fixed a conflict

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

@@ -4,6 +4,7 @@ package eu.dnetlib.dhp.oa.merge;
 import java.text.Normalizer;
 import java.util.*;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.apache.commons.lang3.StringUtils;
 
@@ -32,27 +33,33 @@ public class AuthorMerger {
 
 	}
 
-	public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
+	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;
 		int sa = authorsSize(a);
 		int sb = authorsSize(b);
 
-		if (pa == pb) {
+		if (sa == sb) {
-			base = sa > sb ? a : b;
-			enrich = sa > sb ? b : a;
-		} else {
 			base = pa > pb ? a : b;
 			enrich = pa > pb ? b : a;
+		} else {
+			base = sa > sb ? a : b;
+			enrich = sa > sb ? b : a;
 		}
-		enrichPidFromList(base, enrich);
+		enrichPidFromList(base, enrich, threshold);
 		return base;
 	}
 
-	private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
+	public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
+		return mergeAuthor(a, b, THRESHOLD);
+	}
+
+	private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
 		if (base == null || enrich == null)
 			return;
+
+		// <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)
@@ -63,6 +70,7 @@ public class AuthorMerger {
 					.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)
@@ -83,10 +91,10 @@ public class AuthorMerger {
 						.max(Comparator.comparing(Tuple2::_1));
 
 					if (simAuthor.isPresent()) {
-						double th = THRESHOLD;
+						double th = threshold;
 						// increase the threshold if the surname is too short
 						if (simAuthor.get()._2().getSurname() != null
-							&& simAuthor.get()._2().getSurname().length() <= 3)
+							&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
 							th = 0.99;
 
 						if (simAuthor.get()._1() > th) {
@@ -156,7 +164,7 @@ public class AuthorMerger {
 	}
 
 	private static String normalize(final String s) {
-		return nfd(s)
+		String[] normalized = nfd(s)
 			.toLowerCase()
 			// do not compact the regexes in a single expression, would cause StackOverflowError
 			// in case
@@ -166,7 +174,12 @@ public class AuthorMerger {
 			.replaceAll("(\\p{Punct})+", " ")
 			.replaceAll("(\\d)+", " ")
 			.replaceAll("(\\n)+", " ")
-			.trim();
+			.trim()
+			.split(" ");
+
+		Arrays.sort(normalized);
+
+		return String.join(" ", normalized);
 	}
 
 	private static String nfd(final String s) {

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

@@ -0,0 +1,100 @@
+
+package eu.dnetlib.dhp.oa.merge;
+
+import java.io.BufferedReader;
+import java.io.FileReader;
+import java.io.IOException;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeEach;
+import org.junit.jupiter.api.Test;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.oaf.Author;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
+import eu.dnetlib.pace.util.MapDocumentUtil;
+import scala.Tuple2;
+
+public class AuthorMergerTest {
+
+	private String publicationsBasePath;
+
+	private List<List<Author>> authors;
+
+	@BeforeEach
+	public void setUp() throws Exception {
+
+		publicationsBasePath = Paths
+			.get(AuthorMergerTest.class.getResource("/eu/dnetlib/dhp/oa/merge").toURI())
+			.toFile()
+			.getAbsolutePath();
+
+		authors = readSample(publicationsBasePath + "/publications_with_authors.json", Publication.class)
+			.stream()
+			.map(p -> p._2().getAuthor())
+			.collect(Collectors.toList());
+
+	}
+
+	@Test
+	public void mergeTest() { // used in the dedup: threshold set to 0.95
+
+		for (List<Author> authors1 : authors) {
+			System.out.println("List " + (authors.indexOf(authors1) + 1));
+			for (Author author : authors1) {
+				System.out.println(authorToString(author));
+			}
+		}
+
+		List<Author> merge = AuthorMerger.merge(authors);
+
+		System.out.println("Merge ");
+		for (Author author : merge) {
+			System.out.println(authorToString(author));
+		}
+
+		Assertions.assertEquals(7, merge.size());
+
+	}
+
+	public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
+		List<Tuple2<String, T>> res = new ArrayList<>();
+		BufferedReader reader;
+		try {
+			reader = new BufferedReader(new FileReader(path));
+			String line = reader.readLine();
+			while (line != null) {
+				res
+					.add(
+						new Tuple2<>(
+							MapDocumentUtil.getJPathString("$.id", line),
+							new ObjectMapper().readValue(line, clazz)));
+				// read next line
+				line = reader.readLine();
+			}
+			reader.close();
+		} catch (IOException e) {
+			e.printStackTrace();
+		}
+
+		return res;
+	}
+
+	public String authorToString(Author a) {
+
+		String print = "Fullname = ";
+		print += a.getFullname() + " pid = [";
+		if (a.getPid() != null)
+			for (StructuredProperty sp : a.getPid()) {
+				print += sp.toComparableString() + " ";
+			}
+		print += "]";
+		return print;
+	}
+}

