Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/SampleDataProducer.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/SampleDataProducer.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/SampleDataProducer.java	(nonexistent)
@@ -1,61 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.java;
-
-import java.io.IOException;
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
-import eu.dnetlib.iis.core.examples.protobuf.StandardDataStoreExamples;
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentProto.Document;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.java.PortBindings;
-import eu.dnetlib.iis.core.java.Process;
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-import eu.dnetlib.iis.core.java.io.protobuf.IOUtils;
-import eu.dnetlib.iis.core.java.porttype.PortType;
-import eu.dnetlib.iis.core.java.porttype.ProtoBuffPortType;
-
-/** Processes input files in a specific way
- * @author Mateusz Kobos
- */
-public class SampleDataProducer implements Process {
-	
-	private final static String personPort = "person";
-	private final static String documentPort = "document";
-	
-	@Override
-	public Map<String, PortType> getInputPorts() {
-		return new HashMap<String, PortType>();
-	}
-	
-	@Override
-	public Map<String, PortType> getOutputPorts() {
-		return createOutputPorts();
-	}
-
-	private static HashMap<String, PortType> createOutputPorts(){
-		HashMap<String, PortType> outputPorts = 
-				new HashMap<String, PortType>();
-		outputPorts.put(personPort, 
-				new ProtoBuffPortType<Person>(Person.class));
-		outputPorts.put(documentPort, 
-				new ProtoBuffPortType<Document>(Document.class));
-		return outputPorts;	
-	}
-	
-	@Override
-	public void run(PortBindings portBindings, Configuration conf,
-			Map<String, String> parameters)	throws IOException{
-		Map<String, Path> output = portBindings.getOutput();
-		FileSystem fs = FileSystem.get(conf);
-		
-		IOUtils.writeProtobuffDataStore(StandardDataStoreExamples.getDocument(),
-				new FileSystemPath(fs, output.get(documentPort)));
-		IOUtils.writeProtobuffDataStore(StandardDataStoreExamples.getPerson(),
-				new FileSystemPath(fs, output.get(personPort)));
-	}
-
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/Joiner.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/Joiner.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/Joiner.java	(nonexistent)
@@ -1,205 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.java;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentProto.Document;
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments;
-import eu.dnetlib.iis.core.java.PortBindings;
-import eu.dnetlib.iis.core.java.Process;
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-import eu.dnetlib.iis.core.java.io.protobuf.IOUtils;
-import eu.dnetlib.iis.core.java.porttype.PortType;
-import eu.dnetlib.iis.core.java.porttype.ProtoBuffPortType;
-
-/** Processes input files and produces files in a certain way
- *  that would require SQL JOINs when done in context of relational databases 
- * @author Mateusz Kobos
- */
-public class Joiner implements Process {
-	
-	private final static String personPort = "person";
-	private final static String documentPort = "document";
-	private final static String documentWithAuthorsPort = 
-			"document_with_authors";
-	private final static String personWithDocumentsPort =
-			"person_with_documents";
-	private final static String personAgePort = "person_age";
-	
-	@Override
-	public Map<String, PortType> getInputPorts() {
-		return createInputPorts();
-	}
-	
-	@Override
-	public Map<String, PortType> getOutputPorts() {
-		return createOutputPorts();
-	}
-
-	private static HashMap<String, PortType> createInputPorts(){
-		HashMap<String, PortType> inputPorts = 
-				new HashMap<String, PortType>();
-		inputPorts.put(personPort, 
-				new ProtoBuffPortType<Person>(Person.class));
-		inputPorts.put(documentPort, 
-				new ProtoBuffPortType<Document>(Document.class));
-		return inputPorts;
-	}
-	
-	private static HashMap<String, PortType> createOutputPorts(){
-		HashMap<String, PortType> outputPorts = 
-				new HashMap<String, PortType>();
-		outputPorts.put(documentWithAuthorsPort, 
-				new ProtoBuffPortType<DocumentWithAuthors>(
-						DocumentWithAuthors.class));
-		outputPorts.put(personWithDocumentsPort, 
-				new ProtoBuffPortType<PersonWithDocuments>(
-						PersonWithDocuments.class));
-		outputPorts.put(personAgePort, 
-				new ProtoBuffPortType<PersonAge>(PersonAge.class));
-		return outputPorts;	
-	}
-	
-	@Override
-	public void run(PortBindings portBindings, Configuration conf,
-			Map<String, String> parameters)	throws IOException{
-		Map<String, Path> input = portBindings.getInput();
-		Map<String, Path> output = portBindings.getOutput();
-		FileSystem fs = FileSystem.get(conf);
-		
-		List<Document> documents = IOUtils.readProtobuffDataStore(
-				Document.class, 
-				new FileSystemPath(fs, input.get(documentPort)));
-		List<Person> persons = IOUtils.readProtobuffDataStore(
-				Person.class, 
-				new FileSystemPath(fs, input.get(personPort))); 
-		
-		List<DocumentWithAuthors> documentWithAuthors = 
-				makeDocumentWithAuthors(documents, persons);
-		List<PersonWithDocuments> personWithDocuments = 
-				makePersonWithDocuments(documents, persons);
-		List<PersonAge> personAge = makePersonAge(persons);
-
-		IOUtils.writeProtobuffDataStore(documentWithAuthors, 
-				new FileSystemPath(fs, output.get(documentWithAuthorsPort)));
-		IOUtils.writeProtobuffDataStore(personWithDocuments, 
-				new FileSystemPath(fs, output.get(personWithDocumentsPort)));
-		IOUtils.writeProtobuffDataStore(personAge, 
-				new FileSystemPath(fs, output.get(personAgePort)));
-	}
-	
-	private static List<DocumentWithAuthors> makeDocumentWithAuthors(
-			List<Document> documents, List<Person> persons){
-		List<DocumentWithAuthors> list = new ArrayList<DocumentWithAuthors>();
-		for(Document d: documents){
-			List<Person> authors = new ArrayList<Person>();
-			for(int authorId: d.getAuthorIdsList()){
-				Person author = getPerson(persons, authorId);
-				authors.add(author);
-			}
-			list.add(DocumentWithAuthors.newBuilder()
-					.setId(d.getId())
-					.setTitle(d.getTitle())
-					.addAllAuthors(authors)
-					.build());
-		}
-		return list;
-	}
-	
-	private static Person getPerson(List<Person> persons, int id){
-		for(Person p: persons){
-			if(p.getId() == id){
-				return p;
-			}
-		}
-		throw new RuntimeException(
-				String.format("Person with id=%d not found", id));
-	}
-	
-	private static List<PersonWithDocuments> makePersonWithDocuments(
-			List<Document> documents, List<Person> persons){
-		List<PersonWithDocuments> list = new ArrayList<PersonWithDocuments>();
-		for(Person p: persons){
-			List<PersonWithDocuments.Document> personDocs = 
-					new ArrayList<PersonWithDocuments.Document>();
-			for(Document d: documents){
-				for(int authorId: d.getAuthorIdsList()){
-					if(p.getId() == authorId){
-						personDocs.add(PersonWithDocuments.Document.newBuilder()
-								.setId(d.getId())
-								.setTitle(d.getTitle()).build());
-						break;
-					}
-				}
-			}
-			list.add(PersonWithDocuments.newBuilder()
-					.setId(p.getId())
-					.addAllDocuments(personDocs)
-					.build());
-		}
-		return list;
-	}
-	
-	private static List<PersonAge> makePersonAge(List<Person> persons){
-		List<PersonAge> personAge = new ArrayList<PersonAge>();
-		for(Person p: persons){
-			personAge.add(PersonAge.newBuilder().setAge(p.getAge()).build());
-		}
-		return personAge;
-	}
-	
-//	private <T extends GeneratedMessage> List<T> readDataStore(Class<T> clazz,
-//			FileSystem fs, Path path) throws IOException{
-//		DataStoreReaderIterator<T> i = new DataStoreReaderIterator<T>(
-//				new FileSystemPath(fs, path), new ProtoBuffSchema<T>(clazz));
-//		List<T> elems = new ArrayList<T>();
-//		while(i.hasNext()){
-//			elems.add(i.next());
-//		}
-//		return elems;
-//	}
-	
-//	private <T extends GeneratedMessage> List<T> readDataStore(Class<T> clazz,
-//			FileSystem fs, Path path) throws IOException{
-//		GenericProtoBuffIteratorBuilder<T> builder = 
-//				new GenericProtoBuffIteratorBuilder<T>(clazz);
-//		List<T> elems = new ArrayList<T>();
-//		ClosableIterator<T> docI = builder.build(fs, path);
-//		while(docI.hasNext()){
-//			elems.add(docI.next());
-//		}
-//		return elems;
-//	}
-	
-//	private <T extends Message> void writeDataStore(
-//			List<T> elements, Path path, FileSystem fs) 
-//					throws IOException{
-//		DataStoreWriter<T> writer = new StandardDataStoreWriter<T>(
-//				new FileSystemPath(fs, path));
-//		for(T i: elements){
-//			writer.append(i);
-//		}
-//		writer.close();
-//	}
-
-//	private <T extends GeneratedMessage> void writeDataStore(
-//			List<T> elements, Path path, FileSystem fs) 
-//					throws IOException{
-//		SequenceFileDataStoreWriter writer = new SequenceFileDataStoreWriter(
-//				path.toString(), fs);
-//		for(T i: elements){
-//			writer.append(i.toByteArray());
-//		}
-//		writer.close();
-//	}
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/PersonCloner.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/PersonCloner.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/java/PersonCloner.java	(nonexistent)
@@ -1,91 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.java;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.java.PortBindings;
-import eu.dnetlib.iis.core.java.Process;
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-import eu.dnetlib.iis.core.java.io.protobuf.IOUtils;
-import eu.dnetlib.iis.core.java.porttype.PortType;
-import eu.dnetlib.iis.core.java.porttype.ProtoBuffPortType;
-
-/** Processes input files in a specific way
- * @author Mateusz Kobos
- */
-public class PersonCloner implements Process {
-	
-	private final static String personPort = "person";
-	private final static int defaultCopies = 2;
-	private final static String copiesParam = "copies";
-	
-	@Override
-	public Map<String, PortType> getInputPorts() {
-		return createInputPorts();
-	}
-	
-	@Override
-	public Map<String, PortType> getOutputPorts() {
-		return createOutputPorts();
-	}
-
-	private static HashMap<String, PortType> createInputPorts(){
-		HashMap<String, PortType> inputPorts = 
-				new HashMap<String, PortType>();
-		inputPorts.put(personPort, 
-				new ProtoBuffPortType<Person>(Person.class));
-		return inputPorts;
-	}
-		
-	private static HashMap<String, PortType> createOutputPorts(){
-		HashMap<String, PortType> outputPorts = 
-				new HashMap<String, PortType>();
-		outputPorts.put(personPort, 
-				new ProtoBuffPortType<Person>(Person.class));
-		return outputPorts;	
-	}
-	
-	@Override
-	public void run(PortBindings portBindings, Configuration conf,
-			Map<String, String> parameters)	throws IOException{
-		Map<String, Path> input = portBindings.getInput();
-		Map<String, Path> output = portBindings.getOutput();
-		
-		int copies = defaultCopies;
-		if(parameters.containsKey(copiesParam)){
-			copies = Integer.parseInt(parameters.get(copiesParam));
-		}
-		FileSystem fs = FileSystem.get(conf);
-		
-		List<Person> personsIn = IOUtils.readProtobuffDataStore(
-				Person.class, 
-				new FileSystemPath(fs, input.get(personPort))); 
-		
-		List<Person> personsOut = clone(personsIn, copies);
-
-		IOUtils.writeProtobuffDataStore(personsOut, 
-				new FileSystemPath(fs, output.get(personPort)));
-	}
-	
-	private static List<Person> clone(List<Person> persons, int copies){
-		List<Person> list = new ArrayList<Person>();
-		for(int i = 0; i < copies; i++){
-			for(Person p: persons){
-				list.add(Person.newBuilder()
-						.setId(p.getId())
-						.setName(p.getName())
-						.setAge(p.getAge())
-						.build());
-			}
-		}
-		return list;
-	}
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/package-info.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/package-info.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/package-info.java	(nonexistent)
@@ -1,4 +0,0 @@
-/**
- * Contains deprecated code for data stores based on protocol buffers
- */
-package eu.dnetlib.iis.core.examples.protobuf;
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/StandardDataStoreExamples.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/StandardDataStoreExamples.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/StandardDataStoreExamples.java	(nonexistent)
@@ -1,251 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentProto.Document;
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments;
-
-@Deprecated
-public class StandardDataStoreExamples {
-	
-	static String bookTitleExtra = "An extraordinary book";
-	static String bookTitleBasics = "Basics of the basics";
-	static String bookTitleInteresting = "Interesting stuff";
-	static String bookTitleMoreInteresting = "Even more of interesting stuff";
-	static String personDrWho = "Dr. Who";
-	
-	
-	/**
-	 * Sample data on some documents
-	 */
-	public static List<Document> getDocument(){
-		ArrayList<Document> list = new ArrayList<Document>();
-		list.add(Document.newBuilder()
-				.setId(20)
-				.setTitle(bookTitleExtra)
-				.addAuthorIds(1).addAuthorIds(20)
-				.build());
-		list.add(Document.newBuilder()
-				.setId(1)
-				.setTitle(bookTitleBasics)
-				.addAuthorIds(10).addAuthorIds(6).addAuthorIds(1)
-				.build());
-		list.add(Document.newBuilder()
-				.setId(2)
-				.setTitle(bookTitleInteresting)
-				.build());
-		list.add(Document.newBuilder()
-				.setId(6)
-				.setTitle(bookTitleMoreInteresting)
-				.addAuthorIds(1).addAuthorIds(6)
-				.build());
-		return list;
-	}
-	
-	/**
-	 * Sample data on some persons
-	 */
-	public static List<Person> getPerson(){
-		return getPersonRepeated(1);
-	}
-
-	/**
-	 * Similar to {@link getPerson()}, but the records are repeated a 
-	 * couple of times.
