Updates Promotion DBs

- Add a step for promoting the splitted monitor DBs

README.md

@@ -1,2 +1,2 @@
 # dnet-hadoop
-Dnet-hadoop is the project that defined all the OOZIE workflows for the OpenAIRE Graph construction, processing, provisioning.
+Dnet-hadoop is a tool for

dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojo.java

@@ -8,6 +8,8 @@ import java.util.List;
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang.StringUtils;
 import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
 
 /**
  * Generates oozie properties which were not provided from commandline.
@@ -25,7 +27,7 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
 	};
 
 	@Override
-	public void execute() {
+	public void execute() throws MojoExecutionException, MojoFailureException {
 		if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
 			&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
 			String generatedSandboxName = generateSandboxName(
@@ -44,24 +46,24 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
 	/**
 	 * Generates sandbox name from workflow source directory.
 	 *
-	 * @param wfSourceDir workflow source directory
+	 * @param wfSourceDir
 	 * @return generated sandbox name
 	 */
 	private String generateSandboxName(String wfSourceDir) {
 		// utilize all dir names until finding one of the limiters
-		List<String> sandboxNameParts = new ArrayList<>();
+		List<String> sandboxNameParts = new ArrayList<String>();
 		String[] tokens = StringUtils.split(wfSourceDir, File.separatorChar);
 		ArrayUtils.reverse(tokens);
 		if (tokens.length > 0) {
 			for (String token : tokens) {
 				for (String limiter : limiters) {
 					if (limiter.equals(token)) {
-						return !sandboxNameParts.isEmpty()
+						return sandboxNameParts.size() > 0
 							? StringUtils.join(sandboxNameParts.toArray())
 							: null;
 					}
 				}
-				if (!sandboxNameParts.isEmpty()) {
+				if (sandboxNameParts.size() > 0) {
 					sandboxNameParts.add(0, File.separator);
 				}
 				sandboxNameParts.add(0, token);

dhp-build/dhp-build-properties-maven-plugin/src/main/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectProperties.java

@@ -16,7 +16,6 @@ import java.io.File;
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
@@ -290,7 +289,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 */
 	protected List<String> getEscapeChars(String escapeChars) {
 		List<String> tokens = getListFromCSV(escapeChars);
-		List<String> realTokens = new ArrayList<>();
+		List<String> realTokens = new ArrayList<String>();
 		for (String token : tokens) {
 			String realToken = getRealToken(token);
 			realTokens.add(realToken);
@@ -325,7 +324,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 * @return content
 	 */
 	protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
-		List<String> names = new ArrayList<>(properties.stringPropertyNames());
+		List<String> names = new ArrayList<String>(properties.stringPropertyNames());
 		Collections.sort(names);
 		StringBuilder sb = new StringBuilder();
 		if (!StringUtils.isBlank(comment)) {
@@ -353,7 +352,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 		throws MojoExecutionException {
 		try {
 			String content = getContent(comment, properties, escapeTokens);
-			FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8);
+			FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
 		} catch (IOException e) {
 			throw new MojoExecutionException("Error creating properties file", e);
 		}
@@ -400,9 +399,9 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 */
 	protected static final List<String> getListFromCSV(String csv) {
 		if (StringUtils.isBlank(csv)) {
-			return new ArrayList<>();
+			return new ArrayList<String>();
 		}
-		List<String> list = new ArrayList<>();
+		List<String> list = new ArrayList<String>();
 		String[] tokens = StringUtils.split(csv, ",");
 		for (String token : tokens) {
 			list.add(token.trim());

dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/GenerateOoziePropertiesMojoTest.java

@@ -9,18 +9,18 @@ import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 /** @author mhorst, claudio.atzori */
-class GenerateOoziePropertiesMojoTest {
+public class GenerateOoziePropertiesMojoTest {
 
 	private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
 
 	@BeforeEach
-	void clearSystemProperties() {
+	public void clearSystemProperties() {
 		System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
 		System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
 	}
 
 	@Test
-	void testExecuteEmpty() throws Exception {
+	public void testExecuteEmpty() throws Exception {
 		// execute
 		mojo.execute();
 
@@ -29,7 +29,7 @@ class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	void testExecuteSandboxNameAlreadySet() throws Exception {
+	public void testExecuteSandboxNameAlreadySet() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
 		String sandboxName = "originalSandboxName";
@@ -44,7 +44,7 @@ class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	void testExecuteEmptyWorkflowSourceDir() throws Exception {
+	public void testExecuteEmptyWorkflowSourceDir() throws Exception {
 		// given
 		String workflowSourceDir = "";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -57,7 +57,7 @@ class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	void testExecuteNullSandboxNameGenerated() throws Exception {
+	public void testExecuteNullSandboxNameGenerated() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -70,7 +70,7 @@ class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	void testExecute() throws Exception {
+	public void testExecute() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -83,7 +83,7 @@ class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	void testExecuteWithoutRoot() throws Exception {
+	public void testExecuteWithoutRoot() throws Exception {
 		// given
 		String workflowSourceDir = "wf/transformers";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);

dhp-build/dhp-build-properties-maven-plugin/src/test/java/eu/dnetlib/maven/plugin/properties/WritePredefinedProjectPropertiesTest.java

@@ -20,7 +20,7 @@ import org.mockito.junit.jupiter.MockitoExtension;
 
 /** @author mhorst, claudio.atzori */
 @ExtendWith(MockitoExtension.class)
-class WritePredefinedProjectPropertiesTest {
+public class WritePredefinedProjectPropertiesTest {
 
 	@Mock
 	private MavenProject mavenProject;
@@ -39,7 +39,7 @@ class WritePredefinedProjectPropertiesTest {
 	// ----------------------------------- TESTS ---------------------------------------------
 
 	@Test
-	void testExecuteEmpty() throws Exception {
+	public void testExecuteEmpty() throws Exception {
 		// execute
 		mojo.execute();
 
@@ -50,7 +50,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithProjectProperties() throws Exception {
+	public void testExecuteWithProjectProperties() throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -70,7 +70,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test()
-	void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
+	public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -84,7 +84,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
+	public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -108,7 +108,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
+	public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -132,7 +132,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
+	public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -164,7 +164,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
+	public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -194,7 +194,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromBlankLocation() {
+	public void testExecuteIncludingPropertyKeysFromBlankLocation() {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -214,7 +214,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
+	public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -247,7 +247,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
+	public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -273,7 +273,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
+	public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
 		// given
 		mojo.setQuiet(true);
 		mojo.setIncludePropertyKeysFromFiles(new String[] {
@@ -290,7 +290,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteIncludingPropertyKeysFromInvalidFile() {
+	public void testExecuteIncludingPropertyKeysFromInvalidFile() {
 		// given
 		mojo.setIncludePropertyKeysFromFiles(new String[] {
 			"invalid location"
@@ -301,7 +301,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
+	public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
 		// given
 		mojo.setIncludeEnvironmentVariables(true);
 
@@ -318,7 +318,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
+	public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "systemPropertyKey";
 		String value = "systemPropertyValue";
@@ -337,7 +337,7 @@ class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
+	public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "systemPropertyKey ";

dhp-common/pom.xml

@@ -25,11 +25,6 @@
 			<groupId>com.github.sisyphsu</groupId>
 			<artifactId>dateparser</artifactId>
 		</dependency>
-		<dependency>
-			<groupId>me.xuender</groupId>
-			<artifactId>unidecode</artifactId>
-		</dependency>
-
 		<dependency>
 			<groupId>org.apache.spark</groupId>
 			<artifactId>spark-core_2.11</artifactId>
@@ -117,11 +112,6 @@
 			<groupId>eu.dnetlib.dhp</groupId>
 			<artifactId>dhp-schemas</artifactId>
 		</dependency>
-
-		<dependency>
-			<groupId>com.opencsv</groupId>
-			<artifactId>opencsv</artifactId>
-		</dependency>
 	</dependencies>
 
 </project>

dhp-common/src/main/java/eu/dnetlib/dhp/application/ApplicationUtils.java

@@ -0,0 +1,14 @@
+
+package eu.dnetlib.dhp.application;
+
+import java.io.*;
+import java.util.Map;
+import java.util.Properties;
+
+import org.apache.hadoop.conf.Configuration;
+
+import com.google.common.collect.Maps;
+
+public class ApplicationUtils {
+
+}

dhp-common/src/main/java/eu/dnetlib/dhp/application/ArgumentApplicationParser.java

@@ -56,13 +56,13 @@ public class ArgumentApplicationParser implements Serializable {
 			final StringWriter stringWriter = new StringWriter();
 			IOUtils.copy(gis, stringWriter);
 			return stringWriter.toString();
-		} catch (IOException e) {
-			log.error("Wrong value to decompress: {}", abstractCompressed);
-			throw new IllegalArgumentException(e);
+		} catch (Throwable e) {
+			log.error("Wrong value to decompress:" + abstractCompressed);
+			throw new RuntimeException(e);
 		}
 	}
 
-	public static String compressArgument(final String value) throws IOException {
+	public static String compressArgument(final String value) throws Exception {
 		ByteArrayOutputStream out = new ByteArrayOutputStream();
 		GZIPOutputStream gzip = new GZIPOutputStream(out);
 		gzip.write(value.getBytes());

dhp-common/src/main/java/eu/dnetlib/dhp/application/OptionsParameter.java

@@ -9,6 +9,9 @@ public class OptionsParameter {
 	private boolean paramRequired;
 	private boolean compressed;
 
+	public OptionsParameter() {
+	}
+
 	public String getParamName() {
 		return paramName;
 	}

dhp-common/src/main/java/eu/dnetlib/dhp/collection/ApiDescriptor.java

@@ -34,7 +34,7 @@ public class ApiDescriptor {
 		return params;
 	}
 
-	public void setParams(final Map<String, String> params) {
+	public void setParams(final HashMap<String, String> params) {
 		this.params = params;
 	}
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/Constants.java

@@ -12,9 +12,6 @@ public class Constants {
 
 	public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/";
 
-	private Constants() {
-	}
-
 	static {
 		accessRightsCoarMap.put("OPEN", "c_abf2");
 		accessRightsCoarMap.put("RESTRICTED", "c_16ec");
@@ -52,10 +49,4 @@ public class Constants {
 	public static final String CONTENT_INVALIDRECORDS = "InvalidRecords";
 	public static final String CONTENT_TRANSFORMEDRECORDS = "transformedItems";
 
-	// IETF Draft and used by Repositories like ZENODO , not included in APACHE HTTP java packages
-	// see https://ietf-wg-httpapi.github.io/ratelimit-headers/draft-ietf-httpapi-ratelimit-headers.html
-	public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT = "X-RateLimit-Limit";
-	public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING = "X-RateLimit-Remaining";
-	public static final String HTTPHEADER_IETF_DRAFT_RATELIMIT_RESET = "X-RateLimit-Reset";
-
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/GraphResultMapper.java

@@ -84,7 +84,7 @@ public class GraphResultMapper implements Serializable {
 								.setDocumentationUrl(
 									value
 										.stream()
-										.map(Field::getValue)
+										.map(v -> v.getValue())
 										.collect(Collectors.toList())));
 
 					Optional
@@ -100,20 +100,20 @@ public class GraphResultMapper implements Serializable {
 						.setContactgroup(
 							Optional
 								.ofNullable(ir.getContactgroup())
-								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
+								.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
 								.orElse(null));
 
 					out
 						.setContactperson(
 							Optional
 								.ofNullable(ir.getContactperson())
-								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
+								.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
 								.orElse(null));
 					out
 						.setTool(
 							Optional
 								.ofNullable(ir.getTool())
-								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
+								.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
 								.orElse(null));
 
 					out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
@@ -123,8 +123,7 @@ public class GraphResultMapper implements Serializable {
 
 			Optional
 				.ofNullable(input.getAuthor())
-				.ifPresent(
-					ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
+				.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
 
 			// I do not map Access Right UNKNOWN or OTHER
 
@@ -211,7 +210,7 @@ public class GraphResultMapper implements Serializable {
 			if (oInst.isPresent()) {
 				out
 					.setInstance(
-						oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
+						oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
 
 			}
 
@@ -231,7 +230,7 @@ public class GraphResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
 					.collect(Collectors.toList());
-				if (!iTitle.isEmpty()) {
+				if (iTitle.size() > 0) {
 					out.setMaintitle(iTitle.get(0).getValue());
 				}
 
@@ -240,7 +239,7 @@ public class GraphResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
 					.collect(Collectors.toList());
-				if (!iTitle.isEmpty()) {
+				if (iTitle.size() > 0) {
 					out.setSubtitle(iTitle.get(0).getValue());
 				}
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java

@@ -28,7 +28,7 @@ public class HdfsSupport {
 	 * @param configuration Configuration of hadoop env
 	 */
 	public static boolean exists(String path, Configuration configuration) {
-		logger.info("Checking existence for path: {}", path);
+		logger.info("Removing path: {}", path);
 		return rethrowAsRuntimeException(
 			() -> {
 				Path f = new Path(path);

dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java

@@ -14,33 +14,38 @@ public class MakeTarArchive implements Serializable {
 
 	private static TarArchiveOutputStream getTar(FileSystem fileSystem, String outputPath) throws IOException {
 		Path hdfsWritePath = new Path(outputPath);
+		FSDataOutputStream fsDataOutputStream = null;
 		if (fileSystem.exists(hdfsWritePath)) {
 			fileSystem.delete(hdfsWritePath, true);
 
 		}
-		return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+
+		return new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
 	}
 
 	private static void write(FileSystem fileSystem, String inputPath, String outputPath, String dir_name)
 		throws IOException {
 
 		Path hdfsWritePath = new Path(outputPath);
+		FSDataOutputStream fsDataOutputStream = null;
 		if (fileSystem.exists(hdfsWritePath)) {
 			fileSystem.delete(hdfsWritePath, true);
 
 		}
-		try (TarArchiveOutputStream ar = new TarArchiveOutputStream(
-			fileSystem.create(hdfsWritePath).getWrappedStream())) {
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
 
-			RemoteIterator<LocatedFileStatus> iterator = fileSystem
-				.listFiles(
-					new Path(inputPath), true);
+		TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
 
-			while (iterator.hasNext()) {
-				writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
-			}
+		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			.listFiles(
+				new Path(inputPath), true);
 
+		while (fileStatusListIterator.hasNext()) {
+			writeCurrentFile(fileSystem, dir_name, fileStatusListIterator, ar, 0);
 		}
+
+		ar.close();
 	}
 
 	public static void tarMaxSize(FileSystem fileSystem, String inputPath, String outputPath, String dir_name,
@@ -85,13 +90,6 @@ public class MakeTarArchive implements Serializable {
 		String p_string = p.toString();
 		if (!p_string.endsWith("_SUCCESS")) {
 			String name = p_string.substring(p_string.lastIndexOf("/") + 1);
-			if (name.startsWith("part-") & name.length() > 10) {
-				String tmp = name.substring(0, 10);
-				if (name.contains(".")) {
-					tmp += name.substring(name.indexOf("."));
-				}
-				name = tmp;
-			}
 			TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name);
 			entry.setSize(fileStatus.getLen());
 			current_size += fileStatus.getLen();

dhp-common/src/main/java/eu/dnetlib/dhp/common/MdstoreClient.java

@@ -10,6 +10,8 @@ import java.util.Optional;
 import java.util.stream.StreamSupport;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.bson.Document;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -19,7 +21,6 @@ import com.mongodb.BasicDBObject;
 import com.mongodb.MongoClient;
 import com.mongodb.MongoClientURI;
 import com.mongodb.QueryBuilder;
-import com.mongodb.client.FindIterable;
 import com.mongodb.client.MongoCollection;
 import com.mongodb.client.MongoDatabase;
 
@@ -45,7 +46,7 @@ public class MdstoreClient implements Closeable {
 
 		final String currentId = Optional
 			.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
-			.map(FindIterable::first)
+			.map(r -> r.first())
 			.map(d -> d.getString("currentId"))
 			.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
 