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

@@ -105,6 +105,8 @@ public class ModelConstants {
 	public static final KeyValue UNKNOWN_REPOSITORY = keyValue(
 		"10|openaire____::55045bd2a65019fd8e6741a755395c8c", "Unknown Repository");
 
+	public static final Qualifier UNKNOWN_COUNTRY = qualifier(UNKNOWN, "Unknown", DNET_COUNTRY_TYPE, DNET_COUNTRY_TYPE);
+
 	private static Qualifier qualifier(
 		final String classid,
 		final String classname,

dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/oaf/Result.java

@@ -243,7 +243,7 @@ public class Result extends OafEntity implements Serializable {
 
 		Result r = (Result) e;
 
-		// TODO consider merging also Measures
+		measures = mergeLists(measures, r.getMeasures());
 
 		instance = mergeLists(instance, r.getInstance());
 

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

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

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

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

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

@@ -0,0 +1,85 @@
+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.Optional;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+/**
+ * Just collects all the atomic actions produced for the different results and saves them in
+ * outputpath for the ActionSet
+ */
+public class CollectAndSave implements Serializable {
+
+	private static final Logger log = LoggerFactory.getLogger(CollectAndSave.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				CollectAndSave.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}: ", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}: ", outputPath);
+
+		SparkConf conf = new SparkConf();
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				removeOutputDir(spark, outputPath);
+				collectAndSave(spark, inputPath, outputPath);
+			});
+	}
+
+	private static void collectAndSave(SparkSession spark, String inputPath, String outputPath) {
+		JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		sc
+			.sequenceFile(inputPath + "/publication", Text.class, Text.class)
+			.union(sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class))
+			.union(sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class))
+			.union(sc.sequenceFile(inputPath + "/software", Text.class, Text.class))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+		;
+	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
+}

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

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

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

@@ -0,0 +1,28 @@
+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.Serializable;
+
+/**
+ * Subset of the information of the generic results that are needed to create the atomic action
+ */
+public class PreparedResult implements Serializable {
+	private String id; // openaire id
+	private String value; // doi
+
+	public String getId() {
+		return id;
+	}
+
+	public void setId(String id) {
+		this.id = id;
+	}
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+}

