[maven-release-plugin] prepare release dspace-5.9

DS-3936 bower registry needs updating (5.x port)

.gitignore

@@ -3,6 +3,7 @@ target/
 
 ## Ignore project files created by Eclipse
 .settings/
+/bin/
 .project
 .classpath
 

.travis.yml

@@ -1,4 +1,5 @@
 language: java
+sudo: false
 
 env: 
   # Give Maven 1GB of memory to work with
@@ -6,6 +7,8 @@ env:
 
 # Install prerequisites for building Mirage2 more rapidly
 before_install:
+  # Remove outdated settings.xml from Travis builds. Workaround for https://github.com/travis-ci/travis-ci/issues/4629
+  - rm ~/.m2/settings.xml
   # Install latest Node.js 0.10.x & print version info
   - nvm install 0.10
   - node --version
@@ -17,10 +20,10 @@ before_install:
   # Print ruby version info (should be installed)
   - ruby -v
   # Install Sass & print version info
-  - gem install sass
+  - gem install sass -v 3.3.14
   - sass -v
   # Install Compass & print version info
-  - gem install compass
+  - gem install compass -v 1.0.1
   - compass version
 
 # Skip install stage, as we'll do it below

LICENSE

@@ -1,7 +1,7 @@
 DSpace source code license:
 
 
-Copyright (c) 2002-2013, DuraSpace.  All rights reserved.
+Copyright (c) 2002-2017, DuraSpace.  All rights reserved.
 
 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are

LICENSES_THIRD_PARTY

@@ -266,22 +266,24 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Morfologik Stemming Dictionary for Polish (org.carrot2:morfologik-polish:1.7.1 - http://morfologik.blogspot.com/morfologik-polish/)
         * Morfologik Stemming APIs (org.carrot2:morfologik-stemming:1.7.1 - http://morfologik.blogspot.com/morfologik-stemming/)
         * databene ContiPerf (org.databene:contiperf:2.2.0 - http://databene.org/contiperf)
-        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
-        * DSpace JSP-UI (org.dspace:dspace-jspui:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
-        * DSpace OAI-PMH (org.dspace:dspace-oai:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
-        * DSpace RDF (org.dspace:dspace-rdf:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
-        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:5.0-rc4-SNAPSHOT - http://demo.dspace.org)
-        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
-        * Apache Solr Webapp (org.dspace:dspace-solr:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
-        * DSpace SWORD (org.dspace:dspace-sword:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
-        * DSpace SWORD v2 (org.dspace:dspace-swordv2:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
-        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
+        * DSpace Kernel :: API and Implementation (org.dspace:dspace-api:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-api)
+        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:5.0.4 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-api-lang)
+        * DSpace JSP-UI (org.dspace:dspace-jspui:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-jspui)
+        * DSpace OAI-PMH (org.dspace:dspace-oai:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-oai)
+        * DSpace RDF (org.dspace:dspace-rdf:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-rdf)
+        * DSpace REST :: API and Implementation (org.dspace:dspace-rest:5.3-SNAPSHOT - http://demo.dspace.org)
+        * DSpace Services Framework :: API and Implementation (org.dspace:dspace-services:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-services)
+        * Apache Solr Webapp (org.dspace:dspace-solr:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-solr)
+        * DSpace SWORD (org.dspace:dspace-sword:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-sword)
+        * DSpace SWORD v2 (org.dspace:dspace-swordv2:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-swordv2)
+        * DSpace XML-UI (Manakin) (org.dspace:dspace-xmlui:5.3-SNAPSHOT - https://github.com/dspace/DSpace/dspace-xmlui)
+        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:5.0.5 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-xmlui-lang)
         * handle (org.dspace:handle:6.2 - no url defined)
         * jargon (org.dspace:jargon:1.4.25 - no url defined)
         * mets (org.dspace:mets:1.5.2 - no url defined)
         * oclc-harvester2 (org.dspace:oclc-harvester2:0.1.12 - no url defined)
         * Repackaged Cocoon Servlet Service Implementation (org.dspace.dependencies.cocoon:dspace-cocoon-servlet-service-impl:1.0.3 - http://projects.dspace.org/dspace-pom/dspace-cocoon-servlet-service-impl)
-        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:5.0-rc4-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
+        * DSpace Kernel :: Additions and Local Customizations (org.dspace.modules:additions:5.3-SNAPSHOT - https://github.com/dspace/DSpace/modules/additions)
         * Hamcrest All (org.hamcrest:hamcrest-all:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-all)
         * Hamcrest Core (org.hamcrest:hamcrest-core:1.3 - https://github.com/hamcrest/JavaHamcrest/hamcrest-core)
         * JBibTeX (org.jbibtex:jbibtex:1.0.10 - http://www.jbibtex.org)
@@ -386,8 +388,3 @@ https://wiki.duraspace.org/display/DSPACE/Code+Contribution+Guidelines
         * Dough Lea's util.concurrent package (concurrent:concurrent:1.3.4 - no url defined)
         * Reflections (org.reflections:reflections:0.9.9-RC1 - http://code.google.com/p/reflections/reflections/)
         * XZ for Java (org.tukaani:xz:1.4 - http://tukaani.org/xz/java.html)
-
-    Unknown license:
-
-        * DSpace I18N :: Language Packs (org.dspace:dspace-api-lang:5.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-api-lang)
-        * DSpace XML-UI (Manakin) I18N :: Language Packs (org.dspace:dspace-xmlui-lang:5.0.2 - http://nexus.sonatype.org/oss-repository-hosting.html/dspace-xmlui-lang)

build.properties

@@ -66,14 +66,12 @@ db.password=dspace
 #db.username=dspace
 #db.password=dspace
 
-# Schema name - if your database contains multiple schemas, you can avoid problems with
-# retrieving the definitions of duplicate object names by specifying
-# the schema name here that is used for DSpace by uncommenting the following entry
-
-# NOTE: this configuration option is for PostgreSQL only. For Oracle, schema is equivalent
-# to user name. DSpace depends on the PostgreSQL understanding of schema. If you are using
-# Oracle, just leave this this value blank.
-
+# Schema name - if your database contains multiple schemas, you can avoid
+# problems with retrieving the definitions of duplicate object names by
+# specifying the schema name that is used for DSpace.
+# ORACLE USAGE NOTE: In Oracle, schema is equivalent to "username". This means
+# specifying a "db.schema" is often unnecessary (i.e. you can leave it blank),
+# UNLESS your Oracle DB Account (in db.username) has access to multiple schemas.
 db.schema = 
 
 # Maximum number of DB connections in pool

dspace-api/pom.xml

@@ -12,7 +12,7 @@
     <parent>
         <groupId>org.dspace</groupId>
         <artifactId>dspace-parent</artifactId>
-        <version>5.0</version>
+        <version>5.9</version>
         <relativePath>..</relativePath>
     </parent>
 
@@ -209,7 +209,7 @@
                             </execution>
                         </executions>
                     </plugin>
-                    
+
                     <!-- FileWeaver plugin is in charge of initializing & "weaving" together
                          the dspace.cfg file to be used by the Unit Testing environment.
                          It weaves two files, the default 'dspace.cfg' and 'dspace.cfg.more',
@@ -528,9 +528,9 @@
             <version>1.8</version>
         </dependency>
         <dependency>
-            <groupId>com.maxmind.geoip</groupId>
-            <artifactId>geoip-api</artifactId>
-            <version>1.2.11</version>
+            <groupId>com.maxmind.geoip2</groupId>
+            <artifactId>geoip2</artifactId>
+            <version>2.11.0</version>
         </dependency>
         <dependency>
             <groupId>org.apache.ant</groupId>
@@ -569,10 +569,10 @@
 
 
         <dependency>
-            <groupId>postgresql</groupId>
+            <groupId>org.postgresql</groupId>
             <artifactId>postgresql</artifactId>
         </dependency>
-		
+
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-api</artifactId>
@@ -590,7 +590,7 @@
             <artifactId>im4java</artifactId>
             <version>1.4.0</version>
         </dependency>
-        
+
         <!-- Flyway DB API (flywaydb.org) is used to manage DB upgrades automatically. -->
         <dependency>
             <groupId>org.flywaydb</groupId>
@@ -603,13 +603,21 @@
             <groupId>com.google.apis</groupId>
             <artifactId>google-api-services-analytics</artifactId>
         </dependency>
+        <dependency>
+            <groupId>com.google.api-client</groupId>
+            <artifactId>google-api-client</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.google.http-client</groupId>
+            <artifactId>google-http-client</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.google.http-client</groupId>
             <artifactId>google-http-client-jackson2</artifactId>
         </dependency>
         <dependency>
             <groupId>com.google.oauth-client</groupId>
-            <artifactId>google-oauth-client-jetty</artifactId>
+            <artifactId>google-oauth-client</artifactId>
         </dependency>
         <!-- FindBugs -->
         <dependency>
@@ -631,6 +639,66 @@
             <version>1</version>
             <type>jar</type>
         </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-impl</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.ws.commons.axiom</groupId>
+            <artifactId>axiom-api</artifactId>
+            <!-- NOTE: SWORDv2 needs 1.2.14, required by Abdera: https://abdera.apache.org/ -->
+            <version>1.2.14</version>
+        </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.core</groupId>
+            <artifactId>jersey-client</artifactId>
+            <version>2.22.1</version>
+        </dependency>
+        <!-- S3 -->
+        <dependency>
+            <groupId>com.amazonaws</groupId>
+            <artifactId>aws-java-sdk-s3</artifactId>
+            <version>1.10.50</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>joda-time</groupId>
+                    <artifactId>joda-time</artifactId>
+                </exclusion>
+                <exclusion>
+                    <groupId>com.fasterxml.jackson.core</groupId>
+                    <artifactId>jackson-databind</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <!-- S3 also wanted jackson... -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-databind</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-annotations</artifactId>
+        </dependency>
+
+        <!-- For ORCID v2 integration -->
+        <dependency>
+            <groupId>org.dspace</groupId>
+            <artifactId>orcid-jaxb-api</artifactId>
+            <version>2.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.json</groupId>
+            <artifactId>json</artifactId>
+            <version>20180130</version>
+        </dependency>
     </dependencies>
 
 </project>

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

@@ -113,8 +113,8 @@ public class CommunityFiliator
         CommunityFiliator filiator = new CommunityFiliator();
         Context c = new Context();
 
-        // ve are superuser!
-        c.setIgnoreAuthorization(true);
+        // we are superuser!
+        c.turnOffAuthorisationSystem();
 
         try
         {

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

@@ -228,7 +228,7 @@ public final class CreateAdministrator
     {
     	// Of course we aren't an administrator yet so we need to
     	// circumvent authorisation
-    	context.setIgnoreAuthorization(true);
+    	context.turnOffAuthorisationSystem();
     	
     	// Find administrator group
     	Group admins = Group.find(context, 1);

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

@@ -88,7 +88,7 @@ public class MetadataExporter
     {
         // create a context
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
 
         OutputFormat xmlFormat = new OutputFormat(Method.XML, "UTF-8", true);
         xmlFormat.setLineWidth(120);

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

@@ -187,7 +187,7 @@ public class DSpaceCSV implements Serializable
             StringBuilder lineBuilder = new StringBuilder();
             String lineRead;
 
-            while (StringUtils.isNotBlank(lineRead = input.readLine()))
+            while ((lineRead = input.readLine()) != null)
             {
                 if (lineBuilder.length() > 0) {
                     // Already have a previously read value - add this line

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

@@ -1169,10 +1169,8 @@ public class MetadataImport
      */
     private static boolean isAuthorityControlledField(String md)
     {
-        int pos = md.indexOf("[");
-        String mdf = (pos > -1 ? md.substring(0, pos) : md);
-        pos = md.indexOf(":");
-        mdf = (pos > -1 ? md.substring(pos+1) : md);
+        String mdf = StringUtils.substringAfter(md, ":");
+        mdf = StringUtils.substringBefore(mdf, "[");
         return authorityControlled.contains(mdf);
     }
 

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

@@ -89,16 +89,16 @@ public class MetadataImportInvalidHeadingException extends Exception
     {
         if (type == SCHEMA)
         {
-            return "Unknown metadata schema in row " + column + ": " + badHeading;
+            return "Unknown metadata schema in column " + column + ": " + badHeading;
         } else if (type == ELEMENT)
         {
-            return "Unknown metadata element in row " + column + ": " + badHeading;
+            return "Unknown metadata element in column " + column + ": " + badHeading;
         } else if (type == MISSING)
         {
-            return "Row with missing header: Row " + column;
+            return "Row with missing header: column " + column;
         } else
         {
-            return "Bad metadata declaration in row " + column + ": " + badHeading;
+            return "Bad metadata declaration in column" + column + ": " + badHeading;
         }
     }
-}
+}

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

@@ -209,7 +209,7 @@ public class ItemExport
         }
 
         Context c = new Context();
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         if (myType == Constants.ITEM)
         {

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

@@ -284,7 +284,7 @@ public class ItemImport
             if (line.hasOption('z'))
             {
                 zip = true;
-                zipfilename = sourcedir + System.getProperty("file.separator") + line.getOptionValue('z');
+                zipfilename = line.getOptionValue('z');
             }
 
             //By default assume collections will be given on the command line
@@ -733,7 +733,7 @@ public class ItemImport
                 {
                     clist = mycollections;
                 }
-                addItem(c, mycollections, sourceDir, dircontents[i], mapOut, template);
+                addItem(c, clist, sourceDir, dircontents[i], mapOut, template);
                 System.out.println(i + " " + dircontents[i]);
                 c.clearCache();
             }
@@ -1108,6 +1108,10 @@ public class ItemImport
         {
             value = "";
         }
+        else
+        {
+        	value = value.trim();
+        }
         // //getElementData(n, "element");
         String element = getAttributeValue(n, "element");
         String qualifier = getAttributeValue(n, "qualifier"); //NodeValue();
@@ -1129,8 +1133,8 @@ public class ItemImport
         {
             qualifier = null;
         }
-
-        if (!isTest)
+        // only add metadata if it is no test and there is an real value
+        if (!isTest && !value.equals(""))
         {
             i.addMetadata(schema, element, qualifier, language, value);
         }
@@ -2148,7 +2152,7 @@ public class ItemImport
 					context = new Context();
 					eperson = EPerson.find(context, oldEPerson.getID());
 					context.setCurrentUser(eperson);
-					context.setIgnoreAuthorization(true);
+					context.turnOffAuthorisationSystem();
 					
 					boolean isResume = theResumeDir!=null;
 					

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

@@ -351,7 +351,7 @@ public class ItemUpdate {
 	               	
 	        context = new Context();  
 	        iu.setEPerson(context, iu.eperson);	
-	        context.setIgnoreAuthorization(true);
+	        context.turnOffAuthorisationSystem();
 	        
 	    	HANDLE_PREFIX = ConfigurationManager.getProperty("handle.canonical.prefix");
 	    	if (HANDLE_PREFIX == null || HANDLE_PREFIX.length() == 0)
@@ -362,19 +362,20 @@ public class ItemUpdate {
         	iu.processArchive(context, sourcedir, itemField, metadataIndexName, alterProvenance, isTest);		        	            
 
 	        context.complete();  // complete all transactions
-	        context.setIgnoreAuthorization(false);
         }
         catch (Exception e)
         {
             if (context != null && context.isValid())
             {
                 context.abort();
-            	context.setIgnoreAuthorization(false);
             }
             e.printStackTrace();
             pr(e.toString());
             status = 1;
         }
+        finally {
+        	context.restoreAuthSystemState();
+        }
 
         if (isTest)
         {

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

@@ -11,6 +11,7 @@ import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.lang.reflect.Method;
 import java.util.List;
+import java.util.TreeMap;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.servicemanager.DSpaceKernelImpl;
 import org.dspace.servicemanager.DSpaceKernelInit;
@@ -275,9 +276,21 @@ public class ScriptLauncher
      */
     private static void display()
     {
+        // List all command elements
         List<Element> commands = commandConfigs.getRootElement().getChildren("command");
-        System.out.println("Usage: dspace [command-name] {parameters}");
+
+        // Sort the commands by name.
+        // We cannot just use commands.sort() because it tries to remove and
+        // reinsert Elements within other Elements, and that doesn't work.
+        TreeMap<String, Element> sortedCommands = new TreeMap<>();
         for (Element command : commands)
+        {
+            sortedCommands.put(command.getChild("name").getValue(), command);
+        }
+
+        // Display the sorted list
+        System.out.println("Usage: dspace [command-name] {parameters}");
+        for (Element command : sortedCommands.values())
         {
             System.out.println(" - " + command.getChild("name").getValue() +
                                ": " + command.getChild("description").getValue());

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

@@ -7,9 +7,10 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.InputStream;
+import java.nio.file.Files;
 
 
 /**
@@ -30,9 +31,24 @@ public class ImageMagickImageThumbnailFilter extends ImageMagickThumbnailFilter
             throws Exception
     {
 		File f = inputStreamToTempFile(source, "imthumb", ".tmp");
-    	File f2 = getThumbnailFile(f);
-		return new FileInputStream(f2);
-    }
+    	File f2 = null;
+	    try
+	    {
+		    f2 = getThumbnailFile(f);
+		    byte[] bytes = Files.readAllBytes(f2.toPath());
+		    return new ByteArrayInputStream(bytes);
+	    }
+	    finally
+	    {
+		    //noinspection ResultOfMethodCallIgnored
+		    f.delete();
+		    if (f2 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f2.delete();
+		    }
+	    }
+	}
 
 
 }

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

@@ -7,24 +7,40 @@
  */
 package org.dspace.app.mediafilter;
 
+import java.io.ByteArrayInputStream;
 import java.io.File;
-import java.io.FileInputStream;
 import java.io.InputStream;
+import java.nio.file.Files;
 
 public class ImageMagickPdfThumbnailFilter extends ImageMagickThumbnailFilter {
    public InputStream getDestinationStream(InputStream source)
         throws Exception
     {
 		File f = inputStreamToTempFile(source, "impdfthumb", ".pdf");
-		File f2 = getImageFile(f, 0);
-    	File f3 = getThumbnailFile(f2);
-    	return new FileInputStream(f3);
+		File f2 = null;
+	    File f3 = null;
+	    try
+	    {
+		    f2 = getImageFile(f, 0);
+		    f3 = getThumbnailFile(f2);
+		    byte[] bytes = Files.readAllBytes(f3.toPath());
+		    return new ByteArrayInputStream(bytes);
+	    }
+		finally
+	    {
+		    //noinspection ResultOfMethodCallIgnored
+		    f.delete();
+		    if (f2 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f2.delete();
+		    }
+		    if (f3 != null)
+		    {
+			    //noinspection ResultOfMethodCallIgnored
+			    f3.delete();
+		    }
+	    }
     }
 
-   public static final String[] PDF = {"Adobe PDF"};
-   public String[] getInputMIMETypes()
-  {
-      return PDF;
-  }
-
 }

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

@@ -23,6 +23,7 @@ import org.dspace.content.Bundle;
 import org.dspace.content.Item;
 import org.dspace.core.Context;
 import org.im4java.core.ConvertCmd;
+import org.im4java.core.Info;
 import org.im4java.core.IM4JavaException;
 import org.im4java.core.IMOperation;
 import org.im4java.process.ProcessStarter;
@@ -34,161 +35,163 @@ import org.dspace.core.ConfigurationManager;
  * thumbnail.maxwidth, thumbnail.maxheight, the size we want our thumbnail to be
  * no bigger than. Creates only JPEGs.
  */
-public abstract class ImageMagickThumbnailFilter extends MediaFilter implements SelfRegisterInputFormats
-{
-	private static int width = 180;
-	private static int height = 120;
-	static String bitstreamDescription = "IM Thumbnail";
-	static final String defaultPattern = "Generated Thumbnail";
-	static Pattern replaceRegex = Pattern.compile(defaultPattern);
-	
-	static {
-		String pre = ImageMagickThumbnailFilter.class.getName();
-		String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
-		ProcessStarter.setGlobalSearchPath(s);
-		width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
-		height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
-		String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
-		if (description != null) {
-			bitstreamDescription = description;
-		}
-		try {
-			String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
-		    replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
-		} catch(PatternSyntaxException e) {
-			System.err.println("Invalid thumbnail replacement pattern: "+e.getMessage());
-		}
-		
-	}
-	
-	public ImageMagickThumbnailFilter() {
-	}
-	
-	
-    public String getFilteredName(String oldFilename)
-    {
-        return oldFilename + ".jpg";
-    }
+public abstract class ImageMagickThumbnailFilter extends MediaFilter {
+        private static int width = 180;
+        private static int height = 120;
+        private static boolean flatten = true;
+        static String bitstreamDescription = "IM Thumbnail";
+        static final String defaultPattern = "Generated Thumbnail";
+        static Pattern replaceRegex = Pattern.compile(defaultPattern);
+        static String cmyk_profile;
+        static String srgb_profile;
 
-    /**
-     * @return String bundle name
-     *  
-     */
-    public String getBundleName()
-    {
-        return "THUMBNAIL";
-    }
+        static {
+                String pre = ImageMagickThumbnailFilter.class.getName();
+                String s = ConfigurationManager.getProperty(pre + ".ProcessStarter");
+                ProcessStarter.setGlobalSearchPath(s);
+                width = ConfigurationManager.getIntProperty("thumbnail.maxwidth", width);
+                height = ConfigurationManager.getIntProperty("thumbnail.maxheight", height);
+                flatten = ConfigurationManager.getBooleanProperty(pre + ".flatten", flatten);
+                String description = ConfigurationManager.getProperty(pre + ".bitstreamDescription");
+                cmyk_profile = ConfigurationManager.getProperty(pre + ".cmyk_profile");
+                srgb_profile = ConfigurationManager.getProperty(pre + ".srgb_profile");
+                if (description != null) {
+                        bitstreamDescription = description;
+                }
+                try {
+                        String patt = ConfigurationManager.getProperty(pre + ".replaceRegex");
+                        replaceRegex = Pattern.compile(patt == null ? defaultPattern : patt);
+                } catch (PatternSyntaxException e) {
+                        System.err.println("Invalid thumbnail replacement pattern: " + e.getMessage());
+                }
 
-    /**
-     * @return String bitstreamformat
-     */
-    public String getFormatString()
-    {
-        return "JPEG";
-    }
-
-    /**
-     * @return String bitstreamDescription
-     */
-    public String getDescription()
-    {
-        return bitstreamDescription;
-    }
-
-    public static File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
-		File f = File.createTempFile(prefix, suffix);
-		f.deleteOnExit();
-    	FileOutputStream fos = new FileOutputStream(f);
-    	
-    	byte[] buffer = new byte[1024];
-    	int len = source.read(buffer);
-    	while (len != -1) {
-    		fos.write(buffer, 0, len);
-    		len = source.read(buffer);
-    	}
-    	fos.close();
-		return f;
-    }
-    
-    public static File getThumbnailFile(File f) throws IOException, InterruptedException, IM4JavaException {
-    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-    	f2.deleteOnExit();
-    	ConvertCmd cmd = new ConvertCmd();
-		IMOperation op = new IMOperation();
-		op.addImage(f.getAbsolutePath());
-		op.thumbnail(width, height);
-		op.addImage(f2.getAbsolutePath());
-        if (MediaFilterManager.isVerbose) {
-		    System.out.println("IM Thumbnail Param: "+op);
         }
-		cmd.run(op);
-		return f2;
-    }
-    
-    public static File getImageFile(File f, int page) throws IOException, InterruptedException, IM4JavaException {
-    	File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
-    	f2.deleteOnExit();
-    	ConvertCmd cmd = new ConvertCmd();
-		IMOperation op = new IMOperation();
-		String s = "[" + page + "]";
-		op.addImage(f.getAbsolutePath()+s);
-		op.addImage(f2.getAbsolutePath());
-        if (MediaFilterManager.isVerbose) {
-		    System.out.println("IM Image Param: "+op);
+
+        public ImageMagickThumbnailFilter() {
         }
-		cmd.run(op);
-		return f2;
-    }
-    
-    public boolean preProcessBitstream(Context c, Item item, Bitstream source)
-            throws Exception
-    {
-    	String nsrc = source.getName();
-    	for(Bundle b: item.getBundles("THUMBNAIL")) {
-    		for(Bitstream bit: b.getBitstreams()) {
-    			String n = bit.getName();
-    			if (n != null) {
-    				if (nsrc != null) {
-    					if (!n.startsWith(nsrc)) continue;
-    				}
-    			}
-     	    	String description = bit.getDescription();
-    	    	//If anything other than a generated thumbnail is found, halt processing
-    	    	if (description != null) {
-        	    	if (replaceRegex.matcher(description).matches()) {
-        	            if (MediaFilterManager.isVerbose) {
-        	    		    System.out.println(description + " " + nsrc + " matches pattern and is replacable.");
-        	            }
-        	    		continue;
-        	    	}
-        	    	if (description.equals(bitstreamDescription)) {
-        	            if (MediaFilterManager.isVerbose) {
-        	    		    System.out.println(bitstreamDescription + " " + nsrc + " is replacable.");
-        	            }
-        	    		continue;    	    		
-        	    	}
-    	    	}
-    			System.out.println("Custom Thumbnail exists for " + nsrc + " for item " + item.getHandle() + ".  Thumbnail will not be generated. ");
-    			return false;
-    		}
-    	}
-    	
-    	
-        return true; //assume that the thumbnail is a custom one
-    }
 
-     public String[] getInputMIMETypes()
-    {
-        return ImageIO.getReaderMIMETypes();
-    }
+        public String getFilteredName(String oldFilename) {
+                return oldFilename + ".jpg";
+        }
 
-    public String[] getInputDescriptions()
-    {
-        return null;
-    }
+        /**
+         * @return String bundle name
+         * 
+         */
+        public String getBundleName() {
+                return "THUMBNAIL";
+        }
+
+        /**
+         * @return String bitstreamformat
+         */
+        public String getFormatString() {
+                return "JPEG";
+        }
+
+        /**
+         * @return String bitstreamDescription
+         */
+        public String getDescription() {
+                return bitstreamDescription;
+        }
+
+        public static File inputStreamToTempFile(InputStream source, String prefix, String suffix) throws IOException {
+                File f = File.createTempFile(prefix, suffix);
+                f.deleteOnExit();
+                FileOutputStream fos = new FileOutputStream(f);
+
+                byte[] buffer = new byte[1024];
+                int len = source.read(buffer);
+                while (len != -1) {
+                        fos.write(buffer, 0, len);
+                        len = source.read(buffer);
+                }
+                fos.close();
+                return f;
+        }
+
+        public static File getThumbnailFile(File f) throws IOException, InterruptedException, IM4JavaException {
+                File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+                f2.deleteOnExit();
+                ConvertCmd cmd = new ConvertCmd();
+                IMOperation op = new IMOperation();
+                op.autoOrient();
+                op.addImage(f.getAbsolutePath());
+                op.thumbnail(width, height);
+                op.addImage(f2.getAbsolutePath());
+                if (MediaFilterManager.isVerbose) {
+                        System.out.println("IM Thumbnail Param: " + op);
+                }
+                cmd.run(op);
+                return f2;
+        }
+
+        public static File getImageFile(File f, int page) throws IOException, InterruptedException, IM4JavaException {
+                File f2 = new File(f.getParentFile(), f.getName() + ".jpg");
+                f2.deleteOnExit();
+                ConvertCmd cmd = new ConvertCmd();
+                IMOperation op = new IMOperation();
+                String s = "[" + page + "]";
+                op.addImage(f.getAbsolutePath() + s);
+                if (flatten) {
+                        op.flatten();
+                }
+                // PDFs using the CMYK color system can be handled specially if
+                // profiles are defined
+                if (cmyk_profile != null && srgb_profile != null) {
+                        Info imageInfo = new Info(f.getAbsolutePath(), true);
+                        String imageClass = imageInfo.getImageClass();
+                        if (imageClass.contains("CMYK")) {
+                                op.profile(cmyk_profile);
+                                op.profile(srgb_profile);
+                        }
+                }
+                op.addImage(f2.getAbsolutePath());
+                if (MediaFilterManager.isVerbose) {
+                        System.out.println("IM Image Param: " + op);
+                }
+                cmd.run(op);
+                return f2;
+        }
+
+        public boolean preProcessBitstream(Context c, Item item, Bitstream source) throws Exception {
+                String nsrc = source.getName();
+                for (Bundle b : item.getBundles("THUMBNAIL")) {
+                        for (Bitstream bit : b.getBitstreams()) {
+                                String n = bit.getName();
+                                if (n != null) {
+                                        if (nsrc != null) {
+                                                if (!n.startsWith(nsrc))
+                                                        continue;
+                                        }
+                                }
+                                String description = bit.getDescription();
+                                // If anything other than a generated thumbnail
+                                // is found, halt processing
+                                if (description != null) {
+                                        if (replaceRegex.matcher(description).matches()) {
+                                                if (MediaFilterManager.isVerbose) {
+                                                        System.out.println(description + " " + nsrc
+                                                                        + " matches pattern and is replacable.");
+                                                }
+                                                continue;
+                                        }
+                                        if (description.equals(bitstreamDescription)) {
+                                                if (MediaFilterManager.isVerbose) {
+                                                        System.out.println(bitstreamDescription + " " + nsrc
+                                                                        + " is replacable.");
+                                                }
+                                                continue;
+                                        }
+                                }
+                                System.out.println("Custom Thumbnail exists for " + nsrc + " for item "
+                                                + item.getHandle() + ".  Thumbnail will not be generated. ");
+                                return false;
+                        }
+                }
+
+                return true; // assume that the thumbnail is a custom one
+        }
 
-    public String[] getInputExtensions()
-    {
-        return ImageIO.getReaderFileSuffixes();
-    }
 }

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

@@ -33,7 +33,7 @@ import java.util.zip.GZIPOutputStream;
  *   }
  *   g.finish();
  * </pre>
- * 
+ *
  * @author Robert Tansley
  */
 public abstract class AbstractGenerator
@@ -59,7 +59,7 @@ public abstract class AbstractGenerator
     /**
      * Initialize this generator to write to the given directory. This must be
      * called by any subclass constructor.
-     * 
+     *
      * @param outputDirIn
      *            directory to write sitemap files to
      */
@@ -73,7 +73,7 @@ public abstract class AbstractGenerator
 
     /**
      * Start writing a new sitemap file.
-     * 
+     *
      * @throws IOException
      *             if an error occurs creating the file
      */
@@ -97,7 +97,7 @@ public abstract class AbstractGenerator
 
     /**
      * Add the given URL to the sitemap.
-     * 
+     *
      * @param url
      *            Full URL to add
      * @param lastMod
@@ -129,7 +129,7 @@ public abstract class AbstractGenerator
 
     /**
      * Finish with the current sitemap file.
-     * 
+     *
      * @throws IOException
      *             if an error occurs writing
      */
@@ -144,15 +144,18 @@ public abstract class AbstractGenerator
      * Complete writing sitemap files and write the index files. This is invoked
      * when all calls to {@link AbstractGenerator#addURL(String, Date)} have
      * been completed, and invalidates the generator.
-     * 
+     *
      * @return number of sitemap files written.
-     * 
+     *
      * @throws IOException
      *             if an error occurs writing
      */
     public int finish() throws IOException
     {
-        closeCurrentFile();
+        if (null != currentOutput)
+        {
+            closeCurrentFile();
+        }
 
         OutputStream fo = new FileOutputStream(new File(outputDir,
                 getIndexFilename()));
@@ -165,13 +168,13 @@ public abstract class AbstractGenerator
         PrintStream out = new PrintStream(fo);
         writeIndex(out, fileCount);
         out.close();
-        
+
         return fileCount;
     }
 
     /**
      * Return marked-up text to be included in a sitemap about a given URL.
-     * 
+     *
      * @param url
      *            URL to add information about
      * @param lastMod
@@ -183,14 +186,14 @@ public abstract class AbstractGenerator
 
     /**
      * Return the boilerplate at the top of a sitemap file.
-     * 
+     *
      * @return The boilerplate markup.
      */
     public abstract String getLeadingBoilerPlate();
 
     /**
      * Return the boilerplate at the end of a sitemap file.
-     * 
+     *
      * @return The boilerplate markup.
      */
     public abstract String getTrailingBoilerPlate();
@@ -198,7 +201,7 @@ public abstract class AbstractGenerator
     /**
      * Return the maximum size in bytes that an individual sitemap file should
      * be.
-     * 
+     *
      * @return the size in bytes.
      */
     public abstract int getMaxSize();
@@ -206,7 +209,7 @@ public abstract class AbstractGenerator
     /**
      * Return the maximum number of URLs that an individual sitemap file should
      * contain.
-     * 
+     *
      * @return the maximum number of URLs.
      */
     public abstract int getMaxURLs();
@@ -214,7 +217,7 @@ public abstract class AbstractGenerator
     /**
      * Return whether the written sitemap files and index should be
      * GZIP-compressed.
-     * 
+     *
      * @return {@code true} if GZIP compression should be used, {@code false}
      *         otherwise.
      */
@@ -222,7 +225,7 @@ public abstract class AbstractGenerator
 
     /**
      * Return the filename a sitemap at the given index should be stored at.
-     * 
+     *
      * @param number
      *            index of the sitemap file (zero is first).
      * @return the filename to write the sitemap to.
@@ -231,14 +234,14 @@ public abstract class AbstractGenerator
 