@@ -83,7 +84,7 @@ public class MdstoreClient implements Closeable {
 		if (!Iterables.contains(client.listDatabaseNames(), dbName)) {
 			final String err = String.format("Database '%s' not found in %s", dbName, client.getAddress());
 			log.warn(err);
-			throw new IllegalArgumentException(err);
+			throw new RuntimeException(err);
 		}
 		return client.getDatabase(dbName);
 	}
@@ -96,7 +97,7 @@ public class MdstoreClient implements Closeable {
 					String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
 			log.warn(err);
 			if (abortIfMissing) {
-				throw new IllegalArgumentException(err);
+				throw new RuntimeException(err);
 			} else {
 				return null;
 			}

dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java

@@ -24,6 +24,7 @@ import com.google.common.hash.Hashing;
  */
 public class PacePerson {
 
+	private static final String UTF8 = "UTF-8";
 	private List<String> name = Lists.newArrayList();
 	private List<String> surname = Lists.newArrayList();
 	private List<String> fullname = Lists.newArrayList();

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/ZenodoAPIClient.java

@@ -5,9 +5,6 @@ import java.io.*;
 import java.io.IOException;
 import java.util.concurrent.TimeUnit;
 
-import org.apache.http.HttpHeaders;
-import org.apache.http.entity.ContentType;
-
 import com.google.gson.Gson;
 
 import eu.dnetlib.dhp.common.api.zenodo.ZenodoModel;
@@ -46,7 +43,7 @@ public class ZenodoAPIClient implements Serializable {
 		this.deposition_id = deposition_id;
 	}
 
-	public ZenodoAPIClient(String urlString, String access_token) {
+	public ZenodoAPIClient(String urlString, String access_token) throws IOException {
 
 		this.urlString = urlString;
 		this.access_token = access_token;
@@ -66,8 +63,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString)
-			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
 			.post(body)
 			.build();
 
@@ -106,8 +103,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(bucket + "/" + file_name)
-			.addHeader(HttpHeaders.CONTENT_TYPE, "application/zip") // add request headers
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Content-Type", "application/zip") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
 			.put(InputStreamRequestBody.create(MEDIA_TYPE_ZIP, is, len))
 			.build();
 
@@ -133,8 +130,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString + "/" + deposition_id)
-			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
 			.put(body)
 			.build();
 
@@ -200,7 +197,7 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString + "/" + deposition_id + "/actions/newversion")
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Authorization", "Bearer " + access_token)
 			.post(body)
 			.build();
 
@@ -273,8 +270,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString)
-			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
 			.get()
 			.build();
 
@@ -296,8 +293,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(url)
-			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
+			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader("Authorization", "Bearer " + access_token)
 			.get()
 			.build();
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/Creator.java

@@ -32,13 +32,13 @@ public class Creator {
 
 	public static Creator newInstance(String name, String affiliation, String orcid) {
 		Creator c = new Creator();
-		if (name != null) {
+		if (!(name == null)) {
 			c.name = name;
 		}
-		if (affiliation != null) {
+		if (!(affiliation == null)) {
 			c.affiliation = affiliation;
 		}
-		if (orcid != null) {
+		if (!(orcid == null)) {
 			c.orcid = orcid;
 		}
 

dhp-common/src/main/java/eu/dnetlib/dhp/common/api/zenodo/File.java

@@ -3,12 +3,17 @@ package eu.dnetlib.dhp.common.api.zenodo;
 
 import java.io.Serializable;
 
+import net.minidev.json.annotate.JsonIgnore;
+
 public class File implements Serializable {
 	private String checksum;
 	private String filename;
 	private long filesize;
 	private String id;
 
+	@JsonIgnore
+	// private Links links;
+
 	public String getChecksum() {
 		return checksum;
 	}
@@ -41,4 +46,13 @@ public class File implements Serializable {
 		this.id = id;
 	}
 
+//    @JsonIgnore
+//    public Links getLinks() {
+//        return links;
+//    }
+//
+//    @JsonIgnore
+//    public void setLinks(Links links) {
+//        this.links = links;
+//    }
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/GetCSV.java

@@ -1,56 +0,0 @@
-
-package eu.dnetlib.dhp.common.collection;
-
-import java.io.*;
-import java.nio.charset.StandardCharsets;
-import java.util.List;
-
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.opencsv.bean.CsvToBeanBuilder;
-
-public class GetCSV {
-
-	public static final char DEFAULT_DELIMITER = ',';
-
-	private GetCSV() {
-	}
-
-	public static void getCsv(FileSystem fileSystem, BufferedReader reader, String hdfsPath,
-		String modelClass) throws IOException, ClassNotFoundException {
-		getCsv(fileSystem, reader, hdfsPath, modelClass, DEFAULT_DELIMITER);
-	}
-
-	public static void getCsv(FileSystem fileSystem, Reader reader, String hdfsPath,
-		String modelClass, char delimiter) throws IOException, ClassNotFoundException {
-
-		Path hdfsWritePath = new Path(hdfsPath);
-		FSDataOutputStream fsDataOutputStream = null;
-		if (fileSystem.exists(hdfsWritePath)) {
-			fileSystem.delete(hdfsWritePath, false);
-		}
-		fsDataOutputStream = fileSystem.create(hdfsWritePath);
-
-		try (BufferedWriter writer = new BufferedWriter(
-			new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8))) {
-
-			final ObjectMapper mapper = new ObjectMapper();
-
-			@SuppressWarnings("unchecked")
-			final List lines = new CsvToBeanBuilder(reader)
-				.withType(Class.forName(modelClass))
-				.withSeparator(delimiter)
-				.build()
-				.parse();
-
-			for (Object line : lines) {
-				writer.write(mapper.writeValueAsString(line));
-				writer.newLine();
-			}
-		}
-	}
-
-}

dhp-common/src/main/java/eu/dnetlib/dhp/common/rest/DNetRestClient.java

@@ -1,11 +1,11 @@
 
 package eu.dnetlib.dhp.common.rest;
 
-import java.io.IOException;
 import java.util.Arrays;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpGet;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.client.methods.HttpUriRequest;
@@ -23,20 +23,17 @@ public class DNetRestClient {
 
 	private static final ObjectMapper mapper = new ObjectMapper();
 
-	private DNetRestClient() {
-	}
-
 	public static <T> T doGET(final String url, Class<T> clazz) throws Exception {
 		final HttpGet httpGet = new HttpGet(url);
 		return doHTTPRequest(httpGet, clazz);
 	}
 
-	public static String doGET(final String url) throws IOException {
+	public static String doGET(final String url) throws Exception {
 		final HttpGet httpGet = new HttpGet(url);
 		return doHTTPRequest(httpGet);
 	}
 
-	public static <V> String doPOST(final String url, V objParam) throws IOException {
+	public static <V> String doPOST(final String url, V objParam) throws Exception {
 		final HttpPost httpPost = new HttpPost(url);
 
 		if (objParam != null) {
@@ -48,25 +45,25 @@ public class DNetRestClient {
 		return doHTTPRequest(httpPost);
 	}
 
-	public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws IOException {
+	public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws Exception {
 		return mapper.readValue(doPOST(url, objParam), clazz);
 	}
 
-	private static String doHTTPRequest(final HttpUriRequest r) throws IOException {
-		try (CloseableHttpClient client = HttpClients.createDefault()) {
+	private static String doHTTPRequest(final HttpUriRequest r) throws Exception {
+		CloseableHttpClient client = HttpClients.createDefault();
 
-			log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
-			log
-				.info(
-					"request headers: {}",
-					Arrays
-						.asList(r.getAllHeaders())
-						.stream()
-						.map(h -> h.getName() + ":" + h.getValue())
-						.collect(Collectors.joining(",")));
+		log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
+		log
+			.info(
+				"request headers: {}",
+				Arrays
+					.asList(r.getAllHeaders())
+					.stream()
+					.map(h -> h.getName() + ":" + h.getValue())
+					.collect(Collectors.joining(",")));
 
-			return IOUtils.toString(client.execute(r).getEntity().getContent());
-		}
+		CloseableHttpResponse response = client.execute(r);
+		return IOUtils.toString(response.getEntity().getContent());
 	}
 
 	private static <T> T doHTTPRequest(final HttpUriRequest r, Class<T> clazz) throws Exception {

dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java

@@ -46,7 +46,7 @@ public class Vocabulary implements Serializable {
 	}
 
 	public VocabularyTerm getTerm(final String id) {
-		return Optional.ofNullable(id).map(String::toLowerCase).map(terms::get).orElse(null);
+		return Optional.ofNullable(id).map(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null);
 	}
 
 	protected void addTerm(final String id, final String name) {
@@ -81,6 +81,7 @@ public class Vocabulary implements Serializable {
 			.ofNullable(getTermBySynonym(syn))
 			.map(term -> getTermAsQualifier(term.getId()))
 			.orElse(null);
+		// .orElse(OafMapperUtils.unknown(getId(), getName()));
 	}
 
 }

dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java

@@ -46,6 +46,7 @@ public class VocabularyGroup implements Serializable {
 				}
 
 				vocs.addTerm(vocId, termId, termName);
+				// vocs.addSynonyms(vocId, termId, termId);
 			}
 		}
 
@@ -57,6 +58,7 @@ public class VocabularyGroup implements Serializable {
 				final String syn = arr[2].trim();
 
 				vocs.addSynonyms(vocId, termId, syn);
+				// vocs.addSynonyms(vocId, termId, termId);
 			}
 		}
 
@@ -96,7 +98,7 @@ public class VocabularyGroup implements Serializable {
 			.getTerms()
 			.values()
 			.stream()
-			.map(VocabularyTerm::getId)
+			.map(t -> t.getId())
 			.collect(Collectors.toCollection(HashSet::new));
 	}
 
@@ -152,19 +154,16 @@ public class VocabularyGroup implements Serializable {
 		return Optional
 			.ofNullable(vocId)
 			.map(String::toLowerCase)
-			.map(vocs::containsKey)
+			.map(id -> vocs.containsKey(id))
 			.orElse(false);
 	}
 
 	private void addSynonyms(final String vocId, final String termId, final String syn) {
 		String id = Optional
 			.ofNullable(vocId)
-			.map(String::toLowerCase)
+			.map(s -> s.toLowerCase())
 			.orElseThrow(
-				() -> new IllegalArgumentException(
-					String
-						.format(
-							"empty vocabulary id for [term:%s, synonym:%s]", termId, syn)));
+				() -> new IllegalArgumentException(String.format("empty vocabulary id for [term:%s, synonym:%s]")));
 		Optional
 			.ofNullable(vocs.get(id))
 			.orElseThrow(() -> new IllegalArgumentException("missing vocabulary id: " + vocId))

dhp-common/src/main/java/eu/dnetlib/dhp/message/Message.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.message;
 
 import java.io.Serializable;
+import java.util.HashMap;
 import java.util.LinkedHashMap;
 import java.util.Map;
 
@@ -9,8 +10,8 @@ public class Message implements Serializable {
 
 	private static final long serialVersionUID = 401753881204524893L;
 
-	public static final String CURRENT_PARAM = "current";
-	public static final String TOTAL_PARAM = "total";
+	public static String CURRENT_PARAM = "current";
+	public static String TOTAL_PARAM = "total";
 
 	private MessageType messageType;
 

dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge;
 import java.text.Normalizer;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.apache.commons.lang3.StringUtils;
 
@@ -18,9 +19,6 @@ public class AuthorMerger {
 
 	private static final Double THRESHOLD = 0.95;
 
-	private AuthorMerger() {
-	}
-
 	public static List<Author> merge(List<List<Author>> authors) {
 
 		authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)));
@@ -38,8 +36,7 @@ public class AuthorMerger {
 	public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
 		int pa = countAuthorsPids(a);
 		int pb = countAuthorsPids(b);
-		List<Author> base;
-		List<Author> enrich;
+		List<Author> base, enrich;
 		int sa = authorsSize(a);
 		int sb = authorsSize(b);
 
@@ -65,24 +62,22 @@ public class AuthorMerger {
 		// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
 		final Map<String, Author> basePidAuthorMap = base
 			.stream()
-			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
+			.filter(a -> a.getPid() != null && a.getPid().size() > 0)
 			.flatMap(
 				a -> a
 					.getPid()
 					.stream()
-					.filter(Objects::nonNull)
 					.map(p -> new Tuple2<>(pidToComparableString(p), a)))
 			.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
 
 		// <pid, Author> (list of pid that are missing in the other list)
 		final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
 			.stream()
-			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
+			.filter(a -> a.getPid() != null && a.getPid().size() > 0)
 			.flatMap(
 				a -> a
 					.getPid()
 					.stream()
-					.filter(Objects::nonNull)
 					.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
 					.map(p -> new Tuple2<>(p, a)))
 			.collect(Collectors.toList());
@@ -120,9 +115,9 @@ public class AuthorMerger {
 	}
 
 	public static String pidToComparableString(StructuredProperty pid) {
-		final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
-			: "";
-		return (pid.getQualifier() != null ? classid : "")
+		return (pid.getQualifier() != null
+			? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
+			: "")
 			+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
 	}
 
@@ -155,7 +150,7 @@ public class AuthorMerger {
 	}
 
 	private static boolean hasPid(Author a) {
-		if (a == null || a.getPid() == null || a.getPid().isEmpty())
+		if (a == null || a.getPid() == null || a.getPid().size() == 0)
 			return false;
 		return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
 	}
@@ -164,10 +159,7 @@ public class AuthorMerger {
 		if (StringUtils.isNotBlank(author.getSurname())) {
 			return new Person(author.getSurname() + ", " + author.getName(), false);
 		} else {
-			if (StringUtils.isNotBlank(author.getFullname()))
-				return new Person(author.getFullname(), false);
-			else
-				return new Person("", false);
+			return new Person(author.getFullname(), false);
 		}
 	}
 

dhp-common/src/main/java/eu/dnetlib/dhp/parser/utility/VtdUtilityParser.java

@@ -12,9 +12,6 @@ import com.ximpleware.VTDNav;
 /** Created by sandro on 9/29/16. */
 public class VtdUtilityParser {
 
-	private VtdUtilityParser() {
-	}
-
 	public static List<Node> getTextValuesWithAttributes(
 		final AutoPilot ap, final VTDNav vn, final String xpath, final List<String> attributes)
 		throws VtdException {

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java

@@ -7,19 +7,22 @@ import java.time.format.DateTimeFormatter;
 import java.time.format.DateTimeParseException;
 import java.util.*;
 import java.util.function.Function;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.apache.commons.lang3.StringUtils;
+import org.jetbrains.annotations.NotNull;
 
 import com.github.sisyphsu.dateparser.DateParserUtils;
 import com.google.common.collect.Lists;
+import com.google.common.collect.Maps;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.*;
-import me.xuender.unidecode.Unidecode;
 
 public class GraphCleaningFunctions extends CleaningFunctions {
 
@@ -27,11 +30,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 	public static final int ORCID_LEN = 19;
 	public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
 	public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
-
-	public static final String TITLE_TEST = "test";
-	public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
-
-	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
+	public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]";
+	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10;
 
 	public static <T extends Oaf> T fixVocabularyNames(T value) {
 		if (value instanceof Datasource) {
@@ -194,21 +194,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 							.filter(Objects::nonNull)
 							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 							.filter(
-								sp -> {
-									final String title = sp
-										.getValue()
-										.toLowerCase();
-									final String decoded = Unidecode.decode(title);
-
-									if (StringUtils.contains(decoded, TITLE_TEST)) {
-										return decoded
-											.replaceAll(TITLE_FILTER_REGEX, "")
-											.length() > TITLE_FILTER_RESIDUAL_LENGTH;
-									}
-									return !decoded
-										.replaceAll("\\W|\\d", "")
-										.isEmpty();
-								})
+								sp -> sp
+									.getValue()
+									.toLowerCase()
+									.replaceAll(TITLE_FILTER_REGEX, "")
+									.length() > TITLE_FILTER_RESIDUAL_LENGTH)
 							.map(GraphCleaningFunctions::cleanValue)
 							.collect(Collectors.toList()));
 			}
@@ -293,7 +283,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						r
 							.getAuthor()
 							.stream()
-							.filter(Objects::nonNull)
+							.filter(a -> Objects.nonNull(a))
 							.filter(a -> StringUtils.isNotBlank(a.getFullname()))
 							.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
 							.collect(Collectors.toList()));

dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java

@@ -17,16 +17,13 @@ import eu.dnetlib.dhp.schema.oaf.*;
 
 public class OafMapperUtils {
 
-	private OafMapperUtils() {
-	}
-
 	public static Oaf merge(final Oaf left, final Oaf right) {
 		if (ModelSupport.isSubClass(left, OafEntity.class)) {
 			return mergeEntities((OafEntity) left, (OafEntity) right);
 		} else if (ModelSupport.isSubClass(left, Relation.class)) {
 			((Relation) left).mergeFrom((Relation) right);
 		} else {
-			throw new IllegalArgumentException("invalid Oaf type:" + left.getClass().getCanonicalName());
+			throw new RuntimeException("invalid Oaf type:" + left.getClass().getCanonicalName());
 		}
 		return left;
 	}
@@ -41,7 +38,7 @@ public class OafMapperUtils {
 		} else if (ModelSupport.isSubClass(left, Project.class)) {
 			left.mergeFrom(right);
 		} else {
-			throw new IllegalArgumentException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
+			throw new RuntimeException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
 		}
 		return left;
 	}
@@ -65,7 +62,7 @@ public class OafMapperUtils {
 
 	public static List<KeyValue> listKeyValues(final String... s) {
 		if (s.length % 2 > 0) {
-			throw new IllegalArgumentException("Invalid number of parameters (k,v,k,v,....)");
+			throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)");
 		}
 
 		final List<KeyValue> list = new ArrayList<>();
@@ -91,7 +88,7 @@ public class OafMapperUtils {
 			.stream(values)
 			.map(v -> field(v, info))
 			.filter(Objects::nonNull)
-			.filter(distinctByKey(Field::getValue))
+			.filter(distinctByKey(f -> f.getValue()))
 			.collect(Collectors.toList());
 	}
 
