cleanup

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

@@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test;
 /** @author mhorst, claudio.atzori */
 public class GenerateOoziePropertiesMojoTest {
 
-	private GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
+	private final GenerateOoziePropertiesMojo mojo = new GenerateOoziePropertiesMojo();
 
 	@BeforeEach
 	public void clearSystemProperties() {

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

@@ -366,7 +366,7 @@ public class WritePredefinedProjectPropertiesTest {
 	}
 
 	private Properties getStoredProperties(File testFolder)
-		throws FileNotFoundException, IOException {
+		throws IOException {
 		Properties properties = new Properties();
 		properties.load(new FileInputStream(getPropertiesFileLocation(testFolder)));
 		return properties;

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

@@ -21,7 +21,7 @@ public class DHPUtils {
 	public static String md5(final String s) {
 		try {
 			final MessageDigest md = MessageDigest.getInstance("MD5");
-			md.update(s.getBytes("UTF-8"));
+			md.update(s.getBytes(StandardCharsets.UTF_8));
 			return new String(Hex.encodeHex(md.digest()));
 		} catch (final Exception e) {
 			System.err.println("Error creating id");

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

@@ -17,7 +17,7 @@ public class NormalizeDate extends AbstractExtensionFunction {
 		"yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "yyyy/MM/dd", "yyyy"
 	};
 
-	private static final String normalizeOutFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
+	private static final String normalizeOutFormat = "yyyy-MM-dd'T'hh:mm:ss'Z'";
 
 	@Override
 	public String getName() {

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

@@ -21,7 +21,7 @@ public class MessageManager {
 
 	private Connection connection;
 
-	private Map<String, Channel> channels = new HashMap<>();
+	private final Map<String, Channel> channels = new HashMap<>();
 
 	private boolean durable;
 

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/action/AtomicActionDeserializer.java

@@ -16,7 +16,7 @@ public class AtomicActionDeserializer extends JsonDeserializer {
 
 	@Override
 	public Object deserialize(JsonParser jp, DeserializationContext ctxt)
-		throws IOException, JsonProcessingException {
+		throws IOException {
 		JsonNode node = jp.getCodec().readTree(jp);
 		String classTag = node.get("clazz").asText();
 		JsonNode payload = node.get("payload");

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelSupport.java

@@ -13,7 +13,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
 public class ModelSupport {
 
 	/** Defines the mapping between the actual entity type and the main entity type */
-	private static Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
+	private static final Map<EntityType, MainEntityType> entityMapping = Maps.newHashMap();
 
 	static {
 		entityMapping.put(EntityType.publication, MainEntityType.result);

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

@@ -32,7 +32,7 @@ public class ISClient implements Serializable {
 
 	private static final String INPUT_ACTION_SET_ID_SEPARATOR = ",";
 
-	private ISLookUpService isLookup;
+	private final ISLookUpService isLookup;
 
 	public ISClient(String isLookupUrl) {
 		isLookup = ISLookupClientFactory.getLookUpService(isLookupUrl);

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

@@ -123,10 +123,10 @@ public class PromoteActionPayloadFunctions {
 	 * @param <G> Type of graph table row
 	 */
 	public static class TableAggregator<G extends Oaf> extends Aggregator<G, G, G> {
-		private SerializableSupplier<G> zeroFn;
+		private final SerializableSupplier<G> zeroFn;
-		private SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
+		private final SerializableSupplier<BiFunction<G, G, G>> mergeAndGetFn;
-		private SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
+		private final SerializableSupplier<Function<G, Boolean>> isNotZeroFn;
-		private Class<G> rowClazz;
+		private final Class<G> rowClazz;
 
 		public TableAggregator(
 			SerializableSupplier<G> zeroFn,

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

@@ -20,7 +20,7 @@ public class DnetCollectorWorkerApplication {
 
 	private static final Logger log = LoggerFactory.getLogger(DnetCollectorWorkerApplication.class);
 
-	private static CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
+	private static final CollectorPluginFactory collectorPluginFactory = new CollectorPluginFactory();
 
 	private static ArgumentApplicationParser argumentParser;
 

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/CollectorPluginErrorLogList.java

@@ -9,7 +9,7 @@ public class CollectorPluginErrorLogList extends LinkedList<String> {
 
