Merge branch 'master' into DS-3363-csv-import-error-messages

.travis.yml

@@ -5,6 +5,20 @@ env:
   # Give Maven 1GB of memory to work with
   - MAVEN_OPTS=-Xmx1024M
 
+jdk:
+  # DS-3384 Oracle JDK 8 has DocLint enabled by default.
+  # Let's use this to catch any newly introduced DocLint issues.
+  - oraclejdk8
+  - oraclejdk7
+
+## Should we run into any problems with oraclejdk8 on Travis, we may try the following workaround.
+## https://docs.travis-ci.com/user/languages/java#Testing-Against-Multiple-JDKs
+## https://github.com/travis-ci/travis-ci/issues/3259#issuecomment-130860338
+#addons:
+#  apt:
+#    packages:
+#      - oracle-java8-installer
+
 # Install prerequisites for building Mirage2 more rapidly
 before_install:
   # Install Node.js 6.5.0 & print version info

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>6.0-rc5-SNAPSHOT</version>
+        <version>7.0-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

dspace-api/src/main/java/org/apache/solr/handler/extraction/ExtractingParams.java

@@ -72,10 +72,10 @@ public interface ExtractingParams {
   /**
    * Restrict the extracted parts of a document to be indexed
    * by passing in an XPath expression.  All content that satisfies the XPath expr.
-   * will be passed to the {@link SolrContentHandler}.
+   * will be passed to the {@link org.apache.solr.handler.extraction.SolrContentHandler}.
    * <p>
    * See Tika's docs for what the extracted document looks like.
-   * <p>
+   *
    * @see #CAPTURE_ELEMENTS
    */
   public static final String XPATH_EXPRESSION = "xpath";
@@ -105,7 +105,7 @@ public interface ExtractingParams {
    * Capture the specified fields (and everything included below it that isn't capture by some other capture field) separately from the default.  This is different
    * then the case of passing in an XPath expression.
    * <p>
-   * The Capture field is based on the localName returned to the {@link SolrContentHandler}
+   * The Capture field is based on the localName returned to the {@link org.apache.solr.handler.extraction.SolrContentHandler}
    * by Tika, not to be confused by the mapped field.  The field name can then
    * be mapped into the index schema.
    * <p>

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

@@ -48,7 +48,7 @@ public class CommunityFiliator
 
     /**
      *
-     * @param argv arguments
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception

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

@@ -57,8 +57,7 @@ public final class CreateAdministrator
      * For invoking via the command line.  If called with no command line arguments,
      * it will negotiate with the user for the administrator details
      * 
-     * @param argv
+     * @param argv the command line arguments given
-     *            command-line arguments
      * @throws Exception if error
      */
     public static void main(String[] argv)

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

@@ -71,7 +71,8 @@ public class MetadataImporter
 
     /**
      * main method for reading user input from the command line
-     * @param args arguments
+     *
+     * @param args the command line arguments given
      * @throws ParseException if parse error
      * @throws SQLException if database error
      * @throws IOException if IO error

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

@@ -54,8 +54,7 @@ public class RegistryLoader
     /**
      * For invoking via the command line
      * 
-     * @param argv
+     * @param argv the command line arguments given
-     *            command-line arguments
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception

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

@@ -92,7 +92,8 @@ public class StructBuilder
      * 
      * The output file will contain exactly the same as the source xml document, but
      * with the handle for each imported item added as an attribute.
-     * @param argv commandline arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if an error occurs
      */
     public static void main(String[] argv) 

dspace-api/src/main/java/org/dspace/app/checker/ChecksumChecker.java

@@ -53,7 +53,6 @@ public final class ChecksumChecker
     /**
      * Command line access to the checksum package.
      * 
-     * @param args
      * <dl>
      *   <dt>-h</dt>
      *   <dd>Print help on command line options</dd>
@@ -72,6 +71,7 @@ public final class ChecksumChecker
      *   <dt>-p</dt>
      *   <dd>Don't prune results before running checker</dd>
      * </dl>
+     * @param args the command line arguments given
      * @throws SQLException if error
      */
     public static void main(String[] args) throws SQLException {
@@ -98,8 +98,7 @@ public final class ChecksumChecker
         options.addOption(useBitstreamIds);
 
         options.addOption("p", "prune", false, "Prune configuration file");
-        options
+        options.addOption(OptionBuilder
-                .addOption(OptionBuilder
             .withArgName("prune")
             .hasOptionalArgs(1)
             .withDescription(
@@ -233,7 +232,7 @@ public final class ChecksumChecker
             context.complete();
             context = null;
         } finally {
-            if(context != null){
+            if (context != null) {
                 context.abort();
             }
         }
@@ -249,19 +248,15 @@ public final class ChecksumChecker
         HelpFormatter myhelp = new HelpFormatter();
 
         myhelp.printHelp("Checksum Checker\n", options);
-        System.out
+        System.out.println("\nSpecify a duration for checker process, using s(seconds),"
-                .println("\nSpecify a duration for checker process, using s(seconds),"
             + "m(minutes), or h(hours): ChecksumChecker -d 30s"
             + " OR ChecksumChecker -d 30m"
             + " OR ChecksumChecker -d 2h");
-        System.out
+        System.out.println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
-                .println("\nSpecify bitstream IDs: ChecksumChecker -b 13 15 17 20");
         System.out.println("\nLoop once through all bitstreams: "
             + "ChecksumChecker -l");
-        System.out
+        System.out.println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
-                .println("\nLoop continuously through all bitstreams: ChecksumChecker -L");
+        System.out.println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
-        System.out
-                .println("\nCheck a defined number of bitstreams: ChecksumChecker -c 10");
         System.out.println("\nReport all processing (verbose)(default reports only errors): ChecksumChecker -v");
         System.out.println("\nDefault (no arguments) is equivalent to '-c 1'");
         System.exit(0);

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

@@ -67,12 +67,18 @@ public class Harvest
         options.addOption("P", "purge", false, "purge all harvestable collections");
         
 
-        options.addOption("e", "eperson", true, "eperson");
+        options.addOption("e", "eperson", true,
-        options.addOption("c", "collection", true, "harvesting collection (handle or id)");
+            "eperson");
-        options.addOption("t", "type", true, "type of harvesting (0 for none)");
+        options.addOption("c", "collection", true,
-        options.addOption("a", "address", true, "address of the OAI-PMH server");
+            "harvesting collection (handle or id)");
-        options.addOption("i", "oai_set_id", true, "id of the PMH set representing the harvested collection");
+        options.addOption("t", "type", true,
-        options.addOption("m", "metadata_format", true, "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
+            "type of harvesting (0 for none)");
+        options.addOption("a", "address", true,
+            "address of the OAI-PMH server");
+        options.addOption("i", "oai_set_id", true,
+            "id of the PMH set representing the harvested collection");
+        options.addOption("m", "metadata_format", true,
+            "the name of the desired metadata format for harvesting, resolved to namespace and crosswalk in dspace.cfg");
 
         options.addOption("h", "help", false, "help");
 
@@ -90,22 +96,14 @@ public class Harvest
         {
             HelpFormatter myhelp = new HelpFormatter();
             myhelp.printHelp("Harvest\n", options);
-            System.out
+            System.out.println("\nPING OAI server: Harvest -g -s oai_source -i oai_set_id");
-    				.println("\nPING OAI server: Harvest -g -s oai_source -i oai_set_id");
+            System.out.println("RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
-            System.out
+            System.out.println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
-					.println("RUNONCE harvest with arbitrary options: Harvest -o -e eperson -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
+            System.out.println("RUN harvest once: Harvest -r -e eperson -c collection");
-            System.out
+            System.out.println("START harvest scheduler: Harvest -S");
-                    .println("SETUP a collection for harvesting: Harvest -s -c collection -t harvest_type -a oai_source -i oai_set_id -m metadata_format");
+            System.out.println("RESET all harvest status: Harvest -R");
-            System.out
+            System.out.println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            		.println("RUN harvest once: Harvest -r -e eperson -c collection");
+            System.out.println("PURGE all harvestable collections: Harvest -P -e eperson");
-            System.out
-    				.println("START harvest scheduler: Harvest -S");
-            System.out
-					.println("RESET all harvest status: Harvest -R");
-            System.out
-                    .println("PURGE a collection of items and settings: Harvest -p -e eperson -c collection");
-            System.out
-					.println("PURGE all harvestable collections: Harvest -P -e eperson");
             
             
 

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

@@ -31,7 +31,7 @@ public class BitstreamFilterByFilename extends BitstreamFilter {
      * 
      * @param bitstream Bitstream
      * @return whether bitstream name matches the regular expression
-         * @exception BitstreamFilterException if filter error
+     * @throws BitstreamFilterException if filter error
      */
     @Override
     public boolean accept(Bitstream bitstream) throws BitstreamFilterException

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

@@ -113,7 +113,7 @@ public class ItemUpdate {
    
     /**
      * 
-     * @param argv commandline args
+     * @param argv the command line arguments given
      */
     public static void main(String[] argv)
     {
@@ -138,13 +138,13 @@ public class ItemUpdate {
         delBitstreamOption.setArgName("BitstreamFilter");
         options.addOption(delBitstreamOption);
                                
-//other params        
+        //other params        
         options.addOption("e", "eperson", true, "email of eperson doing the update");
         options.addOption("i", "itemfield", true, "optional metadata field that containing item identifier; default is dc.identifier.uri");
         options.addOption("F", "filter-properties", true, "filter class name; only for deleting bitstream");  
         options.addOption("v", "verbose", false, "verbose logging");
       
-//special run states        
+        //special run states        
         options.addOption("t", "test", false, "test run - do not actually import items");
         options.addOption("P", "provenance", false, "suppress altering provenance field for bitstream changes");
         options.addOption("h", "help", false, "help");
@@ -395,6 +395,7 @@ public class ItemUpdate {
 
     /**
      * process an archive
+     *
      * @param context DSpace Context
      * @param sourceDirPath source path
      * @param itemField item field
@@ -516,7 +517,6 @@ public class ItemUpdate {
            
     
     /**
-     * 
      * to avoid overwriting the undo source tree on repeated processing
      * sequence numbers are added and checked 
      * 
@@ -606,6 +606,7 @@ public class ItemUpdate {
      * poor man's logging
      * As with ItemImport, API logging goes through log4j to the DSpace.log files
      * whereas the batch logging goes to the console to be captured there.
+     * 
      * @param s String
      */
     static void pr(String s)

dspace-api/src/main/java/org/dspace/app/launcher/CommandRunner.java

@@ -25,7 +25,7 @@ public class CommandRunner
 {
     /**
      * 
-     * @param args commandline args
+     * @param args the command line arguments given
      * @throws IOException if IO error
      * @throws FileNotFoundException if file doesn't exist
      */

dspace-api/src/main/java/org/dspace/app/launcher/ScriptLauncher.java

@@ -92,8 +92,9 @@ public class ScriptLauncher
 
     /**
      * Recognize and execute a single command.
+     *
      * @param doc Document
-     * @param args arguments
+     * @param args the command line arguments given
      */
     static int runOneCommand(Document commandConfigs, String[] args)
     {

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

@@ -61,7 +61,7 @@ public abstract class MediaFilter implements FormatFilter
      * @param generatedBitstream
      *            the bitstream which was generated by
      *            this filter.
-     * @throws java.lang.Exception
+     * @throws Exception if error
      */
     @Override
     public void postProcessBitstream(Context c, Item item, Bitstream generatedBitstream)

dspace-api/src/main/java/org/dspace/app/requestitem/service/RequestItemService.java

@@ -24,13 +24,20 @@ public interface RequestItemService {
 
     /**
      * Generate a request item representing the request and put it into the DB
-     * @param context context
+     * @param context
-     * @param bitstream bitstream
+     *     The relevant DSpace Context.
-     * @param item item
+     * @param bitstream
-     * @param reqMessage message
+     *     The requested bitstream
-     * @param allFiles all files flag
+     * @param item
+     *     The requested item
+     * @param reqMessage
+     *     Request message text
+     * @param allFiles
+     *     true indicates that all bitstreams of this item are requested
      * @param reqEmail email
-     * @param reqName name
+     *     Requester email
+     * @param reqName
+     *     Requester name
      * @return the token of the request item
      * @throws SQLException if database error
      */
@@ -41,8 +48,11 @@ public interface RequestItemService {
 
     /**
      * Save updates to the record. Only accept_request, and decision_date are set-able.
+     *
      * @param context
+     *     The relevant DSpace Context.
      * @param requestItem
+     *     requested item
      */
     public void update(Context context, RequestItem requestItem);
 

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

@@ -212,7 +212,7 @@ public class LogAnalyser
     /**
      * main method to be run from command line.  See usage information for
      * details as to how to use the command line flags (-help)
-     * @param argv arguments
+     * @param argv the command line arguments given
      * @throws Exception if error
      * @throws SQLException if database error
      */
@@ -1187,13 +1187,13 @@ public class LogAnalyser
         // that
 
         DiscoverQuery discoverQuery = new DiscoverQuery();
-        if(StringUtils.isNotBlank(type))
+        if (StringUtils.isNotBlank(type))
         {
             discoverQuery.addFilterQueries("dc.type=" + type +"*");
         }
         StringBuilder accessionedQuery = new StringBuilder();
         accessionedQuery.append("dc.date.accessioned_dt:[");
-        if(startDate != null)
+        if (startDate != null)
         {
             accessionedQuery.append(unParseDate(startDate));
         }
@@ -1202,7 +1202,7 @@ public class LogAnalyser
             accessionedQuery.append("*");
         }
         accessionedQuery.append(" TO ");
-        if(endDate != null)
+        if (endDate != null)
         {
             accessionedQuery.append(unParseDate(endDate));
         }

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

@@ -152,9 +152,10 @@ public class ReportGenerator
     /**
      * main method to be run from command line.  See usage information for
      * details as to how to use the command line flags
-     * @param argv
+     * @param argv the command line arguments given
-     * @throws java.lang.Exception
+     * @throws Exception on generic exception
-     * @throws java.sql.SQLException
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public static void main(String [] argv)
         throws Exception, SQLException

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

@@ -30,6 +30,8 @@ public class CollectionDropDown {
      * Get full path starting from a top-level community via subcommunities down to a collection.
      * The full path will not be truncated.
      * 
+     * @param context
+     *     The relevant DSpace Context.
      * @param col 
      *     Get full path for this collection
      * @return Full path to the collection
@@ -44,6 +46,8 @@ public class CollectionDropDown {
      * Get full path starting from a top-level community via subcommunities down to a collection.
      * The full cat will be truncated to the specified number of characters and prepended with an ellipsis.
      * 
+     * @param context
+     *     The relevant DSpace Context.
      * @param col 
      *     Get full path for this collection
      * @param maxchars 
@@ -84,6 +88,8 @@ public class CollectionDropDown {
 
     /**
      * Annotates an array of collections with their respective full paths (@see #collectionPath() method in this class).
+     * @param context
+     *     The relevant DSpace Context.
      * @param collections An array of collections to annotate with their hierarchical paths.
      *     The array and all its entries must be non-null.
      * @return A sorted array of collection path entries (essentially collection/path pairs).

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

@@ -36,8 +36,7 @@ public class Configuration
      * </ul>
      * If the property does not exist, nothing is written.
      *
-     * @param argv
+     * @param argv the command line arguments given
-     *            command-line arguments
      */
     public static void main(String[] argv)
     {

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

@@ -94,8 +94,10 @@ public class DCInput
      * a HashMap
      * 
      * @param fieldMap
-     *            ???
+     *     named field values.
+     *     
      * @param listMap
+     *     value-pairs map, computed from the forms definition XML file
      */
     public DCInput(Map<String, String> fieldMap, Map<String, List<String>> listMap)
     {

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

@@ -120,7 +120,7 @@ public class DCInputSet
      * Does the current input set define the named field?
      * Scan through every field in every page of the input set
      *
-     * @param fieldName
+     * @param fieldName selects the field.
      * @return true if the current set has the named field
      */
     public boolean isFieldPresent(String fieldName)
@@ -152,7 +152,7 @@ public class DCInputSet
      */
      public boolean isFieldPresent(String fieldName, String documentType)
      {
-     	if(documentType == null){
+         if (documentType == null) {
              documentType = "";
          }
          for (int i = 0; i < inputPages.length; i++)
@@ -164,7 +164,7 @@ public class DCInputSet
                                      pageInputs[row].getQualifier();
                  if (fullName.equals(fieldName) )
                  {
-     				if(pageInputs[row].isAllowedFor(documentType)){
+                     if (pageInputs[row].isAllowedFor(documentType)) {
                          return true;
                      }
                  }

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

@@ -82,6 +82,7 @@ public class DCInputsReader
      * level structures: a map between collections and forms, the definition for
      * each page of each form, and lists of pairs of values that populate
      * selection boxes.
+     *
      * @throws DCInputsReaderException if input reader error
      */
 
@@ -197,6 +198,9 @@ public class DCInputsReader
      * Process the top level child nodes in the passed top-level node. These
      * should correspond to the collection-form maps, the form definitions, and
      * the display/storage word pairs.
+     *
+     * @param n
+     *     top-level DOM node
      */
     private void doNodes(Node n)
         throws SAXException, DCInputsReaderException
@@ -337,7 +341,6 @@ public class DCInputsReader
 
                                 // we omit the duplicate validation, allowing multiple fields definition for 
                                 // the same metadata and different visibility/type-bind
-
                             }
                         }
                     } // ignore any child that is not a 'page'
@@ -545,7 +548,6 @@ public class DCInputsReader
                     String errString =
                         "Missing name attribute for value-pairs for DC term " + dcTerm;
                     throw new SAXException(errString);
-
                 }
                 List<String> pairs = new ArrayList<String>();
                 valuePairs.put(pairsName, pairs);
@@ -626,7 +628,6 @@ public class DCInputsReader
                 
                         // we omit the "required" and "visibility" validation, provided this must be checked in the processing class
                         // only when it makes sense (if the field isn't visible means that it is not applicable, therefore it can't be required)
-
                 }
             }
         }

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

@@ -30,6 +30,7 @@ public class DSpaceContextListener implements ServletContextListener
     /**
      * Initialize any resources required by the application.
      * @param event
+     *     This is the event class for notifications about changes to the servlet context of a web application.
      */
     @Override
     public void contextInitialized(ServletContextEvent event)
@@ -63,6 +64,7 @@ public class DSpaceContextListener implements ServletContextListener
      * Clean up resources used by the application when stopped
      * 
      * @param event
+     8     Event class for notifications about changes to the servlet context of a web application.
      */
     @Override
     public void contextDestroyed(ServletContextEvent event)

