Merge branch 'main' into CST-4509-assignAnEntityTypeToCollection

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/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/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;
@@ -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.

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) {
-
+                    LOG.warn("DSpace uses an unsupported encoding", e);
-                    e.printStackTrace();
                 }
 
                 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/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/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
+ * <ul>
- * A list of allowed locations (eg. institutional repository, personal homepage, non-commercial repository)
+ *   <li>A list of general conditions / terms for deposit of this version of work</li>
- * A list of prerequisite conditions for deposit (eg. attribution, linking to published version)
+ *   <li>A list of allowed locations (e.g. institutional repository, personal homepage, non-commercial repository)</li>
- * A list of required licences for the deposited work (eg. CC-BY-NC)
+ *   <li>A list of prerequisite conditions for deposit (e.g. attribution, linking to published version)</li>
- * Embargo requirements, if any
+ *   <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/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/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;
+            DocumentBuilder dBuilder = dbFactory.newDocumentBuilder();
-            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/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/PasswordAuthentication.java

@@ -15,6 +15,7 @@ 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.LogHelper;
@@ -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();
 
 
     /**
@@ -142,7 +142,7 @@ 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) {
@@ -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.

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/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/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 this.getID().equals(otherBitstream.getID());
-            return false;
-        }
-
-        return true;
     }
 
     @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 this.getID().equals(otherBitstreamFormat.getID());
-            return false;
-        }
-
-        return true;
     }
 
     @Override

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

@@ -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)
@@ -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 this.getID().equals(other.getID());
-            return false;
-        }
-        return true;
     }
 
     @Override

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

@@ -318,7 +318,7 @@ 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);

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

@@ -24,7 +24,6 @@ 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 +41,12 @@ 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;
 
@@ -215,7 +208,7 @@ 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 +216,7 @@ public class Community extends DSpaceObject implements DSpaceObjectLegacySupport
             return false;
         }
         final Community otherCommunity = (Community) other;
-        if (!this.getID().equals(otherCommunity.getID())) {
+        return this.getID().equals(otherCommunity.getID());
-            return false;
-        }
-
-        return true;
     }
 
     @Override

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

@@ -195,7 +195,7 @@ 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);

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>,
+ * Examples: {@code 1994-05-03T15:30:24}, {@code 1995-10-04},
- * <code>2001-10</code>,<code>1975</code>
+ * {@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

@@ -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()

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;
+            String newValueLanguage = Item.ANY.equals(language) ? null : language;
-            addMetadata(context, dso, field.SCHEMA, field.ELEMENT, field.QUALIFIER,
+            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 StringUtils.equals(this.getLabel(), entityType.getLabel());
-            return false;
-        }
-        return true;
     }
 
     /**

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

@@ -27,8 +27,6 @@ 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 +47,10 @@ 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
      */
@@ -297,7 +288,7 @@ 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 +319,7 @@ 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 +327,7 @@ 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 +335,7 @@ public class Item extends DSpaceObject implements DSpaceObjectLegacySupport {
             return false;
         }
         final Item otherItem = (Item) obj;
-        if (!this.getID().equals(otherItem.getID())) {
+        return this.getID().equals(otherItem.getID());
-            return false;
-        }
-        return true;
     }
 
     @Override

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 getMetadataSchema().equals(other.getMetadataSchema());
-            return false;
-        }
-        return true;
     }
 
     @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;
+        this.schema = schema;
-        ELEMENT = element;
+        this.element = element;
-        QUALIFIER = qualifier;
+        this.qualifier = qualifier;
     }
 
     /**
@@ -59,9 +59,9 @@ public class MetadataFieldName {
             throw new NullPointerException("Element must not be null.");
         }
 
-        SCHEMA = schema;
+        this.schema = schema;
-        ELEMENT = element;
+        this.element = element;
-        QUALIFIER = null;
+        qualifier = null;
     }
 
     /**
@@ -79,9 +79,9 @@ public class MetadataFieldName {
             throw new IllegalArgumentException("Element must not be null.");
         }
 
-        SCHEMA = schema.getName();
+        this.schema = schema.getName();
-        ELEMENT = element;
+        this.element = element;
-        QUALIFIER = qualifier;
+        this.qualifier = qualifier;
     }
 
     /**
@@ -98,9 +98,9 @@ public class MetadataFieldName {
             throw new IllegalArgumentException("Element must not be null.");
         }
 
-        SCHEMA = schema.getName();
+        this.schema = schema.getName();
-        ELEMENT = element;
+        this.element = element;
-        QUALIFIER = null;
+        qualifier = null;
     }
 
     /**
@@ -110,9 +110,9 @@ public class MetadataFieldName {
      */
     public MetadataFieldName(@Nonnull String name) {
         String[] elements = parse(name);
-        SCHEMA = elements[0];
+        schema = elements[0];
-        ELEMENT = elements[1];
+        element = elements[1];
-        QUALIFIER = elements[2];
+        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);
+                .append(element);
-        if (null != QUALIFIER) {
+        if (null != qualifier) {
             buffer.append('.')
-                    .append(QUALIFIER);
+                    .append(qualifier);
         }
         return buffer.toString();
     }

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/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 this.getDSpaceObject().getID().equals(other.getDSpaceObject().getID());
-            return false;
-        }
-        return true;
     }
 
     @Override

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 org.apache.commons.collections4.CollectionUtils;
@@ -250,7 +250,7 @@ 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;
@@ -266,6 +266,7 @@ 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;
@@ -407,7 +408,7 @@ 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/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/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;
@@ -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<>();
+        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/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/logic/Filter.java

@@ -20,7 +20,6 @@ import org.dspace.core.Context;
  * logical statement that shouldn't be use as root element. A filter may contain only one substatement.
  *
  * @author Kim Shepherd
- * @version $Revision$
  * @see org.dspace.content.logic.DefaultFilter
  */
 public interface Filter extends LogicalStatement {
@@ -31,5 +30,6 @@ public interface Filter extends LogicalStatement {
      * @return boolean
      * @throws LogicalStatementException
      */
+    @Override
     boolean getResult(Context context, Item item) throws LogicalStatementException;
 }

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

@@ -45,9 +45,10 @@ public interface Condition extends LogicalStatement {
      * Get the result of logical evaluation for an item
      * @param context   DSpace context
      * @param item      Item to evaluate
-     * @return boolean
+     * @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/operator/Nor.java

@@ -15,10 +15,9 @@ import org.dspace.content.logic.LogicalStatementException;
 import org.dspace.core.Context;
 
 /**
- * An operator that implements NIR by negating an OR operation
+ * An operator that implements NOR by negating an OR operation.
  *
  * @author Kim Shepherd
- * @version $Revision$
  */
 public class Nor extends AbstractOperator {
 

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

@@ -11,6 +11,7 @@ import java.io.ByteArrayInputStream;
 import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.Iterator;
@@ -656,7 +657,7 @@ public class METSManifest {
 
                         String mimeType = mdWrap.getAttributeValue("MIMETYPE");
                         if (mimeType != null && mimeType.equalsIgnoreCase("text/xml")) {
-                            byte value[] = Base64.decodeBase64(bin.getText().getBytes());
+                            byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                             Document mdd = parser.build(new ByteArrayInputStream(value));
                             List<Element> result = new ArrayList<>(1);
                             result.add(mdd.getRootElement());
@@ -724,13 +725,13 @@ public class METSManifest {
                     throw new MetadataValidationException(
                         "Invalid METS Manifest: mdWrap element with neither xmlData nor binData child.");
                 } else {
-                    byte value[] = Base64.decodeBase64(bin.getText().getBytes());
+                    byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                     return new ByteArrayInputStream(value);
                 }
             } else {
                 XMLOutputter outputPretty = new XMLOutputter(Format.getPrettyFormat());
                 return new ByteArrayInputStream(
-                    outputPretty.outputString(xmlData.getChildren()).getBytes());
+                    outputPretty.outputString(xmlData.getChildren()).getBytes(StandardCharsets.UTF_8));
             }
         } else {
             mdRef = mdSec.getChild("mdRef", metsNS);
@@ -1176,7 +1177,7 @@ public class METSManifest {
                                     "Invalid METS Manifest: mdWrap element for streaming crosswalk without binData " +
                                         "child.");
                             } else {
-                                byte value[] = Base64.decodeBase64(bin.getText().getBytes());
+                                byte value[] = Base64.decodeBase64(bin.getText().getBytes(StandardCharsets.UTF_8));
                                 sxwalk.ingest(context, dso,
                                               new ByteArrayInputStream(value),
                                               mdWrap.getAttributeValue("MIMETYPE"));
@@ -1302,6 +1303,6 @@ public class METSManifest {
         XMLOutputter outputPretty = new XMLOutputter(Format.getPrettyFormat());
 
         return new ByteArrayInputStream(
-            outputPretty.outputString(mets).getBytes());
+            outputPretty.outputString(mets).getBytes(StandardCharsets.UTF_8));
     }
 }

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

@@ -19,7 +19,6 @@ import org.apache.logging.log4j.Logger;
  * exceptions. This class is intended for declarations and catch clauses.
  *
  * @author Larry Stone
- * @version $Revision$
  */
 public class PackageException extends Exception {
     /**
@@ -76,10 +75,4 @@ public class PackageException extends Exception {
             log.error(sw.toString());
         }
     }
-
-    public String toString() {
-        String base = getClass().getName() + ": " + getMessage();
-        return (getCause() == null) ? base :
-            base + ", Reason: " + getCause().toString();
-    }
 }

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

@@ -57,7 +57,7 @@ public class PackageParameters extends Properties {
             } else if (v.length == 1) {
                 result.setProperty(name, v[0]);
             } else {
-                StringBuffer sb = new StringBuffer();
+                StringBuilder sb = new StringBuilder();
                 for (int i = 0; i < v.length; ++i) {
                     if (i > 0) {
                         sb.append(SEPARATOR);

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

@@ -33,6 +33,7 @@ import org.dspace.core.Context;
  */
 public interface BitstreamService extends DSpaceObjectService<Bitstream>, DSpaceObjectLegacySupportService<Bitstream> {
 
+    @Override
     public Bitstream find(Context context, UUID id) throws SQLException;
 
     public List<Bitstream> findAll(Context context) throws SQLException;

dspace-api/src/main/java/org/dspace/content/virtual/UUIDValue.java

@@ -8,7 +8,6 @@
 package org.dspace.content.virtual;
 
 import java.sql.SQLException;
-import java.util.LinkedList;
 import java.util.List;
 
 import org.dspace.content.Item;
@@ -24,9 +23,7 @@ public class UUIDValue implements VirtualMetadataConfiguration {
 
     @Override
     public List<String> getValues(Context context, Item item) throws SQLException {
-        List<String> list = new LinkedList<>();
+        return List.of(String.valueOf(item.getID()));
-        list.add(String.valueOf(item.getID()));
-        return list;
     }
 