-	 * @param copies number of times the records are repeated
-	 */
-	public static List<Person> getPersonRepeated(int copies){
-		ArrayList<Person> list = new ArrayList<Person>();
-		for(int i = 0; i < copies; i++){
-			list.add(Person.newBuilder()
-					.setId(1)
-					.setName(personDrWho)
-					.setAge(2349)
-					.build());
-			list.add(Person.newBuilder()
-					.setId(10)
-					.setName("Mikael Blomkvist")
-					.setAge(46)
-					.build());
-			list.add(Person.newBuilder()
-					.setId(5)
-					.setName("Daniel Craig")
-					.setAge(40)
-					.build());
-			list.add(Person.newBuilder()
-					.setId(20)
-					.setName("Stieg Larsson")
-					.setAge(50)
-					.build());
-			list.add(Person.newBuilder()
-					.setId(6)
-					.setName("Lisbeth Salander")
-					.setAge(12)
-					.build());
-		}
-		return list;
-	}
-	
-	/**
-	 * Gets person age objects.
-	 * @param copies number of times the records are repeated
-	 */
-	public static List<PersonAge> getPersonAgeRepeated(int copies){
-		List<Person> persons = getPersonRepeated(copies);
-		List<PersonAge> personsAges = new ArrayList<PersonAge>(copies);
-		for (Person currentPerson : persons) {
-			PersonAge.Builder personAgeBuilder = PersonAge.newBuilder();
-			personAgeBuilder.setAge(currentPerson.getAge());
-			personsAges.add(personAgeBuilder.build());
-		}
-		return personsAges;
-		
-	}
-	
-	/**
-	 * @return age of each person contained in the output of the
-	 *  {@link getPerson()} 
-	 */
-	public static List<PersonAge> getPersonAge(){
-		ArrayList<PersonAge> list = 
-				new ArrayList<PersonAge>();
-		int[] age = new int[]{2349, 46, 40, 50, 12};
-		for(int i = 0; i < age.length; i++){
-			list.add(PersonAge.newBuilder().setAge(age[i]).build());
-		}
-		return list;
-	}
-	
-	/**
-	 * @return information about documents and their authors. This data comes 
-	 * from joining the data returned by 
-	 * {@link getPerson()} and {@link getDocument} 
-	 */
-	public static List<DocumentWithAuthors> getDocumentWithAuthors(){
-		ArrayList<DocumentWithAuthors> list = 
-				new ArrayList<DocumentWithAuthors>();
-		list.add(DocumentWithAuthors.newBuilder()
-				.setId(20)
-				.setTitle(bookTitleExtra)
-				.addAuthors(Person.newBuilder()
-						.setId(1)
-						.setName(personDrWho)
-						.setAge(2349)
-						.build())
-				.addAuthors(Person.newBuilder()
-						.setId(20)
-						.setName("Stieg Larsson")
-						.setAge(50)
-						.build())
-				.build());
-		list.add(DocumentWithAuthors.newBuilder()
-				.setId(1)
-				.setTitle(bookTitleBasics)
-				.addAuthors(Person.newBuilder()
-						.setId(10)
-						.setName("Mikael Blomkvist")
-						.setAge(46)
-						.build())
-				.addAuthors(Person.newBuilder()
-						.setId(6)
-						.setName("Lisbeth Salander")
-						.setAge(12)
-						.build())
-				.addAuthors(Person.newBuilder()
-						.setId(1)
-						.setName(personDrWho)
-						.setAge(2349)
-						.build())
-				.build());
-		list.add(DocumentWithAuthors.newBuilder()
-				.setId(2)
-				.setTitle(bookTitleInteresting)
-				.build());
-		list.add(DocumentWithAuthors.newBuilder()
-				.setId(6)
-				.setTitle(bookTitleMoreInteresting)
-				.addAuthors(Person.newBuilder()
-						.setId(1)
-						.setName(personDrWho)
-						.setAge(2349)
-						.build())
-				.addAuthors(Person.newBuilder()
-						.setId(6)
-						.setName("Lisbeth Salander")
-						.setAge(12)
-						.build())
-				.build());
-		return list;
-	}
-
-	/**
-	 * @return information about person and documents authored by them. 
-	 * This data comes from joining the data returned by 
-	 * {@link getPerson()} and {@link getDocument} 
-	 */
-	public static List<PersonWithDocuments> getPersonWithDocuments(){
-		ArrayList<PersonWithDocuments> list = 
-				new ArrayList<PersonWithDocuments>();
-		list.add(PersonWithDocuments.newBuilder()
-				.setId(1)
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(20)
-						.setTitle(bookTitleExtra))
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(1)
-						.setTitle(bookTitleBasics))
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(6)
-						.setTitle(bookTitleMoreInteresting))
-				.build());
-		list.add(PersonWithDocuments.newBuilder()
-				.setId(10)
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(1)
-						.setTitle(bookTitleBasics))
-				.build());
-		list.add(PersonWithDocuments.newBuilder()
-				.setId(5)
-				.build());
-		list.add(PersonWithDocuments.newBuilder()
-				.setId(20)
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(20)
-						.setTitle(bookTitleExtra))
-				.build());
-		list.add(PersonWithDocuments.newBuilder()
-				.setId(6)
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(1)
-						.setTitle(bookTitleBasics))
-				.addDocuments(PersonWithDocuments.Document.newBuilder()
-						.setId(6)
-						.setTitle(bookTitleMoreInteresting))
-				.build());
-		return list;
-	}
-	
-	/**
-	 * Write some of the example data stores to the current directory.
-	 * 
-	 * This is a code for generating data for some manual tests.
-	 */
-/*	public static void main(String[] args) throws IOException, URISyntaxException{
-		FileSystem fs = new RawLocalFileSystem();
-		fs.initialize(new URI("file:///"), new Configuration());
-		FileSystemPath path = new FileSystemPath(fs, new Path("document"));
-		IOUtils.writeDataStore(getDocument(), path);
-		List<Document> elements = IOUtils.readDataStore(Document.class, path);
-		for(Document e: elements){
-			System.out.println("document data:\n==============");
-			System.out.println(e.toString());
-		}
-		IOUtils.writeDataStore(getPerson(),
-				new FileSystemPath(fs, new Path("person")));
-		
-	}*/
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerMapper.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerMapper.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerMapper.java	(nonexistent)
@@ -1,36 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.javamapreduce;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapreduce.Mapper;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.javamapreduce.protobuf.MapRedUtils;
-
-/**
- * @author Mateusz Kobos
- */
-public class PersonClonerMapper extends Mapper<Text, BytesWritable, Text, BytesWritable> {
-	
-	private int copiesCount;
-	
-	/** This is the place you can access map-reduce workflow node parameters */
-	@Override
-	protected void setup(Context context) throws IOException,
-			InterruptedException {
-		copiesCount = Integer.parseInt(
-				context.getConfiguration().get("copiesCount"));
-	}
-	
-	@Override
-	public void map(Text key, BytesWritable value, Context context)
-			throws IOException, InterruptedException {
-		Person person = MapRedUtils.parse(Person.class, key, value);
-		for(int i = 0; i < copiesCount; i++){
-			MapRedUtils.write(context, person);
-		}
-	}
-
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/MultipleOutputPersonProcessor.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/MultipleOutputPersonProcessor.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/MultipleOutputPersonProcessor.java	(nonexistent)
@@ -1,68 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.javamapreduce;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapreduce.Mapper;
-import org.apache.hadoop.mapreduce.lib.output.MultipleOutputs;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.javamapreduce.protobuf.MapRedUtils;
-
-/**
- * Mapper writing to multiple output.
- * Clones person objects and additionally writes age to second output.
- * Number of objects written to both outputs are defined by copiesCount property.
- * @author mhorst
- *
- */
-public class MultipleOutputPersonProcessor extends Mapper<Text, BytesWritable, Text, BytesWritable> {/*-?|2013-01-07 Cermine integration and MR multiple in-out|mafju|c3|?*/
-	
-	private int copiesCount;
-	private String namedOutputPerson;
-	private String namedOutputAge;
-	
-	@SuppressWarnings("rawtypes")
-	private MultipleOutputs mos = null;
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#setup(org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@SuppressWarnings({ "rawtypes", "unchecked" })
-	@Override
-	protected void setup(Context context) throws IOException,
-			InterruptedException {
-		this.copiesCount = Integer.parseInt(
-				context.getConfiguration().get("copiesCount"));
-		this.namedOutputPerson = context.getConfiguration().get("named.output.person");
-		this.namedOutputAge = context.getConfiguration().get("named.output.age");
-		this.mos = new MultipleOutputs(context);
-	}
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#cleanup(org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@Override
-    public void cleanup(Context context) throws IOException, InterruptedException {
-        mos.close();
-    }
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#map(KEYIN, VALUEIN, org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@Override
-	public void map(Text key, BytesWritable value, Context context)
-			throws IOException, InterruptedException {
-		Person person = MapRedUtils.parse(Person.class, key, value);
-		for(int i = 0; i < copiesCount; i++){
-			MapRedUtils.write(mos, namedOutputPerson, person);
-//			writing metrics to other output
-			PersonAge.Builder personAgeBuilder = PersonAge.newBuilder();
-			personAgeBuilder.setAge(person.getAge());
-			MapRedUtils.write(mos, namedOutputAge, personAgeBuilder.build());
-		}
-	}
-
-}

Property changes on: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/MultipleOutputPersonProcessor.java
___________________________________________________________________
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerReducer.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerReducer.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonClonerReducer.java	(nonexistent)
@@ -1,27 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.javamapreduce;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapreduce.Reducer;
-
-/**
- * @author Mateusz Kobos
- */
-public class PersonClonerReducer extends Reducer<Text, BytesWritable, Text, BytesWritable> {
-	
-	private final Text emptyText = new Text("");
-	
-	/**
-	 * Copy the data without introducing any changes
-	 */
-	@Override
-	public void reduce(Text key, Iterable<BytesWritable> values, Context context)
-			throws IOException, InterruptedException {
-		for(BytesWritable value: values){
-			context.write(emptyText, value);
-		}
-	}
-
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonByAgeSplitter.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonByAgeSplitter.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonByAgeSplitter.java	(nonexistent)
@@ -1,62 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf.javamapreduce;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapreduce.Mapper;
-import org.apache.hadoop.mapreduce.lib.output.MultipleOutputs;
-
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.javamapreduce.protobuf.MapRedUtils;
-
-/**
- * Mapper writing to multiple output splitting data by age.
