Merge branch 'beta' into beta

README.md

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

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

@@ -8,8 +8,6 @@ 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.
@@ -27,7 +25,7 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
 	};
 
 	@Override
-	public void execute() throws MojoExecutionException, MojoFailureException {
+	public void execute() {
 		if (System.getProperties().containsKey(PROPERTY_NAME_WF_SOURCE_DIR)
 			&& !System.getProperties().containsKey(PROPERTY_NAME_SANDBOX_NAME)) {
 			String generatedSandboxName = generateSandboxName(
@@ -46,24 +44,24 @@ public class GenerateOoziePropertiesMojo extends AbstractMojo {
 	/**
 	 * Generates sandbox name from workflow source directory.
 	 *
-	 * @param wfSourceDir
+	 * @param wfSourceDir workflow source directory
 	 * @return generated sandbox name
 	 */
 	private String generateSandboxName(String wfSourceDir) {
 		// utilize all dir names until finding one of the limiters
-		List<String> sandboxNameParts = new ArrayList<String>();
+		List<String> sandboxNameParts = new ArrayList<>();
 		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.size() > 0
+						return !sandboxNameParts.isEmpty()
 							? StringUtils.join(sandboxNameParts.toArray())
 							: null;
 					}
 				}
-				if (sandboxNameParts.size() > 0) {
+				if (!sandboxNameParts.isEmpty()) {
 					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

@@ -16,6 +16,7 @@ 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;
@@ -289,7 +290,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 */
 	protected List<String> getEscapeChars(String escapeChars) {
 		List<String> tokens = getListFromCSV(escapeChars);
-		List<String> realTokens = new ArrayList<String>();
+		List<String> realTokens = new ArrayList<>();
 		for (String token : tokens) {
 			String realToken = getRealToken(token);
 			realTokens.add(realToken);
@@ -324,7 +325,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 * @return content
 	 */
 	protected String getContent(String comment, Properties properties, List<String> escapeTokens) {
-		List<String> names = new ArrayList<String>(properties.stringPropertyNames());
+		List<String> names = new ArrayList<>(properties.stringPropertyNames());
 		Collections.sort(names);
 		StringBuilder sb = new StringBuilder();
 		if (!StringUtils.isBlank(comment)) {
@@ -352,7 +353,7 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 		throws MojoExecutionException {
 		try {
 			String content = getContent(comment, properties, escapeTokens);
-			FileUtils.writeStringToFile(file, content, ENCODING_UTF8);
+			FileUtils.writeStringToFile(file, content, StandardCharsets.UTF_8);
 		} catch (IOException e) {
 			throw new MojoExecutionException("Error creating properties file", e);
 		}
@@ -399,9 +400,9 @@ public class WritePredefinedProjectProperties extends AbstractMojo {
 	 */
 	protected static final List<String> getListFromCSV(String csv) {
 		if (StringUtils.isBlank(csv)) {
-			return new ArrayList<String>();
+			return new ArrayList<>();
 		}
-		List<String> list = new ArrayList<String>();
+		List<String> list = new ArrayList<>();
 		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 */
-public class GenerateOoziePropertiesMojoTest {
+class GenerateOoziePropertiesMojoTest {
 
 	private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
 
 	@BeforeEach
-	public void clearSystemProperties() {
+	void clearSystemProperties() {
 		System.clearProperty(PROPERTY_NAME_SANDBOX_NAME);
 		System.clearProperty(PROPERTY_NAME_WF_SOURCE_DIR);
 	}
 
 	@Test
-	public void testExecuteEmpty() throws Exception {
+	void testExecuteEmpty() throws Exception {
 		// execute
 		mojo.execute();
 
@@ -29,7 +29,7 @@ public class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	public void testExecuteSandboxNameAlreadySet() throws Exception {
+	void testExecuteSandboxNameAlreadySet() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
 		String sandboxName = "originalSandboxName";
@@ -44,7 +44,7 @@ public class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	public void testExecuteEmptyWorkflowSourceDir() throws Exception {
+	void testExecuteEmptyWorkflowSourceDir() throws Exception {
 		// given
 		String workflowSourceDir = "";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -57,7 +57,7 @@ public class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	public void testExecuteNullSandboxNameGenerated() throws Exception {
+	void testExecuteNullSandboxNameGenerated() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -70,7 +70,7 @@ public class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	public void testExecute() throws Exception {
+	void testExecute() throws Exception {
 		// given
 		String workflowSourceDir = "eu/dnetlib/dhp/wf/transformers";
 		System.setProperty(PROPERTY_NAME_WF_SOURCE_DIR, workflowSourceDir);
@@ -83,7 +83,7 @@ public class GenerateOoziePropertiesMojoTest {
 	}
 
 	@Test
-	public void testExecuteWithoutRoot() throws Exception {
+	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)
-public class WritePredefinedProjectPropertiesTest {
+class WritePredefinedProjectPropertiesTest {
 
 	@Mock
 	private MavenProject mavenProject;
@@ -39,7 +39,7 @@ public class WritePredefinedProjectPropertiesTest {
 	// ----------------------------------- TESTS ---------------------------------------------
 
 	@Test
-	public void testExecuteEmpty() throws Exception {
+	void testExecuteEmpty() throws Exception {
 		// execute
 		mojo.execute();
 
@@ -50,7 +50,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithProjectProperties() throws Exception {
+	void testExecuteWithProjectProperties() throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -70,7 +70,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test()
-	public void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
+	void testExecuteWithProjectPropertiesAndInvalidOutputFile(@TempDir File testFolder) {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -84,7 +84,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
+	void testExecuteWithProjectPropertiesExclusion(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -108,7 +108,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
+	void testExecuteWithProjectPropertiesInclusion(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -132,7 +132,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
+	void testExecuteIncludingPropertyKeysFromFile(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -164,7 +164,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
+	void testExecuteIncludingPropertyKeysFromClasspathResource(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -194,7 +194,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromBlankLocation() {
+	void testExecuteIncludingPropertyKeysFromBlankLocation() {
 		// given
 		String key = "projectPropertyKey";
 		String value = "projectPropertyValue";
@@ -214,7 +214,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
+	void testExecuteIncludingPropertyKeysFromXmlFile(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -247,7 +247,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
+	void testExecuteIncludingPropertyKeysFromInvalidXmlFile(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "projectPropertyKey";
@@ -273,7 +273,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
+	void testExecuteWithQuietModeOn(@TempDir File testFolder) throws Exception {
 		// given
 		mojo.setQuiet(true);
 		mojo.setIncludePropertyKeysFromFiles(new String[] {
@@ -290,7 +290,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteIncludingPropertyKeysFromInvalidFile() {
+	void testExecuteIncludingPropertyKeysFromInvalidFile() {
 		// given
 		mojo.setIncludePropertyKeysFromFiles(new String[] {
 			"invalid location"
@@ -301,7 +301,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
+	void testExecuteWithEnvironmentProperties(@TempDir File testFolder) throws Exception {
 		// given
 		mojo.setIncludeEnvironmentVariables(true);
 
@@ -318,7 +318,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
+	void testExecuteWithSystemProperties(@TempDir File testFolder) throws Exception {
 		// given
 		String key = "systemPropertyKey";
 		String value = "systemPropertyValue";
@@ -337,7 +337,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	@Test
-	public void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
+	void testExecuteWithSystemPropertiesAndEscapeChars(@TempDir File testFolder)
 		throws Exception {
 		// given
 		String key = "systemPropertyKey ";

dhp-common/pom.xml

@@ -25,6 +25,11 @@
 			<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>
@@ -112,6 +117,11 @@
 			<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

@@ -1,14 +0,0 @@
-
-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 (Throwable e) {
+		} catch (IOException e) {
-			log.error("Wrong value to decompress:" + abstractCompressed);
+			log.error("Wrong value to decompress: {}", abstractCompressed);
-			throw new RuntimeException(e);
+			throw new IllegalArgumentException(e);
 		}
 	}
 
-	public static String compressArgument(final String value) throws Exception {
+	public static String compressArgument(final String value) throws IOException {
 		ByteArrayOutputStream out = new ByteArrayOutputStream();
 		GZIPOutputStream gzip = new GZIPOutputStream(out);
 		gzip.write(value.getBytes());

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

@@ -9,9 +9,6 @@ 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 HashMap<String, String> params) {
+	public void setParams(final Map<String, String> params) {
 		this.params = params;
 	}
 

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

@@ -12,6 +12,9 @@ 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");
@@ -49,4 +52,10 @@ 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(v -> v.getValue())
+										.map(Field::getValue)
 										.collect(Collectors.toList())));
 
 					Optional
@@ -100,20 +100,20 @@ public class GraphResultMapper implements Serializable {
 						.setContactgroup(
 							Optional
 								.ofNullable(ir.getContactgroup())
-								.map(value -> value.stream().map(cg -> cg.getValue()).collect(Collectors.toList()))
+								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
 								.orElse(null));
 
 					out
 						.setContactperson(
 							Optional
 								.ofNullable(ir.getContactperson())
-								.map(value -> value.stream().map(cp -> cp.getValue()).collect(Collectors.toList()))
+								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
 								.orElse(null));
 					out
 						.setTool(
 							Optional
 								.ofNullable(ir.getTool())
-								.map(value -> value.stream().map(t -> t.getValue()).collect(Collectors.toList()))
+								.map(value -> value.stream().map(Field::getValue).collect(Collectors.toList()))
 								.orElse(null));
 
 					out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname());
@@ -123,7 +123,8 @@ public class GraphResultMapper implements Serializable {
 
 			Optional
 				.ofNullable(input.getAuthor())
-				.ifPresent(ats -> out.setAuthor(ats.stream().map(at -> getAuthor(at)).collect(Collectors.toList())));
+				.ifPresent(
+					ats -> out.setAuthor(ats.stream().map(GraphResultMapper::getAuthor).collect(Collectors.toList())));
 