     @Override

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

@@ -9,13 +9,14 @@ package org.dspace.core;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.EmptyStackException;
+import java.util.Deque;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Locale;
+import java.util.NoSuchElementException;
 import java.util.Set;
-import java.util.Stack;
 import java.util.UUID;
+import java.util.concurrent.ConcurrentLinkedDeque;
 import java.util.concurrent.atomic.AtomicBoolean;
 
 import org.apache.logging.log4j.Logger;
@@ -46,8 +47,6 @@ import org.springframework.util.CollectionUtils;
  * changes and free up the resources.
  * <P>
  * The context object is also used as a cache for CM API objects.
- *
- * @version $Revision$
  */
 public class Context implements AutoCloseable {
     private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(Context.class);
@@ -81,13 +80,13 @@ public class Context implements AutoCloseable {
     /**
      * A stack with the history of authorisation system check modify
      */
-    private Stack<Boolean> authStateChangeHistory;
+    private Deque<Boolean> authStateChangeHistory;
 
     /**
      * A stack with the name of the caller class that modify authorisation
      * system check
      */
-    private Stack<String> authStateClassCallHistory;
+    private Deque<String> authStateClassCallHistory;
 
     /**
      * Group IDs of special groups user is a member of
@@ -117,7 +116,7 @@ public class Context implements AutoCloseable {
     /**
      * Cache that is only used the context is in READ_ONLY mode
      */
-    private ContextReadOnlyCache readOnlyCache = new ContextReadOnlyCache();
+    private final ContextReadOnlyCache readOnlyCache = new ContextReadOnlyCache();
 
     protected EventService eventService;
 
@@ -159,8 +158,6 @@ public class Context implements AutoCloseable {
 
     /**
      * Initializes a new context object.
-     *
-     * @throws SQLException if there was an error obtaining a database connection
      */
     protected void init() {
         updateDatabase();
@@ -185,8 +182,8 @@ public class Context implements AutoCloseable {
 
         specialGroups = new ArrayList<>();
 
-        authStateChangeHistory = new Stack<>();
+        authStateChangeHistory = new ConcurrentLinkedDeque<>();
-        authStateClassCallHistory = new Stack<>();
+        authStateClassCallHistory = new ConcurrentLinkedDeque<>();
         setMode(this.mode);
     }
 
@@ -312,10 +309,10 @@ public class Context implements AutoCloseable {
         Boolean previousState;
         try {
             previousState = authStateChangeHistory.pop();
-        } catch (EmptyStackException ex) {
+        } catch (NoSuchElementException ex) {
             log.warn(LogHelper.getHeader(this, "restore_auth_sys_state",
-                                          "not previous state info available "
+                    "not previous state info available:  {}"),
-                                              + ex.getLocalizedMessage()));
+                    ex::getLocalizedMessage);
             previousState = Boolean.FALSE;
         }
         if (log.isDebugEnabled()) {
@@ -323,13 +320,19 @@ public class Context implements AutoCloseable {
             StackTraceElement[] stackTrace = currThread.getStackTrace();
             String caller = stackTrace[stackTrace.length - 1].getClassName();
 
-            String previousCaller = (String) authStateClassCallHistory.pop();
+            String previousCaller;
+            try {
+                previousCaller = (String) authStateClassCallHistory.pop();
+            } catch (NoSuchElementException ex) {
+                previousCaller = "none";
+                log.warn(LogHelper.getHeader(this, "restore_auth_sys_state",
+                        "no previous caller info available:  {}"),
+                        ex::getLocalizedMessage);
+            }
 
             // if previousCaller is not the current caller *only* log a warning
             if (!previousCaller.equals(caller)) {
-                log
+                log.warn(LogHelper.getHeader(
-                    .warn(LogHelper
-                              .getHeader(
                                   this,
                                   "restore_auth_sys_state",
                                   "Class: "
@@ -338,7 +341,7 @@ public class Context implements AutoCloseable {
                                       + previousCaller));
             }
         }
-        ignoreAuth = previousState.booleanValue();
+        ignoreAuth = previousState;
     }
 
     /**
@@ -490,7 +493,7 @@ public class Context implements AutoCloseable {
             throw new IllegalStateException("Attempt to mutate object in read-only context");
         }
         if (events == null) {
-            events = new LinkedList<Event>();
+            events = new LinkedList<>();
         }
 
         events.add(event);
@@ -628,11 +631,7 @@ public class Context implements AutoCloseable {
      * @return true if member
      */
     public boolean inSpecialGroup(UUID groupID) {
-        if (specialGroups.contains(groupID)) {
+        return specialGroups.contains(groupID);
-            return true;
-        }
-
-        return false;
     }
 
     /**
@@ -642,7 +641,7 @@ public class Context implements AutoCloseable {
      * @throws SQLException if database error
      */
     public List<Group> getSpecialGroups() throws SQLException {
-        List<Group> myGroups = new ArrayList<Group>();
+        List<Group> myGroups = new ArrayList<>();
         for (UUID groupId : specialGroups) {
             myGroups.add(EPersonServiceFactory.getInstance().getGroupService().find(this, groupId));
         }
@@ -667,7 +666,7 @@ public class Context implements AutoCloseable {
 
         currentUserPreviousState = currentUser;
         specialGroupsPreviousState = specialGroups;
-        specialGroups = new ArrayList<UUID>();
+        specialGroups = new ArrayList<>();
         currentUser = newUser;
     }
 
@@ -709,11 +708,13 @@ public class Context implements AutoCloseable {
 
 
     /**
-     * Returns the size of the cache of all object that have been read from the database so far. A larger number
+     * Returns the size of the cache of all object that have been read from the
-     * means that more memory is consumed by the cache. This also has a negative impact on the query performance. In
+     * database so far.  A larger number means that more memory is consumed by
-     * that case you should consider uncaching entities when they are no longer needed (see
+     * the cache. This also has a negative impact on the query performance. In
-     * {@link Context#uncacheEntity(ReloadableEntity)} () uncacheEntity}).
+     * that case you should consider uncaching entities when they are no longer
+     * needed (see {@link Context#uncacheEntity(ReloadableEntity)} () uncacheEntity}).
      *
+     * @return cache size.
      * @throws SQLException When connecting to the active cache fails.
      */
     public long getCacheSize() throws SQLException {
@@ -749,7 +750,7 @@ public class Context implements AutoCloseable {
                     dbConnection.setConnectionMode(false, false);
                     break;
                 default:
-                    log.warn("New context mode detected that has nog been configured.");
+                    log.warn("New context mode detected that has not been configured.");
                     break;
             }
         } catch (SQLException ex) {
@@ -811,7 +812,7 @@ public class Context implements AutoCloseable {
      * entity. This means changes to the entity will be tracked and persisted to the database.
      *
      * @param entity The entity to reload
-     * @param <E>    The class of the enity. The entity must implement the {@link ReloadableEntity} interface.
+     * @param <E>    The class of the entity. The entity must implement the {@link ReloadableEntity} interface.
      * @return A (possibly) <b>NEW</b> reference to the entity that should be used for further processing.
      * @throws SQLException When reloading the entity from the database fails.
      */
@@ -824,7 +825,7 @@ public class Context implements AutoCloseable {
      * Remove an entity from the cache. This is necessary when batch processing a large number of items.
      *
      * @param entity The entity to reload
-     * @param <E>    The class of the enity. The entity must implement the {@link ReloadableEntity} interface.
+     * @param <E>    The class of the entity. The entity must implement the {@link ReloadableEntity} interface.
      * @throws SQLException When reloading the entity from the database fails.
      */
     @SuppressWarnings("unchecked")

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

@@ -571,7 +571,7 @@ public class Email {
     /**
      * @author arnaldo
      */
-    public class InputStreamDataSource implements DataSource {
+    public static class InputStreamDataSource implements DataSource {
         private final String name;
         private final String contentType;
         private final ByteArrayOutputStream baos;
@@ -612,7 +612,7 @@ public class Email {
      * Wrap ConfigurationService to prevent templates from modifying
      * the configuration.
      */
-    public class UnmodifiableConfigurationService {
+    public static class UnmodifiableConfigurationService {
         private final ConfigurationService configurationService;
 
         /**

dspace-api/src/main/java/org/dspace/core/I18nUtil.java

@@ -217,12 +217,11 @@ public class I18nUtil {
      */
     public static String getInputFormsFileName(Locale locale) {
         /** Name of the form definition XML file */
-        String fileName = "";
         final String FORM_DEF_FILE = "submission-forms";
         final String FILE_TYPE = ".xml";
         String defsFilename = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("dspace.dir")
             + File.separator + "config" + File.separator + FORM_DEF_FILE;
-        fileName = getFilename(locale, defsFilename, FILE_TYPE);
+        String fileName = getFilename(locale, defsFilename, FILE_TYPE);
         return fileName;
     }
 
@@ -286,14 +285,13 @@ public class I18nUtil {
      */
     public static String getDefaultLicense(Context context) {
         Locale locale = context.getCurrentLocale();
-        String fileName = "";
         /** Name of the default license */
         final String DEF_LIC_FILE = "default";
         final String FILE_TYPE = ".license";
         String defsFilename = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("dspace.dir")
             + File.separator + "config" + File.separator + DEF_LIC_FILE;
 
-        fileName = getFilename(locale, defsFilename, FILE_TYPE);
+        String fileName = getFilename(locale, defsFilename, FILE_TYPE);
 
         return fileName;
     }
@@ -316,18 +314,17 @@ public class I18nUtil {
         // with Language, Country
         String fileNameLC = null;
         // with Language
-        String fileNameL = null;
+        String fileNameL = fileName + "_" + locale.getLanguage();
-        fileNameL = fileName + "_" + locale.getLanguage();
 
         if (fileType == null) {
             fileType = "";
         }
 
-        if (!("".equals(locale.getCountry()))) {
+        if (!locale.getCountry().isEmpty()) {
             fileNameLC = fileName + "_" + locale.getLanguage() + "_"
                 + locale.getCountry();
 
-            if (!("".equals(locale.getVariant()))) {
+            if (!locale.getVariant().isEmpty()) {
                 fileNameLCV = fileName + "_" + locale.getLanguage() + "_"
                     + locale.getCountry() + "_" + locale.getVariant();
             }
@@ -372,12 +369,11 @@ public class I18nUtil {
      * String - localized filename of an email template
      */
     public static String getEmailFilename(Locale locale, String name) {
-        String templateName = "";
         String templateFile = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("dspace.dir")
             + File.separator + "config" + File.separator + "emails"
             + File.separator + name;
 
-        templateName = getFilename(locale, templateFile, "");
+        String templateName = getFilename(locale, templateFile, "");
         return templateName;
     }
 
@@ -389,7 +385,7 @@ public class I18nUtil {
      * @return array of locale results, possibly empty
      */
     public static Locale[] parseLocales(String[] locales) {
-        List<Locale> resultList = new ArrayList<Locale>();
+        List<Locale> resultList = new ArrayList<>();
         for (String ls : locales) {
             Locale lc = makeLocale(ls);
             if (lc != null) {

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

@@ -20,6 +20,7 @@ import java.net.URI;
 import java.net.URISyntaxException;
 import java.net.URL;
 import java.net.UnknownHostException;
+import java.nio.charset.StandardCharsets;
 import java.rmi.dgc.VMID;
 import java.security.MessageDigest;
 import java.security.NoSuchAlgorithmException;
@@ -38,6 +39,7 @@ import java.util.regex.Pattern;
 import com.coverity.security.Escape;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.text.StringSubstitutor;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.services.ConfigurationService;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -46,13 +48,12 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  * Utility functions for DSpace.
  *
  * @author Peter Breton
- * @version $Revision$
  */
 public final class Utils {
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Utils.class);
+    private static final Logger log = LogManager.getLogger(Utils.class);
 
     private static final Pattern DURATION_PATTERN = Pattern
         .compile("(\\d+)([smhdwy])");
@@ -71,12 +72,12 @@ public final class Utils {
 
     private static int counter = 0;
 