     /**
      * Get the filename the index should be written to.
-     * 
+     *
      * @return the filename of the index.
      */
     public abstract String getIndexFilename();
 
     /**
      * Write the index file.
-     * 
+     *
      * @param output
      *            stream to write the index to
      * @param sitemapCount

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

@@ -92,7 +92,7 @@ public class CreateStatReport {
         
         // create context as super user
         context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         //get paths to directories
         outputLogDirectory = ConfigurationManager.getProperty("log.dir") + File.separator;

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

@@ -215,7 +215,7 @@ public class LogAnalyser
         
         // create context as super user
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         // set up our command line variables
         String myLogDir = null;

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

@@ -151,7 +151,7 @@ public class ReportGenerator
     {
         // create context as super user
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
         
         String myFormat = null;
         String myInput = null;

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

@@ -7,37 +7,31 @@
  */
 package org.dspace.app.util;
 
-import java.sql.SQLException;
-
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.ListMultimap;
-import org.dspace.authorize.AuthorizeManager;
-import org.dspace.content.*;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Properties;
 import org.apache.log4j.Logger;
+import org.dspace.authorize.AuthorizeManager;
+import org.dspace.content.Bitstream;
+import org.dspace.content.Bundle;
+import org.dspace.content.Item;
+import org.dspace.content.Metadatum;
 import org.dspace.core.ConfigurationManager;
-
-import java.io.File;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map.Entry;
-import java.util.Set;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
 import org.dspace.handle.HandleManager;
-
 import org.jdom.Element;
 
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.UnsupportedEncodingException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.sql.SQLException;
+import java.util.*;
+import java.util.Map.Entry;
+
 /**
  * Configuration and mapping for Google Scholar output metadata
  * @author Sands Fish
@@ -125,6 +119,7 @@ public class GoogleMetadata
 
     private static final int ALL_FIELDS_IN_OPTION = 2;
 
+    private Context ourContext;
     // Load configured fields from google-metadata.properties
     static
     {
@@ -216,7 +211,11 @@ public class GoogleMetadata
         // Hold onto the item in case we need to refresh a stale parse
         this.item = item;
         itemURL = HandleManager.resolveToURL(context, item.getHandle());
+        ourContext=context;
+        EPerson currentUser = ourContext.getCurrentUser();
+        ourContext.setCurrentUser(null);
         parseItem();
+        ourContext.setCurrentUser(currentUser);
     }
 
     /**
@@ -757,16 +756,17 @@ public class GoogleMetadata
     }
 
     /**
-     * Fetch all metadata mappings
-     * 
+     * Fetch retaining the order of the values for any given key in which they
+     * where added (like authors).
+     *
      * Usage: GoogleMetadata gmd = new GoogleMetadata(item); for(Entry<String,
      * String> mapping : googlemd.getMappings()) { ... }
      * 
      * @return Iterable of metadata fields mapped to Google-formatted values
      */
-    public Set<Entry<String, String>> getMappings()
+    public Collection<Entry<String, String>> getMappings()
     {
-        return new HashSet<>(metadataMappings.entries());
+        return metadataMappings.entries();
     }
 
     /**
@@ -1041,7 +1041,6 @@ public class GoogleMetadata
 	 */
 	private Bitstream findLinkableFulltext(Item item) throws SQLException {
 		Bitstream bestSoFar = null;
-		int bitstreamCount = 0;
 		Bundle[] contentBundles = item.getBundles("ORIGINAL");
 		for (Bundle bundle : contentBundles) {
 			int primaryBitstreamId = bundle.getPrimaryBitstreamID();
@@ -1050,16 +1049,16 @@ public class GoogleMetadata
 				if (candidate.getID() == primaryBitstreamId) { // is primary -> use this one
 					if (isPublic(candidate)) {
 						return candidate;
+					}					
+				} else 
+					{
+						
+						if (bestSoFar == null && isPublic(candidate)) { //if bestSoFar is null but the candidate is not public you don't use it and try to find another
+						bestSoFar = candidate;
+						}					
 					}
-				} else if (bestSoFar == null) {
-					bestSoFar = candidate;
-				}
-				bitstreamCount++;
 			}
 		}
-		if (bitstreamCount > 1 || !isPublic(bestSoFar)) {
-			bestSoFar = null;
-		}
 
 		return bestSoFar;
 	}
@@ -1069,16 +1068,10 @@ public class GoogleMetadata
 			return false;
 		}
 		boolean result = false;
-		Context context = null;
 		try {
-			context = new Context();
-			result = AuthorizeManager.authorizeActionBoolean(context, bitstream, Constants.READ, true);
+            result = AuthorizeManager.authorizeActionBoolean(ourContext, bitstream, Constants.READ, true);
 		} catch (SQLException e) {
 			log.error("Cannot determine whether bitstream is public, assuming it isn't. bitstream_id=" + bitstream.getID(), e);
-		} finally {
-			if (context != null) {
-				context.abort();
-			}
 		}
 		return result;
 	}

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

@@ -279,11 +279,11 @@ public class LDAPAuthentication
                         {
                             log.info(LogManager.getHeader(context,
                                     "type=ldap-login", "type=ldap_but_already_email"));
-                            context.setIgnoreAuthorization(true);
+                            context.turnOffAuthorisationSystem();
                             eperson.setNetid(netid.toLowerCase());
                             eperson.update();
                             context.commit();
-                            context.setIgnoreAuthorization(false);
+                            context.restoreAuthSystemState();
                             context.setCurrentUser(eperson);
 
                             // assign user to groups based on ldap dn
@@ -298,7 +298,7 @@ public class LDAPAuthentication
                                 // TEMPORARILY turn off authorisation
                                 try
                                 {
-                                    context.setIgnoreAuthorization(true);
+                                    context.turnOffAuthorisationSystem();
                                     eperson = EPerson.create(context);
                                     if (StringUtils.isNotEmpty(email))
                                     {
@@ -332,7 +332,7 @@ public class LDAPAuthentication
                                 }
                                 finally
                                 {
-                                    context.setIgnoreAuthorization(false);
+                                    context.restoreAuthSystemState();
                                 }
 
                                 log.info(LogManager.getHeader(context, "authenticate",
@@ -354,7 +354,7 @@ public class LDAPAuthentication
                     }
                     finally
                     {
-                        context.setIgnoreAuthorization(false);
+                        context.restoreAuthSystemState();
                     }
                 }
             }

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

@@ -7,11 +7,7 @@
  */
 package org.dspace.authenticate;
 
-import java.sql.SQLException;
-
-import javax.servlet.http.HttpServletRequest;
-import javax.servlet.http.HttpServletResponse;
-
+import org.apache.commons.lang3.StringUtils;
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.core.ConfigurationManager;
@@ -20,6 +16,10 @@ import org.dspace.core.LogManager;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
 
+import javax.servlet.http.HttpServletRequest;
+import javax.servlet.http.HttpServletResponse;
+import java.sql.SQLException;
+
 /**
  * A stackable authentication method
  * based on the DSpace internal "EPerson" database.
@@ -128,7 +128,7 @@ public class PasswordAuthentication
 		// ensures they are password users
 		try
 		{
-			if (context.getCurrentUser().getPasswordHash() != null && !context.getCurrentUser().getPasswordHash().toString().equals(""))
+		if (context.getCurrentUser() != null && context.getCurrentUser().getPasswordHash()!=null && StringUtils.isNotBlank(context.getCurrentUser().getPasswordHash().toString()))
 			{
 				String groupName = ConfigurationManager.getProperty("authentication-password", "login.specialgroup");
 				if ((groupName != null) && (!groupName.trim().equals("")))
@@ -149,7 +149,7 @@ public class PasswordAuthentication
 			}
 		}
 		catch (Exception e) {
-			// The user is not a password user, so we don't need to worry about them
+            log.error(LogManager.getHeader(context,"getSpecialGroups",""),e);
 		}
 		return new int[0];
     }

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

@@ -612,7 +612,7 @@ public class X509Authentication implements AuthenticationMethod
                                 "from=x.509, email=" + email));
 
                         // TEMPORARILY turn off authorisation
-                        context.setIgnoreAuthorization(true);
+                        context.turnOffAuthorisationSystem();
                         eperson = EPerson.create(context);
                         eperson.setEmail(email);
                         eperson.setCanLogIn(true);
@@ -620,7 +620,7 @@ public class X509Authentication implements AuthenticationMethod
                                 eperson);
                         eperson.update();
                         context.commit();
-                        context.setIgnoreAuthorization(false);
+                        context.restoreAuthSystemState();
                         context.setCurrentUser(eperson);
                         setSpecialGroupsFlag(request, email);
                         return SUCCESS;

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

@@ -0,0 +1,20 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.authority;
+
+import java.util.List;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public interface SolrAuthorityInterface {
+
+    List<AuthorityValue> queryAuthorities(String text, int max);
+
+    AuthorityValue queryAuthorityID(String id);
+}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcid.java

@@ -1,86 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid;
-
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.Work;
-import org.dspace.authority.orcid.xml.XMLtoBio;
-import org.dspace.authority.orcid.xml.XMLtoWork;
-import org.dspace.authority.rest.RestSource;
-import org.apache.log4j.Logger;
-import org.dspace.utils.DSpace;
-import org.w3c.dom.Document;
-
-import java.net.URLEncoder;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Orcid extends RestSource {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(Orcid.class);
-
-    private static Orcid orcid;
-
-    public static Orcid getOrcid() {
-        if (orcid == null) {
-            orcid = new DSpace().getServiceManager().getServiceByName("OrcidSource", Orcid.class);
-        }
-        return orcid;
-    }
-
-    private Orcid(String url) {
-        super(url);
-    }
-
-    public Bio getBio(String id) {
-        Document bioDocument = restConnector.get(id + "/orcid-bio");
-        XMLtoBio converter = new XMLtoBio();
-        Bio bio = converter.convert(bioDocument).get(0);
-        bio.setOrcid(id);
-        return bio;
-    }
-
-    public List<Work> getWorks(String id) {
-        Document document = restConnector.get(id + "/orcid-works");
-        XMLtoWork converter = new XMLtoWork();
-        return converter.convert(document);
-    }
-
-    public List<Bio> queryBio(String name, int start, int rows) {
-        Document bioDocument = restConnector.get("search/orcid-bio?q=" + URLEncoder.encode("\"" + name + "\"") + "&start=" + start + "&rows=" + rows);
-        XMLtoBio converter = new XMLtoBio();
-        return converter.convert(bioDocument);
-    }
-
-    @Override
-    public List<AuthorityValue> queryAuthorities(String text, int max) {
-        List<Bio> bios = queryBio(text, 0, max);
-        List<AuthorityValue> authorities = new ArrayList<AuthorityValue>();
-        for (Bio bio : bios) {
-            authorities.add(OrcidAuthorityValue.create(bio));
-        }
-        return authorities;
-    }
-
-    @Override
-    public AuthorityValue queryAuthorityID(String id) {
-        Bio bio = getBio(id);
-        return OrcidAuthorityValue.create(bio);
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/OrcidAuthorityValue.java

@@ -1,316 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid;
-
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.AuthorityValueGenerator;
-import org.dspace.authority.PersonAuthorityValue;
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.BioExternalIdentifier;
-import org.dspace.authority.orcid.model.BioName;
-import org.dspace.authority.orcid.model.BioResearcherUrl;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.apache.solr.common.SolrDocument;
-import org.apache.solr.common.SolrInputDocument;
-
-import java.util.*;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class OrcidAuthorityValue extends PersonAuthorityValue {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(OrcidAuthorityValue.class);
-
-    private String orcid_id;
-    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
-    private boolean update; // used in setValues(Bio bio)
-
-
-    /**
-     * Creates an instance of OrcidAuthorityValue with only uninitialized fields.
-     * This is meant to be filled in with values from an existing record.
-     * To create a brand new OrcidAuthorityValue, use create()
-     */
-    public OrcidAuthorityValue() {
-    }
-
-    public OrcidAuthorityValue(SolrDocument document) {
-        super(document);
-    }
-
-    public String getOrcid_id() {
-        return orcid_id;
-    }
-
-    public void setOrcid_id(String orcid_id) {
-        this.orcid_id = orcid_id;
-    }
-
-    public Map<String, List<String>> getOtherMetadata() {
-        return otherMetadata;
-    }
-
-    public void addOtherMetadata(String label, String data) {
-        List<String> strings = otherMetadata.get(label);
-        if (strings == null) {
-            strings = new ArrayList<String>();
-        }
-        strings.add(data);
-        otherMetadata.put(label, strings);
-    }
-
-    @Override
-    public SolrInputDocument getSolrInputDocument() {
-        SolrInputDocument doc = super.getSolrInputDocument();
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            doc.addField("orcid_id", getOrcid_id());
-        }
-
-        for (String t : otherMetadata.keySet()) {
-            List<String> data = otherMetadata.get(t);
-            for (String data_entry : data) {
-                doc.addField("label_" + t, data_entry);
-            }
-        }
-        return doc;
-    }
-
-    @Override
-    public void setValues(SolrDocument document) {
-        super.setValues(document);
-        this.orcid_id = String.valueOf(document.getFieldValue("orcid_id"));
-
-        otherMetadata = new HashMap<String, List<String>>();
-        for (String fieldName : document.getFieldNames()) {
-            String labelPrefix = "label_";
-            if (fieldName.startsWith(labelPrefix)) {
-                String label = fieldName.substring(labelPrefix.length());
-                List<String> list = new ArrayList<String>();
-                Collection<Object> fieldValues = document.getFieldValues(fieldName);
-                for (Object o : fieldValues) {
-                    list.add(String.valueOf(o));
-                }
-                otherMetadata.put(label, list);
-            }
-        }
-    }
-
-    public static OrcidAuthorityValue create() {
-        OrcidAuthorityValue orcidAuthorityValue = new OrcidAuthorityValue();
-        orcidAuthorityValue.setId(UUID.randomUUID().toString());
-        orcidAuthorityValue.updateLastModifiedDate();
-        orcidAuthorityValue.setCreationDate(new Date());
-        return orcidAuthorityValue;
-    }
-
-    /**
-     * Create an authority based on a given orcid bio
-     */
-    public static OrcidAuthorityValue create(Bio bio) {
-        OrcidAuthorityValue authority = OrcidAuthorityValue.create();
-
-        authority.setValues(bio);
-
-        return authority;
-    }
-
-    public boolean setValues(Bio bio) {
-        BioName name = bio.getName();
-
-        if (updateValue(bio.getOrcid(), getOrcid_id())) {
-            setOrcid_id(bio.getOrcid());
-        }
-
-        if (updateValue(name.getFamilyName(), getLastName())) {
-            setLastName(name.getFamilyName());
-        }
-
-        if (updateValue(name.getGivenNames(), getFirstName())) {
-            setFirstName(name.getGivenNames());
-        }
-
-        if (StringUtils.isNotBlank(name.getCreditName())) {
-            if (!getNameVariants().contains(name.getCreditName())) {
-                addNameVariant(name.getCreditName());
-                update = true;
-            }
-        }
-        for (String otherName : name.getOtherNames()) {
-            if (!getNameVariants().contains(otherName)) {
-                addNameVariant(otherName);
-                update = true;
-            }
-        }
-
-        if (updateOtherMetadata("country", bio.getCountry())) {
-            addOtherMetadata("country", bio.getCountry());
-        }
-
-        for (String keyword : bio.getKeywords()) {
-            if (updateOtherMetadata("keyword", keyword)) {
-                addOtherMetadata("keyword", keyword);
-            }
-        }
-
-        for (BioExternalIdentifier externalIdentifier : bio.getBioExternalIdentifiers()) {
-            if (updateOtherMetadata("external_identifier", externalIdentifier.toString())) {
-                addOtherMetadata("external_identifier", externalIdentifier.toString());
-            }
-        }
-
-        for (BioResearcherUrl researcherUrl : bio.getResearcherUrls()) {
-            if (updateOtherMetadata("researcher_url", researcherUrl.toString())) {
-                addOtherMetadata("researcher_url", researcherUrl.toString());
-            }
-        }
-
-        if (updateOtherMetadata("biography", bio.getBiography())) {
-            addOtherMetadata("biography", bio.getBiography());
-        }
-
-        setValue(getName());
-
-        if (update) {
-            update();
-        }
-        boolean result = update;
-        update = false;
-        return result;
-    }
-
-    private boolean updateOtherMetadata(String label, String data) {
-        List<String> strings = getOtherMetadata().get(label);
-        boolean update;
-        if (strings == null) {
-            update = StringUtils.isNotBlank(data);
-        } else {
-            update = !strings.contains(data);
-        }
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    private boolean updateValue(String incoming, String resident) {
-        boolean update = StringUtils.isNotBlank(incoming) && !incoming.equals(resident);
-        if (update) {
-            this.update = true;
-        }
-        return update;
-    }
-
-    @Override
-    public Map<String, String> choiceSelectMap() {
-
-        Map<String, String> map = super.choiceSelectMap();
-
-        map.put("orcid", getOrcid_id());
-
-        return map;
-    }
-
-    public String getAuthorityType() {
-        return "orcid";
-    }
-
-    @Override
-    public String generateString() {
-        String generateString = AuthorityValueGenerator.GENERATE + getAuthorityType() + AuthorityValueGenerator.SPLIT;
-        if (StringUtils.isNotBlank(getOrcid_id())) {
-            generateString += getOrcid_id();
-        }
-        return generateString;
-    }
-
-
-    @Override
-    public AuthorityValue newInstance(String info) {
-        AuthorityValue authorityValue = null;
-        if (StringUtils.isNotBlank(info)) {
-            Orcid orcid = Orcid.getOrcid();
-            authorityValue = orcid.queryAuthorityID(info);
-        } else {
-            authorityValue = OrcidAuthorityValue.create();
-        }
-        return authorityValue;
-    }
-
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        return orcid_id != null ? orcid_id.hashCode() : 0;
-    }
-
-    public boolean hasTheSameInformationAs(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-        if (!super.hasTheSameInformationAs(o)) {
-            return false;
-        }
-
-        OrcidAuthorityValue that = (OrcidAuthorityValue) o;
-
-        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
-            return false;
-        }
-
-        for (String key : otherMetadata.keySet()) {
-            if(otherMetadata.get(key) != null){
-                List<String> metadata = otherMetadata.get(key);
-                List<String> otherMetadata = that.otherMetadata.get(key);
-                if (otherMetadata == null) {
-                    return false;
-                } else {
-                    HashSet<String> metadataSet = new HashSet<String>(metadata);
-                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
-                    if (!metadataSet.equals(otherMetadataSet)) {
-                        return false;
-                    }
-                }
-            }else{
-                if(that.otherMetadata.get(key) != null){
-                    return false;
-                }
-            }
-        }
-
-        return true;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2.java

@@ -0,0 +1,185 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.authority.orcid;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.http.HttpResponse;
+import org.apache.http.client.HttpClient;
+import org.apache.http.client.methods.HttpPost;
+import org.apache.http.impl.client.HttpClientBuilder;
+import org.apache.log4j.Logger;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.SolrAuthorityInterface;
+import org.dspace.authority.orcid.xml.XMLtoBio;
+import org.dspace.authority.rest.RESTConnector;
+import org.json.JSONObject;
+import org.orcid.jaxb.model.record_v2.Person;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URLEncoder;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ * This class contains all methods for retrieving "Person" objects calling the ORCID (version 2) endpoints.
+ * Additionally, this can also create AuthorityValues based on these returned Person objects
+ */
+public class Orcidv2 implements SolrAuthorityInterface {
+
+    private static Logger log = Logger.getLogger(Orcidv2.class);
+
+    public RESTConnector restConnector;
+    private String OAUTHUrl;
+    private String clientId;
+
+    private String clientSecret;
+
+    private String accessToken;
+
+    /**
+     *  Initialize the accessToken that is required for all subsequent calls to ORCID
+     */
+    public void init() throws IOException {
+        if (StringUtils.isNotBlank(accessToken) && StringUtils.isNotBlank(clientSecret)) {
+            String authenticationParameters = "?client_id=" + clientId + "&client_secret=" + clientSecret + "&scope=/read-public&grant_type=client_credentials";
+            HttpPost httpPost = new HttpPost(OAUTHUrl + authenticationParameters);
+            httpPost.addHeader("Accept", "application/json");
+            httpPost.addHeader("Content-Type", "application/x-www-form-urlencoded");
+
+            HttpClient httpClient = HttpClientBuilder.create().build();
+            HttpResponse getResponse = httpClient.execute(httpPost);
+
+            InputStream is = getResponse.getEntity().getContent();
+            BufferedReader streamReader = new BufferedReader(new InputStreamReader(is, "UTF-8"));
+
+            JSONObject responseObject = null;
+            String inputStr;
+            while ((inputStr = streamReader.readLine()) != null && responseObject == null) {
+                if (inputStr.startsWith("{") && inputStr.endsWith("}") && inputStr.contains("access_token")) {
+                    try {
+                        responseObject = new JSONObject(inputStr);
+                    } catch (Exception e) {
+                        //Not as valid as I'd hoped, move along
+                        responseObject = null;
+                    }
+                }
+            }
+
+            if (responseObject != null && responseObject.has("access_token")) {
+                accessToken = (String) responseObject.get("access_token");
+            }
+        }
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url, String OAUTHUrl, String clientId, String clientSecret) {
+        this.restConnector = new RESTConnector(url);
+        this.OAUTHUrl = OAUTHUrl;
+        this.clientId = clientId;
+        this.clientSecret = clientSecret;
+    }
+
+    /**
+     * Makes an instance of the Orcidv2 class based on the provided parameters.
+     * This constructor is called through the spring bean initialization
+     */
+    private Orcidv2(String url) {
+        this.restConnector = new RESTConnector(url);
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param text search string
+     * @return List<AuthorityValue>
+     */
+    @Override
+    public List<AuthorityValue> queryAuthorities(String text, int max) {
+        List<Person> bios = queryBio(text, max);
+        List<AuthorityValue> result = new ArrayList<>();
+        for (Person person : bios) {
+            AuthorityValue orcidAuthorityValue = Orcidv2AuthorityValue.create(person);
+            if (orcidAuthorityValue != null) {
+                result.add(orcidAuthorityValue);
+            }
+        }
+        return result;
+    }
+
+    /**
+     * Create an AuthorityValue from a Person retrieved using the given orcid identifier.
+     * @param id orcid identifier
+     * @return AuthorityValue
+     */
+    public AuthorityValue queryAuthorityID(String id) {
+        Person person = getBio(id);
+        AuthorityValue valueFromPerson = Orcidv2AuthorityValue.create(person);
+        return valueFromPerson;
+    }
+
+    /**
+     * Retrieve a Person object based on a given orcid identifier
+     * @param id orcid identifier
+     * @return Person
+     */
+    public Person getBio(String id) {
+        log.debug("getBio called with ID=" + id);
+        if(!isValid(id)){
+            return null;
+        }
+        InputStream bioDocument = restConnector.get(id + ((id.endsWith("/person")) ? "" : "/person"), accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        Person person = converter.convertSinglePerson(bioDocument);
+        return person;
+    }
+
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param start offset to use
+     * @param rows how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int start, int rows) {
+        if (rows > 100) {
+            throw new IllegalArgumentException("The maximum number of results to retrieve cannot exceed 100.");
+        }
+
+        String searchPath = "search?q=" + URLEncoder.encode(text) + "&start=" + start + "&rows=" + rows;
+        log.debug("queryBio searchPath=" + searchPath + " accessToken=" + accessToken);
+        InputStream bioDocument = restConnector.get(searchPath, accessToken);
+        XMLtoBio converter = new XMLtoBio();
+        List<Person> bios = converter.convert(bioDocument);
+        return bios;
+    }
+
+    /**
+     * Retrieve a list of Person objects.
+     * @param text search string
+     * @param max how many rows to return
+     * @return List<Person>
+     */
+    public List<Person> queryBio(String text, int max) {
+        return queryBio(text, 0, max);
+    }
+
+    /**
+     * Check to see if the provided text has the correct ORCID syntax.
+     * Since only searching on ORCID id is allowed, this way, we filter out any queries that would return a blank result anyway
+     */
+    private boolean isValid(String text) {
+        return StringUtils.isNotBlank(text) && text.matches(Orcidv2AuthorityValue.ORCID_ID_SYNTAX);
+    }
+}

dspace-api/src/main/java/org/dspace/authority/orcid/Orcidv2AuthorityValue.java

@@ -0,0 +1,330 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.authority.orcid;
+
+import org.apache.commons.lang.StringUtils;
+import org.apache.solr.common.SolrDocument;
+import org.apache.solr.common.SolrInputDocument;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.AuthorityValueGenerator;
+import org.dspace.authority.PersonAuthorityValue;
+import org.dspace.utils.DSpace;
+import org.orcid.jaxb.model.common_v2.ExternalId;
+import org.orcid.jaxb.model.record_v2.*;
+
+import java.util.*;
+
+/**
+ * @author Jonas Van Goolen (jonas at atmire dot com)
+ */
+public class Orcidv2AuthorityValue extends PersonAuthorityValue {
+
+    /*
+     * The ORCID identifier
+     */
+    private String orcid_id;
+
+    /*
+     * Map containing key-value pairs filled in by "setValues(Person person)".
+     * This represents all dynamic information of the object.
+     */
+    private Map<String, List<String>> otherMetadata = new HashMap<String, List<String>>();
+
+    /**
+     * The syntax that the ORCID id needs to conform to
+     */
+    public static final String ORCID_ID_SYNTAX = "\\d{4}-\\d{4}-\\d{4}-(\\d{3}X|\\d{4})";
+
+
+    /**
+     * Creates an instance of Orcidv2AuthorityValue with only uninitialized fields.
+     * This is meant to be filled in with values from an existing record.
+     * To create a brand new Orcidv2AuthorityValue, use create()
+     */
+    public Orcidv2AuthorityValue() {
+    }
+
+    public Orcidv2AuthorityValue(SolrDocument document) {
+        super(document);
+    }
+
+
+    public String getOrcid_id() {
+        return orcid_id;
+    }
+
+    public void setOrcid_id(String orcid_id) {
+        this.orcid_id = orcid_id;
+    }
+
+    /**
+     * Create an empty authority.
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create() {
+        Orcidv2AuthorityValue orcidAuthorityValue = new Orcidv2AuthorityValue();
+        orcidAuthorityValue.setId(UUID.randomUUID().toString());
+        orcidAuthorityValue.updateLastModifiedDate();
+        orcidAuthorityValue.setCreationDate(new Date());
+        return orcidAuthorityValue;
+    }
+
+    /**
+     * Create an authority based on a given orcid bio
+     * @return OrcidAuthorityValue
+     */
+    public static Orcidv2AuthorityValue create(Person person) {
+        if (person == null) {
+            return null;
+        }
+        Orcidv2AuthorityValue authority = Orcidv2AuthorityValue.create();
+
+        authority.setValues(person);
+
+        return authority;
+    }
+
+    /**
+     * Initialize this instance based on a Person object
+     * @param person Person
+     */
+    protected void setValues(Person person) {
+        NameType name = person.getName();
+
+        if (!StringUtils.equals(name.getPath(), this.getOrcid_id())) {
+            this.setOrcid_id(name.getPath());
+        }
+
+        if (!StringUtils.equals(name.getFamilyName().getValue(), this.getLastName())) {
+            this.setLastName(name.getFamilyName().getValue());
+        }
+
+        if (!StringUtils.equals(name.getGivenNames().getValue(), this.getFirstName())) {
+            this.setFirstName(name.getGivenNames().getValue());
+        }
+
+        if (name.getCreditName() != null && StringUtils.isNotBlank(name.getCreditName().getValue())) {
+            if (!this.getNameVariants().contains(name.getCreditName())) {
+                this.addNameVariant(name.getCreditName().getValue());
+            }
+        }
+
+        if (person.getKeywords() != null) {
+            for (KeywordType keyword : person.getKeywords().getKeyword()) {
+                if (this.isNewMetadata("keyword", keyword.getContent())) {
+                    this.addOtherMetadata("keyword", keyword.getContent());
+                }
+            }
+        }
+
+        ExternalIdentifiers externalIdentifiers = person.getExternalIdentifiers();
+        if (externalIdentifiers != null) {
+            for (ExternalId externalIdentifier : externalIdentifiers.getExternalIdentifier()) {
+                if (this.isNewMetadata("external_identifier", externalIdentifier.getExternalIdValue())) {
+                    this.addOtherMetadata("external_identifier", externalIdentifier.getExternalIdValue());
+
+                }
+            }
+        }
+        if (person.getResearcherUrls() != null) {
+            for (ResearcherUrlType researcherUrl : person.getResearcherUrls().getResearcherUrl()) {
+                if (this.isNewMetadata("researcher_url", researcherUrl.getUrl().getValue())) {
+                    this.addOtherMetadata("researcher_url", researcherUrl.getUrl().getValue());
+                }
+            }
+
+        }
+        if (person.getBiography() != null) {
+            if (this.isNewMetadata("biography", person.getBiography().getContent())) {
+                this.addOtherMetadata("biography", person.getBiography().getContent());
+            }
+        }
+
+        this.setValue(this.getName());
+
+    }
+
+    /**
+     * Makes an instance of the AuthorityValue with the given information.
+     * @param info string info
+     * @return AuthorityValue
+     */
+    @Override
+    public AuthorityValue newInstance(String info) {
+        AuthorityValue authorityValue = null;
+        if (StringUtils.isNotBlank(info)) {
+            Orcidv2 orcid = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
+            authorityValue = orcid.queryAuthorityID(info);
+        } else {
+            authorityValue = this.create();
+        }
+        return authorityValue;
+    }
+
+    @Override
+    public void setValue(String value) {
+        super.setValue(value);
+    }
+
+    /**
+     * Check to see if the provided label / data pair is already present in the "otherMetadata" or not
+     * */
+    public boolean isNewMetadata(String label, String data) {
+        List<String> strings = getOtherMetadata().get(label);
+        boolean update;
+        if (strings == null) {
+            update = StringUtils.isNotBlank(data);
+        } else {
+            update = !strings.contains(data);
+        }
+        return update;
+    }
+
+    /**
+     * Add additional metadata to the otherMetadata map*/
+    public void addOtherMetadata(String label, String data) {
+        List<String> strings = otherMetadata.get(label);
+        if (strings == null) {
+            strings = new ArrayList<>();
+        }
+        strings.add(data);
+        otherMetadata.put(label, strings);
+    }
+
+    public Map<String, List<String>> getOtherMetadata() {
+        return otherMetadata;
+    }
+
+
+    /**
+     * Generate a solr record from this instance
+     * @return SolrInputDocument
+     */
+    @Override
+    public SolrInputDocument getSolrInputDocument() {
+        SolrInputDocument doc = super.getSolrInputDocument();
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            doc.addField("orcid_id", getOrcid_id());
+        }
+
+        for (String t : otherMetadata.keySet()) {
+            List<String> data = otherMetadata.get(t);
+            for (String data_entry : data) {
+                doc.addField("label_" + t, data_entry);
+            }
+        }
+        return doc;
+    }
+
+    /**
+     * Information that can be used the choice ui
+     * @return map
+     */
+    @Override
+    public Map<String, String> choiceSelectMap() {
+
+        Map<String, String> map = super.choiceSelectMap();
+
+        String orcid_id = getOrcid_id();
+        if (StringUtils.isNotBlank(orcid_id)) {
+            map.put("orcid", orcid_id);
+        }
+
+        return map;
+    }
+
+    @Override
+    public String getAuthorityType() {
+        return "orcid";
+    }
+
+    /**
+     * Provides a string that will allow this AuthorityType to be recognized and provides information to create a new instance to be created using public Orcidv2AuthorityValue newInstance(String info).
+     * @return see {@link org.dspace.authority.AuthorityValueGenerator#GENERATE AuthorityValueGenerator.GENERATE}
+     */
+    @Override
+    public String generateString() {
+        String generateString = AuthorityValueGenerator.GENERATE + getAuthorityType() + AuthorityValueGenerator.SPLIT;
+        if (StringUtils.isNotBlank(getOrcid_id())) {
+            generateString += getOrcid_id();
+        }
+        return generateString;
+    }
+
+
+    @Override
+    public boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        return true;
+    }
+
+    @Override
+    public int hashCode() {
+        return orcid_id != null ? orcid_id.hashCode() : 0;
+    }
+
+    /**
+     * The regular equals() only checks if both AuthorityValues describe the same authority.
+     * This method checks if the AuthorityValues have different information
+     * E.g. it is used to decide when lastModified should be updated.
+     * @param o object
+     * @return true or false
+     */
+    @Override
+    public boolean hasTheSameInformationAs(Object o) {
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
+        if (!super.hasTheSameInformationAs(o)) {
+            return false;
+        }
+
+        Orcidv2AuthorityValue that = (Orcidv2AuthorityValue) o;
+
+        if (orcid_id != null ? !orcid_id.equals(that.orcid_id) : that.orcid_id != null) {
+            return false;
+        }
+
+        for (String key : otherMetadata.keySet()) {
+            if (otherMetadata.get(key) != null) {
+                List<String> metadata = otherMetadata.get(key);
+                List<String> otherMetadata = that.otherMetadata.get(key);
+                if (otherMetadata == null) {
+                    return false;
+                } else {
+                    HashSet<String> metadataSet = new HashSet<String>(metadata);
+                    HashSet<String> otherMetadataSet = new HashSet<String>(otherMetadata);
+                    if (!metadataSet.equals(otherMetadataSet)) {
+                        return false;
+                    }
+                }
+            } else {
+                if (that.otherMetadata.get(key) != null) {
+                    return false;
+                }
+            }
+        }
+
+        return true;
+    }
+}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Bio.java