@@ -100,7 +97,7 @@ public class OafMapperUtils {
 			.stream()
 			.map(v -> field(v, info))
 			.filter(Objects::nonNull)
-			.filter(distinctByKey(Field::getValue))
+			.filter(distinctByKey(f -> f.getValue()))
 			.collect(Collectors.toList());
 	}
 
@@ -345,10 +342,10 @@ public class OafMapperUtils {
 		if (instanceList != null) {
 			final Optional<AccessRight> min = instanceList
 				.stream()
-				.map(Instance::getAccessright)
+				.map(i -> i.getAccessright())
 				.min(new AccessRightComparator<>());
 
-			final Qualifier rights = min.map(OafMapperUtils::qualifier).orElseGet(Qualifier::new);
+			final Qualifier rights = min.isPresent() ? qualifier(min.get()) : new Qualifier();
 
 			if (StringUtils.isBlank(rights.getClassid())) {
 				rights.setClassid(UNKNOWN);

dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java

@@ -4,19 +4,19 @@ package eu.dnetlib.dhp.utils;
 import java.io.*;
 import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
-import java.util.*;
-import java.util.stream.Collectors;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+import java.util.zip.GZIPInputStream;
+import java.util.zip.GZIPOutputStream;
 
+import org.apache.commons.codec.binary.Base64;
+import org.apache.commons.codec.binary.Base64OutputStream;
 import org.apache.commons.codec.binary.Hex;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
-import org.apache.http.client.methods.CloseableHttpResponse;
-import org.apache.http.client.methods.HttpGet;
-import org.apache.http.impl.client.CloseableHttpClient;
-import org.apache.http.impl.client.HttpClients;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.SaveMode;
 import org.slf4j.Logger;
@@ -26,8 +26,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.collect.Maps;
 import com.jayway.jsonpath.JsonPath;
 
-import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
 import net.minidev.json.JSONArray;
 import scala.collection.JavaConverters;
 import scala.collection.Seq;
@@ -36,9 +34,6 @@ public class DHPUtils {
 
 	private static final Logger log = LoggerFactory.getLogger(DHPUtils.class);
 
-	private DHPUtils() {
-	}
-
 	public static Seq<String> toSeq(List<String> list) {
 		return JavaConverters.asScalaIteratorConverter(list.iterator()).asScala().toSeq();
 	}
@@ -49,59 +44,40 @@ public class DHPUtils {
 			md.update(s.getBytes(StandardCharsets.UTF_8));
 			return new String(Hex.encodeHex(md.digest()));
 		} catch (final Exception e) {
-			log.error("Error creating id from {}", s);
+			System.err.println("Error creating id");
 			return null;
 		}
 	}
 
-	/**
-	 * Retrieves from the metadata store manager application the list of paths associated with mdstores characterized
-	 * by he given format, layout, interpretation
-	 * @param mdstoreManagerUrl the URL of the mdstore manager service
-	 * @param format the mdstore format
-	 * @param layout the mdstore layout
-	 * @param interpretation the mdstore interpretation
-	 * @param includeEmpty include Empty mdstores
-	 * @return the set of hdfs paths
-	 * @throws IOException in case of HTTP communication issues
-	 */
-	public static Set<String> mdstorePaths(final String mdstoreManagerUrl,
-		final String format,
-		final String layout,
-		final String interpretation,
-		boolean includeEmpty) throws IOException {
-		final String url = mdstoreManagerUrl + "/mdstores/";
-		final ObjectMapper objectMapper = new ObjectMapper();
-
-		final HttpGet req = new HttpGet(url);
-
-		try (final CloseableHttpClient client = HttpClients.createDefault()) {
-			try (final CloseableHttpResponse response = client.execute(req)) {
-				final String json = IOUtils.toString(response.getEntity().getContent());
-				final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class);
-				return Arrays
-					.stream(mdstores)
-					.filter(md -> md.getFormat().equalsIgnoreCase(format))
-					.filter(md -> md.getLayout().equalsIgnoreCase(layout))
-					.filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation))
-					.filter(md -> StringUtils.isNotBlank(md.getHdfsPath()))
-					.filter(md -> StringUtils.isNotBlank(md.getCurrentVersion()))
-					.filter(md -> includeEmpty || md.getSize() > 0)
-					.map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store")
-					.collect(Collectors.toSet());
-			}
-		}
-	}
-
 	public static String generateIdentifier(final String originalId, final String nsPrefix) {
 		return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
 	}
 
-	public static String generateUnresolvedIdentifier(final String pid, final String pidType) {
+	public static String compressString(final String input) {
+		try (ByteArrayOutputStream out = new ByteArrayOutputStream();
+			Base64OutputStream b64os = new Base64OutputStream(out)) {
+			GZIPOutputStream gzip = new GZIPOutputStream(b64os);
+			gzip.write(input.getBytes(StandardCharsets.UTF_8));
+			gzip.close();
+			return out.toString();
+		} catch (Throwable e) {
+			return null;
+		}
+	}
 
-		final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid);
-
-		return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim());
+	public static String decompressString(final String input) {
+		byte[] byteArray = Base64.decodeBase64(input.getBytes());
+		int len;
+		try (GZIPInputStream gis = new GZIPInputStream(new ByteArrayInputStream((byteArray)));
+			ByteArrayOutputStream bos = new ByteArrayOutputStream(byteArray.length)) {
+			byte[] buffer = new byte[1024];
+			while ((len = gis.read(buffer)) != -1) {
+				bos.write(buffer, 0, len);
+			}
+			return bos.toString();
+		} catch (Exception e) {
+			return null;
+		}
 	}
 
 	public static String getJPathString(final String jsonPath, final String json) {

dhp-common/src/main/java/eu/dnetlib/dhp/utils/ISLookupClientFactory.java

@@ -18,16 +18,13 @@ public class ISLookupClientFactory {
 	private static final int requestTimeout = 60000 * 10;
 	private static final int connectTimeout = 60000 * 10;
 
-	private ISLookupClientFactory() {
-	}
-
 	public static ISLookUpService getLookUpService(final String isLookupUrl) {
 		return getServiceStub(ISLookUpService.class, isLookupUrl);
 	}
 
 	@SuppressWarnings("unchecked")
 	private static <T> T getServiceStub(final Class<T> clazz, final String endpoint) {
-		log.info("creating {} stub from {}", clazz.getName(), endpoint);
+		log.info(String.format("creating %s stub from %s", clazz.getName(), endpoint));
 		final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
 		jaxWsProxyFactory.setServiceClass(clazz);
 		jaxWsProxyFactory.setAddress(endpoint);
@@ -41,10 +38,12 @@ public class ISLookupClientFactory {
 
 			log
 				.info(
-					"setting connectTimeout to {}, requestTimeout to {} for service {}",
-					connectTimeout,
-					requestTimeout,
-					clazz.getCanonicalName());
+					String
+						.format(
+							"setting connectTimeout to %s, requestTimeout to %s for service %s",
+							connectTimeout,
+							requestTimeout,
+							clazz.getCanonicalName()));
 
 			policy.setConnectionTimeout(connectTimeout);
 			policy.setReceiveTimeout(requestTimeout);

dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/AbstractExtensionFunction.java

@@ -10,7 +10,7 @@ import net.sf.saxon.trans.XPathException;
 
 public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition {
 
-	public static final String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
+	public static String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
 
 	public abstract String getName();
 

dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/ExtractYear.java

@@ -26,7 +26,7 @@ public class ExtractYear extends AbstractExtensionFunction {
 
 	@Override
 	public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
-		if (arguments == null || arguments.length == 0) {
+		if (arguments == null | arguments.length == 0) {
 			return new StringValue("");
 		}
 		final Item item = arguments[0].head();
@@ -63,7 +63,8 @@ public class ExtractYear extends AbstractExtensionFunction {
 		for (String format : dateFormats) {
 			try {
 				c.setTime(new SimpleDateFormat(format).parse(s));
-				return String.valueOf(c.get(Calendar.YEAR));
+				String year = String.valueOf(c.get(Calendar.YEAR));
+				return year;
 			} catch (ParseException e) {
 			}
 		}

dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/NormalizeDate.java

@@ -30,7 +30,7 @@ public class NormalizeDate extends AbstractExtensionFunction {
 
 	@Override
 	public Sequence doCall(XPathContext context, Sequence[] arguments) throws XPathException {
-		if (arguments == null || arguments.length == 0) {
+		if (arguments == null | arguments.length == 0) {
 			return new StringValue(BLANK);
 		}
 		String s = arguments[0].head().getStringValue();

dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/PickFirst.java

@@ -1,8 +1,6 @@
 
 package eu.dnetlib.dhp.utils.saxon;
 
-import static org.apache.commons.lang3.StringUtils.isNotBlank;
-
 import org.apache.commons.lang3.StringUtils;
 
 import net.sf.saxon.expr.XPathContext;
@@ -28,8 +26,7 @@ public class PickFirst extends AbstractExtensionFunction {
 		final String s1 = getValue(arguments[0]);
 		final String s2 = getValue(arguments[1]);
 
-		final String value = isNotBlank(s1) ? s1 : isNotBlank(s2) ? s2 : "";
-		return new StringValue(value);
+		return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
 	}
 
 	private String getValue(final Sequence arg) throws XPathException {

dhp-common/src/main/java/eu/dnetlib/dhp/utils/saxon/SaxonTransformerFactory.java

@@ -12,9 +12,6 @@ import net.sf.saxon.TransformerFactoryImpl;
 
 public class SaxonTransformerFactory {
 
-	private SaxonTransformerFactory() {
-	}
-
 	/**
 	 * Creates the index record transformer from the given XSLT
 	 *

dhp-common/src/test/java/eu/dnetlib/dhp/application/ArgumentApplicationParserTest.java

@@ -7,10 +7,10 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
 import org.apache.commons.io.IOUtils;
 import org.junit.jupiter.api.Test;
 
-class ArgumentApplicationParserTest {
+public class ArgumentApplicationParserTest {
 
 	@Test
-	void testParseParameter() throws Exception {
+	public void testParseParameter() throws Exception {
 		final String jsonConfiguration = IOUtils
 			.toString(
 				this.getClass().getResourceAsStream("/eu/dnetlib/application/parameters.json"));

dhp-common/src/test/java/eu/dnetlib/dhp/common/HdfsSupportTest.java

@@ -21,13 +21,13 @@ public class HdfsSupportTest {
 	class Remove {
 
 		@Test
-		void shouldThrowARuntimeExceptionOnError() {
+		public void shouldThrowARuntimeExceptionOnError() {
 			// when
 			assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
 		}
 
 		@Test
-		void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
+		public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
 			// when
 			HdfsSupport.remove(tempDir.toString(), new Configuration());
 
@@ -36,7 +36,7 @@ public class HdfsSupportTest {
 		}
 
 		@Test
-		void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
+		public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
 			// given
 			Path file = Files.createTempFile(tempDir, "p", "s");
 
@@ -52,13 +52,13 @@ public class HdfsSupportTest {
 	class ListFiles {
 
 		@Test
-		void shouldThrowARuntimeExceptionOnError() {
+		public void shouldThrowARuntimeExceptionOnError() {
 			// when
 			assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
 		}
 
 		@Test
-		void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
+		public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
 			Path subDir1 = Files.createTempDirectory(tempDir, "list_me");
 			Path subDir2 = Files.createTempDirectory(tempDir, "list_me");
 

dhp-common/src/test/java/eu/dnetlib/dhp/common/PacePersonTest.java

@@ -5,10 +5,10 @@ import static org.junit.jupiter.api.Assertions.*;
 
 import org.junit.jupiter.api.Test;
 
-class PacePersonTest {
+public class PacePersonTest {
 
 	@Test
-	void pacePersonTest1() {
+	public void pacePersonTest1() {
 
 		PacePerson p = new PacePerson("Artini, Michele", false);
 		assertEquals("Artini", p.getSurnameString());
@@ -17,7 +17,7 @@ class PacePersonTest {
 	}
 
 	@Test
-	void pacePersonTest2() {
+	public void pacePersonTest2() {
 		PacePerson p = new PacePerson("Michele G. Artini", false);
 		assertEquals("Artini, Michele G.", p.getNormalisedFullname());
 		assertEquals("Michele G", p.getNameString());

dhp-common/src/test/java/eu/dnetlib/dhp/common/SparkSessionSupportTest.java

@@ -18,8 +18,7 @@ public class SparkSessionSupportTest {
 	class RunWithSparkSession {
 
 		@Test
-		@SuppressWarnings("unchecked")
-		void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
+		public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
 			throws Exception {
 			// given
 			SparkSession spark = mock(SparkSession.class);
@@ -38,8 +37,7 @@ public class SparkSessionSupportTest {
 		}
 
 		@Test
-		@SuppressWarnings("unchecked")
-		void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
+		public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
 			throws Exception {
 			// given
 			SparkSession spark = mock(SparkSession.class);

dhp-common/src/test/java/eu/dnetlib/dhp/common/api/ZenodoAPIClientTest.java

@@ -12,7 +12,7 @@ import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Test;
 
 @Disabled
-class ZenodoAPIClientTest {
+public class ZenodoAPIClientTest {
 
 	private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
 	private final String ACCESS_TOKEN = "";
@@ -22,7 +22,7 @@ class ZenodoAPIClientTest {
 	private final String depositionId = "674915";
 
 	@Test
-	void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
+	public void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
 		Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId));
@@ -44,7 +44,7 @@ class ZenodoAPIClientTest {
 	}
 
 	@Test
-	void testNewDeposition() throws IOException {
+	public void testNewDeposition() throws IOException {
 
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
@@ -67,7 +67,7 @@ class ZenodoAPIClientTest {
 	}
 
 	@Test
-	void testNewVersionNewName() throws IOException, MissingConceptDoiException {
+	public void testNewVersionNewName() throws IOException, MissingConceptDoiException {
 
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
@@ -87,7 +87,7 @@ class ZenodoAPIClientTest {
 	}
 
 	@Test
-	void testNewVersionOldName() throws IOException, MissingConceptDoiException {
+	public void testNewVersionOldName() throws IOException, MissingConceptDoiException {
 
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);

dhp-common/src/test/java/eu/dnetlib/dhp/oa/merge/AuthorMergerTest.java

@@ -21,7 +21,7 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.pace.util.MapDocumentUtil;
 import scala.Tuple2;
 