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

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

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

@@ -0,0 +1,200 @@
+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
+
+import java.io.Serializable;
+import java.util.List;
+import java.util.Optional;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.hadoop.mapred.SequenceFileOutputFormat;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.api.java.function.MapGroupsFunction;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.SparkSession;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.KeyValue;
+import scala.Tuple2;
+
+/**
+ * created the Atomic Action for each tipe of results
+ */
+public class SparkAtomicActionScoreJob implements Serializable {
+
+	private static String DOI = "doi";
+	private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class);
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	public static <I extends Result> void main(String[] args) throws Exception {
+
+		String jsonConfiguration = IOUtils
+			.toString(
+				SparkAtomicActionScoreJob.class
+					.getResourceAsStream(
+						"/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json"));
+
+		final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
+
+		parser.parseArgument(args);
+
+		Boolean isSparkSessionManaged = Optional
+			.ofNullable(parser.get("isSparkSessionManaged"))
+			.map(Boolean::valueOf)
+			.orElse(Boolean.TRUE);
+
+		log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
+
+		final String inputPath = parser.get("inputPath");
+		log.info("inputPath {}: ", inputPath);
+
+		final String outputPath = parser.get("outputPath");
+		log.info("outputPath {}: ", outputPath);
+
+		final String bipScorePath = parser.get("bipScorePath");
+		log.info("bipScorePath: {}", bipScorePath);
+
+		final String resultClassName = parser.get("resultTableName");
+		log.info("resultTableName: {}", resultClassName);
+
+		Class<I> inputClazz = (Class<I>) Class.forName(resultClassName);
+
+		SparkConf conf = new SparkConf();
+
+		runWithSparkSession(
+			conf,
+			isSparkSessionManaged,
+			spark -> {
+				removeOutputDir(spark, outputPath);
+				prepareResults(spark, inputPath, outputPath, bipScorePath, inputClazz);
+			});
+	}
+
+	private static <I extends Result> void prepareResults(SparkSession spark, String inputPath, String outputPath,
+		String bipScorePath, Class<I> inputClazz) {
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
+			.textFile(bipScorePath)
+			.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
+
+		Dataset<BipScore> bipScores = spark
+			.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
+				BipScore bs = new BipScore();
+				bs.setId(key);
+				bs.setScoreList(entry.get(key));
+				return bs;
+			}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
+
+		System.out.println(bipScores.count());
+
+		Dataset<I> results = readPath(spark, inputPath, inputClazz);
+
+		results.createOrReplaceTempView("result");
+
+		Dataset<PreparedResult> preparedResult = spark
+			.sql(
+				"select pIde.value value, id " +
+					"from result " +
+					"lateral view explode (pid) p as pIde " +
+					"where dataInfo.deletedbyinference = false and pIde.qualifier.classid = '" + DOI + "'")
+			.as(Encoders.bean(PreparedResult.class));
+
+		bipScores
+			.joinWith(
+				preparedResult, bipScores.col("id").equalTo(preparedResult.col("value")),
+				"inner")
+			.map((MapFunction<Tuple2<BipScore, PreparedResult>, BipScore>) value -> {
+				BipScore ret = value._1();
+				ret.setId(value._2().getId());
+				return ret;
+			}, Encoders.bean(BipScore.class))
+			.groupByKey((MapFunction<BipScore, String>) value -> value.getId(), Encoders.STRING())
+			.mapGroups((MapGroupsFunction<String, BipScore, Result>) (k, it) -> {
+				Result ret = new Result();
+				ret.setDataInfo(getDataInfo());
+				BipScore first = it.next();
+				ret.setId(first.getId());
+
+				ret.setMeasures(getMeasure(first));
+				it.forEachRemaining(value -> ret.getMeasures().addAll(getMeasure(value)));
+
+				return ret;
+			}, Encoders.bean(Result.class))
+			.toJavaRDD()
+			.map(p -> new AtomicAction(inputClazz, p))
+			.mapToPair(
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))))
+			.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
+
+	}
+
+	private static List<Measure> getMeasure(BipScore value) {
+		return value
+			.getScoreList()
+			.stream()
+			.map(score -> {
+				Measure m = new Measure();
+				m.setId(score.getId());
+				m
+					.setUnit(
+						score
+							.getUnit()
+							.stream()
+							.map(unit -> {
+								KeyValue kv = new KeyValue();
+								kv.setValue(unit.getValue());
+								kv.setKey(unit.getKey());
+								kv.setDataInfo(getDataInfo());
+								return kv;
+							})
+							.collect(Collectors.toList()));
+				return m;
+			})
+			.collect(Collectors.toList());
+	}
+
+	private static DataInfo getDataInfo() {
+		DataInfo di = new DataInfo();
+		di.setInferred(false);
+		di.setInvisible(false);
+		di.setDeletedbyinference(false);
+		di.setTrust("");
+		Qualifier qualifier = new Qualifier();
+		qualifier.setClassid("sysimport:actionset");
+		qualifier.setClassname("Harvested");
+		qualifier.setSchemename("dnet:provenanceActions");
+		qualifier.setSchemeid("dnet:provenanceActions");
+		di.setProvenanceaction(qualifier);
+		return di;
+	}
+
+	private static void removeOutputDir(SparkSession spark, String path) {
+		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
+	}
+
+	public static <R> Dataset<R> readPath(
+		SparkSession spark, String inputPath, Class<R> clazz) {
+		return spark
+			.read()
+			.textFile(inputPath)
+			.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
+	}
+
+}

