumentBuilder dBuilder = null;
-            dBuilder = dbFactory.newDocumentBuilder();
+            DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
             Document doc = dBuilder.parse(fXmlFile);
 
             doc.getDocumentElement().normalize();
 
             NodeList nList = doc.getElementsByTagName("type");
-            List<RelationshipType> relationshipTypes = new LinkedList<>();
             for (int i = 0; i < nList.getLength(); i++) {
                 Node nNode = nList.item(i);
 

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

@@ -0,0 +1,69 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.util;
+
+import java.util.List;
+
+import org.dspace.content.RelationshipType;
+
+public class RelationshipUtils {
+
+    private RelationshipUtils() {
+    }
+
+    /**
+     * Matches two Entity types to a Relationship Type from a set of Relationship Types.
+     *
+     * Given a list of Relationship Types, this method will find a Relationship Type that
+     * is configured between the originType and the targetType, with the matching originTypeName.
+     * It will match a relationship between these two entities in either direction (eg leftward
+     * or rightward).
+     * 
+     * Example: originType = Author, targetType = Publication, originTypeName = isAuthorOfPublication.
+     * 
+     * @param relTypes set of Relationship Types in which to find a match.
+     * @param targetType entity type of target (eg. Publication).
+     * @param originType entity type of origin referer (eg. Author).
+     * @param originTypeName the name of the relationship (eg. isAuthorOfPublication)
+     * @return null or matched Relationship Type.
+     */
+    public static RelationshipType matchRelationshipType(List<RelationshipType> relTypes, String targetType,
+            String originType, String originTypeName) {
+        RelationshipType foundRelationshipType = null;
+        if (originTypeName.split("\\.").length > 1) {
+            originTypeName = originTypeName.split("\\.")[1];
+        }
+        for (RelationshipType relationshipType : relTypes) {
+            // Is origin type leftward or righward
+            boolean isLeft = false;
+            if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType)) {
+                isLeft = true;
+            }
+            if (isLeft) {
+                // Validate typeName reference
+                if (!relationshipType.getLeftwardType().equalsIgnoreCase(originTypeName)) {
+                    continue;
+                }
+                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(originType)
+                        && relationshipType.getRightType().getLabel().equalsIgnoreCase(targetType)) {
+                    foundRelationshipType = relationshipType;
+                }
+            } else {
+                if (!relationshipType.getRightwardType().equalsIgnoreCase(originTypeName)) {
+                    continue;
+                }
+                if (relationshipType.getLeftType().getLabel().equalsIgnoreCase(targetType)
+                        && relationshipType.getRightType().getLabel().equalsIgnoreCase(originType)) {
+                    foundRelationshipType = relationshipType;
+                }
+            }
+        }
+        return foundRelationshipType;
+    }
+
+}

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

@@ -38,13 +38,12 @@ import org.dspace.core.Utils;
  *
  * @author Robert Tansley
  * @author Mark Diggory
- * @version $Revision$
  */
 public class Util {
     // cache for source version result
     private static String sourceVersion = null;
 
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Util.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
 
     /**
      * Default constructor. Must be protected as org.dspace.xmlworkflow.WorkflowUtils extends it
@@ -60,7 +59,7 @@ public class Util {
      * spaces
      */
     public static String nonBreakSpace(String s) {
-        StringBuffer newString = new StringBuffer();
+        StringBuilder newString = new StringBuilder();
 
         for (int i = 0; i < s.length(); i++) {
             char ch = s.charAt(i);
@@ -99,7 +98,7 @@ public class Util {
             return "";
         }
 
-        StringBuffer out = new StringBuffer();
+        StringBuilder out = new StringBuilder();
 
         final String[] pctEncoding = {"%00", "%01", "%02", "%03", "%04",
             "%05", "%06", "%07", "%08", "%09", "%0a", "%0b", "%0c", "%0d",
@@ -263,7 +262,7 @@ public class Util {
             return null;
         }
 
-        List<UUID> return_values = new ArrayList<UUID>(request_values.length);
+        List<UUID> return_values = new ArrayList<>(request_values.length);
 
         for (String s : request_values) {
             try {
@@ -402,7 +401,7 @@ public class Util {
         Item item, List<MetadataValue> values, String schema, String element,
         String qualifier, Locale locale) throws SQLException,
         DCInputsReaderException {
-        List<String> toReturn = new ArrayList<String>();
+        List<String> toReturn = new ArrayList<>();
         DCInput myInputs = null;
         boolean myInputsFound = false;
         String formFileName = I18nUtil.getInputFormsFileName(locale);
@@ -478,8 +477,9 @@ public class Util {
     }
 
     /**
-     * Split a list in an array of i sub-lists uniformly sized
+     * Split a list in an array of i sub-lists uniformly sized.
      *
+     * @param <T> type of objects in the list.
      * @param idsList the list to split
      * @param i the number of sublists to return
      *

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

@@ -58,6 +58,7 @@ public class WebApp implements ReloadableEntity<Integer> {
 
     }
 
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -8,7 +8,6 @@
 package org.dspace.app.util;
 
 import java.util.ArrayList;
-import java.util.LinkedList;
 import java.util.List;
 
 import org.apache.commons.lang3.StringUtils;
@@ -29,13 +28,13 @@ public class XMLUtils {
 
     /**
      * @param dataRoot the starting node
-     * @param name     the name of the subelement to find
+     * @param name     the tag name of the child element to find.
      * @return the list of all DOM Element with the provided name direct child
      * of the starting node
      */
     public static List<Element> getElementList(Element dataRoot, String name) {
         NodeList list = dataRoot.getElementsByTagName(name);
-        List<Element> listElements = new ArrayList<Element>();
+        List<Element> listElements = new ArrayList<>();
         for (int i = 0; i < list.getLength(); i++) {
             Element item = (Element) list.item(i);
             if (item.getParentNode().equals(dataRoot)) {
@@ -105,7 +104,7 @@ public class XMLUtils {
 
     /**
      * @param rootElement    the starting node
-     * @param subElementName the name of the subelement to find
+     * @param subElementName the tag name of the child element to find.
      * @return a list of string including all the text contents of the sub
      * element with the specified name. If there are not sub element
      * with the supplied name the method will return null
@@ -121,7 +120,7 @@ public class XMLUtils {
             return null;
         }
 
-        List<String> result = new LinkedList<String>();
+        List<String> result = new ArrayList<>();
         for (Element el : subElements) {
             if (StringUtils.isNotBlank(el.getTextContent())) {
                 result.add(el.getTextContent().trim());
@@ -152,7 +151,7 @@ public class XMLUtils {
             return null;
         }
 
-        List<String[]> result = new LinkedList<String[]>();
+        List<String[]> result = new ArrayList<>();
         for (Element el : subElements) {
             String[] tmp = new String[fieldsName.length];
             for (int idx = 0; idx < fieldsName.length; idx++) {

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

@@ -19,7 +19,7 @@ import javax.servlet.http.HttpServletResponse;
 
 import org.apache.logging.log4j.Logger;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
@@ -194,7 +194,7 @@ public class IPAuthentication implements AuthenticationMethod {
 
                                 groups.add(group);
                             } else {
-                                log.warn(LogManager.getHeader(context,
+                                log.warn(LogHelper.getHeader(context,
                                                               "configuration_error", "unknown_group="
                                                                   + groupName));
                             }
@@ -202,7 +202,7 @@ public class IPAuthentication implements AuthenticationMethod {
                     }
                 }
             } catch (IPMatcherException ipme) {
-                log.warn(LogManager.getHeader(context, "configuration_error",
+                log.warn(LogHelper.getHeader(context, "configuration_error",
                                               "bad_ip=" + addr), ipme);
             }
         }
@@ -228,7 +228,7 @@ public class IPAuthentication implements AuthenticationMethod {
 
                                 groups.remove(group);
                             } else {
-                                log.warn(LogManager.getHeader(context,
+                                log.warn(LogHelper.getHeader(context,
                                                               "configuration_error", "unknown_group="
                                                                   + groupName));
                             }
@@ -236,7 +236,7 @@ public class IPAuthentication implements AuthenticationMethod {
                     }
                 }
             } catch (IPMatcherException ipme) {
-                log.warn(LogManager.getHeader(context, "configuration_error",
+                log.warn(LogHelper.getHeader(context, "configuration_error",
                                               "bad_ip=" + addr), ipme);
             }
         }
@@ -248,7 +248,7 @@ public class IPAuthentication implements AuthenticationMethod {
                 gsb.append(group.getID()).append(", ");
             }
 
-            log.debug(LogManager.getHeader(context, "authenticated",
+            log.debug(LogHelper.getHeader(context, "authenticated",
                                            "special_groups=" + gsb.toString()
                                            + " (by IP=" + addr + ", useProxies=" + useProxies.toString() + ")"
                                           ));

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

@@ -36,7 +36,7 @@ import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
@@ -156,7 +156,7 @@ public class LDAPAuthentication
                     Group ldapGroup = groupService.findByName(context, groupName);
                     if (ldapGroup == null) {
                         // Oops - the group isn't there.
-                        log.warn(LogManager.getHeader(context,
+                        log.warn(LogHelper.getHeader(context,
                                                       "ldap_specialgroup",
                                                       "Group defined in login.specialgroup does not exist"));
                         return Collections.EMPTY_LIST;
@@ -211,7 +211,7 @@ public class LDAPAuthentication
                             String realm,
                             HttpServletRequest request)
         throws SQLException {
-        log.info(LogManager.getHeader(context, "auth", "attempting trivial auth of user=" + netid));
+        log.info(LogHelper.getHeader(context, "auth", "attempting trivial auth of user=" + netid));
 
         // Skip out when no netid or password is given.
         if (netid == null || password == null) {
@@ -245,7 +245,7 @@ public class LDAPAuthentication
 
         // Check a DN was found
         if ((dn == null) || (dn.trim().equals(""))) {
-            log.info(LogManager
+            log.info(LogHelper
                          .getHeader(context, "failed_login", "no DN found for user " + netid));
             return BAD_CREDENTIALS;
         }
@@ -265,7 +265,7 @@ public class LDAPAuthentication
                 // assign user to groups based on ldap dn
                 assignGroups(dn, ldap.ldapGroup, context);
 
-                log.info(LogManager
+                log.info(LogHelper
                              .getHeader(context, "authenticate", "type=ldap"));
                 return SUCCESS;
             } else {
@@ -277,7 +277,7 @@ public class LDAPAuthentication
 
             if (ldap.ldapAuthenticate(dn, password, context)) {
                 // Register the new user automatically
-                log.info(LogManager.getHeader(context,
+                log.info(LogHelper.getHeader(context,
                                               "autoregister", "netid=" + netid));
 
                 String email = ldap.ldapEmail;
@@ -290,7 +290,7 @@ public class LDAPAuthentication
                         email = netid + configurationService.getProperty("authentication-ldap.netid_email_domain");
                     } else {
                         // We don't have a valid email address. We'll default it to 'netid' but log a warning
-                        log.warn(LogManager.getHeader(context, "autoregister",
+                        log.warn(LogHelper.getHeader(context, "autoregister",
                                                       "Unable to locate email address for account '" + netid + "', so" +
                                                           " it has been set to '" + netid + "'. " +
                                                           "Please check the LDAP 'email_field' OR consider " +
@@ -303,7 +303,7 @@ public class LDAPAuthentication
                     try {
                         eperson = ePersonService.findByEmail(context, email);
                         if (eperson != null) {
-                            log.info(LogManager.getHeader(context,
+                            log.info(LogHelper.getHeader(context,
                                                           "type=ldap-login", "type=ldap_but_already_email"));
                             context.turnOffAuthorisationSystem();
                             eperson.setNetid(netid.toLowerCase());
@@ -350,12 +350,12 @@ public class LDAPAuthentication
                                     context.restoreAuthSystemState();
                                 }
 
-                                log.info(LogManager.getHeader(context, "authenticate",
+                                log.info(LogHelper.getHeader(context, "authenticate",
                                                               "type=ldap-login, created ePerson"));
                                 return SUCCESS;
                             } else {
                                 // No auto-registration for valid certs
-                                log.info(LogManager.getHeader(context,
+                                log.info(LogHelper.getHeader(context,
                                                               "failed_login", "type=ldap_but_no_record"));
                                 return NO_SUCH_USER;
                             }
@@ -429,7 +429,7 @@ public class LDAPAuthentication
             } catch (NumberFormatException e) {
                 // Log the error if it has been set but is invalid
                 if (ldap_search_scope != null) {
-                    log.warn(LogManager.getHeader(context,
+                    log.warn(LogHelper.getHeader(context,
                                                   "ldap_authentication", "invalid search scope: " + ldap_search_scope));
                 }
             }
@@ -548,19 +548,19 @@ public class LDAPAuthentication
                             // Ambiguous user, can't continue
 
                         } else {
-                            log.debug(LogManager.getHeader(context, "got DN", resultDN));
+                            log.debug(LogHelper.getHeader(context, "got DN", resultDN));
                             return resultDN;
                         }
                     }
                 } catch (NamingException e) {
                     // if the lookup fails go ahead and create a new record for them because the authentication
                     // succeeded
-                    log.warn(LogManager.getHeader(context,
+                    log.warn(LogHelper.getHeader(context,
                                                   "ldap_attribute_lookup", "type=failed_search "
                                                       + e));
                 }
             } catch (NamingException | IOException e) {
-                log.warn(LogManager.getHeader(context,
+                log.warn(LogHelper.getHeader(context,
                                               "ldap_authentication", "type=failed_auth " + e));
             } finally {
                 // Close the context when we're done
@@ -630,7 +630,7 @@ public class LDAPAuthentication
                     }
                 } catch (NamingException | IOException e) {
                     // something went wrong (like wrong password) so return false
-                    log.warn(LogManager.getHeader(context,
+                    log.warn(LogHelper.getHeader(context,
                                                   "ldap_authentication", "type=failed_auth " + e));
                     return false;
                 } finally {
@@ -714,18 +714,18 @@ public class LDAPAuthentication
                             groupService.update(context, ldapGroup);
                         } else {
                             // The group does not exist
-                            log.warn(LogManager.getHeader(context,
+                            log.warn(LogHelper.getHeader(context,
                                                           "ldap_assignGroupsBasedOnLdapDn",
                                                           "Group defined in authentication-ldap.login.groupmap." + i
                                                               + " does not exist :: " + dspaceGroupName));
                         }
                     } catch (AuthorizeException ae) {
-                        log.debug(LogManager.getHeader(context,
+                        log.debug(LogHelper.getHeader(context,
                                                        "assignGroupsBasedOnLdapDn could not authorize addition to " +
                                                            "group",
                                                        dspaceGroupName));
                     } catch (SQLException e) {
-                        log.debug(LogManager.getHeader(context, "assignGroupsBasedOnLdapDn could not find group",
+                        log.debug(LogHelper.getHeader(context, "assignGroupsBasedOnLdapDn could not find group",
                                                        dspaceGroupName));
                     }
                 }

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

@@ -15,9 +15,10 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
@@ -41,7 +42,6 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  * Basic Auth username and password to the <code>AuthenticationManager</code>.
  *
  * @author Larry Stone
- * @version $Revision$
  */
 public class PasswordAuthentication
     implements AuthenticationMethod {
@@ -49,7 +49,7 @@ public class PasswordAuthentication
     /**
      * log4j category
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(PasswordAuthentication.class);
+    private static final Logger log = LogManager.getLogger();
 
 
     /**
@@ -142,12 +142,12 @@ public class PasswordAuthentication
                                      .toString())) {
                 String groupName = DSpaceServicesFactory.getInstance().getConfigurationService()
                                                         .getProperty("authentication-password.login.specialgroup");
-                if ((groupName != null) && (!groupName.trim().equals(""))) {
+                if ((groupName != null) && !groupName.trim().isEmpty()) {
                     Group specialGroup = EPersonServiceFactory.getInstance().getGroupService()
                                                               .findByName(context, groupName);
                     if (specialGroup == null) {
                         // Oops - the group isn't there.
-                        log.warn(LogManager.getHeader(context,
+                        log.warn(LogHelper.getHeader(context,
                                                       "password_specialgroup",
                                                       "Group defined in modules/authentication-password.cfg login" +
                                                           ".specialgroup does not exist"));
@@ -158,7 +158,7 @@ public class PasswordAuthentication
                 }
             }
         } catch (Exception e) {
-            log.error(LogManager.getHeader(context, "getSpecialGroups", ""), e);
+            log.error(LogHelper.getHeader(context, "getSpecialGroups", ""), e);
         }
         return Collections.EMPTY_LIST;
     }
@@ -181,7 +181,7 @@ public class PasswordAuthentication
      * SUCCESS, BAD_CREDENTIALS, CERT_REQUIRED, NO_SUCH_USER, BAD_ARGS
      * <p>Meaning:
      * <br>SUCCESS         - authenticated OK.
-     * <br>BAD_CREDENTIALS - user exists, but assword doesn't match
+     * <br>BAD_CREDENTIALS - user exists, but password doesn't match
      * <br>CERT_REQUIRED   - not allowed to login this way without X.509 cert.
      * <br>NO_SUCH_USER    - no EPerson with matching email address.
      * <br>BAD_ARGS        - missing username, or user matched but cannot login.
@@ -196,7 +196,7 @@ public class PasswordAuthentication
         throws SQLException {
         if (username != null && password != null) {
             EPerson eperson = null;
-            log.info(LogManager.getHeader(context, "authenticate", "attempting password auth of user=" + username));
+            log.info(LogHelper.getHeader(context, "authenticate", "attempting password auth of user=" + username));
             eperson = EPersonServiceFactory.getInstance().getEPersonService()
                                            .findByEmail(context, username.toLowerCase());
 