 	@Override
 	public String toString() {
-		String log = new String();
+		String log = "";
 		int index = 0;
 		for (final String errorMessage : this) {
 			log += String.format("Retry #%s: %s / ", index++, errorMessage);

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/worker/utils/XmlCleaner.java

@@ -11,22 +11,22 @@ import java.util.regex.Pattern;
 public class XmlCleaner {
 
 	/** Pattern for numeric entities. */
-	private static Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); // $NON-NLS-1$
+	private static final Pattern validCharacterEntityPattern = Pattern.compile("^&#x?\\d{2,4};"); // $NON-NLS-1$
 	// private static Pattern validCharacterEntityPattern = Pattern.compile("^&#?\\d{2,4};");
 	// //$NON-NLS-1$
 
 	// see https://www.w3.org/TR/REC-xml/#charsets , not only limited to 
-	private static Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];");
+	private static final Pattern invalidControlCharPattern = Pattern.compile("&#x?1[0-9a-fA-F];");
 
 	/**
 	 * Pattern that negates the allowable XML 4 byte unicode characters. Valid are: #x9 | #xA | #xD | [#x20-#xD7FF] |
 	 * [#xE000-#xFFFD] | [#x10000-#x10FFFF]
 	 */
-	private static Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); // $NON-NLS-1$
+	private static final Pattern invalidCharacterPattern = Pattern.compile("[^\t\r\n\u0020-\uD7FF\uE000-\uFFFD]"); // $NON-NLS-1$
 
 	// Map entities to their unicode equivalent
-	private static Set<String> goodEntities = new HashSet<>();
+	private static final Set<String> goodEntities = new HashSet<>();
-	private static Map<String, String> badEntities = new HashMap<>();
+	private static final Map<String, String> badEntities = new HashMap<>();
 
 	static {
 		// pre-defined XML entities

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collector/worker/DnetCollectorWorkerApplicationTests.java

@@ -21,8 +21,8 @@ import eu.dnetlib.message.MessageManager;
 
 public class DnetCollectorWorkerApplicationTests {
 
-	private ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);
+	private final ArgumentApplicationParser argumentParser = mock(ArgumentApplicationParser.class);
-	private MessageManager messageManager = mock(MessageManager.class);
+	private final MessageManager messageManager = mock(MessageManager.class);
 
 	private DnetCollectorWorker worker;
 

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.oa.dedup;
 
 import java.io.StringReader;
+import java.nio.charset.StandardCharsets;
 import java.security.MessageDigest;
 import java.text.Normalizer;
 import java.util.*;
@@ -73,7 +74,7 @@ public class DedupUtility {
 	public static String md5(final String s) {
 		try {
 			final MessageDigest md = MessageDigest.getInstance("MD5");
-			md.update(s.getBytes("UTF-8"));
+			md.update(s.getBytes(StandardCharsets.UTF_8));
 			return new String(Hex.encodeHex(md.digest()));
 		} catch (final Exception e) {
 			System.err.println("Error creating id");

dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkReporter.java

@@ -15,7 +15,7 @@ public class SparkReporter implements Serializable, Reporter {
 
 	private final List<Tuple2<String, String>> relations = new ArrayList<>();
 
-	private Map<String, LongAccumulator> accumulators;
+	private final Map<String, LongAccumulator> accumulators;
 
 	public SparkReporter(Map<String, LongAccumulator> accumulators) {
 		this.accumulators = accumulators;

dhp-workflows/dhp-dedup-scholexplorer/src/main/java/eu/dnetlib/dedup/DedupUtility.java

@@ -106,7 +106,7 @@ public class DedupUtility {
 	public static String md5(final String s) {
 		try {
 			final MessageDigest md = MessageDigest.getInstance("MD5");
-			md.update(s.getBytes("UTF-8"));
+			md.update(s.getBytes(StandardCharsets.UTF_8));
 			return new String(Hex.encodeHex(md.digest()));
 		} catch (final Exception e) {
 			System.err.println("Error creating id");

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java

@@ -410,14 +410,10 @@ public abstract class AbstractMdRecordToOafMapper {
 
 		final String identifier = n.valueOf("./*[local-name()='identifier']");
 		final String baseURL = n.valueOf("./*[local-name()='baseURL']");
-		;
 		final String metadataNamespace = n.valueOf("./*[local-name()='metadataNamespace']");
-		;
 		final boolean altered = n.valueOf("@altered").equalsIgnoreCase("true");
 		final String datestamp = n.valueOf("./*[local-name()='datestamp']");
-		;
 		final String harvestDate = n.valueOf("@harvestDate");
-		;
 
 		return oaiIProvenance(identifier, baseURL, metadataNamespace, altered, datestamp, harvestDate);
 	}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java