- * @author mhorst
- *
- */
-public class PersonByAgeSplitter extends Mapper<Text, BytesWritable, Text, BytesWritable> {
-	
-	private String namedOutputPersonEvenAge;
-	private String namedOutputPersonOddAge;
-	
-	@SuppressWarnings("rawtypes")
-	private MultipleOutputs mos = null;
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#setup(org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@SuppressWarnings({ "rawtypes", "unchecked" })
-	@Override
-	protected void setup(Context context) throws IOException,
-			InterruptedException {
-		this.namedOutputPersonEvenAge = context.getConfiguration().get(
-				"named.output.person.age.even");
-		this.namedOutputPersonOddAge = context.getConfiguration().get(
-				"named.output.person.age.odd");
-		this.mos = new MultipleOutputs(context);
-	}
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#cleanup(org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@Override
-    public void cleanup(Context context) throws IOException, InterruptedException {
-        mos.close();
-    }
-	
-	/* (non-Javadoc)
-	 * @see org.apache.hadoop.mapreduce.Mapper#map(KEYIN, VALUEIN, org.apache.hadoop.mapreduce.Mapper.Context)
-	 */
-	@Override
-	public void map(Text key, BytesWritable value, Context context)
-			throws IOException, InterruptedException {
-		Person person = MapRedUtils.parse(Person.class, key, value);
-		if (person.getAge()%2==0) {
-			MapRedUtils.write(mos, namedOutputPersonEvenAge, person);	
-		} else {
-			MapRedUtils.write(mos, namedOutputPersonOddAge, person);
-		}
-	}
-
-}

Property changes on: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/PersonByAgeSplitter.java
___________________________________________________________________
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/WorkflowTest.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/WorkflowTest.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/WorkflowTest.java	(nonexistent)
@@ -1,159 +0,0 @@
-package eu.dnetlib.iis.core.examples.protobuf;
-
-import java.io.IOException;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.oozie.client.OozieClientException;
-import org.junit.Test;
-import org.junit.experimental.categories.Category;
-
-import eu.dnetlib.iis.IntegrationTest;
-import eu.dnetlib.iis.core.AbstractWorkflowTestCase;
-import eu.dnetlib.iis.core.RemoteOozieAppManager;
-import eu.dnetlib.iis.core.TestsIOUtils;
-import eu.dnetlib.iis.core.WorkflowConfiguration;
-import eu.dnetlib.iis.core.examples.protobuf.StandardDataStoreExamples;
-import eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-import eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments;
-
-
-/**
- * Tests of various types of workflow nodes
- * @author Mateusz Kobos
- */
-@Deprecated
-@Category(IntegrationTest.class)
-public class WorkflowTest extends AbstractWorkflowTestCase {
-
-	@Test 
-	public void testJavaNodeWithClonerWithPassingParameter() 
-			throws IOException, OozieClientException{
-		RemoteOozieAppManager appManager = 
-				runWorkflow("eu/dnetlib/iis/core/examples/protobuf/java/cloner/oozie_app");
-		
-		List<Person> person = appManager.readProtoBuffDataStoreFromWorkingDir(
-				Person.class, "cloner/person");
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(3),
-				person);		
-	}
-	
-	@Test
-	public void testJavaNodeWithJoinTask() throws Exception{
-		RemoteOozieAppManager appManager = 
-				runWorkflow("eu/dnetlib/iis/core/examples/protobuf/java/joiner/oozie_app");
-		
-		List<DocumentWithAuthors> documentWithAuthors = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					DocumentWithAuthors.class, 
-					"data_processor/document_with_authors");
-		List<PersonWithDocuments> personWithDocuments = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					PersonWithDocuments.class, 
-					"data_processor/person_with_documents");
-		List<PersonAge> personAge =
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					PersonAge.class, 
-					"data_processor/person_age");
-
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getDocumentWithAuthors(),
-				documentWithAuthors);
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonWithDocuments(),
-				personWithDocuments);	
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonAge(),
-				personAge);	
-	}
-	
-	@Test 
-	public void testSubworkflowWithCloners() throws IOException, OozieClientException{
-		RemoteOozieAppManager appManager = 
-				runWorkflow("eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app");
-		
-		List<Person> person = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					Person.class, "cloner2/person");
-	
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(48),
-				person);		
-	}
-
-	@Test
-	public void testMapReduceWithCloners() throws IOException, OozieClientException{
-		RemoteOozieAppManager appManager = 
-				runWorkflow("eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner/oozie_app");
-		
-		List<Person> person = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					Person.class, "cloner/person");
-	
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(4),
-				person);		
-	}
-	
-	@Test 
-	public void testMapReduceWithClonersWithoutReducer() 
-			throws IOException, OozieClientException{
-		RemoteOozieAppManager appManager = 
-				runWorkflow("eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_without_reducer/oozie_app");
-		
-		List<Person> person = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					Person.class, "cloner/person");
-	
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(4),person);		
-	}
-
-	@Test 
-	public void testMapReduceWithClonersWithMultipleOutput() 
-			throws IOException, OozieClientException{
-		Properties jobProps = new Properties();
-		jobProps.load(Thread.currentThread().getContextClassLoader().getResourceAsStream(
-				"eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/job.properties"));
-		RemoteOozieAppManager appManager = 
-			runWorkflow("eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/oozie_app", 
-					new WorkflowConfiguration().setJobProps(jobProps));
-		
-		List<Person> person = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					Person.class, "cloner/person");
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(4), 
-				person);		
-		
-		List<PersonAge> personAge = 
-				appManager.readProtoBuffDataStoreFromWorkingDir(
-						PersonAge.class, "mr_cloner/age");
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonAgeRepeated(2), 
-				personAge);
-	}
-	
-	@Test 
-	public void testMapReduceWithClonersWithMultipleSameTypeInputAndOutput() 
-			throws IOException, OozieClientException{
-		Properties jobProps = new Properties();
-		jobProps.load(Thread.currentThread().getContextClassLoader().getResourceAsStream(
-				"eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/job.properties"));
-		RemoteOozieAppManager appManager = 
-			runWorkflow("eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/oozie_app", 
-					new WorkflowConfiguration().setJobProps(jobProps));
-		
-		List<Person> person = 
-			appManager.readProtoBuffDataStoreFromWorkingDir(
-					Person.class, "cloner/person");
-	
-		TestsIOUtils.assertEqualSets(
-				StandardDataStoreExamples.getPersonRepeated(4),
-				person);
-		
-	}
-}
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonAgeProto.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonAgeProto.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonAgeProto.java	(nonexistent)
@@ -1,390 +0,0 @@
-// Generated by the protocol buffer compiler.  DO NOT EDIT!
-// source: person_age.proto
-
-package eu.dnetlib.iis.core.examples.protobuf.generated;
-
-public final class PersonAgeProto {
-  private PersonAgeProto() {}
-  public static void registerAllExtensions(
-      com.google.protobuf.ExtensionRegistry registry) {
-  }
-  public interface PersonAgeOrBuilder
-      extends com.google.protobuf.MessageOrBuilder {
-    
-    // optional int32 age = 1;
-    boolean hasAge();
-    int getAge();
-  }
-  public static final class PersonAge extends
-      com.google.protobuf.GeneratedMessage
-      implements PersonAgeOrBuilder {
-    // Use PersonAge.newBuilder() to construct.
-    private PersonAge(Builder builder) {
-      super(builder);
-    }
-    private PersonAge(boolean noInit) {}
-    
-    private static final PersonAge defaultInstance;
-    public static PersonAge getDefaultInstance() {
-      return defaultInstance;
-    }
-    
-    public PersonAge getDefaultInstanceForType() {
-      return defaultInstance;
-    }
-    
-    public static final com.google.protobuf.Descriptors.Descriptor
-        getDescriptor() {
-      return eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.internal_static_proto_iis_PersonAge_descriptor;
-    }
-    
-    protected com.google.protobuf.GeneratedMessage.FieldAccessorTable
-        internalGetFieldAccessorTable() {
-      return eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.internal_static_proto_iis_PersonAge_fieldAccessorTable;
-    }
-    
-    private int bitField0_;
-    // optional int32 age = 1;
-    public static final int AGE_FIELD_NUMBER = 1;
-    private int age_;
-    public boolean hasAge() {
-      return ((bitField0_ & 0x00000001) == 0x00000001);
-    }
-    public int getAge() {
-      return age_;
-    }
-    
-    private void initFields() {
-      age_ = 0;
-    }
-    private byte memoizedIsInitialized = -1;
-    public final boolean isInitialized() {
-      byte isInitialized = memoizedIsInitialized;
-      if (isInitialized != -1) return isInitialized == 1;
-      
-      memoizedIsInitialized = 1;
-      return true;
-    }
-    
-    public void writeTo(com.google.protobuf.CodedOutputStream output)
-                        throws java.io.IOException {
-      getSerializedSize();
-      if (((bitField0_ & 0x00000001) == 0x00000001)) {
-        output.writeInt32(1, age_);
-      }
-      getUnknownFields().writeTo(output);
-    }
-    
-    private int memoizedSerializedSize = -1;
-    public int getSerializedSize() {
-      int size = memoizedSerializedSize;
-      if (size != -1) return size;
-    
-      size = 0;
-      if (((bitField0_ & 0x00000001) == 0x00000001)) {
-        size += com.google.protobuf.CodedOutputStream
-          .computeInt32Size(1, age_);
-      }
-      size += getUnknownFields().getSerializedSize();
-      memoizedSerializedSize = size;
-      return size;
-    }
-    
-    private static final long serialVersionUID = 0L;
-    @java.lang.Override
-    protected java.lang.Object writeReplace()
-        throws java.io.ObjectStreamException {
-      return super.writeReplace();
-    }
-    
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        com.google.protobuf.ByteString data)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        com.google.protobuf.ByteString data,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data, extensionRegistry)
-               .buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(byte[] data)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        byte[] data,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data, extensionRegistry)
-               .buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(java.io.InputStream input)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        java.io.InputStream input,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input, extensionRegistry)
-               .buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseDelimitedFrom(java.io.InputStream input)
-        throws java.io.IOException {
-      Builder builder = newBuilder();
-      if (builder.mergeDelimitedFrom(input)) {
-        return builder.buildParsed();
-      } else {
-        return null;
-      }
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseDelimitedFrom(
-        java.io.InputStream input,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws java.io.IOException {
-      Builder builder = newBuilder();
-      if (builder.mergeDelimitedFrom(input, extensionRegistry)) {
-        return builder.buildParsed();
-      } else {
-        return null;
-      }
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        com.google.protobuf.CodedInputStream input)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.PersonAgeProto.PersonAge parseFrom(
-        com.google.protobuf.CodedInputStream input,
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Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonWithDocumentsProto.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonWithDocumentsProto.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonWithDocumentsProto.java	(nonexistent)
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-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
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-        com.google.protobuf.CodedInputStream input,
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-      
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-        return this;
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-      public Builder setDocuments(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder builderForValue) {
-        if (documentsBuilder_ == null) {
-          ensureDocumentsIsMutable();
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-          documentsBuilder_.setMessage(index, builderForValue.build());
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-        return this;
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-      public Builder addDocuments(eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document value) {
-        if (documentsBuilder_ == null) {
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-            throw new NullPointerException();
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-          ensureDocumentsIsMutable();
-          documents_.add(value);
-          onChanged();
-        } else {
-          documentsBuilder_.addMessage(value);
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-        return this;
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-      public Builder addDocuments(
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-        if (documentsBuilder_ == null) {
-          if (value == null) {
-            throw new NullPointerException();
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-          documentsBuilder_.addMessage(index, value);
-        }
-        return this;
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-      public Builder addDocuments(
-          eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder builderForValue) {
-        if (documentsBuilder_ == null) {
-          ensureDocumentsIsMutable();
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-          onChanged();
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-          documentsBuilder_.addMessage(builderForValue.build());
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-        return this;
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-      public Builder addDocuments(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder builderForValue) {
-        if (documentsBuilder_ == null) {
-          ensureDocumentsIsMutable();
-          documents_.add(index, builderForValue.build());
-          onChanged();
-        } else {
-          documentsBuilder_.addMessage(index, builderForValue.build());
-        }
-        return this;
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-      public Builder addAllDocuments(
-          java.lang.Iterable<? extends eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document> values) {
-        if (documentsBuilder_ == null) {
-          ensureDocumentsIsMutable();
-          super.addAll(values, documents_);
-          onChanged();
-        } else {
-          documentsBuilder_.addAllMessages(values);
-        }
-        return this;
-      }
-      public Builder clearDocuments() {
-        if (documentsBuilder_ == null) {
-          documents_ = java.util.Collections.emptyList();
-          bitField0_ = (bitField0_ & ~0x00000002);
-          onChanged();
-        } else {
-          documentsBuilder_.clear();
-        }
-        return this;
-      }
-      public Builder removeDocuments(int index) {
-        if (documentsBuilder_ == null) {
-          ensureDocumentsIsMutable();
-          documents_.remove(index);
-          onChanged();
-        } else {
-          documentsBuilder_.remove(index);
-        }
-        return this;
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder getDocumentsBuilder(
-          int index) {
-        return getDocumentsFieldBuilder().getBuilder(index);
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.DocumentOrBuilder getDocumentsOrBuilder(
-          int index) {
-        if (documentsBuilder_ == null) {
-          return documents_.get(index);  } else {
-          return documentsBuilder_.getMessageOrBuilder(index);
-        }
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-      public java.util.List<? extends eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.DocumentOrBuilder> 
-           getDocumentsOrBuilderList() {
-        if (documentsBuilder_ != null) {
-          return documentsBuilder_.getMessageOrBuilderList();
-        } else {
-          return java.util.Collections.unmodifiableList(documents_);
-        }
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder addDocumentsBuilder() {
-        return getDocumentsFieldBuilder().addBuilder(
-            eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.getDefaultInstance());
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder addDocumentsBuilder(
-          int index) {
-        return getDocumentsFieldBuilder().addBuilder(
