Another batch of Error Prone fixes. (#3061)

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/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;
 
@@ -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/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;
@@ -42,20 +39,18 @@ import org.xml.sax.SAXException;
 /**
  * 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/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/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/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/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/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/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/discovery/indexobject/AbstractIndexableObject.java

@@ -33,7 +33,7 @@ public abstract class AbstractIndexableObject<T extends ReloadableEntity<PK>, PK
         if (!(obj instanceof IndexableObject)) {
             return false;
         }
-        AbstractIndexableObject other = (AbstractIndexableObject) obj;
+        IndexableObject other = (IndexableObject) obj;
         return other.getIndexedObject().equals(getIndexedObject());
     }
 

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/external/provider/impl/SHERPAv2JournalDataProvider.java

@@ -15,7 +15,6 @@ import java.util.stream.Collectors;
 
 import org.apache.commons.collections4.CollectionUtils;
 import org.apache.commons.lang3.StringUtils;
-import org.apache.logging.log4j.Logger;
 import org.dspace.app.sherpa.SHERPAService;
 import org.dspace.app.sherpa.v2.SHERPAJournal;
 import org.dspace.app.sherpa.v2.SHERPAResponse;
@@ -33,8 +32,6 @@ import org.dspace.external.provider.ExternalDataProvider;
  */
 public class SHERPAv2JournalDataProvider implements ExternalDataProvider {
 
-    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(SHERPAv2JournalDataProvider.class);
-
     // Source identifier (configured in spring configuration)
     private String sourceIdentifier;
 

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
                             + " as the resource types of the object it was"
                             + " 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/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/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")) {
@@ -173,7 +174,7 @@ 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")) {
@@ -195,7 +196,8 @@ public class DatabaseUtils {
                             // 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 +233,7 @@ 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 +249,7 @@ 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 +264,7 @@ 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 +307,7 @@ 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 +334,7 @@ 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")) {
@@ -384,7 +386,7 @@ public class DatabaseUtils {
 
         } catch (Exception e) {
             System.err.println("Caught exception:");
-            e.printStackTrace();
+            e.printStackTrace(System.err);
             System.exit(1);
         }
     }

dspace-api/src/test/resources/log4j2-test.xml

@@ -0,0 +1,56 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<Configuration strict='true'
+               xmlns='http://logging.apache.org/log4j/2.0/config'>
+
+    <Properties>
+        <!-- Log level for all DSpace-specific code (org.dspace.*)
+             Possible values (from most to least info):
+             DEBUG, INFO, WARN, ERROR, FATAL -->
+        <Property name='loglevel.dspace'>DEBUG</Property>
+
+        <!-- Log level for other third-party tools/APIs used by DSpace
+             Possible values (from most to least info):
+             DEBUG, INFO, WARN, ERROR, FATAL -->
+        <Property name='loglevel.other'>INFO</Property>
+    </Properties>
+
+    <Appenders>
+        <!-- A1 is for most DSpace activity -->
+        <Appender name='A1'
+                  type='Console'>
+            <Layout type='PatternLayout'
+                    pattern='%d %-5p %c @ %m%n'/>
+        </Appender>
+    </Appenders>
+
+    <Loggers>
+        <!-- Most parts of DSpace -->
+        <Logger name='org.dspace'
+                level='${loglevel.dspace}'
+                additivity='false'>
+            <AppenderRef ref='A1'/>
+        </Logger>
+
+        <!-- Block services logging except on exceptions -->
+        <Logger name='org.dspace.kernel'
+                level='ERROR'/>
+        <Logger name='org.dspace.services'
+                level='ERROR'/>
+        <Logger name='org.dspace.servicemanager'
+                level='WARN'/>
+        <Logger name='org.dspace.providers'
+                level='ERROR'/>
+        <Logger name='org.dspace.utils'
+                level='ERROR'/>
+
+        <!-- Block passwords from being exposed in Axis logs.
+             (DEBUG exposes passwords in Basic Auth) -->
+        <Logger name='org.apache.axis.handlers.http.HTTPAuthHandler'
+                level='INFO'/>
+
+                <!-- Anything not a part of DSpace -->
+        <Root level='${loglevel.other}'>
+            <AppenderRef ref='A1'/>
+        </Root>
+    </Loggers>
+</Configuration>