@@ -514,9 +514,7 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication
 			if (arr.length == 3) {
 				final String issn = StringUtils.isNotBlank(arr[0]) ? arr[0] : null;
 				final String eissn = StringUtils.isNotBlank(arr[1]) ? arr[1] : null;
-				;
 				final String lissn = StringUtils.isNotBlank(arr[2]) ? arr[2] : null;
-				;
 				if (issn != null || eissn != null || lissn != null) {
 					return journal(name, issn, eissn, eissn, null, null, null, null, null, null, null, info);
 				}

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/DbClient.java

@@ -14,7 +14,7 @@ public class DbClient implements Closeable {
 
 	private static final Log log = LogFactory.getLog(DbClient.class);
 
-	private Connection connection;
+	private final Connection connection;
 
 	public DbClient(final String address, final String login, final String password) {
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/PacePerson.java

@@ -2,6 +2,7 @@
 package eu.dnetlib.dhp.oa.graph.raw.common;
 
 import java.nio.charset.Charset;
+import java.nio.charset.StandardCharsets;
 import java.text.Normalizer;
 import java.util.HashSet;
 import java.util.List;
@@ -141,7 +142,7 @@ public class PacePerson {
 	public String hash() {
 		return Hashing
 			.murmur3_128()
-			.hashString(getNormalisedFullname(), Charset.forName(UTF8))
+			.hashString(getNormalisedFullname(), StandardCharsets.UTF_8)
 			.toString();
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/parser/AbstractScholexplorerParser.java

@@ -25,7 +25,7 @@ public abstract class AbstractScholexplorerParser {
 
 	protected static final Log log = LogFactory.getLog(AbstractScholexplorerParser.class);
 	static final Pattern pattern = Pattern.compile("10\\.\\d{4,9}/[-._;()/:A-Z0-9]+$", Pattern.CASE_INSENSITIVE);
-	private List<String> datasetSubTypes = Arrays
+	private final List<String> datasetSubTypes = Arrays
 		.asList(
 			"dataset",
 			"software",

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/CrossRefParserJSON.java

@@ -18,7 +18,7 @@ import eu.dnetlib.dhp.utils.DHPUtils;
 
 public class CrossRefParserJSON {
 
-	private static List<ScholixCollectedFrom> collectedFrom = generateCrossrefCollectedFrom("complete");
+	private static final List<ScholixCollectedFrom> collectedFrom = generateCrossrefCollectedFrom("complete");
 
 	public static ScholixResource parseRecord(final String record) {
 		if (record == null)

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/update/DataciteClient.java

@@ -16,7 +16,7 @@ public class DataciteClient {
 	private String host;
 	private String index = "datacite";
 	private String indexType = "dump";
-	private Datacite2Scholix d2s;
+	private final Datacite2Scholix d2s;
 
 	public DataciteClient(String host) {
 		this.host = host;

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/RelationPartitioner.java

@@ -12,7 +12,7 @@ import eu.dnetlib.dhp.oa.provision.model.SortableRelation;
  */
 public class RelationPartitioner extends Partitioner {
 
-	private int numPartitions;
+	private final int numPartitions;
 
 	public RelationPartitioner(int numPartitions) {
 		this.numPartitions = numPartitions;

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/StreamingInputDocumentFactory.java

@@ -46,7 +46,7 @@ public class StreamingInputDocumentFactory {
 
 	private static final String INDEX_RECORD_ID = INDEX_FIELD_PREFIX + "indexrecordidentifier";
 
-	private static final String outFormat = new String("yyyy-MM-dd'T'hh:mm:ss'Z'");
+	private static final String outFormat = "yyyy-MM-dd'T'hh:mm:ss'Z'";
 
 	private static final List<String> dateFormats = Arrays
 		.asList("yyyy-MM-dd'T'hh:mm:ss", "yyyy-MM-dd", "dd-MM-yyyy", "dd/MM/yyyy", "yyyy");
@@ -61,15 +61,18 @@ public class StreamingInputDocumentFactory {
 
 	private static final int MAX_FIELD_LENGTH = 25000;
 