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

@@ -229,6 +229,7 @@ public class GoogleMetadata
      * first-encountered instance of the field for this Item.
      * 
      * @param fieldName
+     *     metadata field name
      * @return successful?
      */
     protected boolean addSingleField(String fieldName)
@@ -262,7 +263,7 @@ public class GoogleMetadata
         if (config.equals("$simple-pdf"))
         {
             String pdf_url = getPDFSimpleUrl(item);
-            if(pdf_url.length() > 0)
+            if (pdf_url.length() > 0)
             {
                 metadataMappings.put(fieldName, pdf_url);
                 return true;
@@ -291,6 +292,7 @@ public class GoogleMetadata
      * instead of an aggregate.
      * 
      * @param configFilter
+     *     list of DC metadata fields separated by "|" characters
      * @return The first configured match of metadata field for the item.
      */
     protected MetadataValue resolveMetadataField(String configFilter)
@@ -309,6 +311,7 @@ public class GoogleMetadata
      * A plural version of resolveMetadata for aggregate fields.
      * 
      * @param configFilter
+     *     list of DC metadata fields separated by "|" characters
      * @return Aggregate of all matching metadata fields configured in the first
      *         option field-set to return any number of filter matches.
      */
@@ -328,7 +331,9 @@ public class GoogleMetadata
      * configuration filter.
      * 
      * @param configFilter
+     *     list of DC metadata fields separated by "|" characters
      * @param returnType
+     *     GoogleMetadata.SINGLE / GoogleMetadata.MULTI / GoogleMetadata.ALL_FIELDS_IN_OPTION
      * @return Array of configuration to item-field matches
      */
     protected ArrayList<MetadataValue> resolveMetadata(String configFilter,
@@ -350,8 +355,7 @@ public class GoogleMetadata
 
         if (log.isDebugEnabled())
         {
-            log
+            log.debug("Resolved Fields For This Item Per Configuration Filter:");
-                    .debug("Resolved Fields For This Item Per Configuration Filter:");
             for (int i = 0; i < parsedOptions.size(); i++)
             {
                 ArrayList<String> optionFields = parsedOptions.get(i);
@@ -445,6 +449,7 @@ public class GoogleMetadata
      * configuration.
      * 
      * @param configFilter
+     *     list of DC metadata fields separated by "|" characters
      * @return array of parsed options or null
      */
     protected ArrayList<ArrayList<String>> parseOptions(String configFilter)
@@ -720,7 +725,7 @@ public class GoogleMetadata
         // Dissertations
         if (itemIsDissertation())
         {
-            if(log.isDebugEnabled()) {
+            if (log.isDebugEnabled()) {
                 log.debug("ITEM TYPE:  DISSERTATION");
             }
 
@@ -731,7 +736,7 @@ public class GoogleMetadata
         // Patents
         if (itemIsPatent())
         {
-            if(log.isDebugEnabled()) {
+            if (log.isDebugEnabled()) {
                 log.debug("ITEM TYPE:  PATENT");
             }
 
@@ -750,7 +755,7 @@ public class GoogleMetadata
         // Tech Reports
         if (itemIsTechReport())
         {
-            if(log.isDebugEnabled()) {
+            if (log.isDebugEnabled()) {
                 log.debug("ITEM TYPE:  TECH REPORT");
             }
             addSingleField(TECH_REPORT_NUMBER);
@@ -758,7 +763,7 @@ public class GoogleMetadata
         }
 
 
-        if(!itemIsDissertation() && !itemIsTechReport()) {
+        if (!itemIsDissertation() && !itemIsTechReport()) {
             // PUBLISHER
             addSingleField(PUBLISHER);
         }
@@ -1004,7 +1009,7 @@ public class GoogleMetadata
      * is in the default content bundle, and that the item only has one public bitstream
      * and it is a PDF.
      *
-     * @param item
+     * @param item item to get PDF URL from
      * @return URL that the PDF can be directly downloaded from
      */
     protected String getPDFSimpleUrl(Item item)
@@ -1045,7 +1050,9 @@ public class GoogleMetadata
      *     <li>the primary bitstream</li>
      * </ul>
      * Additionally, this bitstream must be publicly viewable.
+     *
      * @param item
+     *     bitstream's parent item
      * @return a linkable bitstream or null if none found
      * @throws SQLException if database error
      */
@@ -1071,6 +1078,13 @@ public class GoogleMetadata
         return bestSoFar;
     }
 
+    /**
+     * Find out whether bitstream is readable by the public.
+     * 
+     * @param bitstream
+     *     the target bitstream
+     * @return whether bitstream is readable by the Anonymous group
+     */
     protected boolean isPublic(Bitstream bitstream) {
         if (bitstream == null) {
             return false;
@@ -1122,6 +1136,7 @@ public class GoogleMetadata
     /**
      * If metadata field contains multiple values, then add each value to the map separately
      * @param FIELD
+     *     metadata field
      */
     protected void addMultipleValues(String FIELD)
     {
@@ -1201,6 +1216,7 @@ public class GoogleMetadata
      * metadata practice.
      * 
      * @param dConfig
+     *     configured fields (from google-metadata.properties)
      * @return item matches configuration
      */
     protected boolean identifyItemType(String dConfig)
@@ -1223,7 +1239,7 @@ public class GoogleMetadata
                 if (mdPairs.containsKey(parsedPair[0].trim()))
                 {
                     mdPairs.get(parsedPair[0].trim()).add(parsedPair[1]);
-                    if(log.isDebugEnabled()) {
+                    if (log.isDebugEnabled()) {
                         log.debug("Registering Type Identifier:  " + parsedPair[0] + " => " + parsedPair[1]);
                     }
                 }

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

@@ -197,7 +197,7 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
         {
             osq.setSearchTerms(URLEncoder.encode(query, "UTF-8"));
         }
-        catch(UnsupportedEncodingException e)
+        catch (UnsupportedEncodingException e)
         {
             log.error(e);
         }
@@ -281,7 +281,9 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
     
     /**
      * Converts a JDOM document to a W3C one
+     *
      * @param jdomDoc
+     *     jDOM document to convert
      * @return W3C Document object
      * @throws IOException if IO error
      */
@@ -292,7 +294,7 @@ public class OpenSearchServiceImpl implements OpenSearchService, InitializingBea
         {
             return domOut.output(jdomDoc);
         }
-        catch(JDOMException jde)
+        catch (JDOMException jde)
         {
             throw new IOException("JDOM output exception", jde);
         }

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

@@ -39,7 +39,7 @@ public class SubmissionStepConfig implements Serializable
 
     /**
      * the id for this step ('id' only exists if this step is defined in the
-     * <step-definitions> section)
+     * &lt;step-definitions&gt; section)
      */
     private String id = null;
 

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

@@ -13,13 +13,15 @@ import java.net.Inet6Address;
 import java.net.UnknownHostException;
 
 /**
+ * <p>
  * Quickly tests whether a given IP address matches an IP range. An
  * {@code IPMatcher} is initialized with a particular IP range specification.
  * Calls to {@link IPMatcher#match(String) match} method will then quickly
  * determine whether a given IP falls within that range.
+ * </p>
  * <p>
  * Supported range specifications are:
- * <p>
+ * </p>
  * <ul>
  * <li>Full IPv4 address, e.g. {@code 12.34.56.78}</li>
  * <li>Full IPv6 address, e.g. {@code 2001:18e8:3:171:218:8bff:fe2a:56a4}</li>

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

@@ -242,8 +242,9 @@ public class AuthorityValue {
     }
 
     /**
-     * Provides a string that will allow this AuthorityType to be recognized and provides information to create a new instance to be created using public AuthorityValue newInstance(String info).
+     * Provides a string that will allow this AuthorityType to be recognized and
-     * See the implementation of {@link com.atmire.org.dspace.authority.AuthorityValueGenerator#generateRaw(java.lang.String, java.lang.String) AuthorityValueGenerator#generateRaw(java.lang.String, java.lang.String)} for more details.
+     * provides information to create a new instance to be created using {@link #newInstance(String)}.
+     * See the implementation of {@link org.dspace.authority.AuthorityValueServiceImpl#generateRaw(java.lang.String, java.lang.String, java.lang.String)} for more details.
      * @return see {@link org.dspace.authority.service.AuthorityValueService#GENERATE AuthorityValueService.GENERATE}
      */
     public String generateString() {

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

@@ -37,6 +37,7 @@ public class AuthorizeException extends Exception
      * create an exception with only a message
      * 
      * @param message
+     *     Exception message
      */
     public AuthorizeException(String message)
     {

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

@@ -624,7 +624,7 @@ public class AuthorizeServiceImpl implements AuthorizeService
 
         List<Group> groups = new ArrayList<Group>();
         for (ResourcePolicy resourcePolicy : policies) {
-            if(resourcePolicy.getGroup() != null)
+            if (resourcePolicy.getGroup() != null)
             {
                 groups.add(resourcePolicy.getGroup());
             }
@@ -653,7 +653,7 @@ public class AuthorizeServiceImpl implements AuthorizeService
         if (CollectionUtils.isNotEmpty(policies))
         {
             return policies.iterator().next();
-        }else{
+        } else {
             return null;
         }
     }
@@ -664,16 +664,22 @@ public class AuthorizeServiceImpl implements AuthorizeService
      * have right on the collection. E.g., if the anonymous can access the collection policies are assigned to anonymous.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param embargoDate
+     *     embargo end date
      * @param reason
+     *     embargo reason
      * @param dso
+     *     DSpace object
      * @param owningCollection
+     *     collection to get group policies from
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      */
     @Override
     public void generateAutomaticPolicies(Context context, Date embargoDate,
-                                                 String reason, DSpaceObject dso, Collection owningCollection) throws SQLException, AuthorizeException
+        String reason, DSpaceObject dso, Collection owningCollection)
+        throws SQLException, AuthorizeException
     {
 
         if (embargoDate != null || (embargoDate == null && dso instanceof Bitstream))
@@ -714,7 +720,7 @@ public class AuthorizeServiceImpl implements AuthorizeService
 
     @Override
     public ResourcePolicy createResourcePolicy(Context context, DSpaceObject dso, Group group, EPerson eperson, int type, String rpType) throws SQLException, AuthorizeException {
-        if(group == null && eperson == null)
+        if (group == null && eperson == null)
         {
             throw new IllegalArgumentException("We need at least an eperson or a group in order to create a resource policy.");
         }

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

@@ -34,7 +34,8 @@ public class FixDefaultPolicies
 {
     /**
      * Command line interface to setPolicies - run to see arguments
-     * @param argv arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception

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

@@ -43,7 +43,8 @@ public class PolicySet
 
     /**
      * Command line interface to setPolicies - run to see arguments
-     * @param argv arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception
@@ -130,17 +131,30 @@ public class PolicySet
     /**
      *
      * @param c
+     *            current context
      * @param containerType
+     *            type, Constants.ITEM or Constants.COLLECTION
      * @param containerID
+     *            ID of container (DB primary key)
      * @param contentType
+     *            ID of container (DB primary key)
      * @param actionID
+     *            action ID (e.g. Constants.READ)
      * @param groupID
+     *            group ID (database key)
      * @param isReplace
+     *            if <code>true</code>, existing policies are removed first,
+     *            otherwise add to existing policies
      * @param clearOnly
+     *            if non-null, only process bitstreams whose names contain filter
      * @param name
+     *            policy name
      * @param description
+     *            policy descrption
      * @param startDate
+     *            policy start date
      * @param endDate
+     *            policy end date
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      */
@@ -166,7 +180,7 @@ public class PolicySet
      * @param contentType
      *            type (BUNDLE, ITEM, or BITSTREAM)
      * @param actionID
-     *            action ID
+     *            action ID (e.g. Constants.READ)
      * @param groupID
      *            group ID (database key)
      * @param isReplace
@@ -214,9 +228,13 @@ public class PolicySet
      * @param filter
      *            if non-null, only process bitstreams whose names contain filter
      * @param name
+     *            policy name
      * @param description
+     *            policy description
      * @param startDate
+     *            policy start date
      * @param endDate
+     *            policy end date
      * @throws SQLException if database error
      *             if database problem
      * @throws AuthorizeException if authorization error
@@ -250,7 +268,7 @@ public class PolicySet
                     {
 
                         // before create a new policy check if an identical policy is already in place
-                        if(!authorizeService.isAnIdenticalPolicyAlreadyInPlace(c, myitem, group, actionID, -1)){
+                        if (!authorizeService.isAnIdenticalPolicyAlreadyInPlace(c, myitem, group, actionID, -1)) {
                             // now add the policy
                             ResourcePolicy rp = resourcePolicyService.create(c);
 

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

@@ -96,6 +96,7 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
      * Return true if this object equals obj, false otherwise.
      *
      * @param obj
+     *     object to compare (eperson, group, start date, end date, ...)
      * @return true if ResourcePolicy objects are equal
      */
     @Override
@@ -144,23 +145,22 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
     {
         int hash = 7;
         hash = 19 * hash + this.getAction();
-        if(this.getGroup() != null)
+        if (this.getGroup() != null)
         {
             hash = 19 * hash + this.getGroup().hashCode();
-        }else{
+        } else {
             hash = 19 * hash + -1;
         }
 
-        if(this.getEPerson() != null)
+        if (this.getEPerson() != null)
         {
             hash = 19 * hash + this.getEPerson().hashCode();
-        }else{
+        } else {
             hash = 19 * hash + -1;
-
         }
 
-        hash = 19 * hash + (this.getStartDate() != null? this.getStartDate().hashCode():0);
+        hash = 19 * hash + (this.getStartDate() != null ? this.getStartDate().hashCode() : 0);
-        hash = 19 * hash + (this.getEndDate() != null? this.getEndDate().hashCode():0);
+        hash = 19 * hash + (this.getEndDate() != null ? this.getEndDate().hashCode() : 0);
         return hash;
     }
 
@@ -185,7 +185,7 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
     /**
      * set the action this policy authorizes
      *
-     * @param myid  action ID from <code>org.dspace.core.Constants</code>
+     * @param myid  action ID from {@link org.dspace.core.Constants#Constants Constants}
      */
     public void setAction(int myid)
     {
@@ -279,24 +279,24 @@ public class ResourcePolicy implements ReloadableEntity<Integer> {
         this.endDate = d;
     }
 
-    public String getRpName(){
+    public String getRpName() {
         return rpname;
     }
-    public void setRpName(String name){
+    public void setRpName(String name) {
         this.rpname = name;
     }
 
-    public String getRpType(){
+    public String getRpType() {
         return rptype;
     }
-    public void setRpType(String type){
+    public void setRpType(String type) {
         this.rptype = type;
     }
 
-    public String getRpDescription(){
+    public String getRpDescription() {
         return rpdescription;
     }
-    public void setRpDescription(String description){
+    public void setRpDescription(String description) {
         this.rpdescription = description;
     }
 }

dspace-api/src/main/java/org/dspace/authorize/service/AuthorizeService.java

@@ -47,7 +47,8 @@ public interface AuthorizeService {
      *     <code>org.dspace.core.Constants</code>
      * @throws AuthorizeException if any one of the specified actions cannot be 
      *     performed by the current user on the given object.
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void authorizeAnyOf(Context c, DSpaceObject o, int[] actions) throws AuthorizeException, SQLException;
 
@@ -59,8 +60,11 @@ public interface AuthorizeService {
      * @param c context
      * @param o a DSpaceObject
      * @param action action to perform from <code>org.dspace.core.Constants</code>
-     * @throws AuthorizeException if the user is denied
+     * @throws AuthorizeException
-     * @throws SQLException if database error
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void authorizeAction(Context c, DSpaceObject o, int action) throws AuthorizeException, SQLException;
 
@@ -75,8 +79,11 @@ public interface AuthorizeService {
      *         flag to say if ADMIN action on the current object or parent
      *         object can be used
      * @param action action to perform from <code>org.dspace.core.Constants</code>
-     * @throws AuthorizeException if the user is denied
+     * @throws AuthorizeException
-     * @throws SQLException if database error
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void authorizeAction(Context c, DSpaceObject o, int action, boolean useInheritance)
             throws AuthorizeException, SQLException;
@@ -93,8 +100,11 @@ public interface AuthorizeService {
      *         flag to say if ADMIN action on the current object or parent
      *         object can be used
      * @param action action to perform from <code>org.dspace.core.Constants</code>
-     * @throws AuthorizeException if the user is denied
+     * @throws AuthorizeException
-     * @throws SQLException if database error
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void authorizeAction(Context c, EPerson e, DSpaceObject o, int action, boolean useInheritance)
             throws AuthorizeException, SQLException;
@@ -109,7 +119,8 @@ public interface AuthorizeService {
      *         <code>org.dspace.core.Constants</code>
      * @return {@code true} if the current user in the context is
      *         authorized to perform the given action on the given object
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean authorizeActionBoolean(Context c, DSpaceObject o, int a) throws SQLException;
 
@@ -126,7 +137,8 @@ public interface AuthorizeService {
      *         object can be used
      * @return {@code true} if the current user in the context is
      *         authorized to perform the given action on the given object
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean authorizeActionBoolean(Context c, DSpaceObject o, int a, boolean useInheritance) throws SQLException;
     
@@ -144,7 +156,8 @@ public interface AuthorizeService {
      *         object can be used
      * @return {@code true} if the requested user is
      *         authorized to perform the given action on the given object
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean authorizeActionBoolean(Context c, EPerson e, DSpaceObject o, int a, boolean useInheritance) throws SQLException;
 
@@ -163,7 +176,8 @@ public interface AuthorizeService {
      *         method
      * @return {@code true} if user has administrative privileges on the
      *         given DSpace object
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean isAdmin(Context c, DSpaceObject o) throws SQLException;
 
@@ -176,7 +190,8 @@ public interface AuthorizeService {
      * @param c current context
      * @return {@code true} if user is an admin or ignore authorization
      *         flag set
-     * @throws SQLException if database error
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean isAdmin(Context c) throws SQLException;
     
@@ -437,6 +452,7 @@ public interface AuthorizeService {
      * specified object to the new action (toPolicy)
      * 
      * @param context
+     *     The relevant DSpace Context.
      * @param dso
      *     the dspace object
      * @param fromAction
@@ -444,7 +460,10 @@ public interface AuthorizeService {
      * @param toAction
      *     the new action to set
      * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     void switchPoliciesAction(Context context, DSpaceObject dso, int fromAction, int toAction)
             throws SQLException, AuthorizeException;

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

@@ -155,6 +155,7 @@ public interface BrowseDAO
      * to only items or values within items that appear in the given container.
      *
      * @param containerID
+     *     community/collection internal ID (UUID)
      */
     public void setContainerID(UUID containerID);
 
@@ -234,7 +235,7 @@ public interface BrowseDAO
      * normal browse operations can be completed without it.  The default is -1, which
      * means do not offset.
      *
-     * @return      the offset
+     * @return      paging offset
      */
     public int getOffset();
 
@@ -245,6 +246,7 @@ public interface BrowseDAO
      * means do not offset.
      *
      * @param offset
+     *     paging offset
      */
     public void setOffset(int offset);
 

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

@@ -139,6 +139,7 @@ public class BrowseInfo
      * set the number of metadata fields at which to truncate with "et al"
      *
      * @param etAl
+     *     the number of metadata fields at which to truncate with "et al"
      */
     public void setEtAl(int etAl)
     {