@@ -1,113 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-package org.dspace.authority.orcid.model;
-
-import java.util.LinkedHashSet;
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Bio {
-
-    protected String orcid;
-
-    protected BioName name;
-
-    protected String country;
-
-    protected Set<String> keywords;
-
-    protected Set<BioExternalIdentifier> bioExternalIdentifiers;
-
-    protected Set<BioResearcherUrl> researcherUrls;
-
-    protected String biography;
-
-    public Bio() {
-        this.name = new BioName();
-        keywords = new LinkedHashSet<String>();
-        bioExternalIdentifiers = new LinkedHashSet<BioExternalIdentifier>();
-        researcherUrls = new LinkedHashSet<BioResearcherUrl>();
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public BioName getName() {
-        return name;
-    }
-
-    public void setName(BioName name) {
-        this.name = name;
-    }
-
-    public String getCountry() {
-        return country;
-    }
-
-    public void setCountry(String country) {
-        this.country = country;
-    }
-
-    public Set<String> getKeywords() {
-        return keywords;
-    }
-
-    public void addKeyword(String keyword) {
-        this.keywords.add(keyword);
-    }
-
-    public Set<BioExternalIdentifier> getBioExternalIdentifiers() {
-        return bioExternalIdentifiers;
-    }
-
-    public void addExternalIdentifier(BioExternalIdentifier externalReference) {
-        bioExternalIdentifiers.add(externalReference);
-    }
-
-    public Set<BioResearcherUrl> getResearcherUrls() {
-        return researcherUrls;
-    }
-
-    public void addResearcherUrl(BioResearcherUrl researcherUrl) {
-        researcherUrls.add(researcherUrl);
-    }
-
-    public String getBiography() {
-        return biography;
-    }
-
-    public void setBiography(String biography) {
-        this.biography = biography;
-    }
-
-    @Override
-    public String toString() {
-        return "Bio{" +
-                "orcid='" + orcid + '\'' +
-                ", name=" + name +
-                ", country='" + country + '\'' +
-                ", keywords=" + keywords +
-                ", bioExternalIdentifiers=" + bioExternalIdentifiers +
-                ", researcherUrls=" + researcherUrls +
-                ", biography='" + biography + '\'' +
-                '}';
-    }
-}
-

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioExternalIdentifier.java

@@ -1,109 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioExternalIdentifier {
-
-
-    protected String id_orcid;
-    protected String id_common_name;
-    protected String id_reference;
-    protected String id_url;
-
-    public BioExternalIdentifier(String id_orcid, String id_common_name, String id_reference, String id_url) {
-        this.id_orcid = id_orcid;
-        this.id_common_name = id_common_name;
-        this.id_reference = id_reference;
-        this.id_url = id_url;
-    }
-
-    public String getId_orcid() {
-        return id_orcid;
-    }
-
-    public void setId_orcid(String id_orcid) {
-        this.id_orcid = id_orcid;
-    }
-
-    public String getId_common_name() {
-        return id_common_name;
-    }
-
-    public void setId_common_name(String id_common_name) {
-        this.id_common_name = id_common_name;
-    }
-
-    public String getId_reference() {
-        return id_reference;
-    }
-
-    public void setId_reference(String id_reference) {
-        this.id_reference = id_reference;
-    }
-
-    public String getId_url() {
-        return id_url;
-    }
-
-    public void setId_url(String id_url) {
-        this.id_url = id_url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioExternalIdentifier{" +
-                "id_orcid='" + id_orcid + '\'' +
-                ", id_common_name='" + id_common_name + '\'' +
-                ", id_reference='" + id_reference + '\'' +
-                ", id_url='" + id_url + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioExternalIdentifier that = (BioExternalIdentifier) o;
-
-        if (id_common_name != null ? !id_common_name.equals(that.id_common_name) : that.id_common_name != null) {
-            return false;
-        }
-        if (id_orcid != null ? !id_orcid.equals(that.id_orcid) : that.id_orcid != null) {
-            return false;
-        }
-        if (id_reference != null ? !id_reference.equals(that.id_reference) : that.id_reference != null) {
-            return false;
-        }
-        if (id_url != null ? !id_url.equals(that.id_url) : that.id_url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = id_orcid != null ? id_orcid.hashCode() : 0;
-        result = 31 * result + (id_common_name != null ? id_common_name.hashCode() : 0);
-        result = 31 * result + (id_reference != null ? id_reference.hashCode() : 0);
-        result = 31 * result + (id_url != null ? id_url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioName.java

@@ -1,115 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioName {
-
-    protected String givenNames;
-    protected String familyName;
-    protected String creditName;
-    protected List<String> otherNames;
-
-    BioName() {
-        otherNames = new ArrayList<String>();
-    }
-
-    BioName(String givenNames, String familyName, String creditName, List<String> otherNames) {
-        this.givenNames = givenNames;
-        this.familyName = familyName;
-        this.creditName = creditName;
-        this.otherNames = otherNames;
-    }
-
-    public String getGivenNames() {
-        return givenNames;
-    }
-
-    public void setGivenNames(String givenNames) {
-        this.givenNames = givenNames;
-    }
-
-    public String getFamilyName() {
-        return familyName;
-    }
-
-    public void setFamilyName(String familyName) {
-        this.familyName = familyName;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public List<String> getOtherNames() {
-        return otherNames;
-    }
-
-    public void setOtherNames(List<String> otherNames) {
-        this.otherNames = otherNames;
-    }
-
-    @Override
-    public String toString() {
-        return "BioName{" +
-                "givenNames='" + givenNames + '\'' +
-                ", familyName='" + familyName + '\'' +
-                ", creditName='" + creditName + '\'' +
-                ", otherNames=" + otherNames +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioName bioName = (BioName) o;
-
-        if (creditName != null ? !creditName.equals(bioName.creditName) : bioName.creditName != null) {
-            return false;
-        }
-        if (familyName != null ? !familyName.equals(bioName.familyName) : bioName.familyName != null) {
-            return false;
-        }
-        if (givenNames != null ? !givenNames.equals(bioName.givenNames) : bioName.givenNames != null) {
-            return false;
-        }
-        if (otherNames != null ? !otherNames.equals(bioName.otherNames) : bioName.otherNames != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = givenNames != null ? givenNames.hashCode() : 0;
-        result = 31 * result + (familyName != null ? familyName.hashCode() : 0);
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (otherNames != null ? otherNames.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/BioResearcherUrl.java

@@ -1,78 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class BioResearcherUrl {
-
-    protected String name;
-    protected String url;
-
-    public BioResearcherUrl(String name, String url) {
-        this.name = name;
-        this.url = url;
-    }
-
-    public String getName() {
-        return name;
-    }
-
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    @Override
-    public String toString() {
-        return "BioResearcherUrl{" +
-                "name='" + name + '\'' +
-                ", url='" + url + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        BioResearcherUrl that = (BioResearcherUrl) o;
-
-        if (name != null ? !name.equals(that.name) : that.name != null) {
-            return false;
-        }
-        if (url != null ? !url.equals(that.url) : that.url != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = name != null ? name.hashCode() : 0;
-        result = 31 * result + (url != null ? url.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Citation.java

@@ -1,50 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Citation {
-
-    private CitationType type;
-    private String citation;
-
-    public Citation(CitationType type, String citation) {
-        this.type = type;
-        this.citation = citation;
-    }
-
-    public CitationType getType() {
-        return type;
-    }
-
-    public void setType(CitationType type) {
-        this.type = type;
-    }
-
-    public String getCitation() {
-        return citation;
-    }
-
-    public void setCitation(String citation) {
-        this.citation = citation;
-    }
-
-    @Override
-    public String toString() {
-        return "Citation{" +
-                "type=" + type +
-                ", citation='" + citation + '\'' +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/CitationType.java

@@ -1,29 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-package org.dspace.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum CitationType {
-
-    FORMATTED_UNSPECIFIED,
-    BIBTEX,
-    FORMATTED_APA,
-    FORMATTED_HARVARD,
-    FORMATTED_IEEE,
-    FORMATTED_MLA,
-    FORMATTED_VANCOUVER,
-    FORMATTED_CHICAGO
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Contributor.java

@@ -1,111 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-package org.dspace.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Contributor {
-
-    private String orcid;
-    private String creditName;
-    private String email;
-    private Set<ContributorAttribute> contributorAttributes;
-
-    public Contributor(String orcid, String creditName, String email, Set<ContributorAttribute> contributorAttributes) {
-        this.orcid = orcid;
-        this.creditName = creditName;
-        this.email = email;
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    public String getOrcid() {
-        return orcid;
-    }
-
-    public void setOrcid(String orcid) {
-        this.orcid = orcid;
-    }
-
-    public String getCreditName() {
-        return creditName;
-    }
-
-    public void setCreditName(String creditName) {
-        this.creditName = creditName;
-    }
-
-    public String getEmail() {
-        return email;
-    }
-
-    public void setEmail(String email) {
-        this.email = email;
-    }
-
-    public Set<ContributorAttribute> getContributorAttributes() {
-        return contributorAttributes;
-    }
-
-    public void setContributorAttributes(Set<ContributorAttribute> contributorAttributes) {
-        this.contributorAttributes = contributorAttributes;
-    }
-
-    @Override
-    public String toString() {
-        return "Contributor{" +
-                "orcid='" + orcid + '\'' +
-                ", creditName='" + creditName + '\'' +
-                ", email='" + email + '\'' +
-                ", contributorAttributes=" + contributorAttributes +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        Contributor that = (Contributor) o;
-
-        if (contributorAttributes != null ? !contributorAttributes.equals(that.contributorAttributes) : that.contributorAttributes != null) {
-            return false;
-        }
-        if (creditName != null ? !creditName.equals(that.creditName) : that.creditName != null) {
-            return false;
-        }
-        if (email != null ? !email.equals(that.email) : that.email != null) {
-            return false;
-        }
-        if (orcid != null ? !orcid.equals(that.orcid) : that.orcid != null) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = orcid != null ? orcid.hashCode() : 0;
-        result = 31 * result + (creditName != null ? creditName.hashCode() : 0);
-        result = 31 * result + (email != null ? email.hashCode() : 0);
-        result = 31 * result + (contributorAttributes != null ? contributorAttributes.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttribute.java

@@ -1,79 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-
-package org.dspace.authority.orcid.model;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class ContributorAttribute {
-
-    private ContributorAttributeRole role;
-    private ContributorAttributeSequence sequence;
-
-    public ContributorAttribute(ContributorAttributeRole role, ContributorAttributeSequence sequence) {
-        this.role = role;
-        this.sequence = sequence;
-    }
-
-    public ContributorAttributeRole getRole() {
-        return role;
-    }
-
-    public void setRole(ContributorAttributeRole role) {
-        this.role = role;
-    }
-
-    public ContributorAttributeSequence getSequence() {
-        return sequence;
-    }
-
-    public void setSequence(ContributorAttributeSequence sequence) {
-        this.sequence = sequence;
-    }
-
-    @Override
-    public String toString() {
-        return "ContributorAttribute{" +
-                "role=" + role +
-                ", sequence=" + sequence +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        ContributorAttribute that = (ContributorAttribute) o;
-
-        if (role != that.role) {
-            return false;
-        }
-        if (sequence != that.sequence) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = role != null ? role.hashCode() : 0;
-        result = 31 * result + (sequence != null ? sequence.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeRole.java

@@ -1,32 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeRole {
-
-    AUTHOR,
-    ASSIGNEE,
-    EDITOR,
-    CHAIR_OR_TRANSLATOR,
-    CO_INVESTIGATOR,
-    CO_INVENTOR,
-    GRADUATE_STUDENT,
-    OTHER_INVENTOR,
-    PRINCIPAL_INVESTIGATOR,
-    POSTDOCTORAL_RESEARCHER,
-    SUPPORT_STAFF
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/ContributorAttributeSequence.java

@@ -1,23 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118843-anatomy-of-a-contributor
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum ContributorAttributeSequence {
-
-    FIRST,
-    ADDITIONAL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/Work.java

@@ -1,117 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-import java.util.Set;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class Work {
-
-    private WorkTitle workTitle;
-    private String description;
-    private Citation citation;
-    private WorkType workType;
-    private String publicationDate;
-    private WorkExternalIdentifier workExternalIdentifier;
-    private String url;
-    private Set<Contributor> contributors;
-    private String workSource;
-
-    public WorkTitle getWorkTitle() {
-        return workTitle;
-    }
-
-    public void setWorkTitle(WorkTitle workTitle) {
-        this.workTitle = workTitle;
-    }
-
-    public String getDescription() {
-        return description;
-    }
-
-    public void setDescription(String description) {
-        this.description = description;
-    }
-
-    public Citation getCitation() {
-        return citation;
-    }
-
-    public void setCitation(Citation citation) {
-        this.citation = citation;
-    }
-
-    public WorkType getWorkType() {
-        return workType;
-    }
-
-    public void setWorkType(WorkType workType) {
-        this.workType = workType;
-    }
-
-    public String getPublicationDate() {
-        return publicationDate;
-    }
-
-    public void setPublicationDate(String publicationDate) {
-        this.publicationDate = publicationDate;
-    }
-
-    public WorkExternalIdentifier getWorkExternalIdentifier() {
-        return workExternalIdentifier;
-    }
-
-    public void setWorkExternalIdentifier(WorkExternalIdentifier workExternalIdentifier) {
-        this.workExternalIdentifier = workExternalIdentifier;
-    }
-
-    public String getUrl() {
-        return url;
-    }
-
-    public void setUrl(String url) {
-        this.url = url;
-    }
-
-    public Set<Contributor> getContributors() {
-        return contributors;
-    }
-
-    public void setContributors(Set<Contributor> contributors) {
-        this.contributors = contributors;
-    }
-
-    public String getWorkSource() {
-        return workSource;
-    }
-
-    public void setWorkSource(String workSource) {
-        this.workSource = workSource;
-    }
-
-    @Override
-    public String toString() {
-        return "Work{" +
-                "workTitle=" + workTitle +
-                ", description='" + description + '\'' +
-                ", citation=" + citation +
-                ", workType=" + workType +
-                ", publicationDate='" + publicationDate + '\'' +
-                ", workExternalIdentifier=" + workExternalIdentifier +
-                ", url='" + url + '\'' +
-                ", contributors=" + contributors +
-                ", workSource='" + workSource + '\'' +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifier.java

@@ -1,71 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkExternalIdentifier {
-
-    private WorkExternalIdentifierType workExternalIdentifierType;
-    private String workExternalIdenfitierID;
-
-    public WorkExternalIdentifier(WorkExternalIdentifierType workExternalIdentifierType, String workExternalIdenfitierID) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-        this.workExternalIdenfitierID = workExternalIdenfitierID;
-    }
-
-    public WorkExternalIdentifierType getWorkExternalIdentifierType() {
-        return workExternalIdentifierType;
-    }
-
-    public void setWorkExternalIdentifierType(WorkExternalIdentifierType workExternalIdentifierType) {
-        this.workExternalIdentifierType = workExternalIdentifierType;
-    }
-
-    @Override
-    public String toString() {
-        return "WorkExternalIdentifier{" +
-                "workExternalIdentifierType=" + workExternalIdentifierType +
-                ", workExternalIdenfitierID='" + workExternalIdenfitierID + '\'' +
-                '}';
-    }
-
-    @Override
-    public boolean equals(Object o) {
-        if (this == o) {
-            return true;
-        }
-        if (o == null || getClass() != o.getClass()) {
-            return false;
-        }
-
-        WorkExternalIdentifier that = (WorkExternalIdentifier) o;
-
-        if (workExternalIdenfitierID != null ? !workExternalIdenfitierID.equals(that.workExternalIdenfitierID) : that.workExternalIdenfitierID != null) {
-            return false;
-        }
-        if (workExternalIdentifierType != that.workExternalIdentifierType) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        int result = workExternalIdentifierType != null ? workExternalIdentifierType.hashCode() : 0;
-        result = 31 * result + (workExternalIdenfitierID != null ? workExternalIdenfitierID.hashCode() : 0);
-        return result;
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkExternalIdentifierType.java

@@ -1,42 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkExternalIdentifierType {
-
-//    OTHER_ID,
-    ARXIV,
-    ASIN,
-    ASIN_TLD,
-    BIBCODE,
-    DOI,
-    EID,
-    ISBN,
-    ISSN,
-    JFM,
-    JSTOR,
-    LCCN,
-    MR,
-    OCLC,
-    OL,
-    OSTI,
-    PMC,
-    PMID,
-    RFC,
-    SSRN,
-    ZBL
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkTitle.java

@@ -1,64 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-import java.util.Map;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118807
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class WorkTitle {
-
-    private String title;
-    private String subtitle;
-    private Map<String, String> translatedTitles;
-
-    public WorkTitle(String title, String subtitle, Map<String, String> translatedTitles) {
-        this.title = title;
-        this.subtitle = subtitle;
-        this.translatedTitles = translatedTitles;
-    }
-
-    public String getTitle() {
-        return title;
-    }
-
-    public void setTitle(String title) {
-        this.title = title;
-    }
-
-    public String getSubtitle() {
-        return subtitle;
-    }
-
-    public void setSubtitle(String subtitle) {
-        this.subtitle = subtitle;
-    }
-
-    public String getTranslatedTitles(String languageCode) {
-        return translatedTitles.get(languageCode);
-    }
-
-    public void setTranslatedTitle(String languageCode, String translatedTitle) {
-        translatedTitles.put(languageCode, translatedTitle);
-    }
-
-    @Override
-    public String toString() {
-        return "WorkTitle{" +
-                "title='" + title + '\'' +
-                ", subtitle='" + subtitle + '\'' +
-                ", translatedTitles=" + translatedTitles +
-                '}';
-    }
-}

dspace-api/src/main/java/org/dspace/authority/orcid/model/WorkType.java

@@ -1,57 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.model;
-
-/**
- * http://support.orcid.org/knowledgebase/articles/118795
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public enum WorkType {
-
-    BOOK,
-    BOOK_CHAPTER,
-    BOOK_REVIEW,
-    DICTIONARY_ENTRY,
-    DISSERTATION,
-    ENCYCLOPEDIA_ARTICLE,
-    EDITED_BOOK,
-    JOURNAL_ARTICLE,
-    JOURNAL_ISSUE,
-    MAGAZINE_ARTICLE,
-    MANUAL,
-    ONLINE_RESOURCE,
-    NEWSLETTER_ARTICLE,
-    NEWSPAPER_ARTICLE,
-    REPORT,
-    RESEARCH_TOOL,
-    SUPERVISED_STUDENT_PUBLICATION,
-    TEST,
-    TRANSLATION,
-    WEBSITE,
-    CONFERENCE_ABSTRACT,
-    CONFERENCE_PAPER,
-    CONFERENCE_POSTER,
-    DISCLOSURE,
-    LICENSE,
-    PATENT,
-    REGISTERED_COPYRIGHT,
-    ARTISTIC_PERFORMANCE,
-    DATA_SET,
-    INVENTION,
-    LECTURE_SPEECH,
-    RESEARCH_TECHNIQUE,
-    SPIN_OFF_COMPANY,
-    STANDARDS_AND_POLICY,
-    TECHNICAL_STANDARD,
-    OTHER
-
-}

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

@@ -8,7 +8,13 @@
 package org.dspace.authority.orcid.xml;
 
 import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
+import org.xml.sax.SAXException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.Unmarshaller;
+import java.io.InputStream;
+import java.net.URISyntaxException;
 
 /**
  *
@@ -24,11 +30,15 @@ public abstract class Converter<T> {
      */
     private static Logger log = Logger.getLogger(Converter.class);
 
+    public abstract T convert(InputStream document);
 
-    protected void processError(Document xml) {
-        String errorMessage = XMLErrors.getErrorMessage(xml);
-        log.error("The orcid-message reports an error: " + errorMessage);
+    protected Object unmarshall(InputStream input, Class<?> type) throws SAXException, URISyntaxException {
+        try {
+            JAXBContext context = JAXBContext.newInstance(type);
+            Unmarshaller unmarshaller = context.createUnmarshaller();
+            return unmarshaller.unmarshal(input);
+        } catch (JAXBException e) {
+            throw new RuntimeException("Unable to unmarshall orcid message" + e);
+        }
     }
-
-    public abstract T convert(Document document);
 }

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLErrors.java

@@ -1,73 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.xml;
-
-import org.dspace.authority.util.XMLUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-
-import javax.xml.xpath.XPathExpressionException;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class XMLErrors {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(XMLErrors.class);
-
-    private static final String ERROR_DESC = "/orcid-message/error-desc";
-
-    /**
-     * Evaluates whether a given xml document contains errors or not.
-     *
-     * @param xml The given xml document
-     * @return true if the given xml document is null
-     * or if it contains errors
-     */
-    public static boolean check(Document xml) {
-
-        if (xml == null) {
-            return true;
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent == null;
-    }
-
-    public static String getErrorMessage(Document xml) {
-
-        if (xml == null) {
-            return "Did not receive an XML document.";
-        }
-
-        String textContent = null;
-
-        try {
-            textContent = XMLUtils.getTextContent(xml, ERROR_DESC);
-        } catch (XPathExpressionException e) {
-            log.error("Error while checking for errors in orcid message", e);
-        }
-
-        return textContent;
-    }
-
-}

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoBio.java

@@ -7,23 +7,22 @@
  */
 package org.dspace.authority.orcid.xml;
 
-import org.dspace.authority.orcid.model.Bio;
-import org.dspace.authority.orcid.model.BioExternalIdentifier;
-import org.dspace.authority.orcid.model.BioName;
-import org.dspace.authority.orcid.model.BioResearcherUrl;
-import org.dspace.authority.util.XMLUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
 
-import javax.xml.xpath.XPathExpressionException;
+import org.apache.log4j.Logger;
+import org.dspace.authority.orcid.Orcidv2;
+import org.dspace.utils.DSpace;
+import org.orcid.jaxb.model.common_v2.OrcidId;
+import org.orcid.jaxb.model.record_v2.Person;
+import org.orcid.jaxb.model.search_v2.Result;
+import org.orcid.jaxb.model.search_v2.Search;
+import org.xml.sax.SAXException;
+
+import java.io.InputStream;
+import java.net.URISyntaxException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 
 /**
- *
  * @author Antoine Snyers (antoine at atmire.com)
  * @author Kevin Van de Velde (kevin at atmire dot com)
  * @author Ben Bosman (ben at atmire dot com)
@@ -36,216 +35,39 @@ public class XMLtoBio extends Converter {
      */
     private static Logger log = Logger.getLogger(XMLtoBio.class);
 
-    /**
-     * orcid-message XPATHs
-     */
-
-    protected String ORCID_BIO = "//orcid-bio";
-
-//    protected String ORCID = "parent::*/orcid";
-    protected String ORCID = "parent::*/orcid-identifier/path";
-
-    protected String PERSONAL_DETAILS = "personal-details";
-    protected String GIVEN_NAMES = PERSONAL_DETAILS + "/given-names";
-    protected String FAMILY_NAME = PERSONAL_DETAILS + "/family-name";
-    protected String CREDIT_NAME = PERSONAL_DETAILS + "/credit-name";
-    protected String OTHER_NAMES = PERSONAL_DETAILS + "/other-names";
-    protected String OTHER_NAME = OTHER_NAMES + "/other-name";
-
-    protected String CONTACT_DETAILS = "contact-details";
-    protected String COUNTRY = CONTACT_DETAILS + "/address/country";
-
-    protected String KEYWORDS = "keywords";
-    protected String KEYWORD = KEYWORDS + "/keyword";
-
-    protected String EXTERNAL_IDENTIFIERS = "external-identifiers";
-    protected String EXTERNAL_IDENTIFIER = EXTERNAL_IDENTIFIERS + "/external-identifier";
-    protected String EXTERNAL_ID_ORCID = "external-id-orcid";
-    protected String EXTERNAL_ID_COMMNON_NAME = "external-id-common-name";
-    protected String EXTERNAL_ID_REFERENCE = "external-id-reference";
-    protected String EXTERNAL_ID_URL = "external-id-url";
-
-    protected String RESEARCHER_URLS = "researcher-urls";
-    protected String RESEARCHER_URL = "researcher-urls/researcher-url";
-    protected String URL_NAME = "url-name";
-    protected String URL = "url";
-
-    protected String BIOGRAPHY = ORCID_BIO + "/biography";
-
-    protected String AFFILIATIONS = ORCID_BIO + "/affiliation";
-
-    /**
-     * Regex
-     */
-
-    protected String ORCID_NOT_FOUND = "ORCID [\\d-]* not found";
-
-
-    public List<Bio> convert(Document xml) {
-        List<Bio> result = new ArrayList<Bio>();
-
-        if (XMLErrors.check(xml)) {
-
-            try {
-                Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, ORCID_BIO);
-                while (iterator.hasNext()) {
-                    Bio bio = convertBio(iterator.next());
-                    result.add(bio);
-                }
-            } catch (XPathExpressionException e) {
-                log.error("Error in xpath syntax", e);
-            }
-        } else {
-            processError(xml);
-        }
-
-        return result;
-    }
-
-    private Bio convertBio(Node node) {
-        Bio bio = new Bio();
-
-        setOrcid(node,bio);
-        setPersonalDetails(node, bio);
-        setContactDetails(node, bio);
-        setKeywords(node, bio);
-        setExternalIdentifiers(node, bio);
-        setResearcherUrls(node, bio);
-        setBiography(node, bio);
-
-        return bio;
-    }
-
-    protected void processError(Document xml)  {
-        String errorMessage = XMLErrors.getErrorMessage(xml);
-
-        if(errorMessage.matches(ORCID_NOT_FOUND))
-        {
-            // do something?
-        }
-
-        log.error("The orcid-message reports an error: " + errorMessage);
-    }
-
-
-    private void setOrcid(Node node, Bio bio) {
+    @Override
+    public List<Person> convert(InputStream xml) {
+        List<Person> bios= new ArrayList<>();
         try {
-            String orcid = XMLUtils.getTextContent(node, ORCID);
-            bio.setOrcid(orcid);
-        } catch (XPathExpressionException e) {
-            log.debug("Error in finding the biography in bio xml.", e);
-        }
-    }
+            Orcidv2 connector = new DSpace().getServiceManager().getServiceByName("AuthoritySource", Orcidv2.class);
 
-    protected void setBiography(Node xml, Bio bio) {
-        try {
-            String biography = XMLUtils.getTextContent(xml, BIOGRAPHY);
-            bio.setBiography(biography);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the biography in bio xml.", e);
-        }
-    }
-
-    protected void setResearcherUrls(Node xml, Bio bio) {
-        try {
-            NodeList researcher_urls = XMLUtils.getNodeList(xml, RESEARCHER_URL);
-            if (researcher_urls != null) {
-                for (int i = 0; i < researcher_urls.getLength(); i++) {
-                    Node researcher_url = researcher_urls.item(i);
-                    if (researcher_url.getNodeType() != Node.TEXT_NODE) {
-                        String url_name = XMLUtils.getTextContent(researcher_url, URL_NAME);
-                        String url = XMLUtils.getTextContent(researcher_url, URL);
-                        BioResearcherUrl researcherUrl = new BioResearcherUrl(url_name, url);
-                        bio.addResearcherUrl(researcherUrl);
+            Search search = (Search) unmarshall(xml, Search.class);
+            for(Result result : search.getResult()){
+                OrcidId orcidIdentifier = result.getOrcidIdentifier();
+                if(orcidIdentifier!=null){
+                    log.debug("Found OrcidId=" + orcidIdentifier.toString());
+                    String orcid = orcidIdentifier.getUriPath();
+                    Person bio = connector.getBio(orcid);
+                    if(bio!=null){
+                        bios.add(bio);
                     }
                 }
             }
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the researcher url in bio xml.", e);
+        } catch (SAXException | URISyntaxException e) {
+            log.error(e);
         }
+        return bios;
     }
 
-    protected void setExternalIdentifiers(Node xml, Bio bio) {
+    public Person convertSinglePerson(InputStream xml) {
+        Person person = null;
         try {
-
-            Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, EXTERNAL_IDENTIFIER);
-            while (iterator.hasNext()) {
-                Node external_identifier = iterator.next();
-                String id_orcid = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_ORCID);
-                String id_common_name = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_COMMNON_NAME);
-                String id_reference = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_REFERENCE);
-                String id_url = XMLUtils.getTextContent(external_identifier, EXTERNAL_ID_URL);
-                BioExternalIdentifier externalIdentifier = new BioExternalIdentifier(id_orcid, id_common_name, id_reference, id_url);
-                bio.addExternalIdentifier(externalIdentifier);
-            }
-
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the external identifier in bio xml.", e);
-        }
-    }
-
-    protected void setKeywords(Node xml, Bio bio) {
-        try {
-            NodeList keywords = XMLUtils.getNodeList(xml, KEYWORD);
-            if (keywords != null) {
-                for (int i = 0; i < keywords.getLength(); i++) {
-                    String keyword = keywords.item(i).getTextContent();
-                    String[] split = keyword.split(",");
-                    for (String k : split) {
-                        bio.addKeyword(k.trim());
-                    }
-                }
-            }
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the keywords in bio xml.", e);
-        }
-    }
-
-    protected void setContactDetails(Node xml, Bio bio) {
-        try {
-            String country = XMLUtils.getTextContent(xml, COUNTRY);
-            bio.setCountry(country);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the country in bio xml.", e);
-        }
-    }
-
-    protected void setPersonalDetails(Node xml, Bio bio) {
-        BioName name = bio.getName();
-
-        try {
-            String givenNames = XMLUtils.getTextContent(xml, GIVEN_NAMES);
-            name.setGivenNames(givenNames);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the given names in bio xml.", e);
-        }
-
-        try {
-            String familyName = XMLUtils.getTextContent(xml, FAMILY_NAME);
-            name.setFamilyName(familyName);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the family name in bio xml.", e);
-        }
-
-        try {
-            String creditName = XMLUtils.getTextContent(xml, CREDIT_NAME);
-            name.setCreditName(creditName);
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the credit name in bio xml.", e);
-        }
-
-        try {
-
-            Iterator<Node> iterator = XMLUtils.getNodeListIterator(xml, OTHER_NAME);
-            while (iterator.hasNext()) {
-                Node otherName = iterator.next();
-                String textContent = otherName.getTextContent();
-                name.getOtherNames().add(textContent.trim());
-            }
-
-        } catch (XPathExpressionException e) {
-            log.error("Error in finding the other names in bio xml.", e);
+            person = (Person) unmarshall(xml, Person.class);
+            return person;
+        } catch (SAXException | URISyntaxException e) {
+            log.error(e);
         }
+        return null;
     }
 
