[maven-release-plugin] prepare release dspace-4.3

Backport Travis CI enhancements to 4.x branch

.travis.yml

@@ -1,2 +1,24 @@
 language: java
-script: "mvn clean package license:check -Dmaven.test.skip=false"
+
+env: 
+  # Give Maven 1GB of memory to work with
+  - MAVEN_OPTS=-Xmx1024M
+
+# Skip install stage, as we'll do it below
+install: "echo 'Skipping install stage, dependencies will be downloaded during build and test stages.'"
+
+# Two stage Build and Test
+# 1. Install & Unit Test APIs
+# 2. Assemble DSpace
+script:
+  # 1. [Install & Unit Test] Check source code licenses and run source code Unit Tests
+  #    (This explicitly skips building the 'dspace' assembly module, since we only want to do that ONCE.)
+  #        license:check => Validate all source code license headers
+  #        -Dmaven.test.skip=false => Enable DSpace Unit Tests
+  #        -P !dspace => SKIP full DSpace assembly (will do below)
+  #        -B => Maven batch/non-interactive mode (recommended for CI)
+  #        -V => Display Maven version info before build
+  - "mvn clean install license:check -Dmaven.test.skip=false -P !dspace -B -V"
+  # 2. [Assemble DSpace] Ensure overlay & assembly process works (from [src]/dspace/)
+  #        -P !assembly => SKIP the actual building of [src]/dspace/dspace-installer (as it can be memory intensive)
+  - "cd dspace && mvn package -P !assembly -B -V"

README

@@ -1,6 +1,9 @@
-Installation instructions are included in this release package under
+Installation instructions may be found in DSpace-Manual.pdf, offered 
+with the source archives in the SourceForge project:
 
- - dspace/docs/DSpace-Manual.pdf
+  http://sourceforge.net/projects/dspace/files/DSpace%20Stable/VERSION/
+
+(Replace "VERSION" with the version you are installing, such as "4.0".)
 
 DSpace version information can be viewed online at
  - https://wiki.duraspace.org/display/DSDOC/

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -436,12 +436,12 @@
         <dependency>
             <groupId>gr.ekt.bte</groupId>
             <artifactId>bte-core</artifactId>
-            <version>0.9.3.3</version>
+            <version>0.9.2.4</version>
         </dependency>
         <dependency>
             <groupId>gr.ekt.bte</groupId>
             <artifactId>bte-io</artifactId>
-            <version>0.9.3.3</version>
+            <version>0.9.2.4</version>
         </dependency>
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
@@ -463,6 +463,21 @@
                 </exclusion>
             </exclusions>
         </dependency>
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-cell</artifactId>
+            <version>${solr.version}</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>jcl-over-slf4j</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-api</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
         <dependency>
             <groupId>commons-configuration</groupId>
             <artifactId>commons-configuration</artifactId>

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.app.statistics;
 
+import org.dspace.content.MetadataSchema;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
@@ -153,10 +154,10 @@ public class LogAnalyser
    private static Pattern logRegex = null;
    
    /** pattern to match commented out lines from the config file */
-   private static Pattern comment = Pattern.compile("^#");
+   private static final Pattern comment = Pattern.compile("^#");
         
    /** pattern to match genuine lines from the config file */
-   private static Pattern real = Pattern.compile("^(.+)=(.+)");
+   private static final Pattern real = Pattern.compile("^(.+)=(.+)");
    
    /** pattern to match all search types */
    private static Pattern typeRX = null;
@@ -1165,8 +1166,12 @@ public class LogAnalyser
                         "AND metadata_field_id = (" +
                         " SELECT metadata_field_id " +
                         " FROM metadatafieldregistry " +
-                        " WHERE element = 'type' " +
+                        " WHERE metadata_schema_id = (" +
-                        " AND qualifier IS NULL) ";
+                        "  SELECT metadata_schema_id" +
+                        "   FROM MetadataSchemaRegistry" +
+                        "   WHERE short_id = '" + MetadataSchema.DC_SCHEMA + "')" +
+                        "  AND element = 'type' " +
+                        "  AND qualifier IS NULL) ";
         }
         
         // start the date constraint query buffer
@@ -1184,8 +1189,12 @@ public class LogAnalyser
                           "WHERE metadata_field_id = (" +
                           " SELECT metadata_field_id " +
                           " FROM metadatafieldregistry " +
-                          " WHERE element = 'date' " +
+                          " WHERE metadata_schema_id = (" +
-                          " AND qualifier = 'accessioned') ");
+                          "  SELECT metadata_schema_id" +
+                          "   FROM MetadataSchemaRegistry" +
+                          "   WHERE short_id = '" + MetadataSchema.DC_SCHEMA + "')" +
+                          "  AND element = 'date' " +
+                          "  AND qualifier = 'accessioned') ");
 
         // Verifies that the metadata contains a valid date, otherwise the
         // postgres queries blow up when doing the ::timestamp cast.

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

@@ -26,6 +26,7 @@ import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.logging.Level;
 
 import javax.servlet.http.HttpServletResponse;
 
@@ -1094,6 +1095,22 @@ public class ShibAuthentication implements AuthenticationMethod
 			value = request.getHeader(name.toLowerCase());
 		if (StringUtils.isEmpty(value))
 			value = request.getHeader(name.toUpperCase());
+                
+                boolean reconvertAttributes = 
+                        ConfigurationManager.getBooleanProperty(
+                            "authentication-shibboleth",
+                            "reconvert.attributes",
+                            false);
+                
+                if (!StringUtils.isEmpty(value) && reconvertAttributes)
+                {
+                    try {
+                        value = new String(value.getBytes("ISO-8859-1"), "UTF-8");
+                    } catch (UnsupportedEncodingException ex) {
+                        log.warn("Failed to reconvert shibboleth attribute ("
+                                + name + ").", ex);
+                    }
+                }
 		
 		return value;
 	}

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

@@ -31,7 +31,8 @@ import org.dspace.utils.DSpace;
 /**
  * 
  * @author Andrea Bollini (CILEA)
- *
+ * @author Adán Román Ruiz at arvo.es (bugfix)
+ * 
  */
 public class SolrBrowseDAO implements BrowseDAO
 {
@@ -337,11 +338,11 @@ public class SolrBrowseDAO implements BrowseDAO
         query.addFilterQueries("search.resourcetype:" + Constants.ITEM);
         if (isAscending)
         {
-            query.setQuery("bi_"+column + "_sort" + ": [* TO \"" + value + "\"]");
+            query.setQuery("bi_"+column + "_sort" + ": [* TO \"" + value + "\"}");
         }
         else
         {
-            query.setQuery("bi_" + column + "_sort" + ": [\"" + value + "\" TO *]");
+            query.setQuery("bi_" + column + "_sort" + ": {\"" + value + "\" TO *]");
         }
         DiscoverResult resp = null;
         try

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

@@ -65,12 +65,16 @@ public class DailyReportEmailer
     public void sendReport(File attachment, int numberOfBitstreams) 
             throws IOException, javax.mail.MessagingException 
     { 
-        Email email = new Email(); 
+        if(numberOfBitstreams > 0)
-        email.setSubject("Checksum checker Report - " + numberOfBitstreams + " Bitstreams found with POSSIBLE issues"); 
+        {
-        email.setContent("report is attached ..."); 
+            String hostname = ConfigurationManager.getProperty("dspace.hostname");
-        email.addAttachment(attachment, "checksum_checker_report.txt"); 
+            Email email = new Email();
-        email.addRecipient(ConfigurationManager.getProperty("mail.admin")); 
+            email.setSubject("Checksum checker Report - " + numberOfBitstreams + " Bitstreams found with POSSIBLE issues on " + hostname);
-        email.send(); 
+            email.setContent("report is attached ...");
+            email.addAttachment(attachment, "checksum_checker_report.txt");
+            email.addRecipient(ConfigurationManager.getProperty("mail.admin"));
+            email.send();
+        }
     } 
 
     /**

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

@@ -9,25 +9,107 @@ package org.dspace.content.dao;
 
 import org.dspace.core.Context;
 import org.dspace.content.Bitstream;
+import org.dspace.storage.rdbms.DatabaseManager;
+import org.dspace.storage.rdbms.TableRowIterator;
+import org.dspace.storage.rdbms.TableRow;
 
 import java.sql.SQLException;
 
 public class ItemDAOOracle extends ItemDAO
-{
+{		
+		private static final String selectPrimaryBitstreamID =
+            "SELECT bundle.primary_bitstream_id FROM item2bundle, bundle " +
+            "WHERE item2bundle.item_id=? AND item2bundle.bundle_id=bundle.bundle_id AND bundle.name=?";
+
+    private static final String selectFirstBitstreamID =
+        "SELECT bundle2bitstream.bitstream_id FROM item2bundle, bundle, bundle2bitstream " +
+        "WHERE item2bundle.item_id=? AND item2bundle.bundle_id=bundle.bundle_id AND bundle.name=? " +
+        "AND bundle.bundle_id=bundle2bitstream.bundle_id";
+    
+		private static final String selectNamedBitstreamID =
+        "SELECT bitstream.bitstream_id FROM item2bundle, bundle, bundle2bitstream, bitstream " +
+        "WHERE item2bundle.item_id=? AND item2bundle.bundle_id=bundle.bundle_id AND bundle.name=? " +
+        "AND bundle.bundle_id=bundle2bitstream.bundle_id AND bundle2bitstream.bitstream_id=bitstream.bitstream_id " +
+        "AND bitstream.name=?";
+    
     ItemDAOOracle(Context ctx)
     {
         super(ctx);
     }
 
-    public Bitstream getPrimaryBitstream(int itemId, String bundleName) throws SQLException {
+    public Bitstream getPrimaryBitstream(int itemId, String bundleName) throws SQLException
-        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    {
+        TableRowIterator tri = null;
+
+        try
+        {
+            tri = DatabaseManager.query(context, selectPrimaryBitstreamID, itemId, bundleName);
+
+            if (tri.hasNext())
+            {
+                TableRow row = tri.next();
+                int bid = row.getIntColumn("primary_bitstream_id");
+                return Bitstream.find(context, bid);
+            }
+        }        
+        finally
+        {
+            if (tri != null)
+            {
+                tri.close();
+            }
+        }
+
+        return null;
     }
 
-    public Bitstream getFirstBitstream(int itemId, String bundleName) throws SQLException {
+    public Bitstream getFirstBitstream(int itemId, String bundleName) throws SQLException
-        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    {
+        TableRowIterator tri = null;
+
+        try
+        {
+            tri = DatabaseManager.query(context, selectFirstBitstreamID, itemId, bundleName);
+            if (tri.hasNext())
+            {
+                TableRow row = tri.next();
+                int bid = row.getIntColumn("bitstream_id");
+                return Bitstream.find(context, bid);
+            }
+        }
+        finally
+        {
+            if (tri != null)
+            {
+                tri.close();
+            }
+        }
+
+        return null;
     }
 
-    public Bitstream getNamedBitstream(int itemId, String bundleName, String fileName) throws SQLException {
+    public Bitstream getNamedBitstream(int itemId, String bundleName, String fileName) throws SQLException
-        return null;  //To change body of implemented methods use File | Settings | File Templates.
+    {
+        TableRowIterator tri = null;
+
+        try
+        {
+            tri = DatabaseManager.query(context, selectNamedBitstreamID, itemId, bundleName, fileName);
+            if (tri.hasNext())
+            {
+                TableRow row = tri.next();
+                int bid = row.getIntColumn("bitstream_id");
+                return Bitstream.find(context, bid);
+            }
+        }
+        finally
+        {
+            if (tri != null)
+            {
+                tri.close();
+            }
+        }
+
+        return null;
     }
 }

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

@@ -0,0 +1,73 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.discovery;
+
+import org.apache.log4j.Logger;
+import org.apache.solr.common.util.ContentStreamBase;
+import org.dspace.content.Bitstream;
+
+import java.io.ByteArrayInputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.nio.charset.StandardCharsets;
+
+/**
+ * Construct a <code>ContentStream</code> from a <code>File</code>
+ */
+public class BitstreamContentStream extends ContentStreamBase
+{
+    private static final Logger log = Logger.getLogger(BitstreamContentStream.class);
+    private final Bitstream file;
+
+    public BitstreamContentStream( Bitstream f ) {
+        file = f;
+
+        contentType = f.getFormat().getMIMEType();
+        name = file.getName();
+        size = file.getSize();
+        sourceInfo = file.getName();
+    }
+
+    @Override
+    public String getContentType() {
+        if(contentType==null) {
+            InputStream stream = null;
+            try {
+                stream = file.retrieve();
+                char first = (char)stream.read();
+                if(first == '<') {
+                    return "application/xml";
+                }
+                if(first == '{') {
+                    return "application/json";
+                }
+            } catch(Exception ex) {
+                log.error("Error determining content type for bitstream:" + file.getID(), ex);
+            } finally {
+                if (stream != null) try {
+                    stream.close();
+                } catch (IOException ioe) {
+                    log.error("Error closing stream:" + file.getID(), ioe);
+
+                }
+            }
+        }
+        return contentType;
+    }
+
+    @Override
+    public InputStream getStream() throws IOException {
+        try {
+            return file.retrieve();
+        } catch (Exception e) {
+            log.error(e.getMessage(),e);
+            return new ByteArrayInputStream(e.getMessage().getBytes(StandardCharsets.UTF_8));
+        }
+    }
+}
+

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

@@ -66,6 +66,10 @@ public class IndexClient {
                 "(re)build index, wiping out current one if it exists").create(
                 "b"));
 
+        options.addOption(OptionBuilder.isRequired(false).withDescription(
+                "Rebuild the spellchecker, can be combined with -b and -f.").create(
+                "s"));
+
         options
                 .addOption(OptionBuilder
                         .isRequired(false)
@@ -111,15 +115,32 @@ public class IndexClient {
         } else if (line.hasOption("b")) {
             log.info("(Re)building index from scratch.");
             indexer.createIndex(context);
+            checkRebuildSpellCheck(line, indexer);
         } else if (line.hasOption("o")) {
             log.info("Optimizing search core.");
             indexer.optimize();
+        } else if(line.hasOption('s')) {
+            checkRebuildSpellCheck(line, indexer);
         } else {
             log.info("Updating and Cleaning Index");
             indexer.cleanIndex(line.hasOption("f"));
             indexer.updateIndex(context, line.hasOption("f"));
+            checkRebuildSpellCheck(line, indexer);
         }
 
         log.info("Done with indexing");
 	}
+
+    /**
+     * Check the command line options and rebuild the spell check if active.
+     * @param line the command line options
+     * @param indexer the solr indexer
+     * @throws SearchServiceException in case of a solr exception
+     */
+    protected static void checkRebuildSpellCheck(CommandLine line, IndexingService indexer) throws SearchServiceException {
+        if (line.hasOption("s")) {
+            log.info("Rebuilding spell checker.");
+            indexer.buildSpellCheck();
+        }
+    }
 }

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

@@ -7,6 +7,7 @@
  */
 package org.dspace.discovery;
 
+import org.apache.solr.client.solrj.SolrServerException;
 import org.dspace.content.DSpaceObject;
 import org.dspace.core.Context;
 
@@ -58,4 +59,6 @@ public interface IndexingService {
     void commit() throws SearchServiceException;
 
     void optimize() throws SearchServiceException;
+
+    void buildSpellCheck() throws SearchServiceException;
 }

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

@@ -7,12 +7,7 @@
  */
 package org.dspace.discovery;
 
-import java.io.IOException;
+import java.io.*;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.io.StringWriter;
-import java.net.MalformedURLException;
 import java.net.URI;
 import java.net.URISyntaxException;
 import java.sql.SQLException;
@@ -31,7 +26,6 @@ import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
 import java.util.TimeZone;
-import java.util.TreeMap;
 import java.util.Vector;
 
 import org.apache.commons.collections.CollectionUtils;
@@ -39,7 +33,6 @@ import org.apache.commons.collections.MapUtils;
 import org.apache.commons.collections.Transformer;
 import org.apache.commons.httpclient.HttpClient;
 import org.apache.commons.httpclient.methods.GetMethod;
-import org.apache.commons.io.IOUtils;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.lang.time.DateFormatUtils;
@@ -53,6 +46,8 @@ import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.impl.HttpSolrServer;
+import org.apache.solr.client.solrj.request.AbstractUpdateRequest;
+import org.apache.solr.client.solrj.request.ContentStreamUpdateRequest;
 import org.apache.solr.client.solrj.response.FacetField;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.client.solrj.util.ClientUtils;
@@ -61,6 +56,7 @@ import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.SolrInputDocument;
 import org.apache.solr.common.params.*;
 import org.apache.solr.common.util.NamedList;
+import org.apache.solr.handler.extraction.ExtractingParams;
 import org.dspace.content.Bitstream;
 import org.dspace.content.Bundle;
 import org.dspace.content.Collection;
@@ -148,7 +144,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     solr = new HttpSolrServer(solrService);
 
                     solr.setBaseURL(solrService);
-
+                    solr.setUseMultiPartPost(true);
                     SolrQuery solrQuery = new SolrQuery()
                             .setQuery("search.resourcetype:2 AND search.resourceid:1");
 
@@ -504,11 +500,11 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 return;
             }
             long start = System.currentTimeMillis();
-            System.out.println("SOLR Search Optimize -- Process Started:"+start);
+            System.out.println("SOLR Search Optimize -- Process Started:" + start);
             getSolr().optimize();
             long finish = System.currentTimeMillis();
-            System.out.println("SOLR Search Optimize -- Process Finished:"+finish);
+            System.out.println("SOLR Search Optimize -- Process Finished:" + finish);
-            System.out.println("SOLR Search Optimize -- Total time taken:"+(finish-start) + " (ms).");
+            System.out.println("SOLR Search Optimize -- Total time taken:" + (finish - start) + " (ms).");
         } catch (SolrServerException sse)
         {
             System.err.println(sse.getMessage());
@@ -518,6 +514,23 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         }
     }
 
+    public void buildSpellCheck() throws SearchServiceException {
+        try {
+            if (getSolr() == null) {
+                return;
+            }
+            SolrQuery solrQuery = new SolrQuery();
+            solrQuery.set("spellcheck", true);
+            solrQuery.set(SpellingParams.SPELLCHECK_BUILD, true);
+            getSolr().query(solrQuery);
+        }catch (SolrServerException e)
+        {
+            //Make sure to also log the exception since this command is usually run from a crontab.
+            log.error(e, e);
+            throw new SearchServiceException(e);
+        }
+    }
+
     // //////////////////////////////////
     // Private
     // //////////////////////////////////
@@ -666,15 +679,47 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     /**
      * Write the document to the index under the appropriate handle.
+     *
      * @param doc the solr document to be written to the server
+     * @param streams
      * @throws IOException IO exception
      */
-    protected void writeDocument(SolrInputDocument doc) throws IOException {
+    protected void writeDocument(SolrInputDocument doc, List<BitstreamContentStream> streams) throws IOException {
 
         try {
             if(getSolr() != null)
             {
-                getSolr().add(doc);
+                if(CollectionUtils.isNotEmpty(streams))
+                {
+                    ContentStreamUpdateRequest req = new ContentStreamUpdateRequest("/update/extract");
+
+                    for(BitstreamContentStream bce : streams)
+                    {
+                        req.addContentStream(bce);
+                    }
+
+                    ModifiableSolrParams params = new ModifiableSolrParams();
+
+                    //req.setParam(ExtractingParams.EXTRACT_ONLY, "true");
+                    for(String name : doc.getFieldNames())
+                    {
+                        for(Object val : doc.getFieldValues(name))
+                        {
+                             params.add(ExtractingParams.LITERALS_PREFIX + name,val.toString());
+                        }
+                    }
+
+                    req.setParams(params);
+                    req.setParam(ExtractingParams.UNKNOWN_FIELD_PREFIX, "attr_");
+                    req.setParam(ExtractingParams.MAP_PREFIX + "content", "fulltext");
+                    req.setParam(ExtractingParams.EXTRACT_FORMAT, "text");
+                    req.setAction(AbstractUpdateRequest.ACTION.COMMIT, true, true);
+                    req.process(getSolr());
+                }
+                else
+                {
+                    getSolr().add(doc);
+                }
             }
         } catch (SolrServerException e)
         {
@@ -727,7 +772,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrServiceIndexPlugin.additionalIndex(context, community, doc);
         }
 