@@ -208,7 +208,7 @@ public class PasswordAuthentication
                 return BAD_ARGS;
             } else if (eperson.getRequireCertificate()) {
                 // this user can only login with x.509 certificate
-                log.warn(LogManager.getHeader(context, "authenticate",
+                log.warn(LogHelper.getHeader(context, "authenticate",
                                               "rejecting PasswordAuthentication because " + username + " requires " +
                                                   "certificate."));
                 return CERT_REQUIRED;
@@ -216,7 +216,7 @@ public class PasswordAuthentication
                                             .checkPassword(context, eperson, password)) {
                 // login is ok if password matches:
                 context.setCurrentUser(eperson);
-                log.info(LogManager.getHeader(context, "authenticate", "type=PasswordAuthentication"));
+                log.info(LogHelper.getHeader(context, "authenticate", "type=PasswordAuthentication"));
                 return SUCCESS;
             } else {
                 return BAD_CREDENTIALS;

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

@@ -35,7 +35,7 @@ import org.dspace.authenticate.factory.AuthenticateServiceFactory;
 import org.dspace.authenticate.service.AuthenticationService;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
@@ -286,7 +286,7 @@ public class X509Authentication implements AuthenticationMethod {
         try {
             certificate.checkValidity();
         } catch (CertificateException e) {
-            log.info(LogManager.getHeader(context, "authentication",
+            log.info(LogHelper.getHeader(context, "authentication",
                                           "X.509 Certificate is EXPIRED or PREMATURE: "
                                               + e.toString()));
             return false;
@@ -298,7 +298,7 @@ public class X509Authentication implements AuthenticationMethod {
                 certificate.verify(caPublicKey);
                 return true;
             } catch (GeneralSecurityException e) {
-                log.info(LogManager.getHeader(context, "authentication",
+                log.info(LogHelper.getHeader(context, "authentication",
                                               "X.509 Certificate FAILED SIGNATURE check: "
                                                   + e.toString()));
             }
@@ -322,11 +322,11 @@ public class X509Authentication implements AuthenticationMethod {
                     }
                 }
                 log
-                    .info(LogManager
+                    .info(LogHelper
                               .getHeader(context, "authentication",
                                          "Keystore method FAILED SIGNATURE check on client cert."));
             } catch (GeneralSecurityException e) {
-                log.info(LogManager.getHeader(context, "authentication",
+                log.info(LogHelper.getHeader(context, "authentication",
                                               "X.509 Certificate FAILED SIGNATURE check: "
                                                   + e.toString()));
             }
@@ -461,7 +461,7 @@ public class X509Authentication implements AuthenticationMethod {
                         if (group != null) {
                             groups.add(group);
                         } else {
-                            log.warn(LogManager.getHeader(context,
+                            log.warn(LogHelper.getHeader(context,
                                                           "configuration_error", "unknown_group="
                                                               + groupName));
                         }
@@ -513,7 +513,7 @@ public class X509Authentication implements AuthenticationMethod {
             try {
                 if (!isValid(context, certs[0])) {
                     log
-                        .warn(LogManager
+                        .warn(LogHelper
                                   .getHeader(context, "authenticate",
                                              "type=x509certificate, status=BAD_CREDENTIALS (not valid)"));
                     return BAD_CREDENTIALS;
@@ -530,7 +530,7 @@ public class X509Authentication implements AuthenticationMethod {
                     if (email != null
                         && canSelfRegister(context, request, null)) {
                         // Register the new user automatically
-                        log.info(LogManager.getHeader(context, "autoregister",
+                        log.info(LogHelper.getHeader(context, "autoregister",
                                                       "from=x.509, email=" + email));
 
                         // TEMPORARILY turn off authorisation
@@ -549,25 +549,25 @@ public class X509Authentication implements AuthenticationMethod {
                     } else {
                         // No auto-registration for valid certs
                         log
-                            .warn(LogManager
+                            .warn(LogHelper
                                       .getHeader(context, "authenticate",
                                                  "type=cert_but_no_record, cannot auto-register"));
                         return NO_SUCH_USER;
                     }
                 } else if (!eperson.canLogIn()) { // make sure this is a login account
-                    log.warn(LogManager.getHeader(context, "authenticate",
+                    log.warn(LogHelper.getHeader(context, "authenticate",
                                                   "type=x509certificate, email=" + email
                                                       + ", canLogIn=false, rejecting."));
                     return BAD_ARGS;
                 } else {
-                    log.info(LogManager.getHeader(context, "login",
+                    log.info(LogHelper.getHeader(context, "login",
                                                   "type=x509certificate"));
                     context.setCurrentUser(eperson);
                     setSpecialGroupsFlag(request, email);
                     return SUCCESS;
                 }
             } catch (AuthorizeException ce) {
-                log.warn(LogManager.getHeader(context, "authorize_exception",
+                log.warn(LogHelper.getHeader(context, "authorize_exception",
                                               ""), ce);
             }
 

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

@@ -21,7 +21,7 @@ import org.apache.solr.common.SolrDocument;
 import org.dspace.authority.service.AuthorityValueService;
 import org.dspace.content.authority.SolrAuthority;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -220,7 +220,7 @@ public class AuthorityValueServiceImpl implements AuthorityValueService {
                 }
             }
         } catch (Exception e) {
-            log.error(LogManager.getHeader(context, "Error while retrieving AuthorityValue from solr",
+            log.error(LogHelper.getHeader(context, "Error while retrieving AuthorityValue from solr",
                                            "query: " + queryString), e);
         }
 

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

@@ -11,7 +11,6 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Date;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.UUID;
 
@@ -62,7 +61,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class AuthorizeServiceImpl implements AuthorizeService {
 
-    private static Logger log = LogManager.getLogger(AuthorizeServiceImpl.class);
+    private static final Logger log = LogManager.getLogger();
 
     @Autowired(required = true)
     protected BitstreamService bitstreamService;
@@ -243,7 +242,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
         // If authorization was given before and cached
         Boolean cachedResult = c.getCachedAuthorizationResult(o, action, e);
         if (cachedResult != null) {
-            return cachedResult.booleanValue();
+            return cachedResult;
         }
 
         // is eperson set? if not, userToCheck = null (anonymous)
@@ -308,7 +307,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
                 }
 
                 if ((rp.getGroup() != null)
-                    && (groupService.isMember(c, e, rp.getGroup()))) {
+                    && groupService.isMember(c, e, rp.getGroup())) {
                     // group was set, and eperson is a member
                     // of that group
                     c.cacheAuthorizedAction(o, action, e, true, rp);
@@ -366,7 +365,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
 
         Boolean cachedResult = c.getCachedAuthorizationResult(o, Constants.ADMIN, e);
         if (cachedResult != null) {
-            return cachedResult.booleanValue();
+            return cachedResult;
         }
 
         //
@@ -383,7 +382,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
                 }
 
                 if ((rp.getGroup() != null)
-                    && (groupService.isMember(c, e, rp.getGroup()))) {
+                    && groupService.isMember(c, e, rp.getGroup())) {
                     // group was set, and eperson is a member
                     // of that group
                     c.cacheAuthorizedAction(o, Constants.ADMIN, e, true, rp);
@@ -502,7 +501,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
         List<ResourcePolicy> policies = getPolicies(c, src);
 
         //Only inherit non-ADMIN policies (since ADMIN policies are automatically inherited)
-        List<ResourcePolicy> nonAdminPolicies = new ArrayList<ResourcePolicy>();
+        List<ResourcePolicy> nonAdminPolicies = new ArrayList<>();
         for (ResourcePolicy rp : policies) {
             if (rp.getAction() != Constants.ADMIN) {
                 nonAdminPolicies.add(rp);
@@ -525,7 +524,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
     public void addPolicies(Context c, List<ResourcePolicy> policies, DSpaceObject dest)
         throws SQLException, AuthorizeException {
         // now add them to the destination object
-        List<ResourcePolicy> newPolicies = new LinkedList<>();
+        List<ResourcePolicy> newPolicies = new ArrayList<>(policies.size());
 
         for (ResourcePolicy srp : policies) {
             ResourcePolicy rp = resourcePolicyService.create(c);
@@ -600,7 +599,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
                                            int actionID) throws java.sql.SQLException {
         List<ResourcePolicy> policies = getPoliciesActionFilter(c, o, actionID);
 
-        List<Group> groups = new ArrayList<Group>();
+        List<Group> groups = new ArrayList<>();
         for (ResourcePolicy resourcePolicy : policies) {
             if (resourcePolicy.getGroup() != null && resourcePolicyService.isDateValid(resourcePolicy)) {
                 groups.add(resourcePolicy.getGroup());
@@ -768,6 +767,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
      * @param context   context with the current user
      * @return          true if the current user is a community admin in the site
      *                  false when this is not the case, or an exception occurred
+     * @throws java.sql.SQLException passed through.
      */
     @Override
     public boolean isCommunityAdmin(Context context) throws SQLException {
@@ -780,6 +780,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
      * @param context   context with the current user
      * @return          true if the current user is a collection admin in the site
      *                  false when this is not the case, or an exception occurred
+     * @throws java.sql.SQLException passed through.
      */
     @Override
     public boolean isCollectionAdmin(Context context) throws SQLException {
@@ -792,6 +793,7 @@ public class AuthorizeServiceImpl implements AuthorizeService {
      * @param context   context with the current user
      * @return          true if the current user is a community or collection admin in the site
      *                  false when this is not the case, or an exception occurred
+     * @throws java.sql.SQLException passed through.
      */
     @Override
     public boolean isComColAdmin(Context context) throws SQLException {

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

@@ -169,6 +169,7 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
      *
      * @return the internal identifier
      */
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -11,13 +11,12 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 
-import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.Logger;
 import org.dspace.content.Collection;
 import org.dspace.content.Community;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.sort.OrderFormat;
 import org.dspace.sort.SortOption;
 
@@ -85,7 +84,7 @@ public class BrowseEngine {
      */
     public BrowseInfo browse(BrowserScope bs)
         throws BrowseException {
-        log.debug(LogManager.getHeader(context, "browse", ""));
+        log.debug(LogHelper.getHeader(context, "browse", ""));
 
         // first, load the browse scope into the object
         this.scope = bs;
@@ -119,7 +118,7 @@ public class BrowseEngine {
      */
     public BrowseInfo browseMini(BrowserScope bs)
         throws BrowseException {
-        log.info(LogManager.getHeader(context, "browse_mini", ""));
+        log.info(LogHelper.getHeader(context, "browse_mini", ""));
 
         // load the scope into the object
         this.scope = bs;
@@ -198,7 +197,7 @@ public class BrowseEngine {
      */
     private BrowseInfo browseByItem(BrowserScope bs)
         throws BrowseException {
-        log.info(LogManager.getHeader(context, "browse_by_item", ""));
+        log.info(LogHelper.getHeader(context, "browse_by_item", ""));
         try {
             // get the table name that we are going to be getting our data from
             dao.setTable(browseIndex.getTableName());
@@ -374,14 +373,14 @@ public class BrowseEngine {
      */
     private BrowseInfo browseByValue(BrowserScope bs)
         throws BrowseException {
-        log.info(LogManager.getHeader(context, "browse_by_value", "focus=" + bs.getJumpToValue()));
+        log.info(LogHelper.getHeader(context, "browse_by_value", "focus=" + bs.getJumpToValue()));
 
         try {
             // get the table name that we are going to be getting our data from
             // this is the distinct table constrained to either community or collection
             dao.setTable(browseIndex.getDistinctTableName());
 
-            dao.setStartsWith(StringUtils.lowerCase(scope.getStartsWith()));
+            dao.setStartsWith(normalizeJumpToValue(scope.getStartsWith()));
             // remind the DAO that this is a distinct value browse, so it knows what sort
             // of query to build
             dao.setDistinct(true);
@@ -518,17 +517,17 @@ public class BrowseEngine {
      */
     private String getJumpToValue()
         throws BrowseException {
-        log.debug(LogManager.getHeader(context, "get_focus_value", ""));
+        log.debug(LogHelper.getHeader(context, "get_focus_value", ""));
 
         // if the focus is by value, just return it
         if (scope.hasJumpToValue()) {
-            log.debug(LogManager.getHeader(context, "get_focus_value_return", "return=" + scope.getJumpToValue()));
+            log.debug(LogHelper.getHeader(context, "get_focus_value_return", "return=" + scope.getJumpToValue()));
             return scope.getJumpToValue();
         }
 
         // if the focus is to start with, then we need to return the value of the starts with
         if (scope.hasStartsWith()) {
-            log.debug(LogManager.getHeader(context, "get_focus_value_return", "return=" + scope.getStartsWith()));
+            log.debug(LogHelper.getHeader(context, "get_focus_value_return", "return=" + scope.getStartsWith()));
             return scope.getStartsWith();
         }
 
@@ -565,7 +564,7 @@ public class BrowseEngine {
         // item (I think)
         String max = dao.doMaxQuery(col, tableName, id);
 
-        log.debug(LogManager.getHeader(context, "get_focus_value_return", "return=" + max));
+        log.debug(LogHelper.getHeader(context, "get_focus_value_return", "return=" + max));
 
         return max;
     }
@@ -671,7 +670,7 @@ public class BrowseEngine {
      */
     private int getTotalResults(boolean distinct)
         throws SQLException, BrowseException {
-        log.debug(LogManager.getHeader(context, "get_total_results", "distinct=" + distinct));
+        log.debug(LogHelper.getHeader(context, "get_total_results", "distinct=" + distinct));
 
         // tell the browse query whether we are distinct
         dao.setDistinct(distinct);
@@ -706,7 +705,7 @@ public class BrowseEngine {
         dao.setOffset(offset);
         dao.setCountValues(null);
 
-        log.debug(LogManager.getHeader(context, "get_total_results_return", "return=" + count));
+        log.debug(LogHelper.getHeader(context, "get_total_results_return", "return=" + count));
 
         return count;
     }

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

@@ -170,7 +170,7 @@ public class MostRecentChecksum implements Serializable {
             return true;
         }
 
-        if (o == null || getClass() != o.getClass()) {
+        if (o == null || !(o instanceof MostRecentChecksum)) {
             return false;
         }
 

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

@@ -109,7 +109,7 @@ public class ResultsLogger implements ChecksumResultsCollector {
             "unknown"));
         LOG.info(msg("new-checksum") + ": " + info.getCurrentChecksum());
         LOG.info(msg("checksum-comparison-result") + ": "
-                     + (info.getChecksumResult().getResultCode()));
+                     + info.getChecksumResult().getResultCode());
         LOG.info("\n\n");
     }
 }

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

@@ -77,7 +77,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         osw.write(applyDateFormatShort(endDate));
         osw.write("\n\n\n");
 
-        if (recentChecksums.size() == 0) {
+        if (recentChecksums.isEmpty()) {
             osw.write("\n\n");
             osw.write(msg("no-bitstreams-to-delete"));
             osw.write("\n");
@@ -119,7 +119,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         osw.write(applyDateFormatShort(endDate));
         osw.write("\n\n\n");
 
-        if (history.size() == 0) {
+        if (history.isEmpty()) {
             osw.write("\n\n");
             osw.write(msg("no-changed-bitstreams"));
             osw.write("\n");
@@ -159,7 +159,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         osw.write(applyDateFormatShort(endDate));
         osw.write("\n\n\n");
 
-        if (history.size() == 0) {
+        if (history.isEmpty()) {
             osw.write("\n\n");
             osw.write(msg("no-bitstreams-changed"));
             osw.write("\n");
@@ -201,7 +201,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         osw.write(applyDateFormatShort(endDate));
         osw.write("\n\n\n");
 
-        if (mostRecentChecksums.size() == 0) {
+        if (mostRecentChecksums.isEmpty()) {
             osw.write("\n\n");
             osw.write(msg("no-bitstreams-to-no-longer-be-processed"));
             osw.write("\n");
@@ -233,7 +233,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         osw.write(applyDateFormatShort(new Date()));
         osw.write("\n\n\n");
 
-        if (bitstreams.size() == 0) {
+        if (bitstreams.isEmpty()) {
             osw.write("\n\n");
             osw.write(msg("no-unchecked-bitstreams"));
             osw.write("\n");
@@ -257,7 +257,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
     protected void printHistoryRecords(List<MostRecentChecksum> mostRecentChecksums, OutputStreamWriter osw)
         throws IOException {
         for (MostRecentChecksum mostRecentChecksum : mostRecentChecksums) {
-            StringBuffer buf = new StringBuffer(1000);
+            StringBuilder buf = new StringBuilder(1000);
             buf.append("------------------------------------------------ \n");
             buf.append(msg("bitstream-id")).append(" = ").append(
                 mostRecentChecksum.getBitstream().getID()).append("\n");
@@ -292,7 +292,7 @@ public class SimpleReporterServiceImpl implements SimpleReporterService {
         throws IOException, SQLException {
 
         for (Bitstream info : bitstreams) {
-            StringBuffer buf = new StringBuffer(1000);
+            StringBuilder buf = new StringBuilder(1000);
             buf.append("------------------------------------------------ \n");
             buf.append(msg("format-id")).append(" =  ").append(
                 info.getFormat(context).getID()).append("\n");

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

@@ -21,7 +21,7 @@ import org.dspace.core.Context;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the ChecksumResult object.
- * This class is responsible for all database calls for the ChecksumResult object and is autowired by spring
+ * This class is responsible for all database calls for the ChecksumResult object and is autowired by Spring.
  * This class should never be accessed directly.
  *
  * @author kevinvandevelde at atmire.com
@@ -39,6 +39,6 @@ public class ChecksumResultDAOImpl extends AbstractHibernateDAO<ChecksumResult>
         Root<ChecksumResult> checksumResultRoot = criteriaQuery.from(ChecksumResult.class);
         criteriaQuery.select(checksumResultRoot);
         criteriaQuery.where(criteriaBuilder.equal(checksumResultRoot.get(ChecksumResult_.resultCode), code));
-        return uniqueResult(context, criteriaQuery, false, ChecksumResult.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, ChecksumResult.class);
     }
 }