-class AuthorMergerTest {
+public class AuthorMergerTest {
 
 	private String publicationsBasePath;
 
@@ -43,7 +43,7 @@ class AuthorMergerTest {
 	}
 
 	@Test
-	void mergeTest() { // used in the dedup: threshold set to 0.95
+	public void mergeTest() { // used in the dedup: threshold set to 0.95
 
 		for (List<Author> authors1 : authors) {
 			System.out.println("List " + (authors.indexOf(authors1) + 1));

dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java

@@ -4,8 +4,12 @@ package eu.dnetlib.dhp.schema.oaf.utils;
 import static org.junit.jupiter.api.Assertions.*;
 
 import java.io.IOException;
+import java.time.LocalDate;
+import java.time.format.DateTimeFormatter;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
+import java.util.Optional;
 import java.util.stream.Collectors;
 
 import org.apache.commons.io.IOUtils;
@@ -15,34 +19,15 @@ import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Dataset;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Publication;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import me.xuender.unidecode.Unidecode;
+import eu.dnetlib.dhp.schema.oaf.*;
 
-class OafMapperUtilsTest {
+public class OafMapperUtilsTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
 		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
 	@Test
-	public void testUnidecode() {
-
-		assertEquals("Liu Ben Mu hiruzuSen tawa", Unidecode.decode("六本木ヒルズ森タワ"));
-		assertEquals("Nan Wu A Mi Tuo Fo", Unidecode.decode("南无阿弥陀佛"));
-		assertEquals("Yi Tiao Hui Zou Lu De Yu", Unidecode.decode("一条会走路的鱼"));
-		assertEquals("amidaniyorai", Unidecode.decode("あみだにょらい"));
-		assertEquals("T`owrk`iayi", Unidecode.decode("Թուրքիայի"));
-		assertEquals("Obzor tematiki", Unidecode.decode("Обзор тематики"));
-		assertEquals("GERMANSKIE IaZYKI", Unidecode.decode("ГЕРМАНСКИЕ ЯЗЫКИ"));
-		assertEquals("Diereunese tes ikanopoieses", Unidecode.decode("Διερεύνηση της ικανοποίησης"));
-		assertEquals("lqDy l'wly@", Unidecode.decode("القضايا الأولية"));
-		assertEquals("abc def ghi", Unidecode.decode("abc def ghi"));
-	}
-
-	@Test
-	void testDateValidation() {
+	public void testDateValidation() {
 
 		assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z  ").isPresent());
 		assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent());
@@ -147,46 +132,44 @@ class OafMapperUtilsTest {
 	}
 
 	@Test
-	void testDate() {
-		final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
-		assertNotNull(date);
-		System.out.println(date);
+	public void testDate() {
+		System.out.println(GraphCleaningFunctions.cleanDate("23-FEB-1998"));
 	}
 
 	@Test
-	void testMergePubs() throws IOException {
+	public void testMergePubs() throws IOException {
 		Publication p1 = read("publication_1.json", Publication.class);
 		Publication p2 = read("publication_2.json", Publication.class);
 		Dataset d1 = read("dataset_1.json", Dataset.class);
 		Dataset d2 = read("dataset_2.json", Dataset.class);
 
-		assertEquals(1, p1.getCollectedfrom().size());
-		assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
-		assertEquals(1, d2.getCollectedfrom().size());
+		assertEquals(p1.getCollectedfrom().size(), 1);
+		assertEquals(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
+		assertEquals(d2.getCollectedfrom().size(), 1);
 		assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
-		assertEquals(
-			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
+		assertTrue(
 			OafMapperUtils
 				.mergeResults(p1, d2)
 				.getResulttype()
-				.getClassid());
+				.getClassid()
+				.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
 
-		assertEquals(1, p2.getCollectedfrom().size());
+		assertEquals(p2.getCollectedfrom().size(), 1);
 		assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
-		assertEquals(1, d1.getCollectedfrom().size());
+		assertEquals(d1.getCollectedfrom().size(), 1);
 		assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
-		assertEquals(
-			ModelConstants.DATASET_RESULTTYPE_CLASSID,
+		assertTrue(
 			OafMapperUtils
 				.mergeResults(p2, d1)
 				.getResulttype()
-				.getClassid());
+				.getClassid()
+				.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
 	}
 
 	protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
-		return collectedfrom.stream().map(KeyValue::getKey).collect(Collectors.toCollection(HashSet::new));
+		return collectedfrom.stream().map(c -> c.getKey()).collect(Collectors.toCollection(HashSet::new));
 	}
 
 	protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {

dhp-common/src/test/java/eu/dnetlib/scholexplorer/relation/RelationMapperTest.java

@@ -3,10 +3,10 @@ package eu.dnetlib.scholexplorer.relation;
 
 import org.junit.jupiter.api.Test;
 
-class RelationMapperTest {
+public class RelationMapperTest {
 
 	@Test
-	void testLoadRels() throws Exception {
+	public void testLoadRels() throws Exception {
 
 		RelationMapper relationMapper = RelationMapper.load();
 		relationMapper.keySet().forEach(System.out::println);

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/ISClient.java

@@ -3,37 +3,40 @@ package eu.dnetlib.dhp.actionmanager;
 
 import java.io.Serializable;
 import java.io.StringReader;
-import java.util.List;
-import java.util.NoSuchElementException;
-import java.util.Optional;
-import java.util.Set;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang3.tuple.Triple;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
+import org.dom4j.Element;
 import org.dom4j.io.SAXReader;
+import org.jetbrains.annotations.NotNull;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.xml.sax.SAXException;
 
 import com.google.common.base.Joiner;
 import com.google.common.base.Splitter;
 import com.google.common.collect.Iterables;
+import com.google.common.collect.Lists;
 import com.google.common.collect.Sets;
 
 import eu.dnetlib.actionmanager.rmi.ActionManagerException;
+import eu.dnetlib.actionmanager.set.ActionManagerSet;
+import eu.dnetlib.actionmanager.set.ActionManagerSet.ImpactTypes;
+import eu.dnetlib.dhp.actionmanager.partition.PartitionActionSetsByPayloadTypeJob;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
 import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
+import scala.Tuple2;
 
 public class ISClient implements Serializable {
 
-	private static final Logger log = LoggerFactory.getLogger(ISClient.class);
+	private static final Logger log = LoggerFactory.getLogger(PartitionActionSetsByPayloadTypeJob.class);
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
 
-	private final transient ISLookUpService isLookup;
+	private final ISLookUpService isLookup;
 
 	public ISClient(String isLookupUrl) {
 		isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
@@ -60,7 +63,7 @@ public class ISClient implements Serializable {
 				.map(
 					sets -> sets
 						.stream()
-						.map(ISClient::parseSetInfo)
+						.map(set -> parseSetInfo(set))
 						.filter(t -> ids.contains(t.getLeft()))
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
@@ -70,17 +73,15 @@ public class ISClient implements Serializable {
 		}
 	}
 
-	private static Triple<String, String, String> parseSetInfo(String set) {
+	private Triple<String, String, String> parseSetInfo(String set) {
 		try {
-			final SAXReader reader = new SAXReader();
-			reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
-			Document doc = reader.read(new StringReader(set));
+			Document doc = new SAXReader().read(new StringReader(set));
 			return Triple
 				.of(
 					doc.valueOf("//SET/@id"),
 					doc.valueOf("//SET/@directory"),
 					doc.valueOf("//SET/@latest"));
-		} catch (DocumentException | SAXException e) {
+		} catch (DocumentException e) {
 			throw new IllegalStateException(e);
 		}
 	}
@@ -98,7 +99,7 @@ public class ISClient implements Serializable {
 		final String q = "for $x in /RESOURCE_PROFILE[.//RESOURCE_TYPE/@value='ActionManagerServiceResourceType'] return $x//SERVICE_PROPERTIES/PROPERTY[./@ key='"
 			+ propertyName
 			+ "']/@value/string()";
-		log.debug("quering for service property: {}", q);
+		log.debug("quering for service property: " + q);
 		try {
 			final List<String> value = isLookup.quickSearchProfile(q);
 			return Iterables.getOnlyElement(value);

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGet.java

@@ -62,7 +62,6 @@ public class MergeAndGet {
 					x.getClass().getCanonicalName(), y.getClass().getCanonicalName()));
 	}
 
-	@SuppressWarnings("unchecked")
 	private static <G extends Oaf, A extends Oaf> G selectNewerAndGet(G x, A y) {
 		if (x.getClass().equals(y.getClass())
 			&& x.getLastupdatetimestamp() > y.getLastupdatetimestamp()) {

dhp-workflows/dhp-actionmanager/src/main/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJob.java

@@ -74,9 +74,7 @@ public class PromoteActionPayloadForGraphTableJob {
 			.orElse(true);
 		logger.info("shouldGroupById: {}", shouldGroupById);
 
-		@SuppressWarnings("unchecked")
 		Class<? extends Oaf> rowClazz = (Class<? extends Oaf>) Class.forName(graphTableClassName);
-		@SuppressWarnings("unchecked")
 		Class<? extends Oaf> actionPayloadClazz = (Class<? extends Oaf>) Class.forName(actionPayloadClassName);
 
 		throwIfGraphTableClassIsNotSubClassOfActionPayloadClass(rowClazz, actionPayloadClazz);
@@ -154,7 +152,7 @@ public class PromoteActionPayloadForGraphTableJob {
 		return spark
 			.read()
 			.parquet(path)
-			.map((MapFunction<Row, String>) PromoteActionPayloadForGraphTableJob::extractPayload, Encoders.STRING())
+			.map((MapFunction<Row, String>) value -> extractPayload(value), Encoders.STRING())
 			.map(
 				(MapFunction<String, A>) value -> decodePayload(actionPayloadClazz, value),
 				Encoders.bean(actionPayloadClazz));

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml

@@ -107,7 +107,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.sql.shuffle.partitions=2560
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
@@ -159,7 +159,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.sql.shuffle.partitions=2560
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${workingDir}/publication</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>

dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml

@@ -99,7 +99,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=5000
+                --conf spark.sql.shuffle.partitions=2560
             </spark-opts>
             <arg>--inputGraphTablePath</arg><arg>${inputGraphRootPath}/relation</arg>
             <arg>--graphTableClassName</arg><arg>eu.dnetlib.dhp.schema.oaf.Relation</arg>

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/partition/PartitionActionSetsByPayloadTypeJobTest.java

@@ -80,7 +80,7 @@ public class PartitionActionSetsByPayloadTypeJobTest {
 		private ISClient isClient;
 
 		@Test
-		void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
+		public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
 			// given
 			Path inputActionSetsBaseDir = workingDir.resolve("input").resolve("action_sets");
 			Path outputDir = workingDir.resolve("output");

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/MergeAndGetTest.java

@@ -20,7 +20,7 @@ public class MergeAndGetTest {
 	class MergeFromAndGetStrategy {
 
 		@Test
-		void shouldThrowForOafAndOaf() {
+		public void shouldThrowForOafAndOaf() {
 			// given
 			Oaf a = mock(Oaf.class);
 			Oaf b = mock(Oaf.class);
@@ -33,7 +33,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafAndRelation() {
+		public void shouldThrowForOafAndRelation() {
 			// given
 			Oaf a = mock(Oaf.class);
 			Relation b = mock(Relation.class);
@@ -46,7 +46,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafAndOafEntity() {
+		public void shouldThrowForOafAndOafEntity() {
 			// given
 			Oaf a = mock(Oaf.class);
 			OafEntity b = mock(OafEntity.class);
@@ -59,7 +59,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForRelationAndOaf() {
+		public void shouldThrowForRelationAndOaf() {
 			// given
 			Relation a = mock(Relation.class);
 			Oaf b = mock(Oaf.class);
@@ -72,7 +72,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForRelationAndOafEntity() {
+		public void shouldThrowForRelationAndOafEntity() {
 			// given
 			Relation a = mock(Relation.class);
 			OafEntity b = mock(OafEntity.class);
@@ -85,7 +85,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldBehaveProperlyForRelationAndRelation() {
+		public void shouldBehaveProperlyForRelationAndRelation() {
 			// given
 			Relation a = mock(Relation.class);
 			Relation b = mock(Relation.class);
@@ -101,7 +101,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafEntityAndOaf() {
+		public void shouldThrowForOafEntityAndOaf() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Oaf b = mock(Oaf.class);
@@ -114,7 +114,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafEntityAndRelation() {
+		public void shouldThrowForOafEntityAndRelation() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Relation b = mock(Relation.class);
@@ -127,7 +127,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
+		public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
 			// given
 			class OafEntitySub1 extends OafEntity {
 			}
@@ -145,7 +145,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldBehaveProperlyForOafEntityAndOafEntity() {
+		public void shouldBehaveProperlyForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			OafEntity b = mock(OafEntity.class);
@@ -165,7 +165,7 @@ public class MergeAndGetTest {
 	class SelectNewerAndGetStrategy {
 
 		@Test
-		void shouldThrowForOafEntityAndRelation() {
+		public void shouldThrowForOafEntityAndRelation() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Relation b = mock(Relation.class);
@@ -178,7 +178,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForRelationAndOafEntity() {
+		public void shouldThrowForRelationAndOafEntity() {
 			// given
 			Relation a = mock(Relation.class);
 			OafEntity b = mock(OafEntity.class);
@@ -191,7 +191,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowForOafEntityAndResult() {
+		public void shouldThrowForOafEntityAndResult() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Result b = mock(Result.class);
@@ -204,7 +204,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
+		public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
 			// given
 			// real types must be used because subclass-superclass resolution does not work for
 			// mocks
@@ -221,7 +221,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldShouldReturnLeftForOafEntityAndOafEntity() {
+		public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			when(a.getLastupdatetimestamp()).thenReturn(1L);
@@ -238,7 +238,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		void shouldShouldReturnRightForOafEntityAndOafEntity() {
+		public void shouldShouldReturnRightForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			when(a.getLastupdatetimestamp()).thenReturn(2L);

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java

@@ -77,7 +77,7 @@ public class PromoteActionPayloadForGraphTableJobTest {
 	class Main {
 
 		@Test
-		void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
+		public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
 			// given
 			Class<Relation> rowClazz = Relation.class;
 			Class<OafEntity> actionPayloadClazz = OafEntity.class;
@@ -116,7 +116,7 @@ public class PromoteActionPayloadForGraphTableJobTest {
 
 		@ParameterizedTest(name = "strategy: {0}, graph table: {1}, action payload: {2}")
 		@MethodSource("eu.dnetlib.dhp.actionmanager.promote.PromoteActionPayloadForGraphTableJobTest#promoteJobTestParams")
-		void shouldPromoteActionPayloadForGraphTable(
+		public void shouldPromoteActionPayloadForGraphTable(
 			MergeAndGet.Strategy strategy,
 			Class<? extends Oaf> rowClazz,
 			Class<? extends Oaf> actionPayloadClazz)

dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadFunctionsTest.java

@@ -44,7 +44,7 @@ public class PromoteActionPayloadFunctionsTest {
 	class JoinTableWithActionPayloadAndMerge {
 
 		@Test
-		void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
+		public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
 			// given
 			class OafImpl extends Oaf {
 			}
@@ -58,7 +58,7 @@ public class PromoteActionPayloadFunctionsTest {
 		}
 
 		@Test
-		void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
+		public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
 			// given
 			String id0 = "id0";
 			String id1 = "id1";
@@ -138,7 +138,7 @@ public class PromoteActionPayloadFunctionsTest {
 		}
 
 		@Test
-		void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
+		public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
 			// given
 			String id0 = "id0";
 			String id1 = "id1";
@@ -218,7 +218,7 @@ public class PromoteActionPayloadFunctionsTest {
 	class GroupTableByIdAndMerge {
 