-            index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.getDefaultInstance());
-      }
-      public java.util.List<eu.dnetlib.iis.core.examples.protobuf.generated.PersonWithDocumentsProto.PersonWithDocuments.Document.Builder> 
-           getDocumentsBuilderList() {
-        return getDocumentsFieldBuilder().getBuilderList();
-      }
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Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonProto.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonProto.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/PersonProto.java	(nonexistent)
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Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentProto.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentProto.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentProto.java	(nonexistent)
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Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentWithAuthorsProto.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentWithAuthorsProto.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/protobuf/generated/DocumentWithAuthorsProto.java	(nonexistent)
@@ -1,781 +0,0 @@
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-    public java.util.List<eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person> getAuthorsList() {
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-      return true;
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-      for (int i = 0; i < authors_.size(); i++) {
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-      return newBuilder().mergeFrom(data).buildParsed();
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-        com.google.protobuf.ByteString data,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data, extensionRegistry)
-               .buildParsed();
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-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data).buildParsed();
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-    public static eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors parseFrom(
-        byte[] data,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws com.google.protobuf.InvalidProtocolBufferException {
-      return newBuilder().mergeFrom(data, extensionRegistry)
-               .buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors parseFrom(java.io.InputStream input)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors parseFrom(
-        java.io.InputStream input,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input, extensionRegistry)
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-      Builder builder = newBuilder();
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-    public static eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors parseDelimitedFrom(
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-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws java.io.IOException {
-      Builder builder = newBuilder();
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-        return builder.buildParsed();
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-        com.google.protobuf.CodedInputStream input)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input).buildParsed();
-    }
-    public static eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors parseFrom(
-        com.google.protobuf.CodedInputStream input,
-        com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-        throws java.io.IOException {
-      return newBuilder().mergeFrom(input, extensionRegistry)
-               .buildParsed();
-    }
-    
-    public static Builder newBuilder() { return Builder.create(); }
-    public Builder newBuilderForType() { return newBuilder(); }
-    public static Builder newBuilder(eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors prototype) {
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-    }
-    public Builder toBuilder() { return newBuilder(this); }
-    
-    @java.lang.Override
-    protected Builder newBuilderForType(
-        com.google.protobuf.GeneratedMessage.BuilderParent parent) {
-      Builder builder = new Builder(parent);
-      return builder;
-    }
-    public static final class Builder extends
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-       implements eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthorsOrBuilder {
-      public static final com.google.protobuf.Descriptors.Descriptor
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-      // Construct using eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors.newBuilder()
-      private Builder() {
-        maybeForceBuilderInitialization();
-      }
-      
-      private Builder(BuilderParent parent) {
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-        title_ = "";
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-          return this;
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-      public Builder mergeFrom(eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors other) {
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-        if (other.hasId()) {
-          setId(other.getId());
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-        if (other.hasTitle()) {
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-          com.google.protobuf.CodedInputStream input,
-          com.google.protobuf.ExtensionRegistryLite extensionRegistry)
-          throws java.io.IOException {
-        com.google.protobuf.UnknownFieldSet.Builder unknownFields =
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-            this.getUnknownFields());
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-              onChanged();
-              return this;
-            default: {
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-                onChanged();
-                return this;
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-              break;
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-            case 18: {
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-              title_ = input.readBytes();
-              break;
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-            case 26: {
-              eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder subBuilder = eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.newBuilder();
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-        onChanged();
-        return this;
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-      public Builder clearId() {
-        bitField0_ = (bitField0_ & ~0x00000001);
-        id_ = 0;
-        onChanged();
-        return this;
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-      
-      // optional string title = 2;
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-      public Builder setTitle(String value) {
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-  bitField0_ |= 0x00000002;
-        title_ = value;
-        onChanged();
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-      public Builder clearTitle() {
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-        onChanged();
-        return this;
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-        bitField0_ |= 0x00000002;
-        title_ = value;
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-      private java.util.List<eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person> authors_ =
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-      private void ensureAuthorsIsMutable() {
-        if (!((bitField0_ & 0x00000004) == 0x00000004)) {
-          authors_ = new java.util.ArrayList<eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person>(authors_);
-          bitField0_ |= 0x00000004;
-         }
-      }
-      
-      private com.google.protobuf.RepeatedFieldBuilder<
-          eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.PersonOrBuilder> authorsBuilder_;
-      
-      public java.util.List<eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person> getAuthorsList() {
-        if (authorsBuilder_ == null) {
-          return java.util.Collections.unmodifiableList(authors_);
-        } else {
-          return authorsBuilder_.getMessageList();
-        }
-      }
-      public int getAuthorsCount() {
-        if (authorsBuilder_ == null) {
-          return authors_.size();
-        } else {
-          return authorsBuilder_.getCount();
-        }
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person getAuthors(int index) {
-        if (authorsBuilder_ == null) {
-          return authors_.get(index);
-        } else {
-          return authorsBuilder_.getMessage(index);
-        }
-      }
-      public Builder setAuthors(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person value) {
-        if (authorsBuilder_ == null) {
-          if (value == null) {
-            throw new NullPointerException();
-          }
-          ensureAuthorsIsMutable();
-          authors_.set(index, value);
-          onChanged();
-        } else {
-          authorsBuilder_.setMessage(index, value);
-        }
-        return this;
-      }
-      public Builder setAuthors(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder builderForValue) {
-        if (authorsBuilder_ == null) {
-          ensureAuthorsIsMutable();
-          authors_.set(index, builderForValue.build());
-          onChanged();
-        } else {
-          authorsBuilder_.setMessage(index, builderForValue.build());
-        }
-        return this;
-      }
-      public Builder addAuthors(eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person value) {
-        if (authorsBuilder_ == null) {
-          if (value == null) {
-            throw new NullPointerException();
-          }
-          ensureAuthorsIsMutable();
-          authors_.add(value);
-          onChanged();
-        } else {
-          authorsBuilder_.addMessage(value);
-        }
-        return this;
-      }
-      public Builder addAuthors(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person value) {
-        if (authorsBuilder_ == null) {
-          if (value == null) {
-            throw new NullPointerException();
-          }
-          ensureAuthorsIsMutable();
-          authors_.add(index, value);
-          onChanged();
-        } else {
-          authorsBuilder_.addMessage(index, value);
-        }
-        return this;
-      }
-      public Builder addAuthors(
-          eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder builderForValue) {
-        if (authorsBuilder_ == null) {
-          ensureAuthorsIsMutable();
-          authors_.add(builderForValue.build());
-          onChanged();
-        } else {
-          authorsBuilder_.addMessage(builderForValue.build());
-        }
-        return this;
-      }
-      public Builder addAuthors(
-          int index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder builderForValue) {
-        if (authorsBuilder_ == null) {
-          ensureAuthorsIsMutable();
-          authors_.add(index, builderForValue.build());
-          onChanged();
-        } else {
-          authorsBuilder_.addMessage(index, builderForValue.build());
-        }
-        return this;
-      }
-      public Builder addAllAuthors(
-          java.lang.Iterable<? extends eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person> values) {
-        if (authorsBuilder_ == null) {
-          ensureAuthorsIsMutable();
-          super.addAll(values, authors_);
-          onChanged();
-        } else {
-          authorsBuilder_.addAllMessages(values);
-        }
-        return this;
-      }
-      public Builder clearAuthors() {
-        if (authorsBuilder_ == null) {
-          authors_ = java.util.Collections.emptyList();
-          bitField0_ = (bitField0_ & ~0x00000004);
-          onChanged();
-        } else {
-          authorsBuilder_.clear();
-        }
-        return this;
-      }
-      public Builder removeAuthors(int index) {
-        if (authorsBuilder_ == null) {
-          ensureAuthorsIsMutable();
-          authors_.remove(index);
-          onChanged();
-        } else {
-          authorsBuilder_.remove(index);
-        }
-        return this;
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder getAuthorsBuilder(
-          int index) {
-        return getAuthorsFieldBuilder().getBuilder(index);
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.PersonOrBuilder getAuthorsOrBuilder(
-          int index) {
-        if (authorsBuilder_ == null) {
-          return authors_.get(index);  } else {
-          return authorsBuilder_.getMessageOrBuilder(index);
-        }
-      }
-      public java.util.List<? extends eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.PersonOrBuilder> 
-           getAuthorsOrBuilderList() {
-        if (authorsBuilder_ != null) {
-          return authorsBuilder_.getMessageOrBuilderList();
-        } else {
-          return java.util.Collections.unmodifiableList(authors_);
-        }
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder addAuthorsBuilder() {
-        return getAuthorsFieldBuilder().addBuilder(
-            eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.getDefaultInstance());
-      }
-      public eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder addAuthorsBuilder(
-          int index) {
-        return getAuthorsFieldBuilder().addBuilder(
-            index, eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.getDefaultInstance());
-      }
-      public java.util.List<eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person.Builder> 
-           getAuthorsBuilderList() {
-        return getAuthorsFieldBuilder().getBuilderList();
-      }
-      private com.google.protobuf.RepeatedFieldBuilder<
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-          getAuthorsFieldBuilder() {
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-                  ((bitField0_ & 0x00000004) == 0x00000004),
-                  getParentForChildren(),
-                  isClean());
-          authors_ = null;
-        }
-        return authorsBuilder_;
-      }
-      
-      // @@protoc_insertion_point(builder_scope:proto.iis.DocumentWithAuthors)
-    }
-    
-    static {
-      defaultInstance = new DocumentWithAuthors(true);
-      defaultInstance.initFields();
-    }
-    
-    // @@protoc_insertion_point(class_scope:proto.iis.DocumentWithAuthors)
-  }
-  
-  private static com.google.protobuf.Descriptors.Descriptor
-    internal_static_proto_iis_DocumentWithAuthors_descriptor;
-  private static
-    com.google.protobuf.GeneratedMessage.FieldAccessorTable
-      internal_static_proto_iis_DocumentWithAuthors_fieldAccessorTable;
-  
-  public static com.google.protobuf.Descriptors.FileDescriptor
-      getDescriptor() {
-    return descriptor;
-  }
-  private static com.google.protobuf.Descriptors.FileDescriptor
-      descriptor;
-  static {
-    java.lang.String[] descriptorData = {
-      "\n\033document_with_authors.proto\022\tproto.iis" +
-      "\032\014person.proto\"T\n\023DocumentWithAuthors\022\n\n" +
-      "\002id\030\001 \002(\005\022\r\n\005title\030\002 \001(\t\022\"\n\007authors\030\003 \003(" +
-      "\0132\021.proto.iis.PersonBF\n*eu.dnetlib.iis.e" +
-      "xamples.protobuf.generatedB\030DocumentWith" +
-      "AuthorsProto"
-    };
-    com.google.protobuf.Descriptors.FileDescriptor.InternalDescriptorAssigner assigner =
-      new com.google.protobuf.Descriptors.FileDescriptor.InternalDescriptorAssigner() {
-        public com.google.protobuf.ExtensionRegistry assignDescriptors(
-            com.google.protobuf.Descriptors.FileDescriptor root) {
-          descriptor = root;
-          internal_static_proto_iis_DocumentWithAuthors_descriptor =
-            getDescriptor().getMessageTypes().get(0);
-          internal_static_proto_iis_DocumentWithAuthors_fieldAccessorTable = new
-            com.google.protobuf.GeneratedMessage.FieldAccessorTable(
-              internal_static_proto_iis_DocumentWithAuthors_descriptor,
-              new java.lang.String[] { "Id", "Title", "Authors", },
-              eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors.class,
-              eu.dnetlib.iis.core.examples.protobuf.generated.DocumentWithAuthorsProto.DocumentWithAuthors.Builder.class);
-          return null;
-        }
-      };
-    com.google.protobuf.Descriptors.FileDescriptor
-      .internalBuildGeneratedFileFrom(descriptorData,
-        new com.google.protobuf.Descriptors.FileDescriptor[] {
-          eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.getDescriptor(),
-        }, assigner);
-  }
-  
-  // @@protoc_insertion_point(outer_class_scope)
-}
Index: modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/javamapreduce/PersonByAgeSplitter.java
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/javamapreduce/PersonByAgeSplitter.java	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/java/eu/dnetlib/iis/core/examples/javamapreduce/PersonByAgeSplitter.java	(nonexistent)
@@ -1,76 +0,0 @@
-package eu.dnetlib.iis.core.examples.javamapreduce;
-//package eu.dnetlib.iis.core.examples.mapreduce;
-//
-//import java.io.IOException;
-//
-//import org.apache.avro.mapred.AvroMapper;
-//import org.apache.avro.mapred.Pair;
-//import org.apache.hadoop.io.BytesWritable;
-//import org.apache.hadoop.io.Text;
-//import org.apache.hadoop.mapred.JobConf;
-//import org.apache.hadoop.mapreduce.Mapper;
-//import org.apache.hadoop.mapreduce.lib.output.MultipleOutputs;
-//
-//import eu.dnetlib.iis.io.MapRedUtils;
-//import eu.dnetlib.iis.core.examples.protobuf.generated.PersonProto.Person;
-//
-///**
-// * Mapper writing to multiple output splitting data by age.