 }

dspace-api/src/main/java/org/dspace/authority/orcid/xml/XMLtoWork.java

@@ -1,239 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.authority.orcid.xml;
-
-import org.dspace.authority.orcid.model.*;
-import org.dspace.authority.util.*;
-import org.apache.commons.lang.StringUtils;
-import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import javax.xml.xpath.XPathExpressionException;
-import java.util.*;
-
-/**
- *
- * @author Antoine Snyers (antoine at atmire.com)
- * @author Kevin Van de Velde (kevin at atmire dot com)
- * @author Ben Bosman (ben at atmire dot com)
- * @author Mark Diggory (markd at atmire dot com)
- */
-public class XMLtoWork extends Converter {
-
-    /**
-     * log4j logger
-     */
-    private static Logger log = Logger.getLogger(XMLtoWork.class);
-
-    /**
-     * orcid-message XPATHs
-     */
-
-    protected String ORCID_WORKS = "//orcid-works";
-    protected String ORCID_WORK = ORCID_WORKS + "/orcid-work";
-
-    protected String WORK_TITLE = "work-title";
-    protected String TITLE = WORK_TITLE + "/title";
-    protected String SUBTITLE = WORK_TITLE + "/subtitle";
-    protected String TRANSLATED_TITLES = WORK_TITLE + "/translated-title";
-    protected String TRANSLATED_TITLES_LANGUAGE = "@language-code";
-
-    protected String SHORT_DESCRIPTION = "short-description";
-
-    protected String WORK_CITATION = "work-citation";
-    protected String CITATION_TYPE = WORK_CITATION + "/work-citation-type";
-    protected String CITATION = WORK_CITATION + "/citation";
-
-    protected String WORK_TYPE = "work-type";
-
-    protected String PUBLICATION_DATE = "publication-date";
-    protected String YEAR = PUBLICATION_DATE + "/year";
-    protected String MONTH = PUBLICATION_DATE + "/month";
-    protected String DAY = PUBLICATION_DATE + "/day";
-
-    protected String WORK_EXTERNAL_IDENTIFIERS = "work-external-identifiers";
-    protected String WORK_EXTERNAL_IDENTIFIER = WORK_EXTERNAL_IDENTIFIERS + "/work-external-identifier";
-    protected String WORK_EXTERNAL_IDENTIFIER_TYPE = "work-external-identifier-type";
-    protected String WORK_EXTERNAL_IDENTIFIER_ID = "work-external-identifier-id";
-
-    protected String URL = "url";
-
-    protected String WORK_CONTRIBUTOR = "work-contributors";
-    protected String CONTRIBUTOR = WORK_CONTRIBUTOR+"/contributor";
-    protected String CONTRIBUTOR_ORCID = "contributor-orcid";
-    protected String CREDIT_NAME = "credit-name";
-    protected String CONTRIBUTOR_EMAIL = "contributor-email";
-    protected String CONTRIBUTOR_ATTRIBUTES = "contributor-attributes";
-    protected String CONTRIBUTOR_SEQUENCE = "contributor-sequence";
-    protected String CONTRIBUTOR_ROLE = "contributor-role";
-
-    protected String WORK_SOURCE = "work-source";
-
-
-    public List<Work> convert(Document document) {
-        List<Work> result = new ArrayList<Work>();
-
-        if (XMLErrors.check(document)) {
-
-            try {
-                Iterator<Node> iterator = XMLUtils.getNodeListIterator(document, ORCID_WORK);
-                while (iterator.hasNext()) {
-                    Work work = convertWork(iterator.next());
-                    result.add(work);
-                }
-            } catch (XPathExpressionException e) {
-                log.error("Error in xpath syntax", e);
-            }
-        } else {
-            processError(document);
-        }
-
-        return result;
-    }
-
-    protected Work convertWork(Node node) throws XPathExpressionException {
-        Work work = new Work();
-        setTitle(node, work);
-        setDescription(node, work);
-        setCitation(node, work);
-        setWorkType(node, work);
-        setPublicationDate(node, work);
-        setExternalIdentifiers(node, work);
-        setUrl(node, work);
-        setContributors(node, work);
-        setWorkSource(node, work);
-
-        return work;
-    }
-
-    protected void setWorkSource(Node node, Work work) throws XPathExpressionException {
-        String workSource = XMLUtils.getTextContent(node, WORK_SOURCE);
-        work.setWorkSource(workSource);
-    }
-
-    protected void setContributors(Node node, Work work) throws XPathExpressionException {
-
-        Set<Contributor> contributors = new HashSet<Contributor>();
-
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, CONTRIBUTOR);
-        while (iterator.hasNext()) {
-            Node nextContributorNode = iterator.next();
-            String orcid = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_ORCID);
-            String creditName = XMLUtils.getTextContent(nextContributorNode, CREDIT_NAME);
-            String email = XMLUtils.getTextContent(nextContributorNode, CONTRIBUTOR_EMAIL);
-
-            Set<ContributorAttribute> contributorAttributes = new HashSet<ContributorAttribute>();
-            NodeList attributeNodes = XMLUtils.getNodeList(nextContributorNode, CONTRIBUTOR_ATTRIBUTES);
-            Iterator<Node> attributesIterator = XMLUtils.getNodeListIterator(attributeNodes);
-            while (attributesIterator.hasNext()) {
-                Node nextAttribute = attributesIterator.next();
-
-                String roleText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_ROLE);
-                ContributorAttributeRole role = EnumUtils.lookup(ContributorAttributeRole.class, roleText);
-
-                String sequenceText = XMLUtils.getTextContent(nextAttribute, CONTRIBUTOR_SEQUENCE);
-                ContributorAttributeSequence sequence = EnumUtils.lookup(ContributorAttributeSequence.class, sequenceText);
-
-                ContributorAttribute attribute = new ContributorAttribute(role, sequence);
-                contributorAttributes.add(attribute);
-            }
-
-            Contributor contributor = new Contributor(orcid, creditName, email, contributorAttributes);
-            contributors.add(contributor);
-        }
-
-        work.setContributors(contributors);
-    }
-
-    protected void setUrl(Node node, Work work) throws XPathExpressionException {
-        String url = XMLUtils.getTextContent(node, URL);
-        work.setUrl(url);
-    }
-
-    protected void setExternalIdentifiers(Node node, Work work) throws XPathExpressionException {
-
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(node, WORK_EXTERNAL_IDENTIFIER);
-        while (iterator.hasNext()) {
-            Node work_external_identifier = iterator.next();
-            String typeText = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_TYPE);
-
-            WorkExternalIdentifierType type = EnumUtils.lookup(WorkExternalIdentifierType.class, typeText);
-
-            String id = XMLUtils.getTextContent(work_external_identifier, WORK_EXTERNAL_IDENTIFIER_ID);
-
-            WorkExternalIdentifier externalID = new WorkExternalIdentifier(type, id);
-            work.setWorkExternalIdentifier(externalID);
-        }
-    }
-
-    protected void setPublicationDate(Node node, Work work) throws XPathExpressionException {
-
-        String year = XMLUtils.getTextContent(node, YEAR);
-        String month = XMLUtils.getTextContent(node, MONTH);
-        String day = XMLUtils.getTextContent(node, DAY);
-
-        String publicationDate = year;
-        if (StringUtils.isNotBlank(month)) {
-            publicationDate += "-" + month;
-            if (StringUtils.isNotBlank(day)) {
-                publicationDate += "-" + day;
-            }
-        }
-
-        work.setPublicationDate(publicationDate);
-    }
-
-    protected void setWorkType(Node node, Work work) throws XPathExpressionException {
-
-        String workTypeText = XMLUtils.getTextContent(node, WORK_TYPE);
-        WorkType workType = EnumUtils.lookup(WorkType.class, workTypeText);
-
-        work.setWorkType(workType);
-    }
-
-    protected void setCitation(Node node, Work work) throws XPathExpressionException {
-
-        String typeText = XMLUtils.getTextContent(node, CITATION_TYPE);
-        CitationType type = EnumUtils.lookup(CitationType.class, typeText);
-
-        String citationtext = XMLUtils.getTextContent(node, CITATION);
-
-        Citation citation = new Citation(type, citationtext);
-        work.setCitation(citation);
-    }
-
-    protected void setDescription(Node node, Work work) throws XPathExpressionException {
-
-        String description = null;
-        description = XMLUtils.getTextContent(node, SHORT_DESCRIPTION);
-        work.setDescription(description);
-    }
-
-    protected void setTitle(Node node, Work work) throws XPathExpressionException {
-
-        String title = XMLUtils.getTextContent(node, TITLE);
-
-        String subtitle = XMLUtils.getTextContent(node, SUBTITLE);
-
-        Map<String, String> translatedTitles = new HashMap<String, String>();
-        NodeList nodeList = XMLUtils.getNodeList(node, TRANSLATED_TITLES);
-        Iterator<Node> iterator = XMLUtils.getNodeListIterator(nodeList);
-        while (iterator.hasNext()) {
-            Node languageNode = iterator.next();
-            String language = XMLUtils.getTextContent(languageNode, TRANSLATED_TITLES_LANGUAGE);
-            String translated_title = XMLUtils.getTextContent(languageNode, ".");
-            translatedTitles.put(language, translated_title);
-        }
-
-        WorkTitle workTitle = new WorkTitle(title, subtitle, translatedTitles);
-        work.setWorkTitle(workTitle);
-    }
-
-}

dspace-api/src/main/java/org/dspace/authority/rest/RESTConnector.java

@@ -7,13 +7,12 @@
  */
 package org.dspace.authority.rest;
 
-import org.apache.http.impl.client.HttpClientBuilder;
-import org.dspace.authority.util.XMLUtils;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.HttpClient;
 import org.apache.http.client.methods.HttpGet;
+import org.apache.http.impl.client.HttpClientBuilder;
 import org.apache.log4j.Logger;
-import org.w3c.dom.Document;
 
 import java.io.InputStream;
 import java.util.Scanner;
@@ -38,26 +37,28 @@ public class RESTConnector {
         this.url = url;
     }
 
-    public Document get(String path) {
-        Document document = null;
+    public InputStream get(String path, String accessToken) {
 
         InputStream result = null;
         path = trimSlashes(path);
 
         String fullPath = url + '/' + path;
         HttpGet httpGet = new HttpGet(fullPath);
+        if(StringUtils.isNotBlank(accessToken)){
+            httpGet.addHeader("Content-Type", "application/vnd.orcid+xml");
+            httpGet.addHeader("Authorization","Bearer "+accessToken);
+        }
         try {
             HttpClient httpClient = HttpClientBuilder.create().build();
             HttpResponse getResponse = httpClient.execute(httpGet);
             //do not close this httpClient
             result = getResponse.getEntity().getContent();
-            document = XMLUtils.convertStreamToXML(result);
 
         } catch (Exception e) {
             getGotError(e, fullPath);
         }
 
-        return document;
+        return result;
     }
 
     protected void getGotError(Exception e, String fullPath) {

dspace-api/src/main/java/org/dspace/authority/rest/RestSource.java

@@ -7,9 +7,7 @@
  */
 package org.dspace.authority.rest;
 
-import org.dspace.authority.AuthorityValue;
-
-import java.util.List;
+import org.dspace.authority.SolrAuthorityInterface;
 
 /**
  *
@@ -18,21 +16,11 @@ import java.util.List;
  * @author Ben Bosman (ben at atmire dot com)
  * @author Mark Diggory (markd at atmire dot com)
  */
-public abstract class RestSource {
+public abstract class RestSource implements SolrAuthorityInterface {
 
     protected RESTConnector restConnector;
 
     public RestSource(String url) {
         this.restConnector = new RESTConnector(url);
     }
-
-    /**
-     * TODO
-     * com.atmire.org.dspace.authority.rest.RestSource#queryAuthorities -> add field, so the source can decide whether to query /users or something else.
-     * -> implement subclasses
-     * -> implement usages
-     */
-    public abstract List<AuthorityValue> queryAuthorities(String text, int max);
-
-    public abstract AuthorityValue queryAuthorityID(String id);
 }

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

@@ -20,6 +20,7 @@ import org.dspace.eperson.Group;
 import org.dspace.storage.rdbms.DatabaseManager;
 import org.dspace.storage.rdbms.TableRow;
 import org.dspace.storage.rdbms.TableRowIterator;
+import org.dspace.workflow.WorkflowItem;
 
 /**
  * AuthorizeManager handles all authorization checks for DSpace. For better
@@ -295,8 +296,43 @@ public class AuthorizeManager
             }
         }
 
+        // In case the dso is an bundle or bitstream we must ignore custom 
+        // policies if it does not belong to at least one installed item (see 
+        // DS-2614).
+        // In case the dso is an item and a corresponding workspace or workflow
+        // item exist, we have to ignore custom policies (see DS-2614).
+        boolean ignoreCustomPolicies = false;
+        if (o instanceof Bitstream)
+        {
+            Bitstream b = (Bitstream) o;
+
+            // Ensure that this is not a collection or community logo
+            DSpaceObject parent = b.getParentObject();
+            if (!(parent instanceof Collection) && !(parent instanceof Community))
+            {
+                ignoreCustomPolicies = !isAnyItemInstalled(c, b.getBundles());
+            }
+        }
+        if (o instanceof Bundle)
+        {
+            ignoreCustomPolicies = !isAnyItemInstalled(c, new Bundle[] {(Bundle) o});
+        }
+        if (o instanceof Item)
+        {
+            if (WorkspaceItem.findByItem(c, (Item) o) != null ||
+                    WorkflowItem.findByItem(c, (Item) o) != null)
+            {
+                ignoreCustomPolicies = true;
+            }
+        }
+        
         for (ResourcePolicy rp : getPoliciesActionFilter(c, o, action))
         {
+            if (ignoreCustomPolicies 
+                    && ResourcePolicy.TYPE_CUSTOM.equals(rp.getRpType()))
+            {
+                continue;
+            }
             // check policies for date validity
             if (rp.isDateValid())
             {
@@ -306,7 +342,7 @@ public class AuthorizeManager
                 }
 
                 if ((rp.getGroupID() != -1)
-                        && (Group.isMember(c, rp.getGroupID())))
+                        && (Group.isMember(c, e, rp.getGroupID())))
                 {
                     // group was set, and eperson is a member
                     // of that group
@@ -318,7 +354,26 @@ public class AuthorizeManager
         // default authorization is denial
         return false;
     }
-
+    
+    // check whether any bundle belongs to any item that passed submission 
+    // and workflow process
+    protected static boolean isAnyItemInstalled(Context ctx, Bundle[] bundles)
+            throws SQLException
+    {
+        for (Bundle bundle : bundles)
+        {
+            for (Item item : bundle.getItems())
+            {
+                if (WorkspaceItem.findByItem(ctx, item) == null
+                        && WorkflowItem.findByItem(ctx, item) == null)
+                {
+                    return true;
+                }
+            }
+        }
+        return false;
+    }
+    
     ///////////////////////////////////////////////
     // admin check methods
     ///////////////////////////////////////////////
@@ -480,7 +535,9 @@ public class AuthorizeManager
 
         rp.update();
 
+        c.turnOffAuthorisationSystem();
         o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -534,8 +591,10 @@ public class AuthorizeManager
         rp.setRpType(type);
 
         rp.update();
-
+        
+        c.turnOffAuthorisationSystem();
         o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -799,7 +858,9 @@ public class AuthorizeManager
             drp.update();
         }
 
+        c.turnOffAuthorisationSystem();
         dest.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -815,12 +876,14 @@ public class AuthorizeManager
     public static void removeAllPolicies(Context c, DSpaceObject o)
             throws SQLException
     {
-        o.updateLastModified();
-
         // FIXME: authorization check?
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? ",
                 o.getType(), o.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -837,7 +900,7 @@ public class AuthorizeManager
             throws SQLException
     {
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
-                + "resource_type_id= ? AND resource_id= ? AND rptype <> ? ",
+                + "resource_type_id= ? AND resource_id= ? AND (rptype <> ? OR rptype IS NULL)",
                 o.getType(), o.getID(), type);
     }
 
@@ -861,6 +924,29 @@ public class AuthorizeManager
                 + "resource_type_id= ? AND resource_id= ? AND rptype=? ",
                 o.getType(), o.getID(), type);
     }
+    
+	/**
+	 * Change all the policies related to the action (fromPolicy) of the
+	 * specified object to the new action (toPolicy)
+	 * 
+	 * @param context
+	 * @param dso
+	 *            the dspace object
+	 * @param fromAction
+	 *            the action to change
+	 * @param toAction
+	 *            the new action to set
+	 * @throws SQLException
+	 * @throws AuthorizeException
+	 */
+	public static void switchPoliciesAction(Context context, DSpaceObject dso, int fromAction, int toAction)
+			throws SQLException, AuthorizeException {
+		List<ResourcePolicy> rps = getPoliciesActionFilter(context, dso, fromAction);
+		for (ResourcePolicy rp : rps) {
+			rp.setAction(toAction);
+			rp.update();
+		}
+	}
 
     /**
      * Remove all policies from an object that match a given action. FIXME
@@ -879,7 +965,6 @@ public class AuthorizeManager
     public static void removePoliciesActionFilter(Context context,
                                                   DSpaceObject dso, int actionID) throws SQLException
     {
-        dso.updateLastModified();
         if (actionID == -1)
         {
             // remove all policies from object
@@ -891,6 +976,10 @@ public class AuthorizeManager
                             "resource_id= ? AND action_id= ? ",
                     dso.getType(), dso.getID(), actionID);
         }
+        
+        context.turnOffAuthorisationSystem();
+        dso.updateLastModified();
+        context.restoreAuthSystemState();
     }
 
     /**
@@ -927,11 +1016,13 @@ public class AuthorizeManager
     public static void removeGroupPolicies(Context c, DSpaceObject o, Group g)
             throws SQLException
     {
-        o.updateLastModified();
-
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? AND epersongroup_id= ? ",
                 o.getType(), o.getID(), g.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**
@@ -950,10 +1041,13 @@ public class AuthorizeManager
     public static void removeEPersonPolicies(Context c, DSpaceObject o, EPerson e)
             throws SQLException
     {
-        o.updateLastModified();
         DatabaseManager.updateQuery(c, "DELETE FROM resourcepolicy WHERE "
                 + "resource_type_id= ? AND resource_id= ? AND eperson_id= ? ",
                 o.getType(), o.getID(), e.getID());
+        
+        c.turnOffAuthorisationSystem();
+        o.updateLastModified();
+        c.restoreAuthSystemState();
     }
 
     /**

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

@@ -36,7 +36,7 @@ public class FixDefaultPolicies
         Context c = new Context();
 
         // turn off authorization
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         //////////////////////
         // carnage begins here

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

@@ -63,7 +63,7 @@ public class PolicySet
         Context c = new Context();
 
         // turn off authorization
-        c.setIgnoreAuthorization(true);
+        c.turnOffAuthorisationSystem();
 
         //////////////////////
         // carnage begins here

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

@@ -354,7 +354,7 @@ public class BrowserScope
      */
     public void setResultsPerPage(int resultsPerPage)
     {
-        if (resultsPerPage > -1 || browseIndex.isTagCloudEnabled())
+        if (resultsPerPage > -1 || (browseIndex != null && browseIndex.isTagCloudEnabled()))
         {
             this.resultsPerPage = resultsPerPage;
         }

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

@@ -32,6 +32,8 @@ import org.dspace.utils.DSpace;
  * 
  * @author Andrea Bollini (CILEA)
  * @author Adán Román Ruiz at arvo.es (bugfix)
+ * @author Panagiotis Koutsourakis (National Documentation Centre) (bugfix)
+ * @author Kostas Stamatis (National Documentation Centre) (bugfix)
  * 
  */
 public class SolrBrowseDAO implements BrowseDAO
@@ -336,6 +338,22 @@ public class SolrBrowseDAO implements BrowseDAO
         addStatusFilter(query);
         query.setMaxResults(0);
         query.addFilterQueries("search.resourcetype:" + Constants.ITEM);
+
+        // We need to take into account the fact that we may be in a subset of the items
+        if (authority != null)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_authority_filter}"
+                    + authority);
+        }
+        else if (this.value != null && !valuePartial)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_value_filter}" + this.value);
+        }
+        else if (valuePartial)
+        {
+            query.addFilterQueries("{!field f="+facetField + "_partial}" + this.value);
+        }
+
         if (isAscending)
         {
             query.setQuery("bi_"+column + "_sort" + ": [* TO \"" + value + "\"}");
@@ -343,6 +361,7 @@ public class SolrBrowseDAO implements BrowseDAO
         else
         {
             query.setQuery("bi_" + column + "_sort" + ": {\"" + value + "\" TO *]");
+	        query.addFilterQueries("-(bi_" + column + "_sort" + ":" + value + "*)");
         }
 	    boolean includeUnDiscoverable = itemsWithdrawn || !itemsDiscoverable;
         DiscoverResult resp = null;

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

@@ -28,6 +28,7 @@ import org.dspace.workflow.WorkflowItem;
 import org.dspace.xmlworkflow.storedcomponents.CollectionRole;
 import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 
+import java.io.Serializable;
 import java.io.IOException;
 import java.io.InputStream;
 import java.sql.PreparedStatement;
@@ -47,7 +48,6 @@ import java.util.*;
  * effect.
  *
  * @author Robert Tansley
- * @version $Revision$
  */
 public class Collection extends DSpaceObject
 {
@@ -294,31 +294,48 @@ public class Collection extends DSpaceObject
      * @return the collections in the system
      * @throws SQLException
      */
-    public static Collection[] findAll(Context context) throws SQLException {
+    public static Collection[] findAll(Context context) throws SQLException
+    {
         TableRowIterator tri = null;
-        try {
-            String query = "SELECT c.* FROM collection c " +
-                    "LEFT JOIN metadatavalue m on (m.resource_id = c.collection_id and m.resource_type_id = ? and m.metadata_field_id = ?) ";
-            if(DatabaseManager.isOracle()){
-                query += " ORDER BY cast(m.text_value as varchar2(128))";
-            }else{
-                query += " ORDER BY m.text_value";
-            }
+        List<Collection> collections = null;
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer query = new StringBuffer(
+            "SELECT c.*" +
+            "FROM collection c " +
+            "LEFT JOIN metadatavalue m ON (" +
+              "m.resource_id = c.collection_id AND " +
+              "m.resource_type_id = ? AND " +
+              "m.metadata_field_id = ?" +
+            ")"
+        );
 
-            tri = DatabaseManager.query(context,
-                    query,
-                    Constants.COLLECTION,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(), "title", null).getFieldID()
-            );
-        } catch (SQLException e) {
-            log.error("Find all Collections - ",e);
-            throw e;
+        if (DatabaseManager.isOracle())
+        {
+            query.append(" ORDER BY cast(m.text_value as varchar2(128))");
+        }
+        else
+        {
+            query.append(" ORDER BY m.text_value");
         }
 
-        List<Collection> collections = new ArrayList<Collection>();
+        params.add(Constants.COLLECTION);
+        params.add(
+          MetadataField.findByElement(
+            context,
+            MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(),
+            "title",
+            null
+          ).getFieldID()
+        );
 
         try
         {
+            tri = DatabaseManager.query(
+              context, query.toString(), params.toArray()
+            );
+
+            collections = new ArrayList<Collection>();
+
             while (tri.hasNext())
             {
                 TableRow row = tri.next();
@@ -337,6 +354,11 @@ public class Collection extends DSpaceObject
                 }
             }
         }
+        catch (SQLException e)
+        {
+            log.error("Find all Collections - ", e);
+            throw e;
+        }
         finally
         {
             // close the TableRowIterator to free up resources
@@ -363,31 +385,47 @@ public class Collection extends DSpaceObject
     public static Collection[] findAll(Context context, Integer limit, Integer offset) throws SQLException
     {
         TableRowIterator tri = null;
-        try{
-            String query = "SELECT c.* FROM collection c " +
-                    "LEFT JOIN metadatavalue m on (m.resource_id = c.collection_id and m.resource_type_id = ? and m.metadata_field_id = ?) ";
+        List<Collection> collections = null;
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer query = new StringBuffer(
+            "SELECT c.*" +
+            "FROM collection c " +
+            "LEFT JOIN metadatavalue m ON (" +
+              "m.resource_id = c.collection_id AND " +
+              "m.resource_type_id = ? AND " +
+              "m.metadata_field_id = ?" +
+            ")"
+        );
 
-            if(DatabaseManager.isOracle()){
-                query += " ORDER BY cast(m.text_value as varchar2(128))";
-            }else{
-                query += " ORDER BY m.text_value";
-            }
-            query += " limit ? offset ?";
-            tri = DatabaseManager.query(context,
-                    query,
-                    Constants.COLLECTION,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(), "title", null).getFieldID(),
-                    limit,
-                    offset
-            );
-        } catch (SQLException e) {
-            log.error("Find all Collections offset/limit - ",e);
-            throw e;
+        if (DatabaseManager.isOracle())
+        {
+            query.append(" ORDER BY cast(m.text_value as varchar2(128))");
         }
-        List<Collection> collections = new ArrayList<Collection>();
+        else
+        {
+            query.append(" ORDER BY m.text_value");
+        }
+
+        params.add(Constants.COLLECTION);
+        params.add(
+          MetadataField.findByElement(
+            context,
+            MetadataSchema.find(context, MetadataSchema.DC_SCHEMA).getSchemaID(),
+            "title",
+            null
+          ).getFieldID()
+        );
+
+        DatabaseManager.applyOffsetAndLimit(query, params, offset, limit);
 
         try
         {
+            tri = DatabaseManager.query(
+              context, query.toString(), params.toArray()
+            );
+
+            collections = new ArrayList<Collection>();
+
             while (tri.hasNext())
             {
                 TableRow row = tri.next();
@@ -406,6 +444,11 @@ public class Collection extends DSpaceObject
                 }
             }
         }
+        catch (SQLException e)
+        {
+            log.error("Find all Collections offset/limit - ", e);
+            throw e;
+        }
         finally
         {
             // close the TableRowIterator to free up resources
@@ -450,13 +493,20 @@ public class Collection extends DSpaceObject
      */
     public ItemIterator getItems(Integer limit, Integer offset) throws SQLException
     {
-        String myQuery = "SELECT item.* FROM item, collection2item WHERE "
-                + "item.item_id=collection2item.item_id AND "
-                + "collection2item.collection_id= ? "
-                + "AND item.in_archive='1' limit ? offset ?";
+        List<Serializable> params = new ArrayList<Serializable>();
+        StringBuffer myQuery = new StringBuffer(
+            "SELECT item.* " + 
+            "FROM item, collection2item " + 
+            "WHERE item.item_id = collection2item.item_id " +
+              "AND collection2item.collection_id = ? " +
+              "AND item.in_archive = '1'"
+        );
 
-        TableRowIterator rows = DatabaseManager.queryTable(ourContext, "item",
-                myQuery,getID(), limit, offset);
+        params.add(getID());
+        DatabaseManager.applyOffsetAndLimit(myQuery, params, offset, limit);
+
+        TableRowIterator rows = DatabaseManager.query(ourContext,
+                myQuery.toString(), params.toArray());
 
         return new ItemIterator(ourContext, rows);
     }
@@ -679,8 +729,6 @@ public class Collection extends DSpaceObject
             g.setName("COLLECTION_" + getID() + "_WORKFLOW_STEP_" + step);
             g.update();
             setWorkflowGroup(step, g);
-
-            AuthorizeManager.addPolicy(ourContext, this, Constants.ADD, g);
         }
 
         return workflowGroup[step - 1];
@@ -689,26 +737,82 @@ public class Collection extends DSpaceObject
     /**
      * Set the workflow group corresponding to a particular workflow step.
      * <code>null</code> can be passed in if there should be no associated
-     * group for that workflow step; any existing group is NOT deleted.
+     * group for that workflow step.  Any existing group is NOT deleted.
      *
      * @param step
      *            the workflow step (1-3)
-     * @param g
+     * @param newGroup
      *            the new workflow group, or <code>null</code>
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException passed through.
      */
-    public void setWorkflowGroup(int step, Group g)
+    public void setWorkflowGroup(int step, Group newGroup)
+            throws SQLException, AuthorizeException
     {
-        workflowGroup[step - 1] = g;
-
-        if (g == null)
+        Group oldGroup = getWorkflowGroup(step);
+        String stepColumn;
+        int action;
+        switch(step)
         {
-            collectionRow.setColumnNull("workflow_step_" + step);
+        case 1:
+            action = Constants.WORKFLOW_STEP_1;
+            stepColumn = "workflow_step_1";
+            break;
+        case 2:
+            action = Constants.WORKFLOW_STEP_2;
+            stepColumn = "workflow_step_2";
+            break;
+        case 3:
+            action = Constants.WORKFLOW_STEP_3;
+            stepColumn = "workflow_step_3";
+            break;
+        default:
+            throw new IllegalArgumentException("Illegal step count:  " + step);
         }
+        workflowGroup[step-1] = newGroup;
+        if (newGroup != null)
+            collectionRow.setColumn(stepColumn, newGroup.getID());
         else
-        {
-            collectionRow.setColumn("workflow_step_" + step, g.getID());
-        }
+            collectionRow.setColumnNull(stepColumn);
         modified = true;
+
+        // Deal with permissions.
+        try {
+            ourContext.turnOffAuthorisationSystem();
+            // remove the policies for the old group
+            if (oldGroup != null)
+            {
+                List<ResourcePolicy> oldPolicies = AuthorizeManager
+                        .getPoliciesActionFilter(ourContext, this, action);
+                int oldGroupID = oldGroup.getID();
+                for (ResourcePolicy rp : oldPolicies)
+                {
+                    if (rp.getGroupID() == oldGroupID)
+                        rp.delete();
+                }
+
+                oldPolicies = AuthorizeManager
+                        .getPoliciesActionFilter(ourContext, this, Constants.ADD);
+                for (ResourcePolicy rp : oldPolicies)
+                {
+                    if ((rp.getGroupID() == oldGroupID)
+                            && ResourcePolicy.TYPE_WORKFLOW.equals(rp.getRpType()))
+                        rp.delete();
+                }
+           }
+
+            // New group can be null to delete workflow step.
+            // We need to grant permissions if new group is not null.
+            if (newGroup != null)
+            {
+                AuthorizeManager.addPolicy(ourContext, this, action, newGroup,
+                        ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(ourContext, this, Constants.ADD, newGroup,
+                        ResourcePolicy.TYPE_WORKFLOW);
+            }
+        } finally {
+            ourContext.restoreAuthSystemState();
+        }
     }
 
     /**
@@ -1513,7 +1617,7 @@ public class Collection extends DSpaceObject
 
     public static Collection[] findAuthorizedOptimized(Context context, int actionID) throws java.sql.SQLException
     {
-        if(! ConfigurationManager.getBooleanProperty("org.dspace.content.Collection.findAuthorizedPerformanceOptimize", true)) {
+        if(! ConfigurationManager.getBooleanProperty("org.dspace.content.Collection.findAuthorizedPerformanceOptimize", false)) {
             // Fallback to legacy query if config says so. The rationale could be that a site found a bug.
             return findAuthorized(context, null, actionID);
         }

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

@@ -280,7 +280,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(context);
 
                 // First check the cache
                 Community fromCache = (Community) context.fromCache(
@@ -350,7 +350,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(context);
 
                 // First check the cache
                 Community fromCache = (Community) context.fromCache(
@@ -683,7 +683,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Collection fromCache = (Collection) ourContext.fromCache(
@@ -757,7 +757,7 @@ public class Community extends DSpaceObject
         {
             while (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Community fromCache = (Community) ourContext.fromCache(
@@ -812,7 +812,7 @@ public class Community extends DSpaceObject
         {
             if (tri.hasNext())
             {
-                TableRow row = tri.next();
+                TableRow row = tri.next(ourContext);
 
                 // First check the cache
                 Community fromCache = (Community) ourContext.fromCache(

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

@@ -60,6 +60,8 @@ public class InstallItem
             IOException, AuthorizeException
     {
         Item item = is.getItem();
+        Collection collection = is.getCollection();
+        
         IdentifierService identifierService = new DSpace().getSingletonService(IdentifierService.class);
         try {
             if(suppliedHandle == null)
@@ -74,7 +76,15 @@ public class InstallItem
 
         populateMetadata(c, item);
 
-        return finishItem(c, item, is);
+        // Finish up / archive the item
+        item = finishItem(c, item, is);
+        
+        // As this is a BRAND NEW item, as a final step we need to remove the
+        // submitter item policies created during deposit and replace them with
+        // the default policies from the collection.
+        item.inheritCollectionDefaultPolicies(collection);
+        
+        return item;
     }
 
     /**
@@ -205,8 +215,18 @@ public class InstallItem
         item.addDC("description", "provenance", "en", provDescription);
     }
 
-    // final housekeeping when adding new Item to archive
-    // common between installing and "restoring" items.
+    /**
+     * Final housekeeping when adding a new Item into the archive.
+     * This method is used by *both* installItem() and restoreItem(),
+     * so all actions here will be run for a newly added item or a restored item.
+     *
+     * @param c DSpace Context
+     * @param item Item in question
+     * @param is InProgressSubmission object
+     * @return final "archived" Item
+     * @throws SQLException if database error
+     * @throws AuthorizeException if authorization error
+     */
     private static Item finishItem(Context c, Item item, InProgressSubmission is)
         throws SQLException, IOException, AuthorizeException
     {
@@ -229,10 +249,6 @@ public class InstallItem
         // remove in-progress submission
         is.deleteWrapper();
 
-        // remove the item's policies and replace them with
-        // the defaults from the collection
-        item.inheritCollectionDefaultPolicies(is.getCollection());
-
         // set embargo lift date and take away read access if indicated.
         EmbargoManager.setEmbargo(c, item);
 

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

@@ -24,14 +24,15 @@ import org.dspace.authorize.AuthorizeManager;
 import org.dspace.authorize.ResourcePolicy;
 import org.dspace.browse.BrowseException;
 import org.dspace.browse.IndexBrowse;
+import org.dspace.content.authority.ChoiceAuthorityManager;
+import org.dspace.content.authority.Choices;
+import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
-import org.dspace.content.authority.Choices;
-import org.dspace.content.authority.ChoiceAuthorityManager;
-import org.dspace.event.Event;
 import org.dspace.eperson.EPerson;
 import org.dspace.eperson.Group;
+import org.dspace.event.Event;
 import org.dspace.handle.HandleManager;
 import org.dspace.identifier.IdentifierException;
 import org.dspace.identifier.IdentifierService;
@@ -40,6 +41,8 @@ import org.dspace.storage.rdbms.TableRow;
 import org.dspace.storage.rdbms.TableRowIterator;
 import org.dspace.utils.DSpace;
 import org.dspace.versioning.VersioningService;
+import org.dspace.workflow.WorkflowItem;
+import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 
 /**
  * Class representing an item in DSpace.
@@ -263,7 +266,7 @@ public class Item extends DSpaceObject
         }
 
         String query = "SELECT item.* FROM metadatavalue,item WHERE item.in_archive='1' " +
-                "AND item.item_id = metadatavalue.item_id AND metadata_field_id = ?";
+                "AND item.item_id = metadatavalue.resource_id AND metadatavalue.resource_type_id=2 AND metadata_field_id = ?";
         TableRowIterator rows = null;
         if (Item.ANY.equals(authority)) {
             rows = DatabaseManager.queryTable(context, "item", query, mdf.getFieldID());
@@ -1158,8 +1161,14 @@ public class Item extends DSpaceObject
         ourContext.addEvent(new Event(Event.MODIFY, Constants.ITEM, getID(), 
                 "WITHDRAW", getIdentifiers(ourContext)));
 