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

@@ -21,8 +21,6 @@ import javax.persistence.OneToOne;
 import javax.persistence.Table;
 import javax.persistence.Transient;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.BitstreamService;
 import org.dspace.core.Constants;
@@ -37,17 +35,10 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * the contents of a bitstream; you need to create a new bitstream.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 @Entity
 @Table(name = "bitstream")
 public class Bitstream extends DSpaceObject implements DSpaceObjectLegacySupport {
-
-    /**
-     * log4j logger
-     */
-    private static final Logger log = LogManager.getLogger();
-
     @Column(name = "bitstream_id", insertable = false, updatable = false)
     private Integer legacyId;
 
@@ -412,7 +403,7 @@ public class Bitstream extends DSpaceObject implements DSpaceObjectLegacySupport
      */
     @Override
     public boolean equals(Object other) {
-        if (other == null) {
+        if (!(other instanceof Bitstream)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(other);
@@ -420,11 +411,7 @@ public class Bitstream extends DSpaceObject implements DSpaceObjectLegacySupport
             return false;
         }
         final Bitstream otherBitstream = (Bitstream) other;
-        if (!this.getID().equals(otherBitstream.getID())) {
-            return false;
-        }
-
-        return true;
+        return this.getID().equals(otherBitstream.getID());
     }
 
     @Override

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

@@ -9,7 +9,7 @@ package org.dspace.content;
 
 import java.io.Serializable;
 import java.sql.SQLException;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 import javax.persistence.CollectionTable;
 import javax.persistence.Column;
@@ -40,7 +40,6 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * when <code>update</code> is called.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 @Entity
 @Table(name = "bitstreamformatregistry")
@@ -112,7 +111,7 @@ public class BitstreamFormat implements Serializable, ReloadableEntity<Integer>
      * {@link org.dspace.content.service.BitstreamFormatService#create(Context)}
      */
     protected BitstreamFormat() {
-        fileExtensions = new LinkedList<>();
+        fileExtensions = new ArrayList<>();
     }
 
     /**
@@ -120,6 +119,7 @@ public class BitstreamFormat implements Serializable, ReloadableEntity<Integer>
      *
      * @return the internal identifier
      */
+    @Override
     public final Integer getID() {
         return id;
     }
@@ -267,7 +267,7 @@ public class BitstreamFormat implements Serializable, ReloadableEntity<Integer>
      */
     @Override
     public boolean equals(Object other) {
-        if (other == null) {
+        if (!(other instanceof BitstreamFormat)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(other);
@@ -275,11 +275,7 @@ public class BitstreamFormat implements Serializable, ReloadableEntity<Integer>
             return false;
         }
         final BitstreamFormat otherBitstreamFormat = (BitstreamFormat) other;
-        if (!this.getID().equals(otherBitstreamFormat.getID())) {
-            return false;
-        }
-
-        return true;
+        return this.getID().equals(otherBitstreamFormat.getID());
     }
 
     @Override

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

@@ -18,7 +18,7 @@ import org.dspace.authorize.service.AuthorizeService;
 import org.dspace.content.dao.BitstreamFormatDAO;
 import org.dspace.content.service.BitstreamFormatService;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -68,7 +68,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
 
         if (bitstreamFormat == null) {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context,
+                log.debug(LogHelper.getHeader(context,
                                                "find_bitstream_format",
                                                "not_found,bitstream_format_id=" + id));
             }
@@ -78,7 +78,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
 
         // not null, return format object
         if (log.isDebugEnabled()) {
-            log.debug(LogManager.getHeader(context, "find_bitstream_format",
+            log.debug(LogHelper.getHeader(context, "find_bitstream_format",
                                            "bitstream_format_id=" + id));
         }
 
@@ -129,7 +129,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
         BitstreamFormat bitstreamFormat = bitstreamFormatDAO.create(context, new BitstreamFormat());
 
 
-        log.info(LogManager.getHeader(context, "create_bitstream_format",
+        log.info(LogHelper.getHeader(context, "create_bitstream_format",
                                       "bitstream_format_id="
                                           + bitstreamFormat.getID()));
 
@@ -189,7 +189,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
             }
 
             for (BitstreamFormat bitstreamFormat : bitstreamFormats) {
-                log.info(LogManager.getHeader(context, "update_bitstream_format",
+                log.info(LogHelper.getHeader(context, "update_bitstream_format",
                                               "bitstream_format_id=" + bitstreamFormat.getID()));
 
                 bitstreamFormatDAO.save(context, bitstreamFormat);
@@ -218,7 +218,7 @@ public class BitstreamFormatServiceImpl implements BitstreamFormatService {
         // Delete this format from database
         bitstreamFormatDAO.delete(context, bitstreamFormat);
 
-        log.info(LogManager.getHeader(context, "delete_bitstream_format",
+        log.info(LogHelper.getHeader(context, "delete_bitstream_format",
                                       "bitstream_format_id=" + bitstreamFormat.getID() + ",bitstreams_changed="
                                           + numberChanged));
     }

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

@@ -28,7 +28,7 @@ import org.dspace.content.service.BundleService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.event.Event;
 import org.dspace.storage.bitstore.service.BitstreamStorageService;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -45,7 +45,8 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(BitstreamServiceImpl.class);
+    private static final Logger log
+            = org.apache.logging.log4j.LogManager.getLogger();
 
 
     @Autowired(required = true)
@@ -73,7 +74,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
 
         if (bitstream == null) {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_bitstream",
+                log.debug(LogHelper.getHeader(context, "find_bitstream",
                                                "not_found,bitstream_id=" + id));
             }
 
@@ -82,7 +83,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
 
         // not null, return Bitstream
         if (log.isDebugEnabled()) {
-            log.debug(LogManager.getHeader(context, "find_bitstream",
+            log.debug(LogHelper.getHeader(context, "find_bitstream",
                                            "bitstream_id=" + id));
         }
 
@@ -131,7 +132,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         // Store the bits
         UUID bitstreamID = bitstreamStorageService.store(context, bitstreamDAO.create(context, new Bitstream()), is);
 
-        log.info(LogManager.getHeader(context, "create_bitstream",
+        log.info(LogHelper.getHeader(context, "create_bitstream",
                                       "bitstream_id=" + bitstreamID));
 
         // Set the format to "unknown"
@@ -191,7 +192,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         bitstreamStorageService.register(
             context, bitstream, assetstore, bitstreamPath);
 
-        log.info(LogManager.getHeader(context,
+        log.info(LogHelper.getHeader(context,
                                       "create_bitstream",
                                       "bitstream_id=" + bitstream.getID()));
 
@@ -248,7 +249,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         // Check authorisation
         authorizeService.authorizeAction(context, bitstream, Constants.WRITE);
 
-        log.info(LogManager.getHeader(context, "update_bitstream",
+        log.info(LogHelper.getHeader(context, "update_bitstream",
                                       "bitstream_id=" + bitstream.getID()));
         super.update(context, bitstream);
         if (bitstream.isModified()) {
@@ -273,7 +274,7 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         // changed to a check on delete
         // Check authorisation
         authorizeService.authorizeAction(context, bitstream, Constants.DELETE);
-        log.info(LogManager.getHeader(context, "delete_bitstream",
+        log.info(LogHelper.getHeader(context, "delete_bitstream",
                                       "bitstream_id=" + bitstream.getID()));
 
         context.addEvent(new Event(Event.DELETE, Constants.BITSTREAM, bitstream.getID(),
@@ -350,7 +351,8 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
     public void expunge(Context context, Bitstream bitstream) throws SQLException, AuthorizeException {
         authorizeService.authorizeAction(context, bitstream, Constants.DELETE);
         if (!bitstream.isDeleted()) {
-            throw new IllegalStateException("Bitstream must be deleted before it can be removed from the database");
+            throw new IllegalStateException("Bitstream " + bitstream.getID().toString()
+                    + " must be deleted before it can be removed from the database.");
         }
         bitstreamDAO.delete(context, bitstream);
     }

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

@@ -9,7 +9,6 @@ package org.dspace.content;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.LinkedList;
 import java.util.List;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -138,7 +137,7 @@ public class Bundle extends DSpaceObject implements DSpaceObjectLegacySupport {
      * @return the bitstreams
      */
     public List<Bitstream> getBitstreams() {
-        List<Bitstream> bitstreamList = new LinkedList<>(this.bitstreams);
+        List<Bitstream> bitstreamList = new ArrayList<>(this.bitstreams);
         return bitstreamList;
     }
 
@@ -191,7 +190,7 @@ public class Bundle extends DSpaceObject implements DSpaceObjectLegacySupport {
 
     @Override
     public boolean equals(Object obj) {
-        if (obj == null) {
+        if (obj == null || !(obj instanceof Bundle)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(obj);
@@ -202,10 +201,7 @@ public class Bundle extends DSpaceObject implements DSpaceObjectLegacySupport {
         if (this.getType() != other.getType()) {
             return false;
         }
-        if (!this.getID().equals(other.getID())) {
-            return false;
-        }
-        return true;
+        return this.getID().equals(other.getID());
     }
 
     @Override

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

@@ -33,7 +33,7 @@ import org.dspace.content.service.BundleService;
 import org.dspace.content.service.ItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.event.Event;
 import org.springframework.beans.factory.annotation.Autowired;
 
@@ -73,14 +73,14 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
         Bundle bundle = bundleDAO.findByID(context, Bundle.class, id);
         if (bundle == null) {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_bundle",
+                log.debug(LogHelper.getHeader(context, "find_bundle",
                                                "not_found,bundle_id=" + id));
             }
 
             return null;
         } else {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_bundle",
+                log.debug(LogHelper.getHeader(context, "find_bundle",
                                                "bundle_id=" + id));
             }
 
@@ -105,7 +105,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
         }
 
 
-        log.info(LogManager.getHeader(context, "create_bundle", "bundle_id="
+        log.info(LogHelper.getHeader(context, "create_bundle", "bundle_id="
             + bundle.getID()));
 
         // if we ever use the identifier service for bundles, we should
@@ -136,7 +136,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
         // Check authorisation
         authorizeService.authorizeAction(context, bundle, Constants.ADD);
 
-        log.info(LogManager.getHeader(context, "add_bitstream", "bundle_id="
+        log.info(LogHelper.getHeader(context, "add_bitstream", "bundle_id="
             + bundle.getID() + ",bitstream_id=" + bitstream.getID()));
 
         // First check that the bitstream isn't already in the list
@@ -177,7 +177,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
         // Check authorisation
         authorizeService.authorizeAction(context, bundle, Constants.REMOVE);
 
-        log.info(LogManager.getHeader(context, "remove_bitstream",
+        log.info(LogHelper.getHeader(context, "remove_bitstream",
                                       "bundle_id=" + bundle.getID() + ",bitstream_id=" + bitstream.getID()));
 
 
@@ -362,14 +362,14 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
             // If we have an invalid Bitstream ID, just ignore it, but log a warning
             if (bitstream == null) {
                 //This should never occur but just in case
-                log.warn(LogManager.getHeader(context, "Invalid bitstream id while changing bitstream order",
+                log.warn(LogHelper.getHeader(context, "Invalid bitstream id while changing bitstream order",
                                               "Bundle: " + bundle.getID() + ", bitstream id: " + bitstreamId));
                 continue;
             }
 
             // If we have a Bitstream not in the current list, log a warning & exit immediately
             if (!currentBitstreams.contains(bitstream)) {
-                log.warn(LogManager.getHeader(context,
+                log.warn(LogHelper.getHeader(context,
                                               "Encountered a bitstream not in this bundle while changing bitstream " +
                                                   "order. Bitstream order will not be changed.",
                                               "Bundle: " + bundle.getID() + ", bitstream id: " + bitstreamId));
@@ -380,7 +380,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
 
         // If our lists are different sizes, exit immediately
         if (updatedBitstreams.size() != currentBitstreams.size()) {
-            log.warn(LogManager.getHeader(context,
+            log.warn(LogHelper.getHeader(context,
                                           "Size of old list and new list do not match. Bitstream order will not be " +
                                               "changed.",
                                           "Bundle: " + bundle.getID()));
@@ -471,7 +471,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
     public void update(Context context, Bundle bundle) throws SQLException, AuthorizeException {
         // Check authorisation
         //AuthorizeManager.authorizeAction(ourContext, this, Constants.WRITE);
-        log.info(LogManager.getHeader(context, "update_bundle", "bundle_id="
+        log.info(LogHelper.getHeader(context, "update_bundle", "bundle_id="
             + bundle.getID()));
 
         super.update(context, bundle);
@@ -491,7 +491,7 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
 
     @Override
     public void delete(Context context, Bundle bundle) throws SQLException, AuthorizeException, IOException {
-        log.info(LogManager.getHeader(context, "delete_bundle", "bundle_id="
+        log.info(LogHelper.getHeader(context, "delete_bundle", "bundle_id="
             + bundle.getID()));
 
         authorizeService.authorizeAction(context, bundle, Constants.DELETE);

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

@@ -14,6 +14,7 @@ import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.UUID;
 import javax.annotation.Nonnull;
 import javax.persistence.Cacheable;
 import javax.persistence.CascadeType;
@@ -104,6 +105,16 @@ public class Collection extends DSpaceObject implements DSpaceObjectLegacySuppor
 
     }
 
+    /**
+     * Takes a pre-determined UUID to be passed to the object to allow for the
+     * restoration of previously defined UUID's.
+     *
+     * @param uuid Takes a uuid to be passed to the Pre-Defined UUID Generator
+     */
+    protected Collection(UUID uuid) {
+        this.predefinedUUID = uuid;
+    }
+
     @Override
     public String getName() {
         String value = getCollectionService()

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

@@ -39,7 +39,7 @@ import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.core.service.LicenseService;
 import org.dspace.discovery.DiscoverQuery;
 import org.dspace.discovery.DiscoverResult;
@@ -129,12 +129,23 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
     @Override
     public Collection create(Context context, Community community, String handle)
-        throws SQLException, AuthorizeException {
+            throws SQLException, AuthorizeException {
+        return create(context, community, handle, null);
+    }
+
+    @Override
+    public Collection create(Context context, Community community,
+                             String handle, UUID uuid) throws SQLException, AuthorizeException {
         if (community == null) {
             throw new IllegalArgumentException("Community cannot be null when creating a new collection.");
         }
 
-        Collection newCollection = collectionDAO.create(context, new Collection());
+        Collection newCollection;
+        if (uuid != null) {
+            newCollection = collectionDAO.create(context, new Collection(uuid));
+        }  else {
+            newCollection = collectionDAO.create(context, new Collection());
+        }
         //Add our newly created collection to our community, authorization checks occur in THIS method
         communityService.addCollection(context, community, newCollection);
 
@@ -146,9 +157,10 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         authorizeService.createResourcePolicy(context, newCollection, anonymousGroup, null, Constants.READ, null);
         // now create the default policies for submitted items
         authorizeService
-            .createResourcePolicy(context, newCollection, anonymousGroup, null, Constants.DEFAULT_ITEM_READ, null);
+                .createResourcePolicy(context, newCollection, anonymousGroup, null, Constants.DEFAULT_ITEM_READ, null);
         authorizeService
-            .createResourcePolicy(context, newCollection, anonymousGroup, null, Constants.DEFAULT_BITSTREAM_READ, null);
+                .createResourcePolicy(context, newCollection, anonymousGroup, null,
+                        Constants.DEFAULT_BITSTREAM_READ, null);
 
         collectionDAO.save(context, newCollection);
 
@@ -164,12 +176,12 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         }
 
         context.addEvent(new Event(Event.CREATE, Constants.COLLECTION,
-                                   newCollection.getID(), newCollection.getHandle(),
-                                   getIdentifiers(context, newCollection)));
+                newCollection.getID(), newCollection.getHandle(),
+                getIdentifiers(context, newCollection)));
 
-        log.info(LogManager.getHeader(context, "create_collection",
-                                      "collection_id=" + newCollection.getID())
-                     + ",handle=" + newCollection.getHandle());
+        log.info(LogHelper.getHeader(context, "create_collection",
+                "collection_id=" + newCollection.getID())
+                + ",handle=" + newCollection.getHandle());
 
         return newCollection;
     }
@@ -318,7 +330,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
          * whitespace.
          */
         if (value == null) {
-            clearMetadata(context, collection, field.SCHEMA, field.ELEMENT, field.QUALIFIER, Item.ANY);
+            clearMetadata(context, collection, field.schema, field.element, field.qualifier, Item.ANY);
             collection.setMetadataModified();
         } else {
             super.setMetadataSingleValue(context, collection, field, null, value);
@@ -345,7 +357,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
         if (is == null) {
             collection.setLogo(null);
-            log.info(LogManager.getHeader(context, "remove_logo",
+            log.info(LogHelper.getHeader(context, "remove_logo",
                                           "collection_id=" + collection.getID()));
         } else {
             Bitstream newLogo = bitstreamService.create(context, is);
@@ -357,7 +369,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
                 .getPoliciesActionFilter(context, collection, Constants.READ);
             authorizeService.addPolicies(context, policies, newLogo);
 
-            log.info(LogManager.getHeader(context, "set_logo",
+            log.info(LogHelper.getHeader(context, "set_logo",
                                           "collection_id=" + collection.getID() + "logo_bitstream_id="
                                               + newLogo.getID()));
         }
@@ -393,7 +405,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         try {
             workflow = workflowFactory.getWorkflow(collection);
         } catch (WorkflowConfigurationException e) {
-            log.error(LogManager.getHeader(context, "setWorkflowGroup",
+            log.error(LogHelper.getHeader(context, "setWorkflowGroup",
                     "collection_id=" + collection.getID() + " " + e.getMessage()), e);
         }
         if (!StringUtils.equals(workflowFactory.getDefaultWorkflow().getID(), workflow.getID())) {
@@ -524,6 +536,8 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
         // register this as the admin group
         collection.setAdmins(admins);
+        context.addEvent(new Event(Event.MODIFY, Constants.COLLECTION, collection.getID(),
+                                              null, getIdentifiers(context, collection)));
         return admins;
     }
 
@@ -540,6 +554,8 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
         // Remove the link to the collection table.
         collection.setAdmins(null);
+        context.addEvent(new Event(Event.MODIFY, Constants.COLLECTION, collection.getID(),
+                                              null, getIdentifiers(context, collection)));
     }
 