-// * @author mhorst
-// *
-// */
-//public class AvroPersonByAgeSplitter extends AvroMapper<Person, Pair<String, Person>> {
-//	
-//	private String namedOutputPersonEvenAge;
-//	private String namedOutputPersonOddAge;
-//	
-//	@SuppressWarnings("rawtypes")
-//	private MultipleOutputs mos = null;
-//	
-//	/* (non-Javadoc)
-//	 * @see org.apache.hadoop.mapreduce.Mapper#setup(org.apache.hadoop.mapreduce.Mapper.Context)
-//	 */
-//	@SuppressWarnings({ "rawtypes", "unchecked" })
-//	@Override
-//	protected void setup(Context context) throws IOException,
-//			InterruptedException {
-//		this.namedOutputPersonEvenAge = conf.get(
-//				"named.output.person.age.even");
-//		this.namedOutputPersonOddAge = conf.get(
-//				"named.output.person.age.odd");
-//		this.mos = new MultipleOutputs(context);
-//	}
-//	
-//	/** This is the place you can access map-reduce workflow node parameters */
-//	@Override
-//	public void configure(JobConf jobConf) {
-//		this.namedOutputPersonEvenAge = jobConf.get(
-//				"named.output.person.age.even");
-//		this.namedOutputPersonOddAge = jobConf.get(
-//				"named.output.person.age.odd");
-//		this.mos = new MultipleOutputs(jobConf);
-//	}
-//	
-//	/* (non-Javadoc)
-//	 * @see org.apache.hadoop.mapreduce.Mapper#cleanup(org.apache.hadoop.mapreduce.Mapper.Context)
-//	 */
-//	@Override
-//    public void cleanup(Context context) throws IOException, InterruptedException {
-//        mos.close();
-//    }
-//	
-//	/* (non-Javadoc)
-//	 * @see org.apache.hadoop.mapreduce.Mapper#map(KEYIN, VALUEIN, org.apache.hadoop.mapreduce.Mapper.Context)
-//	 */
-//	@Override
-//	public void map(Text key, BytesWritable value, Context context)
-//			throws IOException, InterruptedException {
-//		Person person = MapRedUtils.parse(Person.class, key, value);
-//		if (person.getAge()%2==0) {
-//			MapRedUtils.write(mos, namedOutputPersonEvenAge, person);	
-//		} else {
-//			MapRedUtils.write(mos, namedOutputPersonOddAge, person);
-//		}
-//	}
-//
-//}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/cloner/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/cloner/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/cloner/oozie_app/workflow.xml	(nonexistent)
@@ -1,61 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="java-cloner">
-	<start to="data_producer" />
-	<action name="data_producer">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Operson=${workingDir}/data_producer/person</arg>
-			<arg>-Odocument=${workingDir}/data_producer/document</arg>
-		</java>
-		<ok to="cloner" />
-		<error to="fail" />
-	</action>
-	<action name="cloner">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner" />
-				<mkdir path="${nameNode}${workingDir}/cloner" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Iperson=${workingDir}/data_producer/person</arg>
-			<arg>-Operson=${workingDir}/cloner/person</arg>
-			<arg>-Pcopies=3</arg>
-		</java>
-		<ok to="end" />
-		<error to="fail" />
-	</action>
-	<kill name="fail">
-		<message>Unfortunately, the process failed -- error message:
-			[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-	<end name="end" />
-</workflow-app>
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/joiner/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/joiner/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/joiner/oozie_app/workflow.xml	(nonexistent)
@@ -1,64 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="java-joiner">
-    <start to="data_producer"/>
-    <action name="data_producer">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Operson=${workingDir}/data_producer/person</arg>
-            <arg>-Odocument=${workingDir}/data_producer/document</arg>
-        </java>
-        <ok to="data_processor"/>
-        <error to="fail"/>
-    </action>
-    <action name="data_processor">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_processor" />
-				<mkdir path="${nameNode}${workingDir}/data_processor" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.Joiner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${workingDir}/data_producer/person</arg>
-            <arg>-Idocument=${workingDir}/data_producer/document</arg>
-            <arg>-Odocument_with_authors=${workingDir}/data_processor/document_with_authors</arg>
-            <arg>-Operson_with_documents=${workingDir}/data_processor/person_with_documents</arg>
-            <arg>-Operson_age=${workingDir}/data_processor/person_age</arg>
-        </java>
-        <ok to="end"/>
-        <error to="fail"/>
-    </action>
-    <kill name="fail">
-        <message>Unfortunately, the process failed -- error message: [${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-    <end name="end"/>
-</workflow-app>
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/oozie_app/workflow.xml	(nonexistent)
@@ -1,59 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="line-by-line-copier">
-    <start to="producer"/>
-    <action name="producer">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/producer" />
-				<mkdir path="${nameNode}${workingDir}/producer" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.TextDataProducer</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Operson=${workingDir}/producer/person.csv</arg>
-            <arg>-Odocument=${workingDir}/producer/doc.csv</arg>
-        </java>
-        <ok to="copier"/>
-        <error to="fail"/>
-    </action>
-    <action name="copier">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/copier" />
-				<mkdir path="${nameNode}${workingDir}/copier" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.LineByLineCopier</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${workingDir}/producer/person.csv</arg>
-            <arg>-Idocument=${workingDir}/producer/doc.csv</arg>
-            <arg>-Operson_copy=${workingDir}/copier/person_copy.csv</arg>
-            <arg>-Odocument_copy=${workingDir}/copier/doc_copy.csv</arg>
-        </java>
-        <ok to="end"/>
-        <error to="fail"/>
-    </action>
-    <kill name="fail">
-        <message>Unfortunately, the process failed -- error message: [${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-    <end name="end"/>
-</workflow-app>
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/job.properties
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/job.properties	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier/job.properties	(nonexistent)
@@ -1,9 +0,0 @@
-nameNode=hdfs://localhost:8020
-jobTracker=localhost:8021
-queueName=default
-
-oozieAppDir=oozie_app
-sandboxDir=/user/${user.name}/iis_sandbox
-workingDir=${sandboxDir}/working_dir
-oozie.wf.application.path=${nameNode}${sandboxDir}/${oozieAppDir}
-
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/oozie-log4j.properties
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/oozie-log4j.properties	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/java/oozie-log4j.properties	(nonexistent)
@@ -1,37 +0,0 @@
-#
-# Licensed to the Apache Software Foundation (ASF) under one
-# or more contributor license agreements. See the NOTICE file
-# distributed with this work for additional information
-# regarding copyright ownership. The ASF licenses this file
-# to you under the Apache License, Version 2.0 (the
-# "License"); you may not use this file except in compliance
-# with the License. You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-#
-log4j.rootLogger=DEBUG, test
-
-log4j.appender.test=org.apache.log4j.ConsoleAppender
-log4j.appender.test.Target=System.out
-log4j.appender.test.layout=org.apache.log4j.PatternLayout
-log4j.appender.test.layout.ConversionPattern=%d{ABSOLUTE} %5p %c{1}:%L - %m%n
-
-log4j.appender.none=org.apache.log4j.varia.NullAppender
-
-log4j.logger.oozieops=OFF, none
-log4j.logger.oozieinstrumentation=OFF, none
-log4j.logger.oozieaudit=OFF, none
-
-log4j.logger.openjpa=INFO, test
-log4j.logger.org.apache.openjpa=INFO, test
-log4j.logger.org.apache.hadoop=INFO, test
-log4j.logger.com.yahoo.hadoop=INFO, test
-log4j.logger.org.mortbay=INFO, test
-log4j.logger.org.hsqldb=INFO, test
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_age.proto
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_age.proto	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_age.proto	(nonexistent)
@@ -1,8 +0,0 @@
-package proto.iis;
-
-option java_package = "eu.dnetlib.iis.examples.protobuf.generated";
-option java_outer_classname = "PersonAgeProto";
-
-message PersonAge {
-	optional int32 age = 1;
-}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_with_documents.proto
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_with_documents.proto	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person_with_documents.proto	(nonexistent)
@@ -1,15 +0,0 @@
-package proto.iis;
-
-option java_package = "eu.dnetlib.iis.examples.protobuf.generated";
-option java_outer_classname = "PersonWithDocumentsProto";
-
-message PersonWithDocuments {
-
-	message Document {
-		required int32 id = 1;
-		optional string title = 2;
-	}
-
-	required int32 id = 1;
-	repeated Document documents = 2;
-}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person.proto
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person.proto	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/person.proto	(nonexistent)
@@ -1,10 +0,0 @@
-package proto.iis;
-
-option java_package = "eu.dnetlib.iis.examples.protobuf.generated";
-option java_outer_classname = "PersonProto";
-
-message Person {
-	required int32 id = 1;
-	optional string name = 2;
-	optional int32 age = 3;
-}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/generate-classes.sh
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/generate-classes.sh	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/generate-classes.sh	(nonexistent)
@@ -1,8 +0,0 @@
-#!/bin/bash
-
-
-for file in *.proto
-do
-	echo generating java classes for file: $file
-	protoc --java_out=../../../../../../../java/ $file
-done

Property changes on: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/generate-classes.sh
___________________________________________________________________
Deleted: svn:executable
## -1 +0,0 ##
-*
\ No newline at end of property
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document.proto
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document.proto	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document.proto	(nonexistent)
@@ -1,10 +0,0 @@
-package proto.iis;
-
-option java_package = "eu.dnetlib.iis.examples.protobuf.generated";
-option java_outer_classname = "DocumentProto";
-
-message Document {
-	required int32 id = 1;
-	optional string title = 2;
-	repeated int32 authorIds = 3;
-}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document_with_authors.proto
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document_with_authors.proto	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/schemas/document_with_authors.proto	(nonexistent)
@@ -1,12 +0,0 @@
-package proto.iis;
-
-option java_package = "eu.dnetlib.iis.examples.protobuf.generated";
-option java_outer_classname = "DocumentWithAuthorsProto";
-
-import "person.proto";
-
-message DocumentWithAuthors {
-	required int32 id = 1;
-	optional string title = 2;
-	repeated Person authors = 3;
-}
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/workflow.xml	(nonexistent)
@@ -1,129 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="cloners_chain_with_subworkflows">
-    <start to="data_producer"/>
-    <action name="data_producer">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Operson=${workingDir}/data_producer/person</arg>
-            <arg>-Odocument=${workingDir}/data_producer/document</arg>
-        </java>
-        <ok to="cloner1"/>
-        <error to="fail"/>
-    </action>
-    <action name="cloner1">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner1" />
-				<mkdir path="${nameNode}${workingDir}/cloner1" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${workingDir}/data_producer/person</arg>
-            <arg>-Operson=${workingDir}/cloner1/person</arg>
-        </java>
-        <ok to="my_subworkflow"/>
-        <error to="fail"/>
-    </action>
-    <action name="my_subworkflow">
-        <sub-workflow>
-            <app-path>${wf:appPath()}/my_subworkflow</app-path>
-            <configuration>
-                <property>
-                    <name>jobTracker</name>
-                    <value>${jobTracker}</value>
-                </property>
-                <property>
-                    <name>nameNode</name>
-                    <value>${nameNode}</value>
-                </property>
-                <property>
-                    <name>queueName</name>
-                    <value>${queueName}</value>
-                </property>
-                <!-- Working directory of the subworkflow -->
-                <property>
-                    <name>workingDir</name>
-                    <value>${workingDir}/my_subworkflow/working_dir</value>
-                </property>
-                <!-- Input port "person" bound to given path -->
-                <property>
-                    <name>input_person</name>
-                    <value>${workingDir}/cloner1/person</value>
-                </property>
-                <!-- Output port "person" bound to given path -->
-                <property>
-                    <name>output_person</name>
-                    <value>${workingDir}/my_subworkflow/person</value>
-                </property>
-                <!-- parameters of this workflow node -->
-                <property>
-                	<name>param_copies_count</name>
-                	<value>3</value>
-                </property>
-            </configuration>
-        </sub-workflow>
-        <ok to="cloner2"/>
-        <error to="fail"/>
-    </action>
-    <action name="cloner2">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner2" />
-				<mkdir path="${nameNode}${workingDir}/cloner2" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${workingDir}/my_subworkflow/person</arg>
-            <arg>-Operson=${workingDir}/cloner2/person</arg>
-        </java>
-        <ok to="end"/>
-        <error to="fail"/>
-    </action>
-    <kill name="fail">
-        <message>Sub workflow failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-    <end name="end"/>
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/workflow.xml	(nonexistent)
@@ -1,75 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="my_subworkflow">
-    <start to="cloner1"/>
-    <action name="cloner1">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner1" />
-				<mkdir path="${nameNode}${workingDir}/cloner1" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${input_person}</arg>
-            <arg>-Operson=${workingDir}/cloner1/person</arg>
-        </java>
-        <ok to="my_subsubworkflow"/>
-        <error to="fail"/>
-    </action>
-    <action name="my_subsubworkflow">
-        <sub-workflow>
-            <app-path>${wf:appPath()}/my_subsubworkflow</app-path>
-            <configuration>
-                <property>
-                    <name>jobTracker</name>
-                    <value>${jobTracker}</value>
-                </property>
-                <property>
-                    <name>nameNode</name>
-                    <value>${nameNode}</value>
-                </property>
-                <property>
-                    <name>queueName</name>
-                    <value>${queueName}</value>
-                </property>
-                <!-- Working directory of the subworkflow -->
-                <property>
-                    <name>workingDir</name>
-                    <value>${workingDir}/my_subsubworkflow/working_dir</value>
-                </property>
-                <!-- Input port "person" bound to given path -->
-                <property>
-                    <name>input_person</name>
-                    <value>${workingDir}/cloner1/person</value>
-                </property>
-                <!-- Output port "person" bound to given path -->
-                <property>
-                    <name>output_person</name>
-                    <value>${output_person}</value>
-                </property>
-                <!-- parameters of this workflow node -->
-                <property>
-                	<name>param_copies_count</name>
-                	<value>${param_copies_count}</value>
-                </property>
-            </configuration>
-        </sub-workflow>
-        <ok to="end"/>
-        <error to="fail"/>
-    </action>
-    <kill name="fail">
-        <message>Unfortunately, the process failed -- error message: [${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-    <end name="end"/>
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/my_subsubworkflow/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/my_subsubworkflow/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners/oozie_app/my_subworkflow/my_subsubworkflow/workflow.xml	(nonexistent)
@@ -1,62 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="my_subsubworkflow">
-    <start to="cloner1"/>
-    <action name="cloner1">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
- 			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner1" />
-				<mkdir path="${nameNode}${workingDir}/cloner1" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${input_person}</arg>
-            <arg>-Operson=${workingDir}/cloner1/person</arg>
-            <arg>-Pcopies=${param_copies_count}</arg>
-        </java>
-        <ok to="cloner2"/>
-        <error to="fail"/>
-    </action>
-     <action name="cloner2">
-        <java>
-            <job-tracker>${jobTracker}</job-tracker>
-            <name-node>${nameNode}</name-node>
- 			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner2" />
-				<mkdir path="${nameNode}${workingDir}/cloner2" />
-			</prepare>
-            <configuration>
-                <property>
-                    <name>mapred.job.queue.name</name>
-                    <value>${queueName}</value>
-                </property>
-            </configuration>
-            <!-- This is simple wrapper for the Java code -->
-            <main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-            <!-- The business Java code that gets to be executed -->
-            <arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-            <!-- All input and output ports have to be bound to paths in 
-            HDFS, working directory has to be specified as well -->
-            <arg>-Iperson=${workingDir}/cloner1/person</arg>
-            <arg>-Operson=${output_person}</arg>
-        </java>
-        <ok to="end"/>
-        <error to="fail"/>
-    </action>
-    <kill name="fail">
-        <message>Unfortunately, the process failed -- error message: [${wf:errorMessage(wf:lastErrorNode())}]</message>
-    </kill>
-    <end name="end"/>
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/oozie_app/workflow.xml	(nonexistent)
@@ -1,150 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="map_reduce_cloner_with_multiple_outputs">
-	<!-- 
-		This example writes to multiple datastores: 2 sequence files, person and documents. 