-    private static Random random = new Random();
+    private static final Random random = new Random();
 
-    private static VMID vmid = new VMID();
+    private static final VMID vmid = new VMID();
 
     // for parseISO8601Date
-    private static SimpleDateFormat parseFmt[]  = {
+    private static final SimpleDateFormat parseFmt[]  = {
         // first try at parsing, has milliseconds (note General time zone)
         new SimpleDateFormat("yyyy'-'MM'-'dd'T'HH':'mm':'ss.SSSz"),
 
@@ -91,12 +92,14 @@ public final class Utils {
 
     // for formatISO8601Date
     // output canonical format (note RFC22 time zone, easier to hack)
-    private static SimpleDateFormat outFmtSecond = new SimpleDateFormat("yyyy'-'MM'-'dd'T'HH':'mm':'ssZ");
+    private static final SimpleDateFormat outFmtSecond
+            = new SimpleDateFormat("yyyy'-'MM'-'dd'T'HH':'mm':'ssZ");
 
     // output format with millsecond precision
-    private static SimpleDateFormat outFmtMillisec = new SimpleDateFormat("yyyy'-'MM'-'dd'T'HH':'mm':'ss.SSSZ");
+    private static final SimpleDateFormat outFmtMillisec
+            = new SimpleDateFormat("yyyy'-'MM'-'dd'T'HH':'mm':'ss.SSSZ");
 
-    private static Calendar outCal = GregorianCalendar.getInstance();
+    private static final Calendar outCal = GregorianCalendar.getInstance();
 
     /**
      * Private constructor
@@ -110,7 +113,7 @@ public final class Utils {
      * @return MD5 checksum for the data in hex format.
      */
     public static String getMD5(String data) {
-        return getMD5(data.getBytes());
+        return getMD5(data.getBytes(StandardCharsets.UTF_8));
     }
 
     /**
@@ -153,7 +156,7 @@ public final class Utils {
             return null;
         }
 
-        StringBuffer result = new StringBuffer();
+        StringBuilder result = new StringBuilder();
 
         // This is far from the most efficient way to do things...
         for (int i = 0; i < data.length; i++) {
@@ -197,10 +200,14 @@ public final class Utils {
 
         random.nextBytes(junk);
 
-        String input = new StringBuffer().append(vmid).append(
+        String input = new StringBuilder()
-            new java.util.Date()).append(Arrays.toString(junk)).append(counter++).toString();
+                .append(vmid)
+                .append(new java.util.Date())
+                .append(Arrays.toString(junk))
+                .append(counter++)
+                .toString();
 
-        return getMD5Bytes(input.getBytes());
+        return getMD5Bytes(input.getBytes(StandardCharsets.UTF_8));
     }
 
     // The following two methods are taken from the Jakarta IOUtil class.

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

@@ -13,7 +13,6 @@ import java.util.Iterator;
 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.DSpaceObject;
@@ -39,8 +38,6 @@ public abstract class AbstractCurationTask implements CurationTask {
     protected Curator curator = null;
     // curator-assigned taskId
     protected String taskId = null;
-    // logger
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AbstractCurationTask.class);
     protected CommunityService communityService;
     protected ItemService itemService;
     protected HandleService handleService;

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

@@ -19,7 +19,6 @@ import org.apache.commons.lang3.tuple.Pair;
 import org.apache.logging.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
 import org.dspace.content.Bundle;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
@@ -46,7 +45,7 @@ public class CitationPage extends AbstractCurationTask {
     /**
      * Class Logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(CitationPage.class);
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(CitationPage.class);
 
     protected int status = Curator.CURATE_UNSET;
     protected String result = null;
@@ -97,7 +96,7 @@ public class CitationPage extends AbstractCurationTask {
         //Determine if the DISPLAY bundle exits. If not, create it.
         List<Bundle> dBundles = itemService.getBundles(item, CitationPage.DISPLAY_BUNDLE_NAME);
         Bundle dBundle = null;
-        if (dBundles == null || dBundles.size() == 0) {
+        if (dBundles == null || dBundles.isEmpty()) {
             try {
                 dBundle = bundleService.create(Curator.curationContext(), item, CitationPage.DISPLAY_BUNDLE_NAME);
             } catch (AuthorizeException e) {
@@ -110,7 +109,7 @@ public class CitationPage extends AbstractCurationTask {
 
         //Create a map of the bitstreams in the displayBundle. This is used to
         //check if the bundle being cited is already in the display bundle.
-        Map<String, Bitstream> displayMap = new HashMap<String, Bitstream>();
+        Map<String, Bitstream> displayMap = new HashMap<>();
         for (Bitstream bs : dBundle.getBitstreams()) {
             displayMap.put(bs.getName(), bs);
         }
@@ -143,15 +142,16 @@ public class CitationPage extends AbstractCurationTask {
             // Loop through each file and generate a cover page for documents
             // that are PDFs.
             for (Bitstream bitstream : bitstreams) {
-                BitstreamFormat format = bitstream.getFormat(Curator.curationContext());
 
                 //If bitstream is a PDF document then it is citable.
                 CitationDocumentService citationDocument = DisseminateServiceFactory.getInstance()
                                                                                     .getCitationDocumentService();
 
                 if (citationDocument.canGenerateCitationVersion(Curator.curationContext(), bitstream)) {
-                    this.resBuilder.append(item.getHandle() + " - "
+                    this.resBuilder.append(item.getHandle())
-                                               + bitstream.getName() + " is citable.");
+                            .append(" - ")
+                            .append(bitstream.getName())
+                            .append(" is citable.");
                     try {
                         //Create the cited document
                         Pair<InputStream, Long> citedDocument =
@@ -168,7 +168,9 @@ public class CitationPage extends AbstractCurationTask {
                         StringBuilder stack = new StringBuilder();
                         int numLines = Math.min(stackTrace.length, 12);
                         for (int j = 0; j < numLines; j++) {
-                            stack.append("\t" + stackTrace[j].toString() + "\n");
+                            stack.append("\t")
+                                    .append(stackTrace[j].toString())
+                                    .append("\n");
                         }
                         if (stackTrace.length > numLines) {
                             stack.append("\t. . .\n");
@@ -180,8 +182,10 @@ public class CitationPage extends AbstractCurationTask {
                     }
                 } else {
                     //bitstream is not a document
-                    this.resBuilder.append(item.getHandle() + " - "
+                    this.resBuilder.append(item.getHandle())
-                                               + bitstream.getName() + " is not citable.\n");
+                            .append(" - ")
+                            .append(bitstream.getName())
+                            .append(" is not citable.\n");
                     this.status = Curator.CURATE_SUCCESS;
                 }
             }
@@ -211,11 +215,11 @@ public class CitationPage extends AbstractCurationTask {
         //If we are modifying a file that is not in the
         //preservation bundle then we have to move it there.
         Context context = Curator.curationContext();
-        if (bundle.getID() != pBundle.getID()) {
+        if (!bundle.getID().equals(pBundle.getID())) {
             bundleService.addBitstream(context, pBundle, bitstream);
             bundleService.removeBitstream(context, bundle, bitstream);
             List<Bitstream> bitstreams = bundle.getBitstreams();
-            if (bitstreams == null || bitstreams.size() == 0) {
+            if (bitstreams == null || bitstreams.isEmpty()) {
                 itemService.removeBundle(context, item, bundle);
             }
         }
@@ -235,9 +239,11 @@ public class CitationPage extends AbstractCurationTask {
         bitstreamService.setFormat(context, citedBitstream, bitstream.getFormat(Curator.curationContext()));
         citedBitstream.setDescription(context, bitstream.getDescription());
 
-        this.resBuilder.append(" Added "
+        this.resBuilder.append(" Added ")
-                                   + citedBitstream.getName()
+                .append(citedBitstream.getName())
-                                   + " to the " + CitationPage.DISPLAY_BUNDLE_NAME + " bundle.\n");
+                .append(" to the ")
+                .append(CitationPage.DISPLAY_BUNDLE_NAME)
+                .append(" bundle.\n");
 
         //Run update to propagate changes to the
         //database.

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

@@ -13,16 +13,17 @@ import java.io.File;
 import java.io.FileReader;
 import java.io.FileWriter;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Set;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.services.factory.DSpaceServicesFactory;
 
-
 /**
  * FileTaskQueue provides a TaskQueue implementation based on flat files
  * for the queues and semaphores.
@@ -30,14 +31,16 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  * @author richardrodgers
  */
 public class FileTaskQueue implements TaskQueue {
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(TaskQueue.class);
+    private static final Logger log = LogManager.getLogger(TaskQueue.class);
+
     // base directory for curation task queues
     protected String tqDir;
 
     // ticket for queue readers
     protected long readTicket = -1L;
+
     // list of queues owned by reader
-    protected List<Integer> readList = new ArrayList<Integer>();
+    protected List<Integer> readList = new ArrayList<>();
 
     public FileTaskQueue() {
         tqDir = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("curate.taskqueue.dir");
@@ -72,7 +75,7 @@ public class FileTaskQueue implements TaskQueue {
                 BufferedWriter writer = null;
                 try {
                     File queue = new File(qDir, "queue" + Integer.toString(queueIdx));
-                    writer = new BufferedWriter(new FileWriter(queue, true));
+                    writer = new BufferedWriter(new FileWriter(queue, StandardCharsets.UTF_8, true));
                     Iterator<TaskQueueEntry> iter = entrySet.iterator();
                     while (iter.hasNext()) {
                         writer.write(iter.next().toString());
@@ -96,7 +99,7 @@ public class FileTaskQueue implements TaskQueue {
     @Override
     public synchronized Set<TaskQueueEntry> dequeue(String queueName, long ticket)
         throws IOException {
-        Set<TaskQueueEntry> entrySet = new HashSet<TaskQueueEntry>();
+        Set<TaskQueueEntry> entrySet = new HashSet<>();
         if (readTicket == -1L) {
             // hold the ticket & copy all Ids available, locking queues
             // stop when no more queues or one found locked
@@ -113,8 +116,8 @@ public class FileTaskQueue implements TaskQueue {
                     // read contents from file
                     BufferedReader reader = null;
                     try {
-                        reader = new BufferedReader(new FileReader(queue));
+                        reader = new BufferedReader(new FileReader(queue, StandardCharsets.UTF_8));
-                        String entryStr = null;
+                        String entryStr;
                         while ((entryStr = reader.readLine()) != null) {
                             entryStr = entryStr.trim();
                             if (entryStr.length() > 0) {

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

@@ -24,7 +24,7 @@ public class ResolvedTask {
     private CurationTask cTask;
     private ScriptedTask sTask;
     // local name of task
-    private String taskName;
+    private final String taskName;
     // annotation data
     private boolean distributive = false;
     private boolean mutative = false;
@@ -76,7 +76,7 @@ public class ResolvedTask {
      * @throws IOException if error
      */
     public int perform(DSpaceObject dso) throws IOException {
-        return (unscripted()) ? cTask.perform(dso) : sTask.performDso(dso);
+        return unscripted() ? cTask.perform(dso) : sTask.performDso(dso);
     }
 