     @Override
@@ -569,7 +585,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
             Item template = itemService.createTemplateItem(context, collection);
             collection.setTemplateItem(template);
 
-            log.info(LogManager.getHeader(context, "create_template_item",
+            log.info(LogHelper.getHeader(context, "create_template_item",
                                           "collection_id=" + collection.getID() + ",template_item_id="
                                               + template.getID()));
         }
@@ -584,7 +600,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         Item template = collection.getTemplateItem();
 
         if (template != null) {
-            log.info(LogManager.getHeader(context, "remove_template_item",
+            log.info(LogHelper.getHeader(context, "remove_template_item",
                                           "collection_id=" + collection.getID() + ",template_item_id="
                                               + template.getID()));
             // temporarily turn off auth system, we have already checked the permission on the top of the method
@@ -604,7 +620,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         // Check authorisation
         authorizeService.authorizeAction(context, collection, Constants.ADD);
 
-        log.info(LogManager.getHeader(context, "add_item", "collection_id="
+        log.info(LogHelper.getHeader(context, "add_item", "collection_id="
             + collection.getID() + ",item_id=" + item.getID()));
 
         // Create mapping
@@ -645,7 +661,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         // Check authorisation
         canEdit(context, collection, true);
 
-        log.info(LogManager.getHeader(context, "update_collection",
+        log.info(LogHelper.getHeader(context, "update_collection",
                                       "collection_id=" + collection.getID()));
 
         super.update(context, collection);
@@ -657,8 +673,11 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
             collection.clearModified();
         }
         if (collection.isMetadataModified()) {
-            collection.clearDetails();
+            context.addEvent(new Event(Event.MODIFY_METADATA, Constants.COLLECTION, collection.getID(),
+                                         collection.getDetails(),getIdentifiers(context, collection)));
+            collection.clearModified();
         }
+        collection.clearDetails();
     }
 
     @Override
@@ -702,7 +721,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
 
     @Override
     public void delete(Context context, Collection collection) throws SQLException, AuthorizeException, IOException {
-        log.info(LogManager.getHeader(context, "delete_collection",
+        log.info(LogHelper.getHeader(context, "delete_collection",
                                       "collection_id=" + collection.getID()));
 
         // remove harvested collections.
@@ -944,7 +963,7 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
      * Finds all Indexed Collections where the current user has submit rights. If the user is an Admin,
      * this is all Indexed Collections. Otherwise, it includes those collections where
      * an indexed "submit" policy lists either the eperson or one of the eperson's groups
-     * 
+     *
      * @param context                    DSpace context
      * @param discoverQuery
      * @param community                  parent community, could be null

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

@@ -11,6 +11,7 @@ import java.util.Arrays;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.UUID;
 import javax.persistence.Cacheable;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -24,7 +25,6 @@ import javax.persistence.Table;
 import javax.persistence.Transient;
 
 import org.apache.commons.lang3.builder.HashCodeBuilder;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.comparator.NameAscendingComparator;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.CommunityService;
@@ -42,18 +42,12 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * <code>update</code> is called.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 @Entity
 @Table(name = "community")
 @Cacheable
 @org.hibernate.annotations.Cache(usage = CacheConcurrencyStrategy.NONSTRICT_READ_WRITE, include = "non-lazy")
 public class Community extends DSpaceObject implements DSpaceObjectLegacySupport {
-    /**
-     * log4j category
-     */
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Community.class);
-
     @Column(name = "community_id", insertable = false, updatable = false)
     private Integer legacyId;
 
@@ -96,6 +90,16 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
 
     }
 
+    /**
+     * Takes a pre-determined UUID to be passed to the object to allow for the
+     * restoration of previously defined UUID's.
+     *
+     * @param uuid Takes a uuid to be passed to the Pre-Defined UUID Generator
+     */
+    protected Community(UUID uuid) {
+        this.predefinedUUID = uuid;
+    }
+
     void addSubCommunity(Community subCommunity) {
         subCommunities.add(subCommunity);
         setModified();
@@ -215,7 +219,7 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
      */
     @Override
     public boolean equals(Object other) {
-        if (other == null) {
+        if (!(other instanceof Community)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(other);
@@ -223,11 +227,7 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
             return false;
         }
         final Community otherCommunity = (Community) other;
-        if (!this.getID().equals(otherCommunity.getID())) {
-            return false;
-        }
-
-        return true;
+        return this.getID().equals(otherCommunity.getID());
     }
 
     @Override

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

@@ -33,7 +33,7 @@ import org.dspace.content.service.SiteService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.I18nUtil;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.Group;
 import org.dspace.eperson.service.GroupService;
 import org.dspace.event.Event;
@@ -86,13 +86,24 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
     @Override
     public Community create(Community parent, Context context, String handle) throws SQLException, AuthorizeException {
+        return create(parent, context, handle, null);
+    }
+
+    @Override
+    public Community create(Community parent, Context context, String handle,
+                            UUID uuid) throws SQLException, AuthorizeException {
         if (!(authorizeService.isAdmin(context) ||
-            (parent != null && authorizeService.authorizeActionBoolean(context, parent, Constants.ADD)))) {
+                (parent != null && authorizeService.authorizeActionBoolean(context, parent, Constants.ADD)))) {
             throw new AuthorizeException(
-                "Only administrators can create communities");
+                    "Only administrators can create communities");
         }
 
-        Community newCommunity = communityDAO.create(context, new Community());
+        Community newCommunity;
+        if (uuid != null) {
+            newCommunity = communityDAO.create(context, new Community(uuid));
+        } else {
+            newCommunity = communityDAO.create(context, new Community());
+        }
 
         if (parent != null) {
             parent.addSubCommunity(newCommunity);
@@ -128,9 +139,9 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
                     getIdentifiers(context, newCommunity)));
         }
 
-        log.info(LogManager.getHeader(context, "create_community",
-                                      "community_id=" + newCommunity.getID())
-                     + ",handle=" + newCommunity.getHandle());
+        log.info(LogHelper.getHeader(context, "create_community",
+                "community_id=" + newCommunity.getID())
+                + ",handle=" + newCommunity.getHandle());
 
         return newCommunity;
     }
@@ -195,7 +206,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
          * whitespace.
          */
         if (value == null) {
-            clearMetadata(context, community, field.SCHEMA, field.ELEMENT, field.QUALIFIER, Item.ANY);
+            clearMetadata(context, community, field.schema, field.element, field.qualifier, Item.ANY);
             community.setMetadataModified();
         } else {
             super.setMetadataSingleValue(context, community, field, null, value);
@@ -218,7 +229,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
         // First, delete any existing logo
         Bitstream oldLogo = community.getLogo();
         if (oldLogo != null) {
-            log.info(LogManager.getHeader(context, "remove_logo",
+            log.info(LogHelper.getHeader(context, "remove_logo",
                                           "community_id=" + community.getID()));
             community.setLogo(null);
             bitstreamService.delete(context, oldLogo);
@@ -234,7 +245,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
                 .getPoliciesActionFilter(context, community, Constants.READ);
             authorizeService.addPolicies(context, policies, newLogo);
 
-            log.info(LogManager.getHeader(context, "set_logo",
+            log.info(LogHelper.getHeader(context, "set_logo",
                                           "community_id=" + community.getID() + "logo_bitstream_id="
                                               + newLogo.getID()));
         }
@@ -247,7 +258,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
         // Check authorisation
         canEdit(context, community);
 
-        log.info(LogManager.getHeader(context, "update_community",
+        log.info(LogHelper.getHeader(context, "update_community",
                                       "community_id=" + community.getID()));
 
         super.update(context, community);
@@ -287,6 +298,8 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
         // register this as the admin group
         community.setAdmins(admins);
+        context.addEvent(new Event(Event.MODIFY, Constants.COMMUNITY, community.getID(),
+                                             null, getIdentifiers(context, community)));
         return admins;
     }
 
@@ -302,6 +315,8 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
         // Remove the link to the community table.
         community.setAdmins(null);
+        context.addEvent(new Event(Event.MODIFY, Constants.COMMUNITY, community.getID(),
+                                             null, getIdentifiers(context, community)));
     }
 
     @Override
@@ -365,7 +380,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
         // Check authorisation
         authorizeService.authorizeAction(context, community, Constants.ADD);
 
-        log.info(LogManager.getHeader(context, "add_collection",
+        log.info(LogHelper.getHeader(context, "add_collection",
                                       "community_id=" + community.getID() + ",collection_id=" + collection.getID()));
 
         if (!community.getCollections().contains(collection)) {
@@ -379,17 +394,26 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
     @Override
     public Community createSubcommunity(Context context, Community parentCommunity)
-        throws SQLException, AuthorizeException {
+            throws SQLException, AuthorizeException {
         return createSubcommunity(context, parentCommunity, null);
     }
 
+
     @Override
     public Community createSubcommunity(Context context, Community parentCommunity, String handle)
-        throws SQLException, AuthorizeException {
+            throws SQLException, AuthorizeException {
+        return createSubcommunity(context, parentCommunity, handle, null);
+    }
+
+    @Override
+    public Community createSubcommunity(Context context, Community parentCommunity, String handle,
+                                        UUID uuid) throws SQLException, AuthorizeException {
         // Check authorisation
         authorizeService.authorizeAction(context, parentCommunity, Constants.ADD);
 
-        Community c = create(parentCommunity, context, handle);
+        Community c;
+        c = create(parentCommunity, context, handle, uuid);
+
         addSubcommunity(context, parentCommunity, c);
 
         return c;
@@ -401,7 +425,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
         // Check authorisation
         authorizeService.authorizeAction(context, parentCommunity, Constants.ADD);
 
-        log.info(LogManager.getHeader(context, "add_subcommunity",
+        log.info(LogHelper.getHeader(context, "add_subcommunity",
                                       "parent_comm_id=" + parentCommunity.getID() + ",child_comm_id=" + childCommunity
                                           .getID()));
 
@@ -431,7 +455,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
             collection.removeCommunity(community);
         }
 
-        log.info(LogManager.getHeader(context, "remove_collection",
+        log.info(LogHelper.getHeader(context, "remove_collection",
                                       "community_id=" + community.getID() + ",collection_id=" + collection.getID()));
 
         // Remove any mappings
@@ -451,7 +475,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
 
         rawDelete(context, childCommunity);
 
-        log.info(LogManager.getHeader(context, "remove_subcommunity",
+        log.info(LogHelper.getHeader(context, "remove_subcommunity",
                                       "parent_comm_id=" + parentCommunity.getID() + ",child_comm_id=" + childCommunity
                                           .getID()));
 
@@ -519,7 +543,7 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
      */
     protected void rawDelete(Context context, Community community)
         throws SQLException, AuthorizeException, IOException {
-        log.info(LogManager.getHeader(context, "delete_community",
+        log.info(LogHelper.getHeader(context, "delete_community",
                                       "community_id=" + community.getID()));
 
         context.addEvent(new Event(Event.DELETE, Constants.COMMUNITY, community.getID(), community.getHandle(),

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

@@ -34,12 +34,11 @@ import org.apache.logging.log4j.Logger;
  * There are four levels of granularity, depending on how much date information
  * is available: year, month, day, time.
  * <P>
- * Examples: <code>1994-05-03T15:30:24</code>,<code>1995-10-04</code>,
- * <code>2001-10</code>,<code>1975</code>
+ * Examples: {@code 1994-05-03T15:30:24}, {@code 1995-10-04},
+ * {@code 2001-10}, {@code 1975}
  *
  * @author Robert Tansley
  * @author Larry Stone
- * @version $Revision$
  */
 public class DCDate {
     /**
@@ -262,7 +261,7 @@ public class DCDate {
      * @return the year
      */
     public int getYear() {
-        return (!withinGranularity(DateGran.YEAR)) ? -1 : localCalendar.get(Calendar.YEAR);
+        return !withinGranularity(DateGran.YEAR) ? -1 : localCalendar.get(Calendar.YEAR);
     }
 
     /**
@@ -271,7 +270,7 @@ public class DCDate {
      * @return the month
      */
     public int getMonth() {
-        return (!withinGranularity(DateGran.MONTH)) ? -1 : localCalendar.get(Calendar.MONTH) + 1;
+        return !withinGranularity(DateGran.MONTH) ? -1 : localCalendar.get(Calendar.MONTH) + 1;
     }
 
     /**
@@ -280,7 +279,7 @@ public class DCDate {
      * @return the day
      */
     public int getDay() {
-        return (!withinGranularity(DateGran.DAY)) ? -1 : localCalendar.get(Calendar.DAY_OF_MONTH);
+        return !withinGranularity(DateGran.DAY) ? -1 : localCalendar.get(Calendar.DAY_OF_MONTH);
     }
 
     /**
@@ -289,7 +288,7 @@ public class DCDate {
      * @return the hour
      */
     public int getHour() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : localCalendar.get(Calendar.HOUR_OF_DAY);
+        return !withinGranularity(DateGran.TIME) ? -1 : localCalendar.get(Calendar.HOUR_OF_DAY);
     }
 
     /**
@@ -298,7 +297,7 @@ public class DCDate {
      * @return the minute
      */
     public int getMinute() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : localCalendar.get(Calendar.MINUTE);
+        return !withinGranularity(DateGran.TIME) ? -1 : localCalendar.get(Calendar.MINUTE);
     }
 
     /**
@@ -307,7 +306,7 @@ public class DCDate {
      * @return the second
      */
     public int getSecond() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : localCalendar.get(Calendar.SECOND);
+        return !withinGranularity(DateGran.TIME) ? -1 : localCalendar.get(Calendar.SECOND);
     }
 
     /**
@@ -316,7 +315,7 @@ public class DCDate {
      * @return the year
      */
     public int getYearUTC() {
-        return (!withinGranularity(DateGran.YEAR)) ? -1 : calendar.get(Calendar.YEAR);
+        return !withinGranularity(DateGran.YEAR) ? -1 : calendar.get(Calendar.YEAR);
     }
 
     /**
@@ -325,7 +324,7 @@ public class DCDate {
      * @return the month
      */
     public int getMonthUTC() {
-        return (!withinGranularity(DateGran.MONTH)) ? -1 : calendar.get(Calendar.MONTH) + 1;
+        return !withinGranularity(DateGran.MONTH) ? -1 : calendar.get(Calendar.MONTH) + 1;
     }
 
     /**
@@ -334,7 +333,7 @@ public class DCDate {
      * @return the day
      */
     public int getDayUTC() {
-        return (!withinGranularity(DateGran.DAY)) ? -1 : calendar.get(Calendar.DAY_OF_MONTH);
+        return !withinGranularity(DateGran.DAY) ? -1 : calendar.get(Calendar.DAY_OF_MONTH);
     }
 
     /**
@@ -343,7 +342,7 @@ public class DCDate {
      * @return the hour
      */
     public int getHourUTC() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : calendar.get(Calendar.HOUR_OF_DAY);
+        return !withinGranularity(DateGran.TIME) ? -1 : calendar.get(Calendar.HOUR_OF_DAY);
     }
 
     /**
@@ -352,7 +351,7 @@ public class DCDate {
      * @return the minute
      */
     public int getMinuteUTC() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : calendar.get(Calendar.MINUTE);
+        return !withinGranularity(DateGran.TIME) ? -1 : calendar.get(Calendar.MINUTE);
     }
 
     /**
@@ -361,15 +360,15 @@ public class DCDate {
      * @return the second
      */
     public int getSecondUTC() {
-        return (!withinGranularity(DateGran.TIME)) ? -1 : calendar.get(Calendar.SECOND);
+        return !withinGranularity(DateGran.TIME) ? -1 : calendar.get(Calendar.SECOND);
     }
 
-
     /**
      * Get the date as a string to put back in the Dublin Core. Use the UTC/GMT calendar version.
      *
      * @return The date as a string.
      */
+    @Override
     public String toString() {
         if (calendar == null) {
             return "null";

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

@@ -18,7 +18,6 @@ package org.dspace.content;
  * <em>FIXME:  No policy for dealing with "van"/"van der" and "Jr."</em>
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 public class DCPersonName {
     /**
@@ -89,8 +88,9 @@ public class DCPersonName {
      *
      * @return the name, suitable for putting in the database
      */
+    @Override
     public String toString() {
-        StringBuffer out = new StringBuffer();
+        StringBuilder out = new StringBuilder();
 
         if (lastName != null) {
             out.append(lastName);

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

@@ -8,10 +8,9 @@
 package org.dspace.content;
 
 /**
- * Series and report number, as stored in relation.ispartofseries
+ * Series and report number, as stored in {@code relation.ispartofseries}.
  *
  * @author Robert Tansley
- * @version $Id$
  */
 public class DCSeriesNumber {
     /**
@@ -70,6 +69,7 @@ public class DCSeriesNumber {
      *
      * @return the series and number as they should be stored in the DB
      */
+    @Override
     public String toString() {
         if (series == null) {
             return (null);

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

@@ -38,8 +38,8 @@ import org.hibernate.annotations.GenericGenerator;
 @Table(name = "dspaceobject")
 public abstract class DSpaceObject implements Serializable, ReloadableEntity<java.util.UUID> {
     @Id
-    @GeneratedValue(generator = "system-uuid")
-    @GenericGenerator(name = "system-uuid", strategy = "uuid2")
+    @GeneratedValue(generator = "predefined-uuid")
+    @GenericGenerator(name = "predefined-uuid", strategy = "org.dspace.content.PredefinedUUIDGenerator")
     @Column(name = "uuid", unique = true, nullable = false, insertable = true, updatable = false)
     protected java.util.UUID id;
 
@@ -61,7 +61,7 @@ public abstract class DSpaceObject implements Serializable, ReloadableEntity<jav
     private List<Handle> handles = new ArrayList<>();
 
     @OneToMany(fetch = FetchType.LAZY, mappedBy = "dSpaceObject", cascade = CascadeType.ALL)
-    private List<ResourcePolicy> resourcePolicies = new ArrayList<>();
+    private final List<ResourcePolicy> resourcePolicies = new ArrayList<>();
 