-		The class responsible for writing multiple datastores is: eu.dnetlib.iis.core.examples.javamapreduce.PersonClonerMapperMultipleOutput.
-	-->
-	<start to="data_producer" />
-	<action name="data_producer">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Operson=${workingDir}/data_producer/person</arg>
-			<arg>-Odocument=${workingDir}/data_producer/document</arg>
-		</java>
-		<ok to="mr_cloner" />
-		<error to="fail" />
-	</action>
-	<action name="mr_cloner">
-		<map-reduce>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/mr_cloner" />
-				<!-- multiple output, no need to create mr_cloner, will be created by mapred
-				<mkdir path="${nameNode}${workingDir}/mr_cloner" />
-				-->
-			</prepare>
-			<configuration>
-				<!-- This is required for new api usage -->
-				<property>
-					<name>mapred.mapper.new-api</name>
-					<value>true</value>
-				</property>
-				<property>
-					<name>mapred.reducer.new-api</name>
-					<value>true</value>
-				</property>
-
-				<!-- Standard stuff for our framework -->
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapred.output.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.output.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapreduce.inputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat
-					</value>
-				</property>
-				<property>
-					<name>mapreduce.outputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
-					</value>
-				</property>
-				<!-- Other stuff -->
-				<property>
-					<name>mapreduce.map.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.MultipleOutputPersonProcessor</value>
-				</property>
-				<property>
-					<name>mapred.input.dir</name>
-					<value>${workingDir}/data_producer/person</value>
-				</property>
-				<property>
-					<name>mapred.output.dir</name>
-					<value>${workingDir}/mr_cloner</value>
-				</property>
-				<!-- Workflow node parameters -->
-				<property>
-					<name>copiesCount</name>
-					<value>2</value>
-				</property>
-				<property>
-				    <name>named.output.person</name>
-				   <value>${outputPerson}</value>
-				</property>
-				<property>
-				    <name>named.output.age</name>
-				   <value>${outputAge}</value>
-				</property>
-			</configuration>
-		</map-reduce>
-		<ok to="cloner" />
-		<error to="fail" />
-	</action>
-    
-    <!-- cloner works on duplicated data -->
-	<action name="cloner">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner" /> 
-				<mkdir path="${nameNode}${workingDir}/cloner" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Iperson=${workingDir}/mr_cloner/${outputPerson}</arg>
-			<arg>-Operson=${workingDir}/cloner/person</arg>
-		</java>
-		<ok to="end" />
-		<error to="fail" />
-	</action>
-	<kill name="fail">
-		<message>Unfortunately, the process failed -- error message:
-			[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-	<end name="end" />
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/job.properties
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/job.properties	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output/job.properties	(nonexistent)
@@ -1,2 +0,0 @@
-outputPerson=person
-outputAge=age
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_without_reducer/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_without_reducer/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_without_reducer/oozie_app/workflow.xml	(nonexistent)
@@ -1,142 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="map_reduce_cloner_without_reducer">
-	<start to="data_producer" />
-	<action name="data_producer">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Operson=${workingDir}/data_producer/person</arg>
-			<arg>-Odocument=${workingDir}/data_producer/document</arg>
-		</java>
-		<ok to="mr_cloner" />
-		<error to="fail" />
-	</action>
-	<action name="mr_cloner">
-		<map-reduce>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/mr_cloner" />
-				<mkdir path="${nameNode}${workingDir}/mr_cloner" />
-			</prepare>
-			<configuration>
-				<!-- This is required for new api usage -->
-				<property>
-					<name>mapred.mapper.new-api</name>
-					<value>true</value>
-				</property>
-				<property>
-					<name>mapred.reducer.new-api</name>
-					<value>true</value>
-				</property>
-
-				<!-- Standard stuff for our framework -->
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapred.output.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.output.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapreduce.inputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat
-					</value>
-				</property>
-				<property>
-					<name>mapreduce.outputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
-					</value>
-				</property>
-				<!-- This is an outdated property -->
-				<!-- <property> 
-					<name>mapred.map.tasks</name>
-					<value>1</value> 
-				</property> -->
-
-				<!-- Other stuff -->
-				<property>
-					<name>mapreduce.map.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.PersonClonerMapper</value>
-				</property>
-				<!-- <property> <name>mapreduce.reduce.class</name> <value>eu.dnetlib.iis.core.mapreduce.PersonClonerReducer</value> 
-					</property> -->
-				<property>
-					<name>mapred.input.dir</name>
-					<value>${workingDir}/data_producer/person</value>
-				</property>
-				<property>
-					<name>mapred.output.dir</name>
-					<value>${workingDir}/mr_cloner/person</value>
-				</property>
-				<!-- Workflow node parameters -->
-				<property>
-					<name>copiesCount</name>
-					<value>2</value>
-				</property>
-			</configuration>
-		</map-reduce>
-		<ok to="cloner" />
-		<error to="fail" />
-	</action>
-	<action name="cloner">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner" />
-				<mkdir path="${nameNode}${workingDir}/cloner" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Iperson=${workingDir}/mr_cloner/person</arg>
-			<arg>-Operson=${workingDir}/cloner/person</arg>
-		</java>
-		<ok to="end" />
-		<error to="fail" />
-	</action>
-	<kill name="fail">
-		<message>Unfortunately, the process failed -- error message:
-			[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-	<end name="end" />
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner/oozie_app/workflow.xml	(nonexistent)
@@ -1,145 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="map_reduce_cloners">
-	<start to="data_producer" />
-	<action name="data_producer">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Operson=${workingDir}/data_producer/person</arg>
-			<arg>-Odocument=${workingDir}/data_producer/document</arg>
-		</java>
-		<ok to="mr_cloner" />
-		<error to="fail" />
-	</action>
-	<action name="mr_cloner">
-		<map-reduce>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/mr_cloner" />
-				<mkdir path="${nameNode}${workingDir}/mr_cloner" />
-			</prepare>
-			<configuration>
-				<!-- This is required for new api usage -->
-				<property>
-					<name>mapred.mapper.new-api</name>
-					<value>true</value>
-				</property>
-				<property>
-					<name>mapred.reducer.new-api</name>
-					<value>true</value>
-				</property>
-
-				<!-- Standard stuff for our framework -->
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapred.output.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.output.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapreduce.inputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat
-					</value>
-				</property>
-				<property>
-					<name>mapreduce.outputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
-					</value>
-				</property>
-				<!-- This is an outdated property -->
-				<!-- <property>
-					<name>mapred.map.tasks</name>
-					<value>1</value>
-				</property> -->
-
-				<!-- Other stuff -->
-				<property>
-					<name>mapreduce.map.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.PersonClonerMapper</value>
-				</property>
-				<property>
-					<name>mapreduce.reduce.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.PersonClonerReducer
-					</value>
-				</property>
-				<property>
-					<name>mapred.input.dir</name>
-					<value>${workingDir}/data_producer/person</value>
-				</property>
-				<property>
-					<name>mapred.output.dir</name>
-					<value>${workingDir}/mr_cloner/person</value>
-				</property>
-				<!-- Workflow node parameters -->
-				<property>
-					<name>copiesCount</name>
-					<value>2</value>
-				</property>
-			</configuration>
-		</map-reduce>
-		<ok to="cloner" />
-		<error to="fail" />
-	</action>
-	<action name="cloner">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner" />
-				<mkdir path="${nameNode}${workingDir}/cloner" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Iperson=${workingDir}/mr_cloner/person</arg>
-			<arg>-Operson=${workingDir}/cloner/person</arg>
-		</java>
-		<ok to="end" />
-		<error to="fail" />
-	</action>
-	<kill name="fail">
-		<message>Unfortunately, the process failed -- error message:
-			[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-	<end name="end" />
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/oozie_app/workflow.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/oozie_app/workflow.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/oozie_app/workflow.xml	(nonexistent)
@@ -1,229 +0,0 @@
-<workflow-app xmlns="uri:oozie:workflow:0.3" name="person_by_age_splitter">
-	<!-- 
-		This example writes to multiple datastores: 2 sequence files with persons of odd and even age. 
-		Then another MR job reads both datastores and clones all persons.