-        writeDocument(doc);
+        writeDocument(doc, null);
     }
 
     /**
@@ -783,7 +828,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrServiceIndexPlugin.additionalIndex(context, collection, doc);
         }
 
-        writeDocument(doc);
+        writeDocument(doc, null);
     }
 
     /**
@@ -1300,7 +1345,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         log.debug("  Added Grouping");
 
 
-        Vector<InputStreamReader> readers = new Vector<InputStreamReader>();
+
+        List<BitstreamContentStream> streams = new ArrayList<BitstreamContentStream>();
 
         try {
             // now get full text of any bitstreams in the TEXT bundle
@@ -1318,18 +1364,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     for (Bitstream myBitstream : myBitstreams)
                     {
                         try {
-                            InputStreamReader is = new InputStreamReader(
-                                    myBitstream.retrieve()); // get input
-                            readers.add(is);
 
-                            // Add each InputStream to the Indexed Document
+                            streams.add(new BitstreamContentStream(myBitstream));
-                            String value = IOUtils.toString(is);
-                            doc.addField("fulltext", value);
-
-                            if(hitHighlightingFields.contains("*") || hitHighlightingFields.contains("fulltext"))
-                            {
-                                doc.addField("fulltext_hl", value);
-                            }
 
                             log.debug("  Added BitStream: "
                                     + myBitstream.getStoreNumber() + "	"
@@ -1349,16 +1385,6 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             log.error(e.getMessage(), e);
         }
-        finally {
-            Iterator<InputStreamReader> itr = readers.iterator();
-            while (itr.hasNext()) {
-                InputStreamReader reader = itr.next();
-                if (reader != null) {
-                    reader.close();
-                }
-            }
-            log.debug("closed " + readers.size() + " readers");
-        }
 
         //Do any additional indexing, depends on the plugins
         List<SolrServiceIndexPlugin> solrServiceIndexPlugins = new DSpace().getServiceManager().getServicesByType(SolrServiceIndexPlugin.class);
@@ -1369,7 +1395,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
         // write the index and close the inputstreamreaders
         try {
-            writeDocument(doc);
+            writeDocument(doc, streams);
             log.info("Wrote Item: " + handle + " to Index");
         } catch (RuntimeException e)
         {

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

@@ -29,6 +29,7 @@ import java.util.TimeZone;
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import ORG.oclc.oai.harvester2.verb.*;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
@@ -64,12 +65,6 @@ import org.jdom.input.DOMBuilder;
 import org.jdom.output.XMLOutputter;
 import org.xml.sax.SAXException;
 
-import ORG.oclc.oai.harvester2.verb.GetRecord;
-import ORG.oclc.oai.harvester2.verb.Identify;
-import ORG.oclc.oai.harvester2.verb.ListMetadataFormats;
-import ORG.oclc.oai.harvester2.verb.ListRecords;
-import ORG.oclc.oai.harvester2.verb.ListSets;
-
 
 /**
  * This class handles OAI harvesting of externally located records into this repository.
@@ -369,7 +364,13 @@ public class OAIHarvester {
 				else {
 					listRecords = new ListRecords(oaiSource, resumptionToken);
 				}
-				targetCollection.update();
+                ourContext.turnOffAuthorisationSystem();
+                try {
+                    targetCollection.update();
+                } finally {
+                    //In case of an exception, make sure to restore our authentication state to the previous state
+                    ourContext.restoreAuthSystemState();
+                }
 				ourContext.commit();
 			}
 		}
@@ -394,6 +395,7 @@ public class OAIHarvester {
 		}
 		finally {
 			harvestRow.update();
+            ourContext.turnOffAuthorisationSystem();
 			targetCollection.update();
 			ourContext.commit();
 			ourContext.restoreAuthSystemState();
@@ -954,29 +956,21 @@ public class OAIHarvester {
     	try {
             //If we do not want to harvest from one set, then skip this.
     		if(!"all".equals(oaiSetId)){
-                ListSets ls = new ListSets(oaiSource);
+                ListIdentifiers ls = new ListIdentifiers(oaiSource, null, null, oaiSetId, DMDOAIPrefix);
 
                 // The only error we can really get here is "noSetHierarchy"
                 if (ls.getErrors() != null && ls.getErrors().getLength() > 0) {
                     for (int i=0; i<ls.getErrors().getLength(); i++) {
                         String errorCode = ls.getErrors().item(i).getAttributes().getNamedItem("code").getTextContent();
-                        errorSet.add(errorCode);
+                        errorSet.add(OAI_SET_ERROR + ": The OAI server does not have a set with the specified setSpec (" + errorCode + ")");
                     }
                 }
                 else {
                     // Drilling down to /OAI-PMH/ListSets/set
                     Document reply = db.build(ls.getDocument());
                     Element root = reply.getRootElement();
-                    List<Element> sets= root.getChild("ListSets",OAI_NS).getChildren("set",OAI_NS);
+                    //Check if we can find items, if so this indicates that we have children and our sets exist
-
+                    foundSet = 0 < root.getChild("ListIdentifiers",OAI_NS).getChildren().size();
-                    for (Element set : sets)
-                    {
-                        String setSpec = set.getChildText("setSpec", OAI_NS);
-                        if (setSpec.equals(oaiSetId)) {
-                            foundSet = true;
-                            break;
-                        }
-                    }
 
                     if (!foundSet) {
                         errorSet.add(OAI_SET_ERROR + ": The OAI server does not have a set with the specified setSpec");

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

@@ -545,7 +545,7 @@ public class VersionedHandleIdentifierProvider extends IdentifierProvider {
     protected String getCanonical(Item item)
     {
         String canonical = item.getHandle();
-        if( canonical.lastIndexOf(DOT)!=-1)
+        if( canonical.matches(".*/.*\\.\\d+") && canonical.lastIndexOf(DOT)!=-1)
         {
             canonical =  canonical.substring(0, canonical.lastIndexOf(DOT));
         }
@@ -556,7 +556,7 @@ public class VersionedHandleIdentifierProvider extends IdentifierProvider {
     protected String getCanonical(String identifier)
     {
         String canonical = identifier;
-        if( canonical.lastIndexOf(DOT)!=-1)
+        if( canonical.matches(".*/.*\\.\\d+") && canonical.lastIndexOf(DOT)!=-1)
         {
             canonical =  canonical.substring(0, canonical.lastIndexOf(DOT));
         }

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

@@ -475,6 +475,9 @@ public class DSQuery
             lastModified = reader.getVersion();         
             searcher = new IndexSearcher(reader);
             
+        } else {
+            reader.close();
+            searchDir.close();
         }
 
         return searcher;

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

@@ -7,7 +7,6 @@
  */
 package org.dspace.statistics;
 
-import au.com.bytecode.opencsv.CSVParser;
 import au.com.bytecode.opencsv.CSVReader;
 import au.com.bytecode.opencsv.CSVWriter;
 import com.maxmind.geoip.Location;
@@ -78,8 +77,6 @@ public class SolrLogger
 
     private static final LookupService locationService;
 
-    private static Map<String, String> metadataStorageInfo;
-
     private static final boolean useProxies;
 
     private static List<String> statisticYearCores = new ArrayList<String>();
@@ -330,7 +327,10 @@ public class SolrLogger
                 log.error("Failed DNS Lookup for IP:" + ip);
                 log.debug(e.getMessage(),e);
             }
-
+            if(request.getHeader("User-Agent") != null)
+            {
+                doc1.addField("userAgent", request.getHeader("User-Agent"));
+            }
             // Save the location information if valid, save the event without
             // location information if not valid
             if(locationService != null)
@@ -356,10 +356,7 @@ public class SolrLogger
                     doc1.addField("longitude", location.longitude);
                     doc1.addField("isBot",isSpiderBot);
 
-                    if(request.getHeader("User-Agent") != null)
+
-                    {
-                        doc1.addField("userAgent", request.getHeader("User-Agent"));
-                    }
                 }
             }
         }
@@ -415,7 +412,10 @@ public class SolrLogger
                 log.error("Failed DNS Lookup for IP:" + ip);
                 log.debug(e.getMessage(),e);
             }
-
+            if(userAgent != null)
+            {
+                doc1.addField("userAgent", userAgent);
+            }
             // Save the location information if valid, save the event without
             // location information if not valid
             if(locationService != null)
@@ -441,10 +441,7 @@ public class SolrLogger
                     doc1.addField("longitude", location.longitude);
                     doc1.addField("isBot",isSpiderBot);
 
-                    if(userAgent != null)
+
-                    {
-                        doc1.addField("userAgent", userAgent);
-                    }
                 }
             }
         }
@@ -563,11 +560,6 @@ public class SolrLogger
 
     }
 
-    public static Map<String, String> getMetadataStorageInfo()
-    {
-        return metadataStorageInfo;
-    }
-
     /**
      * Method just used to log the parents.
      * <ul>
@@ -676,18 +668,6 @@ public class SolrLogger
 
             // We have at least one document good
             SolrDocument document = response.getResults().get(0);
-            for (Object storedField : metadataStorageInfo.keySet())
-            {
-                // For each of these fields that are stored we are to create a
-                // list of the values it holds now
-                java.util.Collection collection = document
-                        .getFieldValues((String) storedField);
-                List<String> storedVals = new ArrayList<String>();
-                storedVals.addAll(collection);
-                // Now add it to our hashmap
-                currentValsStored.put((String) storedField, storedVals);
-            }
-
             // System.out.println("HERE");
             // Get the info we need
         }

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

@@ -37,6 +37,7 @@ public class StatisticsLoggingConsumer implements Consumer
 
     private Set<String> toRemoveQueries = null;
 
+    @Override
     public void initialize() throws Exception
     {
 
@@ -45,6 +46,7 @@ public class StatisticsLoggingConsumer implements Consumer
     // TODO: checkout whether moving of collections, communities and bitstreams works
     // TODO: use async threaded consumer as this might require some processing time
     // TODO: we might be able to improve the performance: changing the collection will trigger 4 update commands
+    @Override
     public void consume(Context ctx, Event event) throws Exception
     {
         if (toRemoveQueries == null)
@@ -78,45 +80,9 @@ public class StatisticsLoggingConsumer implements Consumer
                     updateQuery, null, null);
 
             // Get all the metadata
-            Map<String, String> metadataStorageInfo = SolrLogger.getMetadataStorageInfo();
             List<String> storageFieldList = new ArrayList<String>();
             List<List<Object>> storageValuesList = new ArrayList<List<Object>>();
 
-            for (Map.Entry<String, String> entry : metadataStorageInfo.entrySet())
-            {
-                String[] metadataFieldInfo = entry.getValue().split("\\.");
-
-                List<Object> values = new ArrayList<Object>();
-                List<Object> valuesLow = new ArrayList<Object>();
-                for (int i = 0; i < item.getMetadata(metadataFieldInfo[0],
-                        metadataFieldInfo[1], metadataFieldInfo[2], Item.ANY).length; i++)
-                {
-                    values.add(item.getMetadata(metadataFieldInfo[0],
-                            metadataFieldInfo[1], metadataFieldInfo[2],
-                            Item.ANY)[i].value);
-                    
-                    valuesLow.add(item.getMetadata(metadataFieldInfo[0],
-                            metadataFieldInfo[1], metadataFieldInfo[2],
-                            Item.ANY)[i].value.toLowerCase());
-                }
-
-                List<String> indexedVals = indexedValues.get(entry.getKey());
-
-                boolean update = true;
-                if (values.size() == indexedVals.size() && values.containsAll(indexedVals))
-                {
-                    update = false;
-                }
-
-                if (update)
-                {
-                    storageFieldList.add(entry.getKey());
-                    storageFieldList.add(entry.getKey() + "_search");
-                    storageValuesList.add(values);
-                    storageValuesList.add(valuesLow);
-                }
-            }
-
             SolrLogger.update(updateQuery, "replace", storageFieldList,
                     storageValuesList);
 
@@ -202,6 +168,7 @@ public class StatisticsLoggingConsumer implements Consumer
         findComms(comm.getParentCommunity(), parentComms);
     }
 
+    @Override
     public void end(Context ctx) throws Exception
     {
         if (toRemoveQueries != null)
@@ -215,6 +182,7 @@ public class StatisticsLoggingConsumer implements Consumer
         toRemoveQueries = null;
     }
 
+    @Override
     public void finish(Context ctx) throws Exception
     {
     }

dspace-api/src/main/java/org/dspace/statistics/util/ClassicDSpaceLogConverter.java

@@ -33,10 +33,10 @@ import java.text.ParsePosition;
  * @author Stuart Lewis
  */
 public class ClassicDSpaceLogConverter {
-    private Logger log = Logger.getLogger(ClassicDSpaceLogConverter.class);
+    private final Logger log = Logger.getLogger(ClassicDSpaceLogConverter.class);
 
     /** A DSpace context */
-    private Context context;
+    private final Context context;
 
     /** Whether or not to provide verbose output */
     private boolean verbose = false;
@@ -45,19 +45,19 @@ public class ClassicDSpaceLogConverter {
     private boolean newEvents = false;
 
     /** A regular expression for extracting the IP address from a log line */
-    private Pattern ipaddrPattern = Pattern.compile("ip_addr=(\\d*\\.\\d*\\.\\d*\\.\\d*):");
+    private final Pattern ipaddrPattern = Pattern.compile("ip_addr=(\\d*\\.\\d*\\.\\d*\\.\\d*):");
 
     /** Date format (in) from the log line */
-    private SimpleDateFormat dateFormatIn = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+    private final SimpleDateFormat dateFormatIn = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
 
     /** Date format out (for solr) */
-    private SimpleDateFormat dateFormatOut = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
+    private final SimpleDateFormat dateFormatOut = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
 
     /** Date format (in) from the log line for the UID */
-    private SimpleDateFormat dateFormatInUID = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss,SSS");
+    private final SimpleDateFormat dateFormatInUID = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss,SSS");
 
     /** Date format out (for uid) */
-    private SimpleDateFormat dateFormatOutUID = new SimpleDateFormat("yyyyMMddHHmmssSSS");
+    private final SimpleDateFormat dateFormatOutUID = new SimpleDateFormat("yyyyMMddHHmmssSSS");
 
 
     /**
@@ -349,24 +349,33 @@ public class ClassicDSpaceLogConverter {
         {
             // Convert all the files
             final File sample = new File(line.getOptionValue('i'));
-            File dir = sample.getParentFile();
+            File dir = sample.getAbsoluteFile().getParentFile();
             FilenameFilter filter = new FilenameFilter()
             {
+                @Override
                 public boolean accept(File dir, String name)
                 {
                     return name.startsWith(sample.getName());
                 }
             };
             String[] children = dir.list(filter);
-            for (String in : children)
+            if (null == children)
             {
-                System.err.println(in);
+                System.err.println(sample + " could not be used to find a directory of log files.");
-                String out = line.getOptionValue('o') +
+                System.exit(1);
-                             (dir.getAbsolutePath() +
-                              System.getProperty("file.separator") + in).substring(line.getOptionValue('i').length());
-
-                converter.convert(dir.getAbsolutePath() + System.getProperty("file.separator") + in, out);
             }
+            else if (children.length <= 0)
+                System.err.println(sample + " matched no files.");
+            else
+                for (String in : children)
+                {
+                    System.err.println(in);
+                    String out = line.getOptionValue('o') +
+                                 (dir.getAbsolutePath() +
+                                  System.getProperty("file.separator") + in).substring(line.getOptionValue('i').length());
+
+                    converter.convert(dir.getAbsolutePath() + System.getProperty("file.separator") + in, out);
+                }
         }
         else
         {

dspace-api/src/main/java/org/dspace/statistics/util/SpiderDetector.java

@@ -205,7 +205,8 @@ public class SpiderDetector {
 
             for (Pattern candidate : agents)
             {
-                if (candidate.matcher(agent).find())
+                // prevent matcher() invocation from a null Pattern object
+                if (null != candidate && candidate.matcher(agent).find())
                 {
                     return true;
                 }
@@ -236,7 +237,8 @@ public class SpiderDetector {
 
             for (Pattern candidate : domains)
             {
-                if (candidate.matcher(hostname).find())
+                // prevent matcher() invocation from a null Pattern object
+                if (null != candidate && candidate.matcher(hostname).find())
                 {
                     return true;
                 }

dspace-api/src/main/java/org/dspace/statistics/util/StatisticsDataGenerator.java

@@ -16,13 +16,10 @@ import org.dspace.core.Constants;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Bitstream;
-import org.dspace.content.DCValue;
-import org.dspace.content.Item;
 import org.dspace.eperson.EPerson;
 import org.dspace.statistics.SolrLogger;
 
 import java.util.Date;
-import java.util.Map;
 import java.text.SimpleDateFormat;
 
 import com.maxmind.geoip.LookupService;
@@ -196,8 +193,6 @@ public class StatisticsDataGenerator {
 		solr.deleteByQuery("*:*");
 		solr.commit();
 
-		Map<String, String> metadataStorageInfo = SolrLogger.getMetadataStorageInfo();
-
 		String prevIp = null;
 		String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
 		LookupService cl = new LookupService(dbfile,
@@ -366,24 +361,6 @@ public class StatisticsDataGenerator {
                 doc1.addField("dns", dns.toLowerCase());
             }
 
-			if (dso instanceof Item) {
-				Item item = (Item) dso;
-				// Store the metadata
-                for (Map.Entry<String, String> entry : metadataStorageInfo.entrySet())
-				{
-					String dcField = entry.getValue();
-
-					DCValue[] vals = item.getMetadata(dcField.split("\\.")[0],
-							dcField.split("\\.")[1], dcField.split("\\.")[2],
-							Item.ANY);
-					for (DCValue val1 : vals) {
-						String val = val1.value;
-						doc1.addField(entry.getKey(), val);
-						doc1.addField(entry.getKey() + "_search", val.toLowerCase());
-					}
-				}
-			}
-
 			SolrLogger.storeParents(doc1, dso);
 
 			solr.add(doc1);

dspace-api/src/main/java/org/dspace/statistics/util/StatisticsImporter.java

@@ -29,7 +29,7 @@ import com.maxmind.geoip.LookupService;
 import com.maxmind.geoip.Location;
 