     /**
      * True if anything else was changed since last update()
@@ -76,6 +76,15 @@ public abstract class DSpaceObject implements Serializable, ReloadableEntity<jav
     @Transient
     private boolean modified = false;
 
+    /**
+     * This will read our predefinedUUID property to pass it along to the UUID generator
+     */
+    @Transient
+    protected UUID predefinedUUID;
+    public UUID getPredefinedUUID() {
+        return predefinedUUID;
+    }
+
     protected DSpaceObject() {
 
     }

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

@@ -13,11 +13,11 @@ import java.util.Arrays;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.Iterator;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.StringTokenizer;
 import java.util.function.Supplier;
+import java.util.stream.Collectors;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang.NotImplementedException;
@@ -435,7 +435,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     @Override
     public String getMetadataFirstValue(T dso, MetadataFieldName field, String language) {
         List<MetadataValue> metadataValues
-                = getMetadata(dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER, language);
+                = getMetadata(dso, field.schema, field.element, field.qualifier, language);
         if (CollectionUtils.isNotEmpty(metadataValues)) {
             return metadataValues.get(0).getValue();
         }
@@ -462,11 +462,11 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
             String language, String value)
             throws SQLException {
         if (value != null) {
-            clearMetadata(context, dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER,
+            clearMetadata(context, dso, field.schema, field.element, field.qualifier,
                     language);
 
-            String newValueLanguage = (Item.ANY.equals(language)) ? null : language;
-            addMetadata(context, dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER,
+            String newValueLanguage = Item.ANY.equals(language) ? null : language;
+            addMetadata(context, dso, field.schema, field.element, field.qualifier,
                     newValueLanguage, value);
             dso.setMetadataModified();
         }
@@ -610,7 +610,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
              */
             // A map created to store the latest place for each metadata field
             Map<MetadataField, Integer> fieldToLastPlace = new HashMap<>();
-            List<MetadataValue> metadataValues = new LinkedList<>();
+            List<MetadataValue> metadataValues;
             if (dso.getType() == Constants.ITEM) {
                 metadataValues = getMetadata(dso, Item.ANY, Item.ANY, Item.ANY, Item.ANY);
             } else {
@@ -643,7 +643,7 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
                     String authority = metadataValue.getAuthority();
                     String relationshipId = StringUtils.split(authority, "::")[1];
                     Relationship relationship = relationshipService.find(context, Integer.parseInt(relationshipId));
-                    if (relationship.getLeftItem() == (Item) dso) {
+                    if (relationship.getLeftItem().equals((Item) dso)) {
                         relationship.setLeftPlace(mvPlace);
                     } else {
                         relationship.setRightPlace(mvPlace);
@@ -742,12 +742,15 @@ public abstract class DSpaceObjectServiceImpl<T extends DSpaceObject> implements
     @Override
     public void moveMetadata(Context context, T dso, String schema, String element, String qualifier, int from, int to)
             throws SQLException, IllegalArgumentException {
-
         if (from == to) {
             throw new IllegalArgumentException("The \"from\" location MUST be different from \"to\" location");
         }
 
-        List<MetadataValue> list = getMetadata(dso, schema, element, qualifier);
+        List<MetadataValue> list =
+            getMetadata(dso, schema, element, qualifier).stream()
+                                                        .sorted(Comparator.comparing(MetadataValue::getPlace))
+                                                        .collect(Collectors.toList());
+
 
         if (from >= list.size() || to >= list.size() || to < 0 || from < 0) {
             throw new IllegalArgumentException(

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

@@ -78,6 +78,7 @@ public class EntityType implements ReloadableEntity<Integer> {
      *
      * @return The ID for this EntityType
      */
+    @Override
     public Integer getID() {
         return id;
     }
@@ -87,6 +88,7 @@ public class EntityType implements ReloadableEntity<Integer> {
      * @param obj   object to be compared
      * @return
      */
+    @Override
     public boolean equals(Object obj) {
         if (!(obj instanceof EntityType)) {
             return false;
@@ -97,10 +99,7 @@ public class EntityType implements ReloadableEntity<Integer> {
             return false;
         }
 
-        if (!StringUtils.equals(this.getLabel(), entityType.getLabel())) {
-            return false;
-        }
-        return true;
+        return StringUtils.equals(this.getLabel(), entityType.getLabel());
     }
 
     /**

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

@@ -17,7 +17,6 @@ import org.dspace.eperson.EPerson;
  * which stage of submission they are (in workspace or workflow system)
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 public interface InProgressSubmission extends ReloadableEntity<Integer> {
     /**
@@ -25,6 +24,7 @@ public interface InProgressSubmission extends ReloadableEntity<Integer> {
      *
      * @return the internal identifier
      */
+    @Override
     Integer getID();
 
     /**

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

@@ -13,6 +13,7 @@ import java.util.Date;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.UUID;
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -27,8 +28,6 @@ import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 import javax.persistence.Transient;
 
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.comparator.NameAscendingComparator;
 import org.dspace.content.factory.ContentServiceFactory;
 import org.dspace.content.service.ItemService;
@@ -49,17 +48,10 @@ import org.hibernate.proxy.HibernateProxyHelper;
  *
  * @author Robert Tansley
  * @author Martin Hald
- * @version $Revision$
  */
 @Entity
 @Table(name = "item")
 public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
-
-    /**
-     * log4j logger
-     */
-    private static final Logger log = LogManager.getLogger();
-
     /**
      * Wild card for Dublin Core metadata qualifiers/languages
      */
@@ -131,6 +123,16 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
 
     }
 
+    /**
+     * Takes a pre-determined UUID to be passed to the object to allow for the
+     * restoration of previously defined UUID's.
+     *
+     * @param uuid Takes a uuid to be passed to the Pre-Defined UUID Generator
+     */
+    protected Item(UUID uuid) {
+        this.predefinedUUID = uuid;
+    }
+
     /**
      * Find out if the item is part of the main archive
      *
@@ -297,7 +299,7 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
      * @return the bundles in an unordered array
      */
     public List<Bundle> getBundles(String name) {
-        List<Bundle> matchingBundles = new ArrayList<Bundle>();
+        List<Bundle> matchingBundles = new ArrayList<>();
          // now only keep bundles with matching names
         List<Bundle> bunds = getBundles();
         for (Bundle bundle : bunds) {
@@ -328,7 +330,7 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
 
     /**
      * Return <code>true</code> if <code>other</code> is the same Item as
-     * this object, <code>false</code> otherwise
+     * this object, <code>false</code> otherwise.
      *
      * @param obj object to compare to
      * @return <code>true</code> if object passed in represents the same item
@@ -336,7 +338,7 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
      */
     @Override
     public boolean equals(Object obj) {
-        if (obj == null) {
+        if (!(obj instanceof Item)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(obj);
@@ -344,10 +346,7 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
             return false;
         }
         final Item otherItem = (Item) obj;
-        if (!this.getID().equals(otherItem.getID())) {
-            return false;
-        }
-        return true;
+        return this.getID().equals(otherItem.getID());
     }
 
     @Override

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

@@ -47,7 +47,7 @@ import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.content.virtual.VirtualMetadataPopulator;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 import org.dspace.event.Event;
@@ -159,7 +159,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         Item item = itemDAO.findByID(context, Item.class, id);
         if (item == null) {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_item",
+                log.debug(LogHelper.getHeader(context, "find_item",
                                                "not_found,item_id=" + id));
             }
             return null;
@@ -167,7 +167,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
         // not null, return item
         if (log.isDebugEnabled()) {
-            log.debug(LogManager.getHeader(context, "find_item", "item_id="
+            log.debug(LogHelper.getHeader(context, "find_item", "item_id="
                 + id));
         }
 
@@ -176,16 +176,29 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
     @Override
     public Item create(Context context, WorkspaceItem workspaceItem) throws SQLException, AuthorizeException {
+        return create(context, workspaceItem, null);
+    }
+
+    @Override
+    public Item create(Context context, WorkspaceItem workspaceItem,
+                       UUID uuid) throws SQLException, AuthorizeException {
+        Collection collection = workspaceItem.getCollection();
+        authorizeService.authorizeAction(context, collection, Constants.ADD);
         if (workspaceItem.getItem() != null) {
             throw new IllegalArgumentException(
-                "Attempting to create an item for a workspace item that already contains an item");
+                    "Attempting to create an item for a workspace item that already contains an item");
+        }
+        Item item = null;
+        if (uuid != null) {
+            item = createItem(context, uuid);
+        } else {
+            item = createItem(context);
         }
-        Item item = createItem(context);
         workspaceItem.setItem(item);
 
 
-        log.info(LogManager.getHeader(context, "create_item", "item_id="
-            + item.getID()));
+        log.info(LogHelper.getHeader(context, "create_item", "item_id="
+                + item.getID()));
 
         return item;
     }
@@ -202,7 +215,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
             collection.setTemplateItem(template);
             template.setTemplateItemOf(collection);
 
-            log.info(LogManager.getHeader(context, "create_template_item",
+            log.info(LogHelper.getHeader(context, "create_template_item",
                                           "collection_id=" + collection.getID() + ",template_item_id="
                                               + template.getID()));
 
@@ -340,7 +353,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         // Check authorisation
         authorizeService.authorizeAction(context, item, Constants.ADD);
 
-        log.info(LogManager.getHeader(context, "add_bundle", "item_id="
+        log.info(LogHelper.getHeader(context, "add_bundle", "item_id="
             + item.getID() + ",bundle_id=" + bundle.getID()));
 
         // Check it's not already there
@@ -368,7 +381,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         // Check authorisation
         authorizeService.authorizeAction(context, item, Constants.REMOVE);
 
-        log.info(LogManager.getHeader(context, "remove_bundle", "item_id="
+        log.info(LogHelper.getHeader(context, "remove_bundle", "item_id="
             + item.getID() + ",bundle_id=" + bundle.getID()));
 
         context.addEvent(new Event(Event.REMOVE, Constants.ITEM, item.getID(),
@@ -418,6 +431,30 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         return bitstreamList;
     }
 
+    protected Item createItem(Context context, UUID uuid) throws SQLException, AuthorizeException {
+        Item item;
+        if (uuid != null) {
+            item = itemDAO.create(context, new Item(uuid));
+        } else {
+            item = itemDAO.create(context, new Item());
+        }
+        // set discoverable to true (default)
+        item.setDiscoverable(true);
+
+        // Call update to give the item a last modified date. OK this isn't
+        // amazingly efficient but creates don't happen that often.
+        context.turnOffAuthorisationSystem();
+        update(context, item);
+        context.restoreAuthSystemState();
+
+        context.addEvent(new Event(Event.CREATE, Constants.ITEM, item.getID(),
+                null, getIdentifiers(context, item)));
+
+        log.info(LogHelper.getHeader(context, "create_item", "item_id=" + item.getID()));
+
+        return item;
+    }
+
     protected Item createItem(Context context) throws SQLException, AuthorizeException {
         Item item = itemDAO.create(context, new Item());
         // set discoverable to true (default)
@@ -432,7 +469,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         context.addEvent(new Event(Event.CREATE, Constants.ITEM, item.getID(),
                                    null, getIdentifiers(context, item)));
 
-        log.info(LogManager.getHeader(context, "create_item", "item_id=" + item.getID()));
+        log.info(LogHelper.getHeader(context, "create_item", "item_id=" + item.getID()));
 
         return item;
     }
@@ -490,7 +527,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
             authorizeService.authorizeAction(context, item, Constants.WRITE);
         }
 
-        log.info(LogManager.getHeader(context, "update_item", "item_id="
+        log.info(LogHelper.getHeader(context, "update_item", "item_id="
             + item.getID()));
 
         super.update(context, item);
@@ -595,7 +632,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         }
 
         // Write log
-        log.info(LogManager.getHeader(context, "withdraw_item", "user="
+        log.info(LogHelper.getHeader(context, "withdraw_item", "user="
             + e.getEmail() + ",item_id=" + item.getID()));
     }
 
@@ -661,7 +698,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         }
 
         // Write log
-        log.info(LogManager.getHeader(context, "reinstate_item", "user="
+        log.info(LogHelper.getHeader(context, "reinstate_item", "user="
             + e.getEmail() + ",item_id=" + item.getID()));
     }
 
@@ -682,7 +719,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         context.addEvent(new Event(Event.DELETE, Constants.ITEM, item.getID(),
                                    item.getHandle(), getIdentifiers(context, item)));
 
-        log.info(LogManager.getHeader(context, "delete_item", "item_id="
+        log.info(LogHelper.getHeader(context, "delete_item", "item_id="
             + item.getID()));
 
         // Remove relationships
@@ -731,7 +768,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
         bundleService.delete(context, b);
 
-        log.info(LogManager.getHeader(context, "remove_bundle", "item_id="
+        log.info(LogHelper.getHeader(context, "remove_bundle", "item_id="
             + item.getID() + ",bundle_id=" + b.getID()));
         context
             .addEvent(new Event(Event.REMOVE, Constants.ITEM, item.getID(), Constants.BUNDLE, b.getID(), b.getName()));
@@ -802,7 +839,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         adjustItemPolicies(context, item, collection);
         adjustBundleBitstreamPolicies(context, item, collection);
 
-        log.debug(LogManager.getHeader(context, "item_inheritCollectionDefaultPolicies",
+        log.debug(LogHelper.getHeader(context, "item_inheritCollectionDefaultPolicies",
                                        "item_id=" + item.getID()));
     }
 
@@ -890,7 +927,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
         // If we are moving from the owning collection, update that too
         if (isOwningCollection(item, from)) {
             // Update the owning collection
-            log.info(LogManager.getHeader(context, "move_item",
+            log.info(LogHelper.getHeader(context, "move_item",
                                           "item_id=" + item.getID() + ", from " +
                                               "collection_id=" + from.getID() + " to " +
                                               "collection_id=" + to.getID()));
@@ -898,7 +935,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
             // If applicable, update the item policies
             if (inheritDefaultPolicies) {
-                log.info(LogManager.getHeader(context, "move_item",
+                log.info(LogHelper.getHeader(context, "move_item",
                                               "Updating item with inherited policies"));
                 inheritCollectionDefaultPolicies(context, item, to);
             }

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

@@ -32,7 +32,6 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * metadata element belongs in a field.
  *
  * @author Martin Hald
- * @version $Revision$
  * @see org.dspace.content.MetadataValue
  * @see org.dspace.content.MetadataSchema
  */
@@ -77,6 +76,7 @@ public class MetadataField implements ReloadableEntity<Integer> {
      *
      * @return metadata field id
      */
+    @Override
     public Integer getID() {
         return id;
     }
@@ -164,7 +164,7 @@ public class MetadataField implements ReloadableEntity<Integer> {
      */
     @Override
     public boolean equals(Object obj) {
-        if (obj == null) {
+        if (!(obj instanceof MetadataField)) {
             return false;
         }
         Class<?> objClass = HibernateProxyHelper.getClassWithoutInitializingProxy(obj);
@@ -175,10 +175,7 @@ public class MetadataField implements ReloadableEntity<Integer> {
         if (!this.getID().equals(other.getID())) {
             return false;
         }
-        if (!getMetadataSchema().equals(other.getMetadataSchema())) {
-            return false;
-        }
-        return true;
+        return getMetadataSchema().equals(other.getMetadataSchema());
     }
 
     @Override

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

@@ -17,13 +17,13 @@ import javax.annotation.Nonnull;
  */
 public class MetadataFieldName {
     /** Name of the metadata schema which defines this field.  Never null. */
-    public final String SCHEMA;
+    public final String schema;
 
     /** Element name of this field.  Never null. */
-    public final String ELEMENT;
+    public final String element;
 
     /** Qualifier name of this field.  May be {@code null}. */
-    public final String QUALIFIER;
+    public final String qualifier;
 
     /**
      * Initialize a tuple of (schema, element, qualifier) to name a metadata field.
@@ -40,9 +40,9 @@ public class MetadataFieldName {
             throw new NullPointerException("Element must not be null.");
         }
 
-        SCHEMA = schema;
-        ELEMENT = element;
-        QUALIFIER = qualifier;
+        this.schema = schema;
+        this.element = element;
+        this.qualifier = qualifier;
     }
 
     /**
@@ -59,9 +59,9 @@ public class MetadataFieldName {
             throw new NullPointerException("Element must not be null.");
         }
 
-        SCHEMA = schema;
-        ELEMENT = element;
-        QUALIFIER = null;
+        this.schema = schema;
+        this.element = element;
+        qualifier = null;
     }
 
     /**
@@ -79,9 +79,9 @@ public class MetadataFieldName {
             throw new IllegalArgumentException("Element must not be null.");
         }
 
-        SCHEMA = schema.getName();
-        ELEMENT = element;
-        QUALIFIER = qualifier;
+        this.schema = schema.getName();
+        this.element = element;
+        this.qualifier = qualifier;
     }
 
     /**
@@ -98,9 +98,9 @@ public class MetadataFieldName {
             throw new IllegalArgumentException("Element must not be null.");
         }
 
-        SCHEMA = schema.getName();
-        ELEMENT = element;
-        QUALIFIER = null;
+        this.schema = schema.getName();
+        this.element = element;
+        qualifier = null;
     }
 
     /**
@@ -110,9 +110,9 @@ public class MetadataFieldName {
      */
     public MetadataFieldName(@Nonnull String name) {
         String[] elements = parse(name);
-        SCHEMA = elements[0];
-        ELEMENT = elements[1];
-        QUALIFIER = elements[2];
+        schema = elements[0];
+        element = elements[1];
+        qualifier = elements[2];
     }
 
     /**
@@ -138,17 +138,17 @@ public class MetadataFieldName {
 
     /**
      * Format a dotted-atoms representation of this field name.
-     * @return SCHEMA.ELEMENT.QUALIFIER
+     * @return schema.element.qualifier
      */
     @Override
     public String toString() {
         StringBuilder buffer = new StringBuilder(32);
-        buffer.append(SCHEMA)
+        buffer.append(schema)
                 .append('.')
-                .append(ELEMENT);
-        if (null != QUALIFIER) {
+                .append(element);
+        if (null != qualifier) {
             buffer.append('.')
-                    .append(QUALIFIER);
+                    .append(qualifier);
         }
         return buffer.toString();
     }