-	-->
-	<start to="data_producer" />
-	<action name="data_producer">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/data_producer" />
-				<mkdir path="${nameNode}${workingDir}/data_producer" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.SampleDataProducer</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Operson=${workingDir}/data_producer/person</arg>
-			<arg>-Odocument=${workingDir}/data_producer/document</arg>
-		</java>
-		<ok to="mr_splitter" />
-		<error to="fail" />
-	</action>
-	<action name="mr_splitter">
-		<map-reduce>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/mr_splitter" />
-				<!-- multiple output, no need to create mr_splitter, will be created by mapred
-				<mkdir path="${nameNode}${workingDir}/mr_splitter" />
-				-->
-			</prepare>
-			<configuration>
-				<!-- This is required for new api usage -->
-				<property>
-					<name>mapred.mapper.new-api</name>
-					<value>true</value>
-				</property>
-				<property>
-					<name>mapred.reducer.new-api</name>
-					<value>true</value>
-				</property>
-
-				<!-- Standard stuff for our framework -->
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapred.output.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.output.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapreduce.inputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat
-					</value>
-				</property>
-				<property>
-					<name>mapreduce.outputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
-					</value>
-				</property>
-				<!-- Other stuff -->
-				<property>
-					<name>mapreduce.map.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.PersonByAgeSplitter</value>
-				</property>
-				<property>
-					<name>mapred.input.dir</name>
-					<value>${workingDir}/data_producer/person</value>
-				</property>
-				<property>
-					<name>mapred.output.dir</name>
-					<value>${workingDir}/mr_splitter</value>
-				</property>
-				<!-- multiple output definitions -->
-				<property>
-				    <name>named.output.person.age.even</name>
-				   <value>${outputAgeEven}</value>
-				</property>
-				<property>
-				    <name>named.output.person.age.odd</name>
-				   <value>${outputAgeOdd}</value>
-				</property>
-			</configuration>
-		</map-reduce>
-		<ok to="mr_cloner_with_multiple_input" />
-		<error to="fail" />
-	</action>
-    
-    <!-- cloner works on split data, reads from both datastores -->
-	<action name="mr_cloner_with_multiple_input">
-		<map-reduce>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/mr_cloner" />
-				<mkdir path="${nameNode}${workingDir}/mr_cloner" />
-			</prepare>
-			<configuration>
-				<!-- This is required for new api usage -->
-				<property>
-					<name>mapred.mapper.new-api</name>
-					<value>true</value>
-				</property>
-				<property>
-					<name>mapred.reducer.new-api</name>
-					<value>true</value>
-				</property>
-
-				<!-- Standard stuff for our framework -->
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.mapoutput.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapred.output.key.class</name>
-					<value>org.apache.hadoop.io.Text</value>
-				</property>
-				<property>
-					<name>mapred.output.value.class</name>
-					<value>org.apache.hadoop.io.BytesWritable</value>
-				</property>
-				<property>
-					<name>mapreduce.inputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.input.SequenceFileInputFormat
-					</value>
-				</property>
-				<property>
-					<name>mapreduce.outputformat.class</name>
-					<value>org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat
-					</value>
-				</property>
-				<!-- This is an outdated property -->
-				<!-- <property> 
-					<name>mapred.map.tasks</name>
-					<value>1</value> 
-				</property> -->
-
-				<!-- Other stuff -->
-				<property>
-					<name>mapreduce.map.class</name>
-					<value>eu.dnetlib.iis.core.examples.protobuf.javamapreduce.PersonClonerMapper</value>
-				</property>
-				<property>
-					<name>mapred.input.dir</name>
-					<!-- simply setting multiple inputs as CSV -->
-					<value>${workingDir}/mr_splitter/${outputAgeEven},${workingDir}/mr_splitter/${outputAgeOdd}</value>
-				</property>
-				<property>
-					<name>mapred.output.dir</name>
-					<value>${workingDir}/mr_cloner/person</value>
-				</property>
-				<!-- Workflow node parameters -->
-				<property>
-					<name>copiesCount</name>
-					<value>2</value>
-				</property>
-			</configuration>
-		</map-reduce>
-		<ok to="cloner" />
-		<error to="fail" />
-	</action>
-	
-	<action name="cloner">
-		<java>
-			<job-tracker>${jobTracker}</job-tracker>
-			<name-node>${nameNode}</name-node>
-			<!-- The data generated by this node is deleted in this section -->
-			<prepare>
-				<delete path="${nameNode}${workingDir}/cloner" />
-				<mkdir path="${nameNode}${workingDir}/cloner" />
-			</prepare>
-			<configuration>
-				<property>
-					<name>mapred.job.queue.name</name>
-					<value>${queueName}</value>
-				</property>
-			</configuration>
-			<!-- This is simple wrapper for the Java code -->
-			<main-class>eu.dnetlib.iis.core.java.ProcessWrapper</main-class>
-			<!-- The business Java code that gets to be executed -->
-			<arg>eu.dnetlib.iis.core.examples.protobuf.java.PersonCloner</arg>
-			<!-- All input and output ports have to be bound to paths in HDFS -->
-			<arg>-Iperson=${workingDir}/mr_cloner/person</arg>
-			<arg>-Operson=${workingDir}/cloner/person</arg>
-		</java>
-		<ok to="end" />
-		<error to="fail" />
-	</action>
-	
-	<kill name="fail">
-		<message>Unfortunately, the process failed -- error message:
-			[${wf:errorMessage(wf:lastErrorNode())}]</message>
-	</kill>
-	<end name="end" />
-</workflow-app>
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/job.properties
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/job.properties	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter/job.properties	(nonexistent)
@@ -1,2 +0,0 @@
-outputAgeEven=ageeven
-outputAgeOdd=ageodd
\ No newline at end of file
Index: modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/README.txt
===================================================================
--- modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/README.txt	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/test/resources/eu/dnetlib/iis/core/examples/protobuf/README.txt	(nonexistent)
@@ -1 +0,0 @@
-This directory contains deprecated workflow definitions that use Protocol Buffers + Sequence File to represent data stores. It also contains deprecated Protocol Buffers schemas.
\ No newline at end of file
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/porttype/ProtoBuffPortType.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/porttype/ProtoBuffPortType.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/porttype/ProtoBuffPortType.java	(nonexistent)
@@ -1,62 +0,0 @@
-package eu.dnetlib.iis.core.java.porttype;
-
-import org.apache.commons.lang.NotImplementedException;
-
-import com.google.protobuf.Message;
-
-/**
- * Port type for Protocol Buffers-based data stores
- * @author Mateusz Kobos
- */
-@Deprecated
-public class ProtoBuffPortType<T extends Message> 
-implements PortType {
-	private final Class<T> clazz;
-
-
-	/**
-	 * @param clazz class of the Protocol Buffers Message
-	 */
-	public ProtoBuffPortType(Class<T> clazz) {
-		this.clazz = clazz;
-	}
-	
-	@Override
-	public String getName() {
-		return clazz.getName();
-	}
-	
-	@Override
-	/** Simple check if the schema patterns are exactly the same 
-	 * (as defined by the {@code equals} method). 
-	 * 
-	 * TODO: this should work in a more relaxed way - 
-	 * {@code this.accepts(other)} should be true if {@code this} 
-	 * describes a subset of structures defined in {@code other}.*/
-	public boolean accepts(PortType other){
-		return this.equals(other);
-	}
-	
-	public Class<T> getMessageClass(){
-		return clazz;
-	}
-	
-	
-	/**
-	 * Two schemas are equal if their message definitions are the same.
-	 */
-	@SuppressWarnings("unchecked")
-	@Override
-	public boolean equals(Object o){
-		if(!(o instanceof ProtoBuffPortType)){
-			return false;
-		}
-		ProtoBuffPortType<T> other = (ProtoBuffPortType<T>) o;
-		return this.clazz.equals(other.clazz);
-	}
-	
-	@Override
-	public int hashCode(){
-		throw new NotImplementedException();
-	}
-}
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/StandardDataStoreWriter.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/StandardDataStoreWriter.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/StandardDataStoreWriter.java	(nonexistent)
@@ -1,70 +0,0 @@
-package eu.dnetlib.iis.core.java.io.protobuf;
-
-import java.io.IOException;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.SequenceFile.CompressionType;
-import org.apache.hadoop.io.SequenceFile.Writer;
-import org.apache.hadoop.io.Text;
-
-import com.google.protobuf.Message;
-
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-
-
-
-/**
- * Data store writer implementation.
- * @author mhorst
- * @param <T>
- *
- */
-public class StandardDataStoreWriter<T extends Message> 
-implements DataStoreWriter<T> {
-
-	/**
-	 * Sequence file writer.
-	 */
-	private final SequenceFile.Writer writer;
-	
-	/**
-	 * @param path
-	 * @throws IOException 
-	 */
-	public StandardDataStoreWriter(FileSystemPath path) throws IOException {
-		this(path, CompressionType.NONE);
-	}
-
-	/**
-	 * @param path
-	 * @param compressionType
-	 * @throws IOException 
-	 */
-	public StandardDataStoreWriter(FileSystemPath path, 
-			CompressionType compressionType) throws IOException {
-		writer = SequenceFile.createWriter(path.getFileSystem().getConf(), 
-	    		Writer.file(path.getPath()), Writer.compression(compressionType), 
-	    		Writer.keyClass(Text.class), Writer.valueClass(BytesWritable.class));
-	}
-	
-	/* (non-Javadoc)
-	 * @see eu.dnetlib.iis.imp.IDataStoreWriter#append(byte[])
-	 */
-	@Override
-	public void append(T data) throws IOException {
-		writer.append(new Text(""), 
-				new BytesWritable(data.toByteArray()));
-	}
-
-	/* (non-Javadoc)
-	 * @see eu.dnetlib.iis.imp.IDataStoreWriter#close()
-	 */
-	@Override
-	public void close() throws IOException {
-		if (writer!=null) {
-			writer.close();
-		}
-	}
-
-}
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/SequenceFileReaderIterator.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/SequenceFileReaderIterator.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/SequenceFileReaderIterator.java	(nonexistent)
@@ -1,196 +0,0 @@
-package eu.dnetlib.iis.core.java.io.protobuf;
-
-import java.io.IOException;
-import java.util.regex.Pattern;
-
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.LocatedFileStatus;
-import org.apache.hadoop.fs.RemoteIterator;
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.SequenceFile;
-import org.apache.hadoop.io.SequenceFile.Reader;
-import org.apache.hadoop.io.Writable;
-import org.apache.hadoop.util.ReflectionUtils;
-import org.apache.log4j.Logger;
-
-import eu.dnetlib.iis.core.java.io.CloseableIterator;
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-
-/**
- * Iterator that extracts sequence file's consecutive byte array entries 
- * 
- * @author mhorst
- */
-public class SequenceFileReaderIterator implements CloseableIterator<ByteData> {
-
-	private final Logger log = Logger.getLogger(this.getClass());
-	
-	private SequenceFile.Reader sequenceReader;
-
-	private final RemoteIterator<LocatedFileStatus> fileIt;
-
-	private final FileSystem fs;
-	
-	/** Ignore file starting with underscore. Such files are also ignored by
-	 * default by map-reduce jobs.
-	 */
-	private final static String whitelistRegexp = "^(?!_).*";
-	
-	private ByteData toBeReturned;
-	
-	/**
-	 * Default constructor.
-	 * 
-	 * @param fs hadoop filesystem
-	 * @param seqPath sequence file path
-	 * @throws IOException
-	 */
-	public SequenceFileReaderIterator(final FileSystemPath path) 
-			throws IOException {
-		this.fs = path.getFileSystem();
-		if (fs.isDirectory(path.getPath())) {
-			fileIt = fs.listFiles(path.getPath(), false);
-			sequenceReader = getNextSequenceReader();
-		} else {
-			fileIt = null;
-			sequenceReader = new Reader(fs.getConf(),
-					SequenceFile.Reader.file(path.getPath()));
-		}
-	}
-
-	final Reader getNextSequenceReader() throws IOException {
-		while (fileIt != null && fileIt.hasNext()) {
-			LocatedFileStatus currentFileStatus = fileIt.next();
-			if (isValidFile(currentFileStatus)) {
-				return new Reader(this.fs.getConf(),
-						SequenceFile.Reader.file(currentFileStatus.getPath()));
-			}
-		}
-//		fallback
-		return null;
-	}
-
-	/**
-	 * Checks whether file is valid candidate.
-	 * @param fileStatus
-	 * @return true when valid, false otherwise
-	 */
-	private final boolean isValidFile(LocatedFileStatus fileStatus) {
-		if (fileStatus.isFile()) {
-			if (whitelistRegexp!=null) {
-				return Pattern.matches(whitelistRegexp, 
-						fileStatus.getPath().getName());
-			} else {
-				return true;
-			}
-		}
-//		fallback
-		return false;
-	}
-	
-	/**
-	 * Returns next data package.
-	 * @return next data package
-	 * @throws IOException
-	 */
-	protected ByteData getNext() {
-		try {
-			if (sequenceReader==null) {
-				return null;
-			}
-			Writable key = (Writable) ReflectionUtils.newInstance(
-					sequenceReader.getKeyClass(), fs.getConf());
-			Writable value = (Writable) ReflectionUtils.newInstance(
-					sequenceReader.getValueClass(), fs.getConf());
-			if (sequenceReader.next(key, value)) {
-		        return new ByteData(((BytesWritable)value).getBytes(), 
-		        		((BytesWritable)value).getLength());
-		      } else {
-		    	  sequenceReader.close();
-		    	  sequenceReader = getNextSequenceReader();
-		    	  if (sequenceReader!=null) {
-		    		  return getNext();
-		    	  }
-		      }
-//			fallback
-			return null;	
-		} catch (IOException e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	/* (non-Javadoc)
-	 * @see java.util.Iterator#hasNext()
-	 */
-	@Override
-	public boolean hasNext() {
-//		check and provide next when already returned
-		if (toBeReturned==null) {
-			toBeReturned = getNext();
-		} 
-		return toBeReturned!=null;
-	}
-	
-	/* (non-Javadoc)
-	 * @see java.util.Iterator#next()
-	 */
-	@Override
-	public ByteData next() {
-		if (toBeReturned!=null) {
-//			element fetched while executing hasNext()
-			ByteData result = toBeReturned;
-			toBeReturned = null;
-			return result;
-		} else {
-			return getNext();
-		}
-	}
-	
-	/* (non-Javadoc)
-	 * @see eu.dnetlib.iis.exp.iterator.ClosableIterator#close()
-	 */
-	@Override
-	public void close() {
-		if (sequenceReader!=null) {
-			try {
-				sequenceReader.close();
-			} catch (IOException e) {
-				log.error("error occurred when closing sequence reader", e);
-			}
-		}
-	}
-	
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see java.util.Iterator#remove()
-	 */
-	@Override
-	public void remove() {
-		throw new UnsupportedOperationException();
-	}
-}
-
-/**
- * A counterpart of {@code byte[]}. We are not using simply {@code byte[]} 
- * because of performance reasons - the sequence file access library returns 
- * a byte array padded with zeroes along with length of the array occupied 
- * by real data. We don't create an instance of {@code byte[]} out of it 
- * because it would involve creating an excessive copy of the data.