 			// I do not map Access Right UNKNOWN or OTHER
 
@@ -210,7 +211,7 @@ public class GraphResultMapper implements Serializable {
 			if (oInst.isPresent()) {
 				out
 					.setInstance(
-						oInst.get().stream().map(i -> getInstance(i)).collect(Collectors.toList()));
+						oInst.get().stream().map(GraphResultMapper::getInstance).collect(Collectors.toList()));
 
 			}
 
@@ -230,7 +231,7 @@ public class GraphResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title"))
 					.collect(Collectors.toList());
-				if (iTitle.size() > 0) {
+				if (!iTitle.isEmpty()) {
 					out.setMaintitle(iTitle.get(0).getValue());
 				}
 
@@ -239,7 +240,7 @@ public class GraphResultMapper implements Serializable {
 					.stream()
 					.filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle"))
 					.collect(Collectors.toList());
-				if (iTitle.size() > 0) {
+				if (!iTitle.isEmpty()) {
 					out.setSubtitle(iTitle.get(0).getValue());
 				}
 

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

@@ -14,38 +14,33 @@ 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);
 
 		}
-		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+		return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).getWrappedStream());
-
-		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);
 
 		}
-		fsDataOutputStream = fileSystem.create(hdfsWritePath);
+		try (TarArchiveOutputStream ar = new TarArchiveOutputStream(
+			fileSystem.create(hdfsWritePath).getWrappedStream())) {
 
-		TarArchiveOutputStream ar = new TarArchiveOutputStream(fsDataOutputStream.getWrappedStream());
+			RemoteIterator<LocatedFileStatus> iterator = fileSystem
+				.listFiles(
+					new Path(inputPath), true);
 
-		RemoteIterator<LocatedFileStatus> fileStatusListIterator = fileSystem
+			while (iterator.hasNext()) {
-			.listFiles(
+				writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
-				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,
@@ -90,6 +85,13 @@ 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

@@ -10,8 +10,6 @@ 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;
@@ -21,6 +19,7 @@ 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;
 
@@ -46,7 +45,7 @@ public class MdstoreClient implements Closeable {
 
 		final String currentId = Optional
 			.ofNullable(getColl(db, COLL_METADATA_MANAGER, true).find(query))
-			.map(r -> r.first())
+			.map(FindIterable::first)
 			.map(d -> d.getString("currentId"))
 			.orElseThrow(() -> new IllegalArgumentException("cannot find current mdstore id for: " + mdId));
 
@@ -84,7 +83,7 @@ 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 RuntimeException(err);
+			throw new IllegalArgumentException(err);
 		}
 		return client.getDatabase(dbName);
 	}
@@ -97,7 +96,7 @@ public class MdstoreClient implements Closeable {
 					String.format("Missing collection '%s' in database '%s'", collName, db.getName()));
 			log.warn(err);
 			if (abortIfMissing) {
-				throw new RuntimeException(err);
+				throw new IllegalArgumentException(err);
 			} else {
 				return null;
 			}

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

@@ -24,7 +24,6 @@ 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/aggregation/AggregatorReport.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.aggregation.common;
+package eu.dnetlib.dhp.common.aggregation;
 
 import java.io.Closeable;
 import java.io.IOException;
@@ -11,8 +11,6 @@ import java.util.Objects;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.google.gson.Gson;
-
 import eu.dnetlib.dhp.message.MessageSender;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
@@ -20,12 +18,12 @@ public class AggregatorReport extends LinkedHashMap<String, String> implements C
 
 	private static final Logger log = LoggerFactory.getLogger(AggregatorReport.class);
 
-	private MessageSender messageSender;
+	private transient MessageSender messageSender;
 
 	public AggregatorReport() {
 	}
 
-	public AggregatorReport(MessageSender messageSender) throws IOException {
+	public AggregatorReport(MessageSender messageSender) {
 		this.messageSender = messageSender;
 	}
 

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

@@ -5,6 +5,9 @@ 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;
@@ -43,7 +46,7 @@ public class ZenodoAPIClient implements Serializable {
 		this.deposition_id = deposition_id;
 	}
 
-	public ZenodoAPIClient(String urlString, String access_token) throws IOException {
+	public ZenodoAPIClient(String urlString, String access_token) {
 
 		this.urlString = urlString;
 		this.access_token = access_token;
@@ -63,8 +66,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString)
-			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
 			.post(body)
 			.build();
 
@@ -103,8 +106,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(bucket + "/" + file_name)
-			.addHeader("Content-Type", "application/zip") // add request headers
+			.addHeader(HttpHeaders.CONTENT_TYPE, "application/zip") // add request headers
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
 			.put(InputStreamRequestBody.create(MEDIA_TYPE_ZIP, is, len))
 			.build();
 
@@ -130,8 +133,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString + "/" + deposition_id)
-			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
 			.put(body)
 			.build();
 
@@ -197,7 +200,7 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString + "/" + deposition_id + "/actions/newversion")
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
 			.post(body)
 			.build();
 
@@ -270,8 +273,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(urlString)
-			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.AUTHORIZATION, "Bearer " + access_token)
 			.get()
 			.build();
 
@@ -293,8 +296,8 @@ public class ZenodoAPIClient implements Serializable {
 
 		Request request = new Request.Builder()
 			.url(url)
-			.addHeader("Content-Type", "application/json") // add request headers
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
-			.addHeader("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.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

@@ -3,17 +3,12 @@ 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;
 	}
@@ -46,13 +41,4 @@ 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/CollectorException.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 public class CollectorException extends Exception {
 

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

@@ -0,0 +1,56 @@
+
+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/collection/HttpClientParams.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 /**
  * Bundles the http connection parameters driving the client behaviour.

dhp-common/src/main/java/eu/dnetlib/dhp/common/collection/HttpConnector2.java

@@ -1,5 +1,5 @@
 
-package eu.dnetlib.dhp.collection;
+package eu.dnetlib.dhp.common.collection;
 
 import static eu.dnetlib.dhp.utils.DHPUtils.*;
 
@@ -15,12 +15,13 @@ import org.apache.http.HttpHeaders;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
+import eu.dnetlib.dhp.common.Constants;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 
 /**
  * Migrated from https://svn.driver.research-infrastructures.eu/driver/dnet45/modules/dnet-modular-collector-service/trunk/src/main/java/eu/dnetlib/data/collector/plugins/HttpConnector.java
  *
- * @author jochen, michele, andrea, alessia, claudio
+ * @author jochen, michele, andrea, alessia, claudio, andreas
  */
 public class HttpConnector2 {
 
@@ -32,7 +33,7 @@ public class HttpConnector2 {
 
 	private String responseType = null;
 
-	private final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
+	private static final String userAgent = "Mozilla/5.0 (compatible; OAI; +http://www.openaire.eu)";
 
 	public HttpConnector2() {
 		this(new HttpClientParams());
@@ -112,6 +113,17 @@ public class HttpConnector2 {
 			}
 
 			int retryAfter = obtainRetryAfter(urlConn.getHeaderFields());
+			String rateLimit = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_LIMIT);
+			String rateRemaining = urlConn.getHeaderField(Constants.HTTPHEADER_IETF_DRAFT_RATELIMIT_REMAINING);
+
+			if ((rateLimit != null) && (rateRemaining != null) && (Integer.parseInt(rateRemaining) < 2)) {
+				if (retryAfter > 0) {
+					backoffAndSleep(retryAfter);
+				} else {
+					backoffAndSleep(1000);
+				}
+			}
+
 			if (is2xx(urlConn.getResponseCode())) {
 				input = urlConn.getInputStream();
 				responseType = urlConn.getContentType();
@@ -120,7 +132,7 @@ public class HttpConnector2 {
 			if (is3xx(urlConn.getResponseCode())) {
 				// REDIRECTS
 				final String newUrl = obtainNewLocation(urlConn.getHeaderFields());
-				log.info(String.format("The requested url has been moved to %s", newUrl));
+				log.info("The requested url has been moved to {}", newUrl);
 				report
 					.put(
 						REPORT_PREFIX + urlConn.getResponseCode(),
@@ -140,14 +152,14 @@ public class HttpConnector2 {
 						if (retryAfter > 0) {
 							log
 								.warn(
-									requestUrl + " - waiting and repeating request after suggested retry-after "
+									"{} - waiting and repeating request after suggested retry-after {} sec.",
-										+ retryAfter + " sec.");
+									requestUrl, retryAfter);
 							backoffAndSleep(retryAfter * 1000);
 						} else {
 							log
 								.warn(
-									requestUrl + " - waiting and repeating request after default delay of "
+									"{} - waiting and repeating request after default delay of {} sec.",
-										+ getClientParams().getRetryDelay() + " sec.");
+									requestUrl, getClientParams().getRetryDelay());
 							backoffAndSleep(retryNumber * getClientParams().getRetryDelay() * 1000);
 						}
 						report.put(REPORT_PREFIX + urlConn.getResponseCode(), requestUrl);
@@ -181,12 +193,12 @@ public class HttpConnector2 {
 	}
 
 	private void logHeaderFields(final HttpURLConnection urlConn) throws IOException {
-		log.debug("StatusCode: " + urlConn.getResponseMessage());
+		log.debug("StatusCode: {}", urlConn.getResponseMessage());
 
 		for (Map.Entry<String, List<String>> e : urlConn.getHeaderFields().entrySet()) {
 			if (e.getKey() != null) {
 				for (String v : e.getValue()) {
-					log.debug("  key: " + e.getKey() + " - value: " + v);
+					log.debug("  key: {} - value: {}", e.getKey(), v);
 				}
 			}
 		}
@@ -204,7 +216,7 @@ public class HttpConnector2 {
 
 	private int obtainRetryAfter(final Map<String, List<String>> headerMap) {
 		for (String key : headerMap.keySet()) {
-			if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (headerMap.get(key).size() > 0)
+			if ((key != null) && key.equalsIgnoreCase(HttpHeaders.RETRY_AFTER) && (!headerMap.get(key).isEmpty())
 				&& NumberUtils.isCreatable(headerMap.get(key).get(0))) {
 				return Integer.parseInt(headerMap.get(key).get(0)) + 10;
 			}