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_actionset_parameter.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the URL from where to get the programme file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/input_parameters.json

@@ -0,0 +1,32 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the URL from where to get the programme file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "o",
+    "paramLongName": "outputPath",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  },
+  {
+    "paramName": "rtn",
+    "paramLongName": "resultTableName",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  },
+  {
+    "paramName": "bsp",
+    "paramLongName": "bipScorePath",
+    "paramDescription": "the path of the new ActionSet",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipfinder/oozie_app/workflow.xml

@@ -0,0 +1,171 @@
+<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>inputPath</name>
+            <description>the input path of the resources to be extended</description>
+        </property>
+
+        <property>
+            <name>bipScorePath</name>
+            <description>the path where to find the bipFinder scores</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the path where to store the actionset</description>
+        </property>
+    </parameters>
+
+    <start to="deleteoutputpath"/>
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+    <action name="deleteoutputpath">
+        <fs>
+            <delete path="${outputPath}"/>
+            <mkdir path="${outputPath}"/>
+            <delete path="${workingDir}"/>
+            <mkdir path="${workingDir}"/>
+        </fs>
+        <ok to="atomicactions"/>
+        <error to="Kill"/>
+    </action>
+
+    <fork name="atomicactions">
+        <path start="atomicactions_publication"/>
+        <path start="atomicactions_dataset"/>
+        <path start="atomicactions_orp"/>
+        <path start="atomicactions_software"/>
+    </fork>
+
+    <action name="atomicactions_publication">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the atomic action with the bip finder scores for publications</name>
+            <class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/publication</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Publication</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/publication</arg>
+            <arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
+        </spark>
+        <ok to="join_aa"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="atomicactions_dataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the atomic action with the bip finder scores for datasets</name>
+            <class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/dataset</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Dataset</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/dataset</arg>
+            <arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
+        </spark>
+        <ok to="join_aa"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="atomicactions_orp">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the atomic action with the bip finder scores for orp</name>
+            <class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/otherresearchproduct</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.OtherResearchProduct</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/otherresearchproduct</arg>
+            <arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
+        </spark>
+        <ok to="join_aa"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="atomicactions_software">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the atomic action with the bip finder scores for software</name>
+            <class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${inputPath}/software</arg>
+            <arg>--resultTableName</arg><arg>eu.dnetlib.dhp.schema.oaf.Software</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/software</arg>
+            <arg>--bipScorePath</arg><arg>${bipScorePath}</arg>
+        </spark>
+        <ok to="join_aa"/>
+        <error to="Kill"/>
+    </action>
+
+    <join name="join_aa" to="collectandsave"/>
+
+    <action name="collectandsave">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>saves all the aa produced for the several types of results in the as output path</name>
+            <class>eu.dnetlib.dhp.actionmanager.bipfinder.CollectAndSave</class>
+            <jar>dhp-aggregation-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.extraListeners=${spark2ExtraListeners}
+                --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
+                --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
+                --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
+                --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${workingDir}</arg>
+            <arg>--outputPath</arg><arg>${outputPath}</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJobTest.java