- * @author Mateusz Kobos
- *
- */
-class ByteData {
-	private final byte[] data;
-	private final int length;
-	public ByteData(byte[] data, int length) {
-		this.data  = data;
-		this.length = length;
-	}
-	public byte[] getData() {
-		return data;
-	}
-	public int getLength() {
-		return length;
-	}
-}
\ No newline at end of file

Property changes on: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/SequenceFileReaderIterator.java
___________________________________________________________________
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/IOUtils.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/IOUtils.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/IOUtils.java	(nonexistent)
@@ -1,51 +0,0 @@
-package eu.dnetlib.iis.core.java.io.protobuf;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
-
-import com.google.protobuf.Message;
-
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-
-
-/**
- * Utility for doing various IO operations
- * @author Mateusz Kobos
- *
- */
-public final class IOUtils {
-	
-	private IOUtils(){}
-	
-	/**
-	 * Read data store entries and save them in a list.
-	 * @param clazz class of the Protocol Buffers message
-	 * @return
-	 * @throws IOException
-	 */
-	public static <T extends Message> List<T> readProtobuffDataStore(
-			Class<T> clazz, FileSystemPath path) throws IOException{
-		ProtobuffCloseableIterator<T> i = new ProtobuffCloseableIterator<T>(
-				path, clazz);
-		List<T> elems = new ArrayList<T>();
-		while(i.hasNext()){
-			elems.add(i.next());
-		}
-		return elems;
-	}
-	
-	/**
-	 * Create a data store from a list of entries
-	 * @param elements
-	 * @throws IOException
-	 */
-	public static <T extends Message> void writeProtobuffDataStore(
-			List<T> elements, FileSystemPath path) throws IOException{
-		DataStoreWriter<T> writer = new StandardDataStoreWriter<T>(path);
-		for(T i: elements){
-			writer.append(i);
-		}
-		writer.close();
-	}
-}
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/ProtobuffCloseableIterator.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/ProtobuffCloseableIterator.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/ProtobuffCloseableIterator.java	(nonexistent)
@@ -1,74 +0,0 @@
-package eu.dnetlib.iis.core.java.io.protobuf;
-
-import java.io.IOException;
-import java.lang.reflect.Method;
-
-import com.google.protobuf.Message;
-
-import eu.dnetlib.iis.core.java.io.CloseableIterator;
-import eu.dnetlib.iis.core.java.io.FileSystemPath;
-
-/**
- * Reader iterator providing protocol buffer objects.
- * @author mhorst
- *
- */
-public class ProtobuffCloseableIterator<T extends Message> 
-	implements CloseableIterator<T> {
-	
-	/**
-	 * Class of the output protocol buffer object.
-	 */
-	private final Class<T> clazz;
-	private SequenceFileReaderIterator i;
-	
-	/**
-	 * Default constructor.
-	 * @param fs
-	 * @param seqPath
-	 * @param clazz
-	 * @param whitelistRegexp
-	 * @throws IOException
-	 */
-	public ProtobuffCloseableIterator(FileSystemPath path, 
-			Class<T> clazz) throws IOException {
-		this.i = new SequenceFileReaderIterator(path);
-		this.clazz = clazz;
-	}
-
-	@Override
-	public boolean hasNext() {
-		return i.hasNext();
-	}
-
-	@Override
-	public T next() {
-		return buildObject(i.next());
-	}
-
-	@SuppressWarnings("unchecked")
-	private T buildObject(ByteData data) {
-		try {
-			Method newBuilderMethod = clazz.getDeclaredMethod("newBuilder");
-			Object builderObj = newBuilderMethod.invoke(null);
-			Method mergeFromMethod = builderObj.getClass().getMethod("mergeFrom", 
-					byte[].class, Integer.TYPE, Integer.TYPE);
-			builderObj = mergeFromMethod.invoke(builderObj, 
-					data.getData(), 0, data.getLength());
-			Method buildMethod = builderObj.getClass().getDeclaredMethod("build"); 
-			return (T) buildMethod.invoke(builderObj);
-		} catch (Exception e) {
-			throw new RuntimeException(e);
-		}
-	}
-	
-	@Override
-	public void remove() {
-		i.remove();
-	}
-
-	@Override
-	public void close() {
-		i.close();
-	}
-}

Property changes on: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/ProtobuffCloseableIterator.java
___________________________________________________________________
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/DataStoreWriter.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/DataStoreWriter.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/DataStoreWriter.java	(nonexistent)
@@ -1,27 +0,0 @@
-package eu.dnetlib.iis.core.java.io.protobuf;
-
-import java.io.IOException;
-
-import com.google.protobuf.Message;
-
-/**
- * Data store writer interface.
- * @author mhorst
- *
- */
-public interface DataStoreWriter<T extends Message> {
-   
-    /**
-     * Appends data to writer output.
-     * @param data
-     * @throws IOException
-     */
-    public void append(T data) throws IOException;
-    
-    /**
-     * Closes writer, releases resources.
-     * @throws IOException
-     */
-    public void close() throws IOException;
-    
-}
\ No newline at end of file

Property changes on: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/java/io/protobuf/DataStoreWriter.java
___________________________________________________________________
Deleted: svn:mime-type
## -1 +0,0 ##
-text/plain
\ No newline at end of property
Index: modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/javamapreduce/protobuf/MapRedUtils.java
===================================================================
--- modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/javamapreduce/protobuf/MapRedUtils.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/main/java/eu/dnetlib/iis/core/javamapreduce/protobuf/MapRedUtils.java	(nonexistent)
@@ -1,49 +0,0 @@
-package eu.dnetlib.iis.core.javamapreduce.protobuf;
-
-import java.io.IOException;
-import java.lang.reflect.Method;
-
-import org.apache.hadoop.io.BytesWritable;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapreduce.Mapper;
-import org.apache.hadoop.mapreduce.lib.output.MultipleOutputs;
-
-import com.google.protobuf.Message;
-
-/**
- * Simplifies accessing data from within mapper and reducer, hides the exact
- * implementation details of accessing this data.
- * 
- * @author Mateusz Kobos
- * 
- */
-@SuppressWarnings("unchecked")
-public class MapRedUtils {
-	
-	private static final Text emptyText = new Text("");
-
-	private MapRedUtils() {
-	}
-
-	public static <T extends Message> T parse(Class<T> clazz, Text key,
-			BytesWritable value) {
-		try {
-			Method parseFromMethod = clazz.getMethod("parseFrom", byte[].class);
-			return (T) parseFromMethod.invoke(null, value.copyBytes());
-		} catch (Exception e) {
-			throw new RuntimeException(e);
-		}
-	}
-
-	public static void write(
-			Mapper<Text, BytesWritable, Text, BytesWritable>.Context context,
-			Message message) throws IOException, InterruptedException {
-		context.write(emptyText, new BytesWritable(message.toByteArray()));
-	}
-
-	public static void write(@SuppressWarnings("rawtypes") MultipleOutputs mos, String directoryName,
-			Message message) throws IOException, InterruptedException {
-		mos.write(emptyText,
-				new BytesWritable(message.toByteArray()), directoryName + "/part");
-	}
-}
Index: modules/icm-iis-metadataextraction/trunk/pom.xml
===================================================================
--- modules/icm-iis-metadataextraction/trunk/pom.xml	(revision 39024)
+++ modules/icm-iis-metadataextraction/trunk/pom.xml	(revision 39025)
@@ -54,11 +54,6 @@
 			</exclusions>
 		</dependency>
 		<dependency>
-		  <groupId>com.googlecode.protobuf-java-format</groupId>
-		  <artifactId>protobuf-java-format</artifactId>
-		  <version>1.2</version>
-		</dependency>
-		<dependency>
 	      <groupId>com.googlecode.json-simple</groupId>
 	      <artifactId>json-simple</artifactId>
 	      <version>1.1</version>
Index: modules/icm-iis-metadataextraction/trunk/README.markdown
===================================================================
--- modules/icm-iis-metadataextraction/trunk/README.markdown	(revision 39024)
+++ modules/icm-iis-metadataextraction/trunk/README.markdown	(revision 39025)
@@ -2,6 +2,8 @@
 
 Contains all required classes and testing workflow.
 
+**Mafju review (2015-09-04)**: the input descriptions below are surely outdated since we don't use Protocol Buffers any more
+
 input1:		eu.dnetlib.iis.schemas.protobuf.DocumentContentProto.DocumentContent 
 output1:	eu.dnetlib.iis.schemas.protobuf.DocumentWithBasicMetadataProto.DocumentWithBasicMetadata
 output2:	eu.dnetlib.iis.schemas.protobuf.DocumentTextProto.DocumentText [disabled by default]
Index: modules/icm-iis-core-examples/trunk/src/main/scripts/generate_example_workflow_apps.properties
===================================================================
--- modules/icm-iis-core-examples/trunk/src/main/scripts/generate_example_workflow_apps.properties	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/src/main/scripts/generate_example_workflow_apps.properties	(revision 39025)
@@ -25,14 +25,6 @@
 eu/dnetlib/iis/core/examples/pig/joiner_with_explicit_schema
 eu/dnetlib/iis/core/examples/pig/person_by_docs_filter
 eu/dnetlib/iis/core/examples/pig/person_by_docs_filter_with_subworkflow
-eu/dnetlib/iis/core/examples/protobuf/java/cloner
-eu/dnetlib/iis/core/examples/protobuf/java/joiner
-eu/dnetlib/iis/core/examples/protobuf/java/line_by_line_copier
-eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner
-eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_with_multiple_output
-eu/dnetlib/iis/core/examples/protobuf/javamapreduce/cloner_without_reducer
-eu/dnetlib/iis/core/examples/protobuf/javamapreduce/person_by_age_splitter
-eu/dnetlib/iis/core/examples/protobuf/subworkflow/cloners
 eu/dnetlib/iis/core/examples/subworkflow/cloners
 # remember to leave '\n' after the last line
 
Index: modules/icm-iis-core-examples/trunk/pom.xml
===================================================================
--- modules/icm-iis-core-examples/trunk/pom.xml	(revision 39024)
+++ modules/icm-iis-core-examples/trunk/pom.xml	(revision 39025)
@@ -33,11 +33,6 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>com.google.protobuf</groupId>
-            <artifactId>protobuf-java</artifactId>
-            <version>2.4.1</version>
-        </dependency>
-        <dependency>
             <groupId>org.apache.hadoop</groupId>
             <artifactId>hadoop-common</artifactId>
             <version>${iis.hadoop.common.version}</version>
Index: modules/icm-iis-import/trunk/README.markdown
===================================================================
--- modules/icm-iis-import/trunk/README.markdown	(revision 39024)
+++ modules/icm-iis-import/trunk/README.markdown	(revision 39025)
@@ -1,6 +1,9 @@
 IIS module importing data from Information Space HBase.
 Contains classes and import workflow definitions used for testing purposes. 
 
+
+**Mafju review (2015-09-04)**: the input descriptions below are surely outdated since we don't use Protocol Buffers any more
+
 input:		hbase 
 output1:	eu.dnetlib.iis.schemas.protobuf.ProjectFundingProto.ProjectFunding
 output2:	eu.dnetlib.iis.schemas.protobuf.PersonProto.Person
Index: modules/icm-iis-core/trunk/src/test/java/eu/dnetlib/iis/core/RemoteOozieAppManager.java
===================================================================
--- modules/icm-iis-core/trunk/src/test/java/eu/dnetlib/iis/core/RemoteOozieAppManager.java	(revision 39024)
+++ modules/icm-iis-core/trunk/src/test/java/eu/dnetlib/iis/core/RemoteOozieAppManager.java	(revision 39025)
@@ -12,11 +12,9 @@
 import org.apache.hadoop.fs.Path;
 
 import com.google.common.io.Files;
-import com.google.protobuf.Message;
 
 import eu.dnetlib.iis.core.java.io.DataStore;
 import eu.dnetlib.iis.core.java.io.FileSystemPath;
-import eu.dnetlib.iis.core.java.io.protobuf.IOUtils;
 
 /**
  * Provides a facade hiding the complexities of communicating with
@@ -145,16 +143,6 @@
 		return records;
 	}
 
-	@Deprecated
-	public <T extends Message> List<T> readProtoBuffDataStoreFromWorkingDir(
-			Class<T> messageClass, String name) throws IOException{
-		List<T> records =
-				IOUtils.readProtobuffDataStore(
-					messageClass,
-					new FileSystemPath(hdfs, new Path(getWorkingDir(), name)));
-		return records;
-	}
-
 	public void copyResourceFilesToWorkingDir(
 			Map<String, String> resourcePathToHDFSFileNameMap) throws IOException{
 		for(Map.Entry<String, String> entry:
