Last commit

Commented a little the Datacite transformation code

.gitignore

@@ -25,6 +25,10 @@
 /build
 spark-warehouse
 /**/job-override.properties
+<<<<<<< HEAD
+/**/*.log
+=======
 /**/*.log
 /**/.factorypath
 
+>>>>>>> upstream/master

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-build/dhp-code-style/pom.xml

@@ -22,9 +22,20 @@
             <id>dnet45-releases</id>
             <url>https://maven.d4science.org/nexus/content/repositories/dnet45-releases</url>
         </repository>
+        <site>
+            <id>DHPSite</id>
+            <url>${dhp.site.stage.path}/dhp-build/dhp-code-style</url>
+        </site>
     </distributionManagement>
 
     <build>
+        <extensions>
+            <extension>
+                <groupId>org.apache.maven.wagon</groupId>
+                <artifactId>wagon-ssh</artifactId>
+                <version>2.10</version>
+            </extension>
+        </extensions>
         <pluginManagement>
             <plugins>
                 <plugin>
@@ -35,7 +46,7 @@
                 <plugin>
                     <groupId>org.apache.maven.plugins</groupId>
                     <artifactId>maven-site-plugin</artifactId>
-                    <version>3.7.1</version>
+                    <version>3.9.1</version>
                 </plugin>
             </plugins>
         </pluginManagement>
@@ -43,6 +54,7 @@
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <dhp.site.stage.path>sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop</dhp.site.stage.path>
     </properties>
 
 </project>

dhp-build/dhp-code-style/src/site/site.xml

@@ -0,0 +1,21 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
+         name="DHP-Aggregation">
+    <skin>
+        <groupId>org.apache.maven.skins</groupId>
+        <artifactId>maven-fluido-skin</artifactId>
+        <version>1.8</version>
+    </skin>
+    <poweredBy>
+        <logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
+              img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
+    </poweredBy>
+    <body>
+        <links>
+            <item name="Code" href="https://code-repo.d4science.org/" />
+        </links>
+        <menu ref="modules" />
+        <menu ref="reports"/>
+    </body>
+</project>

dhp-build/pom.xml

@@ -10,6 +10,9 @@
 	<packaging>pom</packaging>
 
 	<description>This module is a container for the build tools used in dnet-hadoop</description>
+	<properties>
+		<maven.javadoc.skip>true</maven.javadoc.skip>
+	</properties>
 
 	<modules>
 		<module>dhp-code-style</module>
@@ -17,4 +20,12 @@
 		<module>dhp-build-properties-maven-plugin</module>
 	</modules>
 
+
+ <distributionManagement>
+	 <site>
+		 <id>DHPSite</id>
+		 <url>${dhp.site.stage.path}/dhp-build/</url>
+	 </site>
+ </distributionManagement>
+
 </project>

dhp-build/src/site/site.xml

@@ -0,0 +1,22 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
+         name="DHP-Aggregation">
+    <skin>
+        <groupId>org.apache.maven.skins</groupId>
+        <artifactId>maven-fluido-skin</artifactId>
+        <version>1.8</version>
+    </skin>
+    <poweredBy>
+        <logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
+              img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
+    </poweredBy>
+    <body>
+        <links>
+            <item name="Code" href="https://code-repo.d4science.org/" />
+        </links>
+
+        <menu ref="modules" />
+        <menu ref="reports"/>
+    </body>
+</project>

dhp-common/pom.xml

@@ -13,7 +13,51 @@
 	<artifactId>dhp-common</artifactId>
 	<packaging>jar</packaging>
 