 /**
- * Class to load intermediate statistics files (produced from log files by <code>ClassicDSpaceLogConverter</code>) into Solr
+ * Class to load intermediate statistics files (produced from log files by {@link ClassicDSpaceLogConverter}) into Solr.
  *
  * @see ClassicDSpaceLogConverter
  *
@@ -40,7 +40,7 @@ public class StatisticsImporter
     private static final Logger log = Logger.getLogger(StatisticsImporter.class);
 
     /** Date format (for solr) */
-    private static SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
+    private static final SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss");
 
     /** Solr server connection */
     private static HttpSolrServer solr;
@@ -48,9 +48,6 @@ public class StatisticsImporter
     /** GEOIP lookup service */
     private static LookupService geoipLookup;
 
-    /** Metadata storage information */
-    private static Map<String, String> metadataStorageInfo;
-
     /** Whether to skip the DNS reverse lookup or not */
     private static boolean skipReverseDNS = false;
 
@@ -67,7 +64,7 @@ public class StatisticsImporter
     private List<Integer> localBitstreams;
 
     /** Whether or not to replace item IDs with local values (for testing) */
-    private boolean useLocal;
+    private final boolean useLocal;
 
     /**
      * Constructor. Optionally loads local data to replace foreign data
@@ -339,24 +336,6 @@ public class StatisticsImporter
                     sid.addField("dns", dns.toLowerCase());
                 }
 
-                if (dso instanceof Item) {
-                    Item item = (Item) dso;
-                    // Store the metadata
-                    for (String storedField : metadataStorageInfo.keySet()) {
-                        String dcField = metadataStorageInfo.get(storedField);
-
-                        DCValue[] vals = item.getMetadata(dcField.split("\\.")[0],
-                                dcField.split("\\.")[1], dcField.split("\\.")[2],
-                                Item.ANY);
-                        for (DCValue val1 : vals) {
-                            String val = val1.value;
-                            sid.addField(String.valueOf(storedField), val);
-                            sid.addField(String.valueOf(storedField + "_search"),
-                                    val.toLowerCase());
-                        }
-                    }
-                }
-
                 SolrLogger.storeParents(sid, dso);
                 solr.add(sid);
                 errors--;
@@ -471,7 +450,6 @@ public class StatisticsImporter
         }
 		solr = new HttpSolrServer(sserver);
 
-		metadataStorageInfo = SolrLogger.getMetadataStorageInfo();
         String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
         try
         {
@@ -495,6 +473,7 @@ public class StatisticsImporter
             File dir = sample.getParentFile();
             FilenameFilter filter = new FilenameFilter()
             {
+                @Override
                 public boolean accept(File dir, String name)
                 {
                     return name.startsWith(sample.getName());
@@ -522,7 +501,7 @@ public class StatisticsImporter
      */
     static class DNSCache<K,V> extends LinkedHashMap<K,V>
     {
-        private int maxCapacity;
+        private final int maxCapacity;
 
         public DNSCache(int initialCapacity, float loadFactor, int maxCapacity)
         {

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

@@ -112,11 +112,15 @@ public class MetadataSchemaTest extends AbstractUnitTest
     @Test
     public void testSetName() 
     {
+        String oldname = ms.getName();
         String name = "new name";
         ms.setName(name);
         assertThat("testSetName 0",ms.getName(),notNullValue());
         assertThat("testSetName 1",ms.getName(),not(equalTo("")));
         assertThat("testSetName 2",ms.getName(),equalTo(name));
+
+        //we restore the old name to avoid issues in other tests
+        ms.setName(oldname);
     }
 
     /**
@@ -392,4 +396,4 @@ public class MetadataSchemaTest extends AbstractUnitTest
         assertThat("testFind_Context_String 4",found, nullValue());
     }
 
-}
+}

dspace-jspui/pom.xml

@@ -13,7 +13,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-parent</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace-jspui/src/main/java/org/dspace/app/webui/servlet/AbstractBrowserServlet.java

@@ -14,6 +14,7 @@ import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.app.webui.util.UIUtil;
 import org.dspace.authorize.AuthorizeException;
@@ -30,6 +31,7 @@ import org.dspace.content.Community;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
+import org.dspace.core.Utils;
 
 /**
  * Servlet for browsing through indices, as they are defined in
@@ -86,6 +88,25 @@ public abstract class AbstractBrowserServlet extends DSpaceServlet
             String month = request.getParameter("month");
             String year = request.getParameter("year");
             String startsWith = request.getParameter("starts_with");
+            //validate input to avoid cross-site scripting
+            try {
+            	if (StringUtils.isNotBlank(month) && !"-1".equals(month)) {
+            		Integer.valueOf(month);
+            	}
+            	if (StringUtils.isNotBlank(year) && !"-1".equals(year)) {
+            		Integer.valueOf(year);
+            	}
+            	if(StringUtils.isNotBlank(startsWith)) {
+            		startsWith = Utils.addEntities(startsWith);
+            	}
+            }
+            catch(Exception ex) {
+                log.warn("We were unable to parse the browse request: maybe a cross-site scripting attach?");
+                return null;
+            }
+            
+            
+            
             String valueFocus = request.getParameter("vfocus");
             String valueFocusLang = request.getParameter("vfocus_lang");
             String authority = request.getParameter("authority");
@@ -108,7 +129,7 @@ public abstract class AbstractBrowserServlet extends DSpaceServlet
 
             // process the input, performing some inline validation
             BrowseIndex bi = null;
-            if (type != null && !"".equals(type))
+            if (StringUtils.isNotEmpty(type))
             {
                 bi = BrowseIndex.getBrowseIndex(type);
             }

dspace-jspui/src/main/java/org/dspace/app/webui/servlet/BrowserServlet.java

@@ -65,7 +65,7 @@ public class BrowserServlet extends AbstractBrowserServlet
         // all browse requests currently come to GET.
         BrowserScope scope = getBrowserScopeForRequest(context, request, response);
 
-        if (scope.getBrowseIndex() == null)
+        if (scope == null || scope.getBrowseIndex() == null)
         {
             throw new ServletException("There is no browse index for the request");
         }

dspace-jspui/src/main/java/org/dspace/app/webui/servlet/CommunityListServlet.java

@@ -11,6 +11,7 @@ import java.io.IOException;
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.Map;
+import java.util.concurrent.locks.*;
 
 import javax.servlet.ServletException;
 import javax.servlet.http.HttpServletRequest;
@@ -33,46 +34,71 @@ import org.dspace.core.LogManager;
  */
 public class CommunityListServlet extends DSpaceServlet
 {
+    
+    // This will map community IDs to arrays of collections
+    private Map<Integer, Collection[]> colMap;
+
+    // This will map communityIDs to arrays of sub-communities
+    private Map<Integer, Community[]> commMap;
+    private static final Object staticLock = new Object();
+    
     /** log4j category */
     private static Logger log = Logger.getLogger(CommunityListServlet.class);
 
     protected void doDSGet(Context context, HttpServletRequest request,
             HttpServletResponse response) throws ServletException, IOException,
             SQLException, AuthorizeException
-    {
+    { 
-        log.info(LogManager.getHeader(context, "view_community_list", ""));
+           synchronized (staticLock) 
+           {
+            colMap = new HashMap<Integer, Collection[]>();
+            commMap = new HashMap<Integer, Community[]>();
 
-        // This will map community IDs to arrays of collections
+            log.info(LogManager.getHeader(context, "view_community_list", ""));
-        Map<Integer, Collection[]> colMap = new HashMap<Integer, Collection[]>();
 
-        // This will map communityIDs to arrays of sub-communities
+            Community[] communities = Community.findAllTop(context);
-        Map<Integer, Community[]> commMap = new HashMap<Integer, Community[]>();
 
-        Community[] communities = Community.findAllTop(context);
+            for (int com = 0; com < communities.length; com++) 
+            {
+                build(communities[com]);
+            }
 
-        for (int com = 0; com < communities.length; com++)
+            // can they admin communities?
+            if (AuthorizeManager.isAdmin(context)) 
+            {
+                // set a variable to create an edit button
+                request.setAttribute("admin_button", Boolean.TRUE);
+            }
+
+            request.setAttribute("communities", communities);
+            request.setAttribute("collections.map", colMap);
+            request.setAttribute("subcommunities.map", commMap);
+            JSPManager.showJSP(request, response, "/community-list.jsp");
+           }
+    }
+    /*
+     * Get all subcommunities and collections from a community
+     */
+    private void build(Community c) throws SQLException {
+
+        Integer comID = Integer.valueOf(c.getID());
+
+        // Find collections in community
+        Collection[] colls = c.getCollections();
+        colMap.put(comID, colls);
+
+        // Find subcommunties in community
+        Community[] comms = c.getSubcommunities();
+        
+        // Get all subcommunities for each communities if they have some
+        if (comms.length > 0) 
         {
-            Integer comID = Integer.valueOf(communities[com].getID());
-
-            // Find collections in community
-            Collection[] colls = communities[com].getCollections();
-            colMap.put(comID, colls);
-
-            // Find subcommunties in community
-            Community[] comms = communities[com].getSubcommunities();
             commMap.put(comID, comms);
+            
+            for (int sub = 0; sub < comms.length; sub++) {
+                
+                build(comms[sub]);
+            }
         }
-
-        // can they admin communities?
-        if (AuthorizeManager.isAdmin(context))
-        {
-            // set a variable to create an edit button
-            request.setAttribute("admin_button", Boolean.TRUE);
-        }
-
-        request.setAttribute("communities", communities);
-        request.setAttribute("collections.map", colMap);
-        request.setAttribute("subcommunities.map", commMap);
-        JSPManager.showJSP(request, response, "/community-list.jsp");
     }
 }

dspace-jspui/src/main/java/org/dspace/app/webui/servlet/HandleServlet.java

@@ -19,6 +19,7 @@ import javax.servlet.http.HttpServletRequest;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.app.util.GoogleMetadata;
 import org.dspace.app.webui.util.Authenticate;
@@ -129,8 +130,7 @@ public class HandleServlet extends DSpaceServlet
 
         if (dso == null)
         {
-            log.info(LogManager
+            log.info(LogManager.getHeader(context, "invalid_id", "path=" + path));
-                    .getHeader(context, "invalid_id", "path=" + path));
             JSPManager.showInvalidIDError(request, response, StringEscapeUtils.escapeHtml(path), -1);
 
             return;
@@ -152,8 +152,28 @@ public class HandleServlet extends DSpaceServlet
             // and firing a usage event for the DSO we're reporting for
             return;
 
+        } else if ("/display-statistics.jsp".equals(extraPathInfo))
+        {
+            request.getRequestDispatcher(extraPathInfo).forward(request, response);
+            // If we don't return here, we keep processing and end up
+            // throwing a NPE when checking community authorization
+            // and firing a usage event for the DSO we're reporting for
+            return;
+        } else if ("/browse".equals((extraPathInfo)) || StringUtils.startsWith(extraPathInfo, "/browse?")) {
+            request.getRequestDispatcher(extraPathInfo).forward(request, response);
+            // If we don't return here, we keep processing and end up
+            // throwing a NPE when checking community authorization
+            // and firing a usage event for the DSO we're reporting for
+            return;
+        } else if ("/simple-search".equals(extraPathInfo) || StringUtils.startsWith(extraPathInfo, "simple-search?")) {
+            request.getRequestDispatcher(extraPathInfo).forward(request, response);
+            // If we don't return here, we keep processing and end up
+            // throwing a NPE when checking community authorization
+            // and firing a usage event for the DSO we're reporting for
+            return;
         }
 
+
         // OK, we have a valid Handle. What is it?
         if (dso.getType() == Constants.ITEM)
         {
@@ -195,9 +215,9 @@ public class HandleServlet extends DSpaceServlet
             }
             else
             {
-                // Forward to another servlet
+                log.debug("Found Item with extraPathInfo => Error.");
-                request.getRequestDispatcher(extraPathInfo).forward(request,
+                JSPManager.showInvalidIDError(request, response, StringEscapeUtils.escapeHtml(path), -1);
-                        response);
+                return;
             }
 
         }
@@ -231,9 +251,9 @@ public class HandleServlet extends DSpaceServlet
             }
             else
             {
-                // Forward to another servlet
+                log.debug("Found Collection with extraPathInfo => Error.");
-                request.getRequestDispatcher(extraPathInfo).forward(request,
+                JSPManager.showInvalidIDError(request, response, StringEscapeUtils.escapeHtml(path), -1);
-                        response);
+                return;
             }
         }
         else if (dso.getType() == Constants.COMMUNITY)
@@ -255,9 +275,9 @@ public class HandleServlet extends DSpaceServlet
             }
             else
             {
-                // Forward to another servlet
+                log.debug("Found Community with extraPathInfo => Error.");
-                request.getRequestDispatcher(extraPathInfo).forward(request,
+                JSPManager.showInvalidIDError(request, response, StringEscapeUtils.escapeHtml(path), -1);
-                        response);
+                return;
             }
         }
         else

dspace-jspui/src/main/webapp/collection-home.jsp

@@ -38,6 +38,7 @@
 <%@ page import="org.dspace.content.*"%>
 <%@ page import="org.dspace.core.ConfigurationManager"%>
 <%@ page import="org.dspace.core.Context" %>
+<%@ page import="org.dspace.core.Utils" %>
 <%@ page import="org.dspace.eperson.Group"     %>
 <%@ page import="javax.servlet.jsp.jstl.fmt.LocaleSupport" %>
 <%@ page import="java.net.URLEncoder" %>
@@ -374,7 +375,7 @@
 			{
 				if (dcv.length > 0)
 				{
-					displayTitle = dcv[0].value;
+					displayTitle = Utils.addEntities(dcv[0].value);
 				}
 			}
 			%><p class="recentItem"><a href="<%= request.getContextPath() %>/handle/<%= items[i].getHandle() %>"><%= displayTitle %></a></p><%

dspace-jspui/src/main/webapp/community-home.jsp

@@ -32,6 +32,7 @@
 <%@ page import="org.dspace.browse.ItemCounter" %>
 <%@ page import="org.dspace.content.*" %>
 <%@ page import="org.dspace.core.ConfigurationManager" %>
+<%@ page import="org.dspace.core.Utils" %>
 <%@ page import="javax.servlet.jsp.jstl.fmt.LocaleSupport" %>
 
 
@@ -158,7 +159,7 @@
 			{
 				if (dcv.length > 0)
 				{
-					displayTitle = dcv[0].value;
+					displayTitle = Utils.addEntities(dcv[0].value);
 				}
 			}
 			%>
@@ -401,4 +402,4 @@
 		</div>
   </dspace:sidebar>
     <% } %>
-</dspace:layout>
+</dspace:layout>

dspace-jspui/src/main/webapp/controlledvocabulary/search.jsp

@@ -14,6 +14,7 @@
 	The add-on may be turn off in dspace.cfg
 --%>  
 
+<%@page import="org.dspace.core.Utils"%>
 <%@ page contentType="text/html;charset=UTF-8" %>
 <%@ page  import="javax.servlet.jsp.jstl.fmt.LocaleSupport" %>
 <%@ taglib uri="/WEB-INF/dspace-tags.tld" prefix="dspace" %>
@@ -52,7 +53,7 @@
 	<form name="filterVocabulary" method="post" action="<%= request.getContextPath() %>/subject-search">
 	  <input style="border-width:1px;border-style:solid;" 
 	  		 name="filter" type="text" id="filter" 
-	  		 size="15" value="<%= filter %>" 
+	  		 size="15" value="<%= Utils.addEntities(filter) %>" 
 	  		 title="<%= LocaleSupport.getLocalizedMessage(pageContext, "jsp.controlledvocabulary.search.trimmessage") %>"/>
 	  <input type="submit" name="submit" value="<%= LocaleSupport.getLocalizedMessage(pageContext, "jsp.controlledvocabulary.search.trimbutton") %>"/>
 	  <input type="hidden" name="action" value="filter"/>

dspace-jspui/src/main/webapp/home.jsp

@@ -15,6 +15,7 @@
   -    recent.submissions - RecetSubmissions
   --%>
 
+<%@page import="org.dspace.core.Utils"%>
 <%@page import="org.dspace.content.Bitstream"%>
 <%@ page contentType="text/html;charset=UTF-8" %>
 
@@ -133,13 +134,13 @@ if (submissions != null && submissions.count() > 0)
 		        String displayTitle = "Untitled";
 		        if (dcv != null & dcv.length > 0)
 		        {
-		            displayTitle = dcv[0].value;
+		            displayTitle = Utils.addEntities(dcv[0].value);
 		        }
 		        dcv = item.getMetadata("dc", "description", "abstract", Item.ANY);
 		        String displayAbstract = "";
 		        if (dcv != null & dcv.length > 0)
 		        {
-		            displayAbstract = dcv[0].value;
+		            displayAbstract = Utils.addEntities(dcv[0].value);
 		        }
 		%>
 		    <div style="padding-bottom: 50px; min-height: 200px;" class="item <%= first?"active":""%>">

dspace-jspui/src/main/webapp/search/advanced.jsp

@@ -106,7 +106,7 @@
 						{
 							String key = "jsp.search.advanced.type." + index;
 					%>
-							<option value="<%= index %>" <%= field1.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
+							<option value="<%= StringEscapeUtils.escapeHtml(index) %>" <%= field1.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
 					<%
 						}
 					%>
@@ -136,7 +136,7 @@
 						{
 							String key = "jsp.search.advanced.type." + index;
 					%>
-							<option value="<%= index %>" <%= field2.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
+							<option value="<%= StringEscapeUtils.escapeHtml(index) %>" <%= field2.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
 					<%
 						}
 					%>
@@ -162,7 +162,7 @@
 						{
 							String key = "jsp.search.advanced.type." + index;
 					%>
-							<option value="<%= index %>" <%= field3.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
+							<option value="<%= StringEscapeUtils.escapeHtml(index) %>" <%= field3.equals(index) ? "selected=\"selected\"" : "" %>><fmt:message key="<%= key %>"/></option>
 					<%
 						}
 					%>

dspace-jspui/src/main/webapp/search/discovery.jsp

@@ -33,6 +33,7 @@
   -   admin_button     - If the user is an admin
   --%>
 
+<%@page import="org.dspace.core.Utils"%>
 <%@page import="org.dspace.discovery.configuration.DiscoverySearchFilterFacet"%>
 <%@page import="org.dspace.app.webui.util.UIUtil"%>
 <%@page import="java.util.HashMap"%>
@@ -55,7 +56,6 @@
     prefix="c" %>
 
 <%@ taglib uri="http://www.dspace.org/dspace-tags.tld" prefix="dspace" %>
-<%@ page import="org.apache.commons.lang.StringEscapeUtils" %>
 <%@ page import="java.net.URLEncoder"            %>
 <%@ page import="org.dspace.content.Community"   %>
 <%@ page import="org.dspace.content.Collection"  %>
@@ -149,6 +149,9 @@
 				}
 			});
 	});
+	function validateFilters() {
+		return document.getElementById("filterquery").value.length > 0;
+	}
 </script>		
 </c:set>
 