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

@@ -25,7 +25,7 @@ import org.dspace.content.service.MetadataValueService;
 import org.dspace.content.service.SiteService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.discovery.indexobject.IndexableMetadataField;
 import org.dspace.event.Event;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -83,7 +83,7 @@ public class MetadataFieldServiceImpl implements MetadataFieldService {
         metadataField = metadataFieldDAO.create(context, metadataField);
         metadataFieldDAO.save(context, metadataField);
 
-        log.info(LogManager.getHeader(context, "create_metadata_field",
+        log.info(LogHelper.getHeader(context, "create_metadata_field",
                                       "metadata_field_id=" + metadataField.getID()));
         // Update the index of type metadatafield
         this.triggerEventToUpdateIndex(context, metadataField.getID());
@@ -155,7 +155,7 @@ public class MetadataFieldServiceImpl implements MetadataFieldService {
 
         metadataFieldDAO.save(context, metadataField);
 
-        log.info(LogManager.getHeader(context, "update_metadatafieldregistry",
+        log.info(LogHelper.getHeader(context, "update_metadatafieldregistry",
                                       "metadata_field_id=" + metadataField.getID() + "element=" + metadataField
                                           .getElement()
                                           + "qualifier=" + metadataField.getQualifier()));
@@ -187,7 +187,7 @@ public class MetadataFieldServiceImpl implements MetadataFieldService {
                 .toString() + " cannot be deleted as it is currently used by one or more objects.");
         }
 
-        log.info(LogManager.getHeader(context, "delete_metadata_field",
+        log.info(LogHelper.getHeader(context, "delete_metadata_field",
                                       "metadata_field_id=" + metadataField.getID()));
         // Update the index of type metadatafield
         this.triggerEventToUpdateIndex(context, metadataField.getID());

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

@@ -30,7 +30,6 @@ import org.hibernate.proxy.HibernateProxyHelper;
  * </p>
  *
  * @author Martin Hald
- * @version $Revision$
  * @see org.dspace.content.MetadataValue
  * @see org.dspace.content.MetadataField
  */
@@ -129,6 +128,7 @@ public class MetadataSchema implements ReloadableEntity<Integer> {
      *
      * @return schema record key
      */
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -17,7 +17,7 @@ import org.dspace.content.dao.MetadataSchemaDAO;
 import org.dspace.content.service.MetadataFieldService;
 import org.dspace.content.service.MetadataSchemaService;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -74,7 +74,7 @@ public class MetadataSchemaServiceImpl implements MetadataSchemaService {
         metadataSchema.setNamespace(namespace);
         metadataSchema.setName(name);
         metadataSchemaDAO.save(context, metadataSchema);
-        log.info(LogManager.getHeader(context, "create_metadata_schema",
+        log.info(LogHelper.getHeader(context, "create_metadata_schema",
                                       "metadata_schema_id="
                                           + metadataSchema.getID()));
         return metadataSchema;
@@ -106,7 +106,7 @@ public class MetadataSchemaServiceImpl implements MetadataSchemaService {
                                                      + " unique");
         }
         metadataSchemaDAO.save(context, metadataSchema);
-        log.info(LogManager.getHeader(context, "update_metadata_schema",
+        log.info(LogHelper.getHeader(context, "update_metadata_schema",
                                       "metadata_schema_id=" + metadataSchema.getID() + "namespace="
                                           + metadataSchema.getNamespace() + "name=" + metadataSchema.getName()));
     }
@@ -125,7 +125,7 @@ public class MetadataSchemaServiceImpl implements MetadataSchemaService {
 
         metadataSchemaDAO.delete(context, metadataSchema);
 
-        log.info(LogManager.getHeader(context, "delete_metadata_schema",
+        log.info(LogHelper.getHeader(context, "delete_metadata_schema",
                 "metadata_schema_id=" + metadataSchema.getID()));
     }
 

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

@@ -46,7 +46,7 @@ public class MetadataValue implements ReloadableEntity<Integer> {
     @Column(name = "metadata_value_id")
     @GeneratedValue(strategy = GenerationType.SEQUENCE, generator = "metadatavalue_seq")
     @SequenceGenerator(name = "metadatavalue_seq", sequenceName = "metadatavalue_seq", allocationSize = 1)
-    private Integer id;
+    private final Integer id;
 
     /**
      * The primary key for the metadata value
@@ -104,6 +104,7 @@ public class MetadataValue implements ReloadableEntity<Integer> {
      *
      * @return metadata value ID
      */
+    @Override
     public Integer getID() {
         return id;
     }
@@ -249,10 +250,7 @@ public class MetadataValue implements ReloadableEntity<Integer> {
         if (!this.getID().equals(other.getID())) {
             return false;
         }
-        if (!this.getDSpaceObject().getID().equals(other.getDSpaceObject().getID())) {
-            return false;
-        }
-        return true;
+        return this.getDSpaceObject().getID().equals(other.getDSpaceObject().getID());
     }
 
     @Override

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

@@ -21,7 +21,7 @@ import org.dspace.content.service.DSpaceObjectService;
 import org.dspace.content.service.MetadataValueService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
@@ -80,7 +80,7 @@ public class MetadataValueServiceImpl implements MetadataValueService {
     @Override
     public void update(Context context, MetadataValue metadataValue) throws SQLException {
         metadataValueDAO.save(context, metadataValue);
-        log.info(LogManager.getHeader(context, "update_metadatavalue",
+        log.info(LogHelper.getHeader(context, "update_metadatavalue",
                                       "metadata_value_id=" + metadataValue.getID()));
 
     }
@@ -102,7 +102,7 @@ public class MetadataValueServiceImpl implements MetadataValueService {
 
     @Override
     public void delete(Context context, MetadataValue metadataValue) throws SQLException {
-        log.info(LogManager.getHeader(context, "delete_metadata_value",
+        log.info(LogHelper.getHeader(context, "delete_metadata_value",
                                       " metadata_value_id=" + metadataValue.getID()));
         metadataValueDAO.delete(context, metadataValue);
     }

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

@@ -0,0 +1,33 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content;
+
+import java.io.Serializable;
+import java.util.UUID;
+
+import org.hibernate.engine.spi.SharedSessionContractImplementor;
+import org.hibernate.id.UUIDGenerator;
+
+/**
+ * Allows DSpaceObjects to provide a pre-determined UUID
+ *
+ * @author April Herron
+ */
+public class PredefinedUUIDGenerator extends UUIDGenerator {
+
+    @Override
+    public Serializable generate(SharedSessionContractImplementor session, Object object) {
+        if (object instanceof DSpaceObject) {
+            UUID uuid = ((DSpaceObject) object).getPredefinedUUID();
+            if (uuid != null) {
+                return uuid;
+            }
+        }
+        return super.generate(session, object);
+    }
+}

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

@@ -220,6 +220,7 @@ public class Relationship implements ReloadableEntity<Integer> {
      * Standard getter for the ID for this Relationship
      * @return  The ID of this relationship
      */
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -8,9 +8,9 @@
 package org.dspace.content;
 
 import java.sql.SQLException;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.Comparator;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.UUID;
 
@@ -251,7 +251,7 @@ public class RelationshipServiceImpl implements RelationshipService {
         }
         List<Relationship> rightRelationships = findByItemAndRelationshipType(context, itemToProcess, relationshipType,
                                                                               isLeft);
-        if (maxCardinality != null && rightRelationships.size() >= maxCardinality) {
+        if (rightRelationships.size() >= maxCardinality) {
             return false;
         }
         return true;
@@ -267,6 +267,7 @@ public class RelationshipServiceImpl implements RelationshipService {
         return StringUtils.equals(leftEntityType, entityTypeToProcess.getLabel());
     }
 
+    @Override
     public Relationship find(Context context, int id) throws SQLException {
         Relationship relationship = relationshipDAO.findByID(context, Relationship.class, id);
         return relationship;
@@ -340,7 +341,7 @@ public class RelationshipServiceImpl implements RelationshipService {
     @Override
     public void delete(Context context, Relationship relationship, boolean copyToLeftItem, boolean copyToRightItem)
         throws SQLException, AuthorizeException {
-        log.info(org.dspace.core.LogManager.getHeader(context, "delete_relationship",
+        log.info(org.dspace.core.LogHelper.getHeader(context, "delete_relationship",
                                                       "relationship_id=" + relationship.getID() + "&" +
                                                           "copyMetadataValuesToLeftItem=" + copyToLeftItem + "&" +
                                                           "copyMetadataValuesToRightItem=" + copyToRightItem));
@@ -357,7 +358,7 @@ public class RelationshipServiceImpl implements RelationshipService {
     @Override
     public void forceDelete(Context context, Relationship relationship, boolean copyToLeftItem, boolean copyToRightItem)
         throws SQLException, AuthorizeException {
-        log.info(org.dspace.core.LogManager.getHeader(context, "delete_relationship",
+        log.info(org.dspace.core.LogHelper.getHeader(context, "delete_relationship",
                                                       "relationship_id=" + relationship.getID() + "&" +
                                                           "copyMetadataValuesToLeftItem=" + copyToLeftItem + "&" +
                                                           "copyMetadataValuesToRightItem=" + copyToRightItem));
@@ -408,7 +409,7 @@ public class RelationshipServiceImpl implements RelationshipService {
             // Set a limit on the total depth of relationships to traverse during a relationship change
             int maxDepth = configurationService.getIntProperty("relationship.update.relateditems.maxdepth", 5);
             // This is the list containing all items which will have changes to their virtual metadata
-            List<Item> itemsToUpdate = new LinkedList<>();
+            List<Item> itemsToUpdate = new ArrayList<>();
             itemsToUpdate.add(relationship.getLeftItem());
             itemsToUpdate.add(relationship.getRightItem());
 

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

@@ -208,7 +208,7 @@ public class RelationshipType implements ReloadableEntity<Integer> {
 
     /**
      * Standard setter for the leftMinCardinality Integer for this RelationshipType
-     * @param leftMinCardinality    The leftMinCardinality Integer that this RelationshipType should recieve
+     * @param leftMinCardinality    The leftMinCardinality Integer that this RelationshipType should receive
      */
     public void setLeftMinCardinality(Integer leftMinCardinality) {
         this.leftMinCardinality = leftMinCardinality;
@@ -224,7 +224,7 @@ public class RelationshipType implements ReloadableEntity<Integer> {
 
     /**
      * Standard setter for the leftMaxCardinality Integer for this RelationshipType
-     * @param leftMaxCardinality    The leftMaxCardinality Integer that this RelationshipType should recieve
+     * @param leftMaxCardinality    The leftMaxCardinality Integer that this RelationshipType should receive
      */
     public void setLeftMaxCardinality(Integer leftMaxCardinality) {
         this.leftMaxCardinality = leftMaxCardinality;
@@ -240,7 +240,7 @@ public class RelationshipType implements ReloadableEntity<Integer> {
 
     /**
      * Standard setter for the rightMinCardinality Integer for this RelationshipType
-     * @param rightMinCardinality    The rightMinCardinality Integer that this RelationshipType should recieve
+     * @param rightMinCardinality    The rightMinCardinality Integer that this RelationshipType should receive
      */
     public void setRightMinCardinality(Integer rightMinCardinality) {
         this.rightMinCardinality = rightMinCardinality;
@@ -256,7 +256,7 @@ public class RelationshipType implements ReloadableEntity<Integer> {
 
     /**
      * Standard setter for the rightMaxCardinality Integer for this RelationshipType
-     * @param rightMaxCardinality    The rightMaxCardinality Integer that this RelationshipType should recieve
+     * @param rightMaxCardinality    The rightMaxCardinality Integer that this RelationshipType should receive
      */
     public void setRightMaxCardinality(Integer rightMaxCardinality) {
         this.rightMaxCardinality = rightMaxCardinality;
@@ -318,6 +318,7 @@ public class RelationshipType implements ReloadableEntity<Integer> {
      * Standard getter for the ID of this RelationshipType
      * @return  The ID of this RelationshipType
      */
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -12,6 +12,7 @@ import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
+import java.util.UUID;
 
 import org.apache.logging.log4j.Logger;
 import org.dspace.app.util.DCInputsReaderException;
@@ -25,7 +26,7 @@ import org.dspace.content.service.ItemService;
 import org.dspace.content.service.WorkspaceItemService;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
-import org.dspace.core.LogManager;
+import org.dspace.core.LogHelper;
 import org.dspace.eperson.EPerson;
 import org.dspace.event.Event;
 import org.dspace.workflow.WorkflowItem;
@@ -66,12 +67,12 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
 
         if (workspaceItem == null) {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_workspace_item",
+                log.debug(LogHelper.getHeader(context, "find_workspace_item",
                                                "not_found,workspace_item_id=" + id));
             }
         } else {
             if (log.isDebugEnabled()) {
-                log.debug(LogManager.getHeader(context, "find_workspace_item",
+                log.debug(LogHelper.getHeader(context, "find_workspace_item",
                                                "workspace_item_id=" + id));
             }
         }
@@ -80,6 +81,12 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
 
     @Override
     public WorkspaceItem create(Context context, Collection collection, boolean template)
+            throws AuthorizeException, SQLException {
+        return create(context, collection, null, template);
+    }
+
+    @Override
+    public WorkspaceItem create(Context context, Collection collection, UUID uuid, boolean template)
         throws AuthorizeException, SQLException {
         // Check the user has permission to ADD to the collection
         authorizeService.authorizeAction(context, collection, Constants.ADD);
@@ -89,7 +96,12 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
 
 
         // Create an item
-        Item item = itemService.create(context, workspaceItem);
+        Item item;
+        if (uuid != null) {
+            item = itemService.create(context, workspaceItem, uuid);
+        } else {
+            item = itemService.create(context, workspaceItem);
+        }
         item.setSubmitter(context.getCurrentUser());
 
         // Now create the policies for the submitter to modify item and contents
@@ -126,7 +138,7 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
         itemService.update(context, item);
         workspaceItem.setItem(item);
 
-        log.info(LogManager.getHeader(context, "create_workspace_item",
+        log.info(LogHelper.getHeader(context, "create_workspace_item",
                                       "workspace_item_id=" + workspaceItem.getID()
                                           + "item_id=" + item.getID() + "collection_id="
                                           + collection.getID()));
@@ -191,7 +203,7 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
     public void update(Context context, WorkspaceItem workspaceItem) throws SQLException, AuthorizeException {
         // Authorisation is checked by the item.update() method below
 
-        log.info(LogManager.getHeader(context, "update_workspace_item",
+        log.info(LogHelper.getHeader(context, "update_workspace_item",
                                       "workspace_item_id=" + workspaceItem.getID()));
 
         // Update the item
@@ -219,7 +231,7 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
                                              + "original submitter to delete a workspace item");
         }
 
-        log.info(LogManager.getHeader(context, "delete_workspace_item",
+        log.info(LogHelper.getHeader(context, "delete_workspace_item",
                                       "workspace_item_id=" + workspaceItem.getID() + "item_id=" + item.getID()
                                           + "collection_id=" + workspaceItem.getCollection().getID()));
 
@@ -256,7 +268,7 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
         Item item = workspaceItem.getItem();
         authorizeService.authorizeAction(context, item, Constants.WRITE);
 
-        log.info(LogManager.getHeader(context, "delete_workspace_item",
+        log.info(LogHelper.getHeader(context, "delete_workspace_item",
                                       "workspace_item_id=" + workspaceItem.getID() + "item_id=" + item.getID()
                                           + "collection_id=" + workspaceItem.getCollection().getID()));
 

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

@@ -44,17 +44,16 @@ import org.jdom.xpath.XPath;
 /**
  * ORE ingestion crosswalk
  * <p>
- * Processes an Atom-encoded ORE resource map and attemps to interpret it as a DSpace item
+ * Processes an Atom-encoded ORE resource map and attempts to interpret it as a DSpace item.
  *
  * @author Alexey Maslov
- * @version $Revision: 1 $
  */
 public class OREIngestionCrosswalk
     implements IngestionCrosswalk {
     /**
      * log4j category
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(OREDisseminationCrosswalk.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger();
 
     /* Namespaces */
     public static final Namespace ATOM_NS =
@@ -149,7 +148,7 @@ public class OREIngestionCrosswalk
                 xpathDesc.addNamespace(RDF_NS);
                 desc = (Element) xpathDesc.selectSingleNode(doc);
             } catch (JDOMException e) {
-                e.printStackTrace();
+                log.warn("Could not find description for {}", href, e);
             }
 
             if (desc != null && desc.getChild("type", RDF_NS).getAttributeValue("resource", RDF_NS)

dspace-api/src/main/java/org/dspace/content/dao/RelationshipTypeDAO.java

@@ -122,12 +122,13 @@ public interface RelationshipTypeDAO extends GenericDAO<RelationshipType> {
             throws SQLException;
 
     /**
-     * Count all relationship types that matches provided EntityType object on any side of relationship
+     * Count all RelationshipType objects for which the given EntityType
+     * is equal to either the leftType or the rightType
      * 
-     * @param context         The relevant DSpace context
-     * @param entityType      The EntityType object that will be used to check on
-     * @return
-     * @throws SQLException   If database error
+     * @param context        DSpace context object
+     * @param entityType     The EntityType object used to check the leftType and rightType properties
+     * @return               Total RelationshipType objects
+     * @throws SQLException  If database error
      */
     public int countByEntityType(Context context, EntityType entityType) throws SQLException;
 

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

@@ -23,7 +23,7 @@ import org.dspace.core.Context;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the BitstreamFormat object.
- * This class is responsible for all database calls for the BitstreamFormat object and is autowired by spring
+ * This class is responsible for all database calls for the BitstreamFormat object and is autowired by Spring.
  * This class should never be accessed directly.
  *
  * @author kevinvandevelde at atmire.com
@@ -86,7 +86,7 @@ public class BitstreamFormatDAOImpl extends AbstractHibernateDAO<BitstreamFormat
         Root<BitstreamFormat> bitstreamFormatRoot = criteriaQuery.from(BitstreamFormat.class);
         criteriaQuery.select(bitstreamFormatRoot);
         criteriaQuery.where(criteriaBuilder.equal(bitstreamFormatRoot.get(BitstreamFormat_.shortDescription), desc));
-        return uniqueResult(context, criteriaQuery, false, BitstreamFormat.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, BitstreamFormat.class);
     }
 