     /**
@@ -88,7 +88,7 @@ public class ResolvedTask {
      * @throws IOException if error
      */
     public int perform(Context ctx, String id) throws IOException {
-        return (unscripted()) ? cTask.perform(ctx, id) : sTask.performId(ctx, id);
+        return unscripted() ? cTask.perform(ctx, id) : sTask.performId(ctx, id);
     }
 
     /**

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

@@ -15,11 +15,13 @@ import java.io.FileWriter;
 import java.io.IOException;
 import java.io.Reader;
 import java.io.Writer;
+import java.nio.charset.StandardCharsets;
 import java.util.Properties;
 import javax.script.ScriptEngine;
 import javax.script.ScriptEngineManager;
 import javax.script.ScriptException;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.core.factory.CoreServiceFactory;
 import org.dspace.services.factory.DSpaceServicesFactory;
@@ -64,7 +66,7 @@ import org.dspace.services.factory.DSpaceServicesFactory;
 
 public class TaskResolver {
     // logging service
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(TaskResolver.class);
+    private static final Logger log = LogManager.getLogger(TaskResolver.class);
 
     // base directory of task scripts & catalog name
     protected static final String CATALOG = "task.catalog";
@@ -94,7 +96,7 @@ public class TaskResolver {
         if (script.exists()) {
             BufferedReader reader = null;
             try {
-                reader = new BufferedReader(new FileReader(script));
+                reader = new BufferedReader(new FileReader(script, StandardCharsets.UTF_8));
                 String line = null;
                 while ((line = reader.readLine()) != null) {
                     if (line.startsWith("#") && line.indexOf("$td=") > 0) {
@@ -136,7 +138,7 @@ public class TaskResolver {
         catalog.put(taskName, descriptor);
         Writer writer = null;
         try {
-            writer = new FileWriter(new File(scriptDir, CATALOG));
+            writer = new FileWriter(new File(scriptDir, CATALOG), StandardCharsets.UTF_8);
             catalog.store(writer, "do not edit");
         } catch (IOException ioE) {
             log.error("Error saving scripted task catalog: " + CATALOG);
@@ -179,7 +181,7 @@ public class TaskResolver {
                 File script = new File(scriptDir, tokens[1]);
                 if (script.exists()) {
                     try {
-                        Reader reader = new FileReader(script);
+                        Reader reader = new FileReader(script, StandardCharsets.UTF_8);
                         engine.eval(reader);
                         reader.close();
                         // third token is the constructor expression for the class
@@ -212,7 +214,7 @@ public class TaskResolver {
             File catalogFile = new File(scriptDir, CATALOG);
             if (catalogFile.exists()) {
                 try {
-                    Reader reader = new FileReader(catalogFile);
+                    Reader reader = new FileReader(catalogFile, StandardCharsets.UTF_8);
                     catalog.load(reader);
                     reader.close();
                 } catch (IOException ioE) {

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

@@ -15,7 +15,6 @@ import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.LinkedHashMap;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
@@ -23,7 +22,7 @@ import org.apache.commons.collections4.CollectionUtils;
 import org.dspace.discovery.configuration.DiscoverySearchFilterFacet;
 
 /**
- * This class represents a query which the discovery backend can use
+ * This class represents a query which the discovery back-end can use.
  *
  * @author Kevin Van de Velde (kevin at atmire dot com)
  */
@@ -33,9 +32,9 @@ public class DiscoverQuery {
      * Main attributes for the discovery query
      **/
     private String query;
-    private List<String> filterQueries;
+    private final List<String> filterQueries;
     private List<String> dspaceObjectFilters = new ArrayList<>();
-    private List<String> fieldPresentQueries;
+    private final List<String> fieldPresentQueries;
     private boolean spellCheck;
 
     private int start = 0;
@@ -55,36 +54,35 @@ public class DiscoverQuery {
     /**
      * Attributes required for the faceting of values
      **/
-    private List<DiscoverFacetField> facetFields;
+    private final List<DiscoverFacetField> facetFields;
-    private List<String> facetQueries;
+    private final List<String> facetQueries;
-    private int facetLimit = -1;
     private int facetMinCount = -1;
     private int facetOffset = 0;
-    private Map<String, DiscoverHitHighlightingField> hitHighlighting;
+    private final Map<String, DiscoverHitHighlightingField> hitHighlighting;
 
     /**
      * Used when you want to search for a specific field value
      **/
-    private List<String> searchFields;
+    private final List<String> searchFields;
 
     /**
      * Misc attributes can be implementation dependent
      **/
-    private Map<String, List<String>> properties;
+    private final Map<String, List<String>> properties;
 
     private String discoveryConfigurationName;
 
     public DiscoverQuery() {
         //Initialize all our lists
-        this.filterQueries = new ArrayList<String>();
+        this.filterQueries = new ArrayList<>();
-        this.fieldPresentQueries = new ArrayList<String>();
+        this.fieldPresentQueries = new ArrayList<>();
 
-        this.facetFields = new ArrayList<DiscoverFacetField>();
+        this.facetFields = new ArrayList<>();
-        this.facetQueries = new ArrayList<String>();
+        this.facetQueries = new ArrayList<>();
-        this.searchFields = new ArrayList<String>();
+        this.searchFields = new ArrayList<>();
-        this.hitHighlighting = new HashMap<String, DiscoverHitHighlightingField>();
+        this.hitHighlighting = new HashMap<>();
         //Use a linked hashmap since sometimes insertion order might matter
-        this.properties = new LinkedHashMap<String, List<String>>();
+        this.properties = new LinkedHashMap<>();
     }
 
 
@@ -274,7 +272,7 @@ public class DiscoverQuery {
     /**
      * Sets the fields which you want Discovery to return in the search results.
      * It is HIGHLY recommended to limit the fields returned, as by default
-     * some backends (like Solr) will return everything.
+     * some back-ends (like Solr) will return everything.
      *
      * @param field field to add to the list of fields returned
      */
@@ -309,7 +307,7 @@ public class DiscoverQuery {
     public void addProperty(String property, String value) {
         List<String> toAddList = properties.get(property);
         if (toAddList == null) {
-            toAddList = new ArrayList<String>();
+            toAddList = new ArrayList<>();
         }
 
         toAddList.add(value);
@@ -322,7 +320,7 @@ public class DiscoverQuery {
     }
 
     public List<DiscoverHitHighlightingField> getHitHighlightingFields() {
-        return new ArrayList<DiscoverHitHighlightingField>(hitHighlighting.values());
+        return new ArrayList<>(hitHighlighting.values());
     }
 
     public void addHitHighlightingField(DiscoverHitHighlightingField hitHighlighting) {
@@ -368,7 +366,7 @@ public class DiscoverQuery {
 
     private List<String> buildFacetQueriesWithGap(int newestYear, int oldestYear, String dateFacet, int gap,
                                                   int topYear, int facetLimit) {
-        List<String> facetQueries = new LinkedList<>();
+        List<String> facetQueries = new ArrayList<>();
         for (int year = topYear; year > oldestYear && (facetQueries.size() < facetLimit); year -= gap) {
             //Add a filter to remove the last year only if we aren't the last year
             int bottomYear = year - gap;
@@ -392,7 +390,7 @@ public class DiscoverQuery {
     }
 
     private int getTopYear(int newestYear, int gap) {
-        return (int) (Math.ceil((float) (newestYear) / gap) * gap);
+        return (int) (Math.ceil((float) newestYear / gap) * gap);
     }
 
     /**

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

@@ -16,9 +16,9 @@ import java.io.Reader;
 import java.io.SequenceInputStream;
 import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
+import java.util.ArrayList;
 import java.util.Enumeration;
 import java.util.Iterator;
-import java.util.LinkedList;
 import java.util.List;
 import javax.annotation.Nullable;
 
@@ -55,7 +55,7 @@ public class FullTextContentStreams extends ContentStreamBase {
     }
 
     protected void init(Item parentItem) {
-        fullTextStreams = new LinkedList<>();
+        fullTextStreams = new ArrayList<>();
 
         if (parentItem != null) {
             sourceInfo = parentItem.getHandle();
@@ -149,8 +149,8 @@ public class FullTextContentStreams extends ContentStreamBase {
     }
 
     private class FullTextBitstream {
-        private String itemHandle;
+        private final String itemHandle;
-        private Bitstream bitstream;
+        private final Bitstream bitstream;
 
         public FullTextBitstream(final String parentHandle, final Bitstream file) {
             this.itemHandle = parentHandle;
@@ -179,18 +179,25 @@ public class FullTextContentStreams extends ContentStreamBase {
         }
     }
 
-    private class FullTextEnumeration implements Enumeration<InputStream> {
+    /**
+     * {@link Enumeration} is implemented because instances of this class are
+     * passed to a JDK class that requires this obsolete type.
+     */
+    @SuppressWarnings("JdkObsolete")
+    private static class FullTextEnumeration implements Enumeration<InputStream> {
 
         private final Iterator<FullTextBitstream> fulltextIterator;
 
-        public FullTextEnumeration(final Iterator<FullTextBitstream> fulltextStreams) {
+        public FullTextEnumeration(final Iterator<FullTextBitstream> fulltextIterator) {
-            this.fulltextIterator = fulltextStreams;
+            this.fulltextIterator = fulltextIterator;
         }
 
+        @Override
         public boolean hasMoreElements() {
             return fulltextIterator.hasNext();
         }
 
+        @Override
         public InputStream nextElement() {
             InputStream inputStream = null;
             FullTextBitstream bitstream = null;

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

@@ -55,7 +55,7 @@ public class SolrServiceFileInfoPlugin implements SolrServiceIndexPlugin {
                                 document.addField(SOLR_FIELD_NAME_FOR_FILENAMES, bitstream.getName());
 
                                 String description = bitstream.getDescription();
-                                if ((description != null) && (!description.isEmpty())) {
+                                if ((description != null) && !description.isEmpty()) {
                                     document.addField(SOLR_FIELD_NAME_FOR_DESCRIPTIONS, description);
                                 }
                             }

dspace-api/src/main/java/org/dspace/discovery/indexobject/AbstractIndexableObject.java

@@ -14,10 +14,13 @@ import org.dspace.discovery.IndexableObject;
 
 /**
  * This class exists in order to provide a default implementation for the equals and hashCode methods.
- * Since IndexableObjects can be made multiple times for the same underlying object, we needed a more finetuned
+ * Since IndexableObjects can be made multiple times for the same underlying
- * equals and hashcode methods. We're simply checking that the underlying objects are equal and generating the hashcode
+ * object, we needed more finely-tuned {@link equals} and {@link hashCode} methods.
- * for the underlying object. This way, we'll always get a proper result when calling equals or hashcode on an
+ * We're simply checking that the underlying objects are equal and returning the
- * IndexableObject because it'll depend on the underlying object
+ * hash-code for the underlying object. This way, we'll always get a proper
+ * result when calling {@link equals} or {@link hashCode} on an IndexableObject
+ * because it'll depend on the underlying object.
+ *
  * @param <T>   Refers to the underlying entity that is linked to this object
  * @param <PK>  The type of ID that this entity uses
  */

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

@@ -11,6 +11,7 @@ import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;
 import java.io.IOException;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
@@ -108,7 +109,7 @@ public class LoadLastLogin {
         final SimpleDateFormat dateEncoder = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
 
         for (String logName : args) {
-            BufferedReader logReader = new BufferedReader(new FileReader(logName));
+            BufferedReader logReader = new BufferedReader(new FileReader(logName, StandardCharsets.UTF_8));
             while (true) {
                 String line = logReader.readLine();
                 // End of file?