 		@Test
-		void shouldRunProperly() {
+		public void shouldRunProperly() {
 			// given
 			String id1 = "id1";
 			String id2 = "id2";

dhp-workflows/dhp-aggregation/pom.xml

@@ -29,13 +29,6 @@
                             <goal>testCompile</goal>
                         </goals>
                     </execution>
-                    <execution>
-                        <id>scala-doc</id>
-                        <phase>process-resources</phase> <!-- or wherever -->
-                        <goals>
-                            <goal>doc</goal>
-                        </goals>
-                    </execution>
                 </executions>
                 <configuration>
                     <scalaVersion>${scala.version}</scalaVersion>
@@ -91,6 +84,14 @@
             <artifactId>json</artifactId>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/org.apache.commons/commons-csv -->
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-csv</artifactId>
+            <version>1.8</version>
+        </dependency>
+
+
         <!-- https://mvnrepository.com/artifact/org.apache.poi/poi-ooxml -->
         <dependency>
             <groupId>org.apache.poi</groupId>

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/CollectAndSave.java

@@ -4,7 +4,6 @@ package eu.dnetlib.dhp.actionmanager.bipfinder;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
-import java.util.Objects;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -29,16 +28,15 @@ import eu.dnetlib.dhp.schema.oaf.Result;
 public class CollectAndSave implements Serializable {
 
 	private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	public static void main(String[] args) throws Exception {
+	public static <I extends Result> void main(String[] args) throws Exception {
 
 		String jsonConfiguration = IOUtils
 			.toString(
-				Objects
-					.requireNonNull(
-						CollectAndSave.class
-							.getResourceAsStream(
-								"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json")));
+				CollectAndSave.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java

@@ -87,7 +87,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 	private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
 		String bipScorePath, Class<I> inputClazz) {
 
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
 
 		JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
 			.textFile(bipScorePath)
@@ -101,6 +101,8 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				return bs;
 			}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
 
+		System.out.println(bipScores.count());
+
 		Dataset<I> results = readPath(spark, inputPath, inputClazz);
 
 		results.createOrReplaceTempView("result");
@@ -122,7 +124,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				ret.setId(value._2().getId());
 				return ret;
 			}, Encoders.bean(BipScore.class))
-			.groupByKey((MapFunction<BipScore, String>) BipScore::getId, Encoders.STRING())
+			.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
 				Result ret = new Result();
 				ret.setDataInfo(getDataInfo());

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java

@@ -1,49 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import java.util.Optional;
-
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-
-public class Constants {
-
-	public static final String DOI = "doi";
-
-	public static final String UPDATE_DATA_INFO_TYPE = "update";
-	public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
-	public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE";
-	public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
-
-	public static final String FOS_CLASS_ID = "FOS";
-	public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
-
-	public static final String NULL = "NULL";
-
-	public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	private Constants() {
-	}
-
-	public static Boolean isSparkSessionManaged(ArgumentApplicationParser parser) {
-		return Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-	}
-
-	public static <R> Dataset<R> readPath(
-		SparkSession spark, String inputPath, Class<R> clazz) {
-		return spark
-			.read()
-			.textFile(inputPath)
-			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSData.java

@@ -1,77 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.Serializable;
-import java.util.Objects;
-import java.util.Optional;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.collection.GetCSV;
-
-public class GetFOSData implements Serializable {
-
-	private static final Logger log = LoggerFactory.getLogger(GetFOSData.class);
-
-	public static final char DEFAULT_DELIMITER = '\t';
-
-	public static void main(final String[] args) throws Exception {
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							GetFOSData.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json"))));
-
-		parser.parseArgument(args);
-
-		// the path where the original fos csv file is stored
-		final String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath {}", sourcePath);
-
-		// the path where to put the file as json
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}", outputPath);
-
-		final String hdfsNameNode = parser.get("hdfsNameNode");
-		log.info("hdfsNameNode {}", hdfsNameNode);
-
-		final String classForName = parser.get("classForName");
-		log.info("classForName {}", classForName);
-
-		final char delimiter = Optional
-			.ofNullable(parser.get("delimiter"))
-			.map(s -> s.charAt(0))
-			.orElse(DEFAULT_DELIMITER);
-		log.info("delimiter {}", delimiter);
-
-		Configuration conf = new Configuration();
-		conf.set("fs.defaultFS", hdfsNameNode);
-
-		FileSystem fileSystem = FileSystem.get(conf);
-
-		new GetFOSData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem);
-
-	}
-
-	public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs)
-		throws IOException, ClassNotFoundException {
-
-		// reads the csv and writes it as its json equivalent
-		try (InputStreamReader reader = new InputStreamReader(fs.open(new Path(inputPath)))) {
-			GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter);
-		}
-
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java

@@ -1,145 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
-import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UPDATE_CLASS_NAME;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-import java.util.List;
-import java.util.Optional;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.hdfs.client.HdfsUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipDeserialize;
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipScore;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.HdfsSupport;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.KeyValue;
-import eu.dnetlib.dhp.schema.oaf.Measure;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.utils.DHPUtils;
-
-public class PrepareBipFinder implements Serializable {
-
-	private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class);
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static <I extends Result> void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				PrepareBipFinder.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		final String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath {}: ", sourcePath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}: ", outputPath);
-
-		SparkConf conf = new SparkConf();
-
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
-				prepareResults(spark, sourcePath, outputPath);
-			});
-	}
-
-	private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath) {
-
-		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
-
-		JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
-			.textFile(inputPath)
-			.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
-
-		spark
-			.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
-				BipScore bs = new BipScore();
-				bs.setId(key);
-				bs.setScoreList(entry.get(key));
-				return bs;
-			}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class))
-			.map((MapFunction<BipScore, Result>) v -> {
-				Result r = new Result();
-
-				r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI));
-				r.setMeasures(getMeasure(v));
-				return r;
-			}, Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "/bip");
-	}
-
-	private static List<Measure> getMeasure(BipScore value) {
-		return value
-			.getScoreList()
-			.stream()
-			.map(score -> {
-				Measure m = new Measure();
-				m.setId(score.getId());
-				m
-					.setUnit(
-						score
-							.getUnit()
-							.stream()
-							.map(unit -> {
-								KeyValue kv = new KeyValue();
-								kv.setValue(unit.getValue());
-								kv.setKey(unit.getKey());
-								kv
-									.setDataInfo(
-										OafMapperUtils
-											.dataInfo(
-												false,
-												UPDATE_DATA_INFO_TYPE,
-												true,
-												false,
-												OafMapperUtils
-													.qualifier(
-														UPDATE_MEASURE_BIP_CLASS_ID,
-														UPDATE_CLASS_NAME,
-														ModelConstants.DNET_PROVENANCE_ACTIONS,
-														ModelConstants.DNET_PROVENANCE_ACTIONS),
-												""));
-								return kv;
-							})
-							.collect(Collectors.toList()));
-				return m;
-			})
-			.collect(Collectors.toList());
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java

@@ -1,133 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-import java.util.*;
-import java.util.stream.Collectors;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FlatMapFunction;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.sql.Dataset;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Result;
-import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
-import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
-import eu.dnetlib.dhp.utils.DHPUtils;
-
-public class PrepareFOSSparkJob implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				PrepareFOSSparkJob.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json"));
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath: {}", sourcePath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				distributeFOSdois(
-					spark,
-					sourcePath,
-
-					outputPath);
-			});
-	}
-
-	private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
-		Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
-
-		fosDataset.flatMap((FlatMapFunction<FOSDataModel, FOSDataModel>) v -> {
-			List<FOSDataModel> fosList = new ArrayList<>();
-			final String level1 = v.getLevel1();
-			final String level2 = v.getLevel2();
-			final String level3 = v.getLevel3();
-			Arrays
-				.stream(v.getDoi().split("\u0002"))
-				.forEach(d -> fosList.add(FOSDataModel.newInstance(d, level1, level2, level3)));
-			return fosList.iterator();
-		}, Encoders.bean(FOSDataModel.class))
-			.map((MapFunction<FOSDataModel, Result>) value -> {
-				Result r = new Result();
-				r.setId(DHPUtils.generateUnresolvedIdentifier(value.getDoi(), DOI));
-				r.setSubject(getSubjects(value));
-				return r;
-			}, Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath + "/fos");
-	}
-
-	private static List<StructuredProperty> getSubjects(FOSDataModel fos) {
-		return Arrays
-			.asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3()))
-			.stream()
-			.filter(Objects::nonNull)
-			.collect(Collectors.toList());
-	}
-
-	private static StructuredProperty getSubject(String sbj) {
-		if (sbj.equals(NULL))
-			return null;
-		StructuredProperty sp = new StructuredProperty();
-		sp.setValue(sbj);
-		sp
-			.setQualifier(
-				OafMapperUtils
-					.qualifier(
-						FOS_CLASS_ID,
-						FOS_CLASS_NAME,
-						ModelConstants.DNET_SUBJECT_TYPOLOGIES,
-						ModelConstants.DNET_SUBJECT_TYPOLOGIES));
-		sp
-			.setDataInfo(
-				OafMapperUtils
-					.dataInfo(
-						false,
-						UPDATE_DATA_INFO_TYPE,
-						true,
-						false,
-						OafMapperUtils
-							.qualifier(
-								UPDATE_SUBJECT_FOS_CLASS_ID,
-								UPDATE_CLASS_NAME,
-								ModelConstants.DNET_PROVENANCE_ACTIONS,
-								ModelConstants.DNET_PROVENANCE_ACTIONS),
-						""));
-
-		return sp;
-
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java

@@ -1,79 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
-
-import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*;
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.Serializable;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.MapFunction;
-import org.apache.spark.api.java.function.MapGroupsFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SaveMode;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.oaf.Result;
-
-public class SparkSaveUnresolved implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class);
-
-	public static void main(String[] args) throws Exception {
-
-		String jsonConfiguration = IOUtils
-			.toString(
-				PrepareFOSSparkJob.class
-					.getResourceAsStream(
-						"/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json"));
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
-
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		String sourcePath = parser.get("sourcePath");
-		log.info("sourcePath: {}", sourcePath);
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath: {}", outputPath);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				saveUnresolved(
-					spark,
-					sourcePath,
-
-					outputPath);
-			});
-	}
-
-	private static void saveUnresolved(SparkSession spark, String sourcePath, String outputPath) {
-
-		spark
-			.read()
-			.textFile(sourcePath + "/*")
-			.map(
-				(MapFunction<String, Result>) l -> OBJECT_MAPPER.readValue(l, Result.class),
-				Encoders.bean(Result.class))
-			.groupByKey((MapFunction<Result, String>) r -> r.getId(), Encoders.STRING())
-			.mapGroups((MapGroupsFunction<String, Result, Result>) (k, it) -> {
-				Result ret = it.next();
-				it.forEachRemaining(r -> ret.mergeFrom(r));
-				return ret;
-			}, Encoders.bean(Result.class))
-			.write()
-			.mode(SaveMode.Overwrite)
-			.option("compression", "gzip")
-			.json(outputPath);
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java

@@ -1,28 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-/**
- * Class that maps the model of the bipFinder! input data.
- * Only needed for deserialization purposes
- */
-
-public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
-
-	public BipDeserialize() {
-		super();
-	}
-
-	public List<Score> get(String key) {
-
-		if (super.get(key) == null) {
-			return new ArrayList<>();
-		}
-		return super.get(key);
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java

@@ -1,30 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
-
-import java.io.Serializable;
-import java.util.List;
-
-/**
- * Rewriting of the bipFinder input data by extracting the identifier of the result (doi)
- */
-
-public class BipScore implements Serializable {
-	private String id; // doi
-	private List<Score> scoreList; // unit as given in the inputfile
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(String id) {
-		this.id = id;
-	}
-
-	public List<Score> getScoreList() {
-		return scoreList;
-	}
-
-	public void setScoreList(List<Score> scoreList) {
-		this.scoreList = scoreList;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java

@@ -1,71 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
-
-import java.io.Serializable;
-
-import com.opencsv.bean.CsvBindByPosition;
-
-public class FOSDataModel implements Serializable {
-	@CsvBindByPosition(position = 1)
-//    @CsvBindByName(column = "doi")
-	private String doi;
-
-	@CsvBindByPosition(position = 2)
-//    @CsvBindByName(column = "level1")
-	private String level1;
-
-	@CsvBindByPosition(position = 3)
-//    @CsvBindByName(column = "level2")
-	private String level2;
-
-	@CsvBindByPosition(position = 4)
-//    @CsvBindByName(column = "level3")
-	private String level3;
-
-	public FOSDataModel() {
-
-	}
-
-	public FOSDataModel(String doi, String level1, String level2, String level3) {
-		this.doi = doi;
-		this.level1 = level1;
-		this.level2 = level2;
-		this.level3 = level3;
-	}
-
-	public static FOSDataModel newInstance(String d, String level1, String level2, String level3) {
-		return new FOSDataModel(d, level1, level2, level3);
-	}
-
-	public String getDoi() {
-		return doi;
-	}
-
-	public void setDoi(String doi) {
-		this.doi = doi;
-	}
-
-	public String getLevel1() {
-		return level1;
-	}
-
-	public void setLevel1(String level1) {
-		this.level1 = level1;
-	}
-
-	public String getLevel2() {
-		return level2;
-	}
-
-	public void setLevel2(String level2) {
-		this.level2 = level2;
-	}
-
-	public String getLevel3() {
-		return level3;
-	}
-
-	public void setLevel3(String level3) {
-		this.level3 = level3;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java

@@ -1,26 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
-
-import java.io.Serializable;
-
-public class KeyValue implements Serializable {
-
-	private String key;
-	private String value;
-
-	public String getKey() {
-		return key;
-	}
-
-	public void setKey(String key) {
-		this.key = key;
-	}
-
-	public String getValue() {
-		return value;
-	}
-
-	public void setValue(String value) {
-		this.value = value;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java

@@ -1,30 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model;
-
-import java.io.Serializable;
-import java.util.List;
-
-/**
- * represents the score in the input file
- */
-public class Score implements Serializable {
-
-	private String id;
-	private List<KeyValue> unit;
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(String id) {
-		this.id = id;
-	}
-
-	public List<KeyValue> getUnit() {
-		return unit;
-	}
-
-	public void setUnit(List<KeyValue> unit) {
-		this.unit = unit;
-	}
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala

@@ -0,0 +1,86 @@
+package eu.dnetlib.dhp.actionmanager.datacite
+
+import org.apache.commons.io.IOUtils
+import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
+import org.apache.http.entity.StringEntity
+import org.apache.http.impl.client.HttpClients
+
+import java.io.IOException
+
+abstract class AbstractRestClient extends Iterator[String]{
+
+  var buffer: List[String] = List()
+  var current_index:Int = 0
+
+  var scroll_value: Option[String] = None
+
+  var complete:Boolean = false
+
+
+  def extractInfo(input: String): Unit
+
+  protected def getBufferData(): Unit
+
+
+  def doHTTPGETRequest(url:String): String = {
+    val httpGet = new HttpGet(url)
+    doHTTPRequest(httpGet)
+
+  }
+
+  def doHTTPPOSTRequest(url:String, json:String): String = {
+    val httpPost = new HttpPost(url)
+    if (json != null) {
+      val entity = new StringEntity(json)
+      httpPost.setEntity(entity)
+      httpPost.setHeader("Accept", "application/json")
+      httpPost.setHeader("Content-type", "application/json")
+    }
+    doHTTPRequest(httpPost)
+  }
+
+  def hasNext: Boolean = {
+    buffer.nonEmpty && current_index < buffer.size
+  }
+
+
+  override def next(): String = {
+    val next_item:String = buffer(current_index)
+    current_index = current_index + 1
+    if (current_index == buffer.size)
+      getBufferData()
+    next_item
+  }
+
+
+
+
+  private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
+    val client = HttpClients.createDefault
+    var tries = 4
+    try {
+      while (tries > 0) {
+
+        println(s"requesting ${r.getURI}")
+        val response = client.execute(r)
+        println(s"get response with status${response.getStatusLine.getStatusCode}")
+        if (response.getStatusLine.getStatusCode > 400) {
+          tries -= 1
+        }
+        else
+          return IOUtils.toString(response.getEntity.getContent)
+      }
+      ""
+    } catch {
+      case e: Throwable =>
+        throw new RuntimeException("Error on executing request ", e)
+    } finally try client.close()
+    catch {
+      case e: IOException =>
+        throw new RuntimeException("Unable to close client ", e)
+    }
+  }
+
+  getBufferData()
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala

@@ -1,7 +1,7 @@
-package eu.dnetlib.dhp.datacite
+package eu.dnetlib.dhp.actionmanager.datacite
 
-import org.json4s.jackson.JsonMethods.{compact, parse, render}
 import org.json4s.{DefaultFormats, JValue}
+import org.json4s.jackson.JsonMethods.{compact, parse, render}
 
 class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala

@@ -1,4 +1,4 @@
-package eu.dnetlib.dhp.datacite
+package eu.dnetlib.dhp.actionmanager.datacite
 
 import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
@@ -325,9 +325,8 @@ object DataciteToOAFTransformation {
       val grantId = m.matcher(awardUri).replaceAll("$2")
       val targetId = s"$p${DHPUtils.md5(grantId)}"
       List(
-        generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo)
-// REMOVED INVERSE RELATION since there is a specific method that should generate later
-//        generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo)
+        generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo),
+        generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo)
       )
     }
     else
@@ -368,7 +367,7 @@ object DataciteToOAFTransformation {
 
 
     result.setDateofcollection(ISO8601FORMAT.format(d))
-    result.setDateoftransformation(ISO8601FORMAT.format(d))
+    result.setDateoftransformation(ISO8601FORMAT.format(ts))
     result.setDataInfo(dataInfo)
 
     val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
@@ -581,11 +580,11 @@ object DataciteToOAFTransformation {
         rel.setProperties(List(dateProps).asJava)
 
         rel.setSource(id)
-        rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType))
+        rel.setTarget(s"unresolved::${r.relatedIdentifier}::${r.relatedIdentifierType}")
         rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava)
-        rel.getCollectedfrom.asScala.map(c => c.getValue).toList
+        rel.getCollectedfrom.asScala.map(c => c.getValue)(collection.breakOut)
         rel
-      }).toList
+      })(collection breakOut)
   }
 
   def generateDataInfo(trust: String): DataInfo = {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala

@@ -0,0 +1,41 @@
+package eu.dnetlib.dhp.actionmanager.datacite
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.schema.oaf.Oaf
+import org.apache.hadoop.io.Text
+import org.apache.hadoop.io.compress.GzipCodec
+import org.apache.hadoop.mapred.SequenceFileOutputFormat
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.io.Source
+
+object ExportActionSetJobNode {
+
+  val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass)
+
+  def main(args: Array[String]): Unit = {
+    val conf = new SparkConf
+    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString)
+    parser.parseArgument(args)
+    val master = parser.get("master")
+    val sourcePath = parser.get("sourcePath")
+    val targetPath = parser.get("targetPath")
+
+    val spark: SparkSession = SparkSession.builder().config(conf)
+      .appName(ExportActionSetJobNode.getClass.getSimpleName)
+      .master(master)
+      .getOrCreate()
+    implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
+    implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING)
+
+    spark.read.load(sourcePath).as[Oaf]
+      .map(o =>DataciteToOAFTransformation.toActionSet(o))
+      .filter(o => o!= null)
+      .rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
+
+
+  }
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala

@@ -0,0 +1,46 @@
+package eu.dnetlib.dhp.actionmanager.datacite
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
+import eu.dnetlib.dhp.schema.mdstore.MetadataRecord
+import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import eu.dnetlib.dhp.utils.ISLookupClientFactory
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
+import org.slf4j.{Logger, LoggerFactory}
+
+import scala.io.Source
+
+object FilterCrossrefEntitiesSpark {
+
+  val log: Logger = LoggerFactory.getLogger(getClass.getClass)
+
+  def main(args: Array[String]): Unit = {
+    val conf = new SparkConf
+    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json")).mkString)
+    parser.parseArgument(args)
+    val master = parser.get("master")
+    val sourcePath = parser.get("sourcePath")
+    log.info("sourcePath: {}", sourcePath)
+    val targetPath = parser.get("targetPath")
+    log.info("targetPath: {}", targetPath)
+
+
+
+    val spark: SparkSession = SparkSession.builder().config(conf)
+      .appName(getClass.getSimpleName)
+      .master(master)
+      .getOrCreate()
+
+
+
+    implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
+    implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result]
+
+    val d:Dataset[Oaf]= spark.read.load(sourcePath).as[Oaf]
+
+    d.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]).write.mode(SaveMode.Overwrite).save(targetPath)
+
+  }
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala

@@ -1,14 +1,9 @@
-package eu.dnetlib.dhp.datacite
+package eu.dnetlib.dhp.actionmanager.datacite
 
-import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations
-import eu.dnetlib.dhp.common.Constants.MDSTORE_DATA_PATH
-import eu.dnetlib.dhp.common.Constants.MDSTORE_SIZE_PATH
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
-import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord}
+import eu.dnetlib.dhp.schema.mdstore.MetadataRecord
 import eu.dnetlib.dhp.schema.oaf.Oaf
-import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
@@ -22,10 +17,11 @@ object GenerateDataciteDatasetSpark {
 
   def main(args: Array[String]): Unit = {
     val conf = new SparkConf
-    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString)
+    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString)
     parser.parseArgument(args)
     val master = parser.get("master")
     val sourcePath = parser.get("sourcePath")
+    val targetPath = parser.get("targetPath")
     val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks"))
     val isLookupUrl: String = parser.get("isLookupUrl")
     log.info("isLookupUrl: {}", isLookupUrl)
@@ -37,28 +33,16 @@ object GenerateDataciteDatasetSpark {
       .master(master)
       .getOrCreate()
 
-    import spark.implicits._
-
     implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord]
 
     implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
 
-    val mdstoreOutputVersion = parser.get("mdstoreOutputVersion")
-    val mapper = new ObjectMapper()
-    val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion])
-    val outputBasePath = cleanedMdStoreVersion.getHdfsPath
-
-    log.info("outputBasePath: {}", outputBasePath)
-    val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH"
+    import spark.implicits._
 
     spark.read.load(sourcePath).as[DataciteType]
       .filter(d => d.isActive)
       .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks))
       .filter(d => d != null)
-      .flatMap(i => fixRelations(i)).filter(i => i != null)
       .write.mode(SaveMode.Overwrite).save(targetPath)
-
-    val total_items = spark.read.load(targetPath).as[Oaf].count()
-    writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH)
   }
-}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala

@@ -1,5 +1,6 @@
-package eu.dnetlib.dhp.datacite
+package eu.dnetlib.dhp.actionmanager.datacite
 
+import eu.dnetlib.dhp.actionmanager.datacite.DataciteToOAFTransformation.df_it
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import org.apache.hadoop.conf.Configuration
 import org.apache.hadoop.fs.{FileSystem, LocalFileSystem, Path}
@@ -8,14 +9,14 @@ import org.apache.hadoop.io.{IntWritable, SequenceFile, Text}
 import org.apache.spark.SparkContext
 import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.expressions.Aggregator
-import org.apache.spark.sql.functions.max
 import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession}
 import org.json4s.DefaultFormats
 import org.json4s.jackson.JsonMethods.parse
+import org.apache.spark.sql.functions.max
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.time.format.DateTimeFormatter.ISO_DATE_TIME
-import java.time.{LocalDateTime, ZoneOffset}
+import java.time.format.DateTimeFormatter._
+import java.time.{LocalDate, LocalDateTime, ZoneOffset}
 import scala.io.Source
 
 object ImportDatacite {
@@ -137,11 +138,11 @@ object ImportDatacite {
     }
   }
 
-  private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs: Int): Long = {
-    var from: Long = timestamp * 1000
-    val delta: Long = 100000000L
+  private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
+    var from:Long = timestamp * 1000
+    val delta:Long = 50000000L
     var client: DataciteAPIImporter = null
-    val now: Long = System.currentTimeMillis()
+    val now :Long =System.currentTimeMillis()
     var i = 0
     try {
       val writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfsTargetPath), SequenceFile.Writer.keyClass(classOf[IntWritable]), SequenceFile.Writer.valueClass(classOf[Text]))
@@ -167,7 +168,7 @@ object ImportDatacite {
               start = System.currentTimeMillis
             }
           }
-          println(s"updating from value: $from  -> ${from + delta}")
+          println(s"updating from value: $from  -> ${from+delta}")
           from = from + delta
         }
       } catch {
@@ -182,4 +183,4 @@ object ImportDatacite {
     i
   }
 
-}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java

@@ -1,181 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.opencitations;
-
-import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
-
-import java.io.IOException;
-import java.io.Serializable;
-import java.util.*;
-
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.io.Text;
-import org.apache.hadoop.mapred.SequenceFileOutputFormat;
-import org.apache.spark.SparkConf;
-import org.apache.spark.api.java.function.FilterFunction;
-import org.apache.spark.api.java.function.FlatMapFunction;
-import org.apache.spark.sql.Encoders;
-import org.apache.spark.sql.SparkSession;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
-import scala.Tuple2;
-
-public class CreateActionSetSparkJob implements Serializable {
-	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
-	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
-	private static final String ID_PREFIX = "50|doi_________::";
-	private static final String TRUST = "0.91";
-
-	private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
-
-	public static void main(final String[] args) throws IOException, ParseException {
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							CreateActionSetSparkJob.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json"))));
-
-		parser.parseArgument(args);
-
-		Boolean isSparkSessionManaged = Optional
-			.ofNullable(parser.get("isSparkSessionManaged"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.TRUE);
-
-		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
-
-		final String inputPath = parser.get("inputPath");
-		log.info("inputPath {}", inputPath.toString());
-
-		final String outputPath = parser.get("outputPath");
-		log.info("outputPath {}", outputPath);
-
-		final boolean shouldDuplicateRels = Optional
-			.ofNullable(parser.get("shouldDuplicateRels"))
-			.map(Boolean::valueOf)
-			.orElse(Boolean.FALSE);
-
-		SparkConf conf = new SparkConf();
-		runWithSparkSession(
-			conf,
-			isSparkSessionManaged,
-			spark -> {
-				extractContent(spark, inputPath, outputPath, shouldDuplicateRels);
-			});
-
-	}
-
-	private static void extractContent(SparkSession spark, String inputPath, String outputPath,
-		boolean shouldDuplicateRels) {
-		spark
-			.sqlContext()
-			.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
-			.flatMap(
-				(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
-				Encoders.bean(Relation.class))
-			.filter((FilterFunction<Relation>) value -> value != null)
-			.toJavaRDD()
-			.map(p -> new AtomicAction(p.getClass(), p))
-			.mapToPair(
-				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
-			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
-
-	}
-
-	private static List<Relation> createRelation(String value, boolean duplicate) {
-		String[] line = value.split(",");
-		if (!line[1].startsWith("10.")) {
-			return new ArrayList<>();
-		}
-		List<Relation> relationList = new ArrayList<>();
-
-		String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
-		final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
-
-		relationList
-			.addAll(
-				getRelations(
-					citing,
-					cited));
-
-		if (duplicate && line[1].endsWith(".refs")) {
-			citing = ID_PREFIX + IdentifierFactory
-				.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
-			relationList.addAll(getRelations(citing, cited));
-		}
-
-		return relationList;
-	}
-
-	private static Collection<Relation> getRelations(String citing, String cited) {
-
-		return Arrays
-			.asList(
-				getRelation(citing, cited, ModelConstants.CITES),
-				getRelation(cited, citing, ModelConstants.IS_CITED_BY));
-	}
-
-	public static Relation getRelation(
-		String source,
-		String target,
-		String relclass) {
-		Relation r = new Relation();
-		r.setCollectedfrom(getCollectedFrom());
-		r.setSource(source);
-		r.setTarget(target);
-		r.setRelClass(relclass);
-		r.setRelType(ModelConstants.RESULT_RESULT);
-		r.setSubRelType(ModelConstants.CITATION);
-		r
-			.setDataInfo(
-				getDataInfo());
-		return r;
-	}
-
-	public static List<KeyValue> getCollectedFrom() {
-		KeyValue kv = new KeyValue();
-		kv.setKey(ModelConstants.OPENOCITATIONS_ID);
-		kv.setValue(ModelConstants.OPENOCITATIONS_NAME);
-
-		return Arrays.asList(kv);
-	}
-
-	public static DataInfo getDataInfo() {
-		DataInfo di = new DataInfo();
-		di.setInferred(false);
-		di.setDeletedbyinference(false);
-		di.setTrust(TRUST);
-
-		di
-			.setProvenanceaction(
-				getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS));
-		return di;
-	}
-
-	public static Qualifier getQualifier(String class_id, String class_name,
-		String qualifierSchema) {
-		Qualifier pa = new Qualifier();
-		pa.setClassid(class_id);
-		pa.setClassname(class_name);
-		pa.setSchemeid(qualifierSchema);
-		pa.setSchemename(qualifierSchema);
-		return pa;
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java

@@ -1,93 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.opencitations;
-
-import java.io.*;
-import java.io.Serializable;
-import java.util.Objects;
-import java.util.zip.GZIPOutputStream;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import org.apache.commons.cli.ParseException;
-import org.apache.commons.io.IOUtils;
-import org.apache.hadoop.conf.Configuration;
-import org.apache.hadoop.fs.FSDataInputStream;
-import org.apache.hadoop.fs.FSDataOutputStream;
-import org.apache.hadoop.fs.FileSystem;
-import org.apache.hadoop.fs.Path;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-
-public class GetOpenCitationsRefs implements Serializable {
-	private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class);
-
-	public static void main(final String[] args) throws IOException, ParseException {
-
-		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
-			IOUtils
-				.toString(
-					Objects
-						.requireNonNull(
-							GetOpenCitationsRefs.class
-								.getResourceAsStream(
-									"/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json"))));
-
-		parser.parseArgument(args);
-
-		final String[] inputFile = parser.get("inputFile").split(";");
-		log.info("inputFile {}", inputFile.toString());
-
-		final String workingPath = parser.get("workingPath");
-		log.info("workingPath {}", workingPath);
-
-		final String hdfsNameNode = parser.get("hdfsNameNode");
-		log.info("hdfsNameNode {}", hdfsNameNode);
-
-		Configuration conf = new Configuration();
-		conf.set("fs.defaultFS", hdfsNameNode);
-
-		FileSystem fileSystem = FileSystem.get(conf);
-
-		GetOpenCitationsRefs ocr = new GetOpenCitationsRefs();
-
-		for (String file : inputFile) {
-			ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem);
-		}
-
-	}
-
-	private void doExtract(String inputFile, String workingPath, FileSystem fileSystem)
-		throws IOException {
-
-		final Path path = new Path(inputFile);
-
-		FSDataInputStream oc_zip = fileSystem.open(path);
-
-		int count = 1;
-		try (ZipInputStream zis = new ZipInputStream(oc_zip)) {
-			ZipEntry entry = null;
-			while ((entry = zis.getNextEntry()) != null) {
-
-				if (!entry.isDirectory()) {
-					String fileName = entry.getName();
-					fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count;
-					count++;
-					try (
-						FSDataOutputStream out = fileSystem
-							.create(new Path(workingPath + "/COCI/" + fileName + ".gz"));
-						GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) {
-
-						IOUtils.copy(zis, gzipOs);
-
-					}
-				}
-
-			}
-
-		}
-
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProgramme.java

@@ -20,7 +20,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
+import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import scala.Tuple2;
@@ -171,23 +171,26 @@ public class PrepareProgramme {
 	}
 
 	private static CSVProgramme groupProgrammeByCode(CSVProgramme a, CSVProgramme b) {
-		if (!a.getLanguage().equals("en") && b.getLanguage().equalsIgnoreCase("en")) {
-			a.setTitle(b.getTitle());
-			a.setLanguage(b.getLanguage());
+		if (!a.getLanguage().equals("en")) {
+			if (b.getLanguage().equalsIgnoreCase("en")) {
+				a.setTitle(b.getTitle());
+				a.setLanguage(b.getLanguage());
+			}
 		}
-		if (StringUtils.isEmpty(a.getShortTitle()) && !StringUtils.isEmpty(b.getShortTitle())) {
-			a.setShortTitle(b.getShortTitle());
+		if (StringUtils.isEmpty(a.getShortTitle())) {
+			if (!StringUtils.isEmpty(b.getShortTitle())) {
+				a.setShortTitle(b.getShortTitle());
+			}
 		}
 
 		return a;
 	}
 
-	@SuppressWarnings("unchecked")
 	private static List<CSVProgramme> prepareClassification(JavaRDD<CSVProgramme> h2020Programmes) {
 		Object[] codedescription = h2020Programmes
 			.map(
 				value -> new Tuple2<>(value.getCode(),
-					new Tuple2<>(value.getTitle(), value.getShortTitle())))
+					new Tuple2<String, String>(value.getTitle(), value.getShortTitle())))
 			.collect()
 			.toArray();
 