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

@@ -67,7 +67,7 @@ public class DailyReportEmailer
     public void sendReport(File attachment, int numberOfBitstreams) 
             throws IOException, javax.mail.MessagingException 
     { 
-        if(numberOfBitstreams > 0)
+        if (numberOfBitstreams > 0)
         {
             String hostname = ConfigurationManager.getProperty("dspace.hostname");
             Email email = new Email();
@@ -83,7 +83,6 @@ public class DailyReportEmailer
      * Allows users to have email sent to them. The default is to send all
      * reports in one email
      * 
-     * @param args
      * <dl>
      *   <dt>-h</dt>
      *   <dd>help</dd>
@@ -99,6 +98,7 @@ public class DailyReportEmailer
      *   <dd>Send all reports in one email</dd>
      * </dl>
      * 
+     * @param args the command line arguments given
      */
     public static void main(String[] args)
     {
@@ -110,25 +110,17 @@ public class DailyReportEmailer
         Options options = new Options();
 
         options.addOption("h", "help", false, "Help");
-        options
+        options.addOption("d", "Deleted", false,
-                .addOption("d", "Deleted", false,
             "Send E-mail report for all bitstreams set as deleted for today");
-        options
+        options.addOption("m", "Missing", false,
-                .addOption("m", "Missing", false,
             "Send E-mail report for all bitstreams not found in assetstore for today");
-        options
+        options.addOption("c", "Changed", false,
-                .addOption(
-                        "c",
-                        "Changed",
-                        false,
             "Send E-mail report for all bitstreams where checksum has been changed for today");
-        options.addOption("a", "All", false, "Send all E-mail reports");
+        options.addOption("a", "All", false,
-
+            "Send all E-mail reports");
         options.addOption("u", "Unchecked", false,
             "Send the Unchecked bitstream report");
-
+        options.addOption("n", "Not Processed", false,
-        options
-                .addOption("n", "Not Processed", false,
             "Send E-mail report for all bitstreams set to longer be processed for today");
 
         try
@@ -147,19 +139,11 @@ public class DailyReportEmailer
             HelpFormatter myhelp = new HelpFormatter();
 
             myhelp.printHelp("Checksum Reporter\n", options);
-            System.out
+            System.out.println("\nSend Deleted bitstream email report: DailyReportEmailer -d");
-                    .println("\nSend Deleted bitstream email report: DailyReportEmailer -d");
+            System.out.println("\nSend Missing bitstreams email report: DailyReportEmailer -m");
-            System.out
+            System.out.println("\nSend Checksum Changed email report: DailyReportEmailer -c");
-                    .println("\nSend Missing bitstreams email report: DailyReportEmailer -m");
+            System.out.println("\nSend bitstream not to be processed email report: DailyReportEmailer -n");
-            System.out
+            System.out.println("\nSend Un-checked bitstream report: DailyReportEmailer -u");
-                    .println("\nSend Checksum Changed email report: DailyReportEmailer -c");
-
-            System.out
-                    .println("\nSend bitstream not to be processed email report: DailyReportEmailer -n");
-
-            System.out
-                    .println("\nSend Un-checked bitstream report: DailyReportEmailer -u");
-
             System.out.println("\nSend All email reports: DailyReportEmailer");
             System.exit(0);
         }
@@ -208,27 +192,17 @@ public class DailyReportEmailer
 
             if ((line.hasOption("a")) || (line.getOptions().length == 0))
             {
-                writer
+                writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                        .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
+                numBitstreams += reporter.getDeletedBitstreamReport(context, yesterday, tomorrow, writer);
-                numBitstreams += reporter.getDeletedBitstreamReport(context, yesterday,
+                writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                        tomorrow, writer);
+                numBitstreams += reporter.getChangedChecksumReport(context, yesterday, tomorrow, writer);
-                writer
+                writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                        .write("\n--------------------------------- Report Spacer ---------------------------\n\n");
+                numBitstreams += reporter.getBitstreamNotFoundReport(context, yesterday, tomorrow, writer);
-                numBitstreams += reporter.getChangedChecksumReport(context, yesterday,
+                writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                        tomorrow, writer);
+                numBitstreams += reporter.getNotToBeProcessedReport(context, yesterday, tomorrow, writer);
-                writer
+                writer.write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                        .write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                numBitstreams += reporter.getBitstreamNotFoundReport(context, yesterday,
-                        tomorrow, writer);
-                writer
-                        .write("\n--------------------------------- Report Spacer ---------------------------\n\n");
-                numBitstreams += reporter.getNotToBeProcessedReport(context, yesterday,
-                        tomorrow, writer);
-                writer
-                        .write("\n--------------------------------- Report Spacer ---------------------------\n\n");
                 numBitstreams += reporter.getUncheckedBitstreamsReport(context, writer);
-                writer
+                writer.write("\n--------------------------------- End Report ---------------------------\n\n");
-                        .write("\n--------------------------------- End Report ---------------------------\n\n");
                 writer.flush();
                 writer.close();
                 emailer.sendReport(report, numBitstreams);
@@ -237,8 +211,7 @@ public class DailyReportEmailer
             {
                 if (line.hasOption("d"))
                 {
-                    writer
+                    writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                            .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter.getDeletedBitstreamReport(context,
                         yesterday, tomorrow, writer);
                     writer.flush();
@@ -248,8 +221,7 @@ public class DailyReportEmailer
 
                 if (line.hasOption("m"))
                 {
-                    writer
+                    writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                            .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter.getBitstreamNotFoundReport(context,
                         yesterday, tomorrow, writer);
                     writer.flush();
@@ -259,8 +231,7 @@ public class DailyReportEmailer
 
                 if (line.hasOption("c"))
                 {
-                    writer
+                    writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                            .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter.getChangedChecksumReport(context,
                         yesterday, tomorrow, writer);
                     writer.flush();
@@ -270,8 +241,7 @@ public class DailyReportEmailer
 
                 if (line.hasOption("n"))
                 {
-                    writer
+                    writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                            .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter.getNotToBeProcessedReport(context,
                         yesterday, tomorrow, writer);
                     writer.flush();
@@ -281,8 +251,7 @@ public class DailyReportEmailer
 
                 if (line.hasOption("u"))
                 {
-                    writer
+                    writer.write("\n--------------------------------- Begin Reporting ------------------------\n\n");
-                            .write("\n--------------------------------- Begin Reporting ------------------------\n\n");
                     numBitstreams += reporter
                         .getUncheckedBitstreamsReport(context, writer);
                     writer.flush();
@@ -294,9 +263,10 @@ public class DailyReportEmailer
         catch (MessagingException | SQLException | IOException e)
         {
             log.fatal(e);
-        } finally
+        }
+        finally
         {
-            if(context != null && context.isValid())
+            if (context != null && context.isValid())
             {
                 context.abort();
             }

dspace-api/src/main/java/org/dspace/checker/dao/ChecksumHistoryDAO.java

@@ -30,8 +30,11 @@ public interface ChecksumHistoryDAO extends GenericDAO<ChecksumHistory> {
      * the specified result code.
      *
      * @param context
-     * @param retentionDate row must be older than this to be deleted.
+     *     The relevant DSpace Context.
-     * @param checksumResultCode row must have this result to be deleted.
+     * @param retentionDate
+     *     row must be older than this to be deleted.
+     * @param checksumResultCode
+     *     row must have this result to be deleted.
      * @return number of rows deleted.
      * @throws SQLException if database error
      */
@@ -41,7 +44,9 @@ public interface ChecksumHistoryDAO extends GenericDAO<ChecksumHistory> {
      * Delete all ChecksumHistory rows for the given Bitstream.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param bitstream
+     *     which bitstream's checksums to delete
      * @throws SQLException if database error
      */
     public void deleteByBitstream(Context context, Bitstream bitstream) throws SQLException;

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

@@ -345,6 +345,7 @@ public class Bitstream extends DSpaceObject implements DSpaceObjectLegacySupport
      * bitstream is uncertain, and the format is set to "unknown."
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param desc
      *     the user's description of the format
      * @throws SQLException if database error

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

@@ -379,12 +379,13 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
      * Get the value of a metadata field
      *
      * @param collection
+     *     which collection to operate on
      * @param field
      *     the name of the metadata field to get
      *
      * @return the value of the metadata field
      *
-     * @exception IllegalArgumentException
+     * @throws IllegalArgumentException
      *                if the requested metadata field doesn't exist
      */
     @Override

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

@@ -594,7 +594,6 @@ public class DCDate
      * Get a date representing the current instant in time.
      *
      * @return a DSpaceDate object representing the current instant.
-
      */
     public static DCDate getCurrent()
     {
@@ -607,9 +606,8 @@ public class DCDate
      *
      * @param m
      *     the month number
-     *
      * @param locale
-        * 
+     *     which locale to render the month name in
      * @return the month name.
      */
     public static String getMonthName(int m, Locale locale)

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

@@ -149,8 +149,8 @@ public class ItemComparator implements Comparator, Serializable
     }
 
     /**
-     * @param first
+     * @param first first operand
-     * @param second
+     * @param second second operand
      * @return true if the first string is equal to the second. Either or both
      * may be null.
      */
@@ -224,7 +224,8 @@ public class ItemComparator implements Comparator, Serializable
 
     /**
      * Normalize the title of a Metadatum.
-     * @param value
+     * 
+     * @param value metadata value
      * @return normalized title
      */
     protected String normalizeTitle(MetadataValue value)

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

@@ -932,10 +932,13 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
 
     /**
      * Check if the item is an inprogress submission
+     * 
      * @param context
-     * @param item
+     *     The relevant DSpace Context.
+     * @param item item to check
      * @return <code>true</code> if the item is an inprogress submission, i.e. a WorkspaceItem or WorkflowItem
      * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public boolean isInProgressSubmission(Context context, Item item) throws SQLException {
         return workspaceItemService.findByItem(context, item) != null
@@ -943,7 +946,7 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
     }
     
     /*
-    With every finished submission a bunch of resource policy entries with have null value for the dspace_object column are generated in the database.
+    With every finished submission a bunch of resource policy entries which have null value for the dspace_object column are generated in the database.
 prevent the generation of resource policy entry values with null dspace_object as value
 
     */
@@ -952,10 +955,16 @@ prevent the generation of resource policy entry values with null dspace_object a
      * Add the default policies, which have not been already added to the given DSpace object
      * 
      * @param context
+     *     The relevant DSpace Context.
      * @param dso
+     *     The DSpace Object to add policies to
      * @param defaultCollectionPolicies
+     *     list of policies
      * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      * @throws AuthorizeException 
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     protected void addDefaultPoliciesNotInPlace(Context context, DSpaceObject dso, List<ResourcePolicy> defaultCollectionPolicies) throws SQLException, AuthorizeException
     {
@@ -983,8 +992,12 @@ prevent the generation of resource policy entry values with null dspace_object a
      * @param value field value or Item.ANY to match any value
      * @return an iterator over the items matching that authority value
      * @throws SQLException if database error
+     *     An exception that provides information on a database access error or other errors.
      * @throws AuthorizeException if authorization error
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      * @throws IOException if IO error
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
      *
      */
     @Override

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

@@ -57,10 +57,15 @@ public class LicenseUtils
      * LicenseArgumentFormatter based on his type (map key)
      * 
      * @param locale
+     *     Formatter locale
      * @param collection
+     *     collection to get license from
      * @param item
+     *     the item object of the license
      * @param eperson
+     *     EPerson to get firstname, lastname and email from
      * @param additionalInfo
+     *     additional template arguments beyond 0-6
      * @return the license text obtained substituting the provided argument in
      *         the license template
      */
@@ -104,9 +109,13 @@ public class LicenseUtils
      * supplying {@code null} for the additionalInfo argument)
      *
      * @param locale
+     *     Formatter locale
      * @param collection
+     *     collection to get license from
      * @param item
+     *     the item object of the license
      * @param eperson
+     *     EPerson to get firstname, lastname and email from
      * @return the license text, with no custom substitutions.
      */
     public static String getLicenseText(Locale locale, Collection collection,

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

@@ -27,6 +27,7 @@ public class NonUniqueMetadataException extends Exception
      * Create an exception with only a message
      * 
      * @param message
+     *     message string
      */
     public NonUniqueMetadataException(String message)
     {

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

@@ -57,9 +57,24 @@ public class CrosswalkMetadataValidator {
     /**
      * Scans metadata for elements not defined in this DSpace instance. It then takes action based
      * on a configurable parameter (fail, ignore, add).
+     *
+     * @param context
+     *     The relevant DSpace Context.
+     * @param schema metadata field schema
+     * @param element metadata field element
+     * @param qualifier metadata field qualifier
+     * @param forceCreate if true, force addinga schema or metadata field
+     * @return metadata field
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
+     * @throws CrosswalkException
+     *     Superclass for more-specific crosswalk exceptions.
      */
     public MetadataField checkMetadata(Context context, String schema, String element, String qualifier, boolean forceCreate) throws SQLException, AuthorizeException, CrosswalkException {
-        if(!validatedBefore(schema, element, qualifier)) {
+        if (!validatedBefore(schema, element, qualifier)) {
             // Verify that the schema exists
             MetadataSchema mdSchema = metadataSchemaService.find(context, schema);
             MetadataField mdField = null;

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

@@ -402,9 +402,13 @@ public class METSRightsCrosswalk
      * Ingest a whole XML document, starting at specified root.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param dso
+     *     DSpace object to ingest
      * @param root
+     *     root element
      * @param createMissingMetadataFields
+     *     whether to create missing fields
      * @throws CrosswalkException if crosswalk error
      * @throws IOException if IO error
      * @throws SQLException if database error

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

@@ -311,7 +311,7 @@ public class MODSDisseminationCrosswalk extends SelfNamedPlugin
     /**
      * Returns object's metadata in MODS format, as List of XML structure nodes.
      * @param context context
-     * @throws org.dspace.content.crosswalk.CrosswalkException
+     * @throws CrosswalkException if crosswalk error
      * @throws IOException if IO error
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error

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

@@ -32,6 +32,7 @@ public interface ParameterizedDisseminationCrosswalk
      * <p>
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param dso the DSpace Object whose metadata to export.
      * @param parameters
      *  names and values of parameters to be passed into the transform.

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

@@ -50,7 +50,7 @@ import org.slf4j.LoggerFactory;
  * Configurable XSLT-driven dissemination Crosswalk
  * <p>
  * See the XSLTCrosswalk superclass for details on configuration.
- * <p>
+ * </p>
  * <h3>Additional Configuration of Dissemination crosswalk:</h3>
  * The disseminator also needs to be configured with an XML Namespace
  * (including prefix and URI) and an XML Schema for output format.  This
@@ -524,7 +524,8 @@ public class XSLTDisseminationCrosswalk
     /**
      * Simple command-line rig for testing the DIM output of a stylesheet.
      * Usage:  {@code java XSLTDisseminationCrosswalk  <crosswalk-name> <handle> [output-file]}
-     * @param argv arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception

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

@@ -293,7 +293,8 @@ public class XSLTIngestionCrosswalk
     /**
      * Simple command-line rig for testing the DIM output of a stylesheet.
      * Usage: {@code java XSLTIngestionCrosswalk  <crosswalk-name> <input-file>}
-     * @param argv arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public static void main(String[] argv) throws Exception

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

@@ -15,7 +15,7 @@ import org.dspace.core.GenericDAO;
  * All DSpaceObject DAO classes should implement this class since it ensures that the T object is of type DSpaceObject
  *
  * @author kevinvandevelde at atmire.com
- * @param <T>
+ * @param <T> some implementation of DSpaceObject
  */
 public interface DSpaceObjectDAO<T extends DSpaceObject> extends GenericDAO<T> {
 }

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

@@ -17,7 +17,7 @@ import java.sql.SQLException;
  * to identify DSpaceObjects prior to DSpace 6.0
  *
  * @author kevinvandevelde at atmire.com
- * @param <T>
+ * @param <T> some implementation of DSpaceObject
  */
 public interface DSpaceObjectLegacySupportDAO<T extends DSpaceObject> extends DSpaceObjectDAO<T> {
 

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

@@ -106,6 +106,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
     protected final WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
 
     /**
+     * <p>
      * An instance of ZipMdrefManager holds the state needed to retrieve the
      * contents of an external metadata stream referenced by an
      * <code>mdRef</code> element in a Zipped up METS manifest.
@@ -244,7 +245,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
                     license);
 
             //if ingestion was successful
-            if(dso!=null)
+            if (dso!=null)
             {
                 // Log whether we finished an ingest (create new obj) or a restore
                 // (restore previously existing obj)
@@ -338,7 +339,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
                 // Retrieve the manifest file entry (named mets.xml)
                 ZipEntry manifestEntry = zip.getEntry(METSManifest.MANIFEST_FILE);
 
-                if(manifestEntry!=null)
+                if (manifestEntry!=null)
                 {
                     // parse the manifest and sanity-check it.
                     manifest = METSManifest.create(zip.getInputStream(manifestEntry),
@@ -404,7 +405,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             catch(UnsupportedOperationException e)
             {
                 //If user specified to skip item ingest if any "missing parent" error message occur
-                if(params.getBooleanProperty("skipIfParentMissing", false))
+                if (params.getBooleanProperty("skipIfParentMissing", false))
                 {
                     //log a warning instead of throwing an error
                     log.warn(LogManager.getHeader(context, "package_ingest",
@@ -518,7 +519,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             
             // Finally, if item is still in the workspace, then we actually need
             // to install it into the archive & assign its handle.
-            if(wsi!=null)
+            if (wsi!=null)
             {
                 // Finish creating the item. This actually assigns the handle,
                 // and will either install item immediately or start a workflow, based on params
@@ -531,7 +532,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             // Add logo if one is referenced from manifest
             addContainerLogo(context, dso, manifest, pkgFile, params);
 
-            if(type==Constants.COLLECTION)
+            if (type==Constants.COLLECTION)
             {
                 //Add template item if one is referenced from manifest (only for Collections)
                 addTemplateItem(context, dso, manifest, pkgFile, params, callback);
@@ -670,11 +671,11 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
 
             // have subclass manage license since it may be extra package file.
             Collection owningCollection = (Collection) ContentServiceFactory.getInstance().getDSpaceObjectService(dso).getParentObject(context, dso);
-            if(owningCollection == null)
+            if (owningCollection == null)
             {
                 //We are probably dealing with an item that isn't archived yet
                 InProgressSubmission inProgressSubmission = workspaceItemService.findByItem(context, item);
-                if(inProgressSubmission == null)
+                if (inProgressSubmission == null)
                 {
                     inProgressSubmission = WorkflowServiceFactory.getInstance().getWorkflowItemService().findByItem(context, item);
                 }
@@ -817,7 +818,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
 
              // Set bitstream sequence id, if known
             String seqID = mfile.getAttributeValue("SEQ");
-            if(seqID!=null && !seqID.isEmpty())
+            if (seqID!=null && !seqID.isEmpty())
                 bitstream.setSequenceID(Integer.parseInt(seqID));
             
             // crosswalk this bitstream's administrative metadata located in
@@ -1044,7 +1045,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             CrosswalkException, PackageValidationException
     {
         //Template items only valid for collections
-        if(dso.getType()!=Constants.COLLECTION)
+        if (dso.getType()!=Constants.COLLECTION)
             return;
         
         Collection collection = (Collection) dso;
@@ -1052,18 +1053,18 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
         //retrieve list of all <div>s representing child objects from manifest
         List childObjList = manifest.getChildObjDivs();
 
-        if(childObjList!=null && !childObjList.isEmpty())
+        if (childObjList!=null && !childObjList.isEmpty())
         {
             Element templateItemDiv = null;
 
             Iterator childIterator = childObjList.iterator();
             //Search for the child with a type of "DSpace ITEM Template"
-            while(childIterator.hasNext())
+            while (childIterator.hasNext())
             {
                 Element childDiv = (Element) childIterator.next();
                 String childType = childDiv.getAttributeValue("TYPE");
                 //should be the only child of type "ITEM" with "Template" for a suffix
-                if(childType.contains(Constants.typeText[Constants.ITEM]) &&
+                if (childType.contains(Constants.typeText[Constants.ITEM]) &&
                    childType.endsWith(AbstractMETSDisseminator.TEMPLATE_TYPE_SUFFIX))
                 {
                     templateItemDiv = childDiv;
@@ -1072,11 +1073,11 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             }
 
             //If an Template Item was found, create it with the specified metadata
-            if(templateItemDiv!=null)
+            if (templateItemDiv!=null)
             {
                 //make sure this templateItemDiv is associated with one or more dmdSecs
                 String templateDmdIds = templateItemDiv.getAttributeValue("DMDID");
-                if(templateDmdIds!=null)
+                if (templateDmdIds!=null)
                 {
                     //create our template item & get a reference to it
                     itemService.createTemplateItem(context, collection);
@@ -1193,7 +1194,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
                         null);
 
                 //if ingestion was successful
-                if(dso!=null)
+                if (dso!=null)
                 {
                     // Log that we created an object
                     log.info(LogManager.getHeader(context, "package_replace",
@@ -1222,7 +1223,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             }
 
             //if ingest/restore/replace successful
-            if(dso!=null)
+            if (dso!=null)
             {
                 // Check if the Packager is currently running recursively.
                 // If so, this means the Packager will attempt to recursively
@@ -1547,14 +1548,16 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
      * 
      * @param context the DSpace context
      * @param dso DSpace Object
-     * @param manifest the METSManifest
+     * @param manifest
+     *     the METSManifest
      * @param callback
-*            the MdrefManager (manages all external metadata files
+     *     the MdrefManager (manages all external metadata files
-*            referenced by METS <code>mdref</code> elements)
+     *     referenced by METS <code>mdref</code> elements)
      * @param dmds
-*            array of Elements, each a METS <code>dmdSec</code> that
+     *     array of Elements, each a METS <code>dmdSec</code> that
-*            applies to the Item as a whole.
+     *     applies to the Item as a whole.
      * @param params
+     *     Packager Parameters
      * @throws CrosswalkException if crosswalk error
      * @throws PackageValidationException if package validation error
      * @throws IOException if IO error
@@ -1590,6 +1593,7 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
      * @param license
      *     optional user-supplied Deposit License text (may be null)
      * @param params
+     *     Packager Parameters
      * @throws PackageValidationException if package validation error
      * @throws IOException if IO error
      * @throws SQLException if database error

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

@@ -454,6 +454,7 @@ public class DSpaceAIPDisseminator extends AbstractMETSDisseminator
      * @throws IOException if IO error
      * @throws AuthorizeException if authorization error
      * @throws MetsException
+     *     METS Java toolkit exception class.
      */
     @Override
     public void addStructMap(Context context, DSpaceObject dso,

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

@@ -95,6 +95,21 @@ public class DSpaceAIPIngester
      * 3. If (1) or (2) succeeds, crosswalk it and ignore all other DMDs with
      *    same GROUPID<br>
      * 4. Crosswalk remaining DMDs not eliminated already.
+     *
+     * @param context
+     *     The relevant DSpace Context.
+     * @param dso
+     *     DSpace object
+     * @param manifest
+     *     the METSManifest
+     * @param callback
+     *     the MdrefManager (manages all external metadata files
+     *     referenced by METS <code>mdref</code> elements)
+     * @param dmds
+     *     array of Elements, each a METS <code>dmdSec</code> that
+     *     applies to the Item as a whole.
+     * @param params
+     *     Packager Parameters
      * @throws PackageValidationException validation error
      * @throws CrosswalkException if crosswalk error
      * @throws IOException if IO error
@@ -198,6 +213,15 @@ public class DSpaceAIPIngester
      * license supplied by explicit argument next, else use collection's
      * default deposit license.
      * Normally the rightsMD crosswalks should provide a license.
+     *
+     * @param context
+     *     The relevant DSpace Context.
+     * @param item
+     *     item to add license to
+     * @param collection
+     *     collection to get the default license from
+     * @param params
+     *     Packager Parameters
      * @throws PackageValidationException validation error
      * @throws IOException if IO error
      * @throws SQLException if database error
@@ -211,7 +235,7 @@ public class DSpaceAIPIngester
     {
         boolean newLicense = false;
 
-        if(!params.restoreModeEnabled())
+        if (!params.restoreModeEnabled())
         {
             //AIP is not being restored/replaced, so treat it like a SIP -- every new SIP needs a new license
             newLicense = true;
@@ -225,7 +249,7 @@ public class DSpaceAIPIngester
             newLicense = true;
         }
 
-        if(newLicense)
+        if (newLicense)
         {
             PackageUtils.addDepositLicense(context, license, item, collection);
         }
@@ -233,19 +257,30 @@ public class DSpaceAIPIngester
 
     /**
      * Last change to fix up a DSpace Object.
-     * <P>
+     * <p>
      * For AIPs, if the object is an Item, we may want to make sure all of its
      * metadata fields already exist in the database (otherwise, the database
      * will throw errors when we attempt to save/update the Item)
+     * </p>
      *
-     * @param context DSpace Context
+     * @param context
-     * @param dso DSpace object
+     *     The relevant DSpace Context.
-     * @param params Packager Parameters
+     * @param dso
-     * @throws org.dspace.content.packager.PackageValidationException
+     *     DSpace object
-     * @throws java.sql.SQLException
+     * @param params
-     * @throws org.dspace.content.crosswalk.CrosswalkException
+     *     Packager Parameters
-     * @throws java.io.IOException
+     * @throws PackageValidationException
-     * @throws org.dspace.authorize.AuthorizeException
+     *     Failure when importing or exporting a package
+     *     caused by invalid unacceptable package format or contents
+     * @throws CrosswalkException
+     *     Superclass for more-specific crosswalk exceptions.
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     @Override
     public void finishObject(Context context, DSpaceObject dso, PackageParameters params)
@@ -253,7 +288,7 @@ public class DSpaceAIPIngester
          AuthorizeException, SQLException, IOException
     {
         //Metadata fields are now required before adding, so this logic isn't needed anymore
-        /*if(dso.getType()==Constants.ITEM)
+        /*if (dso.getType()==Constants.ITEM)
         {
             // Check if 'createMetadataFields' option is enabled (default=true)
             // This defaults to true as by default we should attempt to restore as much metadata as we can.

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

@@ -8,15 +8,18 @@
 package org.dspace.content.packager;
 
 /**
+ * <p>
  * This represents a failure when importing or exporting a package
  * caused by invalid unacceptable package format or contents; for
  * example, missing files that were mentioned in the manifest, or
  * extra files not in manifest, or lack of a manifest.
+ * </p>
  * <p>
  * When throwing a PackageValidationException, be sure the message
  * includes enough specific information to let the end user diagnose
  * the problem, i.e. what files appear to be missing from the manifest
  * or package, or the details of a checksum error on a file.
+ * </p>
  *
  * @author Larry Stone
  * @version $Revision$

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

@@ -430,6 +430,7 @@ public class RoleIngester implements PackageIngester
      * @param context DSpace Context
      * @param parent the Parent DSpaceObject
      * @param params package params
+     * @param stream input stream with the roles
      * @throws PackageException if packaging error
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error

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

@@ -77,8 +77,11 @@ public interface CollectionService extends DSpaceObjectService<Collection>, DSpa
     /**
      * Get all collections in the system. Adds support for limit and offset.
      * @param context
+     *     The relevant DSpace Context.
      * @param limit
+     *     paging limit
      * @param offset
+     *     paging offset
      * @return List of Collections
      * @throws SQLException if database error
      */

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

@@ -104,7 +104,7 @@ public interface CommunityService extends DSpaceObjectService<Community>, DSpace
      *
      * @return the value of the metadata field
      *
-     * @exception IllegalArgumentException
+     * @throws IllegalArgumentException
      *                if the requested metadata field doesn't exist
      * @deprecated
      */
@@ -123,9 +123,9 @@ public interface CommunityService extends DSpaceObjectService<Community>, DSpace
      * @param value
      *            value to set the field to
      *
-     * @exception IllegalArgumentException
+     * @throws IllegalArgumentException
      *                if the requested metadata field doesn't exist
-     * @exception java.util.MissingResourceException
+     * @throws MissingResourceException if resource missing
      * @throws SQLException if database error
      * @deprecated
      */
@@ -192,7 +192,12 @@ public interface CommunityService extends DSpaceObjectService<Community>, DSpace
     /**
      * Return an array of parent communities of this collection.
      *
+     * @param context
+     *     The relevant DSpace Context.
+     * @param collection
+     *            collection to check
      * @return an array of parent communities
+     * @throws SQLException if database error
      */
     public List<Community> getAllParents(Context context, Collection collection) throws SQLException;
 

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

@@ -181,7 +181,7 @@ public interface DSpaceObjectService<T extends DSpaceObject> {
      *
      * @return the value of the metadata field (or null if the column is an SQL NULL)
      *
-     * @exception IllegalArgumentException
+     * @throws IllegalArgumentException
      *                if the requested metadata field doesn't exist
      */
     public String getMetadata(T dSpaceObject, String value);

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

@@ -53,7 +53,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      *
      * @param context DSpace context object
      * @param collection Collection (parent)
-     * @return Item
+     * @return empty template item for this collection
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      */
@@ -96,8 +96,10 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
 
     /**
      * Retrieve the list of items submitted by eperson, ordered by recently submitted, optionally limitable
-     * @param context context
+     *
-     * @param eperson eperson
+     * @param context DSpace context object
+     * @param eperson
+     *            the submitter
      * @param limit a positive integer to limit, -1 or null for unlimited
      * @return an iterator over the items submitted by eperson
      * @throws SQLException if database error
@@ -128,7 +130,8 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
 
     /**
      * Get all Items installed or withdrawn, discoverable, and modified since a Date.
-     * @param context context
+     *
+     * @param context DSpace context object
      * @param since earliest interesting last-modified date, or null for no date test.
      * @return an iterator over the items in the collection.
      * @throws SQLException if database error
@@ -148,7 +151,8 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
 
     /**
      * See whether this Item is contained by a given Collection.
-     * @param item Item
+     *
+     * @param item item to check
      * @param collection Collection (parent
      * @return true if {@code collection} contains this Item.
      * @throws SQLException if database error
@@ -161,7 +165,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * communities of the owning collections.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to check
      * @return the communities this item is in.
      * @throws SQLException if database error
      */
@@ -171,7 +175,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
     /**
      * Get the bundles matching a bundle name (name corresponds roughly to type)
      *
-     * @param item Item
+     * @param item item to check
      * @param name
      *            name of bundle (ORIGINAL/TEXT/THUMBNAIL)
      * @throws SQLException if database error
@@ -184,7 +188,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Add an existing bundle to this item. This has immediate effect.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to add the bundle to
      * @param bundle
      *            the bundle to add
      * @throws SQLException if database error
@@ -210,9 +214,10 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
     /**
      * Remove all bundles linked to this item. This may result in the bundle being deleted, if the
      * bundle is orphaned.
+     *
      * @param context DSpace context object
      * @param item
-     *            the item from which to remove our bundles
+     *            the item from which to remove all bundles
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      * @throws IOException if IO error
@@ -224,7 +229,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * method for the most common use.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to create bitstream on
      * @param is
      *            the stream to create the new bitstream from
      * @param name
@@ -241,7 +246,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Convenience method, calls createSingleBitstream() with name "ORIGINAL"
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to create bitstream on
      * @param is
      *            InputStream
      * @return created bitstream
@@ -256,8 +261,9 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Get all non-internal bitstreams in the item. This is mainly used for
      * auditing for provenance messages and adding format.* DC values. The order
      * is indeterminate.
+     *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to check
      * @return non-internal bitstreams.
      * @throws SQLException if database error
      */
@@ -271,7 +277,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * This method is used by the org.dspace.submit.step.LicenseStep class
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to remove DSpace license from
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      * @throws IOException if IO error
@@ -283,7 +289,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Remove all licenses from an item - it was rejected
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to remove all licenses from
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      * @throws IOException if IO error
@@ -295,7 +301,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * and metadata are not deleted, but it is not publicly accessible.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to withdraw
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      */
@@ -306,7 +312,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Reinstate a withdrawn item
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item withdrawn item to reinstate
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
      */
@@ -315,7 +321,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
     /**
      * Return true if this Collection 'owns' this item
      *
-     * @param item Item
+     * @param item item to check
      * @param collection
      *            Collection
      * @return true if this Collection owns this item
@@ -327,7 +333,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * policies
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to replace policies on
      * @param newpolicies -
      *            this will be all of the new policies for the item and its
      *            contents
@@ -342,7 +348,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * them with a new list of policies
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to replace policies on
      * @param newpolicies -
      *            this will be all of the new policies for the bundle and
      *            bitstream contents
@@ -358,7 +364,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * to a given Group
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to remove group policies from
      * @param group
      *            Group referenced by policies that needs to be removed
      * @throws SQLException if database error
@@ -372,7 +378,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * the collection.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to reset policies on
      * @param collection
      *            Collection
      * @throws SQLException if database error
@@ -392,7 +398,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Moves the item from one collection to another one
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to move
      * @param from Collection to move from
      * @param to Collection to move to
      * @throws SQLException if database error
@@ -405,7 +411,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Moves the item from one collection to another one
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to move
      * @param from Collection to move from
      * @param to Collection to move to
      * @param inheritDefaultPolicies whether to inherit policies from new collection
@@ -413,12 +419,12 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * @throws AuthorizeException if authorization error
      * @throws IOException if IO error
      */
-    public void move (Context context, Item item, Collection from, Collection to, boolean inheritDefaultPolicies) throws SQLException, AuthorizeException, IOException;
+    public void move(Context context, Item item, Collection from, Collection to, boolean inheritDefaultPolicies) throws SQLException, AuthorizeException, IOException;
 
     /**
      * Check the bundle ORIGINAL to see if there are any uploaded files
      *
-     * @param item Item
+     * @param item item to check
      * @return true if there is a bundle named ORIGINAL with one or more
      *         bitstreams inside
      * @throws SQLException if database error
@@ -429,7 +435,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Get the collections this item is not in.
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to check
      * @return the collections this item is not in, if any.
      * @throws SQLException if database error
      */
@@ -439,7 +445,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * return TRUE if context's user can edit item, false otherwise
      *
      * @param context DSpace context object
-     * @param item Item
+     * @param item item to check
      * @return boolean true = current user can edit item
      * @throws SQLException if database error
      */
@@ -448,8 +454,10 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
     /**
      * return TRUE if context's user can create new version of the item, false
      * otherwise.
+     * @param context DSpace context object
+     * @param item item to check
      * @return boolean true = current user can create new version of the item
-     * @throws SQLException
+     * @throws SQLException if database error
      */
     public boolean canCreateNewVersion(Context context, Item item) throws SQLException;
      
@@ -500,7 +508,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * Service method for knowing if this Item should be visible in the item list.
      * Items only show up in the "item list" if the user has READ permission
      * and if the Item isn't flagged as unlisted.
-     * @param context context
+     * @param context DSpace context object
      * @param item item
      * @return true or false
      */
@@ -519,7 +527,7 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
     /**
      * Find all Items modified since a Date.
      *
-     * @param context context
+     * @param context DSpace context object
      * @param last Earliest interesting last-modified date.
      * @return iterator over items
      * @throws SQLException if database error
@@ -566,9 +574,10 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
 
     /**
      * Check if the supplied item is an inprogress submission
-	 * @param context
+     * @param context DSpace context object
-	 * @param item
+     * @param item item to check
      * @return <code>true</code> if the item is linked to a workspaceitem or workflowitem
+     * @throws SQLException if database error
      */
     boolean isInProgressSubmission(Context context, Item item) throws SQLException;
 }

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

@@ -37,7 +37,7 @@ public interface MetadataFieldService {
      * @return new MetadataField
      * @throws AuthorizeException if authorization error
      * @throws SQLException if database error
-     * @throws NonUniqueMetadataException
+     * @throws NonUniqueMetadataException if an existing field with an identical element and qualifier is already present
      */
     public MetadataField create(Context context, MetadataSchema metadataSchema, String element, String qualifier, String scopeNote)
             throws AuthorizeException, SQLException, NonUniqueMetadataException;
@@ -102,7 +102,7 @@ public interface MetadataFieldService {
      * @param metadataField metadata field
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
-     * @throws NonUniqueMetadataException
+     * @throws NonUniqueMetadataException if an existing field with an identical element and qualifier is already present
      * @throws IOException if IO error
      */
     public void update(Context context, MetadataField metadataField)

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

@@ -33,7 +33,7 @@ public interface MetadataSchemaService {
      * @return new MetadataSchema
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
-     * @throws NonUniqueMetadataException
+     * @throws NonUniqueMetadataException if an existing field with an identical element and qualifier is already present
      */
     public MetadataSchema create(Context context, String name, String namespace) throws SQLException, AuthorizeException, NonUniqueMetadataException;
 
@@ -54,7 +54,7 @@ public interface MetadataSchemaService {
      * @param metadataSchema metadata schema
      * @throws SQLException if database error
      * @throws AuthorizeException if authorization error
-     * @throws NonUniqueMetadataException
+     * @throws NonUniqueMetadataException if an existing field with an identical element and qualifier is already present
      */
     public void update(Context context, MetadataSchema metadataSchema) throws SQLException, AuthorizeException, NonUniqueMetadataException;
 

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

@@ -43,7 +43,7 @@ public interface MetadataValueService {
      * @param context dspace context
      * @param valueId database key id of value
      * @return recalled metadata value
-     * @throws java.io.IOException
+     * @throws IOException if IO error
      * @throws SQLException if database error
      */
     public MetadataValue find(Context context, int valueId)
@@ -89,7 +89,7 @@ public interface MetadataValueService {
     /**
      * Get the minimum value of a given metadata field across all objects.
      *
-     * @param context
+     * @param context dspace context
      * @param metadataFieldId unique identifier of the interesting field.
      * @return the minimum value of the metadata field
      * @throws SQLException if database error

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

@@ -143,6 +143,7 @@ public interface WorkspaceItemService extends InProgressSubmissionService<Worksp
     /**
      * The map entry returned contains stage reached as the key and count of items in that stage as a value
      * @param context
+     *     The relevant DSpace Context.
      * @return the map
      * @throws SQLException if database error
      */

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

@@ -94,7 +94,9 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
      * Execute a JPA Criteria query and return a collection of results.
      *
      * @param context
-     * @param query JPQL query string
+     *     The relevant DSpace Context.
+     * @param query
+     *     JPQL query string
      * @return list of DAOs specified by the query string
      * @throws SQLException if database error
      */
@@ -134,7 +136,7 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
      * Retrieve a unique result from the query.  If multiple results CAN be
      * retrieved an exception will be thrown,
      * so only use when the criteria state uniqueness in the database.
-     * @param criteria
+     * @param criteria JPA criteria
      * @return a DAO specified by the criteria
      */
     public T uniqueResult(Criteria criteria)
@@ -147,7 +149,7 @@ public abstract class AbstractHibernateDAO<T> implements GenericDAO<T> {
     /**
      * Retrieve a single result from the query.  Best used if you expect a
      * single result, but this isn't enforced on the database.
-     * @param criteria
+     * @param criteria JPA criteria
      * @return a DAO specified by the criteria
      */
     public T singleResult(Criteria criteria)