-        // remove all authorization policies, saving the custom ones
-        AuthorizeManager.removeAllPoliciesByDSOAndTypeNotEqualsTo(ourContext, this, ResourcePolicy.TYPE_CUSTOM);
+        // switch all READ authorization policies to WITHDRAWN_READ
+		AuthorizeManager.switchPoliciesAction(ourContext, this, Constants.READ, Constants.WITHDRAWN_READ);
+		for (Bundle bnd : this.getBundles()) {
+			AuthorizeManager.switchPoliciesAction(ourContext, bnd, Constants.READ, Constants.WITHDRAWN_READ);
+			for (Bitstream bs : bnd.getBitstreams()) {
+				AuthorizeManager.switchPoliciesAction(ourContext, bs, Constants.READ, Constants.WITHDRAWN_READ);
+			}
+		}
 
         // Write log
         log.info(LogManager.getHeader(ourContext, "withdraw_item", "user="
@@ -1217,16 +1226,28 @@ public class Item extends DSpaceObject
         ourContext.addEvent(new Event(Event.MODIFY, Constants.ITEM, getID(), 
                 "REINSTATE", getIdentifiers(ourContext)));
 
-        // authorization policies
-        if (colls.length > 0)
-        {
-            // FIXME: not multiple inclusion friendly - just apply access
-            // policies from first collection
-            // remove the item's policies and replace them with
-            // the defaults from the collection
-            inheritCollectionDefaultPolicies(colls[0]);
+        // restore all WITHDRAWN_READ authorization policies back to READ
+        for (Bundle bnd : this.getBundles()) {
+			AuthorizeManager.switchPoliciesAction(ourContext, bnd, Constants.WITHDRAWN_READ, Constants.READ);
+			for (Bitstream bs : bnd.getBitstreams()) {
+				AuthorizeManager.switchPoliciesAction(ourContext, bs, Constants.WITHDRAWN_READ, Constants.READ);
+			}
+		}
+        
+        // check if the item was withdrawn before the fix DS-3097
+        if (AuthorizeManager.getPoliciesActionFilter(ourContext, this, Constants.WITHDRAWN_READ).size() != 0) {
+        	AuthorizeManager.switchPoliciesAction(ourContext, this, Constants.WITHDRAWN_READ, Constants.READ);
         }
-
+        else {
+	        // authorization policies
+	        if (colls.length > 0)
+	        {
+	            // remove the item's policies and replace them with
+	            // the defaults from the collection
+	        	adjustItemPolicies(getOwningCollection());
+	        }
+        }
+        
         // Write log
         log.info(LogManager.getHeader(ourContext, "reinstate_item", "user="
                 + e.getEmail() + ",item_id=" + getID()));
@@ -1254,9 +1275,6 @@ public class Item extends DSpaceObject
         log.info(LogManager.getHeader(ourContext, "delete_item", "item_id="
                 + getID()));
 
-        // Remove from cache
-        ourContext.removeCached(this, getID());
-
         // Remove from browse indices, if appropriate
         /** XXX FIXME
          ** Although all other Browse index updates are managed through
@@ -1303,6 +1321,8 @@ public class Item extends DSpaceObject
         // remove version attached to the item
         removeVersion();
 
+        // Remove from cache
+        ourContext.removeCached(this, getID());
 
         // Finally remove item row
         DatabaseManager.delete(ourContext, itemRow);
@@ -1750,7 +1770,12 @@ public class Item extends DSpaceObject
         // is this collection not yet created, and an item template is created
         if (getOwningCollection() == null)
         {
-            return true;
+        	if (!isInProgressSubmission()) {
+        		return true;
+        	}
+        	else {
+        		return false;
+        	}
         }
 
         // is this person an COLLECTION_EDITOR for the owning collection?
@@ -1762,6 +1787,20 @@ public class Item extends DSpaceObject
         return false;
     }
     
+    /**
+     * Check if the item is an inprogress submission
+     * @param context
+     * @param item
+     * @return <code>true</code> if the item is an inprogress submission, i.e. a WorkspaceItem or WorkflowItem
+     * @throws SQLException
+     */
+    public boolean isInProgressSubmission() throws SQLException {
+		return WorkspaceItem.findByItem(ourContext, this) != null ||
+				((ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow")
+						&& XmlWorkflowItem.findByItem(ourContext, this) != null)
+						|| WorkflowItem.findByItem(ourContext, this) != null);
+    }
+    
     public String getName()
     {
         return getMetadataFirstValue(MetadataSchema.DC_SCHEMA, "title", null, Item.ANY);

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

@@ -81,6 +81,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            ID of the workspace item
      * 
      * @return the workspace item, or null if the ID is invalid.
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem find(Context context, int id)
             throws SQLException
@@ -131,6 +132,9 @@ public class WorkspaceItem implements InProgressSubmission
      *            of the collection's template item
      * 
      * @return the newly created workspace item
+     * @throws org.dspace.authorize.AuthorizeException passed through.
+     * @throws java.sql.SQLException passed through.
+     * @throws java.io.IOException passed through.
      */
     public static WorkspaceItem create(Context c, Collection coll,
             boolean template) throws AuthorizeException, SQLException,
@@ -140,98 +144,49 @@ public class WorkspaceItem implements InProgressSubmission
         AuthorizeManager.authorizeAction(c, coll, Constants.ADD);
 
         // Create an item
-        Item i = Item.create(c);
-        i.setSubmitter(c.getCurrentUser());
+        Item item = Item.create(c);
+        item.setSubmitter(c.getCurrentUser());
 
-        // Now create the policies for the submitter and workflow
-        // users to modify item and contents
+        // Now create the policies for the submitter to modify item and contents.
         // contents = bitstreams, bundles
         // FIXME: icky hardcoded workflow steps
         Group step1group = coll.getWorkflowGroup(1);
         Group step2group = coll.getWorkflowGroup(2);
         Group step3group = coll.getWorkflowGroup(3);
 
-        EPerson e = c.getCurrentUser();
+        EPerson submitter = c.getCurrentUser();
 
-        // read permission
-        AuthorizeManager.addPolicy(c, i, Constants.READ, e, ResourcePolicy.TYPE_SUBMISSION);
+        // Add policies for the submitter
+        AuthorizeManager.addPolicy(c, item, Constants.READ, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.WRITE, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.ADD, submitter, ResourcePolicy.TYPE_SUBMISSION);
+        AuthorizeManager.addPolicy(c, item, Constants.REMOVE, submitter, ResourcePolicy.TYPE_SUBMISSION);
 
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
+        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow"))
+        {
+            // Add policies for the workflow step administrative groups
             if (step1group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step1group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step1group, ResourcePolicy.TYPE_WORKFLOW);
             }
 
             if (step2group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step2group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step2group, ResourcePolicy.TYPE_WORKFLOW);
             }
 
             if (step3group != null)
             {
-                AuthorizeManager.addPolicy(c, i, Constants.READ, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-
-        // write permission
-        AuthorizeManager.addPolicy(c, i, Constants.WRITE, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.WRITE, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-        // add permission
-        AuthorizeManager.addPolicy(c, i, Constants.ADD, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.ADD, step3group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-        }
-
-        // remove contents permission
-        AuthorizeManager.addPolicy(c, i, Constants.REMOVE, e, ResourcePolicy.TYPE_SUBMISSION);
-
-        if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("originalworkflow")) {
-            if (step1group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step1group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step2group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step2group, ResourcePolicy.TYPE_WORKFLOW);
-            }
-
-            if (step3group != null)
-            {
-                AuthorizeManager.addPolicy(c, i, Constants.REMOVE, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.READ, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.WRITE, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.ADD, step3group, ResourcePolicy.TYPE_WORKFLOW);
+                AuthorizeManager.addPolicy(c, item, Constants.REMOVE, step3group, ResourcePolicy.TYPE_WORKFLOW);
             }
         }
 
@@ -244,22 +199,22 @@ public class WorkspaceItem implements InProgressSubmission
 
             for (int n = 0; n < md.length; n++)
             {
-                i.addMetadata(md[n].schema, md[n].element, md[n].qualifier, md[n].language,
+                item.addMetadata(md[n].schema, md[n].element, md[n].qualifier, md[n].language,
                         md[n].value);
             }
         }
 
-        i.update();
+        item.update();
 
         // Create the workspace item row
         TableRow row = DatabaseManager.row("workspaceitem");
 
-        row.setColumn("item_id", i.getID());
+        row.setColumn("item_id", item.getID());
         row.setColumn("collection_id", coll.getID());
 
         log.info(LogManager.getHeader(c, "create_workspace_item",
                 "workspace_item_id=" + row.getIntColumn("workspace_item_id")
-                        + "item_id=" + i.getID() + "collection_id="
+                        + "item_id=" + item.getID() + "collection_id="
                         + coll.getID()));
 
         DatabaseManager.insert(c, row);
@@ -280,6 +235,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the eperson
      * 
      * @return the corresponding workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findByEPerson(Context context, EPerson ep)
             throws SQLException
@@ -332,6 +288,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the collection
      * 
      * @return the corresponding workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findByCollection(Context context, Collection c)
             throws SQLException
@@ -384,6 +341,7 @@ public class WorkspaceItem implements InProgressSubmission
      *            the item
      *
      * @return workflow item corresponding to the item, or null
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem findByItem(Context context, Item i)
             throws SQLException
@@ -408,6 +366,7 @@ public class WorkspaceItem implements InProgressSubmission
      * @param   context     the context object
      *
      * @return      all workspace items
+     * @throws java.sql.SQLException passed through.
      */
     public static WorkspaceItem[] findAll(Context context)
         throws SQLException
@@ -505,6 +464,8 @@ public class WorkspaceItem implements InProgressSubmission
 
     /**
      * Update the workspace item, including the unarchived item.
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException passed through.
      */
     public void update() throws SQLException, AuthorizeException
     {
@@ -554,6 +515,10 @@ public class WorkspaceItem implements InProgressSubmission
      * Delete the workspace item. The entry in workspaceitem, the unarchived
      * item and its contents are all removed (multiple inclusion
      * notwithstanding.)
+     * @throws java.sql.SQLException passed through.
+     * @throws org.dspace.authorize.AuthorizeException
+     *          if not original submitter or an administrator.
+     * @throws java.io.IOException passed through.
      */
     public void deleteAll() throws SQLException, AuthorizeException,
             IOException

dspace-api/src/main/java/org/dspace/content/authority/SolrAuthority.java

@@ -7,9 +7,6 @@
  */
 package org.dspace.content.authority;
 
-import org.dspace.authority.AuthoritySearchService;
-import org.dspace.authority.AuthorityValue;
-import org.dspace.authority.rest.RestSource;
 import org.apache.commons.lang.StringUtils;
 import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -17,6 +14,9 @@ import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.params.CommonParams;
+import org.dspace.authority.AuthoritySearchService;
+import org.dspace.authority.AuthorityValue;
+import org.dspace.authority.SolrAuthorityInterface;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.utils.DSpace;
 
@@ -35,7 +35,7 @@ import java.util.Map;
 public class SolrAuthority implements ChoiceAuthority {
 
     private static final Logger log = Logger.getLogger(SolrAuthority.class);
-    private RestSource source = new DSpace().getServiceManager().getServiceByName("AuthoritySource", RestSource.class);
+    protected SolrAuthorityInterface source = new DSpace().getServiceManager().getServiceByName("AuthoritySource", SolrAuthorityInterface.class);
     private boolean externalResults = false;
 
     public Choices getMatches(String field, String text, int collection, int start, int limit, String locale, boolean bestMatch) {

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

@@ -0,0 +1,44 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+
+package org.dspace.content.crosswalk;
+
+import org.dspace.core.Context;
+
+import java.sql.SQLException;
+
+/**
+ * Created by jonas - jonas@atmire.com on 21/04/17.
+ * Implementation of the {@link DisseminationCrosswalk} interface that enables the ability to set a Context manually
+ */
+public abstract class ContextAwareDisseminationCrosswalk  implements DisseminationCrosswalk{
+
+    private Context context;
+    private boolean contextCreatedInternally = false;
+
+    public void setContext(Context context){
+        this.context = context;
+    }
+    public Context getContext() throws SQLException {
+        if(context == null|| !context.isValid()){
+            context=new Context();
+            contextCreatedInternally = true;
+        }
+        return context;
+    }
+
+    public void handleContextCleanup() throws SQLException {
+        if(contextCreatedInternally){
+            context.complete();
+        }else{
+            context.commit();
+        }
+    }
+
+
+}

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

@@ -27,7 +27,10 @@ import org.dspace.license.CreativeCommons;
  *
  * @author  Larry Stone
  * @version $Revision: 1.0 $
+ * 
+ * @deprecated to make uniforme JSPUI and XMLUI approach the bitstream with the license in the textual format it is no longer stored see https://jira.duraspace.org/browse/DS-2604 
  */
+@Deprecated
 public class CreativeCommonsTextStreamDisseminationCrosswalk
     implements StreamDisseminationCrosswalk
 {

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

@@ -7,15 +7,15 @@
  */
 package org.dspace.content.crosswalk;
 
-import java.io.IOException;
-import java.sql.SQLException;
-import java.util.List;
-
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.DSpaceObject;
 import org.jdom.Element;
 import org.jdom.Namespace;
 
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.List;
+
 /**
  * Dissemination Crosswalk plugin -- translate DSpace native
  * metadata into an external XML format.
@@ -107,6 +107,9 @@ public interface DisseminationCrosswalk
      * Execute crosswalk, returning one XML root element as
      * a JDOM <code>Element</code> object.
      * This is typically the root element of a document.
+     * Note that, if the implementing class is of type "{@link org.dspace.content.crosswalk.ContextAwareDisseminationCrosswalk}"
+     * and a context is present in the method call, you should set the context before calling this method. -> "{@link org.dspace.content.crosswalk.ContextAwareDisseminationCrosswalk#setContext(org.dspace.core.Context)}"
+     * The implementing class should then use the  "{@link ContextAwareDisseminationCrosswalk#getContext()}" and  "{@link ContextAwareDisseminationCrosswalk#handleContextCleanup()}" to retrieve and commit/complete the context respectively
      * <p>
      *
      * @param dso the  DSpace Object whose metadata to export.

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

@@ -7,17 +7,6 @@
  */
 package org.dspace.content.crosswalk;
 
-import java.io.IOException;
-import java.sql.SQLException;
-import java.text.ParseException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Date;
-
-import java.text.SimpleDateFormat;
-import java.util.logging.Level;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
@@ -33,6 +22,12 @@ import org.dspace.eperson.Group;
 import org.jdom.Element;
 import org.jdom.Namespace;
 
+import java.io.IOException;
+import java.sql.SQLException;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
 /**
  * METSRights Ingestion & Dissemination Crosswalk
  * <p>
@@ -51,7 +46,7 @@ import org.jdom.Namespace;
  * @author Tim Donohue
  * @version $Revision: 2108 $
  */
-public class METSRightsCrosswalk 
+public class METSRightsCrosswalk extends ContextAwareDisseminationCrosswalk
     implements IngestionCrosswalk, DisseminationCrosswalk
 {
     /** log4j category */
@@ -120,14 +115,14 @@ public class METSRightsCrosswalk
      * METSRights PermissionTypes.
      *
      * @param dso DSpace Object
+     * @param context Context Object
      * @return XML Element corresponding to the new <RightsDeclarationMD> translation
      * @throws CrosswalkException
      * @throws IOException
      * @throws SQLException
      * @throws AuthorizeException
      */
-    @Override
-    public Element disseminateElement(DSpaceObject dso)
+    public Element disseminateElement(Context context,DSpaceObject dso)
         throws CrosswalkException,
                IOException, SQLException, AuthorizeException
     {
@@ -156,7 +151,6 @@ public class METSRightsCrosswalk
         // what those rights are -- too many types of content can be stored in DSpace
 
         //Get all policies on this DSpace Object
-        Context context = new Context();
         List<ResourcePolicy> policies = AuthorizeManager.getPolicies(context, dso);
 
         //For each DSpace policy
@@ -282,9 +276,31 @@ public class METSRightsCrosswalk
            
         }//end for each policy
 
-        context.complete();
         return rightsMD;
     }
+    /**
+     * Actually Disseminate into METSRights schema.  This method locates all DSpace
+     * policies (permissions) for the provided object, and translates them into
+     * METSRights PermissionTypes.
+     *
+     * @param dso DSpace Object
+     * @return XML Element corresponding to the new <RightsDeclarationMD> translation
+     * @throws CrosswalkException
+     * @throws IOException
+     * @throws SQLException
+     * @throws AuthorizeException
+     * @deprecated Do not use this method, please opt for "{@link #disseminateElement(Context context, DSpaceObject dso)}" instead, as this does not internally need to create a new Context
+     */
+    @Override
+    @Deprecated
+    public Element disseminateElement(DSpaceObject dso)
+            throws CrosswalkException,
+            IOException, SQLException, AuthorizeException {
+        Context context = getContext();
+        Element element = disseminateElement(context, dso);
+        handleContextCleanup();
+        return element;
+    }
 
     @Override
     public List<Element> disseminateList(DSpaceObject dso)
@@ -435,134 +451,81 @@ public class METSRightsCrosswalk
     public void ingest(Context context, DSpaceObject dso, List<Element> ml)
         throws CrosswalkException, IOException, SQLException, AuthorizeException
     {
-        // we cannot crosswalk METSRights to a SITE object
+        // SITE objects are not supported by the METSRightsCrosswalk
         if (dso.getType() == Constants.SITE)
         {
             throw new CrosswalkObjectNotSupported("Wrong target object type, METSRightsCrosswalk cannot crosswalk a SITE object.");
         }
 
-        //First, clear all existing Policies on this DSpace Object
-        // as we don't want them to conflict with policies we will be adding
-        if(!ml.isEmpty())
+        // If we're fed the top-level <RightsDeclarationMD> wrapper element, recurse into its guts.
+        // What we need to analyze are the <Context> elements underneath it.
+        if(!ml.isEmpty() && ml.get(0).getName().equals("RightsDeclarationMD"))
         {
-            AuthorizeManager.removeAllPolicies(context, dso);
+            ingest(context, dso, ml.get(0).getChildren());
         }
-
-        // Loop through each Element in the List
-        List<ResourcePolicy> policies = new ArrayList<ResourcePolicy>();
-        for (Element element : ml)
+        else
         {
-            // if we're fed a <RightsDeclarationMD> wrapper object, recurse on its guts:
-            if (element.getName().equals("RightsDeclarationMD"))
+            // Loop through each <Context> Element in the passed in List, creating a ResourcePolicy for each
+            List<ResourcePolicy> policies = new ArrayList<>();
+            for (Element element : ml)
             {
-                ingest(context, dso, element.getChildren());
-            }
-            // "Context" section (where permissions are stored)
-            else if (element.getName().equals("Context"))
-            {
-                //get what class of context this is
-                String contextClass = element.getAttributeValue("CONTEXTCLASS");
-
-                if ((element.getAttributeValue("start-date") != null)
-                       || (element.getAttributeValue("end-date") != null)
-                       || (element.getAttributeValue("rpName") != null))
-                {                 
-                    SimpleDateFormat sdf = new SimpleDateFormat( "yyyy-MM-dd" );
-                    try {
-                        ResourcePolicy rp = ResourcePolicy.create(context);
-                        if (element.getAttributeValue("CONTEXTCLASS").equalsIgnoreCase("GENERAL PUBLIC")) {
-                            Group anonGroup = Group.find(context, 0);
-                            rp.setGroup(anonGroup);
-                        }
-                        else
-                        {
-                            if (element.getAttributeValue("CONTEXTCLASS").equalsIgnoreCase("REPOSITORY MGR")) {
-                                Group adminGroup = Group.find(context, 1);
-                                rp.setGroup(adminGroup);
-                            }
-                        }
-                        if (element.getAttributeValue("rpName") != null)
-                        {
-                            rp.setRpName(element.getAttributeValue("rpName"));
-                        }
-                        try {
-                            if (element.getAttributeValue("start-date") != null)
-                            {
-                                rp.setStartDate(sdf.parse(element.getAttributeValue("start-date")));
-                            }
-                            if (element.getAttributeValue("end-date") != null)
-                            {
-                                rp.setEndDate(sdf.parse(element.getAttributeValue("end-date")));
-                            }
-                        }catch (ParseException ex) {
-                            java.util.logging.Logger.getLogger(METSRightsCrosswalk.class.getName()).log(Level.SEVERE, null, ex);
-                        }
-
-                        List<Element> le = new ArrayList<Element>(element.getChildren());
-                        for (Element el : le)
-                        {
-                            if ((el.getAttributeValue("DISCOVER").equalsIgnoreCase("true")) 
-                                    && (el.getAttributeValue("DISPLAY").equalsIgnoreCase("true")))
-                            {
-                                if (el.getAttributeValue("DELETE").equalsIgnoreCase("false"))
-                                {
-                                    if (el.getAttributeValue("MODIFY").equalsIgnoreCase("false"))
-                                    {
-                                        rp.setAction(Constants.READ);
-                                    }
-                                    else
-                                    {
-                                        rp.setAction(Constants.WRITE);
-                                    }
-                                }
-                                else
-                                {
-                                    if (el.getAttributeValue("MODIFY").equalsIgnoreCase("true"))
-                                    {
-                                        rp.setAction(Constants.DELETE);
-                                        if ((el.getAttributeValue("COPY").equalsIgnoreCase("true"))
-                                                &&(el.getAttributeValue("DUPLICATE").equalsIgnoreCase("true"))
-                                                &&(el.getAttributeValue("PRINT").equalsIgnoreCase("true")))
-                                        {
-                                            rp.setAction(Constants.ADMIN);
-                                        }
-                                    }
-                                }
-                            }
-                        }
-                        policies.add(rp);
-                    } catch (NullPointerException ex) {
-                        java.util.logging.Logger.getLogger(METSRightsCrosswalk.class.getName()).log(Level.SEVERE, null, ex);
-                    }
-                    assignPermissions(context, dso, policies);
-                }
-                else
+                // Must be a "Context" section (where permissions are stored)
+                if (element.getName().equals("Context"))
                 {
-                    //also get reference to the <Permissions> element
+                    //get what class of context this is
+                    String contextClass = element.getAttributeValue("CONTEXTCLASS");
+
+                    ResourcePolicy rp = ResourcePolicy.create(context);
+                    SimpleDateFormat sdf = new SimpleDateFormat( "yyyy-MM-dd" );
+
+                    // get reference to the <Permissions> element
+                    // Note: we are assuming here that there will only ever be ONE <Permissions>
+                    //  element. Currently there are no known use cases for multiple.
                     Element permsElement = element.getChild("Permissions", METSRights_NS);
+                    if(permsElement == null) {
+                            log.error("No <Permissions> element was found. Skipping this <Context> element.");
+                            continue;
+                    }
+
+                    if (element.getAttributeValue("rpName") != null)
+                    {
+                        rp.setRpName(element.getAttributeValue("rpName"));
+                    }
+                    try {
+                        if (element.getAttributeValue("start-date") != null)
+                        {
+                            rp.setStartDate(sdf.parse(element.getAttributeValue("start-date")));
+                        }
+                        if (element.getAttributeValue("end-date") != null)
+                        {
+                            rp.setEndDate(sdf.parse(element.getAttributeValue("end-date")));
+                        }
+                    }catch (ParseException ex) {
+                        log.error("Failed to parse embargo date. The date needs to be in the format 'yyyy-MM-dd'.", ex);
+                    }
 
                     //Check if this permission pertains to Anonymous users
                     if(ANONYMOUS_CONTEXTCLASS.equals(contextClass))
                     {
                         //get DSpace Anonymous group, ID=0
-                        Group anonGroup = Group.find(context, 0);
+                        Group anonGroup = Group.find(context, Group.ANONYMOUS_ID);
                         if(anonGroup==null)
                         {
                             throw new CrosswalkInternalException("The DSpace database has not been properly initialized.  The Anonymous Group is missing from the database.");
                         }
 
-                        assignPermissions(context, dso, anonGroup, permsElement);
+                        rp.setGroup(anonGroup);
                     } // else if this permission declaration pertains to Administrators
                     else if(ADMIN_CONTEXTCLASS.equals(contextClass))
                     {
                         //get DSpace Administrator group, ID=1
-                        Group adminGroup = Group.find(context, 1);
+                        Group adminGroup = Group.find(context, Group.ADMIN_ID);
                         if(adminGroup==null)
                         {
                             throw new CrosswalkInternalException("The DSpace database has not been properly initialized.  The Administrator Group is missing from the database.");
                         }
 
-                        assignPermissions(context, dso, adminGroup, permsElement);
+                        rp.setGroup(adminGroup);
                     } // else if this permission pertains to another DSpace group
                     else if(GROUP_CONTEXTCLASS.equals(contextClass))
                     {
@@ -591,8 +554,8 @@ public class METSRightsCrosswalk
                                         + "Please restore this group using the SITE AIP, or recreate it.");
                             }
 
-                            //assign permissions to group on this object
-                            assignPermissions(context, dso, group, permsElement);
+                            //assign group to policy
+                            rp.setGroup(group);
                         }
                         catch(PackageException pe)
                         {
@@ -600,7 +563,7 @@ public class METSRightsCrosswalk
                             //We'll just wrap it as a CrosswalkException and throw it upwards
                             throw new CrosswalkException(pe);
                         }
-                    }//end if Group
+                    }// else if this permission pertains to a DSpace person
                     else if(PERSON_CONTEXTCLASS.equals(contextClass))
                     {
                         //we need to find the person it pertains to
@@ -629,89 +592,26 @@ public class METSRightsCrosswalk
                                     + "Please restore this Person object using the SITE AIP, or recreate it.");
                         }
 
-                        //assign permissions to person on this object
-                        assignPermissions(context, dso, person, permsElement);
+                        //assign person to the policy
+                        rp.setEPerson(person);
                     }//end if Person
-                    else
+                    else {
                         log.error("Unrecognized CONTEXTCLASS:  " + contextClass);
-                }
-            } //end if "Context" element
-        }//end while loop
-    }
+                    }
 
+                    //set permissions on policy add to list of policies
+                    rp.setAction(parsePermissions(permsElement));
+                    policies.add(rp);
+                } //end if "Context" element
+            }//end for loop
 
-    /**
-     * Parses the 'permsElement' (corresponding to a <code>Permissions</code>
-     * element), and assigns those permissions to the specified Group
-     * on the specified DSpace Object.
-     *
-     * @param context DSpace context object
-     * @param dso The DSpace Object
-     * @param group The DSpace Group
-     * @param permsElement The METSRights <code>Permissions</code> element
-     */
-private void assignPermissions(Context context, DSpaceObject dso, List<ResourcePolicy> policies)
-        throws SQLException, AuthorizeException
-    {
-        AuthorizeManager.removeAllPolicies(context, dso);
-        if (policies == null){
-            throw new AuthorizeException("Policies are null");
-        }
-        else{
+            // Finally, we need to remove any existing policies from the current object,
+            // and replace them with the policies provided via METSRights. NOTE:
+            // if the list of policies provided by METSRights is an empty list, then
+            // the final object will have no policies attached.
+            AuthorizeManager.removeAllPolicies(context, dso);
             AuthorizeManager.addPolicies(context, policies, dso);
-        }
-    }
-
-    private void assignPermissions(Context context, DSpaceObject dso, Group group, Element permsElement)
-            throws SQLException, AuthorizeException
-    {
-        //first, parse our permissions to determine which action we are allowing in DSpace
-        int actionID = parsePermissions(permsElement);
-
-        //If action ID is less than base READ permissions (value=0),
-        // then something must've gone wrong in the parsing
-        if(actionID < Constants.READ)
-        {
-            log.warn("Unable to properly restore all access permissions on object ("
-                        + "type=" + Constants.typeText[dso.getType()] + ", "
-                        + "handle=" + dso.getHandle() + ", "
-                        + "ID=" + dso.getID()
-                        + ") for group '" + group.getName() + "'.");
-        }
-
-        //Otherwise, add the appropriate group policy for this object
-        AuthorizeManager.addPolicy(context, dso, actionID, group);
-    }
-
-     /**
-     * Parses the 'permsElement' (corresponding to a <code>Permissions</code>
-     * element), and assigns those permissions to the specified EPerson
-     * on the specified DSpace Object.
-     *
-     * @param context DSpace context object
-     * @param dso The DSpace Object
-     * @param person The DSpace EPerson
-     * @param permsElement The METSRights <code>Permissions</code> element
-     */
-    private void assignPermissions(Context context, DSpaceObject dso, EPerson person, Element permsElement)
-            throws SQLException, AuthorizeException
-    {
-        //first, parse our permissions to determine which action we are allowing in DSpace
-        int actionID = parsePermissions(permsElement);
-
-        //If action ID is less than base READ permissions (value=0),
-        // then something must've gone wrong in the parsing
-        if(actionID < Constants.READ)
-        {
-            log.warn("Unable to properly restore all access permissions on object ("
-                        + "type=" + Constants.typeText[dso.getType()] + ", "
-                        + "handle=" + dso.getHandle() + ", "
-                        + "ID=" + dso.getID()
-                        + ") for person '" + person.getEmail() + "'.");
-        }
-
-        //Otherwise, add the appropriate EPerson policy for this object
-        AuthorizeManager.addPolicy(context, dso, actionID, person);
+        } // end else
     }
 
     /**
@@ -784,4 +684,5 @@ private void assignPermissions(Context context, DSpaceObject dso, List<ResourceP
         // return -1 to signify failure (as 0 = READ permissions)
         return -1;
     }
+
 }

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

@@ -21,15 +21,7 @@ import java.util.zip.ZipFile;
 
 import org.apache.log4j.Logger;
 import org.dspace.authorize.AuthorizeException;
-import org.dspace.content.Bitstream;
-import org.dspace.content.BitstreamFormat;
-import org.dspace.content.Bundle;
-import org.dspace.content.Collection;
-import org.dspace.content.Community;
-import org.dspace.content.DSpaceObject;
-import org.dspace.content.FormatIdentifier;
-import org.dspace.content.Item;
-import org.dspace.content.WorkspaceItem;
+import org.dspace.content.*;
 import org.dspace.content.crosswalk.CrosswalkException;
 import org.dspace.content.crosswalk.MetadataValidationException;
 import org.dspace.core.ConfigurationManager;
@@ -37,6 +29,8 @@ import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.core.LogManager;
 import org.dspace.handle.HandleManager;
+import org.dspace.workflow.WorkflowItem;
+import org.dspace.xmlworkflow.storedcomponents.XmlWorkflowItem;
 import org.jdom.Element;
 
 /**
@@ -324,18 +318,18 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
         }
         else
         {
-            ZipFile zip = new ZipFile(pkgFile);
+            try(ZipFile zip = new ZipFile(pkgFile))
+            {
+                // Retrieve the manifest file entry (named mets.xml)
+                ZipEntry manifestEntry = zip.getEntry(METSManifest.MANIFEST_FILE);
 
-            // Retrieve the manifest file entry (named mets.xml)
-            ZipEntry manifestEntry = zip.getEntry(METSManifest.MANIFEST_FILE);
-
-            // parse the manifest and sanity-check it.
-            manifest = METSManifest.create(zip.getInputStream(manifestEntry),
-                    validate, getConfigurationName());
-
-            // close the Zip file for now
-            // (we'll extract the other files from zip when we need them)
-            zip.close();
+                if(manifestEntry!=null)
+                {
+                    // parse the manifest and sanity-check it.
+                    manifest = METSManifest.create(zip.getInputStream(manifestEntry),
+                        validate, getConfigurationName());
+                }
+            }
         }
 
         // return our parsed out METS manifest
@@ -660,8 +654,24 @@ public abstract class AbstractMETSIngester extends AbstractPackageIngester
             addBitstreams(context, item, manifest, pkgFile, params, callback);
 
             // have subclass manage license since it may be extra package file.
-            addLicense(context, item, license, (Collection) dso
-                    .getParentObject(), params);
+            Collection owningCollection = (Collection) dso.getParentObject();
+            if(owningCollection == null)
+            {
+                //We are probably dealing with an item that isn't archived yet
+                InProgressSubmission inProgressSubmission = WorkspaceItem.findByItem(context, item);
+                if(inProgressSubmission == null)
+                {
+                    if (ConfigurationManager.getProperty("workflow", "workflow.framework").equals("xmlworkflow"))
+                    {
+                        inProgressSubmission = XmlWorkflowItem.findByItem(context, item);
+                    }else{
+                        inProgressSubmission = WorkflowItem.findByItem(context, item);
+                    }
+                }
+                owningCollection = inProgressSubmission.getCollection();
+            }
+
+            addLicense(context, item, license, owningCollection, params);
 
             // FIXME ?
             // should set lastModifiedTime e.g. when ingesting AIP.