@@ -189,10 +192,10 @@
     }
 %>                                </select><br/>
                                 <label for="query"><fmt:message key="jsp.search.results.searchfor"/></label>
-                                <input type="text" size="50" id="query" name="query" value="<%= (query==null ? "" : StringEscapeUtils.escapeHtml(query)) %>"/>
+                                <input type="text" size="50" id="query" name="query" value="<%= (query==null ? "" : Utils.addEntities(query)) %>"/>
                                 <input type="submit" id="main-query-submit" class="btn btn-primary" value="<fmt:message key="jsp.general.go"/>" />
 <% if (StringUtils.isNotBlank(spellCheckQuery)) {%>
-	<p class="lead"><fmt:message key="jsp.search.didyoumean"><fmt:param><a id="spellCheckQuery" data-spell="<%= StringEscapeUtils.escapeHtml(spellCheckQuery) %>" href="#"><%= spellCheckQuery %></a></fmt:param></fmt:message></p>
+	<p class="lead"><fmt:message key="jsp.search.didyoumean"><fmt:param><a id="spellCheckQuery" data-spell="<%= Utils.addEntities(spellCheckQuery) %>" href="#"><%= spellCheckQuery %></a></fmt:param></fmt:message></p>
 <% } %>                  
                                 <input type="hidden" value="<%= rpp %>" name="rpp" />
                                 <input type="hidden" value="<%= sortedBy %>" name="sort_by" />
@@ -211,7 +214,7 @@
 					for (DiscoverySearchFilter searchFilter : availableFilters)
 					{
 					    String fkey = "jsp.search.filter."+searchFilter.getIndexFieldName();
-					    %><option value="<%= searchFilter.getIndexFieldName() %>"<% 
+					    %><option value="<%= Utils.addEntities(searchFilter.getIndexFieldName()) %>"<% 
 					            if (filter[0].equals(searchFilter.getIndexFieldName()))
 					            {
 					                %> selected="selected"<%
@@ -222,7 +225,7 @@
 					if (!found)
 					{
 					    String fkey = "jsp.search.filter."+filter[0];
-					    %><option value="<%= filter[0] %>" selected="selected"><fmt:message key="<%= fkey %>"/></option><%
+					    %><option value="<%= Utils.addEntities(filter[0]) %>" selected="selected"><fmt:message key="<%= fkey %>"/></option><%
 					}
 				%>
 				</select>
@@ -231,11 +234,11 @@
 					for (String opt : options)
 					{
 					    String fkey = "jsp.search.filter.op."+opt;
-					    %><option value="<%= opt %>"<%= opt.equals(filter[1])?" selected=\"selected\"":"" %>><fmt:message key="<%= fkey %>"/></option><%
+					    %><option value="<%= Utils.addEntities(opt) %>"<%= opt.equals(filter[1])?" selected=\"selected\"":"" %>><fmt:message key="<%= fkey %>"/></option><%
 					}
 				%>
 				</select>
-				<input type="text" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= StringEscapeUtils.escapeHtml(filter[2]) %>" size="45"/>
+				<input type="text" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= Utils.addEntities(filter[2]) %>" size="45"/>
 				<input class="btn btn-default" type="submit" id="submit_filter_remove_<%=idx %>" name="submit_filter_remove_<%=idx %>" value="X" />
 				<br/>
 				<%
@@ -252,17 +255,17 @@
 		<h5><fmt:message key="jsp.search.filter.heading" /></h5>
 		<p class="discovery-search-filters-hint"><fmt:message key="jsp.search.filter.hint" /></p>
 		<form action="simple-search" method="get">
-		<input type="hidden" value="<%= StringEscapeUtils.escapeHtml(searchScope) %>" name="location" />
+		<input type="hidden" value="<%= Utils.addEntities(searchScope) %>" name="location" />
-		<input type="hidden" value="<%= StringEscapeUtils.escapeHtml(query) %>" name="query" />
+		<input type="hidden" value="<%= Utils.addEntities(query) %>" name="query" />
 		<% if (appliedFilterQueries.size() > 0 ) { 
 				int idx = 1;
 				for (String[] filter : appliedFilters)
 				{
 				    boolean found = false;
 				    %>
-				    <input type="hidden" id="filter_field_<%=idx %>" name="filter_field_<%=idx %>" value="<%= filter[0] %>" />
+				    <input type="hidden" id="filter_field_<%=idx %>" name="filter_field_<%=idx %>" value="<%= Utils.addEntities(filter[0]) %>" />
-					<input type="hidden" id="filter_type_<%=idx %>" name="filter_type_<%=idx %>" value="<%= filter[1] %>" />
+					<input type="hidden" id="filter_type_<%=idx %>" name="filter_type_<%=idx %>" value="<%= Utils.addEntities(filter[1]) %>" />
-					<input type="hidden" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= StringEscapeUtils.escapeHtml(filter[2]) %>" />
+					<input type="hidden" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= Utils.addEntities(filter[2]) %>" />
 					<%
 					idx++;
 				}
@@ -285,28 +288,28 @@
 			}
 		%>
 		</select>
-		<input type="text" id="filterquery" name="filterquery" size="45"/>
+		<input type="text" id="filterquery" name="filterquery" size="45" required="required" />
-        <input type="hidden" value="<%= rpp %>" name="rpp" />
+		<input type="hidden" value="<%= rpp %>" name="rpp" />
-        <input type="hidden" value="<%= sortedBy %>" name="sort_by" />
+		<input type="hidden" value="<%= sortedBy %>" name="sort_by" />
-        <input type="hidden" value="<%= order %>" name="order" />
+		<input type="hidden" value="<%= order %>" name="order" />
-		<input class="btn btn-default" type="submit" value="<fmt:message key="jsp.search.filter.add"/>" />
+		<input class="btn btn-default" type="submit" value="<fmt:message key="jsp.search.filter.add"/>" onclick="return validateFilters()" />
 		</form>
 		</div>        
 <% } %>
         <%-- Include a component for modifying sort by, order, results per page, and et-al limit --%>
    <div class="discovery-pagination-controls panel-footer">
    <form action="simple-search" method="get">
-   <input type="hidden" value="<%= StringEscapeUtils.escapeHtml(searchScope) %>" name="location" />
+   <input type="hidden" value="<%= Utils.addEntities(searchScope) %>" name="location" />
-   <input type="hidden" value="<%= StringEscapeUtils.escapeHtml(query) %>" name="query" />
+   <input type="hidden" value="<%= Utils.addEntities(query) %>" name="query" />
 	<% if (appliedFilterQueries.size() > 0 ) { 
 				int idx = 1;
 				for (String[] filter : appliedFilters)
 				{
 				    boolean found = false;
 				    %>
-				    <input type="hidden" id="filter_field_<%=idx %>" name="filter_field_<%=idx %>" value="<%= filter[0] %>" />
+				    <input type="hidden" id="filter_field_<%=idx %>" name="filter_field_<%=idx %>" value="<%= Utils.addEntities(filter[0]) %>" />
-					<input type="hidden" id="filter_type_<%=idx %>" name="filter_type_<%=idx %>" value="<%= filter[1] %>" />
+					<input type="hidden" id="filter_type_<%=idx %>" name="filter_type_<%=idx %>" value="<%= Utils.addEntities(filter[1]) %>" />
-					<input type="hidden" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= StringEscapeUtils.escapeHtml(filter[2]) %>" />
+					<input type="hidden" id="filter_value_<%=idx %>" name="filter_value_<%=idx %>" value="<%= Utils.addEntities(filter[2]) %>" />
 					<%
 					idx++;
 				}
@@ -432,7 +435,7 @@ else if( qResults != null)
     
     // create the URLs accessing the previous and next search result pages
     String baseURL =  request.getContextPath()
-                    + searchScope
+                    + (searchScope != "" ? "/handle/" + searchScope : "")
                     + "/simple-search?query="
                     + URLEncoder.encode(query,"UTF-8")
                     + httpFilters
@@ -628,28 +631,30 @@ else
 		
 	for (DiscoverySearchFilterFacet facetConf : facetsConf)
 	{
-	    String f = facetConf.getIndexFieldName();
+		if(qResults!=null) {
-	    List<FacetResult> facet = qResults.getFacetResult(f);
+		    String f = facetConf.getIndexFieldName();
-	    if (facet.size() == 0)
+		    List<FacetResult> facet = qResults.getFacetResult(f);
-	    {
-	        facet = qResults.getFacetResult(f+".year");
 		    if (facet.size() == 0)
 		    {
-		        showFacets.put(f, false);
+		        facet = qResults.getFacetResult(f+".year");
-		        continue;
+			    if (facet.size() == 0)
+			    {
+			        showFacets.put(f, false);
+			        continue;
+			    }
 		    }
-	    }
+		    boolean showFacet = false;
-	    boolean showFacet = false;
+		    for (FacetResult fvalue : facet)
-	    for (FacetResult fvalue : facet)
+		    { 
-	    { 
+				if(!appliedFilterQueries.contains(f+"::"+fvalue.getFilterType()+"::"+fvalue.getAsFilterQuery()))
-			if(!appliedFilterQueries.contains(f+"::"+fvalue.getFilterType()+"::"+fvalue.getAsFilterQuery()))
+			    {
-		    {
+			        showFacet = true;
-		        showFacet = true;
+			        break;
-		        break;
+			    }
 		    }
-	    }
+		    showFacets.put(f, showFacet);
-	    showFacets.put(f, showFacet);
+		    brefine = brefine || showFacet;
-	    brefine = brefine || showFacet;
+		}
 	}
 	if (brefine) {
 %>
@@ -743,5 +748,4 @@ else
 </div>
 <% } %>
 </dspace:sidebar>
-</dspace:layout>
+</dspace:layout>
-

dspace-jspui/src/main/webapp/search/results.jsp

@@ -396,7 +396,7 @@ if (pageTotal > pageCurrent)
 </p>
 
 <form id="dso-display" action="<%=request.getContextPath()%>/dso-display" method="post">
-    <input type="hidden" name="query"   value="<%=query%>"/>
+    <input type="hidden" name="query"   value="<%=StringEscapeUtils.escapeHtml(query)%>"/>
     <input type="hidden" name="rpp"     value="<%=rpp%>"/>
     <input type="hidden" name="page"   value="<%=pageCurrent%>"/>
     <input type="hidden" name="sort_by" value="<%=(so != null ? so.getNumber() : 0)%>"/>

dspace-jspui/src/main/webapp/tools/eperson-list.jsp

@@ -130,7 +130,16 @@
         <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
         <link rel="stylesheet" href="<%= request.getContextPath() %>/styles.css" type="text/css"/>
         <link rel="shortcut icon" href="<%= request.getContextPath() %>/favicon.ico" type="image/x-icon"/>
-
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/jquery-ui-1.10.3.custom/redmond/jquery-ui-1.10.3.custom.css" type="text/css" />
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/bootstrap.min.css" type="text/css" />
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/bootstrap-theme.min.css" type="text/css" />
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/dspace-theme.css" type="text/css" />
+        <script type='text/javascript' src="<%= request.getContextPath() %>/static/js/jquery/jquery-1.10.2.min.js"></script>
+        <script type='text/javascript' src='<%= request.getContextPath() %>/static/js/jquery/jquery-ui-1.10.3.custom.min.js'></script>
+        <script type='text/javascript' src='<%= request.getContextPath() %>/static/js/bootstrap/bootstrap.min.js'></script>
+        <script type='text/javascript' src='<%= request.getContextPath() %>/static/js/holder.js'></script>
+        <script type="text/javascript" src="<%= request.getContextPath() %>/utils.js"></script>
+							
 <script type="text/javascript">
 <!-- Begin
 
@@ -169,73 +178,65 @@ function clearEPeople()
 	<p class="submitFormHelp"><fmt:message key="jsp.tools.eperson-list.info1"/></p>
 <%  } %>
 <center>
-<form method="get">
+	<form method="get">
-    <input type="hidden" name="first" value="<%= first %>" />
+	    <input type="hidden" name="first" value="<%= first %>" />
-    <input type="hidden" name="sortby" value="<%= sortBy %>" />
+	    <input type="hidden" name="sortby" value="<%= sortBy %>" />
-    <input type="hidden" name="multiple" value="<%= multiple %>" />    
+	    <input type="hidden" name="multiple" value="<%= multiple %>" />    
-    <label for="search"><fmt:message key="jsp.tools.eperson-list.search.query" /></label><input type="text" name="search" value="<%= search %>"/>
+	    <label for="search"><fmt:message key="jsp.tools.eperson-list.search.query"/></label>
-    <input type="submit" value="<fmt:message key="jsp.tools.eperson-list.search.submit" />" />
+	    <input class="form-control" style="width:200px;"type="text" name="search" value="<%= search %>"/>
-<%
+	    <input class="btn btn-success" type="submit" value="<fmt:message key="jsp.tools.eperson-list.search.submit" />" />
-    if (search != null && !search.equals(""))
+	<%
-    {   %>
+	    if (search != null && !search.equals("")){   %>
-    <br/>
+	    <a class="btn btn-warning" href="<%= request.getContextPath() + "/tools/eperson-list?multiple=" + multiple + "&sortby=" + sortByParam + "&first="+first %>"><fmt:message key="jsp.tools.eperson-list.search.return-browse" /></a>	
-    <a href="<%= request.getContextPath() + "/tools/eperson-list?multiple=" + multiple + "&sortby=" + sortByParam + "&first="+first %>"><fmt:message key="jsp.tools.eperson-list.search.return-browse" /></a>	
+		<%}%>
-<%
+		
-    }    
+	</form>
-%>
-</form>
 </center>
+
 <%-- Controls for jumping around list--%>
-	<table width="99%">
+<div class="span12" style="text-align:center">
-		<tr>
+	<ul class="pagination">			
-		 <%--   <td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0">First</a></strong></small></td>
+			<li><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.eperson-list.jump.first"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>">&lt; 5 Pages</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.eperson-list.jump.five-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>">&lt; 1 Page</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.eperson-list.jump.one-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>">1 Page &gt;</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.eperson-list.jump.one-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>">5 Pages &gt;</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.eperson-list.jump.five-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>">Last</a></strong></small></td> --%>
+			<li><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.eperson-list.jump.last"/></a></li>
-			
+	</ul>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.eperson-list.jump.first"/></a></strong></small></td>
+</div
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.eperson-list.jump.five-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.eperson-list.jump.one-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.eperson-list.jump.one-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.eperson-list.jump.five-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.eperson-list.jump.last"/></a></strong></small></td>
-		</tr>
-	</table>
 <br/>
 
 	<form method="get" action=""> <%-- Will never actually be posted, it's just so buttons will appear --%>
 
-    <table class="miscTable" align="center" summary="Epeople list">
+    <table class="table table-striped" align="center" summary="Epeople list">
 <% if (search != null && !search.equals(""))
    {  %>
        <tr>
-            <th class="oddRowOddCol">&nbsp;</th>
+            <th>&nbsp;</th>
-            <th class="oddRowEvenCol"><fmt:message key="jsp.tools.eperson-list.th.id" /></th>
+            <th><fmt:message key="jsp.tools.eperson-list.th.id" /></th>
-            <th class="oddRowOddCol"><fmt:message key="jsp.tools.eperson-list.th.email" /></th>
+            <th><fmt:message key="jsp.tools.eperson-list.th.email" /></th>
-            <th class="oddRowEvenCol"><fmt:message key="jsp.tools.eperson-list.th.lastname" /></th>
+            <th><fmt:message key="jsp.tools.eperson-list.th.lastname" /></th>
-            <th class="oddRowOddCol"><fmt:message key="jsp.tools.eperson-list.th.lastname" /></th>
+            <th><fmt:message key="jsp.tools.eperson-list.th.lastname" /></th>
         </tr>
 <% }
    else 
    {  %>
         <tr>
-            <th id="t1" class="oddRowOddCol">&nbsp;</th>
+            <th id="t1">&nbsp;</th>
-            <th id="t2" class="oddRowEvenCol"><%
+            <th id="t2"><%
                 if (sortBy == EPerson.ID)
                 {
-                    %><strong><fmt:message key="jsp.tools.eperson-list.th.id.sortedby" /></strong><%
+                    %><fmt:message key="jsp.tools.eperson-list.th.id"/><span class="glyphicon glyphicon-arrow-down"><%
                 }
                 else
                 {
                     %><a href="<%= sortLink %>id"><fmt:message key="jsp.tools.eperson-list.th.id" /></a><%
                 }
             %></th>
-            <th id="t3" class="oddRowOddCol"><%
+            <th id="t3"><%
                 if (sortBy == EPerson.EMAIL)
                 {
-                    %><strong><fmt:message key="jsp.tools.eperson-list.th.email.sortedby" /></strong><%
+                    %><fmt:message key="jsp.tools.eperson-list.th.email"/><span class="glyphicon glyphicon-arrow-down"><%
                 }
                 else
                 {
@@ -243,10 +244,10 @@ function clearEPeople()
                 }
             %></th>
             <%-- <th class="oddRowEvenCol"><%= sortBy == EPerson.LASTNAME ? "<strong>Last Name &uarr;</strong>" : "<a href=\"" + sortLink + "lastname\">Last Name</a>" %></th> --%>
-            <th id="t4" class="oddRowEvenCol"><%
+            <th id="t4"><%
                 if (sortBy == EPerson.LASTNAME)
                 {
-                    %><fmt:message key="jsp.tools.eperson-list.th.lastname.sortedby" /><%
+                    %><fmt:message key="jsp.tools.eperson-list.th.lastname"/><span class="glyphicon glyphicon-arrow-down"><%
                 }
                 else
                 {
@@ -254,12 +255,12 @@ function clearEPeople()
                 }
             %></th>
 
-            <th id="t5" class="oddRowOddCol"><fmt:message key="jsp.tools.eperson-list.th.firstname"/></th>
+            <th id="t5"><fmt:message key="jsp.tools.eperson-list.th.firstname"/></th>
  
-             <th id="t6" class="oddRowEvenCol"><%
+             <th id="t6"><%
                 if (sortBy == EPerson.LANGUAGE)
                 {
-                    %><fmt:message key="jsp.tools.eperson-list.th.language.sortedby" /><%
+                    %><fmt:message key="jsp.tools.eperson-list.th.language"/><span class="glyphicon glyphicon-arrow-down"></span><%
                 }
                 else
                 {
@@ -285,20 +286,20 @@ function clearEPeople()
         String fullname = StringEscapeUtils.escapeXml(StringEscapeUtils.escapeJavaScript(e.getFullName()));
         String email = StringEscapeUtils.escapeXml(StringEscapeUtils.escapeJavaScript(e.getEmail()));
 %>
-        <tr>
+  <tr>
-			<td headers="t1" class="<%= row %>RowOddCol">
+			<td headers="t1">
-			    <input type="button" value="<%
+			    <input class="btn btn-success" type="button" value="<%
-	if (multiple) { %><fmt:message key="jsp.tools.general.add"/><% }
+			if (multiple) { %><fmt:message key="jsp.tools.general.add"/><% }
-	else {          %><fmt:message key="jsp.tools.general.select"/><% } %>" onclick="javascript:<%= clearList %>addEPerson(<%= e.getID() %>, '<%= email %>', '<%= fullname %>');<%= closeWindow %>"/></td>
+			else {          %><fmt:message key="jsp.tools.general.select"/><% } %>" onclick="javascript:<%= clearList %>addEPerson(<%= e.getID() %>, '<%= email %>', '<%= fullname %>');<%= closeWindow %>"/></td>
-			<td headers="t2" class="<%= row %>RowEvenCol"><%= e.getID() %></td>
+			<td headers="t2"><%= e.getID() %></td>
-			<td headers="t3" class="<%= row %>RowOddCol"><%= (e.getEmail() == null ? "" : Utils.addEntities(e.getEmail())) %></td>
+			<td headers="t3"><%= (e.getEmail() == null ? "" : Utils.addEntities(e.getEmail())) %></td>
-            <td headers="t4" class="<%= row %>RowEvenCol">
+            <td headers="t4">
                 <%= (e.getLastName() == null ? "" : Utils.addEntities(e.getLastName())) %>
             </td>
-            <td headers="t5" class="<%= row %>RowOddCol">
+            <td headers="t5">
                 <%= (e.getFirstName() == null ? "" : Utils.addEntities(e.getFirstName())) %>
             </td>
-            <td headers="t6" class="<%= row %>RowOddCol">
+            <td headers="t6">
                 <%= (e.getLanguage() == null ? "" : Utils.addEntities(e.getLanguage())) %>
             </td>
         </tr>
@@ -311,28 +312,21 @@ function clearEPeople()
 <br/>
 