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

@@ -40,8 +40,11 @@ public abstract class AbstractHibernateDSODAO<T extends DSpaceObject> extends Ab
      * The identifier of the join will be the toString() representation of the metadata field.
      * The joineded metadata fields can then be used to query or sort.
      * @param query
+     *     partial SQL query (to be appended)
      * @param tableIdentifier
+     *     DB table to join with
      * @param metadataFields
+     *     a collection of metadata fields
      */
     protected void addMetadataLeftJoin(StringBuilder query, String tableIdentifier, Collection<MetadataField> metadataFields)
     {
@@ -63,26 +66,26 @@ public abstract class AbstractHibernateDSODAO<T extends DSpaceObject> extends Ab
      */
     protected void addMetadataValueWhereQuery(StringBuilder query, List<MetadataField> metadataFields, String operator, String additionalWhere)
     {
-        if(CollectionUtils.isNotEmpty(metadataFields) || StringUtils.isNotBlank(additionalWhere)){
+        if (CollectionUtils.isNotEmpty(metadataFields) || StringUtils.isNotBlank(additionalWhere)) {
             //Add the where query on metadata
             query.append(" WHERE ");
             for (int i = 0; i < metadataFields.size(); i++) {
                 MetadataField metadataField = metadataFields.get(i);
-                if(StringUtils.isNotBlank(operator))
+                if (StringUtils.isNotBlank(operator))
                 {
                     query.append(" (");
                     query.append("lower(STR(" + metadataField.toString()).append(".value)) ").append(operator).append(" lower(:queryParam)");
                     query.append(")");
-                    if(i < metadataFields.size() - 1)
+                    if (i < metadataFields.size() - 1)
                     {
                         query.append(" OR ");
                     }
                 }
             }
 
-            if(StringUtils.isNotBlank(additionalWhere))
+            if (StringUtils.isNotBlank(additionalWhere))
             {
-                if(CollectionUtils.isNotEmpty(metadataFields))
+                if (CollectionUtils.isNotEmpty(metadataFields))
                 {
                     query.append(" OR ");
                 }
@@ -95,23 +98,23 @@ public abstract class AbstractHibernateDSODAO<T extends DSpaceObject> extends Ab
     protected void addMetadataSortQuery(StringBuilder query, List<MetadataField> metadataSortFields, List<String> columnSortFields)
     {
 
-        if(CollectionUtils.isNotEmpty(metadataSortFields)){
+        if (CollectionUtils.isNotEmpty(metadataSortFields)) {
             query.append(" ORDER BY ");
             for (int i = 0; i < metadataSortFields.size(); i++) {
                 MetadataField metadataField = metadataSortFields.get(i);
                 query.append("STR(").append(metadataField.toString()).append(".value)");
-                if(i != metadataSortFields.size() -1)
+                if (i != metadataSortFields.size() -1)
                 {
                     query.append(",");
                 }
             }
-        }else if(CollectionUtils.isNotEmpty(columnSortFields))
+        } else if (CollectionUtils.isNotEmpty(columnSortFields))
         {
             query.append(" ORDER BY ");
             for (int i = 0; i < columnSortFields.size(); i++) {
                 String sortField = columnSortFields.get(i);
                 query.append(sortField);
-                if(i != columnSortFields.size() -1)
+                if (i != columnSortFields.size() -1)
                 {
                     query.append(",");
                 }

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

@@ -130,7 +130,7 @@ public class Context
     /**
      * Initializes a new context object. 
      *
-     * @exception SQLException
+     * @throws SQLException
      *                if there was an error obtaining a database connection
      */
     private void init()
@@ -337,7 +337,7 @@ public class Context
      * Calling complete() on a Context which is no longer valid (isValid()==false),
      * is a no-op.
      * 
-     * @exception SQLException
+     * @throws SQLException
      *                if there was an error completing the database transaction
      *                or closing the connection
      */
@@ -448,6 +448,7 @@ public class Context
      * Add an event to be dispatched when this context is committed.
      * 
      * @param event
+     *     event to be dispatched
      */
     public void addEvent(Event event)
     {
@@ -630,10 +631,9 @@ public class Context
 
 
     /**
-     * Returns the size of the cache of all object that have been read from the database so far. A larger number
+     * Returns the size of the cache of all object that have been read from the database so far.
-     * means that more memory is consumed by the cache. This also has a negative impact on the query performance. In
-     * that case you should consider clearing the cache (see {@link Context#clearCache() clearCache}).
      *
+     * @return connection cache size
      * @throws SQLException When connecting to the active cache fails.
      */
     public long getCacheSize() throws SQLException {

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

@@ -48,13 +48,20 @@ public interface DBConnection<T> {
 
     /**
      * Reload a DSpace object from the database. This will make sure the object is valid and stored in the cache.
+     * @param <E> the type of entity.
      * @param entity The DSpace object to reload
+     * @return the reloaded entity.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public <E extends ReloadableEntity> E reloadEntity(E entity) throws SQLException;
 
     /**
      * Remove a DSpace object from the cache when batch processing a large number of objects.
+     * @param <E> the type of entity.
      * @param entity The DSpace object to reload
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public <E extends ReloadableEntity> void uncacheEntity(E entity) throws SQLException ;
 }

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

@@ -42,25 +42,28 @@ import org.dspace.services.factory.DSpaceServicesFactory;
 
 /**
  * Class representing an e-mail message, also used to send e-mails.
- * <P>
+ * <p>
  * Typical use:
- * <P>
+ * </p>
+ * <p>
  * <code>Email email = new Email();</code><br>
  * <code>email.addRecipient("foo@bar.com");</code><br>
  * <code>email.addArgument("John");</code><br>
  * <code>email.addArgument("On the Testing of DSpace");</code><br>
  * <code>email.send();</code><br>
- * <P>
+ * </p>
+ * <p>
  * <code>name</code> is the name of an email template in
  * <code>dspace-dir/config/emails/</code> (which also includes the subject.)
  * <code>arg0</code> and <code>arg1</code> are arguments to fill out the
  * message with.
- * <P>
+ * </p>
+ * <p>
  * Emails are formatted using <code>java.text.MessageFormat.</code>
  * Additionally, comment lines (starting with '#') are stripped, and if a line
  * starts with "Subject:" the text on the right of the colon is used for the
  * subject line. For example:
- * <P>
+ * </p>
  *
  * <pre>
  *
@@ -77,10 +80,10 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  *
  * </pre>
  *
- * <P>
+ * <p>
  * If the example code above was used to send this mail, the resulting mail
  * would have the subject <code>Example e-mail</code> and the body would be:
- * <P>
+ * </p>
  *
  * <pre>
  *
@@ -91,9 +94,10 @@ import org.dspace.services.factory.DSpaceServicesFactory;
  *
  * </pre>
  *
- * <P>
+ * <p>
  * Note that parameters like <code>{0}</code> cannot be placed in the subject
  * of the e-mail; they won't get filled out.
+ * </p>
  *
  *
  * @author Robert Tansley
@@ -295,13 +299,14 @@ public class Email
                 message.setText(fullMessage);
             }
         }
-        else{
+        else
+        {
              Multipart multipart = new MimeMultipart();
                 // create the first part of the email
                 BodyPart messageBodyPart = new MimeBodyPart();
                 messageBodyPart.setText(fullMessage);
                 multipart.addBodyPart(messageBodyPart);
-        	 if(!attachments.isEmpty()){
+             if (!attachments.isEmpty()) {
                 for (Iterator<FileAttachment> iter = attachments.iterator(); iter.hasNext();)
                 {
                     FileAttachment f = iter.next();
@@ -314,13 +319,19 @@ public class Email
                 }
                 message.setContent(multipart);
              }
-        	 if(!moreAttachments.isEmpty()){
+             if (!moreAttachments.isEmpty()) {
                  for (Iterator<InputStreamAttachment> iter = moreAttachments.iterator(); iter.hasNext();)
                  {
                      InputStreamAttachment isa = iter.next();
                      // add the stream
                      messageBodyPart = new MimeBodyPart();
- 	                messageBodyPart.setDataHandler(new DataHandler(new InputStreamDataSource(isa.name,isa.mimetype,isa.is)));
+                     messageBodyPart.setDataHandler(
+                         new DataHandler(new InputStreamDataSource(
+                             isa.name,
+                             isa.mimetype, 
+                             isa.is)
+                         )
+                     );
                      messageBodyPart.setFileName(isa.name);
                      multipart.addBodyPart(messageBodyPart);
                  }
@@ -459,7 +470,7 @@ public class Email
     /**
      * Test method to send an email to check email server settings
      *
-     * @param args Command line options
+     * @param args the command line arguments given
      */
     public static void main(String[] args)
     {
@@ -479,7 +490,7 @@ public class Email
         boolean disabled = config.getBooleanProperty("mail.server.disabled", false);
         try
         {
-            if( disabled)
+            if (disabled)
             {
                 System.err.println("\nError sending email:");
                 System.err.println(" - Error: cannot test email because mail.server.disabled is set to true");
@@ -497,7 +508,9 @@ public class Email
             System.err.println("\nPlease see the DSpace documentation for assistance.\n");
             System.err.println("\n");
             System.exit(1);
-        }catch (IOException e1) {
+        }
+        catch (IOException e1)
+        {
             System.err.println("\nError sending email:");
             System.err.println(" - Error: " + e1);
             System.err.println("\nPlease see the DSpace documentation for assistance.\n");

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

@@ -33,6 +33,7 @@ public interface GenericDAO<T>
      * Fetch all persisted instances of a given object type.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param clazz the desired type.
      * @return list of DAOs of the same type as clazz
      * @throws SQLException if database error
@@ -43,6 +44,7 @@ public interface GenericDAO<T>
      * Execute a JPQL query returning a unique result.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param query JPQL query string
      * @return a DAO specified by the query string
      * @throws SQLException if database error
@@ -57,6 +59,7 @@ public interface GenericDAO<T>
      * Execute a JPQL query and return a collection of results.
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param query JPQL query string
      * @return list of DAOs specified by the query string
      * @throws SQLException if database error

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

@@ -23,38 +23,43 @@ import org.dspace.services.ConfigurationService;
 import org.springframework.beans.factory.annotation.Autowired;
 
 /**
+ * <p>
  * The Legacy Plugin Service is a very simple component container (based on the
  * legacy PluginManager class from 5.x or below). It reads defined "plugins" (interfaces)
  * from config file(s) and makes them available to the API. (TODO: Someday, this
  * entire "plugin" framework needs to be replaced by Spring Beans.)
+ * </p>
  * <p>
  * It creates and organizes components (plugins), and helps select a plugin in
  * the cases where there are many possible choices. It also gives some limited
  * control over the lifecycle of a plugin.  It manages three different types
  * (usage patterns) of plugins:
- * <p>
+ * </p>
- * <ol><li> Singleton Plugin
+ * <ol>
- * <br>  There is only one implementation class for the plugin.  It is indicated
+ *   <li>Singleton Plugin<br>
+ *   There is only one implementation class for the plugin.  It is indicated
  *   in the configuration.  This type of plugin chooses an implementations of
  *   a service, for the entire system, at configuration time.  Your
  *   application just fetches the plugin for that interface and gets the
- *   configured-in choice.
+ *   configured-in choice.</li>
  *
- * <p><li> Sequence Plugins
+ *   <li>Sequence Plugins<br>
- *  <br> You need a sequence or series of plugins, to implement a mechanism like
+ *   You need a sequence or series of plugins, to implement a mechanism like
  *   StackableAuthenticationMethods or a pipeline, where each plugin is
  *   called in order to contribute its implementation of a process to the
- *   whole.
+ *   whole.</li>
- *  <p><li> Named Plugins
+ *   <li>Named Plugins<br>
- *  <br> Use a named plugin when the application has to choose one plugin
+ *   Use a named plugin when the application has to choose one plugin
  *   implementation out of many available ones.  Each implementation is bound
- *   to one or more names (symbolic identifiers) in the configuration.
+ *   to one or more names (symbolic identifiers) in the configuration.</li>
- *  </ol><p>
+ *  </ol>
+ *  <p>
  *  The name is just a <code>String</code> to be associated with the
  *  combination of implementation class and interface.  It may contain
  *  any characters except for comma (,) and equals (=).  It may contain
  *  embedded spaces.  Comma is a special character used to separate
  *  names in the configuration entry.
+ *  </p>
  *
  * @author Larry Stone
  * @author Tim Donohue (turned old PluginManager into a PluginService)
@@ -122,7 +127,7 @@ public class LegacyPluginServiceImpl implements PluginService
      *
      * @param interfaceClass interface Class object
      * @return instance of plugin
-     * @throws PluginConfigurationError
+     * @throws PluginConfigurationError if no matching singleton plugin is configured.
      */
     @Override
     public Object getSinglePlugin(Class interfaceClass)
@@ -257,7 +262,7 @@ public class LegacyPluginServiceImpl implements PluginService
                     // If there's no "=" separator in this value, assume it's
                     // just a "name" that belongs with previous class.
                     // (This may occur if there's an unescaped comma between names)
-                    if(prevClassName!=null && valSplit.length==1)
+                    if (prevClassName!=null && valSplit.length==1)
                     {
                         className = prevClassName;
                         name = valSplit[0];
@@ -713,7 +718,8 @@ public class LegacyPluginServiceImpl implements PluginService
      * Invoking this class from the command line just runs
      * <code>checkConfiguration</code> and shows the results.
      * There are no command-line options.
-     * @param argv arguments
+     *
+     * @param argv the command line arguments given
      * @throws Exception if error
      */
     public void main(String[] argv) throws Exception

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

@@ -44,12 +44,12 @@ public class NewsServiceImpl implements NewsService
         this.acceptableFilenames = addLocalesToAcceptableFilenames(acceptableFilenames);
     }
 
-    protected List<String> addLocalesToAcceptableFilenames(List<String> acceptableFilenames){
+    protected List<String> addLocalesToAcceptableFilenames(List<String> acceptableFilenames) {
         String [] locales = configurationService.getArrayProperty("webui.supported.locales");
         List<String> newAcceptableFilenames = new ArrayList<>();
         newAcceptableFilenames.addAll(acceptableFilenames);
-        for(String local : locales){
+        for (String local : locales) {
-            for(String acceptableFilename : acceptableFilenames){
+            for (String acceptableFilename : acceptableFilenames) {
                 int lastPoint = acceptableFilename.lastIndexOf(".");
                 newAcceptableFilenames.add(
                     acceptableFilename.substring(0, lastPoint)
@@ -69,7 +69,7 @@ public class NewsServiceImpl implements NewsService
     public String readNewsFile(String newsFile)
     {
         if (!validate(newsFile)) {
-    		throw new IllegalArgumentException("The file "+ newsFile + " is not a valid news file");
+            throw new IllegalArgumentException("The file " + newsFile + " is not a valid news file");
         }
         String fileName = getNewsFilePath();
 

dspace-api/src/main/java/org/dspace/core/service/NewsService.java

@@ -42,9 +42,10 @@ public interface NewsService {
     public String getNewsFilePath();
 
     /**
-     * Check if the newsName is a valid one
+     * Check if the newsName is an acceptable file name
      * 
      * @param newsName
+     *     news name
      * @return true 
      *     if the newsName is valid
      */

dspace-api/src/main/java/org/dspace/ctask/general/BasicLinkChecker.java

@@ -113,7 +113,10 @@ public class BasicLinkChecker extends AbstractCurationTask
     /**
      * Check the URL and perform appropriate reporting
      *
-     * @param url The URL to check
+     * @param url
+     *     The URL to check
+     * @param results
+     *     Result string with HTTP status codes
      * @return If the URL was OK or not
      */
     protected boolean checkURL(String url, StringBuilder results)

dspace-api/src/main/java/org/dspace/ctask/general/BitstreamsIntoMetadata.java

@@ -113,6 +113,8 @@ public class BitstreamsIntoMetadata extends AbstractCurationTask
      * @param item The item
      * @param bitstream The bitstream
      * @param type The type of bitstream
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     protected void addMetadata(Item item, Bitstream bitstream, String type) throws SQLException {
         String value = bitstream.getFormat(Curator.curationContext()).getMIMEType() + "##";

dspace-api/src/main/java/org/dspace/ctask/general/ClamScan.java

@@ -156,6 +156,9 @@ public class ClamScan extends AbstractCurationTask
     /** openSession
      *
      * This method opens a session.
+     *
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
      */
 
     protected void openSession() throws IOException

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

@@ -149,7 +149,7 @@ public class Curator
      * 
      * @param reporter name of reporting stream. The name '-'
      *                 causes reporting to standard out. 
-     * @return the Curator instance
+     * @return return self (Curator instance) with reporter set
      */
     public Curator setReporter(String reporter)
     {
@@ -166,6 +166,9 @@ public class Curator
      * entire performance is complete, and a scope of 'object'
      * will commit for each object (e.g. item) encountered in
      * a given execution.
+     *
+     * @param scope transactional scope
+     * @return return self (Curator instance) with given scope set
      */
     public Curator setTransactionScope(TxScope scope)
     {
@@ -358,18 +361,20 @@ public class Curator
     /**
      * Returns the context object used in the current curation thread.
      * This is primarily a utility method to allow tasks access to the context when necessary.
-     * <P>
+     * <p>
      * If the context is null or not set, then this just returns
      * a brand new Context object representing an Anonymous User.
      * 
      * @return curation thread's Context object (or a new, anonymous Context if no curation Context exists)
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public static Context curationContext() throws SQLException
     {
         // Return curation context or new context if undefined/invalid
         Context curCtx = curationCtx.get();
         
-        if(curCtx==null || !curCtx.isValid())
+        if (curCtx==null || !curCtx.isValid())
         {
             //Create a new context (represents an Anonymous User)
             curCtx = new Context();
@@ -407,7 +412,7 @@ public class Curator
             
             // Site-wide Tasks really should have an EPerson performer associated with them,
             // otherwise they are run as an "anonymous" user with limited access rights.
-            if(ctx.getCurrentUser()==null && !ctx.ignoreAuthorization())
+            if (ctx.getCurrentUser()==null && !ctx.ignoreAuthorization())
             {
                 log.warn("You are running one or more Site-Wide curation tasks in ANONYMOUS USER mode," +
                          " as there is no EPerson 'performer' associated with this task. To associate an EPerson 'performer' " +
@@ -502,6 +507,9 @@ public class Curator
     /**
      * Record a 'visit' to a DSpace object and enforce any policies set
      * on this curator.
+     * @param dso the DSpace object
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
      */
     protected void visit(DSpaceObject dso) throws IOException
     {
@@ -540,7 +548,7 @@ public class Curator
                 visit(dso);
                 return ! suspend(statusCode);
             }
-            catch(IOException ioe)
+            catch (IOException ioe)
             {
                 //log error & pass exception upwards
                 log.error("Error executing curation task '" + task.getName() + "'", ioe);
@@ -561,7 +569,7 @@ public class Curator
                 visit(null);
                 return ! suspend(statusCode);
             }
-            catch(IOException ioe)
+            catch (IOException ioe)
             {
                 //log error & pass exception upwards
                 log.error("Error executing curation task '" + task.getName() + "'", ioe);