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

@@ -127,6 +127,8 @@ public class Constants
      */
     public static final int ADMIN = 11;
     
+    public static final int WITHDRAWN_READ = 12;
+    
     /** Position of front page news item -- top box */
     public static final int NEWS_TOP = 0;
 
@@ -139,7 +141,7 @@ public class Constants
     public static final String[] actionText = { "READ", "WRITE",
             "OBSOLETE (DELETE)", "ADD", "REMOVE", "WORKFLOW_STEP_1",
             "WORKFLOW_STEP_2", "WORKFLOW_STEP_3", "WORKFLOW_ABORT",
-            "DEFAULT_BITSTREAM_READ", "DEFAULT_ITEM_READ", "ADMIN" };
+            "DEFAULT_BITSTREAM_READ", "DEFAULT_ITEM_READ", "ADMIN", "WITHDRAWN_READ" };
 
     /**
      * generating constants for the relevance array dynamically is simple: just
@@ -175,7 +177,9 @@ public class Constants
             0, // 8 - WORKFLOW_ABORT
             RCOLLECTION, // 9 - DEFAULT_BITSTREAM_READ
             RCOLLECTION, // 10 - DEFAULT_ITEM_READ
-            RITEM | RCOLLECTION | RCOMMUNITY // 11 - ADMIN
+            RITEM | RCOLLECTION | RCOMMUNITY, // 11 - ADMIN
+            RBITSTREAM | RBUNDLE | RITEM // 12 - WITHDRAWN_READ
+
     };
 
     public static final String DEFAULT_ENCODING = "UTF-8";

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

@@ -474,8 +474,18 @@ public class Email
         System.out.println(" - To: " + to);
         System.out.println(" - Subject: " + subject);
         System.out.println(" - Server: " + server);
+        boolean disabled = ConfigurationManager.getBooleanProperty("mail.server.disabled", false);
         try
         {
+            if( disabled)
+            {
+                System.err.println("\nError sending email:");
+                System.err.println(" - Error: cannot test email because mail.server.disabled is set to true");
+                System.err.println("\nPlease see the DSpace documentation for assistance.\n");
+                System.err.println("\n");
+                System.exit(1);
+                return;
+            }
             e.send();
         }
         catch (MessagingException me)

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

@@ -16,6 +16,9 @@ import java.io.IOException;
 import java.io.InputStreamReader;
 import java.io.OutputStreamWriter;
 import java.io.PrintWriter;
+
+import org.dspace.core.service.NewsService;
+import org.dspace.utils.DSpace;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -39,6 +42,10 @@ public class NewsManager
      */
     public static String readNewsFile(String newsFile)
     {
+    	NewsService newsService = new DSpace().getSingletonService(NewsService.class);
+    	if (!newsService.validate(newsFile)) {
+    		throw new IllegalArgumentException("The file "+ newsFile + " is not a valid news file");
+    	}
         String fileName = getNewsFilePath();
 
         fileName += newsFile;
@@ -81,6 +88,10 @@ public class NewsManager
      */
     public static String writeNewsFile(String newsFile, String news)
     {
+    	NewsService newsService = new DSpace().getSingletonService(NewsService.class);
+    	if (!newsService.validate(newsFile)) {
+    		throw new IllegalArgumentException("The file "+ newsFile + " is not a valid news file");
+    	}
         String fileName = getNewsFilePath();
 
         fileName += newsFile;

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

@@ -0,0 +1,29 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.core;
+
+import java.util.List;
+
+import org.dspace.core.service.NewsService;
+
+public class NewsServiceImpl implements NewsService {
+	private List<String> acceptableFilenames;
+	
+	public void setAcceptableFilenames(List<String> acceptableFilenames) {
+		this.acceptableFilenames = acceptableFilenames;
+	}
+	
+	@Override
+	public boolean validate(String newsName) {
+		if (acceptableFilenames != null) {
+			return acceptableFilenames.contains(newsName);
+		}
+		return false;
+	}
+
+}

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

@@ -0,0 +1,12 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.core.service;
+
+public interface NewsService {
+	boolean validate(String newsName);
+}

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

@@ -164,7 +164,7 @@ public class CurationCli
         }
         else
         {
-            c.setIgnoreAuthorization(true);
+            c.turnOffAuthorisationSystem();
         }
 
         Curator curator = new Curator();

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

@@ -29,36 +29,50 @@ import org.dspace.core.PluginManager;
 /**
  * TaskResolver takes a logical name of a curation task and attempts to deliver 
  * a suitable implementation object. Supported implementation types include:
- * (1) Classpath-local Java classes configured and loaded via PluginManager.
- * (2) Local script-based tasks, viz. coded in any scripting language whose
+ * <ol>
+ *  <li> Classpath-local Java classes configured and loaded via PluginManager</li>.
+ *  <li> Local script-based tasks, viz. coded in any scripting language whose
  * runtimes are accessible via the JSR-223 scripting API. This really amounts
- * to the family of dynamic JVM languages: JRuby, Jython, Groovy, Javascript, etc
- * Note that the requisite jars and other resources for these languages must be
- * installed in the DSpace instance for them to be used here.
+ * to the family of dynamic JVM languages: JRuby, Jython, Groovy, Javascript, etc.</li>
+ * </ol>
+ * <p>
+ * Note that the requisite jars and other resources for these languages must
+ * be installed in the DSpace instance for them to be used here.
  * Further work may involve remote URL-loadable code, etc. 
  * 
+ * <p>
  * Scripted tasks are managed in a directory configured with the
- * dspace/config/modules/curate.cfg property "script.dir". A catalog of
- * scripted tasks named 'task.catalog" is kept in this directory.
+ * {@code dspace/config/modules/curate.cfg} property "script.dir".
+ * A catalog of
+ * scripted tasks named "task.catalog" is kept in this directory.
  * Each task has a 'descriptor' property with value syntax:
- * <engine>|<relFilePath>|<implClassCtor>
+ * <br/>
+ * {@code <engine>|<relFilePath>|<implClassCtor>}
+ *
+ * <p>
  * An example property:
- * 
- * linkchecker = ruby|rubytask.rb|LinkChecker.new
- * 
+ * <br/>
+ * {@code linkchecker = ruby|rubytask.rb|LinkChecker.new}
+ *
+ * <p>
  * This descriptor means that a 'ruby' script engine will be created,
- * a script file named 'rubytask.rb' in the directory <script.dir> will be
- * loaded and the resolver will expect an evaluation of 'LinkChecker.new' will 
- * provide a correct implementation object.
- * 
+ * a script file named 'rubytask.rb' in the directory {@code <script.dir>}
+ * will be
+ * loaded and the resolver will expect an evaluation of 'LinkChecker.new'
+ * will provide a correct implementation object.
+ *
+ * <p>
  * Script files may embed their descriptors to facilitate deployment.
- * To accomplish this, a script must include the descriptor string with syntax:
- * $td=<descriptor> somewhere on a comment line. for example:
- * 
- * # My descriptor $td=ruby|rubytask.rb|LinkChecker.new
- * 
- * For portability, the <relFilePath> component may be omitted in this context.
- * Thus, $td=ruby||LinkChecker.new will be expanded to a descriptor
+ * To accomplish this, a script must include the descriptor string with
+ * syntax {@code $td=<descriptor>} somewhere on a comment line. For example:
+ *
+ * <p>
+ * {@code # My descriptor $td=ruby|rubytask.rb|LinkChecker.new}
+ *
+ * <p>
+ * For portability, the {@code <relFilePath>} component may be omitted in
+ * this context.
+ * Thus, {@code $td=ruby||LinkChecker.new} will be expanded to a descriptor
  * with the name of the embedding file.
  * 
  * @author richardrodgers

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

@@ -218,10 +218,20 @@ public class DiscoverQuery {
         this.facetOffset = facetOffset;
     }
 
+    /**
+     * Sets the fields which you want Discovery to return in the search results.
+     * It is HIGHLY recommended to limit the fields returned, as by default
+     * some backends (like Solr) will return everything.
+     * @param field field to add to the list of fields returned
+     */
     public void addSearchField(String field){
         this.searchFields.add(field);
     }
 
+    /**
+     * Get list of fields which Discovery will return in the search results
+     * @return List of field names
+     */
     public List<String> getSearchFields() {
         return searchFields;
     }

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

@@ -39,7 +39,7 @@ public class IndexClient {
     public static void main(String[] args) throws SQLException, IOException, SearchServiceException {
 
         Context context = new Context();
-        context.setIgnoreAuthorization(true);
+        context.turnOffAuthorisationSystem();
 
         String usage = "org.dspace.discovery.IndexClient [-cbhf[r <item handle>]] or nothing to update/clean an existing index.";
         Options options = new Options();

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

@@ -113,4 +113,11 @@ public interface SearchService {
      * @return the indexed field
      */
     String toSortFieldIndex(String metadataField, String type);
+
+    /**
+     * Utility method to escape any special characters in a user's query
+     * @param query
+     * @return query with any special characters escaped
+     */
+    String escapeQueryChars(String query);
 }

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

@@ -119,6 +119,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
     private static final Logger log = Logger.getLogger(SolrServiceImpl.class);
 
     protected static final String LAST_INDEXED_FIELD = "SolrIndexer.lastIndexed";
+    protected static final String HANDLE_FIELD = "handle";
+    protected static final String RESOURCE_TYPE_FIELD = "search.resourcetype";
+    protected static final String RESOURCE_ID_FIELD = "search.resourceid";
 
     public static final String FILTER_SEPARATOR = "\n|||\n";
 
@@ -149,9 +152,11 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
                     solr.setBaseURL(solrService);
                     solr.setUseMultiPartPost(true);
+                    // Dummy/test query to search for Item (type=2) of ID=1
                     SolrQuery solrQuery = new SolrQuery()
-                            .setQuery("search.resourcetype:2 AND search.resourceid:1");
-
+                            .setQuery(RESOURCE_TYPE_FIELD + ":2 AND " + RESOURCE_ID_FIELD + ":1");
+                    // Only return obj identifier fields in result doc
+                    solrQuery.setFields(RESOURCE_TYPE_FIELD, RESOURCE_ID_FIELD);
                     solr.query(solrQuery);
 
                     // As long as Solr initialized, check with DatabaseUtils to see
@@ -323,7 +328,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
         try {
             if(getSolr() != null){
-                getSolr().deleteByQuery("handle:\"" + handle + "\"");
+                getSolr().deleteByQuery(HANDLE_FIELD + ":\"" + handle + "\"");
                 if(commit)
                 {
                     getSolr().commit();
@@ -462,10 +467,13 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             }
             if (force)
             {
-                getSolr().deleteByQuery("search.resourcetype:[2 TO 4]");
+                getSolr().deleteByQuery(RESOURCE_TYPE_FIELD + ":[2 TO 4]");
             } else {
                 SolrQuery query = new SolrQuery();
-                query.setQuery("search.resourcetype:[2 TO 4]");
+                // Query for all indexed Items, Collections and Communities,
+                // returning just their handle
+                query.setFields(HANDLE_FIELD);
+                query.setQuery(RESOURCE_TYPE_FIELD + ":[2 TO 4]");
                 QueryResponse rsp = getSolr().query(query);
                 SolrDocumentList docs = rsp.getResults();
 
@@ -475,7 +483,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
                  SolrDocument doc = (SolrDocument) iter.next();
 
-                String handle = (String) doc.getFieldValue("handle");
+                String handle = (String) doc.getFieldValue(HANDLE_FIELD);
 
                 DSpaceObject o = HandleManager.resolveToObject(context, handle);
 
@@ -616,7 +624,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         boolean inIndex = false;
 
         SolrQuery query = new SolrQuery();
-        query.setQuery("handle:" + handle);
+        query.setQuery(HANDLE_FIELD + ":" + handle);
+        // Specify that we ONLY want the LAST_INDEXED_FIELD returned in the field list (fl)
+        query.setFields(LAST_INDEXED_FIELD);
         QueryResponse rsp;
 
         try {
@@ -1444,9 +1454,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         // New fields to weaken the dependence on handles, and allow for faster
         // list display
 		doc.addField("search.uniqueid", type+"-"+id);
-        doc.addField("search.resourcetype", Integer.toString(type));
+        doc.addField(RESOURCE_TYPE_FIELD, Integer.toString(type));
 
-        doc.addField("search.resourceid", Integer.toString(id));
+        doc.addField(RESOURCE_ID_FIELD, Integer.toString(id));
 
         // want to be able to search for handle, so use keyword
         // (not tokenized, but it is indexed)
@@ -1454,7 +1464,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         {
             // want to be able to search for handle, so use keyword
             // (not tokenized, but it is indexed)
-            doc.addField("handle", handle);
+            doc.addField(HANDLE_FIELD, handle);
         }
 
         if (locations != null)
@@ -1584,7 +1594,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 discoveryQuery.addFilterQueries("location:l" + dso.getID());
             } else if (dso instanceof Item)
             {
-                discoveryQuery.addFilterQueries("handle:" + dso.getHandle());
+                discoveryQuery.addFilterQueries(HANDLE_FIELD + ":" + dso.getHandle());
             }
         }
         return search(context, discoveryQuery, includeUnDiscoverable);
@@ -1620,6 +1630,18 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 		}
 
         solrQuery.setQuery(query);
+
+        // Add any search fields to our query. This is the limited list
+        // of fields that will be returned in the solr result
+        for(String fieldName : discoveryQuery.getSearchFields())
+        {
+            solrQuery.addField(fieldName);
+        }
+        // Also ensure a few key obj identifier fields are returned with every query
+        solrQuery.addField(HANDLE_FIELD);
+        solrQuery.addField(RESOURCE_TYPE_FIELD);
+        solrQuery.addField(RESOURCE_ID_FIELD);
+
         if(discoveryQuery.isSpellCheck())
         {
             solrQuery.setParam(SpellingParams.SPELLCHECK_Q, query);
@@ -1640,7 +1662,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         }
         if(discoveryQuery.getDSpaceObjectFilter() != -1)
         {
-            solrQuery.addFilterQuery("search.resourcetype:" + discoveryQuery.getDSpaceObjectFilter());
+            solrQuery.addFilterQuery(RESOURCE_TYPE_FIELD + ":" + discoveryQuery.getDSpaceObjectFilter());
         }
 
         for (int i = 0; i < discoveryQuery.getFieldPresentQueries().size(); i++)
@@ -1753,7 +1775,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 query.addFilterQueries("location:l" + dso.getID());
             } else if (dso instanceof Item)
             {
-                query.addFilterQueries("handle:" + dso.getHandle());
+                query.addFilterQueries(HANDLE_FIELD + ":" + dso.getHandle());
             }
         }
         return searchJSON(context, query, jsonIdentifier);
@@ -1807,7 +1829,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
                 {
                     result.addDSpaceObject(dso);
                 } else {
-                    log.error(LogManager.getHeader(context, "Error while retrieving DSpace object from discovery index", "Handle: " + doc.getFirstValue("handle")));
+                    log.error(LogManager.getHeader(context, "Error while retrieving DSpace object from discovery index", "Handle: " + doc.getFirstValue(HANDLE_FIELD)));
                     continue;
                 }
 
@@ -1926,9 +1948,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
     protected static DSpaceObject findDSpaceObject(Context context, SolrDocument doc) throws SQLException {
 
-        Integer type = (Integer) doc.getFirstValue("search.resourcetype");
-        Integer id = (Integer) doc.getFirstValue("search.resourceid");
-        String handle = (String) doc.getFirstValue("handle");
+        Integer type = (Integer) doc.getFirstValue(RESOURCE_TYPE_FIELD);
+        Integer id = (Integer) doc.getFirstValue(RESOURCE_ID_FIELD);
+        String handle = (String) doc.getFirstValue(HANDLE_FIELD);
 
         if (type != null && id != null)
         {
@@ -1981,7 +2003,8 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 
             SolrQuery solrQuery = new SolrQuery();
             solrQuery.setQuery(query);
-            solrQuery.setFields("search.resourceid", "search.resourcetype");
+            //Only return obj identifier fields in result doc
+            solrQuery.setFields(RESOURCE_ID_FIELD, RESOURCE_TYPE_FIELD);
             solrQuery.setStart(offset);
             solrQuery.setRows(max);
             if (orderfield != null)
@@ -2001,7 +2024,7 @@ public class SolrServiceImpl implements SearchService, IndexingService {
             {
                 SolrDocument doc = (SolrDocument) iter.next();
 
-                DSpaceObject o = DSpaceObject.find(context, (Integer) doc.getFirstValue("search.resourcetype"), (Integer) doc.getFirstValue("search.resourceid"));
+                DSpaceObject o = DSpaceObject.find(context, (Integer) doc.getFirstValue(RESOURCE_TYPE_FIELD), (Integer) doc.getFirstValue(RESOURCE_ID_FIELD));
 
                 if (o != null)
                 {
@@ -2089,7 +2112,9 @@ public class SolrServiceImpl implements SearchService, IndexingService {
         try{
             SolrQuery solrQuery = new SolrQuery();
             //Set the query to handle since this is unique
-            solrQuery.setQuery("handle: " + item.getHandle());
+            solrQuery.setQuery(HANDLE_FIELD + ": " + item.getHandle());
+            //Only return obj identifier fields in result doc
+            solrQuery.setFields(HANDLE_FIELD, RESOURCE_TYPE_FIELD, RESOURCE_ID_FIELD);
             //Add the more like this parameters !
             solrQuery.setParam(MoreLikeThisParams.MLT, true);
             //Add a comma separated list of the similar fields
@@ -2320,4 +2345,13 @@ public class SolrServiceImpl implements SearchService, IndexingService {
 			throw new SearchServiceException(e.getMessage(), e);
 		}
 	}
+
+    @Override
+    public String escapeQueryChars(String query) {
+        // Use Solr's built in query escape tool
+        // WARNING: You should only escape characters from user entered queries,
+        // otherwise you may accidentally BREAK field-based queries (which often
+        // rely on special characters to separate the field from the query value)
+        return ClientUtils.escapeQueryChars(query);
+    }
 }

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

@@ -91,10 +91,9 @@ public class EmbargoManager
              }
         }
         String slift = myLift.toString();
-        boolean ignoreAuth = context.ignoreAuthorization();
         try
         {
-            context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();
             item.clearMetadata(lift_schema, lift_element, lift_qualifier, Item.ANY);
             item.addMetadata(lift_schema, lift_element, lift_qualifier, null, slift);
             log.info("Set embargo on Item "+item.getHandle()+", expires on: "+slift);
@@ -105,7 +104,7 @@ public class EmbargoManager
         }
         finally
         {
-            context.setIgnoreAuthorization(ignoreAuth);
+            context.restoreAuthSystemState();
         }
     }
 
@@ -267,7 +266,7 @@ public class EmbargoManager
         try
         {
             context = new Context();
-            context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();
             Date now = new Date();
              
             // scan items under embargo

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

@@ -499,7 +499,7 @@ public class EPerson extends DSpaceObject
             break;
 
         case LANGUAGE:
-            s = "m_text_value";
+            s = "m.text_value";
             t = "language";
             break;
         case NETID:
@@ -507,23 +507,26 @@ public class EPerson extends DSpaceObject
             break;
 
         default:
-            s = "m_text_value";
+            s = "m.text_value";
             t = "lastname";
         }
 
         // NOTE: The use of 's' in the order by clause can not cause an SQL
         // injection because the string is derived from constant values above.
-        TableRowIterator rows = DatabaseManager.query(context, "SELECT * FROM eperson e ORDER BY ?",s);
+        TableRowIterator rows;
         if(!t.equals("")) {
             rows = DatabaseManager.query(context,
                     "SELECT * FROM eperson e " +
-                            "LEFT JOIN metadatavalue m on (m.resource_id = e.eperson_id and m.resource_type_id = ? and m.metadata_field_id = ?) " +
-                            "ORDER BY ?",
+                    "LEFT JOIN metadatavalue m on (m.resource_id = e.eperson_id and m.resource_type_id = ? and m.metadata_field_id = ?) " +
+                    "ORDER BY " + s,
                     Constants.EPERSON,
-                    MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), t, null).getFieldID(),
-                    s
+                    MetadataField.findByElement(context, MetadataSchema.find(context, "eperson").getSchemaID(), t, null).getFieldID()
             );
         }
+        else {
+        	rows =  DatabaseManager.query(context, "SELECT * FROM eperson e ORDER BY " + s);
+        }
+        
 
 
 

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

@@ -358,9 +358,9 @@ public class Group extends DSpaceObject
     }
 
     /**
-     * fast check to see if an eperson is a member called with eperson id, does
-     * database lookup without instantiating all of the epeople objects and is
-     * thus a static method
+     * fast check to see if the current EPerson is a member of a Group.  Does
+     * database lookup without instantiating all of the EPerson objects and is
+     * thus a static method.
      * 
      * @param c
      *            context
@@ -380,6 +380,29 @@ public class Group extends DSpaceObject
         return epersonInGroup(c, groupid, currentuser);
     }
 
+    /**
+     * Fast check to see if a given EPerson is a member of a Group.
+     * Does database lookup without instantiating all of the EPerson objects and
+     * is thus a static method.
+     *
+     * @param c current DSpace context.
+     * @param eperson candidate to test for membership.
+     * @param groupid group whose membership is to be tested.
+     * @return true if {@link eperson} is a member of Group {@link groupid}.
+     * @throws SQLException passed through
+     */
+    public static boolean isMember(Context c, EPerson eperson, int groupid)
+            throws SQLException
+    {
+        // Every EPerson is a member of Anonymous
+        if (groupid == 0)
+        {
+            return true;
+        }
+
+        return epersonInGroup(c, groupid, eperson);
+    }
+
     /**
      * Get all of the groups that an eperson is a member of.
      * 

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

@@ -284,14 +284,23 @@ public class EventManager
         {
             Context ctx = new Context();
 
-            for (Iterator ci = ((Dispatcher) dispatcher).getConsumers()
-                    .iterator(); ci.hasNext();)
-            {
-                ConsumerProfile cp = (ConsumerProfile) ci.next();
-                if (cp != null)
+            try {
+
+                for (Iterator ci = ((Dispatcher) dispatcher).getConsumers()
+                        .iterator(); ci.hasNext();)
                 {
-                    cp.getConsumer().finish(ctx);
+                    ConsumerProfile cp = (ConsumerProfile) ci.next();
+                    if (cp != null)
+                    {
+                        cp.getConsumer().finish(ctx);
+                    }
                 }
+
+                ctx.complete();
+
+            } catch (Exception e) {
+                ctx.abort();
+                throw e;
             }
             return;
 

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

@@ -9,89 +9,167 @@ package org.dspace.handle;
 
 import java.io.BufferedReader;
 import java.io.InputStreamReader;
-
+import java.sql.SQLException;
+import org.apache.log4j.Logger;
 import org.dspace.core.Context;
 import org.dspace.storage.rdbms.DatabaseManager;
 import org.dspace.storage.rdbms.TableRow;
-import org.dspace.search.DSIndexer;
-import org.dspace.browse.IndexBrowse;
+import org.dspace.discovery.IndexClient;
 
 /**
  * A script to update the handle values in the database. This is typically used
- * when moving from a test machine (handle = 123456789) to a production service.
+ * when moving from a test machine (handle = 123456789) to a production service
+ * or when make a test clone from production service.
  *
  * @author Stuart Lewis
+ * @author Ivo Prajer (Czech Technical University in Prague)
  */
 public class UpdateHandlePrefix
 {
+
+    private static final Logger log = Logger.getLogger(UpdateHandlePrefix.class);
+
+    /**
+     * When invoked as a command-line tool, updates handle prefix
+     *
+     * @param args the command-line arguments, none used
+     * @throws java.lang.Exception
+     *
+     */
     public static void main(String[] args) throws Exception
     {
-        // There should be two paramters
+        // There should be two parameters
         if (args.length < 2)
         {
             System.out.println("\nUsage: update-handle-prefix <old handle> <new handle>\n");
+            System.exit(1);
         }
         else
         {
-            // Confirm with the user that this is what they want to do
             String oldH = args[0];
             String newH = args[1];
 
-            BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+            // Get info about changes
+            System.out.println("\nGetting information about handles from database...");
             Context context = new Context();
-            System.out.println("If you continue, all handles in your repository with prefix " +
-                                oldH + " will be updated to have handle prefix " + newH + "\n");
-            String sql = "SELECT count(*) as count FROM handle " +
+            String sql = "SELECT count(*) as count " +
+                         "FROM handle " +
                          "WHERE handle LIKE '" + oldH + "%'";
             TableRow row = DatabaseManager.querySingle(context, sql, new Object[] {});
             long count = row.getLongColumn("count");
-            System.out.println(count + " items will be updated.\n");
-            System.out.print("Have you taken a backup, and are you ready to continue? [y/n]: ");
-            String choiceString = input.readLine();
 
-            if (choiceString.equalsIgnoreCase("y"))
+            if (count > 0)
             {
-                // Make the changes
-                System.out.print("Updating handle table... ");
-                sql = "update handle set handle = '" + newH + "' || '/' || handle_id " +
-                      "where handle like '" + oldH + "/%'";
-                int updated = DatabaseManager.updateQuery(context, sql, new Object[] {});
-                System.out.println(updated + " items updated");
+                // Print info text about changes
+                System.out.println(
+                  "In your repository will be updated " + count + " handle" +
+                  ((count > 1) ? "s" : "") + " to new prefix " + newH +
+                  " from original " + oldH + "!\n"
+                );
 
-                System.out.print("Updating metadatavalues table... ");
-                sql = "UPDATE metadatavalue SET text_value= (SELECT 'http://hdl.handle.net/' || " +
-                      "handle FROM handle WHERE handle.resource_id=item_id AND " +
-                      "handle.resource_type_id=2) WHERE  text_value LIKE 'http://hdl.handle.net/%';";
-                updated = DatabaseManager.updateQuery(context, sql, new Object[] {});
-                System.out.println(updated + " metadata values updated");
+                // Confirm with the user that this is what they want to do
+                System.out.print(
+                  "Servlet container (e.g. Apache Tomcat, Jetty, Caucho Resin) must be running.\n" +
+                  "If it is necessary, please make a backup of the database.\n" +
+                  "Are you ready to continue? [y/n]: "
+                );
+                BufferedReader input = new BufferedReader(new InputStreamReader(System.in));
+                String choiceString = input.readLine();
 
-                // Commit the changes
-                context.complete();
-
-                System.out.print("Re-creating browse and search indexes... ");                
-
-                // Reinitialise the browse system
-                IndexBrowse.main(new String[] {"-i"});
-
-                // Reinitialise the browse system
-                try
+                if (choiceString.equalsIgnoreCase("y"))
                 {
-                    DSIndexer.main(new String[0]);
-                }
-                catch (Exception e)
-                {
-                    // Not a lot we can do
-                    System.out.println("Error re-indexing:");
-                    e.printStackTrace();
-                    System.out.println("\nPlease manually run [dspace]/bin/index-all");
-                }
+                    try {
+                        log.info("Updating handle prefix from " + oldH + " to " + newH);
 
-                // All done
-                System.out.println("\nHandles successfully updated.");
+                        // Make the changes
+                        System.out.print("\nUpdating handle table... ");
+                        sql = "UPDATE handle " +
+                              "SET handle = '" + newH + "' || '/' || handle_id " +
+                              "WHERE handle like '" + oldH + "/%'";
+                        int updHdl = DatabaseManager.updateQuery(context, sql, new Object[] {});
+                        System.out.println(
+                          updHdl + " item" + ((updHdl > 1) ? "s" : "") + " updated"
+                        );
+
+                        System.out.print("Updating metadatavalues table... ");
+                        sql = "UPDATE metadatavalue " +
+                              "SET text_value = " +
+                                "(" +
+                                  "SELECT 'http://hdl.handle.net/' || handle " +
+                                  "FROM handle " +
+                                  "WHERE handle.resource_id = metadatavalue.resource_id " +
+                                    "AND handle.resource_type_id = 2" +
+                                ") " +
+                              "WHERE text_value LIKE 'http://hdl.handle.net/" + oldH + "/%'" +
+                                "AND EXISTS " +
+                                  "(" +
+                                    "SELECT 1 " +
+                                    "FROM handle " + 
+                                    "WHERE handle.resource_id = metadatavalue.resource_id " +
+                                      "AND handle.resource_type_id = 2" +
+                                  ")";
+                        int updMeta = DatabaseManager.updateQuery(context, sql, new Object[] {});
+                        System.out.println(
+                          updMeta + " metadata value" + ((updMeta > 1) ? "s" : "") + " updated"
+                        );
+
+                        // Commit the changes
+                        context.complete();
+
+                        log.info(
+                          "Done with updating handle prefix. " +
+                          "It was changed " + updHdl + " handle" + ((updHdl > 1) ? "s" : "") +
+                          " and " + updMeta + " metadata record" + ((updMeta > 1) ? "s" : "")
+                        );
+
+                    }
+                    catch (SQLException sqle)
+                    {
+                        if ((context != null) && (context.isValid()))
+                        {
+                            context.abort();
+                            context = null;
+                        }
+                        System.out.println("\nError during SQL operations.");
+                        throw sqle;
+                    }
+
+                    System.out.println("Handles successfully updated in database.\n");
+                    System.out.println("Re-creating browse and search indexes...");
+
+                    try
+                    {
+                        // Reinitialise the search and browse system
+                        IndexClient.main(new String[] {"-b"});
+                        System.out.println("Browse and search indexes are ready now.");
+                        // All done
+                        System.out.println("\nAll done successfully. Please check the DSpace logs!\n");
+                    }
+                    catch (Exception e)
+                    {
+                        // Not a lot we can do
+                        System.out.println("Error during re-indexing.");
+                        System.out.println(
+                          "\n\nAutomatic re-indexing failed. Please perform it manually.\n" +
+                          "You should run one of the following commands:\n\n" +
+                          "  [dspace]/bin/dspace index-discovery -b\n\n" +
+                          "If you are using Solr for browse (this is the default setting).\n" +
+                          "When launching this command, your servlet container must be running.\n\n" +
+                          "  [dspace]/bin/dspace index-lucene-init\n\n" +
+                          "If you enabled Lucene for search.\n" +
+                          "When launching this command, your servlet container must be shutdown.\n"
+                        );
+                        throw e;
+                    }
+                }
+                else
+                {
+                    System.out.println("No changes have been made to your data.\n");
+                }
             }
             else
             {
-                System.out.println("No changes have been made to your data.");
+                System.out.println("Nothing to do! All handles are up-to-date.\n");
             }
         }
     }

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

@@ -10,7 +10,6 @@ package org.dspace.identifier;
 
 import java.sql.SQLException;
 import java.util.ArrayList;
-import java.util.Iterator;
 import java.util.List;
 import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Metadatum;
@@ -68,12 +67,12 @@ public class DOIIdentifierProvider
     public static final String DOI_QUALIFIER = "uri";
     
     public static final Integer TO_BE_REGISTERED = 1;
-    public static final Integer TO_BE_RESERVERED = 2;
+    public static final Integer TO_BE_RESERVED = 2;
     public static final Integer IS_REGISTERED = 3;
     public static final Integer IS_RESERVED = 4;
-    public static final Integer UPDATE_RESERVERED = 5;
+    public static final Integer UPDATE_RESERVED = 5;
     public static final Integer UPDATE_REGISTERED = 6;
-    public static final Integer UPDATE_BEFORE_REGISTERATION = 7;
+    public static final Integer UPDATE_BEFORE_REGISTRATION = 7;
     public static final Integer TO_BE_DELETED = 8;
     public static final Integer DELETED = 9;
     
@@ -251,7 +250,7 @@ public class DOIIdentifierProvider
             return;
         } 
                 
-        doiRow.setColumn("status", TO_BE_RESERVERED);
+        doiRow.setColumn("status", TO_BE_RESERVED);
         try
         {
             DatabaseManager.update(context, doiRow);
@@ -353,11 +352,11 @@ public class DOIIdentifierProvider
         }
         else if (TO_BE_REGISTERED == doiRow.getIntColumn("status")) 
         {
-            doiRow.setColumn("status", UPDATE_BEFORE_REGISTERATION);
+            doiRow.setColumn("status", UPDATE_BEFORE_REGISTRATION);
         }
         else if (IS_RESERVED == doiRow.getIntColumn("status")) 
         {
-            doiRow.setColumn("status", UPDATE_RESERVERED);
+            doiRow.setColumn("status", UPDATE_RESERVED);
         }
         else
         {
@@ -416,11 +415,11 @@ public class DOIIdentifierProvider
         {
             doiRow.setColumn("status", IS_REGISTERED);
         }
-        else if (UPDATE_BEFORE_REGISTERATION == doiRow.getIntColumn("status")) 
+        else if (UPDATE_BEFORE_REGISTRATION == doiRow.getIntColumn("status"))
         {
             doiRow.setColumn("status", TO_BE_REGISTERED);
         }
-        else if (UPDATE_RESERVERED == doiRow.getIntColumn("status")) 
+        else if (UPDATE_RESERVED == doiRow.getIntColumn("status"))
         {
             doiRow.setColumn("status", IS_RESERVED);
         }

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

@@ -561,7 +561,7 @@ public class EZIDIdentifierProvider
     /**
      * Map selected DSpace metadata to fields recognized by DataCite.
      */
-    private Map<String, String> crosswalkMetadata(DSpaceObject dso)
+    Map<String, String> crosswalkMetadata(DSpaceObject dso)
     {
         if ((null == dso) || !(dso instanceof Item))
         {
@@ -632,18 +632,42 @@ public class EZIDIdentifierProvider
             mapped.put(DATACITE_PUBLICATION_YEAR, year);
         }
 
-        // TODO find a way to get a current direct URL to the object and set _target
-        // mapped.put("_target", url);
+        // Supply _target link back to this object
+        String handle = dso.getHandle();
+        if (null == handle)
+        {
+            log.warn("{} #{} has no handle -- location not set.",
+                    dso.getTypeText(), dso.getID());
+        }
+        else
+        {
+            String url = configurationService.getProperty("dspace.url")
+                    + "/handle/" + item.getHandle();
+            log.info("Supplying location:  {}", url);
+            mapped.put("_target", url);
+        }
 
         return mapped;
     }
 
+    /**
+     * Provide a map from DSO metadata keys to EZID keys.  This will drive the
+     * generation of EZID metadata for the minting of new identifiers.
+     *
+     * @param aCrosswalk
+     */
     @Required
     public void setCrosswalk(Map<String, String> aCrosswalk)
     {
         crosswalk = aCrosswalk;
     }
 