+	<distributionManagement>
+		<site>
+			<id>DHPSite</id>
+			<url>${dhp.site.stage.path}/dhp-common</url>
+		</site>
+	</distributionManagement>
+
 	<description>This module contains common utilities meant to be used across the dnet-hadoop submodules</description>
+	<build>
+		<plugins>
+			<plugin>
+				<groupId>net.alchim31.maven</groupId>
+				<artifactId>scala-maven-plugin</artifactId>
+				<version>${net.alchim31.maven.version}</version>
+				<executions>
+					<execution>
+						<id>scala-compile-first</id>
+						<phase>initialize</phase>
+						<goals>
+							<goal>add-source</goal>
+							<goal>compile</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>scala-test-compile</id>
+						<phase>process-test-resources</phase>
+						<goals>
+							<goal>testCompile</goal>
+						</goals>
+					</execution>
+					<execution>
+						<id>scala-doc</id>
+						<phase>process-resources</phase> <!-- or wherever -->
+						<goals>
+							<goal>doc</goal>
+						</goals>
+					</execution>
+				</executions>
+				<configuration>
+					<scalaVersion>${scala.version}</scalaVersion>
+				</configuration>
+			</plugin>
+		</plugins>
+
+	</build>
 
 	<dependencies>
 
@@ -25,6 +69,11 @@
 			<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 +161,11 @@
 			<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) {
-			log.error("Wrong value to decompress:" + abstractCompressed);
-			throw new RuntimeException(e);
+		} catch (IOException e) {
+			log.error("Wrong value to decompress: {}", abstractCompressed);
+			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/application/SparkScalaApplication.scala

@@ -0,0 +1,72 @@
+package eu.dnetlib.dhp.application
+
+import scala.io.Source
+
+/**
+ * This is the main Interface SparkApplication
+ * where all the Spark Scala class should inherit
+ *
+ */
+trait SparkScalaApplication {
+  /**
+   * This is the path in the classpath of the json
+   * describes all the argument needed to run
+   */
+  val propertyPath: String
+
+  /**
+   * Utility to parse the arguments using the
+   * property json in the classpath identified from
+   * the variable propertyPath
+   *
+   * @param args the list of arguments
+   */
+  def parseArguments(args: Array[String]): ArgumentApplicationParser = {
+    val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString)
+    parser.parseArgument(args)
+    parser
+  }
+
+  /**
+   * Here all the spark applications runs this method
+   * where the whole logic of the spark node is defined
+   */
+  def run(): Unit
+}
+
+
+import org.apache.spark.SparkConf
+import org.apache.spark.sql.SparkSession
+import org.slf4j.Logger
+
+abstract class AbstractScalaApplication (val propertyPath:String, val args:Array[String], log:Logger) extends  SparkScalaApplication {
+
+  var parser: ArgumentApplicationParser = null
+
+  var spark:SparkSession = null
+
+
+  def initialize():SparkScalaApplication = {
+    parser = parseArguments(args)
+    spark = createSparkSession()
+    this
+  }
+
+  /**
+   * Utility for creating a spark session starting from parser
+   *
+   * @return a spark Session
+   */
+  private def createSparkSession():SparkSession = {
+    require(parser!= null)
+
+    val conf:SparkConf = new SparkConf()
+    val master = parser.get("master")
+    log.info(s"Creating Spark session: Master: $master")
+    SparkSession.builder().config(conf)
+      .appName(getClass.getSimpleName)
+      .master(master)
+      .getOrCreate()
+  }
+
+}

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/HdfsSupport.java

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

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(fsDataOutputStream.getWrappedStream());
+		return new TarArchiveOutputStream(fileSystem.create(hdfsWritePath).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
-			.listFiles(
-				new Path(inputPath), true);
+			while (iterator.hasNext()) {
+				writeCurrentFile(fileSystem, dir_name, iterator, ar, 0);
+			}
 