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

@@ -114,6 +114,7 @@ public class ResolvedTask
     /**
      * Returns whether task should be distributed through containers
      * 
+     * @return whether task should be distributed through containers
      */
     public boolean isDistributive()
     {
@@ -123,6 +124,7 @@ public class ResolvedTask
     /**
      * Returns whether task alters (mutates) it's target objects
      * 
+     * @return whether task alters (mutates) it's target objects
      */
     public boolean isMutative()
     {
@@ -139,6 +141,11 @@ public class ResolvedTask
     	return codes;
     }
     
+    /**
+     * Returns whether task is not scripted (curation task)
+     * 
+     * @return true if this task is not scripted
+     */
     private boolean unscripted()
     {
     	return sTask == null;

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

@@ -27,9 +27,13 @@ public final class TaskQueueEntry
      * TaskQueueEntry constructor with enumerated field values.
      * 
      * @param epersonId
+     *     task owner
      * @param submitTime
+     *     time the task was submitted (System.currentTimeMillis())
      * @param taskNames
+     *     list of task names
      * @param objId
+     *     usually a handle or workflow id
      */
     public TaskQueueEntry(String epersonId, long submitTime,
                           List<String> taskNames, String objId)

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

@@ -120,8 +120,8 @@ public class Utils
     /**
      * Performs a buffered copy from one file into another.
      * 
-     * @param inFile
+     * @param inFile input file
-     * @param outFile
+     * @param outFile output file
      * @throws IOException if IO error
      */
     public static void copy(File inFile, File outFile) throws IOException

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

@@ -79,6 +79,7 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService
      * Ensures the configurationService is injected, so that we can read the
      * settings from configuration
      * Called by "init-method" in Spring config.
+     * @throws Exception ...
      */
     public void init() throws Exception {
         File cfgFile = new File(configurationService.getProperty("dspace.dir") +
@@ -87,7 +88,7 @@ public class WorkflowCuratorServiceImpl implements WorkflowCuratorService
         try
         {
             loadTaskConfig(cfgFile);
-            if(workflowServiceFactory.getWorkflowService() instanceof BasicWorkflowItemService)
+            if (workflowServiceFactory.getWorkflowService() instanceof BasicWorkflowItemService)
             {
                 basicWorkflowService = (BasicWorkflowService) workflowServiceFactory.getWorkflowService();
                 basicWorkflowItemService = (BasicWorkflowItemService) workflowServiceFactory.getWorkflowItemService();

dspace-api/src/main/java/org/dspace/curate/service/WorkflowCuratorService.java

@@ -46,8 +46,12 @@ public interface WorkflowCuratorService {
     /**
      * Determines and executes curation of a Workflow item.
      *
+     * @param curator the Curator object
      * @param c the user context
      * @param wfId the workflow id
+     * @return true if curation was completed or not required,
+     *         false if no workflow item found for id
+     *         or item was rejected
      * @throws AuthorizeException if authorization error
      * @throws IOException if IO error
      * @throws SQLException if database error
@@ -55,6 +59,18 @@ public interface WorkflowCuratorService {
     public boolean curate(Curator curator, Context c, String wfId)
             throws AuthorizeException, IOException, SQLException;
 
+    /**
+     * Determines and executes curation of a Workflow item.
+     *
+     * @param curator the Curator object
+     * @param c the user context
+     * @param wfi the workflow item
+     * @return true if curation was completed or not required,
+     *         false if item was rejected
+     * @throws AuthorizeException if authorization error
+     * @throws IOException if IO error
+     * @throws SQLException if database error
+     */
     public boolean curate(Curator curator, Context c, BasicWorkflowItem wfi)
             throws AuthorizeException, IOException, SQLException;
 }

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

@@ -40,12 +40,17 @@ public class DiscoverHitHighlightingField {
      * field containing a matching hit. e.g. If maxChars = 200
      * and a hit is found in the full-text the 200 chars
      * surrounding the hit will be shown
+     *
+     * @return max number of characters shown for a hit
      */
     public int getMaxChars()
     {
         return maxChars;
     }
 
+    /**
+     * @return max number of result snippets
+     */
     public int getMaxSnippets()
     {
         return maxSnippets;

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

@@ -41,12 +41,15 @@ public class IndexClient {
      * from the whole index
      *
      * @param args the command-line arguments, none used
-     * @throws java.io.IOException
+     * @throws SQLException
-     * @throws SQLException if database error
+     *     An exception that provides information on a database access error or other errors.
-     *
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SearchServiceException if something went wrong with querying the solr server
      */
-    public static void main(String[] args) throws SQLException, IOException, SearchServiceException {
+    public static void main(String[] args)
-
+    throws SQLException, IOException, SearchServiceException
+    {
         Context context = new Context();
         context.turnOffAuthorisationSystem();
 
@@ -55,46 +58,49 @@ public class IndexClient {
         HelpFormatter formatter = new HelpFormatter();
         CommandLine line = null;
 
-        options
+        options.addOption(OptionBuilder
-                .addOption(OptionBuilder
             .withArgName("handle to remove")
             .hasArg(true)
             .withDescription(
                 "remove an Item, Collection or Community from index based on its handle")
             .create("r"));
 
-        options
+        options.addOption(OptionBuilder
-                .addOption(OptionBuilder
             .withArgName("handle to add or update")
             .hasArg(true)
             .withDescription(
                 "add or update an Item, Collection or Community based on its handle")
             .create("i"));
 
-        options
+        options.addOption(OptionBuilder
-                .addOption(OptionBuilder
             .isRequired(false)
             .withDescription(
                 "clean existing index removing any documents that no longer exist in the db")
             .create("c"));
 
-        options.addOption(OptionBuilder.isRequired(false).withDescription(
+        options.addOption(OptionBuilder
-                "(re)build index, wiping out current one if it exists").create(
+            .isRequired(false)
-                "b"));
+            .withDescription(
+               "(re)build index, wiping out current one if it exists")
+            .create("b"));
 
-        options.addOption(OptionBuilder.isRequired(false).withDescription(
+        options.addOption(OptionBuilder
-                "Rebuild the spellchecker, can be combined with -b and -f.").create(
+            .isRequired(false)
-                "s"));
+            .withDescription(
+                "Rebuild the spellchecker, can be combined with -b and -f.")
+            .create("s"));
 
-        options
+        options.addOption(OptionBuilder
-                .addOption(OptionBuilder
             .isRequired(false)
             .withDescription(
                 "if updating existing index, force each handle to be reindexed even if uptodate")
             .create("f"));
 
-        options.addOption(OptionBuilder.isRequired(false).withDescription(
+        options.addOption(OptionBuilder
-                "print this help message").create("h"));
+            .isRequired(false)
+            .withDescription(
+                "print this help message")
+            .create("h"));
 
         options.addOption(OptionBuilder.isRequired(false).withDescription(
                 "optimize search core").create("o"));
@@ -118,7 +124,10 @@ public class IndexClient {
          * new DSpace.getServiceManager().getServiceByName("org.dspace.discovery.SolrIndexer");
          */
 
-        IndexingService indexer = DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName(IndexingService.class.getName(),IndexingService.class);
+        IndexingService indexer = DSpaceServicesFactory.getInstance().getServiceManager().getServiceByName(
+            IndexingService.class.getName(),
+            IndexingService.class
+        );
 
         if (line.hasOption("r")) {
             log.info("Removing " + line.getOptionValue("r") + " from Index");
@@ -133,9 +142,9 @@ public class IndexClient {
         } else if (line.hasOption("o")) {
             log.info("Optimizing search core.");
             indexer.optimize();
-        } else if(line.hasOption('s')) {
+        } else if (line.hasOption('s')) {
             checkRebuildSpellCheck(line, indexer);
-        } else if(line.hasOption('i')) {
+        } else if (line.hasOption('i')) {
             final String handle = line.getOptionValue('i');
             final DSpaceObject dso = HandleServiceFactory.getInstance().getHandleService().resolveToObject(context, handle);
             if (dso == null) {
@@ -160,11 +169,27 @@ public class IndexClient {
 
     /**
      * Indexes the given object and all children, if applicable.
+     *
+     * @param indexingService
+     *     
+     * @param itemService
+     *     
+     * @param context
+     *     The relevant DSpace Context.
+     * @param dso
+     *     DSpace object to index recursively
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SearchServiceException in case of a solr exception
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     private static long indexAll(final IndexingService indexingService,
                                  final ItemService itemService,
                                  final Context context,
-                                 final DSpaceObject dso) throws IOException, SearchServiceException, SQLException {
+                                 final DSpaceObject dso)
+    throws IOException, SearchServiceException, SQLException
+    {
         long count = 0;
 
         indexingService.indexContent(context, dso, true, true);
@@ -194,11 +219,27 @@ public class IndexClient {
 
     /**
      * Indexes all items in the given collection.
+     *
+     * @param indexingService
+     *     
+     * @param itemService
+     *     
+     * @param context
+     *     The relevant DSpace Context.
+     * @param collection
+     *     collection to index
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SearchServiceException in case of a solr exception
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     private static long indexItems(final IndexingService indexingService,
                                    final ItemService itemService,
                                    final Context context,
-                                   final Collection collection) throws IOException, SearchServiceException, SQLException {
+                                   final Collection collection)
+    throws IOException, SearchServiceException, SQLException
+    {
         long count = 0;
 
         final Iterator<Item> itemIterator = itemService.findByCollection(context, collection);
@@ -220,7 +261,9 @@ public class IndexClient {
      * @param indexer the solr indexer
      * @throws SearchServiceException in case of a solr exception
      */
-    protected static void checkRebuildSpellCheck(CommandLine line, IndexingService indexer) throws SearchServiceException {
+    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/SearchService.java

@@ -34,6 +34,7 @@ public interface SearchService {
      *            DSpace Context object.
      * @param query
      *            the discovery query object.
+     * @return discovery search result object
      * @throws SearchServiceException if search error
      */
     DiscoverResult search(Context context, DiscoverQuery query)
@@ -50,6 +51,7 @@ public interface SearchService {
      *            within this object)
      * @param query
      *            the discovery query object
+     * @return discovery search result object
      * @throws SearchServiceException if search error
      */
     DiscoverResult search(Context context, DSpaceObject dso, DiscoverQuery query)
@@ -64,6 +66,7 @@ public interface SearchService {
      * @param includeWithdrawn
      *            use <code>true</code> to include in the results also withdrawn
      *            items that match the query.
+     * @return discovery search result object
      * @throws SearchServiceException if search error
      */
     DiscoverResult search(Context context, DiscoverQuery query,
@@ -81,7 +84,7 @@ public interface SearchService {
      * @param includeWithdrawn
      *            use <code>true</code> to include in the results also withdrawn
      *            items that match the query
-     * 
+     * @return discovery search result object
      * @throws SearchServiceException if search error
      */
     DiscoverResult search(Context context, DSpaceObject dso, DiscoverQuery query, boolean includeWithdrawn) throws SearchServiceException;
@@ -97,11 +100,14 @@ public interface SearchService {
 
     /**
      * Transforms the given string field and value into a filter query
-     * @param context the DSpace context
+     * @param context
+     *     The relevant DSpace Context.
      * @param field the field of the filter query
+     * @param operator equals/notequals/notcontains/authority/notauthority
      * @param value the filter query value
      * @return a filter query
      * @throws SQLException if database error
+     *     An exception that provides information on a database access error or other errors.
      */
     DiscoverFilterQuery toFilterQuery(Context context, String field, String operator, String value) throws SQLException;
 
@@ -118,21 +124,27 @@ public interface SearchService {
      * communities/collections only.
      *
      * @param context
-     * @return
+     *     The relevant DSpace Context.
+     * @return query string specific to the user's rights
      * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     String createLocationQueryForAdministrableItems(Context context) throws SQLException;
 
     /**
-     * Transforms the metadata field of the given sort configuration into the indexed field which we can then use in our solr queries
+     * Transforms the metadata field of the given sort configuration into the indexed field which we can then use in our Solr queries.
+     *
      * @param metadataField the metadata field
+     * @param type see {@link org.dspace.discovery.configuration.DiscoveryConfigurationParameters}
      * @return the indexed field
      */
     String toSortFieldIndex(String metadataField, String type);
 
     /**
      * Utility method to escape any special characters in a user's query
+     *
      * @param query
+     *     User's query to escape.
      * @return query with any special characters escaped
      */
     String escapeQueryChars(String query);

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

@@ -31,28 +31,28 @@ public class SearchUtils {
 
     public static SearchService getSearchService()
     {
-        if(searchService ==  null){
+        if (searchService ==  null) {
             org.dspace.kernel.ServiceManager manager = DSpaceServicesFactory.getInstance().getServiceManager();
             searchService = manager.getServiceByName(SearchService.class.getName(),SearchService.class);
         }
         return searchService;
     }
 
-    public static DiscoveryConfiguration getDiscoveryConfiguration(){
+    public static DiscoveryConfiguration getDiscoveryConfiguration() {
         return getDiscoveryConfiguration(null);
     }
 
-    public static DiscoveryConfiguration getDiscoveryConfiguration(DSpaceObject dso){
+    public static DiscoveryConfiguration getDiscoveryConfiguration(DSpaceObject dso) {
         DiscoveryConfigurationService configurationService = getConfigurationService();
 
         DiscoveryConfiguration result = null;
-        if(dso == null){
+        if (dso == null) {
             result = configurationService.getMap().get("site");
         }else{
             result = configurationService.getMap().get(dso.getHandle());
         }
 
-        if(result == null){
+        if (result == null) {
             //No specific configuration, get the default one
             result = configurationService.getMap().get("default");
         }
@@ -73,8 +73,11 @@ public class SearchUtils {
     /**
      * Method that retrieves a list of all the configuration objects from the given item
      * A configuration object can be returned for each parent community/collection
+     *
      * @param item the DSpace item
      * @return a list of configuration objects
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public static List<DiscoveryConfiguration> getAllDiscoveryConfigurations(Item item) throws SQLException {
         Map<String, DiscoveryConfiguration> result = new HashMap<String, DiscoveryConfiguration>();
@@ -82,14 +85,14 @@ public class SearchUtils {
         List<Collection> collections = item.getCollections();
         for (Collection collection : collections) {
             DiscoveryConfiguration configuration = getDiscoveryConfiguration(collection);
-            if(!result.containsKey(configuration.getId())){
+            if (!result.containsKey(configuration.getId())) {
                 result.put(configuration.getId(), configuration);
             }
         }
 
         //Also add one for the default
         DiscoveryConfiguration configuration = getDiscoveryConfiguration(null);
-        if(!result.containsKey(configuration.getId())){
+        if (!result.containsKey(configuration.getId())) {
             result.put(configuration.getId(), configuration);
         }
 

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

@@ -79,7 +79,7 @@ import org.dspace.eperson.factory.EPersonServiceFactory;
  * that cron.
  *
  * The SolrServiceImpl is registered as a Service in the ServiceManager via
- * a spring configuration file located under
+ * a Spring configuration file located under
  * classpath://spring/spring-dspace-applicationContext.xml
  *
  * Its configuration is Autowired by the ApplicationContext
@@ -257,6 +257,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
      * unIndex removes an Item, Collection, or Community
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param dso     DSpace Object, can be Community, Item, or Collection
      * @throws SQLException if database error
      * @throws IOException if IO error
@@ -271,6 +272,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
      * unIndex removes an Item, Collection, or Community
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param dso     DSpace Object, can be Community, Item, or Collection
      * @param commit if <code>true</code> force an immediate commit on SOLR
      * @throws SQLException if database error
@@ -286,7 +288,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             }
             String uniqueID = dso.getType()+"-"+dso.getID();
             getSolr().deleteById(uniqueID);
-            if(commit)
+            if (commit)
             {
                 getSolr().commit();
             }
@@ -320,9 +322,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             throws SQLException, IOException {
 
         try {
-            if(getSolr() != null){
+            if (getSolr() != null) {
                 getSolr().deleteByQuery(HANDLE_FIELD + ":\"" + handle + "\"");
-                if(commit)
+                if (commit)
                 {
                     getSolr().commit();
                 }
@@ -416,7 +418,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 indexContent(context, community, force);
             }
 
-            if(getSolr() != null)
+            if (getSolr() != null)
             {
                 getSolr().commit();
             }
@@ -445,7 +447,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
         try
         {
-            if(getSolr() == null)
+            if (getSolr() == null)
             {
                 return;
             }
@@ -484,7 +486,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 }
             }
             }
-        } catch(Exception e)
+        } catch (Exception e)
         {
 
             throw new SearchServiceException(e.getMessage(), e);
@@ -506,7 +508,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     public void optimize()
     {
         try {
-            if(getSolr() == null)
+            if (getSolr() == null)
             {
                 return;
             }
@@ -613,7 +615,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         QueryResponse rsp;
 
         try {
-            if(getSolr() == null)
+            if (getSolr() == null)
             {
                 return false;
             }
@@ -630,7 +632,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             Object value = doc.getFieldValue(LAST_INDEXED_FIELD);
 
-            if(value instanceof Date)
+            if (value instanceof Date)
             {
                 Date lastIndexed = (Date) value;
 
@@ -711,7 +713,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             List<Collection> allCollections = new ArrayList<>();
             
-            for( ResourcePolicy rp: collectionsPolicies){
+            for( ResourcePolicy rp: collectionsPolicies) {
                 Collection collection = ContentServiceFactory.getInstance().getCollectionService()
                         .find(context, rp.getdSpaceObject().getID());
                 allCollections.add(collection);
@@ -761,16 +763,19 @@ 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 doc
+     *     the solr document to be written to the server
      * @param streams
-     * @throws IOException IO exception
+     *     list of bitstream content streams
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
      */
     protected void writeDocument(SolrInputDocument doc, List<BitstreamContentStream> streams) throws IOException {
 
         try {
-            if(getSolr() != null)
+            if (getSolr() != null)
             {
-                if(CollectionUtils.isNotEmpty(streams))
+                if (CollectionUtils.isNotEmpty(streams))
                 {
                     ContentStreamUpdateRequest req = new ContentStreamUpdateRequest("/update/extract");
 