-	private ThreadLocal<XMLInputFactory> inputFactory = ThreadLocal.withInitial(() -> XMLInputFactory.newInstance());
+	private final ThreadLocal<XMLInputFactory> inputFactory = ThreadLocal
+		.withInitial(() -> XMLInputFactory.newInstance());
 
-	private ThreadLocal<XMLOutputFactory> outputFactory = ThreadLocal.withInitial(() -> XMLOutputFactory.newInstance());
+	private final ThreadLocal<XMLOutputFactory> outputFactory = ThreadLocal
+		.withInitial(() -> XMLOutputFactory.newInstance());
 
-	private ThreadLocal<XMLEventFactory> eventFactory = ThreadLocal.withInitial(() -> XMLEventFactory.newInstance());
+	private final ThreadLocal<XMLEventFactory> eventFactory = ThreadLocal
+		.withInitial(() -> XMLEventFactory.newInstance());
 
-	private String version;
+	private final String version;
 
-	private String dsId;
+	private final String dsId;
 
 	private String resultName = DEFAULTDNETRESULT;
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateFactory.java

@@ -17,7 +17,7 @@ import eu.dnetlib.dhp.schema.oaf.OafEntity;
 
 public class TemplateFactory {
 
-	private TemplateResources resources;
+	private final TemplateResources resources;
 
 	private static final char DELIMITER = '$';
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/TemplateResources.java

@@ -8,17 +8,17 @@ import com.google.common.io.Resources;
 
 public class TemplateResources {
 
-	private String record = read("eu/dnetlib/dhp/oa/provision/template/record.st");
+	private final String record = read("eu/dnetlib/dhp/oa/provision/template/record.st");
 
-	private String instance = read("eu/dnetlib/dhp/oa/provision/template/instance.st");
+	private final String instance = read("eu/dnetlib/dhp/oa/provision/template/instance.st");
 
-	private String rel = read("eu/dnetlib/dhp/oa/provision/template/rel.st");
+	private final String rel = read("eu/dnetlib/dhp/oa/provision/template/rel.st");
 
-	private String webresource = read("eu/dnetlib/dhp/oa/provision/template/webresource.st");
+	private final String webresource = read("eu/dnetlib/dhp/oa/provision/template/webresource.st");
 
-	private String child = read("eu/dnetlib/dhp/oa/provision/template/child.st");
+	private final String child = read("eu/dnetlib/dhp/oa/provision/template/child.st");
 
-	private String entity = read("eu/dnetlib/dhp/oa/provision/template/entity.st");
+	private final String entity = read("eu/dnetlib/dhp/oa/provision/template/entity.st");
 
 	private static String read(final String classpathResource) throws IOException {
 		return Resources.toString(Resources.getResource(classpathResource), StandardCharsets.UTF_8);

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -48,13 +48,13 @@ import eu.dnetlib.dhp.schema.oaf.Result;
 public class XmlRecordFactory implements Serializable {
 
 	public static final String REL_SUBTYPE_DEDUP = "dedup";
-	private Map<String, LongAccumulator> accumulators;
+	private final Map<String, LongAccumulator> accumulators;
 
-	private Set<String> specialDatasourceTypes;
+	private final Set<String> specialDatasourceTypes;
 
-	private ContextMapper contextMapper;
+	private final ContextMapper contextMapper;
 
-	private String schemaLocation;
+	private final String schemaLocation;
 
 	private boolean indent = false;
 

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlSerializationUtils.java

@@ -41,7 +41,7 @@ public class XmlSerializationUtils {
 
 	public static String mapStructuredProperty(String name, StructuredProperty t) {
 		return asXmlElement(
-			name, t.getValue(), t.getQualifier(), t.getDataInfo() != null ? t.getDataInfo() : null);
+			name, t.getValue(), t.getQualifier(), t.getDataInfo());
 	}
 
 	public static String mapQualifier(String name, Qualifier q) {

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/GraphJoinerTest.java

@@ -9,7 +9,7 @@ import org.junit.jupiter.api.BeforeEach;
 
 public class GraphJoinerTest {
 
-	private ClassLoader cl = getClass().getClassLoader();
+	private final ClassLoader cl = getClass().getClassLoader();
 	private Path workingDir;
 	private Path inputDir;
 	private Path outputDir;