+    /**
+     * Provide a map from DSO metadata keys to classes which can transform their
+     * values to something acceptable to EZID.
+     *
+     * @param transformMap
+     */
     public void setCrosswalkTransform(Map<String, Transform> transformMap)
     {
         transforms = transformMap;

dspace-api/src/main/java/org/dspace/identifier/doi/DOIOrganiser.java

@@ -179,19 +179,19 @@ public class DOIOrganiser {
         
         if (line.hasOption('l'))
         {
-            organiser.list("reservation", null, null, DOIIdentifierProvider.TO_BE_RESERVERED);
+            organiser.list("reservation", null, null, DOIIdentifierProvider.TO_BE_RESERVED);
             organiser.list("registration", null, null, DOIIdentifierProvider.TO_BE_REGISTERED);
             organiser.list("update", null, null,
-                    DOIIdentifierProvider.UPDATE_BEFORE_REGISTERATION,
+                    DOIIdentifierProvider.UPDATE_BEFORE_REGISTRATION,
                     DOIIdentifierProvider.UPDATE_REGISTERED,
-                    DOIIdentifierProvider.UPDATE_RESERVERED);
+                    DOIIdentifierProvider.UPDATE_RESERVED);
             organiser.list("deletion", null, null, DOIIdentifierProvider.TO_BE_DELETED);
         }
 
         if (line.hasOption('s'))
         {
             TableRowIterator it = organiser
-                                    .getDOIsByStatus(DOIIdentifierProvider.TO_BE_RESERVERED);
+                                    .getDOIsByStatus(DOIIdentifierProvider.TO_BE_RESERVED);
            
             try { 
                 if (!it.hasNext()) 
@@ -244,8 +244,8 @@ public class DOIOrganiser {
         if (line.hasOption('u'))
         {
             TableRowIterator it = organiser.getDOIsByStatus(
-                    DOIIdentifierProvider.UPDATE_BEFORE_REGISTERATION,
-                    DOIIdentifierProvider.UPDATE_RESERVERED,
+                    DOIIdentifierProvider.UPDATE_BEFORE_REGISTRATION,
+                    DOIIdentifierProvider.UPDATE_RESERVED,
                     DOIIdentifierProvider.UPDATE_REGISTERED);
            
             try { 

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

@@ -259,7 +259,7 @@ public class CCLookup {
 		throws IOException{
 
 		// Determine the issue URL
-		String issueUrl = this.cc_root + "/license/" + licenseId + "/issue";
+		String issueUrl = cc_root + "/license/" + licenseId + "/issue";
 		// Assemble the "answers" document
 		String answer_doc = "<answers>\n<locale>" + lang + "</locale>\n" + "<license-" + licenseId + ">\n";
 		Iterator keys = answers.keySet().iterator();
@@ -411,31 +411,18 @@ public class CCLookup {
 
 	public String getRdf()
 		throws IOException {
-		String myString = null;
-		java.io.ByteArrayOutputStream outputstream = new java.io.ByteArrayOutputStream();
+		String result = ""; 
 		try {
-			outputstream.write("<result>\n".getBytes()); 
-			JDOMXPath xpathRdf 				= new JDOMXPath("//result/rdf");
-			JDOMXPath xpathLicenseRdf 				= new JDOMXPath("//result/licenserdf");
-			XMLOutputter xmloutputter 	= new XMLOutputter();
-			Element rdfParent     				= ((Element)xpathRdf.selectSingleNode(this.license_doc));
-			xmloutputter.output(rdfParent, outputstream);
-			Element licenseRdfParent       = ((Element)xpathLicenseRdf.selectSingleNode(this.license_doc));
-			outputstream.write("\n".getBytes());
-			xmloutputter.output(licenseRdfParent, outputstream);
-			outputstream.write("\n</result>\n".getBytes());
+			result = CreativeCommons.fetchLicenseRDF(license_doc);
 		} catch (Exception e) {
 			log.warn("An error occurred getting the rdf . . ." + e.getMessage() );
 			setSuccess(false);
-		} finally {
-			outputstream.close();
-			return outputstream.toString();
-		}
+		} 
+		return result;
 	}
 
 	public boolean isSuccess() {
 		setSuccess(false);
-		java.io.ByteArrayOutputStream outputstream = new java.io.ByteArrayOutputStream();
 		JDOMXPath xp_Success = null;
 		String text = null;
 		try {

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

@@ -7,13 +7,16 @@
  */
 package org.dspace.license;
 
-import java.io.*;
-import java.net.URL;
-import java.net.URLConnection;
+import java.io.ByteArrayInputStream;
+import java.io.ByteArrayOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.StringWriter;
 import java.sql.SQLException;
 import java.util.ArrayList;
 
 import javax.xml.transform.Templates;
+import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerConfigurationException;
 import javax.xml.transform.TransformerException;
 import javax.xml.transform.TransformerFactory;
@@ -26,11 +29,14 @@ import org.dspace.authorize.AuthorizeException;
 import org.dspace.content.Bitstream;
 import org.dspace.content.BitstreamFormat;
 import org.dspace.content.Bundle;
-import org.dspace.content.Metadatum;
 import org.dspace.content.Item;
+import org.dspace.content.Metadatum;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
 import org.dspace.core.Utils;
+import org.jdom.Document;
+import org.jdom.transform.JDOMResult;
+import org.jdom.transform.JDOMSource;
 
 public class CreativeCommons
 {
@@ -46,9 +52,17 @@ public class CreativeCommons
 
     /**
      * Some BitStream Names (BSN)
+     * 
+     * @deprecated use the metadata retrieved at {@link CreativeCommons#getCCField(String)} (see https://jira.duraspace.org/browse/DS-2604)
      */
+    @Deprecated
     private static final String BSN_LICENSE_URL = "license_url";
 
+    /**
+     * 
+     * @deprecated to make uniform JSPUI and XMLUI approach the bitstream with the license in the textual format it is no longer stored (see https://jira.duraspace.org/browse/DS-2604)
+     */
+    @Deprecated
     private static final String BSN_LICENSE_TEXT = "license_text";
 
     private static final String BSN_LICENSE_RDF = "license_rdf";
@@ -121,41 +135,6 @@ public class CreativeCommons
         setBitstreamFromBytes(item, bundle, BSN_LICENSE_RDF, bs_rdf_format, licenseRdf.getBytes());
     }
     
-
-    /**
-     * This is a bit of the "do-the-right-thing" method for CC stuff in an item
-     */
-    public static void setLicense(Context context, Item item,
-            String cc_license_url) throws SQLException, IOException,
-            AuthorizeException
-    {
-        Bundle bundle = getCcBundle(item);
-
-        // get some more information
-        String license_text = fetchLicenseText(cc_license_url);
-        String license_rdf = fetchLicenseRDF(cc_license_url);
-        
-        // set the formats
-        BitstreamFormat bs_url_format = BitstreamFormat.findByShortDescription(
-                context, "License");
-        BitstreamFormat bs_text_format = BitstreamFormat.findByShortDescription(
-                context, "CC License");
-        BitstreamFormat bs_rdf_format = BitstreamFormat.findByShortDescription(
-                context, "RDF XML");
-
-        // set the URL bitstream
-        setBitstreamFromBytes(item, bundle, BSN_LICENSE_URL, bs_url_format,
-                cc_license_url.getBytes());
-
-        // set the license text bitstream
-        setBitstreamFromBytes(item, bundle, BSN_LICENSE_TEXT, bs_text_format,
-                license_text.getBytes());
-
-        // set the RDF bitstream
-        setBitstreamFromBytes(item, bundle, BSN_LICENSE_RDF, bs_rdf_format,
-                license_rdf.getBytes());
-    }
-
     /**
      * Used by DSpaceMetsIngester
      *
@@ -224,8 +203,7 @@ public class CreativeCommons
         // verify it has correct contents
         try
         {
-            if ((getLicenseURL(item) == null) || (getLicenseText(item) == null)
-                    || (getLicenseRDF(item) == null))
+            if ((getLicenseURL(item) == null))
             {
                 return false;
             }
@@ -238,18 +216,6 @@ public class CreativeCommons
         return true;
     }
 
-    public static String getLicenseURL(Item item) throws SQLException,
-            IOException, AuthorizeException
-    {
-        return getStringFromBitstream(item, BSN_LICENSE_URL);
-    }
-
-    public static String getLicenseText(Item item) throws SQLException,
-            IOException, AuthorizeException
-    {
-        return getStringFromBitstream(item, BSN_LICENSE_TEXT);
-    }
-
     public static String getLicenseRDF(Item item) throws SQLException,
             IOException, AuthorizeException
     {
@@ -269,56 +235,55 @@ public class CreativeCommons
     /**
      * Get Creative Commons license Text, returning Bitstream object.
      * @return bitstream or null.
+     * 
+     * @deprecated to make uniform JSPUI and XMLUI approach the bitstream with the license in the textual format it is no longer stored (see https://jira.duraspace.org/browse/DS-2604)
      */
+    @Deprecated
     public static Bitstream getLicenseTextBitstream(Item item) throws SQLException,
             IOException, AuthorizeException
     {
         return getBitstream(item, BSN_LICENSE_TEXT);
     }
+    
+	/**
+	 * Retrieve the license text
+	 * 
+	 * @param item - the item 
+	 * @return the license in textual format
+	 * @throws SQLException
+	 * @throws IOException
+	 * @throws AuthorizeException
+	 * 
+     * @deprecated to make uniform JSPUI and XMLUI approach the bitstream with the license in the textual format it is no longer stored (see https://jira.duraspace.org/browse/DS-2604)
+	 */
+	public static String getLicenseText(Item item) throws SQLException, IOException, AuthorizeException {
+		return getStringFromBitstream(item, BSN_LICENSE_TEXT);
+	}
+    
+	public static String getLicenseURL(Item item) throws SQLException, IOException, AuthorizeException {
+		String licenseUri = CreativeCommons.getCCField("uri").ccItemValue(item);
+		if (StringUtils.isNotBlank(licenseUri)) {
+			return licenseUri;
+		}
+		// JSPUI backward compatibility see https://jira.duraspace.org/browse/DS-2604
+		return getStringFromBitstream(item, BSN_LICENSE_URL);
+	}
 
-    public static String fetchLicenseRdf(String ccResult) {
-    	StringWriter result 			= new StringWriter();
-    	String licenseRdfString 		= new String("");
-        try {
-    		InputStream inputstream = new ByteArrayInputStream(ccResult.getBytes("UTF-8"));
-    		templates.newTransformer().transform(new StreamSource(inputstream), new StreamResult(result));
-    	} catch (TransformerException te) {
-    		throw new RuntimeException("Transformer exception " + te.getMessage(), te);
-    	} catch (IOException ioe) {
-    		throw new RuntimeException("IOexception " + ioe.getCause().toString(), ioe);
-    	} finally {
-    		return result.getBuffer().toString();
-    	}
-    }
-    
-    
-    /** 
-    *
-    *  The next two methods are old CC.
-    * Remains until prev. usages are eliminated.
-    * @Deprecated
-    *
-    */
     /**
-     * Get a few license-specific properties. We expect these to be cached at
-     * least per server run.
+     * Apply same transformation on the document to retrieve only the most relevant part of the document passed as parameter.
+     * If no transformation is needed then take in consideration to empty the CreativeCommons.xml
+     * 
+     * @param license - an element that could be contains as part of your content the license rdf
+     * @return the document license in textual format after the transformation
      */
-    public static String fetchLicenseText(String license_url)
-    {
-        String text_url = license_url;
-        byte[] urlBytes = fetchURL(text_url);
-
-        return (urlBytes != null) ? new String(urlBytes) : "";
-    }
-    
-    public static String fetchLicenseRDF(String license_url)
+    public static String fetchLicenseRDF(Document license)
     {
         StringWriter result = new StringWriter();
         
         try
         {
             templates.newTransformer().transform(
-                    new StreamSource(license_url + "rdf"),
+                    new JDOMSource(license),
                     new StreamResult(result)
                     );
         }
@@ -421,33 +386,6 @@ public class CreativeCommons
         return baos.toByteArray();
     }
 
-    /**
-     * Fetch the contents of a URL
-     */
-    private static byte[] fetchURL(String url_string)
-    {
-        try
-        {
-            String line = "";
-            URL url = new URL(url_string);
-            URLConnection connection = url.openConnection();
-            InputStream inputStream = connection.getInputStream();
-            BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream));
-            StringBuilder sb = new StringBuilder();
-
-            while ((line = reader.readLine()) != null)
-            {
-                sb.append(line);
-            }
-
-            return sb.toString().getBytes();
-        }
-        catch (Exception exc)
-        {
-            log.error(exc.getMessage());
-            return null;
-        }
-    }
     /**
      * Returns a metadata field handle for given field Id
      */
@@ -564,4 +502,34 @@ public class CreativeCommons
     		item.addMetadata(params[0], params[1], params[2], params[3], value);
     	}
     }
+
+	/**
+	 * Remove license information, delete also the bitstream
+	 * 
+	 * @param context - DSpace Context
+	 * @param uriField - the metadata field for license uri 
+	 * @param nameField - the metadata field for license name
+	 * @param item - the item
+	 * @throws AuthorizeException
+	 * @throws IOException
+	 * @throws SQLException
+	 */
+	public static void removeLicense(Context context, MdField uriField,
+			MdField nameField, Item item) throws AuthorizeException, IOException, SQLException {
+		// only remove any previous licenses
+		String licenseUri = uriField.ccItemValue(item);
+		if (licenseUri != null) {
+			uriField.removeItemValue(item, licenseUri);
+			if (ConfigurationManager.getBooleanProperty("cc.submit.setname"))
+		    {
+		    	String licenseName = nameField.keyedItemValue(item, licenseUri);
+		    	nameField.removeItemValue(item, licenseName);
+		    }
+		    if (ConfigurationManager.getBooleanProperty("cc.submit.addbitstream"))
+		    {
+		    	removeLicense(context, item);
+		    }
+		}
+	}
+
 }

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

@@ -72,7 +72,7 @@ public class LicenseCleanup
     {
 
         Context ctx = new Context();
-        ctx.setIgnoreAuthorization(true);
+        ctx.turnOffAuthorisationSystem();
         ItemIterator iter = Item.findAll(ctx);
 
         Properties props = new Properties();

dspace-api/src/main/java/org/dspace/rdf/RDFConsumer.java

@@ -20,6 +20,7 @@ import org.dspace.content.Bundle;
 import org.dspace.content.DSpaceObject;
 import org.dspace.content.Item;
 import org.dspace.content.Site;
+import org.dspace.content.WorkspaceItem;
 import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.dspace.event.Consumer;
@@ -52,6 +53,8 @@ public class RDFConsumer implements Consumer
         }
         
         int sType = event.getSubjectType();
+        log.debug(event.getEventTypeAsString() + " for " 
+                + event.getSubjectTypeAsString() + ":" + event.getSubjectID());
         switch (sType)
         {
             case (Constants.BITSTREAM) :
@@ -100,7 +103,7 @@ public class RDFConsumer implements Consumer
             Bitstream bitstream = Bitstream.find(ctx, event.getSubjectID());
             if (bitstream == null)
             {
-                log.warn("Cannot find bitstream " + event.getSubjectID() + "! "
+                log.debug("Cannot find bitstream " + event.getSubjectID() + "! "
                         + "Ignoring, as it is likely it was deleted "
                         + "and we'll cover it by a REMOVE event on its bundle.");
                 return;
@@ -111,6 +114,11 @@ public class RDFConsumer implements Consumer
                 Item[] items = b.getItems();
                 for (Item i : items)
                 {
+                    if (WorkspaceItem.findByItem(ctx, i) != null)
+                    {
+                        log.debug("Ignoring Item " + i.getID() + " as a corresponding workspace item exists.");
+                        continue;
+                    }
                     DSOIdentifier id = new DSOIdentifier(i, ctx);
                     if (!this.toDelete.contains(id) && !this.toConvert.contains(id))
                     {
@@ -148,7 +156,7 @@ public class RDFConsumer implements Consumer
             Bundle bundle = Bundle.find(ctx, event.getSubjectID());
             if (bundle == null)
             {
-                log.warn("Cannot find bundle " + event.getSubjectID() + "! "
+                log.debug("Cannot find bundle " + event.getSubjectID() + "! "
                         + "Ignoring, as it is likely it was deleted "
                         + "and we'll cover it by a REMOVE event on its item.");
                 return;
@@ -156,6 +164,11 @@ public class RDFConsumer implements Consumer
             Item[] items = bundle.getItems();
             for (Item i : items)
             {
+                if (WorkspaceItem.findByItem(ctx, i) != null)
+                {
+                    log.debug("Ignoring Item " + i.getID() + " as a corresponding workspace item exists.");
+                    continue;
+                }
                 DSOIdentifier id = new DSOIdentifier(i, ctx);
                 if (!this.toDelete.contains(id) && !this.toConvert.contains(id))
                 {
@@ -216,14 +229,24 @@ public class RDFConsumer implements Consumer
             DSpaceObject dso = event.getSubject(ctx);
             if (dso == null)
             {
-                log.warn("Cannot find " + event.getSubjectTypeAsString() + " " 
+                log.debug("Cannot find " + event.getSubjectTypeAsString() + " " 
                         + event.getSubjectID() + "! " + "Ignoring, as it is "
                         + "likely it was deleted and we'll cover it by another "
                         + "event with the type REMOVE.");
                 return;
             }
-            DSOIdentifier id = new DSOIdentifier(dso, ctx);
+            
+            // ignore unfinished submissions here. Every unfinished submission
+            // has an workspace item. The item flag "in_archive" doesn't help us
+            // here as this is also set to false if a newer version was submitted.
+            if (dso instanceof Item
+                    && WorkspaceItem.findByItem(ctx, (Item) dso) != null)
+            {
+                log.debug("Ignoring Item " + dso.getID() + " as a corresponding workspace item exists.");
+                return;
+            }
 
+            DSOIdentifier id = new DSOIdentifier(dso, ctx);
             // If an item gets withdrawn, a MODIFIY event is fired. We have to
             // delete the item from the triple store instead of converting it.
             // we don't have to take care for reinstantions of items as they can

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

@@ -392,7 +392,7 @@ public class DSIndexer
         {
             setBatchProcessingMode(true);
             Context context = new Context();
-            context.setIgnoreAuthorization(true);
+            context.turnOffAuthorisationSystem();
 
             String usage = "org.dspace.search.DSIndexer [-cbhof[r <item handle>]] or nothing to update/clean an existing index.";
             Options options = new Options();

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

@@ -7,14 +7,24 @@
  */
 package org.dspace.statistics;
 
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.net.InetAddress;
+import java.net.URL;
+import java.sql.SQLException;
+import java.util.*;
+import javax.servlet.http.HttpServletRequest;
 
 import com.google.common.base.Charsets;
 import com.google.common.io.Resources;
-import com.maxmind.geoip.Location;
-import com.maxmind.geoip.LookupService;
+import com.maxmind.geoip2.DatabaseReader;
+import com.maxmind.geoip2.model.CityResponse;
+
 import org.apache.commons.lang.exception.ExceptionUtils;
 import org.apache.commons.lang.time.DateFormatUtils;
 import org.apache.log4j.Logger;
+
 import org.dspace.content.*;
 import org.dspace.content.Collection;
 import org.dspace.core.ConfigurationManager;
@@ -30,7 +40,6 @@ import org.elasticsearch.action.admin.indices.mapping.put.PutMappingRequestBuild
 import org.elasticsearch.action.admin.indices.mapping.put.PutMappingResponse;
 import org.elasticsearch.action.index.IndexRequestBuilder;
 import org.elasticsearch.client.Client;
-
 import org.elasticsearch.client.transport.TransportClient;
 import org.elasticsearch.common.settings.ImmutableSettings;
 import org.elasticsearch.common.settings.Settings;
@@ -41,13 +50,6 @@ import org.elasticsearch.common.xcontent.XContentFactory;
 import org.elasticsearch.node.Node;
 import org.elasticsearch.node.NodeBuilder;
 
-import javax.servlet.http.HttpServletRequest;
-import java.io.FileNotFoundException;
-import java.io.IOException;
-import java.net.URL;
-import java.sql.SQLException;
-import java.util.*;
-
 public class ElasticSearchLogger {
 
     private static Logger log = Logger.getLogger(ElasticSearchLogger.class);
@@ -58,8 +60,6 @@ public class ElasticSearchLogger {
 
     public static final String DATE_FORMAT_DCDATE = "yyyy-MM-dd'T'HH:mm:ss'Z'";
 
-    private static LookupService locationService;
-
     public static String clusterName = "dspacestatslogging";
     public static String indexName = "dspaceindex";
     public static String indexType = "stats";
@@ -68,6 +68,8 @@ public class ElasticSearchLogger {
 
     private static Client client;
 
+    protected static DatabaseReader locationService;
+
     public static enum ClientType {
         NODE, LOCAL, TRANSPORT
     }
@@ -93,16 +95,24 @@ public class ElasticSearchLogger {
     public void initializeElasticSearch() {
         log.info("DSpace ElasticSearchLogger Initializing");
         try {
-        LookupService service = null;
+        DatabaseReader service = null;
         // Get the db file for the location
-        String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
-        if (dbfile != null) {
+        String dbPath = ConfigurationManager.getProperty("usage-statistics.dbfile");
+        if (dbPath != null) {
             try {
-                service = new LookupService(dbfile, LookupService.GEOIP_STANDARD);
+                File dbFile = new File(dbPath);
+                service = new DatabaseReader.Builder(dbFile).build();
             } catch (FileNotFoundException fe) {
-                log.error("The GeoLite Database file is missing (" + dbfile + ")! Usage Statistics cannot generate location based reports! Please see the DSpace installation instructions for instructions to install this file.", fe);
+                log.error(
+                        "The GeoLite Database file is missing (" + dbPath + ")! Usage Statistics cannot generate location"
+                            + " based reports! Please see the DSpace installation instructions for instructions to"
+                            + " install this file.",
+                        fe);
             } catch (IOException e) {
-                log.error("Unable to load GeoLite Database file (" + dbfile + ")! You may need to reinstall it. See the DSpace installation instructions for more details.", e);
+                log.error(
+                        "Unable to load GeoLite Database file (" + dbPath + ")! You may need to reinstall it. See the"
+                            + " DSpace installation instructions for more details.",
+                        e);
             }
         } else {
             log.error("The required 'dbfile' configuration is missing in usage-statistics.cfg!");
@@ -257,21 +267,24 @@ public class ElasticSearchLogger {
 
             // Save the location information if valid, save the event without
             // location information if not valid
-            Location location = locationService.getLocation(ip);
-            if (location != null
-                    && !("--".equals(location.countryCode)
-                    && location.latitude == -180 && location.longitude == -180)) {
+            InetAddress ipAddress = InetAddress.getByName(ip);
+            CityResponse location = locationService.city(ipAddress);
+            String countryCode = location.getCountry().getIsoCode();
+            double latitude = location.getLocation().getLatitude();
+            double longitude = location.getLocation().getLongitude();
+            if (!("--".equals(countryCode)
+                    && latitude == -180 && longitude == -180)) {
                 try {
                     docBuilder.field("continent", LocationUtils
-                            .getContinentCode(location.countryCode));
-                } catch (Exception e) {
+                            .getContinentCode(countryCode));
+                } catch (IOException e) {
                     System.out
-                            .println("COUNTRY ERROR: " + location.countryCode);
+                            .println("COUNTRY ERROR: " + countryCode);
                 }
-                docBuilder.field("countryCode", location.countryCode);
-                docBuilder.field("city", location.city);
-                docBuilder.field("latitude", location.latitude);
-                docBuilder.field("longitude", location.longitude);
+                docBuilder.field("countryCode", countryCode);
+                docBuilder.field("city", location.getCity().getName());
+                docBuilder.field("latitude", latitude);
+                docBuilder.field("longitude", longitude);
                 docBuilder.field("isBot", isSpiderBot);
 
                 if (request.getHeader("User-Agent") != null) {
@@ -373,22 +386,25 @@ public class ElasticSearchLogger {
             }
 
             // Save the location information if valid, save the event without
-            // location information if not valid
-            Location location = locationService.getLocation(ip);
-            if (location != null
-                    && !("--".equals(location.countryCode)
-                    && location.latitude == -180 && location.longitude == -180)) {
+            // location information if not valid.
+            InetAddress ipAddress = InetAddress.getByName(ip);
+            CityResponse location = locationService.city(ipAddress);
+            String countryCode = location.getCountry().getIsoCode();
+            double latitude = location.getLocation().getLatitude();
+            double longitude = location.getLocation().getLongitude();
+            if (!("--".equals(countryCode)
+                    && latitude == -180 && longitude == -180)) {
                 try {
                     docBuilder.field("continent", LocationUtils
-                            .getContinentCode(location.countryCode));
-                } catch (Exception e) {
+                            .getContinentCode(countryCode));
+                } catch (IOException e) {
                     System.out
-                            .println("COUNTRY ERROR: " + location.countryCode);
+                            .println("COUNTRY ERROR: " + countryCode);
                 }
-                docBuilder.field("countryCode", location.countryCode);
-                docBuilder.field("city", location.city);
-                docBuilder.field("latitude", location.latitude);
-                docBuilder.field("longitude", location.longitude);
+                docBuilder.field("countryCode", countryCode);
+                docBuilder.field("city", location.getCity().getName());
+                docBuilder.field("latitude", latitude);
+                docBuilder.field("longitude", longitude);
                 docBuilder.field("isBot", isSpiderBot);
 
                 if (userAgent != null) {

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

@@ -7,10 +7,37 @@
  */
 package org.dspace.statistics;
 
+import java.io.File;
+import java.io.FileFilter;
+import java.io.FileNotFoundException;
+import java.io.FileWriter;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.Reader;
+import java.io.UnsupportedEncodingException;
+import java.net.InetAddress;
+import java.net.URLEncoder;
+import java.sql.SQLException;
+import java.text.DateFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Date;
+import java.util.EnumSet;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import javax.servlet.http.HttpServletRequest;
+
 import au.com.bytecode.opencsv.CSVReader;
 import au.com.bytecode.opencsv.CSVWriter;
-import com.maxmind.geoip.Location;
-import com.maxmind.geoip.LookupService;
+import com.maxmind.geoip2.DatabaseReader;
+import com.maxmind.geoip2.exception.GeoIp2Exception;
+import com.maxmind.geoip2.model.CityResponse;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
@@ -18,23 +45,24 @@ import org.apache.commons.lang.time.DateFormatUtils;
 import org.apache.http.HttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.impl.client.DefaultHttpClient;
-import org.apache.log4j.Logger;
 import org.apache.solr.client.solrj.SolrQuery;
-import org.apache.solr.client.solrj.SolrServer;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.apache.solr.client.solrj.impl.HttpSolrServer;
 import org.apache.solr.client.solrj.request.AbstractUpdateRequest;
 import org.apache.solr.client.solrj.request.ContentStreamUpdateRequest;
 import org.apache.solr.client.solrj.request.CoreAdminRequest;
+import org.apache.solr.client.solrj.request.LukeRequest;
 import org.apache.solr.client.solrj.response.FacetField;
+import org.apache.solr.client.solrj.response.LukeResponse;
 import org.apache.solr.client.solrj.response.QueryResponse;
 import org.apache.solr.client.solrj.response.RangeFacet;
+import org.apache.solr.client.solrj.response.SolrPingResponse;
 import org.apache.solr.client.solrj.util.ClientUtils;
 import org.apache.solr.common.SolrDocument;
 import org.apache.solr.common.SolrDocumentList;
 import org.apache.solr.common.SolrInputDocument;
+import org.apache.solr.common.luke.FieldFlag;
 import org.apache.solr.common.params.*;
-import org.apache.solr.common.util.JavaBinCodec;
 import org.dspace.content.*;
 import org.dspace.content.Collection;
 import org.dspace.core.ConfigurationManager;
@@ -46,15 +74,10 @@ import org.dspace.statistics.util.DnsLookup;
 import org.dspace.statistics.util.LocationUtils;
 import org.dspace.statistics.util.SpiderDetector;
 import org.dspace.usage.UsageWorkflowEvent;
-
-import javax.servlet.http.HttpServletRequest;
-import java.io.*;
-import java.net.URLEncoder;
-import java.sql.SQLException;
-import java.text.DateFormat;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.util.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.InitializingBean;
+import org.springframework.beans.factory.annotation.Autowired;
 
 /**
  * Static holder for a HttpSolrClient connection pool to issue
@@ -63,19 +86,21 @@ import java.util.*;
  * 
  * @author ben at atmire.com
  * @author kevinvandevelde at atmire.com
- * @author mdiggory at atmire.com
+ * @author mdiggory at atmire.com 
  */
 public class SolrLogger
 {
-    private static final Logger log = Logger.getLogger(SolrLogger.class);
-	
+    private static final Logger log = LoggerFactory.getLogger(SolrLogger.class);
+
+    private static final String MULTIPLE_VALUES_SPLITTER = "|";
+    
     private static final HttpSolrServer solr;
 
     public static final String DATE_FORMAT_8601 = "yyyy-MM-dd'T'HH:mm:ss.SSS'Z'";
 
     public static final String DATE_FORMAT_DCDATE = "yyyy-MM-dd'T'HH:mm:ss'Z'";
 
-    private static final LookupService locationService;
+    private static final DatabaseReader locationService;
 
     private static final boolean useProxies;
 
@@ -143,23 +168,24 @@ public class SolrLogger
         // Read in the file so we don't have to do it all the time
         //spiderIps = SpiderDetector.getSpiderIpAddresses();
 
-        LookupService service = null;
+        DatabaseReader service = null;
         // Get the db file for the location
-        String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
-        if (dbfile != null)
-        {
-            try
-            {
-                service = new LookupService(dbfile,
-                        LookupService.GEOIP_STANDARD);
-            }
-            catch (FileNotFoundException fe)
-            {
-                log.error("The GeoLite Database file is missing (" + dbfile + ")! Solr Statistics cannot generate location based reports! Please see the DSpace installation instructions for instructions to install this file.", fe);
-            }
-            catch (IOException e)
-            {
-                log.error("Unable to load GeoLite Database file (" + dbfile + ")! You may need to reinstall it. See the DSpace installation instructions for more details.", e);
+        String dbPath = ConfigurationManager.getProperty("usage-statistics.dbfile");
+        if (dbPath != null) {
+            try {
+                File dbFile = new File(dbPath);
+                service = new DatabaseReader.Builder(dbFile).build();
+            } catch (FileNotFoundException fe) {
+                log.error(
+                    "The GeoLite Database file is missing (" + dbPath + ")! Solr Statistics cannot generate location " +
+                        "based reports! Please see the DSpace installation instructions for instructions to install " +
+                        "this file.",
+                    fe);
+            } catch (IOException e) {
+                log.error(
+                    "Unable to load GeoLite Database file (" + dbPath + ")! You may need to reinstall it. See the " +
+                        "DSpace installation instructions for more details.",
+                    e);
             }
         }
         else
@@ -331,32 +357,35 @@ public class SolrLogger
 		    {
 		        doc1.addField("userAgent", request.getHeader("User-Agent"));
 		    }
+		    doc1.addField("isBot",isSpiderBot);
             // Save the location information if valid, save the event without
             // location information if not valid
-            if(locationService != null)
-            {
-                Location location = locationService.getLocation(ip);
-                if (location != null
-                        && !("--".equals(location.countryCode)
-                        && location.latitude == -180 && location.longitude == -180))
-                {
-                    try
-                    {
-                        doc1.addField("continent", LocationUtils
-                                .getContinentCode(location.countryCode));
+            if (locationService != null) {
+                try {
+                    InetAddress ipAddress = InetAddress.getByName(ip);
+                    CityResponse location = locationService.city(ipAddress);
+                    String countryCode = location.getCountry().getIsoCode();
+                    double latitude = location.getLocation().getLatitude();
+                    double longitude = location.getLocation().getLongitude();
+                    if (!(
+                            "--".equals(countryCode)
+                            && latitude == -180
+                            && longitude == -180)
+                    ) {
+                        try {
+                            doc1.addField("continent", LocationUtils
+                                .getContinentCode(countryCode));
+                        } catch (Exception e) {
+                            System.out
+                                .println("COUNTRY ERROR: " + countryCode);
+                        }
+                        doc1.addField("countryCode", countryCode);
+                        doc1.addField("city", location.getCity().getName());
+                        doc1.addField("latitude", latitude);
+                        doc1.addField("longitude", longitude);
                     }
-                    catch (Exception e)
-                    {
-                        System.out
-                                .println("COUNTRY ERROR: " + location.countryCode);
-                    }
-                    doc1.addField("countryCode", location.countryCode);
-                    doc1.addField("city", location.city);
-                    doc1.addField("latitude", location.latitude);
-                    doc1.addField("longitude", location.longitude);
-                    doc1.addField("isBot",isSpiderBot);
-
-
+                } catch (IOException | GeoIp2Exception e) {
+                    log.error("Unable to get location of request:  {}", e.getMessage());
                 }
             }
         }
@@ -416,32 +445,35 @@ public class SolrLogger
 		    {
 		        doc1.addField("userAgent", userAgent);
 		    }
+		    doc1.addField("isBot",isSpiderBot);
             // Save the location information if valid, save the event without
             // location information if not valid
-            if(locationService != null)
-            {
-                Location location = locationService.getLocation(ip);
-                if (location != null
-                        && !("--".equals(location.countryCode)
-                        && location.latitude == -180 && location.longitude == -180))
-                {
-                    try
-                    {
-                        doc1.addField("continent", LocationUtils
-                                .getContinentCode(location.countryCode));
+            if (locationService != null) {
+                try {
+                    InetAddress ipAddress = InetAddress.getByName(ip);
+                    CityResponse location = locationService.city(ipAddress);
+                    String countryCode = location.getCountry().getIsoCode();
+                    double latitude = location.getLocation().getLatitude();
+                    double longitude = location.getLocation().getLongitude();
+                    if (!(
+                            "--".equals(countryCode)
+                            && latitude == -180
+                            && longitude == -180)
+                    ) {
+                        try {
+                            doc1.addField("continent", LocationUtils
+                                .getContinentCode(countryCode));
+                        } catch (Exception e) {
+                            System.out
+                                .println("COUNTRY ERROR: " + countryCode);
+                        }
+                        doc1.addField("countryCode", countryCode);
+                        doc1.addField("city", location.getCity().getName());
+                        doc1.addField("latitude", latitude);
+                        doc1.addField("longitude", longitude);
                     }
-                    catch (Exception e)
-                    {
-                        System.out
-                                .println("COUNTRY ERROR: " + location.countryCode);
-                    }
-                    doc1.addField("countryCode", location.countryCode);
-                    doc1.addField("city", location.city);
-                    doc1.addField("latitude", location.latitude);
-                    doc1.addField("longitude", location.longitude);
-                    doc1.addField("isBot",isSpiderBot);
-
-
+                } catch (GeoIp2Exception | IOException e) {
+                    log.error("Unable to get location of request:  {}", e.getMessage());
                 }
             }
         }
@@ -1310,8 +1342,12 @@ public class SolrLogger
             yearQueryParams.put(CommonParams.FQ, filterQuery.toString());
             yearQueryParams.put(CommonParams.WT, "csv");
 