-		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("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
+			.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("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.CONTENT_TYPE, "application/zip") // add request headers
+			.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("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
+			.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("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
+			.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("Authorization", "Bearer " + access_token)
+			.addHeader(HttpHeaders.CONTENT_TYPE, ContentType.APPLICATION_JSON.toString()) // add request headers
+			.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 "
-										+ retryAfter + " sec.");
+									"{} - waiting and repeating request after suggested retry-after {} sec.",
+									requestUrl, retryAfter);
 							backoffAndSleep(retryAfter * 1000);
 						} else {
 							log
 								.warn(
-									requestUrl + " - waiting and repeating request after default delay of "
-										+ getClientParams().getRetryDelay() + " sec.");
+									"{} - waiting and repeating request after default delay of {} 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 {
-		CloseableHttpClient client = HttpClients.createDefault();
+	private static String doHTTPRequest(final HttpUriRequest r) throws IOException {
+		try (CloseableHttpClient client = HttpClients.createDefault()) {
 
-		log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
-		log
-			.info(
-				"request headers: {}",
-				Arrays
-					.asList(r.getAllHeaders())
-					.stream()
-					.map(h -> h.getName() + ":" + h.getValue())
-					.collect(Collectors.joining(",")));
+			log.info("performing HTTP request, method {} on URI {}", r.getMethod(), r.getURI().toString());
+			log
+				.info(
+					"request headers: {}",
+					Arrays
+						.asList(r.getAllHeaders())
+						.stream()
+						.map(h -> h.getName() + ":" + h.getValue())
+						.collect(Collectors.joining(",")));
 
-		CloseableHttpResponse response = client.execute(r);
-		return IOUtils.toString(response.getEntity().getContent());
+			return IOUtils.toString(client.execute(r).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);
 			}
 		}
 
@@ -58,10 +57,17 @@ public class VocabularyGroup implements Serializable {
 				final String syn = arr[2].trim();
 
 				vocs.addSynonyms(vocId, termId, syn);
-				// vocs.addSynonyms(vocId, termId, termId);
+
 			}
 		}
 
+		// add the term names as synonyms
+		vocs.vocs.values().forEach(voc -> {
+			voc.getTerms().values().forEach(term -> {
+				voc.addSynonym(term.getName().toLowerCase(), term.getId());
+			});
+		});
+
 		return vocs;
 	}
 
@@ -98,7 +104,7 @@ public class VocabularyGroup implements Serializable {
 			.getTerms()
 			.values()
 			.stream()
-			.map(t -> t.getId())
+			.map(VocabularyTerm::getId)
 			.collect(Collectors.toCollection(HashSet::new));
 	}
 
@@ -154,16 +160,19 @@ 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 String TOTAL_PARAM = "total";
+	public static final String CURRENT_PARAM = "current";
+	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);
 
@@ -62,22 +65,24 @@ 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()
 					.stream()
+					.filter(Objects::nonNull)
 					.map(p -> new Tuple2<>(pidToComparableString(p), a)))
 			.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
 
 		// <pid, Author> (list of pid that are missing in the other list)
 		final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
 			.stream()
-			.filter(a -> a.getPid() != null && a.getPid().size() > 0)
+			.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
 			.flatMap(
 				a -> a
 					.getPid()
 					.stream()
+					.filter(Objects::nonNull)
 					.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
 					.map(p -> new Tuple2<>(p, a)))
 			.collect(Collectors.toList());
@@ -115,9 +120,17 @@ public class AuthorMerger {
 	}
 
 	public static String pidToComparableString(StructuredProperty pid) {
+<<<<<<< HEAD
+		if (pid == null)
+			return "";
 		return (pid.getQualifier() != null
 			? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
 			: "")
+=======
+		final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
+			: "";
+		return (pid.getQualifier() != null ? classid : "")
+>>>>>>> upstream/master
 			+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
 	}
 
@@ -150,7 +163,7 @@ public class AuthorMerger {
 	}
 
 	private static boolean hasPid(Author a) {
-		if (a == null || a.getPid() == null || a.getPid().size() == 0)
+		if (a == null || a.getPid() == null || a.getPid().isEmpty())
 			return false;
 		return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
 	}
@@ -159,7 +172,10 @@ public class AuthorMerger {
 		if (StringUtils.isNotBlank(author.getSurname())) {
 			return new Person(author.getSurname() + ", " + author.getName(), false);
 		} else {
-			return new Person(author.getFullname(), false);
+			if (StringUtils.isNotBlank(author.getFullname()))
+				return new Person(author.getFullname(), false);
+			else
+				return new Person("", false);
 		}
 	}
 

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 +7,21 @@ 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.common.vocabulary.Vocabulary;
+import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
 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 {
 
@@ -30,8 +29,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 	public static final int ORCID_LEN = 19;
 	public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
 	public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
-	public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]";
-	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10;
+
+	public static final String TITLE_TEST = "test";
+	public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
+
+	public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
 
 	public static <T extends Oaf> T fixVocabularyNames(T value) {
 		if (value instanceof Datasource) {
@@ -115,7 +117,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 		return true;
 	}
 
-	public static <T extends Oaf> T cleanup(T value) {
+	public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
 		if (value instanceof Datasource) {
 			// nothing to clean here
 		} else if (value instanceof Project) {
@@ -194,11 +196,21 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 							.filter(Objects::nonNull)
 							.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
 							.filter(
-								sp -> sp
-									.getValue()
-									.toLowerCase()
-									.replaceAll(TITLE_FILTER_REGEX, "")
-									.length() > TITLE_FILTER_RESIDUAL_LENGTH)
+								sp -> {
+									final String title = sp
+										.getValue()
+										.toLowerCase();
+									final String decoded = Unidecode.decode(title);
+
+									if (StringUtils.contains(decoded, TITLE_TEST)) {
+										return decoded
+											.replaceAll(TITLE_FILTER_REGEX, "")
+											.length() > TITLE_FILTER_RESIDUAL_LENGTH;
+									}
+									return !decoded
+										.replaceAll("\\W|\\d", "")
+										.isEmpty();
+								})
 							.map(GraphCleaningFunctions::cleanValue)
 							.collect(Collectors.toList()));
 			}
@@ -224,6 +236,38 @@ public class GraphCleaningFunctions extends CleaningFunctions {
 			if (Objects.nonNull(r.getInstance())) {
 
 				for (Instance i : r.getInstance()) {
+					if (!vocs.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
+						if (r instanceof Publication) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0038", "Other literature type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof Dataset) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof Software) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						} else if (r instanceof OtherResearchProduct) {
+							i
+								.setInstancetype(
+									OafMapperUtils
+										.qualifier(
+											"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
+											ModelConstants.DNET_PUBLICATION_RESOURCE));
+						}
+					}
+
 					if (Objects.nonNull(i.getPid())) {
 						i.setPid(processPidCleaning(i.getPid()));
 					}
@@ -283,7 +327,7 @@ 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

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

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
-						.format(
-							"setting connectTimeout to %s, requestTimeout to %s for service %s",
-							connectTimeout,
-							requestTimeout,
-							clazz.getCanonicalName()));
+					"setting connectTimeout to {}, requestTimeout to {} for service {}",
+					connectTimeout,
+					requestTimeout,
+					clazz.getCanonicalName());
 
 			policy.setConnectionTimeout(connectTimeout);
 			policy.setReceiveTimeout(requestTimeout);

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

@@ -10,7 +10,7 @@ import net.sf.saxon.trans.XPathException;
 
 public abstract class AbstractExtensionFunction extends ExtensionFunctionDefinition {
 
-	public static 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 year;
+				return String.valueOf(c.get(Calendar.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() {
-		System.out.println(GraphCleaningFunctions.cleanDate("23-FEB-1998"));
+	void testDate() {
+		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(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
-		assertEquals(d2.getCollectedfrom().size(), 1);
+		assertEquals(1, p1.getCollectedfrom().size());
+		assertEquals(ModelConstants.CROSSREF_ID, p1.getCollectedfrom().get(0).getKey());
+		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()
-				.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
+				.getClassid());
 
-		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()
-				.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
+				.getClassid());
 	}
 
 	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);