@@ -213,7 +216,7 @@ public class PrepareProgramme {
 			String[] tmp = ent.split("\\.");
 			if (tmp.length <= 2) {
 				if (StringUtils.isEmpty(entry._2()._2())) {
-					map.put(entry._1(), new Tuple2<>(entry._2()._1(), entry._2()._1()));
+					map.put(entry._1(), new Tuple2<String, String>(entry._2()._1(), entry._2()._1()));
 				} else {
 					map.put(entry._1(), entry._2());
 				}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/PrepareProjects.java

@@ -18,7 +18,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
+import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import scala.Tuple2;
@@ -29,7 +29,7 @@ import scala.Tuple2;
  */
 public class PrepareProjects {
 
-	private static final Logger log = LoggerFactory.getLogger(PrepareProjects.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareProgramme.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
 	public static void main(String[] args) throws Exception {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/ReadProjectsFromDB.java

@@ -31,16 +31,15 @@ import eu.dnetlib.dhp.common.DbClient;
  */
 public class ReadProjectsFromDB implements Closeable {
 
-	private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class);
-
-	private static final String query = "SELECT code  " +
-		"from projects where id like 'corda__h2020%' ";
-
 	private final DbClient dbClient;
+	private static final Log log = LogFactory.getLog(ReadProjectsFromDB.class);
 	private final Configuration conf;
 	private final BufferedWriter writer;
 	private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
+	private final static String query = "SELECT code  " +
+		"from projects where id like 'corda__h2020%' ";
+
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
@@ -66,9 +65,9 @@ public class ReadProjectsFromDB implements Closeable {
 		}
 	}
 
-	public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) {
+	public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) throws Exception {
 
-		final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(this::writeProject);
+		final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r));
 
 		dbClient.processResults(sql, consumer);
 	}
@@ -95,20 +94,20 @@ public class ReadProjectsFromDB implements Closeable {
 
 	public ReadProjectsFromDB(
 		final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
-		throws IOException {
+		throws Exception {
 
 		this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
 		this.conf = new Configuration();
 		this.conf.set("fs.defaultFS", hdfsNameNode);
 		FileSystem fileSystem = FileSystem.get(this.conf);
 		Path hdfsWritePath = new Path(hdfsPath);
-
+		FSDataOutputStream fsDataOutputStream = null;
 		if (fileSystem.exists(hdfsWritePath)) {
 			fileSystem.delete(hdfsWritePath, false);
 		}
-		FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
 
-		this.writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
+		this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
 	}
 
 	@Override

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/SparkAtomicActionJob.java

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.actionmanager.project;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.Objects;
 import java.util.Optional;
 
@@ -21,16 +22,15 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
-import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
-import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
+import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme;
+import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject;
+import eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.oaf.H2020Classification;
 import eu.dnetlib.dhp.schema.oaf.H2020Programme;
-import eu.dnetlib.dhp.schema.oaf.OafEntity;
 import eu.dnetlib.dhp.schema.oaf.Project;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import scala.Tuple2;
@@ -47,10 +47,13 @@ import scala.Tuple2;
  *
  * To produce one single entry for each project code a step of groupoing is needed: each project can be associated to more
  * than one programme.
+ *
+ *
  */
 public class SparkAtomicActionJob {
 	private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionJob.class);
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final HashMap<String, String> programmeMap = new HashMap<>();
 
 	public static void main(String[] args) throws Exception {
 
@@ -134,6 +137,7 @@ public class SparkAtomicActionJob {
 						h2020classification.setClassification(csvProgramme.getClassification());
 						h2020classification.setH2020Programme(pm);
 						setLevelsandProgramme(h2020classification, csvProgramme.getClassification_short());
+						// setProgramme(h2020classification, ocsvProgramme.get().getClassification());
 						pp.setH2020classification(Arrays.asList(h2020classification));
 
 						return pp;
@@ -148,16 +152,20 @@ public class SparkAtomicActionJob {
 			.map((MapFunction<Tuple2<Project, EXCELTopic>, Project>) p -> {
 				Optional<EXCELTopic> op = Optional.ofNullable(p._2());
 				Project rp = p._1();
-				op.ifPresent(excelTopic -> rp.setH2020topicdescription(excelTopic.getTitle()));
+				if (op.isPresent()) {
+					rp.setH2020topicdescription(op.get().getTitle());
+				}
 				return rp;
 			}, Encoders.bean(Project.class))
 			.filter(Objects::nonNull)
 			.groupByKey(
-				(MapFunction<Project, String>) OafEntity::getId,
+				(MapFunction<Project, String>) p -> p.getId(),
 				Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
 				Project first = it.next();
-				it.forEachRemaining(first::mergeFrom);
+				it.forEachRemaining(p -> {
+					first.mergeFrom(p);
+				});
 				return first;
 			}, Encoders.bean(Project.class))
 			.toJavaRDD()
@@ -181,6 +189,12 @@ public class SparkAtomicActionJob {
 		h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
 	}
 
+//	private static void setProgramme(H2020Classification h2020Classification, String classification) {
+//		String[] tmp = classification.split(" \\| ");
+//
+//		h2020Classification.getH2020Programme().setDescription(tmp[tmp.length - 1]);
+//	}
+
 	public static <R> Dataset<R> readPath(
 		SparkSession spark, String inputPath, Class<R> clazz) {
 		return spark

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java

@@ -0,0 +1,40 @@
+
+package eu.dnetlib.dhp.actionmanager.project.utils;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.commons.csv.CSVFormat;
+import org.apache.commons.csv.CSVRecord;
+import org.apache.commons.lang.reflect.FieldUtils;
+
+/**
+ * Reads a generic csv and maps it into classes that mirror its schema
+ */
+public class CSVParser {
+
+	public <R> List<R> parse(String csvFile, String classForName)
+		throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException {
+		final CSVFormat format = CSVFormat.EXCEL
+			.withHeader()
+			.withDelimiter(';')
+			.withQuote('"')
+			.withTrim();
+		List<R> ret = new ArrayList<>();
+		final org.apache.commons.csv.CSVParser parser = org.apache.commons.csv.CSVParser.parse(csvFile, format);
+		final Set<String> headers = parser.getHeaderMap().keySet();
+		Class<?> clazz = Class.forName(classForName);
+		for (CSVRecord csvRecord : parser.getRecords()) {
+			final Object cc = clazz.newInstance();
+			for (String header : headers) {
+				FieldUtils.writeField(cc, header, csvRecord.get(header), true);
+
+			}
+			ret.add((R) cc);
+		}
+
+		return ret;
+	}
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProgramme.java

@@ -1,32 +1,20 @@
 
-package eu.dnetlib.dhp.actionmanager.project.utils.model;
+package eu.dnetlib.dhp.actionmanager.project.utils;
 
 import java.io.Serializable;
 
-import com.opencsv.bean.CsvBindByName;
-import com.opencsv.bean.CsvIgnore;
-
 /**
  * The model for the programme csv file
  */
 public class CSVProgramme implements Serializable {
 
-	@CsvBindByName(column = "code")
+	private String rcn;
 	private String code;
 
-	@CsvBindByName(column = "title")
 	private String title;
-
-	@CsvBindByName(column = "shortTitle")
 	private String shortTitle;
-
-	@CsvBindByName(column = "language")
 	private String language;
-
-	@CsvIgnore
 	private String classification;
-
-	@CsvIgnore
 	private String classification_short;
 
 	public String getClassification_short() {
@@ -45,6 +33,14 @@ public class CSVProgramme implements Serializable {
 		this.classification = classification;
 	}
 
+	public String getRcn() {
+		return rcn;
+	}
+
+	public void setRcn(String rcn) {
+		this.rcn = rcn;
+	}
+
 	public String getCode() {
 		return code;
 	}
@@ -77,4 +73,5 @@ public class CSVProgramme implements Serializable {
 		this.language = language;
 	}
 
+//
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVProject.java

@@ -0,0 +1,200 @@
+
+package eu.dnetlib.dhp.actionmanager.project.utils;
+
+import java.io.Serializable;
+
+/**
+ * the mmodel for the projects csv file
+ */
+public class CSVProject implements Serializable {
+	private String rcn;
+	private String id;
+	private String acronym;
+	private String status;
+	private String programme;
+	private String topics;
+	private String frameworkProgramme;
+	private String title;
+	private String startDate;
+	private String endDate;
+	private String projectUrl;
+	private String objective;
+	private String totalCost;
+	private String ecMaxContribution;
+	private String call;
+	private String fundingScheme;
+	private String coordinator;
+	private String coordinatorCountry;
+	private String participants;
+	private String participantCountries;
+	private String subjects;
+
+	public String getRcn() {
+		return rcn;
+	}
+
+	public void setRcn(String rcn) {
+		this.rcn = rcn;
+	}
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public String getAcronym() {
+		return acronym;
+	}
+
+	public void setAcronym(String acronym) {
+		this.acronym = acronym;
+	}
+
+	public String getStatus() {
+		return status;
+	}
+
+	public void setStatus(String status) {
+		this.status = status;
+	}
+
+	public String getProgramme() {
+		return programme;
+	}
+
+	public void setProgramme(String programme) {
+		this.programme = programme;
+	}
+
+	public String getTopics() {
+		return topics;
+	}
+
+	public void setTopics(String topics) {
+		this.topics = topics;
+	}
+
+	public String getFrameworkProgramme() {
+		return frameworkProgramme;
+	}
+
+	public void setFrameworkProgramme(String frameworkProgramme) {
+		this.frameworkProgramme = frameworkProgramme;
+	}
+
+	public String getTitle() {
+		return title;
+	}
+
+	public void setTitle(String title) {
+		this.title = title;
+	}
+
+	public String getStartDate() {
+		return startDate;
+	}
+
+	public void setStartDate(String startDate) {
+		this.startDate = startDate;
+	}
+
+	public String getEndDate() {
+		return endDate;
+	}
+
+	public void setEndDate(String endDate) {
+		this.endDate = endDate;
+	}
+
+	public String getProjectUrl() {
+		return projectUrl;
+	}
+
+	public void setProjectUrl(String projectUrl) {
+		this.projectUrl = projectUrl;
+	}
+
+	public String getObjective() {
+		return objective;
+	}
+
+	public void setObjective(String objective) {
+		this.objective = objective;
+	}
+
+	public String getTotalCost() {
+		return totalCost;
+	}
+
+	public void setTotalCost(String totalCost) {
+		this.totalCost = totalCost;
+	}
+
+	public String getEcMaxContribution() {
+		return ecMaxContribution;
+	}
+
+	public void setEcMaxContribution(String ecMaxContribution) {
+		this.ecMaxContribution = ecMaxContribution;
+	}
+
+	public String getCall() {
+		return call;
+	}
+
+	public void setCall(String call) {
+		this.call = call;
+	}
+
+	public String getFundingScheme() {
+		return fundingScheme;
+	}
+
+	public void setFundingScheme(String fundingScheme) {
+		this.fundingScheme = fundingScheme;
+	}
+
+	public String getCoordinator() {
+		return coordinator;
+	}
+
+	public void setCoordinator(String coordinator) {
+		this.coordinator = coordinator;
+	}
+
+	public String getCoordinatorCountry() {
+		return coordinatorCountry;
+	}
+
+	public void setCoordinatorCountry(String coordinatorCountry) {
+		this.coordinatorCountry = coordinatorCountry;
+	}
+
+	public String getParticipants() {
+		return participants;
+	}
+
+	public void setParticipants(String participants) {
+		this.participants = participants;
+	}
+
+	public String getParticipantCountries() {
+		return participantCountries;
+	}
+
+	public void setParticipantCountries(String participantCountries) {
+		this.participantCountries = participantCountries;
+	}
+
+	public String getSubjects() {
+		return subjects;
+	}
+
+	public void setSubjects(String subjects) {
+		this.subjects = subjects;
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELParser.java

@@ -17,8 +17,6 @@ import org.apache.poi.ss.usermodel.Row;
 import org.apache.poi.xssf.usermodel.XSSFSheet;
 import org.apache.poi.xssf.usermodel.XSSFWorkbook;
 
-import eu.dnetlib.dhp.actionmanager.project.utils.model.EXCELTopic;
-
 /**
  * Reads a generic excel file and maps it into classes that mirror its schema
  */
@@ -28,52 +26,52 @@ public class EXCELParser {
 		throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException,
 		InvalidFormatException {
 
-		try (OPCPackage pkg = OPCPackage.open(file); XSSFWorkbook wb = new XSSFWorkbook(pkg)) {
+		OPCPackage pkg = OPCPackage.open(file);
+		XSSFWorkbook wb = new XSSFWorkbook(pkg);
 
-			XSSFSheet sheet = wb.getSheet(sheetName);
+		XSSFSheet sheet = wb.getSheet(sheetName);
 
-			if (sheet == null) {
-				throw new IllegalArgumentException("Sheet name " + sheetName + " not present in current file");
-			}
+		if (sheetName == null) {
+			throw new RuntimeException("Sheet name " + sheetName + " not present in current file");
+		}
 
-			List<R> ret = new ArrayList<>();
+		List<R> ret = new ArrayList<>();
 
-			DataFormatter dataFormatter = new DataFormatter();
-			Iterator<Row> rowIterator = sheet.rowIterator();
-			List<String> headers = new ArrayList<>();
-			int count = 0;
-			while (rowIterator.hasNext()) {
-				Row row = rowIterator.next();
+		DataFormatter dataFormatter = new DataFormatter();
+		Iterator<Row> rowIterator = sheet.rowIterator();
+		List<String> headers = new ArrayList<>();
+		int count = 0;
+		while (rowIterator.hasNext()) {
+			Row row = rowIterator.next();
 
-				if (count == 0) {
-					Iterator<Cell> cellIterator = row.cellIterator();
+			if (count == 0) {
+				Iterator<Cell> cellIterator = row.cellIterator();
 
-					while (cellIterator.hasNext()) {
-						Cell cell = cellIterator.next();
-						headers.add(dataFormatter.formatCellValue(cell));
-					}
-				} else {
-					Class<?> clazz = Class.forName(classForName);
-					final Object cc = clazz.newInstance();
+				while (cellIterator.hasNext()) {
+					Cell cell = cellIterator.next();
+					headers.add(dataFormatter.formatCellValue(cell));
+				}
+			} else {
+				Class<?> clazz = Class.forName(classForName);
+				final Object cc = clazz.newInstance();
 
-					for (int i = 0; i < headers.size(); i++) {
-						Cell cell = row.getCell(i);
-						FieldUtils.writeField(cc, headers.get(i), dataFormatter.formatCellValue(cell), true);
-
-					}
-
-					EXCELTopic et = (EXCELTopic) cc;
-					if (StringUtils.isNotBlank(et.getRcn())) {
-						ret.add((R) cc);
-					}
+				for (int i = 0; i < headers.size(); i++) {
+					Cell cell = row.getCell(i);
+					FieldUtils.writeField(cc, headers.get(i), dataFormatter.formatCellValue(cell), true);
 
 				}
 
-				count += 1;
+				EXCELTopic et = (EXCELTopic) cc;
+				if (StringUtils.isNotBlank(et.getRcn())) {
+					ret.add((R) cc);
+				}
+
 			}
 
-			return ret;
+			count += 1;
 		}
+
+		return ret;
 	}
 
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/EXCELTopic.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.actionmanager.project.utils.model;
+package eu.dnetlib.dhp.actionmanager.project.utils;
 
 import java.io.Serializable;
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java