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

@@ -53,6 +53,7 @@ public class Subscription implements ReloadableEntity<Integer> {
 
     }
 
+    @Override
     public Integer getID() {
         return id;
     }

dspace-api/src/main/java/org/dspace/eperson/dao/impl/SubscriptionDAOImpl.java

@@ -8,7 +8,7 @@
 package org.dspace.eperson.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;
@@ -97,7 +97,7 @@ public class SubscriptionDAOImpl extends AbstractHibernateDAO<Subscription> impl
         Root<Subscription> subscriptionRoot = criteriaQuery.from(Subscription.class);
         criteriaQuery.select(subscriptionRoot);
 
-        List<javax.persistence.criteria.Order> orderList = new LinkedList<>();
+        List<javax.persistence.criteria.Order> orderList = new ArrayList<>(1);
         orderList.add(criteriaBuilder.asc(subscriptionRoot.get(Subscription_.ePerson)));
         criteriaQuery.orderBy(orderList);
 

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

@@ -104,7 +104,9 @@ public class ConsumerProfile {
                 "No filters configured for consumer named: " + name);
         }
 
-        consumer = (Consumer) Class.forName(className.trim()).getDeclaredConstructor().newInstance();
+        consumer = Class.forName(className.trim())
+                .asSubclass(Consumer.class)
+                .getDeclaredConstructor().newInstance();
 
         // Each "filter" is <objectTypes> + <eventTypes> : ...
         filters = new ArrayList<>();

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

@@ -48,8 +48,6 @@ import org.dspace.event.factory.EventServiceFactory;
  * significance varies by the combination of action and subject type.</li>
  * <li> - timestamp -- exact millisecond timestamp at which event was logged.</li>
  * </ul>
- *
- * @version $Revision$
  */
 public class Event implements Serializable {
     private static final long serialVersionUID = 1L;
@@ -308,6 +306,7 @@ public class Event implements Serializable {
      * @param other the event to compare this one to
      * @return true if events are "equal", false otherwise.
      */
+    @Override
     public boolean equals(Object other) {
         if (other instanceof Event) {
             Event otherEvent = (Event) other;
@@ -315,14 +314,15 @@ public class Event implements Serializable {
                 .equals(otherEvent.detail))
                 && this.eventType == otherEvent.eventType
                 && this.subjectType == otherEvent.subjectType
-                && this.subjectID == otherEvent.subjectID
+                && this.subjectID.equals(otherEvent.subjectID)
                 && this.objectType == otherEvent.objectType
-                && this.objectID == otherEvent.objectID;
+                && this.objectID.equals(otherEvent.objectID);
         }
 
         return false;
     }
 
+    @Override
     public int hashCode() {
         return new HashCodeBuilder().append(this.detail)
                                     .append(eventType)
@@ -634,6 +634,7 @@ public class Event implements Serializable {
      * @return Detailed string representation of contents of this event, to
      * help in logging and debugging.
      */
+    @Override
     public String toString() {
         return "org.dspace.event.Event(eventType="
             + this.getEventTypeAsString()

dspace-api/src/main/java/org/dspace/external/OrcidRestConnector.java

@@ -8,6 +8,7 @@
 package org.dspace.external;
 
 import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
 import java.util.Scanner;
 
 import org.apache.commons.lang3.StringUtils;
@@ -15,6 +16,7 @@ import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 /**
@@ -28,9 +30,9 @@ public class OrcidRestConnector {
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(OrcidRestConnector.class);
+    private static final Logger log = LogManager.getLogger(OrcidRestConnector.class);
 
-    private String url;
+    private final String url;
 
     public OrcidRestConnector(String url) {
         this.url = url;
@@ -74,7 +76,7 @@ public class OrcidRestConnector {
     }
 
     public static String convertStreamToString(InputStream is) {
-        Scanner s = new Scanner(is).useDelimiter("\\A");
+        Scanner s = new Scanner(is, StandardCharsets.UTF_8).useDelimiter("\\A");
         return s.hasNext() ? s.next() : "";
     }
 }

dspace-api/src/main/java/org/dspace/external/model/ExternalDataObject.java

@@ -7,7 +7,7 @@
  */
 package org.dspace.external.model;
 
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 
 import org.dspace.content.dto.MetadataValueDTO;
@@ -32,7 +32,7 @@ public class ExternalDataObject {
     /**
      * The list of Metadata values. These our MetadataValueDTO because they won't exist in the DB
      */
-    private List<MetadataValueDTO> metadata = new LinkedList<>();
+    private List<MetadataValueDTO> metadata = new ArrayList<>();
     /**
      * The display value of the ExternalDataObject
      */
@@ -87,11 +87,11 @@ public class ExternalDataObject {
 
     /**
      * This method will add a Metadata value to the list of metadata values
-     * @param metadataValueDTO The metadatavalue to be added
+     * @param metadataValueDTO The metadata value to be added.
      */
     public void addMetadata(MetadataValueDTO metadataValueDTO) {
         if (metadata == null) {
-            metadata = new LinkedList<>();
+            metadata = new ArrayList<>();
         }
         metadata.add(metadataValueDTO);
     }

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

@@ -13,7 +13,6 @@ import javax.xml.bind.JAXBContext;
 import javax.xml.bind.JAXBException;
 import javax.xml.bind.Unmarshaller;
 
-import org.apache.logging.log4j.Logger;
 import org.xml.sax.SAXException;
 
 /**
@@ -25,11 +24,6 @@ import org.xml.sax.SAXException;
  */
 public abstract class Converter<T> {
 
-    /**
-     * log4j logger
-     */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(Converter.class);
-
     public abstract T convert(InputStream document);
 
     protected Object unmarshall(InputStream input, Class<?> type) throws SAXException, URISyntaxException {

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

@@ -105,7 +105,7 @@ public class Handle implements ReloadableEntity<Integer> {
             return true;
         }
 
-        if (o == null || getClass() != o.getClass()) {
+        if (!(o instanceof Handle)) {
             return false;
         }
 

dspace-api/src/main/java/org/dspace/harvest/HarvestedItem.java

@@ -56,6 +56,7 @@ public class HarvestedItem implements ReloadableEntity<Integer> {
     protected HarvestedItem() {
     }
 
+    @Override
     public Integer getID() {
         return id;
     }
@@ -89,7 +90,6 @@ public class HarvestedItem implements ReloadableEntity<Integer> {
      */
     public void setOaiID(String itemOaiID) {
         this.oaiId = itemOaiID;
-        return;
     }
 
 

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

@@ -62,6 +62,7 @@ public class DOI
     protected DOI() {
     }
 
+    @Override
     public Integer getID() {
         return id;
     }

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

@@ -158,6 +158,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * Spring will use this setter to set the filter from the configured property in identifier-services.xml
      * @param filterService - an object implementing the org.dspace.content.logic.Filter interface
      */
+    @Override
     public void setFilterService(Filter filterService) {
         this.filterService = filterService;
     }
@@ -319,7 +320,6 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * @param skipFilter - boolean indicating whether to skip any filtering of items before performing reservation
      * @throws IdentifierException
      * @throws IllegalArgumentException
-     * @throws SQLException
      */
     @Override
     public void reserve(Context context, DSpaceObject dso, String identifier, boolean skipFilter)
@@ -367,6 +367,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * @param context       - DSpace context
      * @param dso           - DSpaceObject identified by this DOI
      * @param identifier    - String containing the DOI to reserve
+     * @param skipFilter    - skip the filters for {@link checkMintable(Context, DSpaceObject)}
      * @throws IdentifierException
      * @throws IllegalArgumentException
      * @throws SQLException
@@ -410,6 +411,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * @param context       - DSpace context
      * @param dso           - DSpaceObject identified by this DOI
      * @param identifier    - String containing the DOI to register
+     * @param skipFilter    - skip filters for {@link checkMintable(Context, DSpaceObject)}
      * @throws IdentifierException
      * @throws IllegalArgumentException
      * @throws SQLException
@@ -785,7 +787,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * Delete a specific DOI in the registration agency records via the DOI Connector
      * @param context    - DSpace context
      * @param identifier - String containing identifier to delete
-     * @throws IdentifierException
+     * @throws DOIIdentifierException
      */
     public void deleteOnline(Context context, String identifier) throws DOIIdentifierException {
         String doi = doiService.formatIdentifier(identifier);
@@ -826,7 +828,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      *                   {@link org.dspace.identifier.service.DOIService#formatIdentifier(String)}.
      * @return Null if the DOI couldn't be found or the associated DSpaceObject.
      * @throws SQLException if database error
-     * @throws IdentifierException If {@code identifier} is null or an empty string.
+     * @throws DOIIdentifierException If {@code identifier} is null or an empty string.
      * @throws IllegalArgumentException If the identifier couldn't be recognized as DOI.
      */
     public DSpaceObject getObjectByDOI(Context context, String identifier)
@@ -876,10 +878,10 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
     }
 
     /**
-     * Load a DOI from the database or creates it if it does not exist. This
+     * Load a DOI from the database or creates it if it does not exist.
-     * method can be used to ensure that a DOI exists in the database and to
+     * This method can be used to ensure that a DOI exists in the database and
-     * load the appropriate TableRow. As protected method we don't check if the
+     * to load the appropriate TableRow. As protected method we don't check if
-     * DOI is in a decent format, use DOI.formatIdentifier(String) if necessary.
+     * the DOI is in a decent format, use DOI.formatIdentifier(String) if necessary.
      *
      * @param context       The relevant DSpace Context.
      * @param dso           The DSpaceObject the DOI should be loaded or created for.
@@ -889,6 +891,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * @throws SQLException           In case of an error using the database.
      * @throws DOIIdentifierException If {@code doi} is not part of our prefix or
      *                                DOI is registered for another object already.
+     * @throws IdentifierNotApplicableException passed through.
      */
     protected DOI loadOrCreateDOI(Context context, DSpaceObject dso, String doiIdentifier)
             throws SQLException, DOIIdentifierException, IdentifierNotApplicableException {
@@ -896,11 +899,13 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
     }
 