@@ -811,6 +816,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     /**
      * Build a solr document for a DSpace Community.
      *
+     * @param context
+     *     The relevant DSpace Context.
      * @param community Community to be indexed
      * @throws SQLException if database error
      * @throws IOException if IO error
@@ -824,7 +831,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         DiscoveryConfiguration discoveryConfiguration = SearchUtils.getDiscoveryConfiguration(community);
         DiscoveryHitHighlightingConfiguration highlightingConfiguration = discoveryConfiguration.getHitHighlightingConfiguration();
         List<String> highlightedMetadataFields = new ArrayList<String>();
-        if(highlightingConfiguration != null)
+        if (highlightingConfiguration != null)
         {
             for (DiscoveryHitHighlightFieldConfiguration configuration : highlightingConfiguration.getMetadataFields())
             {
@@ -859,6 +866,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     /**
      * Build a solr document for a DSpace Collection.
      *
+     * @param context
+     *     The relevant DSpace Context.
      * @param collection Collection to be indexed
      * @throws SQLException sql exception
      * @throws IOException IO exception
@@ -874,7 +883,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         DiscoveryConfiguration discoveryConfiguration = SearchUtils.getDiscoveryConfiguration(collection);
         DiscoveryHitHighlightingConfiguration highlightingConfiguration = discoveryConfiguration.getHitHighlightingConfiguration();
         List<String> highlightedMetadataFields = new ArrayList<String>();
-        if(highlightingConfiguration != null)
+        if (highlightingConfiguration != null)
         {
             for (DiscoveryHitHighlightFieldConfiguration configuration : highlightingConfiguration.getMetadataFields())
             {
@@ -915,19 +924,21 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     /**
      * Add the metadata value of the community/collection to the solr document
      * IF needed highlighting is added !
+     *
      * @param doc the solr document
      * @param highlightedMetadataFields the list of metadata fields that CAN be highlighted
+     * @param toIgnoreMetadataFields the list of metadata fields to skip adding to Solr
      * @param metadataField the metadata field added
      * @param value the value (can be NULL !)
      */
     protected void addContainerMetadataField(SolrInputDocument doc, List<String> highlightedMetadataFields, List<String> toIgnoreMetadataFields, String metadataField, String value)
     {
-        if(toIgnoreMetadataFields == null || !toIgnoreMetadataFields.contains(metadataField))
+        if (toIgnoreMetadataFields == null || !toIgnoreMetadataFields.contains(metadataField))
         {
-            if(StringUtils.isNotBlank(value))
+            if (StringUtils.isNotBlank(value))
             {
                 doc.addField(metadataField, value);
-                if(highlightedMetadataFields.contains(metadataField))
+                if (highlightedMetadataFields.contains(metadataField))
                 {
                     doc.addField(metadataField + "_hl", value);
                 }
@@ -985,10 +996,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     {
                         String metadataField = discoverySearchFilter.getMetadataFields().get(j);
                         List<DiscoverySearchFilter> resultingList;
-                        if(searchFilters.get(metadataField) != null)
+                        if (searchFilters.get(metadataField) != null)
                         {
                             resultingList = searchFilters.get(metadataField);
-                        }else{
+                        } else {
                             //New metadata field, create a new list for it
                             resultingList = new ArrayList<DiscoverySearchFilter>();
                         }
@@ -999,7 +1010,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 }
 
                 DiscoverySortConfiguration sortConfiguration = discoveryConfiguration.getSearchSortConfiguration();
-                if(sortConfiguration != null)
+                if (sortConfiguration != null)
                 {
                     for (DiscoverySortFieldConfiguration discoverySortConfiguration : sortConfiguration.getSortFields())
                     {
@@ -1008,13 +1019,13 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 }
 
                 DiscoveryRecentSubmissionsConfiguration recentSubmissionConfiguration = discoveryConfiguration.getRecentSubmissionConfiguration();
-                if(recentSubmissionConfiguration != null)
+                if (recentSubmissionConfiguration != null)
                 {
                     recentSubmissionsConfigurationMap.put(recentSubmissionConfiguration.getMetadataSortField(), recentSubmissionConfiguration);
                 }
 
                 DiscoveryHitHighlightingConfiguration hitHighlightingConfiguration = discoveryConfiguration.getHitHighlightingConfiguration();
-                if(hitHighlightingConfiguration != null)
+                if (hitHighlightingConfiguration != null)
                 {
                     List<DiscoveryHitHighlightFieldConfiguration> fieldConfigurations = hitHighlightingConfiguration.getMetadataFields();
                     for (DiscoveryHitHighlightFieldConfiguration fieldConfiguration : fieldConfigurations)
@@ -1023,7 +1034,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     }
                 }
                 DiscoveryMoreLikeThisConfiguration moreLikeThisConfiguration = discoveryConfiguration.getMoreLikeThisConfiguration();
-                if(moreLikeThisConfiguration != null)
+                if (moreLikeThisConfiguration != null)
                 {
                     for(String metadataField : moreLikeThisConfiguration.getSimilarityMetadataFields())
                     {
@@ -1035,7 +1046,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             List<String> toProjectionFields = new ArrayList<String>();
             String[] projectionFields = DSpaceServicesFactory.getInstance().getConfigurationService().getArrayProperty("discovery.index.projection");
-            if(projectionFields != null){
+            if (projectionFields != null) {
                 for (String field : projectionFields) {
                     toProjectionFields.add(field.trim());
                 }
@@ -1128,7 +1139,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 if ((searchFilters.get(field) != null || searchFilters.get(unqualifiedField + "." + Item.ANY) != null))
                 {
                     List<DiscoverySearchFilter> searchFilterConfigs = searchFilters.get(field);
-                    if(searchFilterConfigs == null)
+                    if (searchFilterConfigs == null)
                     {
                         searchFilterConfigs = searchFilters.get(unqualifiedField + "." + Item.ANY);
                     }
@@ -1137,15 +1148,15 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     {
                         Date date = null;
                         String separator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("discovery.solr.facets.split.char");
-                        if(separator == null)
+                        if (separator == null)
                         {
                             separator = FILTER_SEPARATOR;
                         }
-                        if(searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
+                        if (searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
                         {
                             //For our search filters that are dates we format them properly
                             date = MultiFormatDateParser.parse(value);
-                            if(date != null)
+                            if (date != null)
                             {
                                 //TODO: make this date format configurable !
                                 value = DateFormatUtils.formatUTC(date, "yyyy-MM-dd");
@@ -1214,9 +1225,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                             }
                         }
 
-                        if(searchFilter.getFilterType().equals(DiscoverySearchFilterFacet.FILTER_TYPE_FACET))
+                        if (searchFilter.getFilterType().equals(DiscoverySearchFilterFacet.FILTER_TYPE_FACET))
                         {
-                            if(searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_TEXT))
+                            if (searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_TEXT))
                             {
                                 //Add a special filter
                                 //We use a separator to split up the lowercase and regular case, this is needed to get our filters in regular case
@@ -1230,10 +1241,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                                 {
                                     doc.addField(searchFilter.getIndexFieldName() + "_filter", value.toLowerCase() + separator + value);
                                 }
-                            }else
+                            } else
-                                if(searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
+                                if (searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
                                 {
-                                    if(date != null)
+                                    if (date != null)
                                     {
                                         String indexField = searchFilter.getIndexFieldName() + ".year";
                                         String yearUTC = DateFormatUtils.formatUTC(date, "yyyy");
@@ -1264,18 +1275,18 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                                         }
 
                                         //Also save a sort value of this year, this is required for determining the upper & lower bound year of our facet
-                                        if(doc.getField(indexField + "_sort") == null)
+                                        if (doc.getField(indexField + "_sort") == null)
                                         {
                                             //We can only add one year so take the first one
                                             doc.addField(indexField + "_sort", yearUTC);
                                         }
                                 }
-                            }else
+                            } else
-                            if(searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_HIERARCHICAL))
+                            if (searchFilter.getType().equals(DiscoveryConfigurationParameters.TYPE_HIERARCHICAL))
                             {
                                 HierarchicalSidebarFacetConfiguration hierarchicalSidebarFacetConfiguration = (HierarchicalSidebarFacetConfiguration) searchFilter;
                                 String[] subValues = value.split(hierarchicalSidebarFacetConfiguration.getSplitter());
-                                if(hierarchicalSidebarFacetConfiguration.isSkipFirstNodeLevel() && 1 < subValues.length)
+                                if (hierarchicalSidebarFacetConfiguration.isSkipFirstNodeLevel() && 1 < subValues.length)
                                 {
                                     //Remove the first element of our array
                                     subValues = (String[]) ArrayUtils.subarray(subValues, 1, subValues.length);
@@ -1286,7 +1297,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                                     for(int j = 0; j <= i; j++)
                                     {
                                         valueBuilder.append(subValues[j]);
-                                        if(j < i)
+                                        if (j < i)
                                         {
                                             valueBuilder.append(hierarchicalSidebarFacetConfiguration.getSplitter());
                                         }
@@ -1310,34 +1321,34 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 {
                     //Only add sort value once
                     String type;
-                    if(sortFields.get(field) != null)
+                    if (sortFields.get(field) != null)
                     {
                         type = sortFields.get(field).getType();
-                    }else{
+                    } else {
                         type = recentSubmissionsConfigurationMap.get(field).getType();
                     }
 
-                    if(type.equals(DiscoveryConfigurationParameters.TYPE_DATE))
+                    if (type.equals(DiscoveryConfigurationParameters.TYPE_DATE))
                     {
                         Date date = MultiFormatDateParser.parse(value);
-                        if(date != null)
+                        if (date != null)
                         {
                             doc.addField(field + "_dt", date);
-                        }else{
+                        } else {
                             log.warn("Error while indexing sort date field, item: " + item.getHandle() + " metadata field: " + field + " date value: " + date);
                         }
-                    }else{
+                    } else {
                         doc.addField(field + "_sort", value);
                     }
                     sortFieldsAdded.add(field);
                 }
 
-                if(hitHighlightingFields.contains(field) || hitHighlightingFields.contains("*") || hitHighlightingFields.contains(unqualifiedField + "." + Item.ANY))
+                if (hitHighlightingFields.contains(field) || hitHighlightingFields.contains("*") || hitHighlightingFields.contains(unqualifiedField + "." + Item.ANY))
                 {
                     doc.addField(field + "_hl", value);
                 }
 
-                if(moreLikeThisFields.contains(field) || moreLikeThisFields.contains(unqualifiedField + "." + Item.ANY))
+                if (moreLikeThisFields.contains(field) || moreLikeThisFields.contains(unqualifiedField + "." + Item.ANY))
                 {
                     doc.addField(field + "_mlt", value);
                 }
@@ -1384,7 +1395,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             List<MetadataValue> values = itemService.getMetadataByMetadataString(item, "dc.relation.ispartof");
 
-            if(values != null && values.size() > 0 && values.get(0) != null && values.get(0).getValue() != null)
+            if (values != null && values.size() > 0 && values.get(0) != null && values.get(0).getValue() != null)
             {
                 // group on parent
                 String handlePrefix = ConfigurationManager.getProperty("handle.canonical.prefix");
@@ -1472,10 +1483,15 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     /**
      * Create Lucene document with all the shared fields initialized.
      *
-     * @param type      Type of DSpace Object
+     * @param type
+     *     Type of DSpace Object
      * @param id
+     *     internal identifier
      * @param handle
-     * @param locations @return
+     *     handle string
+     * @param locations
+     *     list of collection/community internal identifiers
+     * @return initialized Lucene document
      */
     protected SolrInputDocument buildDocument(int type, UUID id, String handle,
                                             List<String> locations)
@@ -1589,7 +1605,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     }
 
     public String locationToName(Context context, String field, String value) throws SQLException {
-        if("location.comm".equals(field) || "location.coll".equals(field))
+        if ("location.comm".equals(field) || "location.coll".equals(field))
         {
             int type = ("location.comm").equals(field) ? Constants.COMMUNITY : Constants.COLLECTION;
             DSpaceObject commColl = null;
@@ -1597,7 +1613,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             {
                 commColl = contentServiceFactory.getDSpaceObjectService(type).find(context, UUID.fromString(value));
             }
-            if(commColl != null)
+            if (commColl != null)
             {
                 return commColl.getName();
             }
@@ -1623,7 +1639,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     @Override
     public DiscoverResult search(Context context, DSpaceObject dso, DiscoverQuery discoveryQuery, boolean includeUnDiscoverable) throws SearchServiceException {
-        if(dso != null)
+        if (dso != null)
         {
             if (dso instanceof Community)
             {
@@ -1644,7 +1660,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     @Override
     public DiscoverResult search(Context context, DiscoverQuery discoveryQuery, boolean includeUnDiscoverable) throws SearchServiceException {
         try {
-            if(getSolr() == null){
+            if (getSolr() == null) {
                 return new DiscoverResult();
             }
             SolrQuery solrQuery = resolveToSolrQuery(context, discoveryQuery, includeUnDiscoverable);
@@ -1664,7 +1680,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         SolrQuery solrQuery = new SolrQuery();
 
         String query = "*:*";
-        if(discoveryQuery.getQuery() != null)
+        if (discoveryQuery.getQuery() != null)
         {
             query = discoveryQuery.getQuery();
         }
@@ -1682,7 +1698,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         solrQuery.addField(RESOURCE_TYPE_FIELD);
         solrQuery.addField(RESOURCE_ID_FIELD);
 
-        if(discoveryQuery.isSpellCheck())
+        if (discoveryQuery.isSpellCheck())
         {
             solrQuery.setParam(SpellingParams.SPELLCHECK_Q, query);
             solrQuery.setParam(SpellingParams.SPELLCHECK_COLLATE, Boolean.TRUE);
@@ -1700,7 +1716,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             String filterQuery = discoveryQuery.getFilterQueries().get(i);
             solrQuery.addFilterQuery(filterQuery);
         }
-        if(discoveryQuery.getDSpaceObjectFilter() != -1)
+        if (discoveryQuery.getDSpaceObjectFilter() != -1)
         {
             solrQuery.addFilterQuery(RESOURCE_TYPE_FIELD + ":" + discoveryQuery.getDSpaceObjectFilter());
         }
@@ -1711,20 +1727,20 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrQuery.addFilterQuery(filterQuery + ":[* TO *]");
         }
 
-        if(discoveryQuery.getStart() != -1)
+        if (discoveryQuery.getStart() != -1)
         {
             solrQuery.setStart(discoveryQuery.getStart());
         }
 
-        if(discoveryQuery.getMaxResults() != -1)
+        if (discoveryQuery.getMaxResults() != -1)
         {
             solrQuery.setRows(discoveryQuery.getMaxResults());
         }
 
-        if(discoveryQuery.getSortField() != null)
+        if (discoveryQuery.getSortField() != null)
         {
             SolrQuery.ORDER order = SolrQuery.ORDER.asc;
-            if(discoveryQuery.getSortOrder().equals(DiscoverQuery.SORT_ORDER.desc))
+            if (discoveryQuery.getSortOrder().equals(DiscoverQuery.SORT_ORDER.desc))
                 order = SolrQuery.ORDER.desc;
 
             solrQuery.addSortField(discoveryQuery.getSortField(), order);
@@ -1737,7 +1753,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         }
 
         List<DiscoverFacetField> facetFields = discoveryQuery.getFacetFields();
-        if(0 < facetFields.size())
+        if (0 < facetFields.size())
         {
             //Only add facet information if there are any facets
             for (DiscoverFacetField facetFieldConfig : facetFields)
@@ -1748,10 +1764,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 // Setting the facet limit in this fashion ensures that each facet can have its own max
                 solrQuery.add("f." + field + "." + FacetParams.FACET_LIMIT, String.valueOf(facetFieldConfig.getLimit()));
                 String facetSort;
-                if(DiscoveryConfigurationParameters.SORT.COUNT.equals(facetFieldConfig.getSortOrder()))
+                if (DiscoveryConfigurationParameters.SORT.COUNT.equals(facetFieldConfig.getSortOrder()))
                 {
                     facetSort = FacetParams.FACET_SORT_COUNT;
-                }else{
+                } else {
                     facetSort = FacetParams.FACET_SORT_INDEX;
                 }
                 solrQuery.add("f." + field + "." + FacetParams.FACET_SORT, facetSort);
@@ -1761,7 +1777,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                             + FacetParams.FACET_OFFSET,
                             String.valueOf(facetFieldConfig.getOffset()));
                 }
-                if(facetFieldConfig.getPrefix() != null)
+                if (facetFieldConfig.getPrefix() != null)
                 {
                     solrQuery.setFacetPrefix(field, facetFieldConfig.getPrefix());
                 }
@@ -1773,7 +1789,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 solrQuery.addFacetQuery(facetQuery);
             }
 
-            if(discoveryQuery.getFacetMinCount() != -1)
+            if (discoveryQuery.getFacetMinCount() != -1)
             {
                 solrQuery.setFacetMinCount(discoveryQuery.getFacetMinCount());
             }
@@ -1781,7 +1797,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrQuery.setParam(FacetParams.FACET_OFFSET, String.valueOf(discoveryQuery.getFacetOffset()));
         }
 
-        if(0 < discoveryQuery.getHitHighlightingFields().size())
+        if (0 < discoveryQuery.getHitHighlightingFields().size())
         {
             solrQuery.setHighlight(true);
             solrQuery.add(HighlightParams.USE_PHRASE_HIGHLIGHTER, Boolean.TRUE.toString());
@@ -1805,7 +1821,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     @Override
     public InputStream searchJSON(Context context, DiscoverQuery query, DSpaceObject dso, String jsonIdentifier) throws SearchServiceException {
-        if(dso != null)
+        if (dso != null)
         {
             if (dso instanceof Community)
             {
@@ -1824,7 +1840,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     @Override
     public InputStream searchJSON(Context context, DiscoverQuery discoveryQuery, String jsonIdentifier) throws SearchServiceException {
-        if(getSolr() == null)
+        if (getSolr() == null)
         {
             return null;
         }
@@ -1854,7 +1870,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     protected DiscoverResult retrieveResult(Context context, DiscoverQuery query, QueryResponse solrQueryResponse) throws SQLException {
         DiscoverResult result = new DiscoverResult();
 
-        if(solrQueryResponse != null)
+        if (solrQueryResponse != null)
         {
             result.setSearchTime(solrQueryResponse.getQTime());
             result.setStart(query.getStart());
@@ -1866,7 +1882,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             {
                 DSpaceObject dso = findDSpaceObject(context, doc);
 
-                if(dso != null)
+                if (dso != null)
                 {
                     result.addDSpaceObject(dso);
                 } else {
@@ -1887,10 +1903,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 }
                 result.addSearchDocument(dso, resultDoc);
 
-                if(solrQueryResponse.getHighlighting() != null)
+                if (solrQueryResponse.getHighlighting() != null)
                 {
                     Map<String, List<String>> highlightedFields = solrQueryResponse.getHighlighting().get(dso.getType() + "-" + dso.getID());
-                    if(MapUtils.isNotEmpty(highlightedFields))
+                    if (MapUtils.isNotEmpty(highlightedFields))
                     {
                         //We need to remove all the "_hl" appendix strings from our keys
                         Map<String, List<String>> resultMap = new HashMap<String, List<String>>();
@@ -1906,7 +1922,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             //Resolve our facet field values
             List<FacetField> facetFields = solrQueryResponse.getFacetFields();
-            if(facetFields != null)
+            if (facetFields != null)
             {
                 for (int i = 0; i <  facetFields.size(); i++)
                 {
@@ -1915,7 +1931,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     List<FacetField.Count> facetValues = facetField.getValues();
                     if (facetValues != null)
                     {
-                        if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE) && facetFieldConfig.getSortOrder().equals(DiscoveryConfigurationParameters.SORT.VALUE))
+                        if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE) && facetFieldConfig.getSortOrder().equals(DiscoveryConfigurationParameters.SORT.VALUE))
                         {
                             //If we have a date & are sorting by value, ensure that the results are flipped for a proper result
                            Collections.reverse(facetValues);
@@ -1942,7 +1958,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 }
             }
 
-            if(solrQueryResponse.getFacetQuery() != null)
+            if (solrQueryResponse.getFacetQuery() != null)
             {
                 // just retrieve the facets in the order they where requested!
                 // also for the date we ask it in proper (reverse) order
@@ -1967,17 +1983,17 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     Integer count = sortedFacetQueries.get(facetQuery);
 