     @Override

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

@@ -9,7 +9,7 @@ package org.dspace.content.dao.impl;
 
 import java.sql.SQLException;
 import java.util.AbstractMap;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import javax.persistence.Query;
@@ -34,7 +34,7 @@ import org.dspace.eperson.Group;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the Collection object.
- * This class is responsible for all database calls for the Collection object and is autowired by spring
+ * This class is responsible for all database calls for the Collection object and is autowired by Spring.
  * This class should never be accessed directly.
  *
  * @author kevinvandevelde at atmire.com
@@ -95,7 +95,7 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
         Root<Collection> collectionRoot = criteriaQuery.from(Collection.class);
         criteriaQuery.select(collectionRoot);
         criteriaQuery.where(criteriaBuilder.equal(collectionRoot.get(Collection_.template), item));
-        return uniqueResult(context, criteriaQuery, false, Collection.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, Collection.class);
     }
 
     @Override
@@ -119,7 +119,7 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
         CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Collection.class);
         Root<Collection> collectionRoot = criteriaQuery.from(Collection.class);
         Join<Collection, ResourcePolicy> join = collectionRoot.join("resourcePolicies");
-        List<Predicate> orPredicates = new LinkedList<Predicate>();
+        List<Predicate> orPredicates = new ArrayList<>(actions.size());
         for (Integer action : actions) {
             orPredicates.add(criteriaBuilder.equal(join.get(ResourcePolicy_.actionId), action));
         }
@@ -176,7 +176,7 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
         Query query = createQuery(context, q);
 
         List<Object[]> list = query.getResultList();
-        List<Map.Entry<Collection, Long>> returnList = new LinkedList<>();
+        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]));
         }

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

@@ -18,6 +18,15 @@ import org.dspace.content.dao.EntityTypeDAO;
 import org.dspace.core.AbstractHibernateDAO;
 import org.dspace.core.Context;
 
+/**
+ * Hibernate implementation of the Database Access Object interface class for
+ * the EntityType object.
+ * This class is responsible for all database calls for the EntityType object
+ * and is autowired by Spring.
+ * This class should never be accessed directly.
+ *
+ * @author kevinvandevelde at atmire.com
+ */
 public class EntityTypeDAOImpl extends AbstractHibernateDAO<EntityType> implements EntityTypeDAO {
 
     @Override
@@ -28,6 +37,6 @@ public class EntityTypeDAOImpl extends AbstractHibernateDAO<EntityType> implemen
         criteriaQuery.select(entityTypeRoot);
         criteriaQuery.where(criteriaBuilder.equal(criteriaBuilder.upper(entityTypeRoot.get(EntityType_.label)),
                                                   entityType.toUpperCase()));
-        return uniqueResult(context, criteriaQuery, true, EntityType.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, true, EntityType.class);
     }
 }

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

@@ -32,6 +32,7 @@ import org.dspace.eperson.EPerson;
 import org.hibernate.Criteria;
 import org.hibernate.criterion.Criterion;
 import org.hibernate.criterion.DetachedCriteria;
+import org.hibernate.criterion.Order;
 import org.hibernate.criterion.Projections;
 import org.hibernate.criterion.Property;
 import org.hibernate.criterion.Restrictions;
@@ -54,14 +55,14 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
 
     @Override
     public Iterator<Item> findAll(Context context, boolean archived) throws SQLException {
-        Query query = createQuery(context, "FROM Item WHERE inArchive= :in_archive");
+        Query query = createQuery(context, "FROM Item WHERE inArchive=:in_archive ORDER BY id");
         query.setParameter("in_archive", archived);
         return iterate(query);
     }
 
     @Override
     public Iterator<Item> findAll(Context context, boolean archived, int limit, int offset) throws SQLException {
-        Query query = createQuery(context, "FROM Item WHERE inArchive= :in_archive");
+        Query query = createQuery(context, "FROM Item WHERE inArchive=:in_archive ORDER BY id");
         query.setParameter("in_archive", archived);
         query.setFirstResult(offset);
         query.setMaxResults(limit);
@@ -71,7 +72,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
 
     @Override
     public Iterator<Item> findAll(Context context, boolean archived, boolean withdrawn) throws SQLException {
-        Query query = createQuery(context, "FROM Item WHERE inArchive= :in_archive or withdrawn = :withdrawn");
+        Query query = createQuery(context,
+                "FROM Item WHERE inArchive=:in_archive or withdrawn=:withdrawn ORDER BY id");
         query.setParameter("in_archive", archived);
         query.setParameter("withdrawn", withdrawn);
         return iterate(query);
@@ -89,6 +91,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
         if (lastModified != null) {
             queryStr.append(" AND last_modified > :last_modified");
         }
+        queryStr.append(" ORDER BY i.id");
 
         Query query = createQuery(context, queryStr.toString());
         query.setParameter("in_archive", archived);
@@ -102,7 +105,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
 
     @Override
     public Iterator<Item> findBySubmitter(Context context, EPerson eperson) throws SQLException {
-        Query query = createQuery(context, "FROM Item WHERE inArchive= :in_archive and submitter= :submitter");
+        Query query = createQuery(context,
+                "FROM Item WHERE inArchive=:in_archive and submitter=:submitter ORDER BY id");
         query.setParameter("in_archive", true);
         query.setParameter("submitter", eperson);
         return iterate(query);
@@ -114,7 +118,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
         if (!retrieveAllItems) {
             return findBySubmitter(context, eperson);
         }
-        Query query = createQuery(context, "FROM Item WHERE submitter= :submitter");
+        Query query = createQuery(context, "FROM Item WHERE submitter=:submitter ORDER BY id");
         query.setParameter("submitter", eperson);
         return iterate(query);
     }
@@ -146,7 +150,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
         if (value != null) {
             hqlQueryString += " AND STR(metadatavalue.value) = :text_value";
         }
-        Query query = createQuery(context, hqlQueryString);
+        Query query = createQuery(context, hqlQueryString + " ORDER BY item.id");
 
         query.setParameter("in_archive", inArchive);
         query.setParameter("metadata_field", metadataField);
@@ -262,6 +266,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
                 criteria.add(Subqueries.notExists(subcriteria));
             }
         }
+        criteria.addOrder(Order.asc("item.id"));
+
         log.debug(String.format("Running custom query with %d filters", index));
 
         return ((List<Item>) criteria.list()).iterator();
@@ -274,7 +280,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
         Query query = createQuery(context,
                   "SELECT item FROM Item as item join item.metadata metadatavalue " +
                   "WHERE item.inArchive=:in_archive AND metadatavalue.metadataField = :metadata_field AND " +
-                      "metadatavalue.authority = :authority");
+                      "metadatavalue.authority = :authority ORDER BY item.id");
         query.setParameter("in_archive", inArchive);
         query.setParameter("metadata_field", metadataField);
         query.setParameter("authority", authority);
@@ -286,7 +292,7 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
                                                    Integer offset) throws SQLException {
         Query query = createQuery(context,
               "select i from Item i join i.collections c " +
-              "WHERE :collection IN c AND i.inArchive=:in_archive");
+              "WHERE :collection IN c AND i.inArchive=:in_archive ORDER BY i.id");
         query.setParameter("collection", collection);
         query.setParameter("in_archive", true);
         if (offset != null) {
@@ -309,6 +315,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
                 criteriaBuilder.notEqual(itemRoot.get(Item_.owningCollection), collection),
                 criteriaBuilder.isMember(collection, itemRoot.get(Item_.collections)),
                 criteriaBuilder.isTrue(itemRoot.get(Item_.inArchive))));
+        criteriaQuery.orderBy(criteriaBuilder.asc(itemRoot.get(Item_.id)));
+        criteriaQuery.groupBy(itemRoot.get(Item_.id));
         return list(context, criteriaQuery, false, Item.class, limit, offset).iterator();
     }
 
@@ -327,7 +335,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
 
     @Override
     public Iterator<Item> findAllByCollection(Context context, Collection collection) throws SQLException {
-        Query query = createQuery(context, "select i from Item i join i.collections c WHERE :collection IN c");
+        Query query = createQuery(context,
+                "select i from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
         query.setParameter("collection", collection);
 
         return iterate(query);
@@ -336,7 +345,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
     @Override
     public Iterator<Item> findAllByCollection(Context context, Collection collection, Integer limit, Integer offset)
         throws SQLException {
-        Query query = createQuery(context, "select i from Item i join i.collections c WHERE :collection IN c");
+        Query query = createQuery(context,
+                "select i from Item i join i.collections c WHERE :collection IN c ORDER BY i.id");
         query.setParameter("collection", collection);
 
         if (offset != null) {
@@ -381,7 +391,8 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
     @Override
     public Iterator<Item> findByLastModifiedSince(Context context, Date since)
         throws SQLException {
-        Query query = createQuery(context, "SELECT i FROM item i WHERE last_modified > :last_modified");
+        Query query = createQuery(context,
+                "SELECT i FROM item i WHERE last_modified > :last_modified ORDER BY id");
         query.setParameter("last_modified", since, TemporalType.TIMESTAMP);
         return iterate(query);
     }

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

@@ -8,7 +8,7 @@
 package org.dspace.content.dao.impl;
 
 import java.sql.SQLException;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 import javax.persistence.Query;
 import javax.persistence.criteria.CriteriaBuilder;
@@ -63,7 +63,7 @@ public class MetadataSchemaDAOImpl extends AbstractHibernateDAO<MetadataSchema>
         Root<MetadataSchema> metadataSchemaRoot = criteriaQuery.from(MetadataSchema.class);
         criteriaQuery.select(metadataSchemaRoot);
 
-        List<javax.persistence.criteria.Order> orderList = new LinkedList<>();
+        List<javax.persistence.criteria.Order> orderList = new ArrayList<>();
         orderList.add(criteriaBuilder.asc(metadataSchemaRoot.get(MetadataSchema_.id)));
         criteriaQuery.orderBy(orderList);
 

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

@@ -8,6 +8,7 @@
 package org.dspace.content.dao.impl;
 
 import java.sql.SQLException;
+import java.util.LinkedList;
 import java.util.List;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -20,6 +21,15 @@ import org.dspace.content.dao.RelationshipTypeDAO;
 import org.dspace.core.AbstractHibernateDAO;
 import org.dspace.core.Context;
 
+/**
+ * Hibernate implementation of the Database Access Object interface class for
+ * the RelationshipType object.
+ * This class is responsible for all database calls for the RelationshipType
+ * object and is autowired by Spring.
+ * This class should never be accessed directly.
+ *
+ * @author kevinvandevelde at atmire.com
+ */
 public class RelationshipTypeDAOImpl extends AbstractHibernateDAO<RelationshipType> implements RelationshipTypeDAO {
 
     @Override
@@ -36,7 +46,7 @@ public class RelationshipTypeDAOImpl extends AbstractHibernateDAO<RelationshipTy
                 criteriaBuilder.equal(relationshipTypeRoot.get(RelationshipType_.rightType), rightType),
                 criteriaBuilder.equal(relationshipTypeRoot.get(RelationshipType_.leftwardType), leftwardType),
                 criteriaBuilder.equal(relationshipTypeRoot.get(RelationshipType_.rightwardType), rightwardType)));
-        return uniqueResult(context, criteriaQuery, false, RelationshipType.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, RelationshipType.class);
     }
 
     @Override
@@ -83,7 +93,9 @@ public class RelationshipTypeDAOImpl extends AbstractHibernateDAO<RelationshipTy
                                    .equal(relationshipTypeRoot.get(RelationshipType_.rightType), entityType)
             )
         );
-        criteriaQuery.orderBy(criteriaBuilder.asc(relationshipTypeRoot.get(RelationshipType_.ID)));
+        List<javax.persistence.criteria.Order> orderList = new LinkedList<>();
+        orderList.add(criteriaBuilder.asc(relationshipTypeRoot.get(RelationshipType_.ID)));
+        criteriaQuery.orderBy(orderList);
         return list(context, criteriaQuery, false, RelationshipType.class, limit, offset);
     }
 
@@ -119,13 +131,11 @@ public class RelationshipTypeDAOImpl extends AbstractHibernateDAO<RelationshipTy
         CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, RelationshipType.class);
         Root<RelationshipType> relationshipTypeRoot = criteriaQuery.from(RelationshipType.class);
         criteriaQuery.select(relationshipTypeRoot);
-        criteriaQuery.where(
-            criteriaBuilder.or(criteriaBuilder.
-                                    equal(relationshipTypeRoot.get(RelationshipType_.leftType), entityType),
-                               criteriaBuilder
-                                   .equal(relationshipTypeRoot.get(RelationshipType_.rightType), entityType)
-            )
-        );
+        criteriaQuery.where(criteriaBuilder.or(
+                            criteriaBuilder.equal(relationshipTypeRoot.get(RelationshipType_.leftType), entityType),
+                            criteriaBuilder.equal(relationshipTypeRoot.get(RelationshipType_.rightType), entityType)
+                            ));
         return count(context, criteriaQuery, criteriaBuilder, relationshipTypeRoot);
     }
+
 }

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

@@ -19,7 +19,7 @@ import org.dspace.core.Context;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the Site object.
- * This class is responsible for all database calls for the Site object and is autowired by spring
+ * This class is responsible for all database calls for the Site object and is autowired by Spring.
  * This class should never be accessed directly.
  *
  * @author kevinvandevelde at atmire.com
@@ -35,6 +35,6 @@ public class SiteDAOImpl extends AbstractHibernateDAO<Site> implements SiteDAO {
         CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, Site.class);
         Root<Site> siteRoot = criteriaQuery.from(Site.class);
         criteriaQuery.select(siteRoot);
-        return uniqueResult(context, criteriaQuery, true, Site.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, true, Site.class);
     }
 }

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

@@ -31,7 +31,7 @@ import org.dspace.eperson.Group;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the WorkspaceItem object.
- * This class is responsible for all database calls for the WorkspaceItem object and is autowired by spring
+ * This class is responsible for all database calls for the WorkspaceItem object and is autowired by Spring.
  * This class should never be accessed directly.
  *
  * @author kevinvandevelde at atmire.com
@@ -81,7 +81,7 @@ public class WorkspaceItemDAOImpl extends AbstractHibernateDAO<WorkspaceItem> im
         Root<WorkspaceItem> workspaceItemRoot = criteriaQuery.from(WorkspaceItem.class);
         criteriaQuery.select(workspaceItemRoot);
         criteriaQuery.where(criteriaBuilder.equal(workspaceItemRoot.get(WorkspaceItem_.item), i));
-        return uniqueResult(context, criteriaQuery, false, WorkspaceItem.class, -1, -1);
+        return uniqueResult(context, criteriaQuery, false, WorkspaceItem.class);
     }
 
     @Override

dspace-api/src/main/java/org/dspace/content/logic/DefaultFilter.java

@@ -0,0 +1,46 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic;
+
+import org.apache.log4j.Logger;
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+
+/**
+ * The default filter, a very simple implementation of Filter / LogicalStatement
+ * The idea is to have this as a wrapper / root class for all logical operations, so it takes a single
+ * statement as a property (unlike an operator) and takes no parameters (unlike a condition)
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class DefaultFilter implements Filter {
+    private LogicalStatement statement;
+    private static Logger log = Logger.getLogger(Filter.class);
+
+    /**
+     * Set statement from Spring configuration in item-filters.xml
+     * Be aware that this is singular not plural. A filter can have one sub-statement only.
+     *
+     * @param statement LogicalStatement of this filter (operator, condition, or another filter)
+     */
+    public void setStatement(LogicalStatement statement) {
+        this.statement = statement;
+    }
+
+    /**
+     * Get the result of logical evaluation for an item
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean
+     * @throws LogicalStatementException
+     */
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+        return this.statement.getResult(context, item);
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/Filter.java