 <%-- Controls for jumping around list--%>
-	<table width="99%">
+<div class="span12" style="text-align:center">
-		<tr>
+	<ul class="pagination">
-			<%--
+			<li><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.eperson-list.jump.first"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0">First</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.eperson-list.jump.five-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>">&lt; 5 Pages</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.eperson-list.jump.one-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>">&lt; 1 Page</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.eperson-list.jump.one-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>">1 Page &gt;</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.eperson-list.jump.five-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>">5 Pages &gt;</a></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.eperson-list.jump.last"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>">Last</a></strong></small></td> 
+	</ul>
-			--%>
+</div>
-			
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.eperson-list.jump.first"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.eperson-list.jump.five-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.eperson-list.jump.one-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.eperson-list.jump.one-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.eperson-list.jump.five-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.eperson-list.jump.last"/></a></strong></small></td>
-		</tr>
-	</table>
 
 	<%-- <p align="center"><input type="button" value="Close" onClick="window.close();"/></p> --%>
-	<p align="center"><input type="button" value="<fmt:message key="jsp.tools.eperson-list.close.button"/>" onclick="window.close();"/></p>
+	<p align="center">
+		<input type="button" class="btn btn-danger" value="<fmt:message key="jsp.tools.eperson-list.close.button"/>" onclick="window.close();"/>
+			</p>
 
 	</form>
 

dspace-jspui/src/main/webapp/tools/group-select-list.jsp

@@ -75,7 +75,11 @@
         <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
         <link rel="stylesheet" href="<%= request.getContextPath() %>/styles.css" type="text/css"/>
         <link rel="shortcut icon" href="<%= request.getContextPath() %>/favicon.ico" type="image/x-icon"/>
-
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/bootstrap.min.css" type="text/css" />
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/bootstrap-theme.min.css" type="text/css" />
+        <link rel="stylesheet" href="<%= request.getContextPath() %>/static/css/bootstrap/dspace-theme.css" type="text/css" />
+        <script type='text/javascript' src='<%= request.getContextPath() %>/static/js/bootstrap/bootstrap.min.js'></script>
+		
 <script type="text/javascript">
 <!-- Begin
 
@@ -116,35 +120,27 @@ function clearGroups()
 <%  } %>
     
 <%-- Controls for jumping around list--%>
-	<table width="99%">
+<div class="span12" style="text-align:center">
-		<tr>
+	<ul class="pagination">			
-			<%-- <td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0">First</A></strong></small></td>
+			<li><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.group-select-list.jump.first"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>">&lt; 5 Pages</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.group-select-list.jump.five-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>">&lt; 1 Page</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.group-select-list.jump.one-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>">1 Page &gt;</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.group-select-list.jump.one-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>">5 Pages &gt;</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.group-select-list.jump.five-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>">Last</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.group-select-list.jump.last"/></a></li>
-			--%>
+	</ul>
-		
+</div>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.group-select-list.jump.first"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.group-select-list.jump.five-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.group-select-list.jump.one-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.group-select-list.jump.one-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.group-select-list.jump.five-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.group-select-list.jump.last"/></a></strong></small></td>
-		</tr>
-	</table>
 <br/>
 
 	<form method="get" action=""> <%-- Will never actually be posted, it's just so buttons will appear --%>
 
-    <table class="miscTable" align="center" summary="Group list">
+    <table class="table table-striped" align="center" summary="Group list">
         <tr>
             <th id="t1" class="oddRowOddCol">&nbsp;</th>
 			<th id="t2" class="oddRowEvenCol"><%
                 if (sortBy == Group.ID)
                 {
-                    %><strong><fmt:message key="jsp.tools.group-select-list.th.id.sortedby" /></strong><%
+                    %><fmt:message key="jsp.tools.group-select-list.th.id"/><span class="glyphicon glyphicon-arrow-down"><%
                 }
                 else
                 {
@@ -154,7 +150,7 @@ function clearGroups()
             <th id="t3" class="oddRowOddCol"><%
                 if (sortBy == Group.NAME)
                 {
-                    %><strong><fmt:message key="jsp.tools.group-select-list.th.name.sortedby" /></strong><%
+                    %><fmt:message key="jsp.tools.group-select-list.th.name" /><span class="glyphicon glyphicon-arrow-down"><%
                 }
                 else
                 {
@@ -180,12 +176,12 @@ function clearGroups()
         String fullname = g.getName().replace('\'', ' ');
 %>
         <tr>
-			<td headers="t1" class="<%= row %>RowOddCol">
+			<td headers="t1" class="">
-				<input type="button" value="<%
+				<input type="button" class="btn btn-success" value="<%
 	if (multiple) { %><fmt:message key="jsp.tools.general.add"/><% }
 	else {          %><fmt:message key="jsp.tools.general.select"/><% } %>" onclick="javascript:<%= clearList %>addGroup('<%= g.getID() %>', '<%= Utils.addEntities(fullname) %>');<%= closeWindow %>"/></td>
-			<td headers="t2" class="<%= row %>RowEvenCol"><%= g.getID() %></td>
+			<td headers="t2" class=""><%= g.getID() %></td>
-			<td headers="t3" class="<%= row %>RowOddCol"> <%= g.getName()%></td>
+			<td headers="t3" class=""> <%= g.getName()%></td>
         </tr>
 <%
         row = (row.equals("odd") ? "even" : "odd");
@@ -196,27 +192,19 @@ function clearGroups()
 <br/>
 
 <%-- Controls for jumping around list--%>
-	<table width="99%">
+<div class="span12" style="text-align:center">
-		<tr>
+	<ul class="pagination">	
-			<%-- <td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0">First</A></strong></small></td>
+			<li><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.group-select-list.jump.first"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>">&lt; 5 Pages</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.group-select-list.jump.five-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>">&lt; 1 Page</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.group-select-list.jump.one-back"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>">1 Page &gt;</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.group-select-list.jump.one-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>">5 Pages &gt;</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.group-select-list.jump.five-forward"/></a></li>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>">Last</A></strong></small></td>
+			<li><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.group-select-list.jump.last"/></a></li>
-			--%>
+	</ul>
-		
+</div>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %>0"><fmt:message key="jsp.tools.group-select-list.jump.first"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveBack %>"><fmt:message key="jsp.tools.group-select-list.jump.five-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneBack %>"><fmt:message key="jsp.tools.group-select-list.jump.one-back"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpOneForward %>"><fmt:message key="jsp.tools.group-select-list.jump.one-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpFiveForward %>"><fmt:message key="jsp.tools.group-select-list.jump.five-forward"/></a></strong></small></td>
-			<td width="17%" align="center"><small><strong><a href="<%= jumpLink %><%= jumpEnd %>"><fmt:message key="jsp.tools.group-select-list.jump.last"/></a></strong></small></td>
-		</tr>
-	</table>
 
 	<%-- <p align="center"><input type="button" value="Close" onClick="window.close();"></p> --%>
-	<p align="center"><input type="button" value="<fmt:message key="jsp.tools.group-select-list.close.button"/>" onclick="window.close();"/></p>
+	<p align="center"><input type="button" class="btn btn-danger" value="<fmt:message key="jsp.tools.group-select-list.close.button"/>" onclick="window.close();"/></p>
 
 	</form>
 	

dspace-lni/dspace-lni-client/pom.xml

@@ -11,7 +11,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-parent</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>../..</relativePath>
    </parent>
    

dspace-lni/pom.xml

@@ -11,7 +11,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-parent</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace-oai/pom.xml

@@ -8,7 +8,7 @@
     <parent>
         <artifactId>dspace-parent</artifactId>
         <groupId>org.dspace</groupId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-oai/src/main/java/org/dspace/xoai/DSpaceOAIDataProvider.java

@@ -158,6 +158,11 @@ public class DSpaceOAIDataProvider extends HttpServlet
                     "Requested OAI context \""
                     + request.getPathInfo().replace("/", "")
                     + "\" does not exist");
+        } finally {
+            if(context != null && context.isValid())
+            {
+                context.abort();
+            }
         }
 
     }

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

@@ -7,13 +7,14 @@
  */
 package org.dspace.xoai.util;
 
+import org.apache.log4j.LogManager;
+import org.apache.log4j.Logger;
+
 import java.text.ParseException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
 import java.util.Locale;
-
+import java.util.TimeZone;
-import org.apache.log4j.LogManager;
-import org.apache.log4j.Logger;
 
 /**
  * 
@@ -33,8 +34,8 @@ public class DateUtils
         // 2008-01-01T00:00:00Z
     	SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.'000Z'");
     	if (!init) sdf = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.'999Z'");
+        sdf.setTimeZone(TimeZone.getTimeZone("UTC"));
         String ret = sdf.format(date);
-        System.out.println(ret);
         return ret;
     }
 

dspace-oai/src/main/webapp/static/style.xsl

@@ -728,14 +728,20 @@
 									</td>
 									<td class="clear"></td>
 								</tr>
-								<tr class="info">
+                                                                <tr class="info">
-									<td class="name">Description</td>
+                                                                        <td class="name">Repository identifier</td>
-									<td class="value">
+                                                                        <td class="value">
-										<xsl:value-of
+                                                                                <xsl:value-of select="oai:OAI-PMH/oai:Identify/oai:description//*[local-name() = 'repositoryIdentifier']/text()" />
-											select="oai:OAI-PMH/oai:Identify/oai:description/node()/text()" />
+                                                                        </td>
-									</td>
+                                                                        <td class="clear"></td>
-									<td class="clear"></td>
+                                                                </tr>
-								</tr>
+                                                                <tr class="info">
+                                                                        <td class="name">Sample identifier</td>
+                                                                        <td class="value">
+                                                                                <xsl:value-of select="oai:OAI-PMH/oai:Identify/oai:description//*[local-name() = 'sampleIdentifier']/text()" />
+                                                                        </td>
+                                                                        <td class="clear"></td>
+                                                                </tr>
 								<tr>
 									<td class="separator"></td>
 								</tr>

dspace-rest/pom.xml

@@ -3,14 +3,14 @@
     <groupId>org.dspace</groupId>
     <artifactId>dspace-rest</artifactId>
     <packaging>war</packaging>
-    <version>4.0</version>
+    <version>4.3</version>
     <name>DSpace RESTful web services API</name>
     <url>http://demo.dspace.org</url>
 
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-rest/src/main/java/org/dspace/rest/BitstreamResource.java

@@ -36,7 +36,6 @@ import java.sql.SQLException;
 @Path("/bitstreams")
 public class BitstreamResource {
     Logger log = Logger.getLogger(BitstreamResource.class);
-    private static org.dspace.core.Context context;
     
     private static final boolean writeStatistics;
 	
@@ -50,12 +49,9 @@ public class BitstreamResource {
     @Path("/{bitstream_id}")
     @Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
     public Bitstream getBitstream(@PathParam("bitstream_id") Integer bitstream_id, @QueryParam("expand") String expand) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid()) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Bitstream bitstream = org.dspace.content.Bitstream.find(context, bitstream_id);
 
@@ -67,6 +63,14 @@ public class BitstreamResource {
         } catch(SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
 
@@ -75,17 +79,14 @@ public class BitstreamResource {
     public javax.ws.rs.core.Response getFile(@PathParam("bitstream_id") final Integer bitstream_id,
     		@QueryParam("userIP") String user_ip, @QueryParam("userAgent") String user_agent, @QueryParam("xforwarderfor") String xforwarderfor,
     		@Context HttpHeaders headers, @Context HttpServletRequest request) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Bitstream bitstream = org.dspace.content.Bitstream.find(context, bitstream_id);
             if(AuthorizeManager.authorizeActionBoolean(context, bitstream, org.dspace.core.Constants.READ)) {
             	if(writeStatistics){
-    				writeStats(bitstream_id, user_ip, user_agent, xforwarderfor, headers, request);
+    				writeStats(context, bitstream_id, user_ip, user_agent, xforwarderfor, headers, request);
     			}
             	
                 return Response.ok(bitstream.retrieve()).type(bitstream.getFormat().getMIMEType()).build();
@@ -102,10 +103,18 @@ public class BitstreamResource {
         } catch (AuthorizeException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.UNAUTHORIZED);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
     
-	private void writeStats(Integer bitstream_id, String user_ip, String user_agent,
+	private void writeStats(org.dspace.core.Context context, Integer bitstream_id, String user_ip, String user_agent,
 			String xforwarderfor, HttpHeaders headers,
 			HttpServletRequest request) {
 		

dspace-rest/src/main/java/org/dspace/rest/CollectionsResource.java

@@ -37,11 +37,8 @@ http://localhost:8080/<webapp>/collections
 @Path("/collections")
 public class CollectionsResource {
     private static Logger log = Logger.getLogger(CollectionsResource.class);
-    
 
     @javax.ws.rs.core.Context ServletContext servletContext;
-
-    private static org.dspace.core.Context context;
     
     private static final boolean writeStatistics;
 	
@@ -49,46 +46,13 @@ public class CollectionsResource {
 		writeStatistics=ConfigurationManager.getBooleanProperty("rest","stats",false);
 	}
 
-    /*
-    The "GET" annotation indicates this method will respond to HTTP Get requests.
-    The "Produces" annotation indicates the MIME response the method will return.
-     */
-    @GET
-    @Path("/")
-    @Produces(MediaType.TEXT_HTML)
-    public String listHTML() {
-        StringBuilder everything = new StringBuilder();
-        try {
-            if(context == null || !context.isValid() ) {
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
-
-            org.dspace.content.Collection[] collections = org.dspace.content.Collection.findAll(context);
-            for(org.dspace.content.Collection collection : collections) {
-                //TODO check auth...
-                everything.append("<li><a href='" + servletContext.getContextPath() + "/collections/" + collection.getID() + "'>" + collection.getID() + " - " + collection.getName() + "</a></li>\n");
-            }
-
-            return "<html><title>Hello!</title><body>Collections<br/><ul>" + everything.toString() + "</ul>.</body></html> ";
-
-        } catch (SQLException e) {
-            log.error(e.getMessage());
-            throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
-        }
-    }
-
     @GET
     @Path("/")
     @Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
     public org.dspace.rest.common.Collection[] list(@QueryParam("expand") String expand, @QueryParam("limit") @DefaultValue("100") Integer limit, @QueryParam("offset") @DefaultValue("0") Integer offset) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Collection[] collections;
 
@@ -112,6 +76,14 @@ public class CollectionsResource {
         } catch (SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
 
@@ -122,17 +94,14 @@ public class CollectionsResource {
     		@QueryParam("limit") @DefaultValue("100") Integer limit, @QueryParam("offset") @DefaultValue("0") Integer offset,
     		@QueryParam("userIP") String user_ip, @QueryParam("userAgent") String user_agent, @QueryParam("xforwarderfor") String xforwarderfor,
     		@Context HttpHeaders headers, @Context HttpServletRequest request) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Collection collection = org.dspace.content.Collection.find(context, collection_id);
             if(AuthorizeManager.authorizeActionBoolean(context, collection, org.dspace.core.Constants.READ)) {
             	if(writeStatistics){
-    				writeStats(collection_id, user_ip, user_agent, xforwarderfor, headers, request);
+    				writeStats(context, collection_id, user_ip, user_agent, xforwarderfor, headers, request);
     			}
                 return new org.dspace.rest.common.Collection(collection, expand, context, limit, offset);
             } else {
@@ -141,10 +110,18 @@ public class CollectionsResource {
         } catch (SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
     
-    private void writeStats(Integer collection_id, String user_ip, String user_agent,
+    private void writeStats(org.dspace.core.Context context, Integer collection_id, String user_ip, String user_agent,
 			String xforwarderfor, HttpHeaders headers,
 			HttpServletRequest request) {
 		

dspace-rest/src/main/java/org/dspace/rest/CommunitiesResource.java

@@ -36,52 +36,19 @@ http://localhost:8080/<webapp>/communities
 public class CommunitiesResource {
     private static Logger log = Logger.getLogger(CommunitiesResource.class);
 
-    private static org.dspace.core.Context context;
-
     private static final boolean writeStatistics;
 	
 	static{
 		writeStatistics=ConfigurationManager.getBooleanProperty("rest","stats",false);
 	}
-    
-    /*
-    The "GET" annotation indicates this method will respond to HTTP Get requests.
-    The "Produces" annotation indicates the MIME response the method will return.
-     */
-    @GET
-    @Produces(MediaType.TEXT_HTML)
-    public String list() {
-        StringBuilder everything = new StringBuilder();
-        try {
-            if(context == null || !context.isValid() ) {
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
-            org.dspace.content.Community[] communities = org.dspace.content.Community.findAllTop(context);
-            for(org.dspace.content.Community community : communities) {
-                everything.append(community.getName() + "<br/>\n");
-            }
-            return "<html><title>Hello!</title><body>Communities:<br/>" + everything.toString() + ".</body></html> ";
-
-        } catch (SQLException e) {
-            log.error(e.getMessage());
-            throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
-        }
-    }
-
-    //TODO Respond to html for communities/:id
 
     @GET
     @Path("/")
     @Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
     public org.dspace.rest.common.Community[] list(@QueryParam("expand") String expand) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Community[] topCommunities = org.dspace.content.Community.findAllTop(context);
             ArrayList<org.dspace.rest.common.Community> communityArrayList = new ArrayList<org.dspace.rest.common.Community>();
@@ -98,7 +65,15 @@ public class CommunitiesResource {
         } catch (SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
-        } //finally?
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
+        }
     }
 
     @GET
@@ -107,17 +82,14 @@ public class CommunitiesResource {
     public org.dspace.rest.common.Community getCommunity(@PathParam("community_id") Integer community_id, @QueryParam("expand") String expand,
     		@QueryParam("userIP") String user_ip, @QueryParam("userAgent") String user_agent, @QueryParam("xforwarderfor") String xforwarderfor,
     		@Context HttpHeaders headers, @Context HttpServletRequest request) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Community community = org.dspace.content.Community.find(context, community_id);
             if(AuthorizeManager.authorizeActionBoolean(context, community, org.dspace.core.Constants.READ)) {
             	if(writeStatistics){
-    				writeStats(community_id, user_ip, user_agent, xforwarderfor, headers, request);
+    				writeStats(context, community_id, user_ip, user_agent, xforwarderfor, headers, request);
     			}
                 return new org.dspace.rest.common.Community(community, expand, context);
             } else {
@@ -126,10 +98,18 @@ public class CommunitiesResource {
         } catch (SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
-        } //finally?
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
+        }
     }
     