     /**
-     * Load DOI from database, or create one if it doesn't yet exist
+     * Load DOI from database, or create one if it doesn't yet exist.
-     * We need to distinguish several cases. LoadOrCreate can be called with a specifid identifier to load or create.
+     * We need to distinguish several cases.LoadOrCreate can be called with a
-     * It can also be used to create a new unspecified identifier. In the latter case doiIdentifier is set null.
+     * specified identifier to load or create. It can also be used to create a
-     * If doiIdentifier is set, we know which doi we should try to load or create, but even in sucha situation
+     * new unspecified identifier. In the latter case doiIdentifier is set null.
-     * we might be able to find it in the database or might have to create it.
+     * If doiIdentifier is set, we know which doi we should try to load or
+     * create, but even in such a situation we might be able to find it in the
+     * database or might have to create it.
      *
      * @param context       - DSpace context
      * @param dso           - DSpaceObject to identify
@@ -909,6 +914,7 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
      * @return
      * @throws SQLException
      * @throws DOIIdentifierException
+     * @throws org.dspace.identifier.IdentifierNotApplicableException passed through.
      */
     protected DOI loadOrCreateDOI(Context context, DSpaceObject dso, String doiIdentifier, boolean skipFilter)
         throws SQLException, DOIIdentifierException, IdentifierNotApplicableException {
@@ -929,11 +935,11 @@ public class DOIIdentifierProvider extends FilteredIdentifierProvider {
                         && doi.getResourceTypeId() != dso.getType()) {
                         // doi was assigned to another resource type. Don't
                         // reactivate it
-                        throw new DOIIdentifierException("Cannot reassing "
+                        throw new DOIIdentifierException("Cannot reassign"
-                            + "previously deleted DOI " + doiIdentifier
+                            + " previously deleted DOI " + doiIdentifier
-                            + " as the resource types of the object it was "
+                            + " as the resource types of the object it was"
-                            + "previously assigned to and the object it "
+                            + " previously assigned to and the object it"
-                            + "shall be assigned to now divert (was: "
+                            + " shall be assigned to now differ (was: "
                             + Constants.typeText[doi.getResourceTypeId()]
                             + ", trying to assign to "
                             + Constants.typeText[dso.getType()] + ").",

dspace-api/src/main/java/org/dspace/identifier/dao/impl/DOIDAOImpl.java

@@ -8,7 +8,7 @@
 package org.dspace.identifier.dao.impl;
 
 import java.sql.SQLException;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -52,7 +52,7 @@ public class DOIDAOImpl extends AbstractHibernateDAO<DOI> implements DOIDAO {
         Root<DOI> doiRoot = criteriaQuery.from(DOI.class);
         criteriaQuery.select(doiRoot);
 
-        List<Predicate> listToIncludeInOrPredicate = new LinkedList<>();
+        List<Predicate> listToIncludeInOrPredicate = new ArrayList<>(statusToExclude.size() + 1);
 
         for (Integer status : statusToExclude) {
             listToIncludeInOrPredicate.add(criteriaBuilder.notEqual(doiRoot.get(DOI_.status), status));
@@ -75,7 +75,7 @@ public class DOIDAOImpl extends AbstractHibernateDAO<DOI> implements DOIDAO {
         CriteriaQuery criteriaQuery = getCriteriaQuery(criteriaBuilder, DOI.class);
         Root<DOI> doiRoot = criteriaQuery.from(DOI.class);
         criteriaQuery.select(doiRoot);
-        List<Predicate> orPredicates = new LinkedList<>();
+        List<Predicate> orPredicates = new ArrayList<>(statuses.size());
         for (Integer status : statuses) {
             orPredicates.add(criteriaBuilder.equal(doiRoot.get(DOI_.status), status));
         }
@@ -92,13 +92,13 @@ public class DOIDAOImpl extends AbstractHibernateDAO<DOI> implements DOIDAO {
         Root<DOI> doiRoot = criteriaQuery.from(DOI.class);
         criteriaQuery.select(doiRoot);
 
-        List<Predicate> listToIncludeInOrPredicate = new LinkedList<>();
+        List<Predicate> listToIncludeInOrPredicate = new ArrayList<>(excludedStatuses.size());
 
         for (Integer status : excludedStatuses) {
             listToIncludeInOrPredicate.add(criteriaBuilder.notEqual(doiRoot.get(DOI_.status), status));
         }
 
-        List<Predicate> listToIncludeInAndPredicate = new LinkedList<>();
+        List<Predicate> listToIncludeInAndPredicate = new ArrayList<>();
 
         listToIncludeInAndPredicate.add(criteriaBuilder.like(doiRoot.get(DOI_.doi), doi));
         listToIncludeInAndPredicate.add(criteriaBuilder.or(listToIncludeInOrPredicate.toArray(new Predicate[] {})));
@@ -107,8 +107,6 @@ public class DOIDAOImpl extends AbstractHibernateDAO<DOI> implements DOIDAO {
         }
         criteriaQuery.where(listToIncludeInAndPredicate.toArray(new Predicate[] {}));
         return list(context, criteriaQuery, false, DOI.class, -1, -1);
-
-
     }
 
     @Override

dspace-api/src/main/java/org/dspace/importer/external/datamodel/ImportRecord.java

@@ -7,9 +7,9 @@
  */
 package org.dspace.importer.external.datamodel;
 
+import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
-import java.util.LinkedList;
 import java.util.List;
 
 import org.dspace.importer.external.metadatamapping.MetadatumDTO;
@@ -38,7 +38,7 @@ public class ImportRecord {
      */
     public ImportRecord(List<MetadatumDTO> valueList) {
         //don't want to alter the original list. Also now I can control the type of list
-        this.valueList = new LinkedList<>(valueList);
+        this.valueList = new ArrayList<>(valueList);
     }
 
     /**
@@ -81,7 +81,7 @@ public class ImportRecord {
      * @return the MetadatumDTO's that are related to a given schema/element/qualifier pair/triplet
      */
     public Collection<MetadatumDTO> getValue(String schema, String element, String qualifier) {
-        List<MetadatumDTO> values = new LinkedList<MetadatumDTO>();
+        List<MetadatumDTO> values = new ArrayList<MetadatumDTO>();
         for (MetadatumDTO value : valueList) {
             if (value.getSchema().equals(schema) && value.getElement().equals(element)) {
                 if (qualifier == null && value.getQualifier() == null) {

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

@@ -7,18 +7,19 @@
  */
 package org.dspace.importer.external.metadatamapping;
 
+import java.util.ArrayList;
 import java.util.Collection;
-import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.importer.external.metadatamapping.contributor.MetadataContributor;
 import org.dspace.importer.external.metadatamapping.transform.MetadataProcessorService;
 
 /**
- * Abstract class that implements {@link MetadataFieldMapping}
+ * Abstract class that implements {@link MetadataFieldMapping}.
- * This class adds a default implementation for the MetadataFieldMapping methods
+ * This class adds a default implementation for the MetadataFieldMapping methods.
  *
  * @author Roeland Dillen (roeland at atmire dot com)
  */
@@ -30,7 +31,7 @@ public abstract class AbstractMetadataFieldMapping<RecordType>
     /**
      * log4j logger
      */
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(AbstractMetadataFieldMapping.class);
+    private static final Logger log = LogManager.getLogger(AbstractMetadataFieldMapping.class);
 
     /* A map containing what processing has to be done on a given metadataFieldConfig.
      * The processing of a value is used to determine the actual value that will be returned used.
@@ -66,6 +67,7 @@ public abstract class AbstractMetadataFieldMapping<RecordType>
      * @param value The value to map to a MetadatumDTO
      * @return A metadatumDTO created from the field and value
      */
+    @Override
     public MetadatumDTO toDCValue(MetadataFieldConfig field, String value) {
         MetadatumDTO dcValue = new MetadatumDTO();
 
@@ -108,14 +110,15 @@ public abstract class AbstractMetadataFieldMapping<RecordType>
     }
 
     /**
-     * Loop over the MetadataContributors and return their concatenated retrieved metadatumDTO objects
+     * Loop over the MetadataContributors and return their concatenated
+     * retrieved metadatumDTO objects.
      *
      * @param record Used to retrieve the MetadatumDTO
      * @return Lit of metadatumDTO
      */
     @Override
     public Collection<MetadatumDTO> resultToDCValueMapping(RecordType record) {
-        List<MetadatumDTO> values = new LinkedList<MetadatumDTO>();
+        List<MetadatumDTO> values = new ArrayList<>();
 
         for (MetadataContributor<RecordType> query : getMetadataFieldMap().values()) {
             try {

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

@@ -8,7 +8,7 @@
 package org.dspace.importer.external.metadatamapping;
 
 /**
- * A generalised configuration for metadatafields.
+ * A generalised configuration for metadata fields.
  * This is used to make the link between values and the actual MetadatumDTO object.
  *
  * @author Roeland Dillen (roeland at atmire dot com)
@@ -31,7 +31,7 @@ public class MetadataFieldConfig {
         if (this == o) {
             return true;
         }
-        if (o == null || getClass() != o.getClass()) {
+        if (o == null || !(o instanceof MetadataFieldConfig)) {
             return false;
         }
 
@@ -43,11 +43,7 @@ public class MetadataFieldConfig {
         if (qualifier != null ? !qualifier.equals(that.qualifier) : that.qualifier != null) {
             return false;
         }
-        if (!schema.equals(that.schema)) {
+        return schema.equals(that.schema);
-            return false;
-        }
-
-        return true;
     }
 
     /**

dspace-api/src/main/java/org/dspace/license/LicenseCleanup.java

@@ -15,6 +15,7 @@ import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.StringWriter;
+import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.util.Iterator;
 import java.util.List;
@@ -38,7 +39,8 @@ import org.dspace.content.service.ItemService;
 import org.dspace.core.Context;
 
 /**
- * Cleanup class for CC Licenses, corrects XML formating errors by replacing the license_rdf bitstream.
+ * Cleanup class for CC Licenses, corrects XML formatting errors by replacing
+ * the license_rdf bitstream.
  *
  * @author mdiggory
  */
@@ -130,7 +132,7 @@ public class LicenseCleanup {
         AuthorizeException, IOException {
         List<Bundle> bundles = itemService.getBundles(item, "CC-LICENSE");
 
-        if (bundles == null || bundles.size() == 0) {
+        if (bundles == null || bundles.isEmpty()) {
             return;
         }
 
@@ -138,7 +140,7 @@ public class LicenseCleanup {
 
         Bitstream bitstream = bundleService.getBitstreamByName(bundle, "license_rdf");
 
-        String license_rdf = new String(copy(context, bitstream));
+        String license_rdf = new String(copy(context, bitstream), StandardCharsets.UTF_8);
 
         /* quickly fix xml by ripping out offensive parts */
         license_rdf = license_rdf.replaceFirst("<license", "");
@@ -148,7 +150,7 @@ public class LicenseCleanup {
 
         try {
             templates.newTransformer().transform(
-                new StreamSource(new ByteArrayInputStream(license_rdf.getBytes())),
+                new StreamSource(new ByteArrayInputStream(license_rdf.getBytes(StandardCharsets.UTF_8))),
                 new StreamResult(result));
         } catch (TransformerException e) {
             throw new IllegalStateException(e.getMessage(), e);
@@ -158,7 +160,7 @@ public class LicenseCleanup {
 
         Bitstream newBitstream = bitstreamService
             .create(context, bundle, new ByteArrayInputStream(buffer.toString()
-                                                                    .getBytes()));
+                                                                    .getBytes(StandardCharsets.UTF_8)));
 
         newBitstream.setName(context, bitstream.getName());
         newBitstream.setDescription(context, bitstream.getDescription());

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

@@ -14,7 +14,8 @@ import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.builder.HashCodeBuilder;
 
 /**
- * This class serves as a representation of a command line parameter by holding a String name and a String value
+ * This class serves as a representation of a command line parameter by holding
+ * a String name and a String value.
  */
 public class DSpaceCommandLineParameter {
     private String name;
@@ -23,7 +24,7 @@ public class DSpaceCommandLineParameter {
     public static String SEPARATOR = "|||";
 
     /**
-     * This constructor will take a String key and String value and store them in their appriopriate fields
+     * This constructor will take a String key and String value and store them in their appropriate fields.
      * @param key   The String value to be stored as the name of the parameter
      * @param value The String value to be stored as the value of the parameter
      */
@@ -64,9 +65,10 @@ public class DSpaceCommandLineParameter {
 
     /**
      * Converts the DSpaceCommandLineParameter into a String format by concatenating the value and the name String
-     * values by separating them with a space
+     * values by separating them with a space.
      * @return The String representation of a DSpaceCommandlineParameter object
      */
+    @Override
     public String toString() {
         String stringToReturn = "";
         stringToReturn += getName();
@@ -92,7 +94,7 @@ public class DSpaceCommandLineParameter {
     }
 
     /**
-     * Will return a boolean indicating whether the given param is equal to this object
+     * Will return a boolean indicating whether the given parameter is equal to this object.
      * @param other The other object
      * @return      A boolean indicating equality
      */
@@ -101,7 +103,7 @@ public class DSpaceCommandLineParameter {
         if (other == null) {
             return false;
         }
-        if (other.getClass() != DSpaceCommandLineParameter.class) {
+        if (!(other instanceof DSpaceCommandLineParameter)) {
             return false;
         }
         return StringUtils.equals(this.getName(), ((DSpaceCommandLineParameter) other).getName()) && StringUtils

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

@@ -8,7 +8,7 @@
 package org.dspace.scripts;
 
 import java.io.InputStream;
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
@@ -37,7 +37,7 @@ public abstract class DSpaceRunnable<T extends ScriptConfiguration> implements R
     protected CommandLine commandLine;
 
     /**
-     * This EPerson identifier variable is the uuid of the eperson that's running the script
+     * This EPerson identifier variable is the UUID of the EPerson that's running the script
      */
     private UUID epersonIdentifier;
 
@@ -129,7 +129,7 @@ public abstract class DSpaceRunnable<T extends ScriptConfiguration> implements R
      * @return  The list of Strings representing filenames from the options given to the script
      */
     public List<String> getFileNamesFromInputStreamOptions() {
-        List<String> fileNames = new LinkedList<>();
+        List<String> fileNames = new ArrayList<>();
 
         for (Option option : getScriptConfiguration().getOptions().getOptions()) {
             if (option.getType() == InputStream.class &&
@@ -151,8 +151,8 @@ public abstract class DSpaceRunnable<T extends ScriptConfiguration> implements R
     }
 
     /**
-     * Generic setter for the epersonIdentifier
+     * Generic setter for the epersonIdentifier.
-     * This EPerson identifier variable is the uuid of the eperson that's running the script
+     * This EPerson identifier variable is the UUID of the EPerson that's running the script.
      * @param epersonIdentifier   The epersonIdentifier to be set on this DSpaceRunnable
      */
     public void setEpersonIdentifier(UUID epersonIdentifier) {

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

@@ -7,8 +7,8 @@
  */
 package org.dspace.scripts;
 
+import java.util.ArrayList;
 import java.util.Date;
-import java.util.LinkedList;
 import java.util.List;
 import javax.persistence.Column;
 import javax.persistence.Entity;
@@ -91,6 +91,7 @@ public class Process implements ReloadableEntity<Integer> {
      * This method returns the ID that the Process holds within the Database
      * @return  The ID that the process holds within the database
      */
+    @Override
     public Integer getID() {
         return processId;
     }
@@ -162,7 +163,8 @@ public class Process implements ReloadableEntity<Integer> {
 
     /**
      * To get the parameters, use ProcessService.getParameters() to get a parsed list of DSpaceCommandLineParameters
-     * This String representation is the parameter in an unparsed fashion. For example "-c test"
+     * This String representation is the parameter in an unparsed fashion.For example "-c test"
+     * @return the raw parameter string.
      */
     protected String getParameters() {
         return parameters;
@@ -179,7 +181,7 @@ public class Process implements ReloadableEntity<Integer> {
      */
     public List<Bitstream> getBitstreams() {
         if (bitstreams == null) {
-            bitstreams = new LinkedList<>();
+            bitstreams = new ArrayList<>();
         }
         return bitstreams;
     }

dspace-api/src/main/java/org/dspace/search/Harvest.java

@@ -11,7 +11,6 @@ import java.sql.SQLException;
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.Iterator;
-import java.util.LinkedList;
 import java.util.List;
 
 import org.apache.logging.log4j.Logger;
@@ -43,7 +42,6 @@ import org.dspace.handle.service.HandleService;
  * withdrawn within a particular range of dates.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 public class Harvest {
     /**
@@ -129,7 +127,7 @@ public class Harvest {
         // several smaller operations (e.g. for OAI resumption tokens.)
         discoverQuery.setSortField("search.resourceid", DiscoverQuery.SORT_ORDER.asc);
 
-        List<HarvestedItemInfo> infoObjects = new LinkedList<HarvestedItemInfo>();
+        List<HarvestedItemInfo> infoObjects = new ArrayList<>();
 
         // Count of items read from the record set that match the selection criteria.
         // Note : Until 'index > offset' the records are not added to the output set.
@@ -155,7 +153,7 @@ public class Harvest {
 
                 if (collections) {
                     // Add collections data
-                    fillCollections(context, itemInfo);
+                    fillCollections(itemInfo);
                 }
 
                 if (items) {
@@ -163,7 +161,7 @@ public class Harvest {
                     itemInfo.item = itemService.find(context, itemInfo.itemID);
                 }
 
-                if ((nonAnon) || (itemInfo.item == null) || (withdrawn && itemInfo.withdrawn)) {
+                if (nonAnon || (itemInfo.item == null) || (withdrawn && itemInfo.withdrawn)) {
                     index++;
                     if (index > offset) {
                         infoObjects.add(itemInfo);
@@ -221,7 +219,7 @@ public class Harvest {
 
         // Get the sets
         if (collections) {
-            fillCollections(context, itemInfo);
+            fillCollections(itemInfo);
         }
 
         return itemInfo;
@@ -230,12 +228,10 @@ public class Harvest {
     /**
      * Fill out the containers field of the HarvestedItemInfo object
      *
-     * @param context  DSpace context
      * @param itemInfo HarvestedItemInfo object to fill out
      * @throws SQLException if database error
      */
-    private static void fillCollections(Context context,
+    private static void fillCollections(HarvestedItemInfo itemInfo) throws SQLException {
-                                        HarvestedItemInfo itemInfo) throws SQLException {
         // Get the collection Handles from DB
         List<Collection> collections = itemInfo.item.getCollections();
         itemInfo.collectionHandles = new ArrayList<>();

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

@@ -10,6 +10,7 @@ package org.dspace.statistics;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
 import java.text.DecimalFormat;
 import java.text.ParseException;
 import java.util.ArrayList;
@@ -24,7 +25,7 @@ import org.apache.commons.lang3.StringUtils;
 
 /**
  * @author kevinvandevelde at atmire.com
- * Date: 21-jan-2009
+ * Date: 21-Jan-2009
  * Time: 13:44:48
  */
 public class Dataset {
@@ -66,20 +67,20 @@ public class Dataset {
     }
 
     private void initRowLabels(int rows) {
-        rowLabels = new ArrayList<String>(rows);
+        rowLabels = new ArrayList<>(rows);
-        rowLabelsAttrs = new ArrayList<Map<String, String>>();
+        rowLabelsAttrs = new ArrayList<>();
         for (int i = 0; i < rows; i++) {
             rowLabels.add("Row " + (i + 1));
-            rowLabelsAttrs.add(new HashMap<String, String>());
+            rowLabelsAttrs.add(new HashMap<>());
         }
     }
 
     private void initColumnLabels(int nbCols) {
-        colLabels = new ArrayList<String>(nbCols);
+        colLabels = new ArrayList<>(nbCols);
-        colLabelsAttrs = new ArrayList<Map<String, String>>();
+        colLabelsAttrs = new ArrayList<>();
         for (int i = 0; i < nbCols; i++) {
             colLabels.add("Column " + (i + 1));
-            colLabelsAttrs.add(new HashMap<String, String>());
+            colLabelsAttrs.add(new HashMap<>());
         }
     }
 
@@ -233,7 +234,9 @@ public class Dataset {
 
     public ByteArrayOutputStream exportAsCSV() throws IOException {
         ByteArrayOutputStream baos = new ByteArrayOutputStream();
-        ICSVWriter ecsvp = new CSVWriterBuilder(new OutputStreamWriter(baos)).withSeparator(';').build();
+        ICSVWriter ecsvp = new CSVWriterBuilder(new OutputStreamWriter(baos, StandardCharsets.UTF_8))
+                .withSeparator(';')
+                .build();
         //Generate the item row
         List<String> colLabels = getColLabels();
         colLabels.add(0, "");

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

@@ -7,9 +7,10 @@
  */
 package org.dspace.statistics;
 
-import java.util.LinkedList;
+import java.util.ArrayList;
 import java.util.List;
 
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.dspace.eperson.EPerson;
 import org.dspace.services.model.Event;
@@ -28,7 +29,7 @@ import org.springframework.beans.factory.annotation.Autowired;
  */
 public class SolrLoggerUsageEventListener extends AbstractUsageEventListener {
 
-    private static Logger log = org.apache.logging.log4j.LogManager.getLogger(SolrLoggerUsageEventListener.class);
+    private static final Logger log = LogManager.getLogger(SolrLoggerUsageEventListener.class);
 
     protected SolrLoggerService solrLoggerService;
 
@@ -56,7 +57,7 @@ public class SolrLoggerUsageEventListener extends AbstractUsageEventListener {
                     }
                 } else if (UsageEvent.Action.SEARCH == ue.getAction()) {
                     UsageSearchEvent usageSearchEvent = (UsageSearchEvent) ue;
-                    List<String> queries = new LinkedList<>();
+                    List<String> queries = new ArrayList<>();
                     queries.add(usageSearchEvent.getQuery());
                     solrLoggerService.postSearch(usageSearchEvent.getObject(), usageSearchEvent.getRequest(),
                                     currentUser, queries, usageSearchEvent.getPage().getSize(),

dspace-api/src/main/java/org/dspace/statistics/content/StatisticsDataVisits.java

@@ -285,13 +285,8 @@ public class StatisticsDataVisits extends StatisticsData {
             DatasetQuery firsDataset = datasetQueries.get(0);
             //Do the first query
 
-            ObjectCount[] topCounts1 = null;
+            ObjectCount[] topCounts1 =
-//            if (firsDataset.getQueries().size() == 1) {
-            topCounts1 =
                 queryFacetField(firsDataset, firsDataset.getQueries().get(0).getQuery(), filterQuery, facetMinCount);
-//            } else {
-//                TODO: do this
-//            }
             // Check if we have more queries that need to be done
             if (datasetQueries.size() == 2) {
                 DatasetQuery secondDataSet = datasetQueries.get(1);
@@ -313,7 +308,6 @@ public class StatisticsDataVisits extends StatisticsData {
                 }
                 for (int i = 0; i < topCounts1.length; i++) {
                     ObjectCount count1 = topCounts1[i];
-                    ObjectCount[] currentResult = new ObjectCount[topCounts2.length];
 