@@ -0,0 +1,35 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic;
+
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+
+/**
+ * The interface for Filter currently doesn't add anything to LogicalStatement but inherits from it
+ * just to keep naming / reflection clean, and in case Filters should do anything additional in future.
+ * We need this as filters have to be specified in the spring configuration (item-filters.xml).
+ * Filters are the top level elements of the logic. Only logical statements that implement this interface
+ * are allowed to be the root element of a spring configuration (item-filters.xml) of this logic framework.
+ * A filter is just helping to differentiate between logical statement that can be used as root elements and
+ * logical statement that shouldn't be use as root element. A filter may contain only one substatement.
+ *
+ * @author Kim Shepherd
+ * @see org.dspace.content.logic.DefaultFilter
+ */
+public interface Filter extends LogicalStatement {
+    /**
+     * Get the result of logical evaluation for an item
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean
+     * @throws LogicalStatementException
+     */
+    @Override
+    boolean getResult(Context context, Item item) throws LogicalStatementException;
+}

dspace-api/src/main/java/org/dspace/content/logic/LogicalStatement.java

@@ -0,0 +1,31 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic;
+
+import org.dspace.content.Item;
+import org.dspace.core.Context;
+
+/**
+ * The base interface used by all logic classes: all operators and conditions are logical statements.
+ * All statements must accept an Item object and return a boolean result.
+ * The philosophy is that because Filter, Condition, Operator classes implement getResult(), they can all be
+ * used as sub-statements in other Filters and Operators.
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public interface LogicalStatement {
+    /**
+     * Get the result of logical evaluation for an item
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    boolean getResult(Context context, Item item) throws LogicalStatementException;
+}

dspace-api/src/main/java/org/dspace/content/logic/LogicalStatementException.java

@@ -0,0 +1,35 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic;
+
+/**
+ * Exception for errors encountered while evaluating logical statements
+ * defined as spring beans.
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class LogicalStatementException extends RuntimeException {
+
+    public LogicalStatementException() {
+        super();
+    }
+
+    public LogicalStatementException(String s, Throwable t) {
+        super(s, t);
+    }
+
+    public LogicalStatementException(String s) {
+        super(s);
+    }
+
+    public LogicalStatementException(Throwable t) {
+        super(t);
+    }
+
+}

dspace-api/src/main/java/org/dspace/content/logic/TestLogicRunner.java

@@ -0,0 +1,143 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic;
+
+import java.sql.SQLException;
+import java.util.Iterator;
+import java.util.List;
+
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.ParseException;
+import org.apache.commons.cli.PosixParser;
+import org.apache.logging.log4j.Logger;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;
+import org.dspace.kernel.ServiceManager;
+import org.dspace.services.factory.DSpaceServicesFactory;
+
+/**
+ * A command-line runner used for testing a logical filter against an item, or all items
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class TestLogicRunner {
+
+    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(TestLogicRunner.class);
+
+    /**
+     * Default constructor
+     */
+    private TestLogicRunner() { }
+
+    /**
+     * Main runner method for CLI usage
+     * @param argv  array of command-line arguments
+     */
+    public static void main(String[] argv) {
+        System.out.println("Starting impl of main() test spring logic item filter");
+
+        // initialize options
+        Options options = new Options();
+
+        options.addOption("h", "help", false, "Help");
+        options.addOption("l", "list", false, "List filters");
+        options.addOption("f", "filter", true, "Use filter <filter>");
+        options.addOption("i","item", true, "Run filter over item <handle>");
+        options.addOption("a","all", false, "Run filter over all items");
+
+        // initialize parser
+        CommandLineParser parser = new PosixParser();
+        CommandLine line = null;
+        HelpFormatter helpformater = new HelpFormatter();
+
+        try {
+            line = parser.parse(options, argv);
+        } catch (ParseException ex) {
+            System.out.println(ex.getMessage());
+            System.exit(1);
+        }
+
+        if (line.hasOption("help")) {
+            helpformater.printHelp("\nTest the DSpace logical item filters\n", options);
+            System.exit(0);
+        }
+
+        // Create a context
+        Context c = new Context(Context.Mode.READ_ONLY);
+        //c.turnOffAuthorisationSystem();
+        ServiceManager manager = DSpaceServicesFactory.getInstance().getServiceManager();
+
+        if (line.hasOption("list")) {
+            // Lit filters and exit
+            List<Filter> filters = manager.getServicesByType(Filter.class);
+            for (Filter filter : filters) {
+                System.out.println(filter.getClass().toString());
+            }
+            System.out.println("See item-filters.xml spring config for filter names");
+            System.exit(0);
+        }
+
+        Filter filter;
+
+        if (line.hasOption("filter")) {
+            String filterName = line.getOptionValue("filter");
+            filter = manager.getServiceByName(filterName, Filter.class);
+            if (filter == null) {
+                System.out.println("Error loading filter: " + filterName);
+                System.exit(1);
+            }
+
+            if (line.hasOption("item")) {
+                String handle = line.getOptionValue("item");
+
+                HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
+                try {
+                    DSpaceObject dso = handleService.resolveToObject(c, handle);
+                    if (Constants.typeText[dso.getType()].equals("ITEM")) {
+                        Item item = (Item) dso;
+                        System.out.println(filter.getResult(c, item));
+                    } else {
+                        System.out.println(handle + " is not an ITEM");
+                    }
+                } catch (SQLException | LogicalStatementException e) {
+                    System.out.println("Error encountered processing item " + handle + ": " + e.getMessage());
+                }
+
+            } else if (line.hasOption("all")) {
+                ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+                try {
+                    Iterator<Item> itemIterator = itemService.findAll(c);
+                    while (itemIterator.hasNext()) {
+                        Item i = itemIterator.next();
+                        System.out.println(
+                            "Testing '" + filter + "' on item " + i.getHandle() + " ('" + i.getName() + "')"
+                        );
+                        System.out.println(filter.getResult(c, i));
+
+                    }
+                } catch (SQLException | LogicalStatementException e) {
+                    System.out.println("Error encountered processing items: " + e.getMessage());
+                }
+            } else {
+                helpformater.printHelp("\nTest the DSpace logical item filters\n", options);
+            }
+        }
+
+    }
+
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/AbstractCondition.java

@@ -0,0 +1,91 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.util.Map;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.dspace.content.Item;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+import org.dspace.handle.service.HandleService;
+import org.springframework.beans.factory.annotation.Autowired;
+
+/**
+ * Abstract class for conditions, to implement the basic getter and setter parameters
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public abstract class AbstractCondition implements Condition {
+
+    // Parameters map (injected, required -- see setter annotation)
+    private Map<String, Object> parameters;
+
+    // Declare and instantiate spring services
+    //@Autowired(required = true)
+    protected ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    //@Autowired(required = true)
+    protected CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    @Autowired(required = true)
+    protected HandleService handleService;
+
+    // Logging
+    Logger log = LogManager.getLogger(AbstractCondition.class);
+
+    /**
+     * Get parameters set by spring configuration in item-filters.xml
+     * These could be any kind of map that the extending condition class needs for evaluation
+     * @return map of parameters
+     * @throws LogicalStatementException
+     */
+    @Override
+    public Map<String, Object> getParameters() throws LogicalStatementException {
+        return this.parameters;
+    }
+
+    /**
+     * Set parameters - used by Spring when creating beans from item-filters.xml
+     * These could be any kind of map that the extending condition class needs for evaluation
+     * @param parameters
+     * @throws LogicalStatementException
+     */
+    @Autowired(required = true)
+    @Override
+    public void setParameters(Map<String, Object> parameters) throws LogicalStatementException {
+        this.parameters = parameters;
+    }
+
+    /**
+     * Get the result of logical evaluation for an item
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+        if (item == null) {
+            log.error("Error evaluating item. Passed item is null, returning false");
+            return false;
+        }
+        if (context == null) {
+            throw new IllegalStateException("Context is null");
+        }
+        return true;
+    }
+
+    @Override
+    public void setItemService(ItemService itemService) {
+        this.itemService = itemService;
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/BitstreamCountCondition.java

@@ -0,0 +1,72 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.util.List;
+
+import org.dspace.content.Bundle;
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition to evaluate an item based on how many bitstreams it has in a particular bundle
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class BitstreamCountCondition extends AbstractCondition {
+    /**
+     * Return true if bitstream count is within bounds of min and/or max parameters
+     * Return false if out of bounds
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+
+        // This super call just throws some useful exceptions if required objects are null
+        super.getResult(context, item);
+
+        int min = -1;
+        if (getParameters().get("min") != null) {
+            min = Integer.parseInt((String)getParameters().get("min"));
+        }
+        int max = -1;
+        if (getParameters().get("max") != null) {
+            max = Integer.parseInt((String)getParameters().get("max"));
+        }
+        String bundleName = (String)getParameters().get("bundle");
+        if (min < 0 && max < 0) {
+            throw new LogicalStatementException("Either min or max parameter must be 0 or bigger.");
+        }
+
+        List<Bundle> bundles;
+        int count = 0;
+
+        if (bundleName != null) {
+            bundles = item.getBundles(bundleName);
+        } else {
+            bundles = item.getBundles();
+        }
+
+        for (Bundle bundle : bundles) {
+            count += bundle.getBitstreams().size();
+        }
+
+        if (min < 0) {
+            return (count <= max);
+        }
+        if (max < 0) {
+            return (count >= min);
+        }
+        return (count <= max && count >= min);
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/Condition.java

@@ -0,0 +1,56 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.util.Map;
+
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatement;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.content.service.ItemService;
+import org.dspace.core.Context;
+
+/**
+ * The Condition interface
+ *
+ * A condition is one logical statement testing an item for any idea. A condition is always a logical statements. An
+ * operator is not a condition but also a logical statement.
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public interface Condition extends LogicalStatement {
+
+    /**
+     * Set parameters - used by Spring
+     * @param parameters
+     * @throws LogicalStatementException
+     */
+    void setParameters(Map<String, Object> parameters) throws LogicalStatementException;
+
+    /**
+     * Get parameters set by Spring in item-filters.xml
+     * These could be any kind of map that the extending condition class needs for evaluation
+     * @return map of parameters
+     * @throws LogicalStatementException
+     */
+    Map<String, Object> getParameters() throws LogicalStatementException;
+
+    /**
+     * Get the result of logical evaluation for an item
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return result
+     * @throws LogicalStatementException
+     */
+    @Override
+    boolean getResult(Context context, Item item) throws LogicalStatementException;
+
+    public void setItemService(ItemService itemService);
+
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/InCollectionCondition.java

@@ -0,0 +1,80 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.sql.SQLException;
+import java.util.List;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.dspace.content.Collection;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition that accepts a list of collection handles and returns true
+ * if the item belongs to any of them.
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class InCollectionCondition extends AbstractCondition {
+    private static Logger log = LogManager.getLogger(InCollectionCondition.class);
+
+    /**
+     * Return true if item is in one of the specified collections
+     * Return false if not
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+
+        List<String> collectionHandles = (List<String>)getParameters().get("collections");
+
+        // Look for the handle among an archived item's collections - this test will only work after submission
+        // and archival is complete
+        List<Collection> itemCollections = item.getCollections();
+        for (Collection collection : itemCollections) {
+            if (collectionHandles.contains(collection.getHandle())) {
+                log.debug("item " + item.getHandle() + " is in collection "
+                    + collection.getHandle() + ", returning true");
+                return true;
+            }
+        }
+
+        // Look for the parent object of the item. This is important as the item.getOwningCollection method
+        // may return null, even though the item itself does have a parent object, at the point of archival
+        try {
+            DSpaceObject parent = itemService.getParentObject(context, item);
+            if (parent != null) {
+                log.debug("Got parent DSO for item: " + parent.getID().toString());
+                log.debug("Parent DSO handle: " + parent.getHandle());
+                if (collectionHandles.contains(parent.getHandle())) {
+                    log.debug("item " + item.getHandle() + " is in collection "
+                        + parent.getHandle() + ", returning true");
+                    return true;
+                }
+            } else {
+                log.debug("Parent DSO is null...");
+            }
+        } catch (SQLException e) {
+            log.error("Error obtaining parent DSO", e);
+            throw new LogicalStatementException(e);
+        }
+
+        // If we reach this statement, the item did not appear in any of the collections from the parameters
+        log.debug("item " + item.getHandle() + " not found in the passed collection handle list");
+
+        return false;
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/InCommunityCondition.java

@@ -0,0 +1,90 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.sql.SQLException;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.dspace.content.Collection;
+import org.dspace.content.Community;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition that accepts a list of community handles and returns true
+ * if the item belongs to any of them.
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class InCommunityCondition extends AbstractCondition {
+    private static Logger log = Logger.getLogger(InCommunityCondition.class);
+
+    /**
+     * Return true if item is in one of the specified collections
+     * Return false if not
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+
+        List<String> communityHandles = (List<String>)getParameters().get("communities");
+        List<Collection> itemCollections = item.getCollections();
+
+        // Check communities of item.getCollections() - this will only see collections if the item is archived
+        for (Collection collection : itemCollections) {
+            try {
+                List<Community> communities = collection.getCommunities();
+                for (Community community : communities) {
+                    if (communityHandles.contains(community.getHandle())) {
+                        return true;
+                    }
+                }
+            } catch (SQLException e) {
+                log.error(e.getMessage());
+                throw new LogicalStatementException(e);
+            }
+        }
+
+        // Look for the parent object of the item. This is important as the item.getOwningCollection method
+        // may return null, even though the item itself does have a parent object, at the point of archival
+        try {
+            DSpaceObject parent = itemService.getParentObject(context, item);
+            if (parent instanceof Collection) {
+                log.debug("Got parent DSO for item: " + parent.getID().toString());
+                log.debug("Parent DSO handle: " + parent.getHandle());
+                try {
+                    // Now iterate communities of this parent collection
+                    Collection collection = (Collection)parent;
+                    List<Community> communities = collection.getCommunities();
+                    for (Community community : communities) {
+                        if (communityHandles.contains(community.getHandle())) {
+                            return true;
+                        }
+                    }
+                } catch (SQLException e) {
+                    log.error(e.getMessage());
+                    throw new LogicalStatementException(e);
+                }
+            } else {
+                log.debug("Parent DSO is null or is not a Collection...");
+            }
+        } catch (SQLException e) {
+            log.error("Error obtaining parent DSO", e);
+            throw new LogicalStatementException(e);
+        }
+
+        return false;
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/IsWithdrawnCondition.java

@@ -0,0 +1,37 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import org.apache.log4j.Logger;
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition that returns true if the item is withdrawn
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class IsWithdrawnCondition extends AbstractCondition {
+    private static Logger log = Logger.getLogger(IsWithdrawnCondition.class);
+
+    /**
+     * Return true if item is withdrawn
+     * Return false if not
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+        log.debug("Result of isWithdrawn is " + item.isWithdrawn());
+        return item.isWithdrawn();
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/MetadataValueMatchCondition.java

@@ -0,0 +1,66 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition that returns true if a pattern (regex) matches any value
+ * in a given metadata field
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class MetadataValueMatchCondition extends AbstractCondition {
+
+    private static Logger log = Logger.getLogger(MetadataValueMatchCondition.class);
+
+    /**
+     * Return true if any value for a specified field in the item matches a specified regex pattern
+     * Return false if not
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+        String field = (String)getParameters().get("field");
+        if (field == null) {
+            return false;
+        }
+
+        String[] fieldParts = field.split("\\.");
+        String schema = (fieldParts.length > 0 ? fieldParts[0] : null);
+        String element = (fieldParts.length > 1 ? fieldParts[1] : null);
+        String qualifier = (fieldParts.length > 2 ? fieldParts[2] : null);
+
+        List<MetadataValue> values = itemService.getMetadata(item, schema, element, qualifier, Item.ANY);
+        for (MetadataValue value : values) {
+            if (getParameters().get("pattern") instanceof String) {
+                String pattern = (String)getParameters().get("pattern");
+                log.debug("logic for " + item.getHandle() + ": pattern passed is " + pattern
+                    + ", checking value " + value.getValue());
+                Pattern p = Pattern.compile(pattern);
+                Matcher m = p.matcher(value.getValue());
+                if (m.find()) {
+                    return true;
+                }
+            }
+        }
+        return false;
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/MetadataValuesMatchCondition.java

@@ -0,0 +1,73 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.apache.log4j.Logger;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Context;
+
+/**
+ * A condition that returns true if any pattern in a list of patterns matches any value
+ * in a given metadata field
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class MetadataValuesMatchCondition extends AbstractCondition {
+
+    private static Logger log = Logger.getLogger(MetadataValuesMatchCondition.class);
+
+    /**
+     * Return true if any value for a specified field in the item matches any of the specified regex patterns
+     * Return false if not
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+        String field = (String)getParameters().get("field");
+        if (field == null) {
+            return false;
+        }
+
+        String[] fieldParts = field.split("\\.");
+        String schema = (fieldParts.length > 0 ? fieldParts[0] : null);
+        String element = (fieldParts.length > 1 ? fieldParts[1] : null);
+        String qualifier = (fieldParts.length > 2 ? fieldParts[2] : null);
+
+        List<MetadataValue> values = itemService.getMetadata(item, schema, element, qualifier, Item.ANY);
+        for (MetadataValue value : values) {
+            if (getParameters().get("patterns") instanceof List) {
+                List<String> patternList = (List<String>)getParameters().get("patterns");
+                // If the list is empty, just return true and log error?
+                log.error("No patterns were passed for metadata value matching, defaulting to 'true'");
+                if (patternList == null) {
+                    return true;
+                }
+                for (String pattern : patternList) {
+                    log.debug("logic for " + item.getHandle() + ": pattern passed is " + pattern
+                        + ", checking value " + value.getValue());
+                    Pattern p = Pattern.compile(pattern);
+                    Matcher m = p.matcher(value.getValue());
+                    if (m.find()) {
+                        return true;
+                    }
+                }
+            }
+        }
+        return false;
+    }
+}

dspace-api/src/main/java/org/dspace/content/logic/condition/ReadableByGroupCondition.java

@@ -0,0 +1,64 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.content.logic.condition;
+
+import java.sql.SQLException;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.dspace.authorize.ResourcePolicy;
+import org.dspace.authorize.factory.AuthorizeServiceFactory;
+import org.dspace.authorize.service.AuthorizeService;
+import org.dspace.content.Item;
+import org.dspace.content.logic.LogicalStatementException;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+
+/**
+ * A condition that accepts a group and action parameter and returns true if the group
+ * can perform the action on a given item
+ *
+ * @author Kim Shepherd
+ * @version $Revision$
+ */
+public class ReadableByGroupCondition extends AbstractCondition {
+    private static Logger log = Logger.getLogger(ReadableByGroupCondition.class);
+
+    // Authorize service
+    AuthorizeService authorizeService = AuthorizeServiceFactory.getInstance().getAuthorizeService();
+
+    /**
+     * Return true if this item allows a specified action (eg READ, WRITE, ADD) by a specified group
+     * @param context   DSpace context
+     * @param item      Item to evaluate
+     * @return boolean result of evaluation
+     * @throws LogicalStatementException
+     */
+    @Override
+    public boolean getResult(Context context, Item item) throws LogicalStatementException {
+
+        String group = (String)getParameters().get("group");
+        String action = (String)getParameters().get("action");
+
+        try {
+            List<ResourcePolicy> policies = authorizeService
+                .getPoliciesActionFilter(context, item, Constants.getActionID(action));
+            for (ResourcePolicy policy : policies) {
+                if (policy.getGroup().getName().equals(group)) {
+                    return true;
+                }
+            }
+        } catch (SQLException e) {
+            log.error("Error trying to read policies for " + item.getHandle() + ": " + e.getMessage());
+            throw new LogicalStatementException(e);
+        }
+        log.debug("item " + item.getHandle() + " not readable by anonymous group");
+
+        return false;
+    }
+}