-    private void writeStats(Integer community_id, String user_ip, String user_agent,
+    private void writeStats(org.dspace.core.Context context, Integer community_id, String user_ip, String user_agent,
  			String xforwarderfor, HttpHeaders headers,
  			HttpServletRequest request) {
  		

dspace-rest/src/main/java/org/dspace/rest/HandleResource.java

@@ -32,18 +32,14 @@ import java.sql.SQLException;
 @Path("/handle")
 public class HandleResource {
     private static Logger log = Logger.getLogger(HandleResource.class);
-    private static org.dspace.core.Context context;
 
     @GET
     @Path("/{prefix}/{suffix}")
     @Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
     public org.dspace.rest.common.DSpaceObject getObject(@PathParam("prefix") String prefix, @PathParam("suffix") String suffix, @QueryParam("expand") String expand) {
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid() ) {
+            context = new org.dspace.core.Context();
-                context = new Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.DSpaceObject dso = HandleManager.resolveToObject(context, prefix + "/" + suffix);
             if(dso == null) {
@@ -68,6 +64,14 @@ public class HandleResource {
         } catch (SQLException e) {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
 }

dspace-rest/src/main/java/org/dspace/rest/ItemsResource.java

@@ -44,28 +44,22 @@ public class ItemsResource {
     private static final Logger log = Logger.getLogger(ItemsResource.class);
     //ItemList - Not Implemented
 
-    private static org.dspace.core.Context context;
-
     @GET
     @Path("/{item_id}")
     @Produces({MediaType.APPLICATION_JSON, MediaType.APPLICATION_XML})
     public org.dspace.rest.common.Item getItem(@PathParam("item_id") Integer item_id, @QueryParam("expand") String expand,
     		@QueryParam("userIP") String user_ip, @QueryParam("userAgent") String user_agent, @QueryParam("xforwarderfor") String xforwarderfor,
     		@Context HttpHeaders headers, @Context HttpServletRequest request) throws WebApplicationException {
-    	
+
-    	
+        org.dspace.core.Context context = null;
         try {
-            if(context == null || !context.isValid()) {
+            context = new org.dspace.core.Context();
-                context = new org.dspace.core.Context();
-                //Failed SQL is ignored as a failed SQL statement, prevent: current transaction is aborted, commands ignored until end of transaction block
-                context.getDBConnection().setAutoCommit(true);
-            }
 
             org.dspace.content.Item item = org.dspace.content.Item.find(context, item_id);
 
             if(AuthorizeManager.authorizeActionBoolean(context, item, org.dspace.core.Constants.READ)) {
             	if(writeStatistics){
-    				writeStats(item_id, user_ip, user_agent, xforwarderfor, headers, request);
+    				writeStats(context, item_id, user_ip, user_agent, xforwarderfor, headers, request);
     			}
                 return new org.dspace.rest.common.Item(item, expand, context);
             } else {
@@ -75,11 +69,19 @@ public class ItemsResource {
         } catch (SQLException e)  {
             log.error(e.getMessage());
             throw new WebApplicationException(Response.Status.INTERNAL_SERVER_ERROR);
+        } finally {
+            if(context != null) {
+                try {
+                    context.complete();
+                } catch (SQLException e) {
+                    log.error(e.getMessage() + " occurred while trying to close");
+                }
+            }
         }
     }
     
     
-    private void writeStats(Integer item_id, String user_ip, String user_agent,
+    private void writeStats(org.dspace.core.Context context, Integer item_id, String user_ip, String user_agent,
 			String xforwarderfor, HttpHeaders headers,
 			HttpServletRequest request) {
 		

dspace-services/pom.xml

@@ -9,7 +9,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
     </parent>
 
     <properties>

dspace-solr/pom.xml

@@ -20,7 +20,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -126,6 +126,11 @@
             <artifactId>solr-solrj</artifactId>
             <version>${solr.version}</version>
         </dependency>
+        <dependency>
+            <groupId>org.apache.solr</groupId>
+            <artifactId>solr-cell</artifactId>
+            <version>${solr.version}</version>
+        </dependency>
         <dependency>
             <groupId>org.apache.lucene</groupId>
             <artifactId>lucene-core</artifactId>

dspace-sword/pom.xml

@@ -15,7 +15,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-parent</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace-swordv2/pom.xml

@@ -13,7 +13,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-xmlui/pom.xml

@@ -11,7 +11,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>dspace-parent</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace-xmlui/src/main/java/org/dspace/app/xmlui/aspect/artifactbrowser/ConfigurableBrowse.java

@@ -707,7 +707,7 @@ public class ConfigurableBrowse extends AbstractDSpaceTransformer implements
                     // This is so that we can then highlight the correct option in the navigation
                     SortOption bso = bi.getSortOption();
                     SortOption so = SortOption.getSortOption(sortBy);
-                    if ( bso != null && bso.equals(so))
+                    if ( bso != null && !bso.equals(so))
                     {
                         BrowseIndex newBi = BrowseIndex.getBrowseIndex(so);
                         if (newBi != null)

dspace-xmlui/src/main/java/org/dspace/app/xmlui/cocoon/ConcatenationReader.java

@@ -12,6 +12,7 @@ import com.yahoo.platform.yui.compressor.JavaScriptCompressor;
 import org.apache.avalon.framework.parameters.ParameterException;
 import org.apache.avalon.framework.parameters.Parameters;
 import org.apache.cocoon.ProcessingException;
+import org.apache.cocoon.ResourceNotFoundException;
 import org.apache.cocoon.environment.*;
 import org.apache.cocoon.reading.ResourceReader;
 import org.apache.excalibur.source.Source;
@@ -69,10 +70,19 @@ public class ConcatenationReader extends ResourceReader {
 
         // setup list of sources, get relevant parts of path
         this.inputSources = new ArrayList<Source>();
-        String path = src.substring(0, src.lastIndexOf('/'));
+        
+        // Check for an empty path
+        String path = "";
+        if(src.contains("/"))
+        {
+            path = src.substring(0, src.lastIndexOf('/'));
+        }
         String file = src.substring(src.lastIndexOf('/')+1);
 
-        // now build own list of inputsources
+        // Now build own list of inputsources
+        // Several files may be passed in at once, e.g.
+        // "themes/Mirage/lib/css/reset,base,helper,style,print.css"
+        // So, we need to build the fullPath to *each* file individually
         String[] files = file.split(",");
         for (String f : files) {
             if (file.endsWith(".json") && !f.endsWith(".json")) {
@@ -85,8 +95,21 @@ public class ConcatenationReader extends ResourceReader {
                 f += ".css";
             }
 
-            String fullPath = path + "/" + f;
+            // Build full path to this individual file
-            this.inputSources.add(resolver.resolveURI(fullPath));
+            String fullPath;
+            if(!path.isEmpty())
+                fullPath = path + "/" + f;
+            else
+                fullPath = f;
+
+            // Add to list of inputsources if this file exists
+            Source inSource = resolver.resolveURI(fullPath);
+            if(inSource.exists())
+            {
+                this.inputSources.add(inSource);
+            }
+            else // else throw a ResourceNotFound (which triggers a 404)
+                throw new ResourceNotFoundException("Resource not found (" + fullPath + ")");
         }
 
         // do super stuff

dspace-xmlui/src/main/java/org/dspace/app/xmlui/cocoon/SafeResourceReader.java

@@ -0,0 +1,68 @@
+package org.dspace.app.xmlui.cocoon;
+
+import java.io.IOException;
+import java.util.Map;
+
+import org.apache.avalon.framework.configuration.Configurable;
+import org.apache.avalon.framework.parameters.Parameters;
+import org.apache.cocoon.ResourceNotFoundException;
+import org.apache.cocoon.reading.ResourceReader;
+
+import org.apache.cocoon.ProcessingException;
+import org.apache.cocoon.caching.CacheableProcessingComponent;
+import org.apache.cocoon.environment.SourceResolver;
+import org.apache.excalibur.source.Source;
+
+import org.xml.sax.SAXException;
+
+/**
+ * The SafeResourceReader blocks access to specific paths which we do NOT want
+ * to be readable on the web. By default, the Cocoon ResourceReader just loads
+ * whatever local file you request, which is not very secure and exposes XMLUI 
+ * to possible directory traversal vulnerabilities (when encoded dots or slashes
+ * are passed on the URL).
+ */
+public class SafeResourceReader extends ResourceReader
+        implements CacheableProcessingComponent, Configurable {
+
+    /**
+     * Setup the reader.
+     * The resource is opened to get an <code>InputStream</code>,
+     * the length and the last modification date
+     */
+    @Override
+    public void setup(SourceResolver resolver, Map objectModel, String src, Parameters par)
+            throws ProcessingException, SAXException, IOException {
+
+        // If the requested path includes any of the following strings/characters
+        // then block access and return "Resource Not Found"
+        if(src != null && (
+            // %252e = double encoded dot (.)
+            src.toLowerCase().contains("%252e") ||
+            // %2e = encoded dot (.)
+            src.toLowerCase().contains("%2e") ||
+            // %2f = encoded slash (/)
+            src.toLowerCase().contains("%2f") ||
+            // block public access to all Cocoon Sitemaps (*.xmap)
+            src.toLowerCase().contains(".xmap") ||
+            // block public access to all Theme XSLs
+            src.toLowerCase().contains(".xsl")
+        ))
+        {
+            // Block access by throwing a ResourceNotFound (triggers a 404)
+            throw new ResourceNotFoundException("Resource not found (" + src + ")");
+        }
+
+        // See if this resource actually exists by attempting to resolve it
+        // If not, throw a ResourceNotFound (triggers a 404)
+        Source resource = resolver.resolveURI(src);
+        if(!resource.exists())
+        {
+            throw new ResourceNotFoundException("Resource not found (" + src + ")");
+        }    
+        
+        // Otherwise, simply load the requested resource via ResourceReader
+        super.setup(resolver, objectModel, src, par);
+    }
+
+}

dspace-xmlui/src/main/webapp/i18n/messages.xml

@@ -2120,6 +2120,7 @@
 	<message key="xmlui.dri2xhtml.METS-1.0.item-files-view">View</message>
 	<message key="xmlui.dri2xhtml.METS-1.0.item-files-description">Description</message>
 	<message key="xmlui.dri2xhtml.METS-1.0.item-files-viewOpen">View/<wbr/>Open</message>
+	<message key="xmlui.dri2xhtml.METS-1.0.item-files-access-rights">Read access available for</message>
 	<message key="xmlui.dri2xhtml.METS-1.0.item-no-files">There are no files associated with this item.</message>
 
 	<message key="xmlui.dri2xhtml.METS-1.0.size-bytes">bytes</message>

dspace-xmlui/src/main/webapp/sitemap.xmap

@@ -184,7 +184,7 @@
                         <map:selector name="AuthenticatedSelector" src="org.dspace.app.xmlui.aspect.general.AuthenticatedSelector"/>
                 </map:selectors>
                 <map:readers default="resource">
-                    <map:reader name="resource" src="org.apache.cocoon.reading.ResourceReader"
+                    <map:reader name="resource" src="org.dspace.app.xmlui.cocoon.SafeResourceReader"
                             logger="sitemap.reader.resource" pool-max="32">
                             <expires>3600000</expires> <!-- 1000 * 60 * 60 = 3600000 = One hour -->
                     </map:reader>

dspace-xmlui/src/main/webapp/static/js/bitstream-ordering.js

@@ -65,8 +65,8 @@
         }
         orderElement.val(newOrder);
 
-        var upArrow = row.find('input[name$^="submit_order_"][name$="_up"]');
+        var upArrow = row.find('input[name^="submit_order_"][name$="_up"]');
-        var downArrow = row.find('input[name$^="submit_order_"][name$="_down"]');
+        var downArrow = row.find('input[name^="submit_order_"][name$="_down"]');
 
         //Check if we are the first row, if so hide the up arrow
         if(isBundleRow(row.prev())){
@@ -93,7 +93,11 @@
      */
     function isBundleRow(row){
         // Checks if the identifier starts with the bundle head identifier
-        return row.attr("id").indexOf("aspect_administrative_item_EditItemBitstreamsForm_row_bundle_head_") == 0;
+
+        //DS-2027, found error condition in which attribute is not set when reordering original bitstreams
+    	var id = row.attr("id");
+    	if (id === undefined) return false;
+        return id.indexOf("aspect_administrative_item_EditItemBitstreamsForm_row_bundle_head_") == 0;
     }
 
 

dspace-xmlui/src/main/webapp/themes/Mirage/lib/xsl/aspect/artifactbrowser/item-view.xsl

@@ -539,11 +539,15 @@
                   </xsl:otherwise>
               </xsl:choose>
         </xsl:variable>
+        <xsl:variable name="alt-text"><i18n:text>xmlui.dri2xhtml.METS-1.0.item-files-access-rights</i18n:text> <xsl:value-of select="$users"/></xsl:variable>
 
         <xsl:choose>
             <xsl:when test="(not ($rights_context/@CONTEXTCLASS = 'GENERAL PUBLIC') and ($rights_context/rights:Permissions/@DISPLAY = 'true')) or not ($rights_context)">
                 <a href="{mets:FLocat[@LOCTYPE='URL']/@xlink:href}">
-                    <img width="64" height="64" src="{concat($theme-path,'/images/Crystal_Clear_action_lock3_64px.png')}" title="Read access available for {$users}"/>
+                    <img width="64" height="64" src="{concat($theme-path,'/images/Crystal_Clear_action_lock3_64px.png')}">
+                        <xsl:attribute name="title"><xsl:value-of select="$alt-text"/></xsl:attribute>
+                        <xsl:attribute name="alt"><xsl:value-of select="$alt-text"/></xsl:attribute>
+                    </img>
                     <!-- icon source: http://commons.wikimedia.org/wiki/File:Crystal_Clear_action_lock3.png -->
                 </a>
             </xsl:when>

dspace-xmlui/src/main/webapp/themes/dri2xhtml/General-Handler.xsl

@@ -222,11 +222,15 @@
                 <xsl:if test="position() != last()">, </xsl:if>
             </xsl:for-each>
         </xsl:variable>
+        <xsl:variable name="alt-text"><i18n:text>xmlui.dri2xhtml.METS-1.0.item-files-access-rights</i18n:text> <xsl:value-of select="$users"/></xsl:variable>
 
         <xsl:choose>
             <xsl:when test="not ($rights_context/@CONTEXTCLASS = 'GENERAL PUBLIC') and ($rights_context/rights:Permissions/@DISPLAY = 'true')">
                 <a href="{mets:FLocat[@LOCTYPE='URL']/@xlink:href}">
-                    <img width="64" height="64" src="{concat($theme-path,'/images/Crystal_Clear_action_lock3_64px.png')}" title="Read access available for {$users}"/>
+                    <img width="64" height="64" src="{concat($theme-path,'/images/Crystal_Clear_action_lock3_64px.png')}">
+                        <xsl:attribute name="title"><xsl:value-of select="$alt-text"/></xsl:attribute>
+                        <xsl:attribute name="alt"><xsl:value-of select="$alt-text"/></xsl:attribute>
+                    </img>
                     <!-- icon source: http://commons.wikimedia.org/wiki/File:Crystal_Clear_action_lock3.png -->
                 </a>
             </xsl:when>

dspace-xmlui/src/main/webapp/themes/mobile/mobile.xsl

@@ -133,12 +133,6 @@
         <xsl:attribute name="src">
         <xsl:value-of select="$mobile-url"/>
         <xsl:text>/themes/mobile/lib/cookies.js</xsl:text>
-        </xsl:attribute>&#160;</script>
-
-        <script>
-        <xsl:attribute name="src">
-        <xsl:value-of select="$mobile-url"/>
-        <xsl:text>/themes/mobile/lib/m-tweaks.js</xsl:text>
         </xsl:attribute>&#160;</script>
 
             <!-- Add the title in -->
@@ -694,7 +688,7 @@
                            </xsl:attribute>
                             <img alt="Thumbnail">
                                 <xsl:attribute name="src">
-                                <xsl:variable name="request-uri" select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='contextPath'])"/>
+                                <xsl:variable name="request-uri" select="/dri:document/dri:meta/dri:pageMeta/dri:metadata[@element='contextPath']"/>
                                 <xsl:text>/themes/mobile/lib/images/default-thumbnail.png</xsl:text>
                                 </xsl:attribute>
                             </img>

dspace/bin/dspace

@@ -61,6 +61,12 @@ else
 fi
 
 
+# If the user only wants the CLASSPATH, just give it now.
+if [ "$1" = "classpath" ]; then
+  echo $FULLPATH
+  exit 0
+fi
+
 
 
 #Allow user to specify java options through JAVA_OPTS variable

dspace/config/crosswalks/oai/description.xml

@@ -1 +1,6 @@
-<XOAIDescription xmlns="http://www.lyncode.com/XOAIConfiguration">XOAI: OAI-PMH Java Toolkit</XOAIDescription>
+<oai-identifier xmlns="http://www.openarchives.org/OAI/2.0/oai-identifier" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/oai-identifier http://www.openarchives.org/OAI/2.0/oai-identifier.xsd">
+<scheme>oai</scheme>
+<repositoryIdentifier>${dspace.hostname}</repositoryIdentifier>
+<delimiter>:</delimiter>
+<sampleIdentifier>oai:${dspace.hostname}:${handle.prefix}/1234</sampleIdentifier>
+</oai-identifier>

dspace/config/crosswalks/oai/metadataFormats/dim.xsl

@@ -9,78 +9,89 @@
 	
 -->
 <xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
-	xmlns:doc="http://www.lyncode.com/xoai" version="1.0">
+                xmlns:doc="http://www.lyncode.com/xoai"
-	<xsl:output omit-xml-declaration="yes" method="xml" indent="yes" />
+                xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" version="1.0">
+    <xsl:output omit-xml-declaration="yes" method="xml" indent="yes"/>
+
+    <!-- An identity transformation to show the internal XOAI generated XML -->
+    <xsl:template match="/">
+        <dim:dim xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                 xsi:schemaLocation="http://www.dspace.org/xmlns/dspace/dim http://www.dspace.org/schema/dim.xsd">
+            <xsl:apply-templates select="//doc:field[@name='value']"/>
+        </dim:dim>
+    </xsl:template>
+
+    <xsl:template match="/doc:metadata/doc:element[@name='dc']/doc:element/doc:element/doc:field[@name='value']">
+        <xsl:call-template name="dimfield">
+            <xsl:with-param name="mdschema" select="../../../@name"/>
+            <xsl:with-param name="element" select="../../@name"/>
+            <xsl:with-param name="qualifier"/>
+            <xsl:with-param name="language" select="../@name"/>
+            <xsl:with-param name="authority" select="../doc:field[@name='authority']"/>
+            <xsl:with-param name="confidence" select="../doc:field[@name='confidence']"/>
+            <xsl:with-param name="value" select="text()"/>
+        </xsl:call-template>
+    </xsl:template>
+
+    <xsl:template match="/doc:metadata/doc:element[@name='dc']/doc:element/doc:element/doc:element/doc:field[@name='value']">
+        <xsl:call-template name="dimfield">
+            <xsl:with-param name="mdschema" select="../../../../@name"/>
+            <xsl:with-param name="element" select="../../../@name"/>
+            <xsl:with-param name="qualifier" select="../../@name"/>
+            <xsl:with-param name="language" select="../@name" />
+            <xsl:with-param name="authority" select="../doc:field[@name='authority']"/>
+            <xsl:with-param name="confidence" select="../doc:field[@name='confidence']"/>
+            <xsl:with-param name="value" select="text()"/>
+        </xsl:call-template>
+    </xsl:template>
+
+    <xsl:template name="dimfield">
+        <xsl:param name="mdschema"/>
+        <xsl:param name="element"/>
+        <xsl:param name="qualifier"/>
+        <xsl:param name="language"/>
+        <xsl:param name="authority"/>
+        <xsl:param name="confidence"/>
+        <xsl:param name="value"/>
+
+        <dim:field>
+            <xsl:attribute name="mdschema">
+                <xsl:value-of select="$mdschema"/>
+            </xsl:attribute>
+
+            <xsl:attribute name="element">
+                <xsl:value-of select="$element"/>
+            </xsl:attribute>
+
+            <xsl:if test="$qualifier">
+                <xsl:attribute name="qualifier">
+                    <xsl:value-of select="$qualifier"/>
+                </xsl:attribute>
+            </xsl:if>
+
+            <xsl:choose>
+                <xsl:when test="$language='none'"/>
+                <xsl:otherwise>
+                    <xsl:attribute name="lang">
+                        <xsl:value-of select="$language"/>
+                    </xsl:attribute>
+                </xsl:otherwise>
+            </xsl:choose>
+
+            <xsl:if test="$authority">
+                <xsl:attribute name="authority">
+                    <xsl:value-of select="$authority"/>
+                </xsl:attribute>
+            </xsl:if>
+
+            <xsl:if test="$confidence">
+                <xsl:attribute name="confidence">
+                    <xsl:value-of select="$confidence"/>
+                </xsl:attribute>
+            </xsl:if>
+
+            <xsl:value-of select="$value"/>
+        </dim:field>
+    </xsl:template>
 
-	<!-- An identity transformation to show the internal XOAI generated XML -->
-	<xsl:template match="/">
-		<dim:dim xmlns:dim="http://www.dspace.org/xmlns/dspace/dim" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
-			xsi:schemaLocation="http://www.dspace.org/xmlns/dspace/dim http://www.dspace.org/schema/dim.xsd">
-			<xsl:for-each select="doc:metadata/doc:element[@name='dc']/doc:element/doc:element">
-				<xsl:choose>
-					<xsl:when test="doc:element">
-						<dim:field>
-							<xsl:attribute name="mdschema">
-								<xsl:value-of select="../../@name" />
-							</xsl:attribute>
-							<xsl:attribute name="element">
-								<xsl:value-of select="../@name" />
-							</xsl:attribute>
-							<xsl:attribute name="qualifier">
-								<xsl:value-of select="@name" />
-							</xsl:attribute>
-							<xsl:choose>
-								<xsl:when test="doc:element[@name='none']"></xsl:when>
-								<xsl:otherwise>
-									<xsl:attribute name="lang">
-										<xsl:value-of select="doc:element/@name" />
-									</xsl:attribute>
-								</xsl:otherwise>
-							</xsl:choose>
-							<xsl:if test="doc:element/doc:field[@name='authority']">
-								<xsl:attribute name="authority">
-									<xsl:value-of select="doc:element/doc:field[@name='authority']/text()" />
-								</xsl:attribute>
-							</xsl:if>
-							<xsl:if test="doc:element/doc:field[@name='confidence']">
-								<xsl:attribute name="confidence">
-									<xsl:value-of select="doc:element/doc:field[@name='confidence']/text()" />
-								</xsl:attribute>
-							</xsl:if>
-							<xsl:value-of select="doc:element/doc:field[@name='value']/text()"></xsl:value-of>
-						</dim:field>
-					</xsl:when>
-					<xsl:otherwise>
-						<dim:field>
-							<xsl:attribute name="mdschema">
-								<xsl:value-of select="../../@name" />
-							</xsl:attribute>
-							<xsl:attribute name="element">
-								<xsl:value-of select="../@name" />
-							</xsl:attribute>
-							<xsl:choose>
-								<xsl:when test="@name='none'"></xsl:when>
-								<xsl:otherwise>
-									<xsl:attribute name="lang">
-										<xsl:value-of select="@name" />
-									</xsl:attribute>
-								</xsl:otherwise>
-							</xsl:choose>
-							<xsl:if test="doc:field[@name='authority']">
-								<xsl:attribute name="authority">
-									<xsl:value-of select="doc:field[@name='authority']/text()" />
-								</xsl:attribute>
-							</xsl:if>
-							<xsl:if test="doc:field[@name='confidence']">
-								<xsl:attribute name="confidence">
-									<xsl:value-of select="doc:field[@name='confidence']/text()" />
-								</xsl:attribute>
-							</xsl:if>
-							<xsl:value-of select="doc:field[@name='value']/text()"></xsl:value-of>
-						</dim:field>
-					</xsl:otherwise>
-				</xsl:choose>
-			</xsl:for-each>
-		</dim:dim>
-	</xsl:template>
 </xsl:stylesheet>

dspace/config/dspace.cfg

@@ -830,6 +830,10 @@ webui.submit.blocktheses = false
 # Defaults to true; If set to 'false', submitter has option to skip upload
 #webui.submit.upload.required = true
 
+# Whether to enable the AJAX-based upload progress meter.  Defaults to
+# 'true'.
+#webui.submit.upload.ajax = true
+
 # Whether or not to use the 'advanced' form of the access step.
 # Defaults to false, ie the simple form is used.
 #webui.submission.restrictstep.enableAdvancedForm = false

dspace/config/input-forms.xml

@@ -391,12 +391,16 @@ it, please enter the types and the actual numbers or codes below.</hint>
        <displayed-value>Chinese</displayed-value>
        <stored-value>zh</stored-value>
      </pair>
+     <pair>
+       <displayed-value>Turkish</displayed-value>
+       <stored-value>tr</stored-value>
+     </pair>
      <pair>
        <displayed-value>(Other)</displayed-value>
        <stored-value>other</stored-value>
      </pair>
    </value-pairs>
 
-    </form-value-pairs>
+ </form-value-pairs>
 
 </input-forms>

dspace/config/log4j-solr.properties

@@ -1,6 +1,6 @@
 #  Logging level
 solr.log=logs/
-log4j.rootLogger=INFO, file, CONSOLE
+log4j.rootLogger=INFO, file
 
 log4j.appender.CONSOLE=org.apache.log4j.ConsoleAppender
 

dspace/config/modules/authentication-shibboleth.cfg

@@ -137,6 +137,12 @@ lastname-header = SHIB-SURNAME
 # If the eperson metadata field is not found, should it be automatically created?
 eperson.metadata.autocreate = true;
 
+# Shibboleth attributes are by default UTF-8 encoded. Some servlet container
+# automatically converts the attributes from ISO-8859-1 (latin-1) to UTF-8.
+# As the attributes already were UTF-8 encoded it may be necessary to reconvert
+# them. If you detect problems with special characters in shibboleth attributes
+# set this to true (default to false).
+reconvert.attributes = false
 
 ##
 ## Role-based Groups:

dspace/config/spring/api/discovery.xml

@@ -235,6 +235,32 @@
                 <property name="useAsHomePage" value="false"/>
             </bean>
         </property>
+        <property name="hitHighlightingConfiguration">
+            <bean class="org.dspace.discovery.configuration.DiscoveryHitHighlightingConfiguration">
+                <property name="metadataFields">
+                    <list>
+                        <bean class="org.dspace.discovery.configuration.DiscoveryHitHighlightFieldConfiguration">
+                            <property name="field" value="dc.title"/>
+                            <property name="snippets" value="5"/>
+                        </bean>
+                        <bean class="org.dspace.discovery.configuration.DiscoveryHitHighlightFieldConfiguration">
+                            <property name="field" value="dc.contributor.author"/>
+                            <property name="snippets" value="5"/>
+                        </bean>
+                        <bean class="org.dspace.discovery.configuration.DiscoveryHitHighlightFieldConfiguration">
+                            <property name="field" value="dc.description.abstract"/>
+                            <property name="maxSize" value="250"/>
+                            <property name="snippets" value="2"/>
+                        </bean>
+                        <bean class="org.dspace.discovery.configuration.DiscoveryHitHighlightFieldConfiguration">
+                            <property name="field" value="fulltext"/>
+                            <property name="maxSize" value="250"/>
+                            <property name="snippets" value="2"/>
+                        </bean>
+                    </list>
+                </property>
+            </bean>
+        </property>
         <!-- When true a "did you mean" example will be displayed, value can be true or false -->
         <property name="spellCheckEnabled" value="true"/>
     </bean>

dspace/etc/clean-database.sql

@@ -80,6 +80,8 @@ DROP TABLE harvested_item;
 DROP TABLE Group2GroupCache;
 DROP TABLE Group2Group;
 DROP TABLE FileExtension;
+DROP TABLE webapp;
+DROP TABLE requestitem;
 -- Drop main object tables near end as many other tables have dependencies on them
 DROP TABLE versionitem;
 DROP TABLE versionhistory;
@@ -132,6 +134,8 @@ DROP SEQUENCE harvested_collection_seq;
 DROP SEQUENCE harvested_item_seq;
 DROP SEQUENCE versionhistory_seq;
 DROP SEQUENCE versionitem_seq;
+DROP SEQUENCE webapp_seq;
+DROP SEQUENCE requestitem_seq;
 
 -- Drop the getnextid() function
 DROP FUNCTION getnextid;

dspace/etc/oracle/database_schema_3-4.sql

@@ -47,7 +47,7 @@ CREATE TABLE Webapp
 (
     webapp_id INTEGER NOT NULL PRIMARY KEY,
     AppName VARCHAR2(32),
-    URL VARCHAR2,
+    URL VARCHAR2(1000),
     Started TIMESTAMP,
     isUI NUMBER(1)
 );
@@ -62,7 +62,7 @@ CREATE TABLE requestitem
 (
   requestitem_id INTEGER NOT NULL,
   token varchar(48),
-  item_id INDEX,
+  item_id INTEGER,
   bitstream_id INTEGER,
   allfiles NUMBER(1),
   request_email VARCHAR2(64),
@@ -87,4 +87,4 @@ update workflowitem set multiple_titles=1, published_before=1, multiple_files=1;
 -- DS-1811 Removing a collection fails if non-Solr DAO has been used before for item count
 -------------------------------------------------------
 delete from collection_item_count;
-delete from community_item_count;
+delete from community_item_count;

dspace/etc/oracle/xmlworkflow/workflow_migration.sql

@@ -121,7 +121,7 @@ DELETE FROM resourcepolicy
 WHERE resource_type_id = 0 AND resource_id IN
   (SELECT bundle2bitstream.bitstream_id FROM
     ((workflowitem INNER JOIN item2bundle ON workflowitem.item_id = item2bundle.item_id)
-      INNER JOIN bundle2bitstream ON item2bundle.bundle_id = bundle2bitstream.bundle_id);
+      INNER JOIN bundle2bitstream ON item2bundle.bundle_id = bundle2bitstream.bundle_id));
 -- Create policies for claimtasks
 --     public static final int BITSTREAM = 0;
 --     public static final int BUNDLE = 1;
@@ -137,7 +137,7 @@ WHERE resource_type_id = 0 AND resource_id IN
 -- Create a temporarty table with action ID's
 CREATE TABLE temptable(
   action_id INTEGER PRIMARY KEY
-)
+);
 INSERT ALL
   INTO temptable (action_id) VALUES (0)
   INTO temptable (action_id) VALUES (1)
@@ -266,11 +266,11 @@ FROM (((cwf_workflowitem INNER JOIN item ON cwf_workflowitem.item_id = item.item
 );
 
 -- TODO: not tested yet
-INSERT INTO cwf_in_progress_user (in_progress_user_id, workflowitem_id, step_id, user_id, finished)
+INSERT INTO cwf_in_progress_user (in_progress_user_id, workflowitem_id, user_id, finished)
 SELECT
   cwf_in_progress_user_seq.nextval AS in_progress_user_id,
-  cwf_workflowitem.item_id AS workflowitem_id,
+  cwf_workflowitem.workflowitem_id AS workflowitem_id,
-  cwf_claimtask.owner_id AS user_id
+  cwf_claimtask.owner_id AS user_id,
   0 as finished
 FROM
   (cwf_claimtask INNER JOIN cwf_workflowitem ON cwf_workflowitem.workflowitem_id = cwf_claimtask.workflowitem_id);

dspace/etc/oracle/xmlworkflow/xml_workflow.sql

@@ -5,58 +5,55 @@ CREATE SEQUENCE cwf_claimtask_seq;
 CREATE SEQUENCE cwf_in_progress_user_seq;
 CREATE SEQUENCE cwf_pooltask_seq;
 
+
 CREATE TABLE cwf_workflowitem
 (
   workflowitem_id INTEGER PRIMARY KEY,
   item_id        INTEGER REFERENCES item(item_id) UNIQUE,
   collection_id  INTEGER REFERENCES collection(collection_id),
-
+  --
   -- Answers to questions on first page of submit UI
   multiple_titles       NUMBER(1),
   published_before      NUMBER(1),
   multiple_files        NUMBER(1)
   -- Note: stage reached not applicable here - people involved in workflow
   -- can always jump around submission UI
-
 );
 
--- TODO: it seems like this index is already created by the 'unique' constraint in the table creation
+
--- CREATE INDEX xmlwf_wf_item_fk_idx ON xmlwf_workflowitem(item_id);
+CREATE INDEX cwf_workflowitem_coll_fk_idx ON cwf_workflowitem(collection_id);
-CREATE INDEX xmlwf_wf_coll_fk_idx ON xmlwf_workflowitem(collection_id);
 
 
-
+CREATE TABLE cwf_collectionrole (
-CREATE TABLE xmlwf_collectionrole (
 collectionrole_id INTEGER PRIMARY KEY,
 role_id VARCHAR2(256),
 collection_id integer REFERENCES collection(collection_id),
 group_id integer REFERENCES epersongroup(eperson_group_id)
 );
-ALTER TABLE xmlwf_collectionrole ADD CONSTRAINT xmlwf_collectionrole_unique UNIQUE (role_id, collection_id, group_id);
+ALTER TABLE cwf_collectionrole
+ADD CONSTRAINT cwf_collectionrole_unique UNIQUE (role_id, collection_id, group_id);
 
-CREATE INDEX xmlwf_cr_coll_role_fk_idx ON xmlwf_collectionrole(collection_id,role_id);
+CREATE INDEX cwf_cr_coll_role_fk_idx ON cwf_collectionrole(collection_id,role_id);
-CREATE INDEX xmlwf_cr_coll_fk_idx ON xmlwf_collectionrole(collection_id);
+CREATE INDEX cwf_cr_coll_fk_idx ON cwf_collectionrole(collection_id);
 
 
-CREATE TABLE xmlwf_workflowitemrole (
+CREATE TABLE cwf_workflowitemrole (
   workflowitemrole_id INTEGER PRIMARY KEY,
   role_id VARCHAR2(256),
-  workflowitem_id integer REFERENCES xmlwf_workflowitem(workflowitem_id),
+  workflowitem_id integer REFERENCES cwf_workflowitem(workflowitem_id),
   eperson_id integer REFERENCES eperson(eperson_id),
   group_id integer REFERENCES epersongroup(eperson_group_id)
 );
+ALTER TABLE cwf_workflowitemrole
+ADD CONSTRAINT cwf_workflowitemrole_unique UNIQUE (role_id, workflowitem_id, eperson_id, group_id);
 
-ALTER TABLE xmlwf_workflowitemrole
+CREATE INDEX cwf_wfir_item_role_fk_idx ON cwf_workflowitemrole(workflowitem_id,role_id);
-ADD CONSTRAINT xmlwf_workflowitemrole_unique UNIQUE (role_id, workflowitem_id, eperson_id);
+CREATE INDEX cwf_wfir_item_fk_idx ON cwf_workflowitemrole(workflowitem_id);
 
 
-CREATE INDEX xmlwf_wfir_item_role_fk_idx ON xmlwf_workflowitemrole(workflowitem_id,role_id);
+CREATE TABLE cwf_pooltask (
-CREATE INDEX xmlwf_wfir_item_fk_idx ON xmlwf_workflowitemrole(workflowitem_id);
-
-
-CREATE TABLE xmlwf_pooltask (
   pooltask_id   INTEGER PRIMARY KEY,
-  workflowitem_id   INTEGER REFERENCES xmlwf_workflowitem(workflowitem_id),
+  workflowitem_id   INTEGER REFERENCES cwf_workflowitem(workflowitem_id),
   workflow_id   VARCHAR2(256),
   step_id       VARCHAR2(256),
   action_id     VARCHAR2(256),
@@ -64,10 +61,11 @@ CREATE TABLE xmlwf_pooltask (
   group_id      INTEGER REFERENCES epersongroup(eperson_group_id)
 );
 
+CREATE INDEX cwf_pt_eperson_fk_idx ON cwf_pooltask(eperson_id);
+CREATE INDEX cwf_pt_workflow_fk_idx ON cwf_pooltask(workflowitem_id);
+CREATE INDEX cwf_pt_workflow_eperson_fk_idx ON cwf_pooltask(eperson_id,workflowitem_id);
+
 
-CREATE INDEX cwf_pt_epers_fk_idx ON cwf_pooltask(eperson_id);
-CREATE INDEX cwf_pt_wf_fk_idx ON cwf_pooltask(workflowitem_id);
-CREATE INDEX cwf_pt_wf_epers_fk_idx ON cwf_pooltask(eperson_id,workflowitem_id);
 
 CREATE TABLE cwf_claimtask (
   claimtask_id INTEGER PRIMARY KEY,
@@ -81,27 +79,24 @@ CREATE TABLE cwf_claimtask (
 ALTER TABLE cwf_claimtask
 ADD CONSTRAINT cwf_claimtask_unique UNIQUE (step_id, workflowitem_id, workflow_id, owner_id, action_id);
 
-
+CREATE INDEX cwf_ct_workflow_fk_idx ON cwf_claimtask(workflowitem_id);
-CREATE INDEX cwf_ct_wf_fk_idx ON cwf_claimtask(workflowitem_id);
+CREATE INDEX cwf_ct_workflow_eperson_fk_idx ON cwf_claimtask(workflowitem_id,owner_id);
-CREATE INDEX cwf_ct_wf_epers_fk_idx ON cwf_claimtask(workflowitem_id,owner_id);
+CREATE INDEX cwf_ct_eperson_fk_idx ON cwf_claimtask(owner_id);
-CREATE INDEX cwf_ct_epers_fk_idx ON cwf_claimtask(owner_id);
+CREATE INDEX cwf_ct_wfs_fk_idx ON cwf_claimtask(workflowitem_id,step_id);
-CREATE INDEX cwf_ct_wf_step_fk_idx ON cwf_claimtask(workflowitem_id,step_id);
+CREATE INDEX cwf_ct_wfs_action_fk_idx ON cwf_claimtask(workflowitem_id,step_id,action_id);
-CREATE INDEX cwf_ct_wf_step_act_fk_idx ON cwf_claimtask(workflowitem_id,step_id,action_id);
+CREATE INDEX cwf_ct_wfs_action_e_fk_idx ON cwf_claimtask(workflowitem_id,step_id,action_id,owner_id);
-CREATE INDEX cwf_ct_wf_st_ac_ep_fk_idx ON cwf_claimtask(workflowitem_id,step_id,action_id,owner_id);
-
 