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;
@@ -23,17 +23,20 @@ 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 Exception {
+	public static String doGET(final String url) throws IOException {
 		final HttpGet httpGet = new HttpGet(url);
 		return doHTTPRequest(httpGet);
 	}
 
-	public static <V> String doPOST(final String url, V objParam) throws Exception {
+	public static <V> String doPOST(final String url, V objParam) throws IOException {
 		final HttpPost httpPost = new HttpPost(url);
 
 		if (objParam != null) {
@@ -45,25 +48,25 @@ public class DNetRestClient {
 		return doHTTPRequest(httpPost);
 	}
 
-	public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws Exception {
+	public static <T, V> T doPOST(final String url, V objParam, Class<T> clazz) throws IOException {
 		return mapper.readValue(doPOST(url, objParam), clazz);
 	}
 
-	private static String doHTTPRequest(final HttpUriRequest r) throws Exception {
+	private static String doHTTPRequest(final HttpUriRequest r) throws IOException {
-		CloseableHttpClient client = HttpClients.createDefault();
+		try (CloseableHttpClient client = HttpClients.createDefault()) {
 
-		log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
+			log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
-		log
+			log
-			.info(
+				.info(
-				"request headers: {}",
+					"request headers: {}",
-				Arrays
+					Arrays
-					.asList(r.getAllHeaders())
+						.asList(r.getAllHeaders())
-					.stream()
+						.stream()
-					.map(h -> h.getName() + ":" + h.getValue())
+						.map(h -> h.getName() + ":" + h.getValue())
-					.collect(Collectors.joining(",")));
+						.collect(Collectors.joining(",")));
 
-		CloseableHttpResponse response = client.execute(r);
+			return IOUtils.toString(client.execute(r).getEntity().getContent());
-		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(s -> s.toLowerCase()).map(s -> terms.get(s)).orElse(null);
+		return Optional.ofNullable(id).map(String::toLowerCase).map(terms::get).orElse(null);
 	}
 
 	protected void addTerm(final String id, final String name) {
@@ -81,7 +81,6 @@ 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

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

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

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

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

@@ -4,7 +4,6 @@ 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;
 
@@ -19,6 +18,9 @@ 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)));
@@ -36,7 +38,8 @@ 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, enrich;
+		List<Author> base;
+		List<Author> enrich;
 		int sa = authorsSize(a);
 		int sb = authorsSize(b);
 
@@ -62,7 +65,7 @@ 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().size() > 0)
+			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
 			.flatMap(
 				a -> a
 					.getPid()
@@ -74,7 +77,7 @@ public class AuthorMerger {
 		// <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().size() > 0)
+			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
 			.flatMap(
 				a -> a
 					.getPid()
@@ -117,9 +120,9 @@ public class AuthorMerger {
 	}
 
 	public static String pidToComparableString(StructuredProperty pid) {
-		return (pid.getQualifier() != null
+		final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
-			? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
+			: "";
-			: "")
+		return (pid.getQualifier() != null ? classid : "")
 			+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
 	}
 

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

@@ -12,6 +12,9 @@ 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

@@ -7,22 +7,19 @@ 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 {
 
@@ -194,11 +191,15 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 							.filter(Objects::nonNull)
 							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 							.filter(
-								sp -> sp
+								sp -> {
-									.getValue()
+									final String title = sp
-									.toLowerCase()
+										.getValue()
-									.replaceAll(TITLE_FILTER_REGEX, "")
+										.toLowerCase();
-									.length() > TITLE_FILTER_RESIDUAL_LENGTH)
+									final String residual = Unidecode
+										.decode(title)
+										.replaceAll(TITLE_FILTER_REGEX, "");
+									return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
+								})
 							.map(GraphCleaningFunctions::cleanValue)
 							.collect(Collectors.toList()));
 			}
@@ -283,7 +284,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 						r
 							.getAuthor()
 							.stream()
-							.filter(a -> Objects.nonNull(a))
+							.filter(Objects::nonNull)
 							.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

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

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

@@ -34,6 +34,9 @@ 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();
 	}
@@ -44,7 +47,7 @@ public class DHPUtils {
 			md.update(s.getBytes(StandardCharsets.UTF_8));
 			return new String(Hex.encodeHex(md.digest()));
 		} catch (final Exception e) {
-			System.err.println("Error creating id");
+			log.error("Error creating id from {}", s);
 			return null;
 		}
 	}
@@ -53,33 +56,6 @@ public class DHPUtils {
 		return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId));
 	}
 
-	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;
-		}
-	}
-
-	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) {
 		try {
 			Object o = JsonPath.read(json, jsonPath);

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

@@ -18,13 +18,16 @@ 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(String.format("creating %s stub from %s", clazz.getName(), endpoint));
+		log.info("creating {} stub from {}", clazz.getName(), endpoint);
 		final JaxWsProxyFactoryBean jaxWsProxyFactory = new JaxWsProxyFactoryBean();
 		jaxWsProxyFactory.setServiceClass(clazz);
 		jaxWsProxyFactory.setAddress(endpoint);
@@ -38,12 +41,10 @@ public class ISLookupClientFactory {
 
 			log
 				.info(
-					String
+					"setting connectTimeout to {}, requestTimeout to {} for service {}",
-						.format(
+					connectTimeout,
-							"setting connectTimeout to %s, requestTimeout to %s for service %s",
+					requestTimeout,
-							connectTimeout,
+					clazz.getCanonicalName());
-							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 String DEFAULT_SAXON_EXT_NS_URI = "http://www.d-net.research-infrastructures.eu/saxon-extension";
+	public static final 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();
@@ -63,8 +63,7 @@ public class ExtractYear extends AbstractExtensionFunction {
 		for (String format : dateFormats) {
 			try {
 				c.setTime(new SimpleDateFormat(format).parse(s));
-				String year = String.valueOf(c.get(Calendar.YEAR));
+				return 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

@@ -1,6 +1,8 @@
 
 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;
@@ -26,7 +28,8 @@ public class PickFirst extends AbstractExtensionFunction {
 		final String s1 = getValue(arguments[0]);
 		final String s2 = getValue(arguments[1]);
 
-		return new StringValue(StringUtils.isNotBlank(s1) ? s1 : StringUtils.isNotBlank(s2) ? s2 : "");
+		final String value = isNotBlank(s1) ? s1 : isNotBlank(s2) ? s2 : "";
+		return new StringValue(value);
 	}
 
 	private String getValue(final Sequence arg) throws XPathException {

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

@@ -12,6 +12,9 @@ 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;
 
-public class ArgumentApplicationParserTest {
+class ArgumentApplicationParserTest {
 
 	@Test
-	public void testParseParameter() throws Exception {
+	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
-		public void shouldThrowARuntimeExceptionOnError() {
+		void shouldThrowARuntimeExceptionOnError() {
 			// when
 			assertThrows(RuntimeException.class, () -> HdfsSupport.remove(null, new Configuration()));
 		}
 
 		@Test
-		public void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
+		void shouldRemoveADirFromHDFS(@TempDir Path tempDir) {
 			// when
 			HdfsSupport.remove(tempDir.toString(), new Configuration());
 
@@ -36,7 +36,7 @@ public class HdfsSupportTest {
 		}
 
 		@Test
-		public void shouldRemoveAFileFromHDFS(@TempDir Path tempDir) throws IOException {
+		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
-		public void shouldThrowARuntimeExceptionOnError() {
+		void shouldThrowARuntimeExceptionOnError() {
 			// when
 			assertThrows(RuntimeException.class, () -> HdfsSupport.listFiles(null, new Configuration()));
 		}
 
 		@Test
-		public void shouldListFilesLocatedInPath(@TempDir Path tempDir) throws IOException {
+		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;
 
-public class PacePersonTest {
+class PacePersonTest {
 
 	@Test
-	public void pacePersonTest1() {
+	void pacePersonTest1() {
 
 		PacePerson p = new PacePerson("Artini, Michele", false);
 		assertEquals("Artini", p.getSurnameString());
@@ -17,7 +17,7 @@ public class PacePersonTest {
 	}
 
 	@Test
-	public void pacePersonTest2() {
+	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

@@ -18,7 +18,8 @@ public class SparkSessionSupportTest {
 	class RunWithSparkSession {
 
 		@Test
-		public void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
+		@SuppressWarnings("unchecked")
+		void shouldExecuteFunctionAndNotStopSparkSessionWhenSparkSessionIsNotManaged()
 			throws Exception {
 			// given
 			SparkSession spark = mock(SparkSession.class);
@@ -37,7 +38,8 @@ public class SparkSessionSupportTest {
 		}
 
 		@Test
-		public void shouldExecuteFunctionAndStopSparkSessionWhenSparkSessionIsManaged()
+		@SuppressWarnings("unchecked")
+		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
-public class ZenodoAPIClientTest {
+class ZenodoAPIClientTest {
 
 	private final String URL_STRING = "https://sandbox.zenodo.org/api/deposit/depositions";
 	private final String ACCESS_TOKEN = "";
@@ -22,7 +22,7 @@ public class ZenodoAPIClientTest {
 	private final String depositionId = "674915";
 
 	@Test
-	public void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
+	void testUploadOldDeposition() throws IOException, MissingConceptDoiException {
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
 		Assertions.assertEquals(200, client.uploadOpenDeposition(depositionId));
@@ -44,7 +44,7 @@ public class ZenodoAPIClientTest {
 	}
 
 	@Test
-	public void testNewDeposition() throws IOException {
+	void testNewDeposition() throws IOException {
 
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
@@ -67,7 +67,7 @@ public class ZenodoAPIClientTest {
 	}
 
 	@Test
-	public void testNewVersionNewName() throws IOException, MissingConceptDoiException {
+	void testNewVersionNewName() throws IOException, MissingConceptDoiException {
 
 		ZenodoAPIClient client = new ZenodoAPIClient(URL_STRING,
 			ACCESS_TOKEN);
@@ -87,7 +87,7 @@ public class ZenodoAPIClientTest {
 	}
 
 	@Test
-	public void testNewVersionOldName() throws IOException, MissingConceptDoiException {
+	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;
 
-public class AuthorMergerTest {
+class AuthorMergerTest {
 
 	private String publicationsBasePath;
 
@@ -43,7 +43,7 @@ public class AuthorMergerTest {
 	}
 
 	@Test
-	public void mergeTest() { // used in the dedup: threshold set to 0.95
+	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

@@ -4,12 +4,8 @@ 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;
@@ -19,15 +15,34 @@ 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.*;
+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;
 
-public class OafMapperUtilsTest {
+class OafMapperUtilsTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
 		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
 	@Test
-	public void testDateValidation() {
+	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() {
 
 		assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z  ").isPresent());
 		assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent());
@@ -132,44 +147,46 @@ public class OafMapperUtilsTest {
 	}
 
 	@Test
-	public void testDate() {
+	void testDate() {
-		System.out.println(GraphCleaningFunctions.cleanDate("23-FEB-1998"));
+		final String date = GraphCleaningFunctions.cleanDate("23-FEB-1998");
+		assertNotNull(date);
+		System.out.println(date);
 	}
 
 	@Test
-	public void testMergePubs() throws IOException {
+	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(p1.getCollectedfrom().size(), 1);
+		assertEquals(1, p1.getCollectedfrom().size());
-		assertEquals(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
+		assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
-		assertEquals(d2.getCollectedfrom().size(), 1);
+		assertEquals(1, d2.getCollectedfrom().size());
 		assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
-		assertTrue(
+		assertEquals(
+			ModelConstants.PUBLICATION_RESULTTYPE_CLASSID,
 			OafMapperUtils
 				.mergeResults(p1, d2)
 				.getResulttype()
-				.getClassid()
+				.getClassid());
-				.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
 
-		assertEquals(p2.getCollectedfrom().size(), 1);
+		assertEquals(1, p2.getCollectedfrom().size());
 		assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
-		assertEquals(d1.getCollectedfrom().size(), 1);
+		assertEquals(1, d1.getCollectedfrom().size());
 		assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
 
-		assertTrue(
+		assertEquals(
+			ModelConstants.DATASET_RESULTTYPE_CLASSID,
 			OafMapperUtils
 				.mergeResults(p2, d1)
 				.getResulttype()
-				.getClassid()
+				.getClassid());
-				.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
 	}
 
 	protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
-		return collectedfrom.stream().map(c -> c.getKey()).collect(Collectors.toCollection(HashSet::new));
+		return collectedfrom.stream().map(KeyValue::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;
 
-public class RelationMapperTest {
+class RelationMapperTest {
 
 	@Test
-	public void testLoadRels() throws Exception {
+	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

@@ -3,40 +3,37 @@ package eu.dnetlib.dhp.actionmanager;
 
 import java.io.Serializable;
 import java.io.StringReader;
-import java.util.*;
+import java.util.List;
+import java.util.NoSuchElementException;
+import java.util.Optional;
+import java.util.Set;
 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(PartitionActionSetsByPayloadTypeJob.class);
+	private static final Logger log = LoggerFactory.getLogger(ISClient.class);
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
 
-	private final ISLookUpService isLookup;
+	private final transient ISLookUpService isLookup;
 
 	public ISClient(String isLookupUrl) {
 		isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);
@@ -63,7 +60,7 @@ public class ISClient implements Serializable {
 				.map(
 					sets -> sets
 						.stream()
-						.map(set -> parseSetInfo(set))
+						.map(ISClient::parseSetInfo)
 						.filter(t -> ids.contains(t.getLeft()))
 						.map(t -> buildDirectory(basePath, t))
 						.collect(Collectors.toList()))
@@ -73,15 +70,17 @@ public class ISClient implements Serializable {
 		}
 	}
 
-	private Triple<String, String, String> parseSetInfo(String set) {
+	private static Triple<String, String, String> parseSetInfo(String set) {
 		try {
-			Document doc = new SAXReader().read(new StringReader(set));
+			final SAXReader reader = new SAXReader();
+			reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
+			Document doc = reader.read(new StringReader(set));
 			return Triple
 				.of(
 					doc.valueOf("//SET/@id"),
 					doc.valueOf("//SET/@directory"),
 					doc.valueOf("//SET/@latest"));
-		} catch (DocumentException e) {
+		} catch (DocumentException | SAXException e) {
 			throw new IllegalStateException(e);
 		}
 	}
@@ -99,7 +98,7 @@ 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

@@ -62,6 +62,7 @@ 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

@@ -74,7 +74,9 @@ 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);
@@ -152,7 +154,7 @@ public class PromoteActionPayloadForGraphTableJob {
 		return spark
 			.read()
 			.parquet(path)
-			.map((MapFunction<Row, String>) value -> extractPayload(value), Encoders.STRING())
+			.map((MapFunction<Row, String>) PromoteActionPayloadForGraphTableJob::extractPayload, Encoders.STRING())
 			.map(
 				(MapFunction<String, A>) value -> decodePayload(actionPayloadClazz, value),
 				Encoders.bean(actionPayloadClazz));

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
-		public void shouldPartitionActionSetsByPayloadType(@TempDir Path workingDir) throws Exception {
+		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
-		public void shouldThrowForOafAndOaf() {
+		void shouldThrowForOafAndOaf() {
 			// given
 			Oaf a = mock(Oaf.class);
 			Oaf b = mock(Oaf.class);
@@ -33,7 +33,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafAndRelation() {
+		void shouldThrowForOafAndRelation() {
 			// given
 			Oaf a = mock(Oaf.class);
 			Relation b = mock(Relation.class);
@@ -46,7 +46,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafAndOafEntity() {
+		void shouldThrowForOafAndOafEntity() {
 			// given
 			Oaf a = mock(Oaf.class);
 			OafEntity b = mock(OafEntity.class);
@@ -59,7 +59,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForRelationAndOaf() {
+		void shouldThrowForRelationAndOaf() {
 			// given
 			Relation a = mock(Relation.class);
 			Oaf b = mock(Oaf.class);
@@ -72,7 +72,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForRelationAndOafEntity() {
+		void shouldThrowForRelationAndOafEntity() {
 			// given
 			Relation a = mock(Relation.class);
 			OafEntity b = mock(OafEntity.class);
@@ -85,7 +85,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldBehaveProperlyForRelationAndRelation() {
+		void shouldBehaveProperlyForRelationAndRelation() {
 			// given
 			Relation a = mock(Relation.class);
 			Relation b = mock(Relation.class);
@@ -101,7 +101,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafEntityAndOaf() {
+		void shouldThrowForOafEntityAndOaf() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Oaf b = mock(Oaf.class);
@@ -114,7 +114,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafEntityAndRelation() {
+		void shouldThrowForOafEntityAndRelation() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Relation b = mock(Relation.class);
@@ -127,7 +127,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
+		void shouldThrowForOafEntityAndOafEntityButNotSubclasses() {
 			// given
 			class OafEntitySub1 extends OafEntity {
 			}
@@ -145,7 +145,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldBehaveProperlyForOafEntityAndOafEntity() {
+		void shouldBehaveProperlyForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			OafEntity b = mock(OafEntity.class);
@@ -165,7 +165,7 @@ public class MergeAndGetTest {
 	class SelectNewerAndGetStrategy {
 
 		@Test
-		public void shouldThrowForOafEntityAndRelation() {
+		void shouldThrowForOafEntityAndRelation() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Relation b = mock(Relation.class);
@@ -178,7 +178,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForRelationAndOafEntity() {
+		void shouldThrowForRelationAndOafEntity() {
 			// given
 			Relation a = mock(Relation.class);
 			OafEntity b = mock(OafEntity.class);
@@ -191,7 +191,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowForOafEntityAndResult() {
+		void shouldThrowForOafEntityAndResult() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			Result b = mock(Result.class);
@@ -204,7 +204,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldThrowWhenSuperTypeIsNewerForResultAndOafEntity() {
+		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
-		public void shouldShouldReturnLeftForOafEntityAndOafEntity() {
+		void shouldShouldReturnLeftForOafEntityAndOafEntity() {
 			// given
 			OafEntity a = mock(OafEntity.class);
 			when(a.getLastupdatetimestamp()).thenReturn(1L);
@@ -238,7 +238,7 @@ public class MergeAndGetTest {
 		}
 
 		@Test
-		public void shouldShouldReturnRightForOafEntityAndOafEntity() {
+		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
-		public void shouldThrowWhenGraphTableClassIsNotASubClassOfActionPayloadClass() {
+		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")
-		public void shouldPromoteActionPayloadForGraphTable(
+		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
-		public void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
+		void shouldThrowWhenTableTypeIsNotSubtypeOfActionPayloadType() {
 			// given
 			class OafImpl extends Oaf {
 			}
@@ -58,7 +58,7 @@ public class PromoteActionPayloadFunctionsTest {
 		}
 
 		@Test
-		public void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
+		void shouldRunProperlyWhenActionPayloadTypeAndTableTypeAreTheSame() {
 			// given
 			String id0 = "id0";
 			String id1 = "id1";
@@ -138,7 +138,7 @@ public class PromoteActionPayloadFunctionsTest {
 		}
 
 		@Test
-		public void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
+		void shouldRunProperlyWhenActionPayloadTypeIsSuperTypeOfTableType() {
 			// given
 			String id0 = "id0";
 			String id1 = "id1";
@@ -218,7 +218,7 @@ public class PromoteActionPayloadFunctionsTest {
 	class GroupTableByIdAndMerge {
 
 		@Test
-		public void shouldRunProperly() {
+		void shouldRunProperly() {
 			// given
 			String id1 = "id1";
 			String id2 = "id2";

dhp-workflows/dhp-aggregation/pom.xml

@@ -84,14 +84,6 @@
             <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

@@ -4,6 +4,7 @@ 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;
@@ -28,15 +29,16 @@ 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 <I extends Result> void main(String[] args) throws Exception {
+	public static void main(String[] args) throws Exception {
 
 		String jsonConfiguration = IOUtils
 			.toString(
-				CollectAndSave.class
+				Objects
-					.getResourceAsStream(
+					.requireNonNull(
-						"/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 = new JavaSparkContext(spark.sparkContext());
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
 		JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
 			.textFile(bipScorePath)
@@ -101,8 +101,6 @@ 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");
@@ -124,7 +122,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 				ret.setId(value._2().getId());
 				return ret;
 			}, Encoders.bean(BipScore.class))
-			.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
+			.groupByKey((MapFunction<BipScore, String>) BipScore::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/datacite/AbstractRestClient.scala

@@ -1,20 +1,22 @@
 package eu.dnetlib.dhp.actionmanager.datacite
 
 import org.apache.commons.io.IOUtils
+import org.apache.http.client.config.RequestConfig
 import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
 import org.apache.http.entity.StringEntity
-import org.apache.http.impl.client.HttpClients
+import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
 
 import java.io.IOException
 
-abstract class AbstractRestClient extends Iterator[String]{
+
+abstract class AbstractRestClient extends Iterator[String] {
 
   var buffer: List[String] = List()
-  var current_index:Int = 0
+  var current_index: Int = 0
 
   var scroll_value: Option[String] = None
 
-  var complete:Boolean = false
+  var complete: Boolean = false
 
 
   def extractInfo(input: String): Unit
@@ -22,13 +24,13 @@ abstract class AbstractRestClient extends Iterator[String]{
   protected def getBufferData(): Unit
 
 
-  def doHTTPGETRequest(url:String): String = {
+  def doHTTPGETRequest(url: String): String = {
     val httpGet = new HttpGet(url)
     doHTTPRequest(httpGet)
 
   }
 
-  def doHTTPPOSTRequest(url:String, json:String): String = {
+  def doHTTPPOSTRequest(url: String, json: String): String = {
     val httpPost = new HttpPost(url)
     if (json != null) {
       val entity = new StringEntity(json)
@@ -45,7 +47,7 @@ abstract class AbstractRestClient extends Iterator[String]{
 
 
   override def next(): String = {
-    val next_item:String = buffer(current_index)
+    val next_item: String = buffer(current_index)
     current_index = current_index + 1
     if (current_index == buffer.size)
       getBufferData()
@@ -53,34 +55,38 @@ abstract class AbstractRestClient extends Iterator[String]{
   }
 
 
-
+  private def doHTTPRequest[A <: HttpUriRequest](r: A): String = {
-
+    val timeout = 60; // seconds
-  private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
+    val config = RequestConfig.custom()
-    val client = HttpClients.createDefault
+      .setConnectTimeout(timeout * 1000)
-    var tries = 4
+      .setConnectionRequestTimeout(timeout * 1000)
+      .setSocketTimeout(timeout * 1000).build()
+    val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
     try {
+      var tries = 4
       while (tries > 0) {
-
         println(s"requesting ${r.getURI}")
-        val response = client.execute(r)
+        try {
-        println(s"get response with status${response.getStatusLine.getStatusCode}")
+          val response = client.execute(r)
-        if (response.getStatusLine.getStatusCode > 400) {
+          println(s"get response with status${response.getStatusLine.getStatusCode}")
-          tries -= 1
+          if (response.getStatusLine.getStatusCode > 400) {
+            tries -= 1
+          }
+          else
+            return IOUtils.toString(response.getEntity.getContent)
+        } catch {
+          case e: Throwable =>
+            println(s"Error on requesting ${r.getURI}")
+            e.printStackTrace()
+            tries -= 1
         }
-        else
-          return IOUtils.toString(response.getEntity.getContent)
       }
       ""
-    } catch {
+    } finally {
-      case e: Throwable =>
+      if (client != null)
-        throw new RuntimeException("Error on executing request ", e)
+        client.close()
-    } 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/DataciteToOAFTransformation.scala

@@ -367,7 +367,7 @@ object DataciteToOAFTransformation {
 
 
     result.setDateofcollection(ISO8601FORMAT.format(d))
-    result.setDateoftransformation(ISO8601FORMAT.format(ts))
+    result.setDateoftransformation(ISO8601FORMAT.format(d))
     result.setDataInfo(dataInfo)
 
     val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())

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

@@ -140,7 +140,7 @@ object ImportDatacite {
 
   private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
     var from:Long = timestamp * 1000
-    val delta:Long = 50000000L
+    val delta:Long = 100000000L
     var client: DataciteAPIImporter = null
     val now :Long =System.currentTimeMillis()
     var i = 0

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

@@ -0,0 +1,53 @@
+package eu.dnetlib.dhp.actionmanager.datacite
+
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser
+import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import org.apache.hadoop.conf.Configuration
+import org.apache.hadoop.fs.LocalFileSystem
+import org.apache.hadoop.hdfs.DistributedFileSystem
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
+import org.apache.spark.sql.functions.max
+import org.slf4j.{Logger, LoggerFactory}
+
+import java.text.SimpleDateFormat
+import java.util.{Date, Locale}
+import scala.io.Source
+
+object SparkDownloadUpdateDatacite {
+  val log: Logger = LoggerFactory.getLogger(getClass)
+
+  def main(args: Array[String]): Unit = {
+
+    val conf = new SparkConf
+    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 workingPath = parser.get("workingPath")
+
+    val hdfsuri = parser.get("namenode")
+    log.info(s"namenode is $hdfsuri")
+
+
+    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]
+
+    import spark.implicits._
+
+
+    val maxDate:String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0)
+    val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
+    val string_to_date =ISO8601FORMAT.parse(maxDate)
+    val ts = string_to_date.getTime
+
+
+  }
+
+}

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.CSVProgramme;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.common.HdfsSupport;
 import scala.Tuple2;
@@ -171,26 +171,23 @@ public class PrepareProgramme {
 	}
 
 	private static CSVProgramme groupProgrammeByCode(CSVProgramme a, CSVProgramme b) {
-		if (!a.getLanguage().equals("en")) {
+		if (!a.getLanguage().equals("en") && b.getLanguage().equalsIgnoreCase("en")) {
-			if (b.getLanguage().equalsIgnoreCase("en")) {
+			a.setTitle(b.getTitle());
-				a.setTitle(b.getTitle());
+			a.setLanguage(b.getLanguage());
-				a.setLanguage(b.getLanguage());
-			}
 		}
-		if (StringUtils.isEmpty(a.getShortTitle())) {
+		if (StringUtils.isEmpty(a.getShortTitle()) && !StringUtils.isEmpty(b.getShortTitle())) {
-			if (!StringUtils.isEmpty(b.getShortTitle())) {
+			a.setShortTitle(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<String, String>(value.getTitle(), value.getShortTitle())))
+					new Tuple2<>(value.getTitle(), value.getShortTitle())))
 			.collect()
 			.toArray();
 
@@ -216,7 +213,7 @@ public class PrepareProgramme {
 			String[] tmp = ent.split("\\.");
 			if (tmp.length <= 2) {
 				if (StringUtils.isEmpty(entry._2()._2())) {
-					map.put(entry._1(), new Tuple2<String, String>(entry._2()._1(), entry._2()._1()));
+					map.put(entry._1(), new Tuple2<>(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.CSVProject;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.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(PrepareProgramme.class);
+	private static final Logger log = LoggerFactory.getLogger(PrepareProjects.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

@@ -31,15 +31,16 @@ import eu.dnetlib.dhp.common.DbClient;
  */
 public class ReadProjectsFromDB implements Closeable {
 
-	private final DbClient dbClient;
 	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 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
@@ -65,9 +66,9 @@ public class ReadProjectsFromDB implements Closeable {
 		}
 	}
 
-	public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) throws Exception {
+	public void execute(final String sql, final Function<ResultSet, List<ProjectSubset>> producer) {
 
-		final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(r -> writeProject(r));
+		final Consumer<ResultSet> consumer = rs -> producer.apply(rs).forEach(this::writeProject);
 
 		dbClient.processResults(sql, consumer);
 	}
@@ -94,20 +95,20 @@ public class ReadProjectsFromDB implements Closeable {
 
 	public ReadProjectsFromDB(
 		final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
-		throws Exception {
+		throws IOException {
 
 		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 = fileSystem.create(hdfsWritePath);
+		FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
 
-		this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
+		this.writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8));
 	}
 
 	@Override

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

@@ -4,7 +4,6 @@ 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;
 
@@ -22,15 +21,16 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
-import eu.dnetlib.dhp.actionmanager.project.utils.CSVProgramme;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProgramme;
-import eu.dnetlib.dhp.actionmanager.project.utils.CSVProject;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.CSVProject;
-import eu.dnetlib.dhp.actionmanager.project.utils.EXCELTopic;
+import eu.dnetlib.dhp.actionmanager.project.utils.model.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;
@@ -47,13 +47,10 @@ 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 {
 
@@ -137,7 +134,6 @@ 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;
@@ -152,20 +148,16 @@ public class SparkAtomicActionJob {
 			.map((MapFunction<Tuple2<Project, EXCELTopic>, Project>) p -> {
 				Optional<EXCELTopic> op = Optional.ofNullable(p._2());
 				Project rp = p._1();
-				if (op.isPresent()) {
+				op.ifPresent(excelTopic -> rp.setH2020topicdescription(excelTopic.getTitle()));
-					rp.setH2020topicdescription(op.get().getTitle());
-				}
 				return rp;
 			}, Encoders.bean(Project.class))
 			.filter(Objects::nonNull)
 			.groupByKey(
-				(MapFunction<Project, String>) p -> p.getId(),
+				(MapFunction<Project, String>) OafEntity::getId,
 				Encoders.STRING())
 			.mapGroups((MapGroupsFunction<String, Project, Project>) (s, it) -> {
 				Project first = it.next();
-				it.forEachRemaining(p -> {
+				it.forEachRemaining(first::mergeFrom);
-					first.mergeFrom(p);
-				});
 				return first;
 			}, Encoders.bean(Project.class))
 			.toJavaRDD()
@@ -189,12 +181,6 @@ 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

@@ -1,40 +0,0 @@
-
-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/CSVProject.java

@@ -1,200 +0,0 @@
-
-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

@@ -17,6 +17,8 @@ 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
  */
@@ -26,52 +28,52 @@ public class EXCELParser {
 		throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException,
 		InvalidFormatException {
 
-		OPCPackage pkg = OPCPackage.open(file);
+		try (OPCPackage pkg = OPCPackage.open(file); XSSFWorkbook wb = new XSSFWorkbook(pkg)) {
-		XSSFWorkbook wb = new XSSFWorkbook(pkg);
 
-		XSSFSheet sheet = wb.getSheet(sheetName);
+			XSSFSheet sheet = wb.getSheet(sheetName);
-
-		if (sheetName == null) {
-			throw new RuntimeException("Sheet name " + sheetName + " not present in current file");
-		}
-
-		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();
-
-			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();
-
-				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);
-				}
 
+			if (sheet == null) {
+				throw new IllegalArgumentException("Sheet name " + sheetName + " not present in current file");
 			}
 
-			count += 1;
+			List<R> ret = new ArrayList<>();
-		}
 
-		return ret;
+			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();
+
+					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);
+					}
+
+				}
+
+				count += 1;
+			}
+
+			return ret;
+		}
 	}
 
 }

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

@@ -1,34 +1,21 @@
 
 package eu.dnetlib.dhp.actionmanager.project.utils;
 
-import java.io.BufferedWriter;
+import java.io.*;
-import java.io.Closeable;
+import java.util.Optional;
-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.collection.HttpConnector2;
+import eu.dnetlib.dhp.common.collection.GetCSV;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
 
 /**
  * Applies the parsing of a csv file and writes the Serialization of it in hdfs
  */
-public class ReadCSV implements Closeable {
+public class ReadCSV {
-	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(
@@ -44,56 +31,22 @@ public class ReadCSV implements Closeable {
 		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);
 
-		try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL)) {
+		Configuration conf = new Configuration();
+		conf.set("fs.defaultFS", hdfsNameNode);
 
-			log.info("Getting CSV file...");
+		FileSystem fileSystem = FileSystem.get(conf);
-			readCSV.execute(classForName);
+		BufferedReader reader = new BufferedReader(
+			new InputStreamReader(new HttpConnector2().getInputSourceAsStream(fileURL)));
 
-		}
+		GetCSV.getCsv(fileSystem, reader, hdfsPath, classForName, del);
-	}
 
-	public void execute(final String classForName) throws Exception {
+		reader.close();
-		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

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

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

@@ -1,20 +1,32 @@
 
-package eu.dnetlib.dhp.actionmanager.project.utils;
+package eu.dnetlib.dhp.actionmanager.project.utils.model;
 
 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 {
 
-	private String rcn;
+	@CsvBindByName(column = "code")
 	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() {
@@ -33,14 +45,6 @@ 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;
 	}
@@ -73,5 +77,4 @@ public class CSVProgramme implements Serializable {
 		this.language = language;
 	}
 
-//
 }

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

@@ -0,0 +1,46 @@
+
+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/project/utils/model/EXCELTopic.java

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

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

@@ -9,6 +9,7 @@ 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;
@@ -74,7 +75,7 @@ public class GenerateRorActionSetJob {
 
 		final String jsonConfiguration = IOUtils
 			.toString(
-				SparkAtomicActionJob.class
+				GenerateRorActionSetJob.class
 					.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json"));
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
@@ -108,7 +109,7 @@ public class GenerateRorActionSetJob {
 
 	private static void processRorOrganizations(final SparkSession spark,
 		final String inputPath,
-		final String outputPath) throws Exception {
+		final String outputPath) throws IOException {
 
 		readInputPath(spark, inputPath)
 			.map(
@@ -203,7 +204,7 @@ public class GenerateRorActionSetJob {
 
 	private static Dataset<RorOrganization> readInputPath(
 		final SparkSession spark,
-		final String path) throws Exception {
+		final String path) throws IOException {
 
 		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

@@ -7,6 +7,8 @@ import com.fasterxml.jackson.annotation.JsonProperty;
 
 public class Address implements Serializable {
 
+	private static final long serialVersionUID = 2444635485253443195L;
+
 	@JsonProperty("lat")
 	private Float lat;
 
@@ -37,8 +39,6 @@ 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 final static long serialVersionUID = 2616688352998387611L;
+	private static final long serialVersionUID = 2616688352998387611L;
 
 	public ExternalIdType() {
 	}

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

@@ -15,8 +15,7 @@ import com.fasterxml.jackson.databind.JsonNode;
 public class ExternalIdTypeDeserializer extends JsonDeserializer<ExternalIdType> {
 
 	@Override
-	public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt)
+	public ExternalIdType deserialize(final JsonParser p, final DeserializationContext ctxt) throws IOException {
-		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 final static long serialVersionUID = 7294958526269195673L;
+	private static final 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 final static long serialVersionUID = -8389480201526252955L;
+	private static final 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 final static long serialVersionUID = -6576156103297850809L;
+	private static final 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 final static long serialVersionUID = -194308261058176439L;
+	private static final 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

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

@@ -11,6 +11,8 @@ 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<>();
 
@@ -59,8 +61,6 @@ 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

@@ -0,0 +1,69 @@
+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

@@ -0,0 +1,86 @@
+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])
+
+  }
+
+}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/common/ReportingJob.java

@@ -6,6 +6,8 @@ import java.util.concurrent.Executors;
 import java.util.concurrent.ScheduledExecutorService;
 import java.util.concurrent.TimeUnit;
 
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+
 public abstract class ReportingJob {
 
 	/**
@@ -22,7 +24,7 @@ public abstract class ReportingJob {
 
 	protected final AggregatorReport report;
 
-	public ReportingJob(AggregatorReport report) {
+	protected ReportingJob(AggregatorReport report) {
 		this.report = report;
 	}
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/aggregation/mdstore/MDStoreActionNode.java

@@ -25,7 +25,7 @@ public class MDStoreActionNode {
 		NEW_VERSION, ROLLBACK, COMMIT, READ_LOCK, READ_UNLOCK
 	}
 
-	public static String NEW_VERSION_URI = "%s/mdstore/%s/newVersion";
+	public static final String NEW_VERSION_URI = "%s/mdstore/%s/newVersion";
 
 	public static final String COMMIT_VERSION_URL = "%s/version/%s/commit/%s";
 	public static final String ROLLBACK_VERSION_URL = "%s/version/%s/abort";
@@ -70,7 +70,7 @@ public class MDStoreActionNode {
 				if (StringUtils.isBlank(hdfsuri)) {
 					throw new IllegalArgumentException("missing or empty argument namenode");
 				}
-				final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
+				final String mdStoreVersion_params = argumentParser.get(MDSTOREVERSIONPARAM);
 				final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
 
 				if (StringUtils.isBlank(mdStoreVersion.getId())) {
@@ -94,7 +94,7 @@ public class MDStoreActionNode {
 				break;
 			}
 			case ROLLBACK: {
-				final String mdStoreVersion_params = argumentParser.get("mdStoreVersion");
+				final String mdStoreVersion_params = argumentParser.get(MDSTOREVERSIONPARAM);
 				final MDStoreVersion mdStoreVersion = MAPPER.readValue(mdStoreVersion_params, MDStoreVersion.class);
 
 				if (StringUtils.isBlank(mdStoreVersion.getId())) {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java

@@ -16,7 +16,6 @@ import org.apache.hadoop.io.compress.DeflateCodec;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.aggregation.common.ReporterCallback;
 import eu.dnetlib.dhp.aggregation.common.ReportingJob;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
@@ -24,6 +23,9 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
 import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion;
 
 public class CollectorWorker extends ReportingJob {
@@ -116,7 +118,7 @@ public class CollectorWorker extends ReportingJob {
 				final CollectorPlugin.NAME.OTHER_NAME plugin = Optional
 					.ofNullable(api.getParams().get("other_plugin_type"))
 					.map(CollectorPlugin.NAME.OTHER_NAME::valueOf)
-					.get();
+					.orElseThrow(() -> new IllegalArgumentException("invalid other_plugin_type"));
 
 				switch (plugin) {
 					case mdstore_mongodb_dump:

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorkerApplication.java

@@ -13,8 +13,10 @@ import org.apache.hadoop.fs.FileSystem;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
 import eu.dnetlib.dhp.message.MessageSender;
 import eu.dnetlib.dhp.schema.mdstore.MDStoreVersion;
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/GenerateNativeStoreSparkJob.java

@@ -207,6 +207,7 @@ public class GenerateNativeStoreSparkJob {
 			totalItems.add(1);
 		try {
 			SAXReader reader = new SAXReader();
+			reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
 			Document document = reader.read(new ByteArrayInputStream(input.getBytes(StandardCharsets.UTF_8)));
 			Node node = document.selectSingleNode(xpath);
 			final String originalIdentifier = node.getText();

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java

@@ -3,9 +3,9 @@ package eu.dnetlib.dhp.collection.plugin;
 
 import java.util.stream.Stream;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.CollectorException;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
 
 public interface CollectorPlugin {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MDStoreCollectorPlugin.java

@@ -11,15 +11,13 @@ import org.bson.Document;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import com.mongodb.MongoClient;
-import com.mongodb.MongoClientURI;
 import com.mongodb.client.MongoCollection;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.CollectorException;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
 import eu.dnetlib.dhp.common.MdstoreClient;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
 
 public class MDStoreCollectorPlugin implements CollectorPlugin {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/mongodb/MongoDbDumpCollectorPlugin.java

@@ -12,10 +12,10 @@ import java.util.zip.GZIPInputStream;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.CollectorException;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class MongoDbDumpCollectorPlugin implements CollectorPlugin {
@@ -23,7 +23,7 @@ public class MongoDbDumpCollectorPlugin implements CollectorPlugin {
 	public static final String PATH_PARAM = "path";
 	public static final String BODY_JSONPATH = "$.body";
 
-	public FileSystem fileSystem;
+	private final FileSystem fileSystem;
 
 	public MongoDbDumpCollectorPlugin(FileSystem fileSystem) {
 		this.fileSystem = fileSystem;

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java

@@ -13,11 +13,11 @@ import com.google.common.base.Splitter;
 import com.google.common.collect.Iterators;
 import com.google.common.collect.Lists;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.CollectorException;
-import eu.dnetlib.dhp.collection.HttpClientParams;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
 public class OaiCollectorPlugin implements CollectorPlugin {
 
@@ -66,11 +66,11 @@ public class OaiCollectorPlugin implements CollectorPlugin {
 		}
 
 		if (fromDate != null && !fromDate.matches(DATE_REGEX) && !fromDate.matches(UTC_DATETIME_REGEX)) {
-			throw new CollectorException("Invalid date (YYYY-MM-DD): " + fromDate);
+			throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + fromDate);
 		}
 
 		if (untilDate != null && !untilDate.matches(DATE_REGEX) && !untilDate.matches(UTC_DATETIME_REGEX)) {
-			throw new CollectorException("Invalid date (YYYY-MM-DD): " + untilDate);
+			throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + untilDate);
 		}
 
 		final Iterator<Iterator<String>> iters = sets

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java

@@ -2,7 +2,6 @@
 package eu.dnetlib.dhp.collection.plugin.oai;
 
 import java.io.IOException;
-import java.io.StringReader;
 import java.io.StringWriter;
 import java.io.UnsupportedEncodingException;
 import java.net.URLEncoder;
@@ -16,21 +15,21 @@ import org.dom4j.DocumentException;
 import org.dom4j.DocumentHelper;
 import org.dom4j.Node;
 import org.dom4j.io.OutputFormat;
-import org.dom4j.io.SAXReader;
 import org.dom4j.io.XMLWriter;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
-import eu.dnetlib.dhp.collection.CollectorException;
-import eu.dnetlib.dhp.collection.HttpConnector2;
 import eu.dnetlib.dhp.collection.XmlCleaner;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
 
 public class OaiIterator implements Iterator<String> {
 
 	private static final Logger log = LoggerFactory.getLogger(OaiIterator.class);
 
-	private final static String REPORT_PREFIX = "oai:";
+	private static final String REPORT_PREFIX = "oai:";
+	public static final String UTF_8 = "UTF-8";
 
 	private final Queue<String> queue = new PriorityBlockingQueue<>();
 
@@ -68,7 +67,7 @@ public class OaiIterator implements Iterator<String> {
 			try {
 				this.token = firstPage();
 			} catch (final CollectorException e) {
-				throw new RuntimeException(e);
+				throw new IllegalStateException(e);
 			}
 		}
 	}
@@ -90,7 +89,7 @@ public class OaiIterator implements Iterator<String> {
 				try {
 					token = otherPages(token);
 				} catch (final CollectorException e) {
-					throw new RuntimeException(e);
+					throw new IllegalStateException(e);
 				}
 			}
 			return res;
@@ -99,23 +98,24 @@ public class OaiIterator implements Iterator<String> {
 
 	@Override
 	public void remove() {
+		throw new UnsupportedOperationException();
 	}
 
 	private String firstPage() throws CollectorException {
 		try {
-			String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, "UTF-8");
+			String url = baseUrl + "?verb=ListRecords&metadataPrefix=" + URLEncoder.encode(mdFormat, UTF_8);
 			if (set != null && !set.isEmpty()) {
-				url += "&set=" + URLEncoder.encode(set, "UTF-8");
+				url += "&set=" + URLEncoder.encode(set, UTF_8);
 			}
 			if (fromDate != null && (fromDate.matches(OaiCollectorPlugin.DATE_REGEX)
 				|| fromDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) {
-				url += "&from=" + URLEncoder.encode(fromDate, "UTF-8");
+				url += "&from=" + URLEncoder.encode(fromDate, UTF_8);
 			}
 			if (untilDate != null && (untilDate.matches(OaiCollectorPlugin.DATE_REGEX)
 				|| untilDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) {
-				url += "&until=" + URLEncoder.encode(untilDate, "UTF-8");
+				url += "&until=" + URLEncoder.encode(untilDate, UTF_8);
 			}
-			log.info("Start harvesting using url: " + url);
+			log.info("Start harvesting using url: {}", url);
 
 			return downloadPage(url);
 		} catch (final UnsupportedEncodingException e) {
@@ -143,7 +143,7 @@ public class OaiIterator implements Iterator<String> {
 			return downloadPage(
 				baseUrl
 					+ "?verb=ListRecords&resumptionToken="
-					+ URLEncoder.encode(resumptionToken, "UTF-8"));
+					+ URLEncoder.encode(resumptionToken, UTF_8));
 		} catch (final UnsupportedEncodingException e) {
 			report.put(e.getClass().getName(), e.getMessage());
 			throw new CollectorException(e);
@@ -161,7 +161,7 @@ public class OaiIterator implements Iterator<String> {
 			report.put(e.getClass().getName(), e.getMessage());
 			final String cleaned = XmlCleaner.cleanAllEntities(xml);
 			try {
-				doc = DocumentHelper.parseText(xml);
+				doc = DocumentHelper.parseText(cleaned);
 			} catch (final DocumentException e1) {
 				final String resumptionToken = extractResumptionToken(xml);
 				if (resumptionToken == null) {

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIteratorFactory.java

@@ -3,9 +3,9 @@ package eu.dnetlib.dhp.collection.plugin.oai;
 
 import java.util.Iterator;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
-import eu.dnetlib.dhp.collection.HttpClientParams;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
-import eu.dnetlib.dhp.collection.HttpConnector2;
+import eu.dnetlib.dhp.common.collection.HttpConnector2;
 
 public class OaiIteratorFactory {
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestCollectorPlugin.java

@@ -9,11 +9,11 @@ import java.util.stream.StreamSupport;
 
 import org.apache.commons.lang3.StringUtils;
 
-import eu.dnetlib.dhp.aggregation.common.AggregatorReport;
 import eu.dnetlib.dhp.collection.ApiDescriptor;
-import eu.dnetlib.dhp.collection.CollectorException;
-import eu.dnetlib.dhp.collection.HttpClientParams;
 import eu.dnetlib.dhp.collection.plugin.CollectorPlugin;
+import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
 /**
  * TODO: delegate HTTP requests to the common HttpConnector2 implementation.

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java

@@ -30,9 +30,9 @@ import org.w3c.dom.Node;
 import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 
-import eu.dnetlib.dhp.collection.CollectorException;
-import eu.dnetlib.dhp.collection.HttpClientParams;
 import eu.dnetlib.dhp.collection.JsonUtils;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.common.collection.HttpClientParams;
 
 /**
  * log.info(...) equal to  log.trace(...) in the application-logs
@@ -131,7 +131,8 @@ public class RestIterator implements Iterator<String> {
 
 	private void initXmlTransformation(String resultTotalXpath, String resumptionXpath, String entityXpath)
 		throws TransformerConfigurationException, XPathExpressionException {
-		transformer = TransformerFactory.newInstance().newTransformer();
+		final TransformerFactory factory = TransformerFactory.newInstance();
+		transformer = factory.newTransformer();
 		transformer.setOutputProperty(OutputKeys.INDENT, "yes");
 		transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "3");
 		xpath = XPathFactory.newInstance().newXPath();
@@ -142,7 +143,7 @@ public class RestIterator implements Iterator<String> {
 
 	private void initQueue() {
 		query = baseUrl + "?" + queryParams + querySize + queryFormat;
-		log.info("REST calls starting with " + query);
+		log.info("REST calls starting with {}", query);
 	}
 
 	private void disconnect() {
@@ -174,7 +175,7 @@ public class RestIterator implements Iterator<String> {
 				try {
 					query = downloadPage(query);
 				} catch (CollectorException e) {
-					log.debug("CollectorPlugin.next()-Exception: " + e);
+					log.debug("CollectorPlugin.next()-Exception: {}", e);
 					throw new RuntimeException(e);
 				}
 			}
@@ -198,7 +199,7 @@ public class RestIterator implements Iterator<String> {
 
 		// check if cursor=* is initial set otherwise add it to the queryParam URL
 		if (resumptionType.equalsIgnoreCase("deep-cursor")) {
-			log.debug("check resumptionType deep-cursor and check cursor=*?" + query);
+			log.debug("check resumptionType deep-cursor and check cursor=*?{}", query);
 			if (!query.contains("&cursor=")) {
 				query += "&cursor=*";
 			}
@@ -208,16 +209,16 @@ public class RestIterator implements Iterator<String> {
 			log.info("requestig URL [{}]", query);
 
 			URL qUrl = new URL(query);
-			log.debug("authMethod :" + authMethod);
+			log.debug("authMethod: {}", authMethod);
 			if ("bearer".equalsIgnoreCase(this.authMethod)) {
-				log.trace("authMethod before inputStream: " + resultXml);
+				log.trace("authMethod before inputStream: {}", resultXml);
 				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
 				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Bearer " + authToken);
 				conn.setRequestProperty(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.getMimeType());
 				conn.setRequestMethod("GET");
 				theHttpInputStream = conn.getInputStream();
 			} else if (BASIC.equalsIgnoreCase(this.authMethod)) {
-				log.trace("authMethod before inputStream: " + resultXml);
+				log.trace("authMethod before inputStream: {}", resultXml);
 				HttpURLConnection conn = (HttpURLConnection) qUrl.openConnection();
 				conn.setRequestProperty(HttpHeaders.AUTHORIZATION, "Basic " + authToken);
 				conn.setRequestProperty(HttpHeaders.ACCEPT, ContentType.APPLICATION_XML.getMimeType());
@@ -237,13 +238,13 @@ public class RestIterator implements Iterator<String> {
 			if (!(emptyXml).equalsIgnoreCase(resultXml)) {
 				resultNode = (Node) xpath.evaluate("/", new InputSource(resultStream), XPathConstants.NODE);
 				nodeList = (NodeList) xprEntity.evaluate(resultNode, XPathConstants.NODESET);
-				log.debug("nodeList.length: " + nodeList.getLength());
+				log.debug("nodeList.length: {}", nodeList.getLength());
 				for (int i = 0; i < nodeList.getLength(); i++) {
 					StringWriter sw = new StringWriter();
 					transformer.transform(new DOMSource(nodeList.item(i)), new StreamResult(sw));
 					String toEnqueue = sw.toString();
 					if (toEnqueue == null || StringUtils.isBlank(toEnqueue) || emptyXml.equalsIgnoreCase(toEnqueue)) {
-						log.warn("The following record resulted in empty item for the feeding queue: " + resultXml);
+						log.warn("The following record resulted in empty item for the feeding queue: {}", resultXml);
 					} else {
 						recordQueue.add(sw.toString());
 					}
@@ -274,9 +275,9 @@ public class RestIterator implements Iterator<String> {
 							String[] resumptionKeyValue = arrayUrlArgStr.split("=");
 							if (isInteger(resumptionKeyValue[1])) {
 								urlOldResumptionSize = Integer.parseInt(resumptionKeyValue[1]);
-								log.debug("discover OldResumptionSize from Url (int): " + urlOldResumptionSize);
+								log.debug("discover OldResumptionSize from Url (int): {}", urlOldResumptionSize);
 							} else {
-								log.debug("discover OldResumptionSize from Url (str): " + resumptionKeyValue[1]);
+								log.debug("discover OldResumptionSize from Url (str): {}", resumptionKeyValue[1]);
 							}
 						}
 					}
@@ -295,7 +296,7 @@ public class RestIterator implements Iterator<String> {
 							discoverResultSize += nodeList.getLength();
 						}
 					}
-					log.info("discoverResultSize:  {}", discoverResultSize);
+					log.info("discoverResultSize: {}", discoverResultSize);
 					break;
 
 				case "pagination":

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala

@@ -1,14 +1,12 @@
-package eu.dnetlib.dhp.sx.graph.bio
+package eu.dnetlib.dhp.sx.bio
 
 import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
-import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty}
+import eu.dnetlib.dhp.schema.oaf._
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.{compact, parse, render}
-
+import collection.JavaConverters._
-import scala.collection.JavaConverters._
-
 object BioDBToOAF {
 
   case class EBILinkItem(id: Long, links: String) {}
@@ -17,23 +15,23 @@ object BioDBToOAF {
 
   case class UniprotDate(date: String, date_info: String) {}
 
-  case class ScholixResolved(pid:String, pidType:String, typology:String, tilte:List[String], datasource:List[String], date:List[String], authors:List[String]){}
+  case class ScholixResolved(pid: String, pidType: String, typology: String, tilte: List[String], datasource: List[String], date: List[String], authors: List[String]) {}
 
   val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
   val SUBJ_CLASS = "Keywords"
 
   val DATE_RELATION_KEY = "RelationDate"
 
-  val resolvedURL:Map[String,String] = Map(
+  val resolvedURL: Map[String, String] = Map(
-    "genbank"->             "https://www.ncbi.nlm.nih.gov/nuccore/",
+    "genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
-    "ncbi-n" ->             "https://www.ncbi.nlm.nih.gov/nuccore/",
+    "ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
-    "ncbi-wgs" ->           "https://www.ncbi.nlm.nih.gov/nuccore/",
+    "ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
-    "ncbi-p" ->             "https://www.ncbi.nlm.nih.gov/protein/",
+    "ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/",
-    "ena" ->                "https://www.ebi.ac.uk/ena/browser/view/",
+    "ena" -> "https://www.ebi.ac.uk/ena/browser/view/",
-    "clinicaltrials.gov"->  "https://clinicaltrials.gov/ct2/show/",
+    "clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/",
-    "onim"->                "https://omim.org/entry/",
+    "onim" -> "https://omim.org/entry/",
-    "refseq"->              "https://www.ncbi.nlm.nih.gov/nuccore/",
+    "refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/",
-    "geo"->                 "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
+    "geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc="
   )
 
 
@@ -45,7 +43,7 @@ object BioDBToOAF {
     val ElsevierCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier")
     val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature")
     val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)")
-    val pubmedCollectedFrom:KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
+    val pubmedCollectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
 
     UNIPROTCollectedFrom.setDataInfo(DATA_INFO)
     PDBCollectedFrom.setDataInfo(DATA_INFO)
@@ -58,9 +56,9 @@ object BioDBToOAF {
 
     Map(
       "uniprot" -> UNIPROTCollectedFrom,
-      "pdb"-> PDBCollectedFrom,
+      "pdb" -> PDBCollectedFrom,
-      "elsevier" ->ElsevierCollectedFrom,
+      "elsevier" -> ElsevierCollectedFrom,
-      "ebi" ->EBICollectedFrom,
+      "ebi" -> EBICollectedFrom,
       "Springer Nature" -> springerNatureCollectedFrom,
       "NCBI Nucleotide" -> ncbiCollectedFrom,
       "European Nucleotide Archive" -> enaCollectedFrom,
@@ -68,7 +66,7 @@ object BioDBToOAF {
     )
   }
 
-  def crossrefLinksToOaf(input:String):Oaf = {
+  def crossrefLinksToOaf(input: String): Oaf = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json = parse(input)
     val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase
@@ -77,16 +75,16 @@ object BioDBToOAF {
     val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase
     val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase
 
-    val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String]
+    val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String]
 
     val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String])
 
-    createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic, date)
+    createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type), collectedFromMap("elsevier"), "relationship", relation_semantic, date)
 
   }
 
 
-  def scholixResolvedToOAF(input:ScholixResolved):Oaf = {
+  def scholixResolvedToOAF(input: ScholixResolved): Oaf = {
 
     val d = new Dataset
 
@@ -127,18 +125,18 @@ object BioDBToOAF {
     d.setInstance(List(i).asJava)
 
     if (input.authors != null && input.authors.nonEmpty) {
-      val authors = input.authors.map(a =>{
+      val authors = input.authors.map(a => {
         val authorOAF = new Author
         authorOAF.setFullname(a)
         authorOAF
       })
       d.setAuthor(authors.asJava)
     }
-    if (input.date!= null && input.date.nonEmpty) {
+    if (input.date != null && input.date.nonEmpty) {
-        val dt = input.date.head
+      val dt = input.date.head
-        i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
+      i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
-        d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
+      d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO))
-      }
+    }
     d
   }
 
@@ -190,7 +188,7 @@ object BioDBToOAF {
           OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null)
         ).asJava)
     }
-    var i_date:Option[UniprotDate] = None
+    var i_date: Option[UniprotDate] = None
 
     if (dates.nonEmpty) {
       i_date = dates.find(d => d.date_info.contains("entry version"))
@@ -199,7 +197,7 @@ object BioDBToOAF {
         d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
       }
       val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version"))
-        .map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
+        .map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
       if (relevant_dates != null && relevant_dates.nonEmpty)
         d.setRelevantdate(relevant_dates.asJava)
       d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
@@ -218,12 +216,12 @@ object BioDBToOAF {
 
 
     if (references_pmid != null && references_pmid.nonEmpty) {
-      val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if  (i_date.isDefined) i_date.get.date else null)
+      val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
       rel.getCollectedfrom
       List(d, rel)
     }
     else if (references_doi != null && references_doi.nonEmpty) {
-      val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if  (i_date.isDefined) i_date.get.date else null)
+      val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
       List(d, rel)
     }
     else
@@ -231,19 +229,18 @@ object BioDBToOAF {
   }
 
 
-
+  def generate_unresolved_id(pid: String, pidType: String): String = {
-  def generate_unresolved_id(pid:String, pidType:String) :String = {
     s"unresolved::$pid::$pidType"
   }
 
 
-  def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String, date:String):Relation = {
+  def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType: String, relClass: String, date: String): Relation = {
 
     val rel = new Relation
     rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
     rel.setDataInfo(DATA_INFO)
 
-    rel.setRelType("resultResult")
+    rel.setRelType(ModelConstants.RESULT_RESULT)
     rel.setSubRelType(subRelType)
     rel.setRelClass(relClass)
 
@@ -251,7 +248,7 @@ object BioDBToOAF {
     rel.setTarget(s"unresolved::$pid::$pidType")
 
 
-    val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
+    val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date)
 
     rel.setProperties(List(dateProps).asJava)
 
@@ -262,8 +259,8 @@ object BioDBToOAF {
   }
 
 
-  def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
+  def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date: String): Relation = {
-    createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date)
+    createRelation(pid, pidType, sourceId, collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
   }
 
 
@@ -338,7 +335,7 @@ object BioDBToOAF {
 
   def EBITargetLinksFilter(input: EBILinks): Boolean = {
 
-    input.targetPidType.equalsIgnoreCase("ena") ||   input.targetPidType.equalsIgnoreCase("pdb") ||  input.targetPidType.equalsIgnoreCase("uniprot")
+    input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot")
 
   }
 
@@ -392,6 +389,6 @@ object BioDBToOAF {
     i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
     d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
 
-    List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date)))
+    List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date)))
   }
 }