@@ -0,0 +1,323 @@
+
+package eu.dnetlib.dhp.actionmanager.bipfinder;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.io.Text;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.sql.Dataset;
+import org.apache.spark.sql.Encoders;
+import org.apache.spark.sql.Row;
+import org.apache.spark.sql.SparkSession;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+
+import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+
+public class SparkAtomicActionScoreJobTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(SparkAtomicActionScoreJobTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(SparkAtomicActionScoreJobTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(SparkAtomicActionScoreJobTest.class.getSimpleName());
+
+		conf.setMaster("local[*]");
+		conf.set("spark.driver.host", "localhost");
+		conf.set("hive.metastore.local", "true");
+		conf.set("spark.ui.enabled", "false");
+		conf.set("spark.sql.warehouse.dir", workingDir.toString());
+		conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
+
+		spark = SparkSession
+			.builder()
+			.appName(SparkAtomicActionScoreJobTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	public void matchOne() throws Exception {
+		String bipScoresPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
+			.getPath();
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/bipfinder/publication.json")
+			.getPath();
+
+		SparkAtomicActionScoreJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-bipScorePath",
+					bipScoresPath,
+					"-resultTableName",
+					"eu.dnetlib.dhp.schema.oaf.Publication",
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Publication> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Publication) aa.getPayload()));
+
+		Assertions.assertTrue(tmp.count() == 1);
+
+		Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
+		verificationDataset.createOrReplaceTempView("publication");
+
+		Dataset<Row> execVerification = spark
+			.sql(
+				"Select p.id oaid, mes.id, mUnit.value from publication p " +
+					"lateral view explode(measures) m as mes " +
+					"lateral view explode(mes.unit) u as mUnit ");
+
+		Assertions.assertEquals(2, execVerification.count());
+
+		Assertions
+			.assertEquals(
+				"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
+				execVerification.select("oaid").collectAsList().get(0).getString(0));
+
+		Assertions
+			.assertEquals(
+				"1.47565045883e-08",
+				execVerification.filter("id = 'influence'").select("value").collectAsList().get(0).getString(0));
+
+		Assertions
+			.assertEquals(
+				"0.227515392",
+				execVerification.filter("id = 'popularity'").select("value").collectAsList().get(0).getString(0));
+
+	}
+
+	@Test
+	public void matchOneWithTwo() throws Exception {
+		String bipScoresPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
+			.getPath();
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_2.json")
+			.getPath();
+
+		SparkAtomicActionScoreJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-bipScorePath",
+					bipScoresPath,
+					"-resultTableName",
+					"eu.dnetlib.dhp.schema.oaf.Publication",
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Publication> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Publication) aa.getPayload()));
+
+		Assertions.assertTrue(tmp.count() == 1);
+
+		Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
+		verificationDataset.createOrReplaceTempView("publication");
+
+		Dataset<Row> execVerification = spark
+			.sql(
+				"Select p.id oaid, mes.id, mUnit.value from publication p " +
+					"lateral view explode(measures) m as mes " +
+					"lateral view explode(mes.unit) u as mUnit ");
+
+		Assertions.assertEquals(4, execVerification.count());
+
+		Assertions
+			.assertEquals(
+				"50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb",
+				execVerification.select("oaid").collectAsList().get(0).getString(0));
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("id = 'influence'").count());
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("id = 'popularity'").count());
+
+		List<Row> tmp_ds = execVerification.filter("id = 'influence'").select("value").collectAsList();
+		String tmp_influence = tmp_ds.get(0).getString(0);
+		Assertions
+			.assertTrue(
+				"1.47565045883e-08".equals(tmp_influence) ||
+					"1.98956540239e-08".equals(tmp_influence));
+
+		tmp_influence = tmp_ds.get(1).getString(0);
+		Assertions
+			.assertTrue(
+				"1.47565045883e-08".equals(tmp_influence) ||
+					"1.98956540239e-08".equals(tmp_influence));
+
+		Assertions.assertTrue(!tmp_ds.get(0).getString(0).equals(tmp_ds.get(1).getString(0)));
+
+	}
+
+	@Test
+	public void matchTwo() throws Exception {
+		String bipScoresPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores.json")
+			.getPath();
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/bipfinder/publication_3.json")
+			.getPath();
+
+		SparkAtomicActionScoreJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-bipScorePath",
+					bipScoresPath,
+					"-resultTableName",
+					"eu.dnetlib.dhp.schema.oaf.Publication",
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Publication> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Publication) aa.getPayload()));
+
+		Assertions.assertTrue(tmp.count() == 2);
+
+		Dataset<Publication> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
+		verificationDataset.createOrReplaceTempView("publication");
+
+		Dataset<Row> execVerification = spark
+			.sql(
+				"Select p.id oaid, mes.id, mUnit.value from publication p " +
+					"lateral view explode(measures) m as mes " +
+					"lateral view explode(mes.unit) u as mUnit ");
+
+		Assertions.assertEquals(4, execVerification.count());
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb'").count());
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09'").count());
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("id = 'influence'").count());
+
+		Assertions
+			.assertEquals(
+				2,
+				execVerification.filter("id = 'popularity'").count());
+
+		Assertions
+			.assertEquals(
+				"1.47565045883e-08",
+				execVerification
+					.filter(
+						"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
+							"and id = 'influence'")
+					.select("value")
+					.collectAsList()
+					.get(0)
+					.getString(0));
+
+		Assertions
+			.assertEquals(
+				"1.98956540239e-08",
+				execVerification
+					.filter(
+						"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
+							"and id = 'influence'")
+					.select("value")
+					.collectAsList()
+					.get(0)
+					.getString(0));
+
+		Assertions
+			.assertEquals(
+				"0.282046161584",
+				execVerification
+					.filter(
+						"oaid = '50|acm_________::faed5b7a1bd8f51118d13ed29cfaee09' " +
+							"and id = 'popularity'")
+					.select("value")
+					.collectAsList()
+					.get(0)
+					.getString(0));
+
+		Assertions
+			.assertEquals(
+				"0.227515392",
+				execVerification
+					.filter(
+						"oaid = '50|355e65625b88::ffa5bad14f4adc0c9a15c00efbbccddb' " +
+							"and id = 'popularity'")
+					.select("value")
+					.collectAsList()
+					.get(0)
+					.getString(0));
+
+	}
+
+}