                     //No need to show empty years
-                    if(0 < count)
+                    if (0 < count)
                     {
                         result.addFacetResult(facetField, new DiscoverResult.FacetResult(filter, name, null, name, count));
                     }
                 }
             }
 
-            if(solrQueryResponse.getSpellCheckResponse() != null)
+            if (solrQueryResponse.getSpellCheckResponse() != null)
             {
                 String recommendedQuery = solrQueryResponse.getSpellCheckResponse().getCollatedResult();
-                if(StringUtils.isNotBlank(recommendedQuery))
+                if (StringUtils.isNotBlank(recommendedQuery))
                 {
                     result.setSpellCheckQuery(recommendedQuery);
                 }
@@ -1987,6 +2003,17 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         return result;
     }
 
+    /**
+     * Find DSpace object by type and UUID or by handle from given Solr document
+     *
+     * @param context
+     *     The relevant DSpace Context.
+     * @param doc
+     *     the solr document
+     * @return DSpace object
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     */
     protected DSpaceObject findDSpaceObject(Context context, SolrDocument doc) throws SQLException {
 
         Integer type = (Integer) doc.getFirstValue(RESOURCE_TYPE_FIELD);
@@ -2005,9 +2032,17 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     }
 
 
-    /** Simple means to return the search result as an InputStream */
+    /**
+     * Simple means to return the search result as an InputStream
+     *
+     * @param query discovery query
+     * @return input stream
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SearchServiceException if something went wrong with querying the solr server
+     */
     public java.io.InputStream searchAsInputStream(DiscoverQuery query) throws SearchServiceException, java.io.IOException {
-        if(getSolr() == null)
+        if (getSolr() == null)
         {
             return null;
         }
@@ -2038,7 +2073,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     {
 
         try {
-            if(getSolr() == null)
+            if (getSolr() == null)
             {
                 return Collections.emptyList();
             }
@@ -2088,10 +2123,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         DiscoverFilterQuery result = new DiscoverFilterQuery();
 
         StringBuilder filterQuery = new StringBuilder();
-        if(StringUtils.isNotBlank(field) && StringUtils.isNotBlank(value))
+        if (StringUtils.isNotBlank(field) && StringUtils.isNotBlank(value))
         {
             filterQuery.append(field);
-            if("equals".equals(operator))
+            if ("equals".equals(operator))
             {
                 //Query the keyword indexed field !
                 filterQuery.append("_keyword");
@@ -2108,10 +2143,10 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 filterQuery.insert(0, "-");
             }
             filterQuery.append(":");
-            if("equals".equals(operator) || "notequals".equals(operator))
+            if ("equals".equals(operator) || "notequals".equals(operator))
             {
                 //DO NOT ESCAPE RANGE QUERIES !
-                if(!value.matches("\\[.*TO.*\\]"))
+                if (!value.matches("\\[.*TO.*\\]"))
                 {
                     value = ClientUtils.escapeQueryChars(value);
                     filterQuery.append(value);
@@ -2127,9 +2162,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                     filterQuery.append(value);
                 }
             }
-            else{
+            else {
                 //DO NOT ESCAPE RANGE QUERIES !
-                if(!value.matches("\\[.*TO.*\\]"))
+                if (!value.matches("\\[.*TO.*\\]"))
                 {
                     value = ClientUtils.escapeQueryChars(value);
                     filterQuery.append("(").append(value).append(")");
@@ -2176,13 +2211,13 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             solrQuery.setParam(MoreLikeThisParams.DOC_COUNT, String.valueOf(mltConfig.getMax()));
             solrQuery.setParam(MoreLikeThisParams.MIN_WORD_LEN, String.valueOf(mltConfig.getMinWordLength()));
 
-            if(getSolr() == null)
+            if (getSolr() == null)
             {
                 return Collections.emptyList();
             }
             QueryResponse rsp = getSolr().query(solrQuery);
             NamedList mltResults = (NamedList) rsp.getResponse().get("moreLikeThis");
-            if(mltResults != null && mltResults.get(item.getType() + "-" + item.getID()) != null)
+            if (mltResults != null && mltResults.get(item.getType() + "-" + item.getID()) != null)
             {
                 SolrDocumentList relatedDocs = (SolrDocumentList) mltResults.get(item.getType() + "-" + item.getID());
                 for (Object relatedDoc : relatedDocs)
@@ -2207,67 +2242,67 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     @Override
     public String toSortFieldIndex(String metadataField, String type)
     {
-        if(type.equals(DiscoveryConfigurationParameters.TYPE_DATE))
+        if (type.equals(DiscoveryConfigurationParameters.TYPE_DATE))
         {
             return metadataField + "_dt";
-        }else{
+        } else {
             return metadataField + "_sort";
         }
     }
 
     protected String transformFacetField(DiscoverFacetField facetFieldConfig, String field, boolean removePostfix)
     {
-        if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_TEXT))
+        if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_TEXT))
         {
-            if(removePostfix)
+            if (removePostfix)
             {
                 return field.substring(0, field.lastIndexOf("_filter"));
-            }else{
+            } else {
                 return field + "_filter";
             }
-        }else if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
+        } else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_DATE))
         {
-            if(removePostfix)
+            if (removePostfix)
             {
                 return field.substring(0, field.lastIndexOf(".year"));
-            }else{
+            } else {
                 return field + ".year";
             }
-        }else if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_AC))
+        } else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_AC))
         {
-            if(removePostfix)
+            if (removePostfix)
             {
                 return field.substring(0, field.lastIndexOf("_ac"));
-            }else{
+            } else {
                 return field + "_ac";
             }
-        }else if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_HIERARCHICAL))
+        } else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_HIERARCHICAL))
         {
-            if(removePostfix)
+            if (removePostfix)
             {
                 return StringUtils.substringBeforeLast(field, "_tax_");
-            }else{
+            } else {
                 //Only display top level filters !
                 return field + "_tax_0_filter";
             }
-        }else if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_AUTHORITY))
+        } else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_AUTHORITY))
         {
-            if(removePostfix)
+            if (removePostfix)
             {
                 return field.substring(0, field.lastIndexOf("_acid"));
-            }else{
+            } else {
                 return field + "_acid";
             }
-        }else if(facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_STANDARD))
+        } else if (facetFieldConfig.getType().equals(DiscoveryConfigurationParameters.TYPE_STANDARD))
         {
             return field;
-        }else{
+        } else {
             return field;
         }
     }
 
     protected String transformDisplayedValue(Context context, String field, String value) throws SQLException {
-        if(field.equals("location.comm") || field.equals("location.coll"))
+        if (field.equals("location.comm") || field.equals("location.coll"))
         {
             value = locationToName(context, field, value);
         }
@@ -2276,7 +2311,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             //We have a filter make sure we split !
             String separator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("discovery.solr.facets.split.char");
-            if(separator == null)
+            if (separator == null)
             {
                 separator = FILTER_SEPARATOR;
             }
@@ -2291,7 +2326,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 valueBuffer.append(split[0]);
             }
             value = valueBuffer.toString();
-        }else if(value.matches("\\((.*?)\\)"))
+        } else if (value.matches("\\((.*?)\\)"))
         {
             //The brackets where added for better solr results, remove the first & last one
             value = value.substring(1, value.length() -1);
@@ -2300,7 +2335,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     }
 
     protected String transformAuthorityValue(Context context, String field, String value) throws SQLException {
-    	if(field.equals("location.comm") || field.equals("location.coll"))
+        if (field.equals("location.comm") || field.equals("location.coll"))
         {
             return value;
         }
@@ -2309,7 +2344,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             //We have a filter make sure we split !
             String separator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("discovery.solr.facets.split.char");
-            if(separator == null)
+            if (separator == null)
             {
                 separator = FILTER_SEPARATOR;
             }
@@ -2335,7 +2370,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     }
 
     protected String transformSortValue(Context context, String field, String value) throws SQLException {
-        if(field.equals("location.comm") || field.equals("location.coll"))
+        if (field.equals("location.comm") || field.equals("location.coll"))
         {
             value = locationToName(context, field, value);
         }
@@ -2344,7 +2379,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             //We have a filter make sure we split !
             String separator = DSpaceServicesFactory.getInstance().getConfigurationService().getProperty("discovery.solr.facets.split.char");
-            if(separator == null)
+            if (separator == null)
             {
                 separator = FILTER_SEPARATOR;
             }
@@ -2358,7 +2393,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 valueBuffer.append(fqParts[i]);
             }
             value = valueBuffer.toString();
-        }else if(value.matches("\\((.*?)\\)"))
+        } else if (value.matches("\\((.*?)\\)"))
         {
             //The brackets where added for better solr results, remove the first & last one
             value = value.substring(1, value.length() -1);
@@ -2379,7 +2414,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     @Override
     public void commit() throws SearchServiceException {
         try {
-            if(getSolr() != null)
+            if (getSolr() != null)
             {
                 getSolr().commit();
             }

dspace-api/src/main/java/org/dspace/discovery/configuration/DiscoveryHitHighlightFieldConfiguration.java

@@ -55,6 +55,8 @@ public class DiscoveryHitHighlightFieldConfiguration
 
     /**
      * Get the maximum number of highlighted snippets to generate per field
+     *
+     * @return maximum number of highlighted snippets to generate per field
      */
     public int getSnippets()
     {

dspace-api/src/main/java/org/dspace/embargo/EmbargoCLITool.java

@@ -62,10 +62,11 @@ public class EmbargoCLITool {
      *   <dt>-q,--quiet</dt>
      *   <dd>         No output except upon error.</dd>
      * </dl>
+     *
+     * @param argv the command line arguments given
      */
     public static void main(String argv[])
     {
-
         int status = 0;
 
         Options options = new Options();
@@ -197,7 +198,7 @@ public class EmbargoCLITool {
                 if (line.hasOption('a')){
                     embargoService.setEmbargo(context, item);
                 }
-                else{
+                else {
                     log.debug("Testing embargo on item="+item.getHandle()+", date="+liftDate.toString());
                     if (liftDate.toDate().before(now))
                     {
@@ -229,8 +230,8 @@ public class EmbargoCLITool {
             }
             catch (Exception e)
             {
-                log.error("Failed attempting to lift embargo, item="+item.getHandle()+": ", e);
+                log.error("Failed attempting to lift embargo, item=" + item.getHandle() + ": ", e);
-                System.err.println("Failed attempting to lift embargo, item="+item.getHandle()+": "+ e);
+                System.err.println("Failed attempting to lift embargo, item=" + item.getHandle() + ": " + e);
                 status = true;
             }
         }

dspace-api/src/main/java/org/dspace/embargo/EmbargoLifter.java

@@ -28,8 +28,17 @@ public interface EmbargoLifter
      * (access control) by (for example) turning on default read access to all
      * Bitstreams.
      *
-     * @param context the DSpace context
+     * @param context
-     * @param item the Item on which to lift the embargo
+     *     The relevant DSpace Context.
+     * @param item
+     *     the Item on which to lift the embargo
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public void liftEmbargo(Context context, Item item)
         throws SQLException, AuthorizeException, IOException;

dspace-api/src/main/java/org/dspace/embargo/EmbargoServiceImpl.java

@@ -171,6 +171,8 @@ public class EmbargoServiceImpl implements EmbargoService
      * Ensures the configurationService is injected, so that we can
      * get plugins and MD field settings from config.
      * Called by "init-method" in Spring config.
+     *
+     * @throws Exception on generic exception
      */
     public void init() throws Exception
     {

dspace-api/src/main/java/org/dspace/embargo/EmbargoSetter.java

@@ -42,6 +42,11 @@ public interface EmbargoSetter
      * @param item the item to embargo
      * @param terms value of the metadata field configured as embargo terms, if any.
      * @return absolute date on which the embargo is to be lifted, or null if none
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public DCDate parseTerms(Context context, Item item, String terms)
         throws SQLException, AuthorizeException;
@@ -52,6 +57,11 @@ public interface EmbargoSetter
      *
      * @param context the DSpace context
      * @param item the item to embargo
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public void setEmbargo(Context context, Item item)
         throws SQLException, AuthorizeException;
@@ -68,6 +78,13 @@ public interface EmbargoSetter
      *
      * @param context the DSpace context
      * @param item the item to embargo
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public void checkEmbargo(Context context, Item item)
         throws SQLException, AuthorizeException, IOException;

dspace-api/src/main/java/org/dspace/embargo/service/EmbargoService.java

@@ -51,6 +51,11 @@ public interface EmbargoService {
      *
      * @param context the DSpace context
      * @param item the item to embargo
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public void setEmbargo(Context context, Item item)
         throws SQLException, AuthorizeException;
@@ -69,6 +74,11 @@ public interface EmbargoService {
      * @param context the DSpace context
      * @param item the item to embargo
      * @return lift date on which the embargo is to be lifted, or null if none
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public DCDate getEmbargoTermsAsDate(Context context, Item item)
         throws SQLException, AuthorizeException;
@@ -80,6 +90,13 @@ public interface EmbargoService {
      *
      * @param context the DSpace context
      * @param item the item on which to lift the embargo
+     * @throws IOException
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public void liftEmbargo(Context context, Item item)
         throws SQLException, AuthorizeException, IOException;

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

@@ -107,7 +107,7 @@ public class AccountServiceImpl implements AccountService
      * @param token
      *            Account token
      * @return The EPerson corresponding to token, or null.
-     * @exception SQLException
+     * @throws SQLException
      *                If the token or eperson cannot be retrieved from the
      *                database.
      */
@@ -161,7 +161,7 @@ public class AccountServiceImpl implements AccountService
      *            DSpace context
      * @param token
      *            The token to delete
-     * @exception SQLException
+     * @throws SQLException
      *                If a database error occurs
      */
     @Override
@@ -171,7 +171,7 @@ public class AccountServiceImpl implements AccountService
         registrationDataService.deleteByToken(context, token);
     }
 
-    /*
+    /**
      * THIS IS AN INTERNAL METHOD. THE SEND PARAMETER ALLOWS IT TO BE USED FOR
      * TESTING PURPOSES.
      *
@@ -179,15 +179,18 @@ public class AccountServiceImpl implements AccountService
      * is TRUE, this is registration email; otherwise, it is forgot-password
      * email. If send is TRUE, the email is sent; otherwise it is skipped.
      *
-     * Potential error conditions: No EPerson with that email (returns null)
+     * Potential error conditions:
-     * Cannot create registration data in database (throws SQLException) Error
+     * @return null if no EPerson with that email found
-     * sending email (throws MessagingException) Error reading email template
+     * @throws SQLException Cannot create registration data in database 
-     * (throws IOException) Authorization error (throws AuthorizeException)
+     * @throws MessagingException Error sending email
+     * @throws IOException Error reading email template
+     * @throws AuthorizeException Authorization error
      *
-     * @param context DSpace context @param email Email address to send the
+     * @param context DSpace context
-     * forgot-password email to @param isRegister If true, this is for
+     * @param email Email address to send the forgot-password email to
-     * registration; otherwise, it is for forgot-password @param send If true,
+     * @param isRegister If true, this is for registration; otherwise, it is
-     * send email; otherwise do not send any email
+     *     for forgot-password 
+     * @param send If true, send email; otherwise do not send any email
      */
     protected RegistrationData sendInfo(Context context, String email,
             boolean isRegister, boolean send) throws SQLException, IOException,
@@ -234,6 +237,8 @@ public class AccountServiceImpl implements AccountService
      * If isRegister is <code>true</code>, this is registration email;
      * otherwise, it is a forgot-password email.
      *
+     * @param context
+     *     The relevant DSpace Context.
      * @param email
      *     The email address to mail to
      * @param isRegister
@@ -241,10 +246,12 @@ public class AccountServiceImpl implements AccountService
      *     forgot-password email.
      * @param rd
      *     The RDBMS row representing the registration data.
-     * @exception MessagingException
+     * @throws MessagingException
      *     If an error occurs while sending email
-     * @exception IOException
+     * @throws IOException
-     *                If an error occurs while reading the email template.
+     *     A general class of exceptions produced by failed or interrupted I/O operations.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     protected void sendEmail(Context context, String email, boolean isRegister, RegistrationData rd)
             throws MessagingException, IOException, SQLException

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

@@ -104,8 +104,8 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport
     /**
      * Return true if this object equals obj, false otherwise.
      * 
-     * @param obj
+     * @param obj another EPerson.
-     * @return true if ResourcePolicy objects are equal
+     * @return true if EPerson objects are equal in ID, email, and full name
      */
     @Override
     public boolean equals(Object obj)
@@ -165,8 +165,12 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport
      * Locale specification of the form {language} or {language}_{territory},
      * e.g. "en", "en_US", "pt_BR" (the latter is Brazilian Portugese).
      * 
+     * @param context
+     *     The relevant DSpace Context.
      * @param language
      *     language code
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
      public void setLanguage(Context context, String language) throws SQLException {
          getePersonService().setMetadataSingleValue(context, this, "eperson", "language", null, null, language);
@@ -253,8 +257,12 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport
     /**
      * Set the eperson's first name
      * 
+     * @param context
+     *     The relevant DSpace Context.
      * @param firstname
      *     the person's first name
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void setFirstName(Context context, String firstname) throws SQLException {
         getePersonService().setMetadataSingleValue(context, this, "eperson", "firstname", null, null, firstname);
@@ -274,8 +282,12 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport
     /**
      * Set the eperson's last name
      * 
+     * @param context
+     *     The relevant DSpace Context.
      * @param lastname
      *     the person's last name
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
      */
     public void setLastName(Context context, String lastname) throws SQLException {
         getePersonService().setMetadataSingleValue(context, this, "eperson", "lastname", null, null, lastname);
@@ -369,7 +381,7 @@ public class EPerson extends DSpaceObject implements DSpaceObjectLegacySupport
     }
 
     /**
-     * return type found in Constants
+     * @return type found in Constants, see {@link org.dspace.core.Constants#Constants Constants}
      */
     @Override
     public int getType()

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

@@ -45,6 +45,15 @@ public class EPersonCLITool {
 
     /**
      * Tool for manipulating user accounts.
+     *
+     * @param argv the command line arguments given
+     * @throws ParseException
+     *     Base for Exceptions thrown during parsing of a command-line.
+     * @throws SQLException
+     *     An exception that provides information on a database access error or other errors.
+     * @throws AuthorizeException
+     *     Exception indicating the current user of the context does not have permission
+     *     to perform a particular action.
      */
     public static void main(String argv[])
             throws ParseException, SQLException, AuthorizeException {

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

@@ -50,7 +50,9 @@ public class EPersonConsumer implements Consumer
      * Consume the event
      *
      * @param context
+     *     The relevant DSpace Context.
      * @param event
+     *     Which Event to consume
      * @throws Exception if error
      */
     @Override
@@ -116,6 +118,7 @@ public class EPersonConsumer implements Consumer
      * Handle the end of the event
      *
      * @param ctx
+     *     The relevant DSpace Context.
      * @throws Exception if error
      */
     @Override
@@ -129,6 +132,7 @@ public class EPersonConsumer implements Consumer
      * Finish the event
      *
      * @param ctx
+     *     The relevant DSpace Context.
      */
     @Override
     public void finish(Context ctx)