 
 CREATE TABLE cwf_in_progress_user (
   in_progress_user_id INTEGER PRIMARY KEY,
   workflowitem_id integer REFERENCES cwf_workflowitem(workflowitem_id),
   user_id integer REFERENCES eperson(eperson_id),
-  finished NUMBER(1)
+  finished NUMBER(1) DEFAULT  0
 );
 
 ALTER TABLE cwf_in_progress_user
 ADD CONSTRAINT cwf_in_progress_user_unique UNIQUE (workflowitem_id, user_id);
 
-CREATE INDEX cwf_ipu_wf_fk_idx ON cwf_in_progress_user(workflowitem_id);
+CREATE INDEX cwf_ipu_workflow_fk_idx ON cwf_in_progress_user(workflowitem_id);
-CREATE INDEX cwf_ipu_epers_fk_idx ON cwf_in_progress_user(user_id);
+CREATE INDEX cwf_ipu_eperson_fk_idx ON cwf_in_progress_user(user_id);
--- TODO: it seems like this index is already created by the 'unique' constraint in the table creation
+
--- CREATE INDEX xmlwf_ipu_wf_epers_fk_idx ON xmlwf_in_progress_user(workflowitem_id,user_id);

dspace/etc/postgres/update-sequences.sql

@@ -84,7 +84,7 @@ SELECT setval('metadatavalue_seq', max(metadata_value_id)) FROM metadatavalue;
 SELECT setval('metadataschemaregistry_seq', max(metadata_schema_id)) FROM metadataschemaregistry;
 SELECT setval('harvested_collection_seq', max(id)) FROM harvested_collection;
 SELECT setval('harvested_item_seq', max(id)) FROM harvested_item;
-SELECT setval('webapp_seq', max(id)) FROM webapp;
+SELECT setval('webapp_seq', max(webapp_id)) FROM webapp;
 SELECT setval('requestitem_seq', max(requestitem_id)) FROM requestitem;
 
 -- Handle Sequence is a special case.  Since Handles minted by DSpace use the 'handle_seq',

dspace/modules/additions/pom.xml

@@ -17,7 +17,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/modules/jspui/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>modules</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace/modules/lni/pom.xml

@@ -13,7 +13,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/modules/oai/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <artifactId>modules</artifactId>
         <groupId>org.dspace</groupId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace/modules/pom.xml

@@ -9,7 +9,7 @@
 	<parent>
 		<groupId>org.dspace</groupId>
 		<artifactId>dspace-parent</artifactId>
-		<version>4.0</version>
+		<version>4.3</version>
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 

dspace/modules/rest/pom.xml

@@ -11,7 +11,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>modules</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -94,7 +94,7 @@
             <groupId>org.dspace</groupId>
             <artifactId>dspace-rest</artifactId>
             <type>war</type>
-            <version>4.0</version>
+            <version>4.3</version>
         </dependency>
 
         <dependency>

dspace/modules/solr/pom.xml

@@ -2,7 +2,7 @@
    <modelVersion>4.0.0</modelVersion>
    <groupId>org.dspace.modules</groupId>
    <artifactId>solr</artifactId>
-   <version>4.0</version>
+   <version>4.3</version>
    <packaging>war</packaging>
    <name>DSpace SOLR :: Local Customizations</name>
    <description>
@@ -13,7 +13,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 
@@ -58,7 +58,7 @@
        <dependency>
            <groupId>org.dspace</groupId>
            <artifactId>dspace-solr</artifactId>
-           <version>4.0</version>
+           <version>4.3</version>
            <classifier>skinny</classifier>
            <type>war</type>
        </dependency>
@@ -66,7 +66,7 @@
        <dependency>
            <groupId>org.dspace</groupId>
            <artifactId>dspace-solr</artifactId>
-           <version>4.0</version>
+           <version>4.3</version>
            <classifier>classes</classifier>
            <type>jar</type>
        </dependency>

dspace/modules/sword/pom.xml

@@ -16,7 +16,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/modules/swordv2/pom.xml

@@ -16,7 +16,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/modules/xmlui/pom.xml

@@ -12,7 +12,7 @@
    <parent>
       <groupId>org.dspace</groupId>
       <artifactId>modules</artifactId>
-      <version>4.0</version>
+      <version>4.3</version>
       <relativePath>..</relativePath>
    </parent>
 

dspace/pom.xml

@@ -15,7 +15,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>4.0</version>
+        <version>4.3</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -58,23 +58,88 @@
 
     <profiles>
 
-        <!-- Default Profile. This builds all Overlay modules for DSpace -->
+        <!-- Build Profile. This builds all Overlay modules for DSpace -->   
         <profile>
-            <id>default</id>
+            <id>build</id>
             <activation>
-                <activeByDefault>true</activeByDefault>
+                <!-- Enabled as long as we are NOT creating a zip/tarball distribution -->
+                <property>
+                    <name>!distributions</name>
+                </property>
             </activation>
             <!--
                 Builds Overlay Modules for DSpace
             -->
             <modules>
                 <module>modules</module>
-            </modules>
+            </modules> 
         </profile>
 
+        <!--
+            DSpace Assembly profile. By default this is enabled.
+            This profile actually builds all submodules and then assembles
+            the 'dspace-installer' from the resulting JARs/WARs.
+            See 'assembly.xml' for more info.
+            This profile can be optionally deactivated by passing '-P!assembly'.
+        -->
+        <profile>
+            <id>assembly</id>
+            <activation>
+                <!-- Enabled as long as we are NOT creating a zip/tarball distribution -->
+                <property>
+                    <name>!distributions</name>
+                </property>
+            </activation>
+            <build>
+                <plugins>
+                   <!-- Assemble 'target/dspace-installer' using 'assembly.xml' -->
+                   <plugin>
+                        <artifactId>maven-assembly-plugin</artifactId>
+                        <inherited>false</inherited>
+                        <configuration>
+                            <!-- Don't "attach" the assembly results to this project. As
+                                 this assembly builds a directory, setting this to "true"
+                                (default value) will just result in a WARNING message.-->
+                            <attach>false</attach>
+                            <finalName>${project.artifactId}</finalName>
+                            <descriptors>
+                                <descriptor>src/main/assembly/assembly.xml</descriptor>
+                            </descriptors>
+                        </configuration>
+                        <executions>
+                            <execution>
+                                <phase>package</phase>
+                                <goals>
+                                    <goal>single</goal>
+                                </goals>
+                            </execution>
+                        </executions>
+                    </plugin>
+                </plugins>
+            </build>
+        </profile>
+
+        <!-- This profile simply determines whether we are creating 
+             zip / tarball distributions to upload to SourceFore or similar. 
+             By running "mvn package -Ddistributions=true" you'll
+             SKIP normal build & assembly (see above profiles) and
+             INSTEAD just run the "distributions" profile below. -->
+        <profile>
+            <id>build-and-assembly</id>
+            <activation>
+                <!-- This profile should be active at all times, unless the user
+                     specifies a different value for "distributions" -->
+                <property>
+                    <name>!distributions</name>
+                </property>
+            </activation>
+            <properties>
+                <distributions>false</distributions>
+            </properties>
+        </profile> 
 
         <!--
-            Run this profile (e.g. 'mvn package -Pdistributions') to create
+            Run this profile (e.g. 'mvn package -Ddistributions=true') to create
             zip / tarball distributions to upload to SourceForge or similar.
             When this profile is run, DSpace is NOT compiled as normal.
             Instead, a zip/tarball is generated from the parent [dspace-src] directory.
@@ -82,7 +147,11 @@
         <profile>
            <id>distributions</id>
            <activation>
-              <activeByDefault>false</activeByDefault>
+              <!-- Only enabled if "distributions=true" was passed on commandline -->
+              <property>
+                  <name>distributions</name>
+                  <value>true</value>
+              </property>
            </activation>
            <build>
               <plugins>

dspace/solr/search/conf/schema.xml

@@ -544,6 +544,7 @@
 
     <field name="a_spell" type="textSpell" />
     <copyField source="fulltext" dest="a_spell" />
+    <copyField source="fulltext" dest="fulltext_hl" />
 
     <!-- used by the DSpace Discovery Solr Indexer to track the last time a document was indexed -->
    <field name="SolrIndexer.lastIndexed" type="date" indexed="true" stored="true" default="NOW" multiValued="false" omitNorms="true" />

dspace/solr/search/conf/solrconfig.xml

@@ -1042,13 +1042,13 @@
                   startup="lazy"
                   class="solr.extraction.ExtractingRequestHandler" >
     <lst name="defaults">
-      <str name="lowernames">true</str>
+      <!--<str name="lowernames">true</str>-->
       <str name="uprefix">ignored_</str>
 
       <!-- capture link hrefs but ignore div attributes -->
-      <str name="captureAttr">true</str>
+      <str name="captureAttr">false</str>
-      <str name="fmap.a">links</str>
+      <!--<str name="fmap.a">links</str>-->
-      <str name="fmap.div">ignored_</str>
+      <!--<str name="fmap.div">ignored_</str>-->
     </lst>
   </requestHandler>
 
@@ -1244,7 +1244,7 @@
       <str name="name">default</str>
       <str name="field">a_spell</str>
       <str name="spellcheckIndexDir">./spellchecker</str>
-      <str name="buildOnCommit">true</str>
+      <str name="buildOnOptimize">true</str>
       <str name="spellcheck.onlyMorePopular">false</str>
     </lst>
 

dspace/src/main/assembly/assembly.xml

@@ -48,7 +48,6 @@
          <includes>
             <include>bin/**</include>
             <include>config/**</include>
-            <include>docs/**</include>
             <include>etc/**</include>
             <include>solr/**</include>
          </includes>
@@ -82,11 +81,16 @@
          <outputDirectory>config</outputDirectory>
          <filtered>true</filtered>
       </file>
+      <file>
+         <source>config/crosswalks/oai/description.xml</source>
+         <outputDirectory>config</outputDirectory>
+         <filtered>true</filtered>
+      </file>
    </files>
 
    <!--
-   Still allow anyone to put a JAR dependency into
+   Copy ALL JAR dependencies specified in [src]/dspace/pom.xml
-   [src]/dspace/pom.xml and have it go into 'lib' directory
+   into the DSpace 'lib' directory.
    -->
    <dependencySets>
       <dependencySet>
@@ -100,30 +104,30 @@
 
    <moduleSets>
       <!--
-      Take all jar modules in [src]/dspace/modules/ dir
+      Take all JAR modules (and their dependencies) under
-      and add them into 'lib' directory
+      [src]/dspace/modules/ dir and add them into 'lib' directory
       -->
       <moduleSet>
          <includes>
-            <include>*:jar:*</include>
+            <include>org.dspace.modules:*:jar:*</include>
          </includes>
          <binaries>
             <includeDependencies>true</includeDependencies>
             <outputDirectory>lib</outputDirectory>
             <unpack>false</unpack>
+            <!-- Include any dependency JARs as well -->
             <dependencySets>
                <dependencySet>
                   <includes>
                      <include>*:jar:*</include>
                   </includes>
-                  <outputDirectory>lib</outputDirectory>
                </dependencySet>
             </dependencySets>
          </binaries>
       </moduleSet>
 
       <!--
-      Take all war modules (in [src]/dspace/modules/) and explode them into
+      Take all WAR modules (in [src]/dspace/modules/) and unpack them into
       'webapps' directory
       -->
       <moduleSet>

pom.xml

@@ -4,7 +4,7 @@
    <groupId>org.dspace</groupId>
    <artifactId>dspace-parent</artifactId>
    <packaging>pom</packaging>
-   <version>4.0</version>
+   <version>4.3</version>
    <name>DSpace Parent Project</name>
    <description>
    	DSpace open source software is a turnkey institutional repository application.
@@ -20,7 +20,7 @@
     <parent>
         <groupId>org.sonatype.oss</groupId>
         <artifactId>oss-parent</artifactId>
-        <version>7</version>
+        <version>9</version>
         <relativePath />
     </parent>
 
@@ -41,6 +41,14 @@
            (NOTE: individual POMs can override specific settings). -->
       <pluginManagement>
           <plugins>
+	      <plugin>
+                  <groupId>org.apache.maven.plugins</groupId>
+        	  <artifactId>maven-javadoc-plugin</artifactId>
+        	  <configuration>
+          	     <minmemory>128m</minmemory>
+          	     <maxmemory>1g</maxmemory>
+        	  </configuration>
+      	      </plugin>
               <plugin>
                   <artifactId>maven-compiler-plugin</artifactId>
                   <version>2.3.2</version>
@@ -89,6 +97,8 @@
                     <excludes>
                         <exclude>**/Abstract*</exclude>
                     </excludes>
+                    <!-- Detailed logs in reportsDirectory/testName-output.txt instead of stdout -->
+                    <redirectTestOutputToFile>true</redirectTestOutputToFile>
                     <!--
                     Enable to debug Maven Surefire tests in remote proces
                     <debugForkedProcess>true</debugForkedProcess>
@@ -121,7 +131,7 @@
                <id>native2ascii-utf8</id>
                <phase>generate-resources</phase>
                <configuration>
-                 <target name="Encode any UTF-8 chars in [src]/*.properties">
+                 <target name="Encode any UTF-8 chars in properties">
                    <!-- Run 'native2ascii' to encode UTF-8 characters in properties files. Place the resulting file(s) in /target -->
                    <native2ascii encoding="UTF8" src="${root.basedir}" dest="${root.basedir}/target" includes="*.properties" />
                  </target>
@@ -146,7 +156,7 @@
 
          <plugin>
             <artifactId>maven-release-plugin</artifactId>
-            <version>2.3.2</version>
+            <version>2.5</version>
             <configuration>
                 <!-- During release:perform, enable the "release" profile (see below) -->
                 <releaseProfiles>release</releaseProfiles>
@@ -543,102 +553,102 @@
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-api</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
          </dependency>
          <dependency>
             <groupId>org.dspace.modules</groupId>
             <artifactId>additions</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
          </dependency>
 
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-sword</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-sword</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-swordv2</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-swordv2</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
 
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-jspui</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-jspui</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-oai</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-oai</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-lni</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-lni-client</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-lni</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-xmlui</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>jar</type>
             <classifier>classes</classifier>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-xmlui</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
             <type>war</type>
          </dependency>
          <dependency>
             <groupId>org.dspace</groupId>
             <artifactId>dspace-services</artifactId>
-            <version>4.0</version>
+            <version>4.3</version>
          </dependency>
          <!-- DSpace Localization Packages -->
          <dependency>
@@ -1309,7 +1319,7 @@
       <connection>scm:git:git@github.com:DSpace/DSpace.git</connection>
       <developerConnection>scm:git:git@github.com:DSpace/DSpace.git</developerConnection>
       <url>git@github.com:DSpace/DSpace.git</url>
-     <tag>dspace-4.0</tag>
+     <tag>dspace-4.3</tag>
   </scm>
 
     <!--
@@ -1326,8 +1336,8 @@
         <repository>
             <id>sonatype-releases</id>
             <name>Sonatype Releases Repository</name>
-            <url>http://oss.sonatype.org/content/repositories/releases/</url>
+            <url>https://oss.sonatype.org/content/repositories/releases/</url>
         </repository>
     </repositories>
-    
+
 </project>

src/main/assembly/testEnvironment.xml

@@ -21,43 +21,57 @@
     </formats>
     <includeBaseDirectory>false</includeBaseDirectory>
 
+    <!-- First, copy the following from our 'dspace' subfolder assembly project into the
+         same subdirectory in the final ZIP file. NOTE: We do this in a <fileSet> INSTEAD
+         of a <moduleSet> so that we don't have to first build the "dspace" module. -->
+    <fileSets>
+        <fileSet>
+            <!-- Copy necessary DSpace subdirectories into Test environment -->
+            <includes>
+                <include>dspace/bin/**</include>
+                <include>dspace/config/**</include>
+                <include>dspace/etc/**</include>
+                <include>dspace/solr/**</include>
+            </includes>
+            <!-- But, exclude specific configs (which require filtering) -->
+            <excludes>
+                <exclude>dspace/config/dspace.cfg</exclude>
+                <exclude>dspace/config/log4j.properties</exclude>
+                <exclude>dspace/config/modules/**</exclude>
+            </excludes>
+        </fileSet>
+        <fileSet> 
+            <!-- Copy specific configs (filtering their content) also into Test environment -->
+            <includes>
+                <include>dspace/config/modules/**</include>
+                <include>dspace/config/dspace.cfg</include>
+                <include>dspace/config/log4j.properties</include>
+            </includes>
+            <filtered>true</filtered>
+        </fileSet>        
+    </fileSets>
+
     <moduleSets>
+        <!-- Next, search for a 'src/test/data/dspaceFolder' data directory in
+             ANY of our modules. If found, copy its contents into the same "dspace"
+             subdirectory in the final ZIP file, as this is data to be used in testing.
+             NOTE: This *might* overwrite/overlay default files copied from above. -->
         <moduleSet>
+            <includes>
+                <include>org.dspace:*</include>
+            </includes>
             <sources>
                 <outputDirectoryMapping>dspace</outputDirectoryMapping>
                 <fileSets>
-                    <fileSet> <!-- installable DSpace files -->
+                    <fileSet>
-                        <directory />
-                        <outputDirectory />
-                        <!-- Copy necessary DSpace subdirectories into Test environment -->
-                        <includes>
-                            <include>bin/**</include>
-                            <include>config/**</include>
-                            <include>etc/**</include>
-                            <include>solr/**</include>
-                        </includes>
-                        <!-- Exclude specific configs (which require filtering) -->
-                        <excludes>
-                            <exclude>config/dspace.cfg</exclude>
-                            <exclude>config/log4j.properties</exclude>
-                            <exclude>config/modules/**</exclude>
-                        </excludes> 
-                    </fileSet>
-                    <fileSet> <!-- Copy specific configs (filtering their content) also into Test environment -->
-                        <includes>
-                            <include>config/modules/**</include>
-                            <include>config/dspace.cfg</include>
-                            <include>config/log4j.properties</include>
-                        </includes>
-                        <filtered>true</filtered>
-                    </fileSet>
-                    <fileSet> <!-- test data -->
                         <directory>src/test/data/dspaceFolder</directory>
-                        <outputDirectory />
                     </fileSet>
                 </fileSets>
             </sources>
         </moduleSet>
+        <!-- Finally, copy the 'dspace.cfg.more' from the 'dspace-api' into
+             the root directory of the ZIP. This config will be merged/weaved
+             into the default dspace.cfg (see fileweaver maven plugin) -->
         <moduleSet>
             <includes>
                 <include>org.dspace:dspace-api</include>