dhp-workflows/dhp-broker-events/src/main/resources/eu/dnetlib/dhp/broker/oa/opendoarPartition/oozie_app/workflow.xml

@@ -87,7 +87,7 @@
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
                 --conf spark.sql.shuffle.partitions=3840
             </spark-opts>
-            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--outputDir</arg><arg>${outputDir}</arg>
             <arg>--opendoarIds</arg><arg>${opendoarIds}</arg>
         </spark>
         <ok to="End"/>

dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java

@@ -10,10 +10,11 @@ import java.io.Serializable;
 import java.nio.file.Paths;
 import java.util.*;
 
-import org.codehaus.jackson.map.ObjectMapper;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+
 import eu.dnetlib.dhp.oa.merge.AuthorMerger;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.pace.util.MapDocumentUtil;
@@ -100,8 +101,8 @@ public class EntityMergerTest implements Serializable {
 		assertEquals(pub_merged.getDateofacceptance().getValue(), "2018-09-30");
 
 		// verify authors
-		assertEquals(pub_merged.getAuthor().size(), 9);
+		assertEquals(13, pub_merged.getAuthor().size());
-		assertEquals(AuthorMerger.countAuthorsPids(pub_merged.getAuthor()), 4);
+		assertEquals(4, AuthorMerger.countAuthorsPids(pub_merged.getAuthor()));
 
 		// verify title
 		int count = 0;

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

@@ -7,7 +7,6 @@ import java.util.List;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.api.java.JavaPairRDD;
 import org.apache.spark.api.java.JavaRDD;
-import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.api.java.function.PairFunction;
@@ -16,8 +15,8 @@ import org.apache.spark.rdd.RDD;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
-import org.codehaus.jackson.map.ObjectMapper;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.google.common.hash.Hashing;
 
 import eu.dnetlib.dedup.graph.ConnectedComponent;

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

@@ -10,7 +10,8 @@ import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
-import org.codehaus.jackson.map.ObjectMapper;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.schema.oaf.Oaf;

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala

@@ -4,14 +4,13 @@ import eu.dnetlib.dhp.schema.action.AtomicAction
 import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
 import eu.dnetlib.dhp.utils.DHPUtils
 import org.apache.commons.lang3.StringUtils
-import org.codehaus.jackson.map.ObjectMapper
+import com.fasterxml.jackson.databind.ObjectMapper
 import org.json4s
 import org.json4s.DefaultFormats
 import org.json4s.jackson.JsonMethods.parse
 import org.slf4j.{Logger, LoggerFactory}
 
 import scala.collection.JavaConverters._
-import scala.io.Source
 
 
 case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {}
@@ -19,23 +18,18 @@ case class HostedByItemType(id: String, officialname: String, issn: String, eiss
 case class DoiBoostAffiliation(PaperId:Long, AffiliationId:Long, GridId:Option[String], OfficialPage:Option[String], DisplayName:Option[String]){}
 
 object DoiBoostMappingUtil {
-  def getUnknownCountry(): Qualifier = {
-    createQualifier("UNKNOWN","UNKNOWN","dnet:countries","dnet:countries")
-  }
-
-
 
   def generateMAGAffiliationId(affId: String): String = {
     s"20|microsoft___$SEPARATOR${DHPUtils.md5(affId)}"
   }
 