@@ -1,21 +1,34 @@
 
 package eu.dnetlib.dhp.actionmanager.project.utils;
 
-import java.io.*;
-import java.util.Optional;
+import java.io.BufferedWriter;
+import java.io.Closeable;
+import java.io.IOException;
+import java.io.OutputStreamWriter;
+import java.nio.charset.StandardCharsets;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
 import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.Path;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.collection.GetCSV;
-import eu.dnetlib.dhp.common.collection.HttpConnector2;
+import eu.dnetlib.dhp.collection.HttpConnector2;
 
 /**
  * Applies the parsing of a csv file and writes the Serialization of it in hdfs
  */
-public class ReadCSV {
+public class ReadCSV implements Closeable {
+	private static final Log log = LogFactory.getLog(ReadCSV.class);
+	private final Configuration conf;
+	private final BufferedWriter writer;
+	private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private final String csvFile;
 
 	public static void main(final String[] args) throws Exception {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
@@ -31,22 +44,56 @@ public class ReadCSV {
 		final String hdfsPath = parser.get("hdfsPath");
 		final String hdfsNameNode = parser.get("hdfsNameNode");
 		final String classForName = parser.get("classForName");
-		Optional<String> delimiter = Optional.ofNullable(parser.get("delimiter"));
-		char del = ';';
-		if (delimiter.isPresent())
-			del = delimiter.get().charAt(0);
 
-		Configuration conf = new Configuration();
-		conf.set("fs.defaultFS", hdfsNameNode);
+		try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL)) {
 
-		FileSystem fileSystem = FileSystem.get(conf);
-		BufferedReader reader = new BufferedReader(
-			new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL)));
+			log.info("Getting CSV file...");
+			readCSV.execute(classForName);
 
-		GetCSV.getCsv(fileSystem, reader, hdfsPath, classForName, del);
+		}
+	}
 
-		reader.close();
+	public void execute(final String classForName) throws Exception {
+		CSVParser csvParser = new CSVParser();
+		csvParser
+			.parse(csvFile, classForName)
+			.stream()
+			.forEach(p -> write(p));
 
 	}
 
+	@Override
+	public void close() throws IOException {
+		writer.close();
+	}
+
+	public ReadCSV(
+		final String hdfsPath,
+		final String hdfsNameNode,
+		final String fileURL)
+		throws Exception {
+		this.conf = new Configuration();
+		this.conf.set("fs.defaultFS", hdfsNameNode);
+		HttpConnector2 httpConnector = new HttpConnector2();
+		FileSystem fileSystem = FileSystem.get(this.conf);
+		Path hdfsWritePath = new Path(hdfsPath);
+		FSDataOutputStream fsDataOutputStream = null;
+		if (fileSystem.exists(hdfsWritePath)) {
+			fileSystem.delete(hdfsWritePath, false);
+		}
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+
+		this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
+		this.csvFile = httpConnector.getInputSource(fileURL);
+	}
+
+	protected void write(final Object p) {
+		try {
+			writer.write(OBJECT_MAPPER.writeValueAsString(p));
+			writer.newLine();
+		} catch (final Exception e) {
+			throw new RuntimeException(e);
+		}
+	}
+
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java

@@ -11,20 +11,18 @@ import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.FSDataOutputStream;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
-import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
-import eu.dnetlib.dhp.common.collection.CollectorException;
-import eu.dnetlib.dhp.common.collection.HttpConnector2;
+import eu.dnetlib.dhp.collection.HttpConnector2;
 
 /**
  * Applies the parsing of an excel file and writes the Serialization of it in hdfs
  */
 public class ReadExcel implements Closeable {
-	private static final Log log = LogFactory.getLog(ReadExcel.class);
-
+	private static final Log log = LogFactory.getLog(ReadCSV.class);
+	private final Configuration conf;
 	private final BufferedWriter writer;
 	private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 	private final InputStream excelFile;
@@ -33,7 +31,7 @@ public class ReadExcel implements Closeable {
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
 				.toString(
-					ReadExcel.class
+					ReadCSV.class
 						.getResourceAsStream(
 							"/eu/dnetlib/dhp/actionmanager/project/parameters.json")));
 
@@ -53,15 +51,13 @@ public class ReadExcel implements Closeable {
 		}
 	}
 
-	public void execute(final String classForName, final String sheetName)
-		throws IOException, ClassNotFoundException, InvalidFormatException, IllegalAccessException,
-		InstantiationException {
-
+	public void execute(final String classForName, final String sheetName) throws Exception {
 		EXCELParser excelParser = new EXCELParser();
 		excelParser
 			.parse(excelFile, classForName, sheetName)
 			.stream()
-			.forEach(this::write);
+			.forEach(p -> write(p));
+
 	}
 
 	@Override
@@ -72,20 +68,20 @@ public class ReadExcel implements Closeable {
 	public ReadExcel(
 		final String hdfsPath,
 		final String hdfsNameNode,
-		final String fileURL) throws CollectorException, IOException {
-
-		final Configuration conf = new Configuration();
-		conf.set("fs.defaultFS", hdfsNameNode);
+		final String fileURL)
+		throws Exception {
+		this.conf = new Configuration();
+		this.conf.set("fs.defaultFS", hdfsNameNode);
 		HttpConnector2 httpConnector = new HttpConnector2();
-		FileSystem fileSystem = FileSystem.get(conf);
+		FileSystem fileSystem = FileSystem.get(this.conf);
 		Path hdfsWritePath = new Path(hdfsPath);
-
+		FSDataOutputStream fsDataOutputStream = null;
 		if (fileSystem.exists(hdfsWritePath)) {
 			fileSystem.delete(hdfsWritePath, false);
 		}
-		FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
+		fsDataOutputStream = fileSystem.create(hdfsWritePath);
 
-		this.writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
+		this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
 		this.excelFile = httpConnector.getInputSourceAsStream(fileURL);
 	}
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/model/CSVProject.java

@@ -1,46 +0,0 @@
-
-package eu.dnetlib.dhp.actionmanager.project.utils.model;
-
-import java.io.Serializable;
-
-import com.opencsv.bean.CsvBindByName;
-
-/**
- * the mmodel for the projects csv file
- */
-public class CSVProject implements Serializable {
-
-	@CsvBindByName(column = "id")
-	private String id;
-
-	@CsvBindByName(column = "programme")
-	private String programme;
-
-	@CsvBindByName(column = "topics")
-	private String topics;
-
-	public String getId() {
-		return id;
-	}
-
-	public void setId(String id) {
-		this.id = id;
-	}
-
-	public String getProgramme() {
-		return programme;
-	}
-
-	public void setProgramme(String programme) {
-		this.programme = programme;
-	}
-
-	public String getTopics() {
-		return topics;
-	}
-
-	public void setTopics(String topics) {
-		this.topics = topics;
-	}
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/GenerateRorActionSetJob.java

@@ -9,7 +9,6 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
 import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
 
-import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -75,7 +74,7 @@ public class GenerateRorActionSetJob {
 
 		final String jsonConfiguration = IOUtils
 			.toString(
-				GenerateRorActionSetJob.class
+				SparkAtomicActionJob.class
 					.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json"));
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@@ -109,7 +108,7 @@ public class GenerateRorActionSetJob {
 
 	private static void processRorOrganizations(final SparkSession spark,
 		final String inputPath,
-		final String outputPath) throws IOException {
+		final String outputPath) throws Exception {
 
 		readInputPath(spark, inputPath)
 			.map(
@@ -204,7 +203,7 @@ public class GenerateRorActionSetJob {
 
 	private static Dataset<RorOrganization> readInputPath(
 		final SparkSession spark,
-		final String path) throws IOException {
+		final String path) throws Exception {
 
 		try (final FileSystem fileSystem = FileSystem.get(new Configuration());
 			final InputStream is = fileSystem.open(new Path(path))) {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Address.java

@@ -7,8 +7,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class Address implements Serializable {
 
-	private static final long serialVersionUID = 2444635485253443195L;
-
 	@JsonProperty("lat")
 	private Float lat;
 
@@ -39,6 +37,8 @@ public class Address implements Serializable {
 	@JsonProperty("line")
 	private String line;
 
+	private final static long serialVersionUID = 2444635485253443195L;
+
 	public Float getLat() {
 		return lat;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Country.java

@@ -7,14 +7,14 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class Country implements Serializable {
 
-	private static final long serialVersionUID = 4357848706229493627L;
-
 	@JsonProperty("country_code")
 	private String countryCode;
 
 	@JsonProperty("country_name")
 	private String countryName;
 
+	private final static long serialVersionUID = 4357848706229493627L;
+
 	public String getCountryCode() {
 		return countryCode;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/ExternalIdType.java

@@ -13,7 +13,7 @@ public class ExternalIdType implements Serializable {
 
 	private String preferred;
 
-	private static final long serialVersionUID = 2616688352998387611L;
+	private final static long serialVersionUID = 2616688352998387611L;
 
 	public ExternalIdType() {
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/ExternalIdTypeDeserializer.java

@@ -15,7 +15,8 @@ import com.fasterxml.jackson.databind.JsonNode;
 public class ExternalIdTypeDeserializer extends JsonDeserializer<ExternalIdType> {
 
 	@Override
-	public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt) throws IOException {
+	public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt)
+		throws IOException, JsonProcessingException {
 		final ObjectCodec oc = p.getCodec();
 		final JsonNode node = oc.readTree(p);
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/GeonamesAdmin.java

@@ -19,7 +19,7 @@ public class GeonamesAdmin implements Serializable {
 	@JsonProperty("code")
 	private String code;
 
-	private static final long serialVersionUID = 7294958526269195673L;
+	private final static long serialVersionUID = 7294958526269195673L;
 
 	public String getAsciiName() {
 		return asciiName;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/GeonamesCity.java

@@ -31,7 +31,7 @@ public class GeonamesCity implements Serializable {
 	@JsonProperty("license")
 	private License license;
 
-	private static final long serialVersionUID = -8389480201526252955L;
+	private final static long serialVersionUID = -8389480201526252955L;
 
 	public NameAndCode getNutsLevel2() {
 		return nutsLevel2;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Label.java

@@ -13,7 +13,7 @@ public class Label implements Serializable {
 	@JsonProperty("label")
 	private String label;
 
-	private static final long serialVersionUID = -6576156103297850809L;
+	private final static long serialVersionUID = -6576156103297850809L;
 
 	public String getIso639() {
 		return iso639;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/License.java

@@ -13,7 +13,7 @@ public class License implements Serializable {
 	@JsonProperty("license")
 	private String license;
 
-	private static final long serialVersionUID = -194308261058176439L;
+	private final static long serialVersionUID = -194308261058176439L;
 
 	public String getAttribution() {
 		return attribution;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/NameAndCode.java

@@ -7,14 +7,14 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class NameAndCode implements Serializable {
 
-	private static final long serialVersionUID = 5459836979206140843L;
-
 	@JsonProperty("name")
 	private String name;
 
 	@JsonProperty("code")
 	private String code;
 
+	private final static long serialVersionUID = 5459836979206140843L;
+
 	public String getName() {
 		return name;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/Relationship.java

@@ -7,8 +7,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class Relationship implements Serializable {
 
-	private static final long serialVersionUID = 7847399503395576960L;
-
 	@JsonProperty("type")
 	private String type;
 
@@ -18,6 +16,8 @@ public class Relationship implements Serializable {
 	@JsonProperty("label")
 	private String label;
 
+	private final static long serialVersionUID = 7847399503395576960L;
+
 	public String getType() {
 		return type;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/ror/model/RorOrganization.java

@@ -11,8 +11,6 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class RorOrganization implements Serializable {
 
-	private static final long serialVersionUID = -2658312087616043225L;
-
 	@JsonProperty("ip_addresses")
 	private List<String> ipAddresses = new ArrayList<>();
 
@@ -61,6 +59,8 @@ public class RorOrganization implements Serializable {
 	@JsonProperty("status")
 	private String status;
 
+	private final static long serialVersionUID = -2658312087616043225L;
+
 	public List<String> getIpAddresses() {
 		return ipAddresses;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala

@@ -1,69 +0,0 @@
-package eu.dnetlib.dhp.actionmanager.scholix
-
-import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
-import org.apache.spark.SparkConf
-import org.apache.spark.sql._
-import org.slf4j.{Logger, LoggerFactory}
-
-import scala.io.Source
-
-object SparkCreateActionset {
-
-  def main(args: Array[String]): Unit = {
-    val log: Logger = LoggerFactory.getLogger(getClass)
-    val conf: SparkConf = new SparkConf()
-    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
-    parser.parseArgument(args)
-
-
-    val spark: SparkSession =
-      SparkSession
-        .builder()
-        .config(conf)
-        .appName(getClass.getSimpleName)
-        .master(parser.get("master")).getOrCreate()
-
-
-    val sourcePath = parser.get("sourcePath")
-    log.info(s"sourcePath  -> $sourcePath")
-
-    val targetPath = parser.get("targetPath")
-    log.info(s"targetPath  -> $targetPath")
-
-    val workingDirFolder = parser.get("workingDirFolder")
-    log.info(s"workingDirFolder  -> $workingDirFolder")
-
-    implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
-    implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
-    implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
-
-    import spark.implicits._
-
-    val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
-
-    relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
-      .flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
-
-
-    val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
-
-    log.info("extract source and target Identifier involved in relations")
-
-
-    log.info("save relation filtered")
-
-    relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
-      .write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
-
-    log.info("saving entities")
-
-    val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
-
-    entities
-      .joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
-      .map(p => p._1._2)
-      .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
-  }
-
-}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkSaveActionSet.scala

@@ -1,86 +0,0 @@
-package eu.dnetlib.dhp.actionmanager.scholix
-
-import com.fasterxml.jackson.databind.ObjectMapper
-import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.action.AtomicAction
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
-import org.apache.hadoop.io.Text
-import org.apache.hadoop.io.compress.GzipCodec
-import org.apache.hadoop.mapred.SequenceFileOutputFormat
-import org.apache.spark.SparkConf
-import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
-import org.slf4j.{Logger, LoggerFactory}
-
-import scala.io.Source
-
-object SparkSaveActionSet {
-
-
-  def toActionSet(item: Oaf): (String, String) = {
-    val mapper = new ObjectMapper()
-
-    item match {
-      case dataset: OafDataset =>
-        val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
-        a.setClazz(classOf[OafDataset])
-        a.setPayload(dataset)
-        (dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
-      case publication: Publication =>
-        val a: AtomicAction[Publication] = new AtomicAction[Publication]
-        a.setClazz(classOf[Publication])
-        a.setPayload(publication)
-        (publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
-      case software: Software =>
-        val a: AtomicAction[Software] = new AtomicAction[Software]
-        a.setClazz(classOf[Software])
-        a.setPayload(software)
-        (software.getClass.getCanonicalName, mapper.writeValueAsString(a))
-      case orp: OtherResearchProduct =>
-        val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
-        a.setClazz(classOf[OtherResearchProduct])
-        a.setPayload(orp)
-        (orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
-
-      case relation: Relation =>
-        val a: AtomicAction[Relation] = new AtomicAction[Relation]
-        a.setClazz(classOf[Relation])
-        a.setPayload(relation)
-        (relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
-      case _ =>
-        null
-    }
-
-  }
-
-  def main(args: Array[String]): Unit = {
-    val log: Logger = LoggerFactory.getLogger(getClass)
-    val conf: SparkConf = new SparkConf()
-    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
-    parser.parseArgument(args)
-
-
-    val spark: SparkSession =
-      SparkSession
-        .builder()
-        .config(conf)
-        .appName(getClass.getSimpleName)
-        .master(parser.get("master")).getOrCreate()
-
-
-    val sourcePath = parser.get("sourcePath")
-    log.info(s"sourcePath  -> $sourcePath")
-
-    val targetPath = parser.get("targetPath")
-    log.info(s"targetPath  -> $targetPath")
-
-    implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
-    implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
-
-    spark.read.load(sourcePath).as[Oaf]
-      .map(o => toActionSet(o))
-      .filter(o => o != null)
-      .rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
-
-  }
-
-}