                     // Make sure we have a dataSet
                     if (dataset == null) {
@@ -645,7 +639,7 @@ public class StatisticsDataVisits extends StatisticsData {
                     // be null if a handle has not yet been assigned. In this case reference the
                     // item its internal id. In the last case where the bitstream is not associated
                     // with an item (such as a community logo) then reference the bitstreamID directly.
-                    String identifier = null;
+                    String identifier;
                     if (owningItem != null && owningItem.getHandle() != null) {
                         identifier = "handle/" + owningItem.getHandle();
                     } else if (owningItem != null) {

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

@@ -19,8 +19,6 @@ import javax.servlet.http.HttpServletRequest;
 
 import org.apache.commons.codec.CharEncoding;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
 import org.dspace.content.DCDate;
 import org.dspace.content.Entity;
 import org.dspace.content.EntityType;
@@ -42,8 +40,6 @@ import org.dspace.statistics.export.service.OpenUrlService;
  */
 public abstract class ExportEventProcessor {
 
-    private static final Logger log = LogManager.getLogger();
-
     protected static final String ENTITY_TYPE_DEFAULT = "Publication";
 
     protected static final String ITEM_VIEW = "Investigation";
@@ -130,8 +126,10 @@ public abstract class ExportEventProcessor {
 
         //Start adding our data
         StringBuilder data = new StringBuilder();
-        data.append(URLEncoder.encode("url_ver", UTF_8) + "=" +
+        data.append(URLEncoder.encode("url_ver", UTF_8))
-                    URLEncoder.encode(configurationService.getProperty("irus.statistics.tracker.urlversion"), UTF_8));
+                .append("=")
+                .append(URLEncoder.encode(configurationService.getProperty("irus.statistics.tracker.urlversion"),
+                        UTF_8));
         data.append("&").append(URLEncoder.encode("req_id", UTF_8)).append("=")
             .append(URLEncoder.encode(clientIP, UTF_8));
         data.append("&").append(URLEncoder.encode("req_dat", UTF_8)).append("=")

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

@@ -24,9 +24,10 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  */
 public class ItemEventProcessor extends ExportEventProcessor {
 
-    private ConfigurationService configurationService = DSpaceServicesFactory.getInstance().getConfigurationService();
+    private final ConfigurationService configurationService
+            = DSpaceServicesFactory.getInstance().getConfigurationService();
 
-    private Item item;
+    private final Item item;
 
     /**
      * Creates a new ItemEventProcessor that will set the params
@@ -48,6 +49,7 @@ public class ItemEventProcessor extends ExportEventProcessor {
      * @throws SQLException
      * @throws IOException
      */
+    @Override
     public void processEvent() throws SQLException, IOException {
         if (shouldProcessItem(item)) {
             String baseParam = getBaseParameters(item);

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

@@ -15,8 +15,6 @@ import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
 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.Context;
 import org.dspace.storage.bitstore.factory.StorageServiceFactory;
 import org.dspace.storage.bitstore.service.BitstreamStorageService;
@@ -31,8 +29,6 @@ public class BitStoreMigrate {
      */
     private static final Logger log = LogManager.getLogger(BitStoreMigrate.class);
 
-    private static final BitstreamService bitstreamService
-            = ContentServiceFactory.getInstance().getBitstreamService();
     private static final BitstreamStorageService bitstreamStorageService
             = StorageServiceFactory.getInstance().getBitstreamStorageService();
 

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

@@ -12,6 +12,7 @@ import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.nio.charset.StandardCharsets;
 import java.sql.Connection;
 import java.sql.DatabaseMetaData;
 import java.sql.PreparedStatement;
@@ -133,7 +134,7 @@ public class DatabaseUtils {
                     System.err.println("\nError running 'test': ");
                     System.err.println(" - " + sqle);
                     System.err.println("\nPlease see the DSpace documentation for assistance.\n");
-                    sqle.printStackTrace();
+                    sqle.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("info") || argv[0].equalsIgnoreCase("status")) {
@@ -173,15 +174,16 @@ public class DatabaseUtils {
                     }
                 } catch (SQLException e) {
                     System.err.println("Info exception:");
-                    e.printStackTrace();
+                    e.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("migrate")) {
                 try (Connection connection = dataSource.getConnection()) {
                     System.out.println("\nDatabase URL: " + connection.getMetaData().getURL());
 
-                    // "migrate" allows for an OPTIONAL second argument:
+                    // "migrate" allows for an OPTIONAL second argument (only one may be specified):
                     //    - "ignored" = Also run any previously "ignored" migrations during the migration
+                    //    - "force" = Even if no pending migrations exist, still run a migration to trigger callbacks.
                     //    - [version] = ONLY run migrations up to a specific DSpace version (ONLY FOR TESTING)
                     if (argv.length == 2) {
                         if (argv[1].equalsIgnoreCase("ignored")) {
@@ -191,11 +193,14 @@ public class DatabaseUtils {
                             // Update the database to latest version, but set "outOfOrder=true"
                             // This will ensure any old migrations in the "ignored" state are now run
                             updateDatabase(dataSource, connection, null, true);
+                        } else if (argv[1].equalsIgnoreCase("force")) {
+                            updateDatabase(dataSource, connection, null, false, true);
                         } else {
                             // Otherwise, we assume "argv[1]" is a valid migration version number
                             // This is only for testing! Never specify for Production!
                             String migrationVersion = argv[1];
-                            BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+                            BufferedReader input = new BufferedReader(
+                                    new InputStreamReader(System.in, StandardCharsets.UTF_8));
 
                             System.out.println(
                                 "You've specified to migrate your database ONLY to version " + migrationVersion + " " +
@@ -231,7 +236,7 @@ public class DatabaseUtils {
                     System.exit(0);
                 } catch (SQLException e) {
                     System.err.println("Migration exception:");
-                    e.printStackTrace();
+                    e.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("repair")) {
@@ -247,7 +252,7 @@ public class DatabaseUtils {
                     System.exit(0);
                 } catch (SQLException | FlywayException e) {
                     System.err.println("Repair exception:");
-                    e.printStackTrace();
+                    e.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("validate")) {
@@ -262,7 +267,7 @@ public class DatabaseUtils {
                     System.exit(0);
                 } catch (SQLException | FlywayException e) {
                     System.err.println("Validation exception:");
-                    e.printStackTrace();
+                    e.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("clean")) {
@@ -305,7 +310,7 @@ public class DatabaseUtils {
                         }
                     }
 
-                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+                    BufferedReader input = new BufferedReader(new InputStreamReader(System.in, StandardCharsets.UTF_8));
 
                     System.out.println("\nDatabase URL: " + connection.getMetaData().getURL());
                     System.out
@@ -332,7 +337,7 @@ public class DatabaseUtils {
                     }
                 } catch (SQLException e) {
                     System.err.println("Clean exception:");
-                    e.printStackTrace();
+                    e.printStackTrace(System.err);
                     System.exit(1);
                 }
             } else if (argv[0].equalsIgnoreCase("update-sequences")) {
@@ -384,14 +389,14 @@ public class DatabaseUtils {
 
         } catch (Exception e) {
             System.err.println("Caught exception:");
-            e.printStackTrace();
+            e.printStackTrace(System.err);
             System.exit(1);
         }
     }
 
     /**
      * Print basic information about the current database to System.out.
-     * This is utilized by both the 'test' and 'info' commandline options.
+     * This is utilized by both the 'test' and 'info' command line options.
      *
      * @param connection current database connection
      * @throws SQLException if database error occurs
@@ -654,6 +659,34 @@ public class DatabaseUtils {
     protected static synchronized void updateDatabase(DataSource datasource,
                                                       Connection connection, String targetVersion, boolean outOfOrder)
         throws SQLException {
+        updateDatabase(datasource, connection, targetVersion, outOfOrder, false);
+    }
+
+    /**
+     * Ensures the current database is up-to-date with regards
+     * to the latest DSpace DB schema. If the scheme is not up-to-date,
+     * then any necessary database migrations are performed.
+     * <P>
+     * FlywayDB (http://flywaydb.org/) is used to perform database migrations.
+     * If a Flyway DB migration fails it will be rolled back to the last
+     * successful migration, and any errors will be logged.
+     *
+     * @param datasource    DataSource object (retrieved from DatabaseManager())
+     * @param connection    Database connection
+     * @param targetVersion If specified, only migrate the database to a particular *version* of DSpace. This is
+     *                      just useful for testing migrations, and should NOT be used in Production.
+     *                      If null, the database is migrated to the latest version.
+     * @param outOfOrder    If true, Flyway will run any lower version migrations that were previously "ignored".
+     *                      If false, Flyway will only run new migrations with a higher version number.
+     * @param forceMigrate  If true, always run a Flyway migration, even if no "Pending" migrations exist. This can be
+     *                      used to trigger Flyway Callbacks manually.
+     *                      If false, only run migration if pending migrations exist, otherwise do nothing.
+     * @throws SQLException if database error
+     *                      If database cannot be upgraded.
+     */
+    protected static synchronized void updateDatabase(DataSource datasource, Connection connection,
+                                                      String targetVersion, boolean outOfOrder, boolean forceMigrate)
+        throws SQLException {
         if (null == datasource) {
             throw new SQLException("The datasource is a null reference -- cannot continue.");
         }
@@ -730,6 +763,10 @@ public class DatabaseUtils {
 
                 // Flag that Discovery will need reindexing, since database was updated
                 setReindexDiscovery(reindexAfterUpdate);
+            } else if (forceMigrate) {
+                log.info("DSpace database schema is up to date, but 'force' was specified. " +
+                        "Running migrate command to trigger callbacks.");
+                flyway.migrate();
             } else {
                 log.info("DSpace database schema is up to date");
             }

dspace-api/src/main/java/org/dspace/text/filter/InitialArticleWord.java

@@ -110,7 +110,7 @@ public abstract class InitialArticleWord implements TextFilter {
                     return str.substring(cutPos);
                 } else {
                     // No - move the initial article word to the end
-                    return new StringBuffer(str.substring(cutPos))
+                    return new StringBuilder(str.substring(cutPos))
                         .append(wordSeparator)
                         .append(str.substring(initialStart, initialEnd))
                         .toString();
@@ -124,10 +124,12 @@ public abstract class InitialArticleWord implements TextFilter {
     }
 
     protected InitialArticleWord(boolean stripWord) {
+        this.wordSeparator = ", ";
         stripInitialArticle = stripWord;
     }
 
     protected InitialArticleWord() {
+        this.wordSeparator = ", ";
         stripInitialArticle = false;
     }
 
@@ -138,9 +140,8 @@ public abstract class InitialArticleWord implements TextFilter {
      * @return An array of definite/indefinite article words
      */
     protected abstract String[] getArticleWords(String lang);
-
     // Separator to use when appending article to end
-    private String wordSeparator = ", ";
+    private final String wordSeparator;
 
     // Flag to signify initial article word should be removed
     // If false, then the initial article word is appended to the end