+            //Tell SOLR how to escape and separate the values of multi-valued fields
+            yearQueryParams.put("csv.escape", "\\");
+            yearQueryParams.put("csv.mv.separator", MULTIPLE_VALUES_SPLITTER);
+            
             //Start by creating a new core
-            String coreName = "statistics-" + dcStart.getYear();
+            String coreName = "statistics-" + dcStart.getYearUTC();
             HttpSolrServer statisticsYearServer = createCore(solr, coreName);
 
             System.out.println("Moving: " + totalRecords + " into core " + coreName);
@@ -1326,7 +1362,7 @@ public class SolrLogger
                 HttpResponse response = new DefaultHttpClient().execute(get);
                 InputStream csvInputstream = response.getEntity().getContent();
                 //Write the csv ouput to a file !
-                File csvFile = new File(tempDirectory.getPath() + File.separatorChar + "temp." + dcStart.getYear() + "." + i + ".csv");
+                File csvFile = new File(tempDirectory.getPath() + File.separatorChar + "temp." + dcStart.getYearUTC() + "." + i + ".csv");
                 FileUtils.copyInputStreamToFile(csvInputstream, csvFile);
                 filesToUpload.add(csvFile);
 
@@ -1334,13 +1370,22 @@ public class SolrLogger
                 yearQueryParams.put(CommonParams.START, String.valueOf((i + 10000)));
             }
 
+            Set<String> multivaluedFields = getMultivaluedFieldNames();
+            
             for (File tempCsv : filesToUpload) {
                 //Upload the data in the csv files to our new solr core
                 ContentStreamUpdateRequest contentStreamUpdateRequest = new ContentStreamUpdateRequest("/update/csv");
                 contentStreamUpdateRequest.setParam("stream.contentType", "text/plain;charset=utf-8");
+                contentStreamUpdateRequest.setParam("escape", "\\");
+                contentStreamUpdateRequest.setParam("skip", "_version_");
                 contentStreamUpdateRequest.setAction(AbstractUpdateRequest.ACTION.COMMIT, true, true);
                 contentStreamUpdateRequest.addFile(tempCsv, "text/plain;charset=utf-8");
 
+                //Add parsing directives for the multivalued fields so that they are stored as separate values instead of one value
+                for (String multivaluedField : multivaluedFields) {
+                    contentStreamUpdateRequest.setParam("f." + multivaluedField + ".split", Boolean.TRUE.toString());
+                    contentStreamUpdateRequest.setParam("f." + multivaluedField + ".separator", MULTIPLE_VALUES_SPLITTER);
+                }
                 statisticsYearServer.request(contentStreamUpdateRequest);
             }
             statisticsYearServer.commit(true, true);
@@ -1359,6 +1404,14 @@ public class SolrLogger
     private static HttpSolrServer createCore(HttpSolrServer solr, String coreName) throws IOException, SolrServerException {
         String solrDir = ConfigurationManager.getProperty("dspace.dir") + File.separator + "solr" +File.separator;
         String baseSolrUrl = solr.getBaseURL().replace("statistics", "");
+        HttpSolrServer returnServer = new HttpSolrServer(baseSolrUrl + "/" + coreName);
+        try {
+            SolrPingResponse ping = returnServer.ping();
+            log.debug(String.format("Ping of Solr Core [%s] Returned with Status [%d]", coreName, ping.getStatus()));
+            return returnServer;
+        } catch(Exception e) {
+            log.debug(String.format("Ping of Solr Core [%s] Failed with [%s].  New Core Will be Created", coreName, e.getClass().getName()));
+        }
         CoreAdminRequest.Create create = new CoreAdminRequest.Create();
         create.setCoreName(coreName);
         create.setInstanceDir("statistics");
@@ -1366,10 +1419,35 @@ public class SolrLogger
         HttpSolrServer solrServer = new HttpSolrServer(baseSolrUrl);
         create.process(solrServer);
         log.info("Created core with name: " + coreName);
-        return new HttpSolrServer(baseSolrUrl + "/" + coreName);
+        return returnServer;
     }
 
-
+    /**
+     * Retrieves a list of all the multi valued fields in the solr core
+     * @return all fields tagged as multivalued
+     * @throws SolrServerException When getting the schema information from the SOLR core fails
+     * @throws IOException When connection to the SOLR server fails
+     */
+    public static Set<String> getMultivaluedFieldNames() throws SolrServerException, IOException {
+        Set<String> multivaluedFields = new HashSet<String>();
+        LukeRequest lukeRequest = new LukeRequest();
+        lukeRequest.setShowSchema(true);
+        LukeResponse process = lukeRequest.process(solr);
+        Map<String, LukeResponse.FieldInfo> fields = process.getFieldInfo();
+        for(String fieldName : fields.keySet())
+        {
+            LukeResponse.FieldInfo fieldInfo = fields.get(fieldName);
+            EnumSet<FieldFlag> flags = fieldInfo.getFlags();
+            for(FieldFlag fieldFlag : flags)
+            {
+                if(fieldFlag.getAbbreviation() == FieldFlag.MULTI_VALUED.getAbbreviation())
+                {
+                    multivaluedFields.add(fieldName);
+                }
+            }
+        }
+        return multivaluedFields;
+    }
     public static void reindexBitstreamHits(boolean removeDeletedBitstreams) throws Exception {
         Context context = new Context();
 

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

@@ -15,6 +15,7 @@ import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
+import java.util.Collections;
 import java.util.regex.Pattern;
 import javax.servlet.http.HttpServletRequest;
 import org.dspace.core.ConfigurationManager;
@@ -42,10 +43,10 @@ public class SpiderDetector {
     private static IPTable table = null;
 
     /** Collection of regular expressions to match known spiders' agents. */
-    private static List<Pattern> agents = new ArrayList<Pattern>();
+    private static List<Pattern> agents = Collections.synchronizedList(new ArrayList<Pattern>());
 
     /** Collection of regular expressions to match known spiders' domain names. */
-    private static List<Pattern> domains = new ArrayList<Pattern>();
+    private static List<Pattern> domains = Collections.synchronizedList(new ArrayList<Pattern>());
 
     /**
      * Utility method which reads lines from a file & returns them in a Set.
@@ -199,13 +200,15 @@ public class SpiderDetector {
     {
         // See if any agent patterns match
         if (null != agent)
-        {
-            if (agents.isEmpty())
-                loadPatterns("agents", agents);
-
+        {   
+            synchronized(agents)
+            {
+                if (agents.isEmpty())
+                    loadPatterns("agents", agents);
+            }
             for (Pattern candidate : agents)
             {
-                // prevent matcher() invocation from a null Pattern object
+		// prevent matcher() invocation from a null Pattern object
                 if (null != candidate && candidate.matcher(agent).find())
                 {
                     return true;
@@ -230,15 +233,15 @@ public class SpiderDetector {
         // No.  See if any DNS names match
         if (null != hostname)
         {
-            if (domains.isEmpty())
+            synchronized(domains) 
             {
-                loadPatterns("domains", domains);
+                if (domains.isEmpty())
+                    loadPatterns("domains", domains);
             }
-
             for (Pattern candidate : domains)
             {
-                // prevent matcher() invocation from a null Pattern object
-                if (null != candidate && candidate.matcher(hostname).find())
+		// prevent matcher() invocation from a null Pattern object
+		if (null != candidate && candidate.matcher(hostname).find())
                 {
                     return true;
                 }

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

@@ -22,8 +22,10 @@ import org.dspace.statistics.SolrLogger;
 import java.util.Date;
 import java.text.SimpleDateFormat;
 
-import com.maxmind.geoip.LookupService;
-import com.maxmind.geoip.Location;
+import com.maxmind.geoip2.DatabaseReader;
+import com.maxmind.geoip2.model.CityResponse;
+import java.io.File;
+import java.net.InetAddress;
 
 /**
  * Test class to generate random statistics data.
@@ -194,17 +196,17 @@ public class StatisticsDataGenerator {
 		solr.commit();
 
 		String prevIp = null;
-		String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
-		LookupService cl = new LookupService(dbfile,
-				LookupService.GEOIP_STANDARD);
+		String dbPath = ConfigurationManager.getProperty("usage-statistics", "dbfile");
+        File dbFile = new File(dbPath);
+		DatabaseReader cl = new DatabaseReader.Builder(dbFile).build();
 		int countryErrors = 0;
 		for (int i = 0; i < nrLogs; i++) {
 			String ip = "";
 			Date time;
 			String continent;
 			String countryCode;
-			float longitude;
-			float latitude;
+			double longitude;
+			double latitude;
 			String city;
 
 			// 1. Generate an ip for our user
@@ -219,9 +221,11 @@ public class StatisticsDataGenerator {
             ip = ipBuilder.toString();
             
 			// 2 Depending on our ip get all the location info
-			Location location;
+            InetAddress ipAddress;
+			CityResponse location;
 			try {
-				location = cl.getLocation(ip);
+                ipAddress = InetAddress.getByName(ip);
+				location = cl.city(ipAddress);
 			} catch (Exception e) {
 				location = null;
 			}
@@ -233,13 +237,14 @@ public class StatisticsDataGenerator {
                     continue;
                 }
 				ip = prevIp;
-				location = cl.getLocation(ip);
+                ipAddress = InetAddress.getByName(ip);
+				location = cl.city(ipAddress);
 			}
 
-			city = location.city;
-			countryCode = location.countryCode;
-			longitude = location.longitude;
-			latitude = location.latitude;
+			city = location.getCity().getName();
+			countryCode = location.getCountry().getIsoCode();
+			longitude = location.getLocation().getLongitude();
+			latitude = location.getLocation().getLatitude();
 			try {
 				continent = LocationUtils.getContinentCode(countryCode);
 			} catch (Exception e) {

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

@@ -7,7 +7,29 @@
  */
 package org.dspace.statistics.util;
 
-import org.apache.commons.cli.*;
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.FilenameFilter;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.net.InetAddress;
+import java.text.DecimalFormat;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Random;
+
+import com.maxmind.geoip2.DatabaseReader;
+import com.maxmind.geoip2.model.CityResponse;
+import org.apache.commons.cli.CommandLine;
+import org.apache.commons.cli.CommandLineParser;
+import org.apache.commons.cli.HelpFormatter;
+import org.apache.commons.cli.Options;
+import org.apache.commons.cli.PosixParser;
 import org.apache.commons.lang.time.DateFormatUtils;
 import org.apache.log4j.Logger;
 import org.apache.solr.common.SolrInputDocument;
@@ -21,13 +43,6 @@ import org.dspace.core.ConfigurationManager;
 import org.dspace.eperson.EPerson;
 import org.dspace.statistics.SolrLogger;
 
-import java.text.*;
-import java.io.*;
-import java.util.*;
-
-import com.maxmind.geoip.LookupService;
-import com.maxmind.geoip.Location;
-
 /**
  * Class to load intermediate statistics files (produced from log files by {@link ClassicDSpaceLogConverter}) into Solr.
  *
@@ -45,8 +60,10 @@ public class StatisticsImporter
     /** Solr server connection */
     private static HttpSolrServer solr;
 
-    /** GEOIP lookup service */
-    private static LookupService geoipLookup;
+    /**
+     * GEOIP lookup service
+     */
+    private static DatabaseReader geoipLookup;
 
     /** Whether to skip the DNS reverse lookup or not */
     private static boolean skipReverseDNS = false;
@@ -170,8 +187,8 @@ public class StatisticsImporter
             String continent = "";
             String country = "";
             String countryCode = "";
-            float longitude = 0f;
-            float latitude = 0f;
+            double longitude = 0f;
+            double latitude = 0f;
             String city = "";
             String dns;
 
@@ -236,15 +253,15 @@ public class StatisticsImporter
                 }
 
                 // Get the geo information for the user
-                Location location;
                 try {
-                    location = geoipLookup.getLocation(ip);
-                    city = location.city;
-                    country = location.countryName;
-                    countryCode = location.countryCode;
-                    longitude = location.longitude;
-                    latitude = location.latitude;
-                    if(verbose) {
+                    InetAddress ipAddress = InetAddress.getByName(ip);
+                    CityResponse cityResponse = geoipLookup.city(ipAddress);
+                    city = cityResponse.getCity().getName();
+                    country = cityResponse.getCountry().getName();
+                    countryCode = cityResponse.getCountry().getIsoCode();
+                    longitude = cityResponse.getLocation().getLongitude();
+                    latitude = cityResponse.getLocation().getLatitude();
+                    if (verbose) {
                         data += (", country = " + country);
                         data += (", city = " + city);
                         System.out.println(data);
@@ -450,18 +467,21 @@ public class StatisticsImporter
         }
 		solr = new HttpSolrServer(sserver);
 
-        String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
-        try
-        {
-            geoipLookup = new LookupService(dbfile, LookupService.GEOIP_STANDARD);
-        }
-        catch (FileNotFoundException fe)
-        {
-            log.error("The GeoLite Database file is missing (" + dbfile + ")! Solr Statistics cannot generate location based reports! Please see the DSpace installation instructions for instructions to install this file.", fe);
-        }
-        catch (IOException e)
-        {
-            log.error("Unable to load GeoLite Database file (" + dbfile + ")! You may need to reinstall it. See the DSpace installation instructions for more details.", e);
+        String dbPath = ConfigurationManager.getProperty("usage-statistics", "dbfile");
+        try {
+            File dbFile = new File(dbPath);
+            geoipLookup = new DatabaseReader.Builder(dbFile).build();
+        } catch (FileNotFoundException fe) {
+            log.error(
+                "The GeoLite Database file is missing (" + dbPath + ")! Solr Statistics cannot generate location " +
+                    "based reports! Please see the DSpace installation instructions for instructions to install this " +
+                    "file.",
+                fe);
+        } catch (IOException e) {
+            log.error(
+                "Unable to load GeoLite Database file (" + dbPath + ")! You may need to reinstall it. See the DSpace " +
+                    "installation instructions for more details.",
+                e);
         }
 
 

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

@@ -7,8 +7,13 @@
  */
 package org.dspace.statistics.util;
 
-import com.maxmind.geoip.Location;
-import com.maxmind.geoip.LookupService;
+import java.io.*;
+import java.net.InetAddress;
+
+import com.maxmind.geoip2.DatabaseReader;
+import com.maxmind.geoip2.exception.GeoIp2Exception;
+import com.maxmind.geoip2.model.CityResponse;
+
 import org.apache.commons.cli.*;
 import org.apache.commons.lang.time.DateFormatUtils;
 import org.apache.log4j.Logger;
@@ -24,13 +29,10 @@ import org.dspace.statistics.SolrLogger;
 import org.elasticsearch.action.bulk.BulkRequestBuilder;
 import org.elasticsearch.action.bulk.BulkResponse;
 import org.elasticsearch.client.Client;
-
 import org.elasticsearch.common.geo.GeoPoint;
 import org.elasticsearch.common.xcontent.XContentBuilder;
 import org.elasticsearch.common.xcontent.XContentFactory;
 
-
-import java.io.*;
 import java.text.DecimalFormat;
 import java.text.SimpleDateFormat;
 import java.util.Date;
@@ -38,8 +40,6 @@ import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Random;
 
-import static org.elasticsearch.common.xcontent.XContentFactory.jsonBuilder;
-
 /**
  * Class to load intermediate statistics files (produced from log files by <code>ClassicDSpaceLogConverter</code>) into Elastic Search
  *
@@ -56,7 +56,7 @@ public class StatisticsImporterElasticSearch {
     //TODO ES Client
 
     /** GEOIP lookup service */
-    private static LookupService geoipLookup;
+    private static DatabaseReader geoipLookup;
 
     /** Metadata storage information */
     private static Map<String, String> metadataStorageInfo;
@@ -107,8 +107,8 @@ public class StatisticsImporterElasticSearch {
             String continent = "";
             String country = "";
             String countryCode = "";
-            float longitude = 0f;
-            float latitude = 0f;
+            double longitude = 0f;
+            double latitude = 0f;
             String city = "";
             String dns;
 
@@ -176,15 +176,15 @@ public class StatisticsImporterElasticSearch {
                 }
 
                 // Get the geo information for the user
-                Location location;
                 try {
-                    location = geoipLookup.getLocation(ip);
-                    city = location.city;
-                    country = location.countryName;
-                    countryCode = location.countryCode;
-                    longitude = location.longitude;
-                    latitude = location.latitude;
-                    if(verbose) {
+                    InetAddress ipAddress = InetAddress.getByName(ip);
+                    CityResponse cityResponse = geoipLookup.city(ipAddress);
+                    city = cityResponse.getCity().getName();
+                    country = cityResponse.getCountry().getName();
+                    countryCode = cityResponse.getCountry().getIsoCode();
+                    longitude = cityResponse.getLocation().getLongitude();
+                    latitude = cityResponse.getLocation().getLatitude();
+                    if (verbose) {
                         data += (", country = " + country);
                         data += (", city = " + city);
                         System.out.println(data);
@@ -198,7 +198,7 @@ public class StatisticsImporterElasticSearch {
                         }
                         continue;
                     }
-                } catch (Exception e) {
+                } catch (GeoIp2Exception | IOException e) {
                     // No problem - just can't look them up
                 }
 
@@ -386,20 +386,22 @@ public class StatisticsImporterElasticSearch {
         // Verbose option
         boolean verbose = line.hasOption('v');
 
-        String dbfile = ConfigurationManager.getProperty("usage-statistics", "dbfile");
-        try
-        {
-            geoipLookup = new LookupService(dbfile, LookupService.GEOIP_STANDARD);
+        String dbPath = ConfigurationManager.getProperty("usage-statistics", "dbfile");
+        try {
+            File dbFile = new File(dbPath);
+            geoipLookup = new DatabaseReader.Builder(dbFile).build();
+        } catch (FileNotFoundException fe) {
+            log.error(
+                "The GeoLite Database file is missing (" + dbPath + ")! ElasticSearch Statistics cannot generate location " +
+                    "based reports! Please see the DSpace installation instructions for instructions to install this " +
+                    "file.",
+                fe);
+        } catch (IOException e) {
+            log.error(
+                "Unable to load GeoLite Database file (" + dbPath + ")! You may need to reinstall it. See the DSpace " +
+                    "installation instructions for more details.",
+                e);
         }
-        catch (FileNotFoundException fe)
-        {
-            log.error("The GeoLite Database file is missing (" + dbfile + ")! Elastic Search  Statistics cannot generate location based reports! Please see the DSpace installation instructions for instructions to install this file.", fe);
-        }
-        catch (IOException e)
-        {
-            log.error("Unable to load GeoLite Database file (" + dbfile + ")! You may need to reinstall it. See the DSpace installation instructions for more details.", e);
-        }
-
 
         StatisticsImporterElasticSearch elasticSearchImporter = new StatisticsImporterElasticSearch();
         if (line.hasOption('m'))

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

@@ -7,39 +7,21 @@
  */
 package org.dspace.storage.rdbms;
 
-import java.io.*;
-import java.sql.Connection;
-import java.sql.DatabaseMetaData;
-import java.sql.Date;
-import java.sql.PreparedStatement;
-import java.sql.ResultSet;
-import java.sql.ResultSetMetaData;
-import java.sql.SQLException;
-import java.sql.SQLWarning;
-import java.sql.Statement;
-import java.sql.Time;
-import java.sql.Timestamp;
-import java.sql.Types;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Locale;
-import java.util.Map;
-import java.util.Set;
-import java.util.regex.Pattern;
-import javax.naming.InitialContext;
-import javax.sql.DataSource;
 import org.apache.commons.lang.StringUtils;
 import org.dspace.core.ConfigurationManager;
 import org.dspace.core.Context;
-import org.flywaydb.core.Flyway;
-import org.flywaydb.core.api.MigrationInfo;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import javax.naming.InitialContext;
+import javax.sql.DataSource;
+import java.io.Serializable;
+import java.io.UnsupportedEncodingException;
+import java.sql.*;
+import java.sql.Date;
+import java.util.*;
+import java.util.regex.Pattern;
+
 /**
  * Executes SQL queries.
  *
@@ -343,7 +325,7 @@ public class DatabaseManager
         try
         {
             iterator = query(context, query, parameters);
-            retRow = (!iterator.hasNext()) ? null : iterator.next();
+            retRow = (!iterator.hasNext()) ? null : iterator.next(context);
         } catch (SQLException e) {
             log.error("SQL query single Error - ", e);
             throw e;
@@ -389,7 +371,7 @@ public class DatabaseManager
 
         try
         {
-            retRow = (!iterator.hasNext()) ? null : iterator.next();
+            retRow = (!iterator.hasNext()) ? null : iterator.next(context);
         } catch (SQLException e) {
             log.error("SQL query singleTable Error - ", e);
             throw e;
@@ -475,7 +457,7 @@ public class DatabaseManager
 
     {
         try {
-            TableRow row = new TableRow(canonicalize(table), getColumnNames(table));
+            TableRow row = new TableRow(canonicalize(table), getColumnNames(context,table));
             insert(context, row);
             return row;
         } catch (SQLException e) {
@@ -505,7 +487,7 @@ public class DatabaseManager
         String ctable = canonicalize(table);
 
         try {
-            return findByUnique(context, ctable, getPrimaryKeyColumn(ctable),
+            return findByUnique(context, ctable, getPrimaryKeyColumn(context, ctable),
                     Integer.valueOf(id));
         } catch (SQLException e) {
             log.error("SQL find Error - ", e);
@@ -571,7 +553,7 @@ public class DatabaseManager
     {
         try {
             String ctable = canonicalize(table);
-            return deleteByValue(context, ctable, getPrimaryKeyColumn(ctable),
+            return deleteByValue(context, ctable, getPrimaryKeyColumn(context, ctable),
                     Integer.valueOf(id));
         } catch (SQLException e) {
             log.error("SQL delete Error - ", e);
@@ -691,6 +673,10 @@ public class DatabaseManager
      * @return The newly created row
      * @throws SQLException
      */
+    public static TableRow row(Context context, String table) throws SQLException
+    {
+        return new TableRow(canonicalize(table), getColumnNames(context, table));
+    }
     public static TableRow row(String table) throws SQLException
     {
         return new TableRow(canonicalize(table), getColumnNames(table));
@@ -718,7 +704,7 @@ public class DatabaseManager
             newID = doInsertGeneric(context, row);
         }
 
-        row.setColumn(getPrimaryKeyColumn(row), newID);
+        row.setColumn(getPrimaryKeyColumn(context, row), newID);
     }
 
     /**
@@ -741,8 +727,8 @@ public class DatabaseManager
                 .append(" set ");
 
         List<ColumnInfo> columns = new ArrayList<ColumnInfo>();
-        ColumnInfo pk = getPrimaryKeyColumnInfo(table);
-        Collection<ColumnInfo> info = getColumnInfo(table);
+        ColumnInfo pk = getPrimaryKeyColumnInfo(context, table);
+        Collection<ColumnInfo> info = getColumnInfo(context, table);
 
         String separator = "";
         for (ColumnInfo col : info)
@@ -789,7 +775,7 @@ public class DatabaseManager
             throw new IllegalArgumentException("Row not associated with a table");
         }
 
-        String pk = getPrimaryKeyColumn(row);
+        String pk = getPrimaryKeyColumn(context, row);
 
         if (row.isColumnNull(pk))
         {
@@ -808,9 +794,9 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    static Collection<ColumnInfo> getColumnInfo(String table) throws SQLException
+    static Collection<ColumnInfo> getColumnInfo(Context context, String table) throws SQLException
     {
-        Map<String, ColumnInfo> cinfo = getColumnInfoInternal(table);
+        Map<String, ColumnInfo> cinfo = getColumnInfoInternal(context, table);
 
         return (cinfo == null) ? null : cinfo.values();
     }
@@ -826,14 +812,18 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    static ColumnInfo getColumnInfo(String table, String column)
+    static ColumnInfo getColumnInfo(Context context, String table, String column)
             throws SQLException
     {
-        Map<String, ColumnInfo> info = getColumnInfoInternal(table);
+        Map<String, ColumnInfo> info = getColumnInfoInternal(context, table);
 
         return (info == null) ? null : info.get(column);
     }
 
+    static List<String> getColumnNames(String table) throws SQLException{
+        return getColumnNames(null,table);
+    }
+
     /**
      * Return the names of all the columns of the given table.
      *
@@ -844,10 +834,10 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    static List<String> getColumnNames(String table) throws SQLException
+    static List<String> getColumnNames(Context context, String table) throws SQLException
     {
         List<String> results = new ArrayList<String>();
-        Collection<ColumnInfo> info = getColumnInfo(table);
+        Collection<ColumnInfo> info = getColumnInfo(context, table);
 
         for (ColumnInfo col : info)
         {
@@ -881,22 +871,22 @@ public class DatabaseManager
     }
 
     /**
-     * Return the canonical name for a table.
+     * Return the canonical name for a database object.
      *
-     * @param table
-     *            The name of the table.
-     * @return The canonical name of the table.
+     * @param db_object
+     *            The name of the database object.
+     * @return The canonical name of the database object.
      */
-    static String canonicalize(String table)
+    static String canonicalize(String db_object)
     {
-        // Oracle expects upper-case table names
+        // Oracle expects upper-case table names, schemas, etc.
         if (isOracle)
         {
-            return (table == null) ? null : table.toUpperCase();
+            return (db_object == null) ? null : db_object.toUpperCase();
         }
 
         // default database postgres wants lower-case table names
-        return (table == null) ? null : table.toLowerCase();
+        return (db_object == null) ? null : db_object.toLowerCase();
     }
 
     ////////////////////////////////////////
@@ -914,9 +904,21 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
+    static TableRow process(Context context, ResultSet results, String table) throws SQLException
+    {
+        return process(context,results, table, null);
+    }
     static TableRow process(ResultSet results, String table) throws SQLException
     {
-        return process(results, table, null);
+        return process(null,results, table, null);
+    }
+
+    /**
+     * @deprecated You should try to pass an existing database connection to this method to prevent opening a new one.
+     */
+    @Deprecated
+    static TableRow process(ResultSet results, String table, List<String> pColumnNames) throws SQLException{
+        return process(null,results,table,pColumnNames);
     }
 
     /**
@@ -932,14 +934,14 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    static TableRow process(ResultSet results, String table, List<String> pColumnNames) throws SQLException
+    static TableRow process(Context context, ResultSet results, String table, List<String> pColumnNames) throws SQLException
     {
         ResultSetMetaData meta = results.getMetaData();
         int columns = meta.getColumnCount() + 1;
 
         // If we haven't been passed the column names try to generate them from the metadata / table
         List<String> columnNames = pColumnNames != null ? pColumnNames :
-                                        ((table == null) ? getColumnNames(meta) : getColumnNames(table));
+                ((table == null) ? getColumnNames(meta) : getColumnNames(context,table));
 
         TableRow row = new TableRow(canonicalize(table), columnNames);
 
@@ -1062,9 +1064,9 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    public static String getPrimaryKeyColumn(TableRow row) throws SQLException
+    public static String getPrimaryKeyColumn(Context context,TableRow row) throws SQLException
     {
-        return getPrimaryKeyColumn(row.getTable());
+        return getPrimaryKeyColumn(context,row.getTable());
     }
 
     /**
@@ -1079,10 +1081,10 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    protected static String getPrimaryKeyColumn(String table)
+    protected static String getPrimaryKeyColumn(Context context, String table)
             throws SQLException
     {
-        ColumnInfo info = getPrimaryKeyColumnInfo(table);
+        ColumnInfo info = getPrimaryKeyColumnInfo(context, table);
 
         return (info == null) ? null : info.getName();
     }
@@ -1098,9 +1100,9 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    static ColumnInfo getPrimaryKeyColumnInfo(String table) throws SQLException
+    static ColumnInfo getPrimaryKeyColumnInfo(Context context, String table) throws SQLException
     {
-        Collection<ColumnInfo> cinfo = getColumnInfo(canonicalize(table));
+        Collection<ColumnInfo> cinfo = getColumnInfo(context, canonicalize(table));
 
         for (ColumnInfo info : cinfo)
         {
@@ -1202,7 +1204,7 @@ public class DatabaseManager
      * @exception SQLException
      *                If a database error occurs
      */
-    private static Map<String, ColumnInfo> getColumnInfoInternal(String table) throws SQLException
+    private static Map<String, ColumnInfo> getColumnInfoInternal(Context context, String table) throws SQLException
     {
         String ctable = canonicalize(table);
         Map<String, ColumnInfo> results = info.get(ctable);
@@ -1212,7 +1214,7 @@ public class DatabaseManager
             return results;
         }
 
-        results = retrieveColumnInfo(ctable);
+        results = retrieveColumnInfo(context, ctable);
         info.put(ctable, results);
 
         return results;
@@ -1229,7 +1231,7 @@ public class DatabaseManager
      *                If there is a problem retrieving information from the
      *                RDBMS.
      */
-    private static Map<String, ColumnInfo> retrieveColumnInfo(String table) throws SQLException
+    private static Map<String, ColumnInfo> retrieveColumnInfo(Context context, String table) throws SQLException
     {
         Connection connection = null;
         ResultSet pkcolumns = null;
@@ -1237,10 +1239,6 @@ public class DatabaseManager
 
         try
         {
-            String schema = ConfigurationManager.getProperty("db.schema");
-            if(StringUtils.isBlank(schema)){
-                schema = null;
-            }
             String catalog = null;
 
             int dotIndex = table.indexOf('.');
@@ -1252,8 +1250,15 @@ public class DatabaseManager
                 log.warn("table: " + table);
             }
 
-            connection = getConnection();
+            if (context != null && !context.getDBConnection().isClosed()) {
+                connection = context.getDBConnection();
+            } else {
+                connection = getConnection();
+            }
 
+            // Get current database schema name
+            String schema = DatabaseUtils.getSchemaName(connection);
+            
             DatabaseMetaData metadata = connection.getMetaData();
             Map<String, ColumnInfo> results = new HashMap<String, ColumnInfo>();
 
@@ -1301,7 +1306,7 @@ public class DatabaseManager
                 try { columns.close(); } catch (SQLException sqle) { }
             }
 
-            if (connection != null)
+            if (connection != null && context == null) // Only close if connection is newly created in this method
             {
                 try { connection.close(); } catch (SQLException sqle) { }
             }
@@ -1674,10 +1679,10 @@ public class DatabaseManager
     {
         String table = row.getTable();
 
-        Collection<ColumnInfo> info = getColumnInfo(table);
+        Collection<ColumnInfo> info = getColumnInfo(context, table);
         Collection<ColumnInfo> params = new ArrayList<ColumnInfo>();
 
-        String primaryKey = getPrimaryKeyColumn(table);
+        String primaryKey = getPrimaryKeyColumn(context, table);
         String sql = insertSQL.get(table);
 
         boolean firstColumn = true;
@@ -1713,7 +1718,7 @@ public class DatabaseManager
                 }
             }
 
-            sql = insertBuilder.append(valuesBuilder.toString()).append(") RETURNING ").append(getPrimaryKeyColumn(table)).toString();
+            sql = insertBuilder.append(valuesBuilder.toString()).append(") RETURNING ").append(getPrimaryKeyColumn(context, table)).toString();
             insertSQL.put(table, sql);
         }
         else
@@ -1828,8 +1833,8 @@ public class DatabaseManager
         }
 
         // Set the ID in the table row object
-        row.setColumn(getPrimaryKeyColumn(table), newID);
-        Collection<ColumnInfo> info = getColumnInfo(table);
+        row.setColumn(getPrimaryKeyColumn(context, table), newID);
+        Collection<ColumnInfo> info = getColumnInfo(context, table);
 
         String sql = insertSQL.get(table);
         if (sql == null)