-
   val logger: Logger = LoggerFactory.getLogger(getClass)
 
   //STATIC STRING
   val MAG = "microsoft"
   val MAG_NAME = "Microsoft Academic Graph"
-  val ORCID = "ORCID"
+  val ORCID = "orcid"
+  val ORCID_PENDING = "orcid_pending"
   val CROSSREF = "Crossref"
   val UNPAYWALL = "UnpayWall"
   val GRID_AC = "grid.ac"

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDOIBoostActionSet.scala

@@ -39,33 +39,38 @@ object SparkGenerateDOIBoostActionSet {
     val dbaffiliationRelationPath   = parser.get("dbaffiliationRelationPath")
     val dbOrganizationPath          = parser.get("dbOrganizationPath")
     val workingDirPath              = parser.get("targetPath")
+    val sequenceFilePath            = parser.get("sFilePath")
 
-    spark.read.load(dbDatasetPath).as[OafDataset]
+    val asDataset = spark.read.load(dbDatasetPath).as[OafDataset]
       .map(d =>DoiBoostMappingUtil.fixResult(d))
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
+//      .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/actionSet")
 
-    spark.read.load(dbPublicationPath).as[Publication]
+    val asPublication =spark.read.load(dbPublicationPath).as[Publication]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+//      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
-    spark.read.load(dbOrganizationPath).as[Organization]
+    val asOrganization = spark.read.load(dbOrganizationPath).as[Organization]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+//      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
 
-    spark.read.load(crossRefRelation).as[Relation]
+    val asCRelation = spark.read.load(crossRefRelation).as[Relation]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+//      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
-    spark.read.load(dbaffiliationRelationPath).as[Relation]
+    val asRelAffiliation = spark.read.load(dbaffiliationRelationPath).as[Relation]
       .map(d=>DoiBoostMappingUtil.toActionSet(d))(Encoders.tuple(Encoders.STRING, Encoders.STRING))
-      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
+//      .write.mode(SaveMode.Append).save(s"$workingDirPath/actionSet")
 
 
-    val d: Dataset[(String, String)] =spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
 
-    d.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingDirPath/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
+
+    val d: Dataset[(String, String)] = asDataset.union(asPublication).union(asOrganization).union(asCRelation).union(asRelAffiliation)
+
+//      spark.read.load(s"$workingDirPath/actionSet").as[(String,String)]
+
+    d.rdd.repartition(6000).map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$sequenceFilePath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
 
 
 

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala

@@ -2,6 +2,7 @@ package eu.dnetlib.doiboost
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.oa.merge.AuthorMerger
+import eu.dnetlib.dhp.schema.common.ModelConstants
 import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
 import eu.dnetlib.doiboost.mag.ConversionUtil
 import org.apache.commons.io.IOUtils
@@ -30,7 +31,7 @@ object SparkGenerateDoiBoost {
     import spark.implicits._
 
     val hostedByMapPath = parser.get("hostedByMapPath")
-    val workingDirPath = parser.get("workingDirPath")
+    val workingDirPath = parser.get("workingPath")
 
 
     implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
@@ -132,7 +133,7 @@ object SparkGenerateDoiBoost {
           o.setLegalname(DoiBoostMappingUtil.asField(affiliation.DisplayName.get))
         if (affiliation.OfficialPage.isDefined)
           o.setWebsiteurl(DoiBoostMappingUtil.asField(affiliation.OfficialPage.get))
-        o.setCountry(DoiBoostMappingUtil.getUnknownCountry())
+        o.setCountry(ModelConstants.UNKNOWN_COUNTRY)
         o
       }
       else

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala

@@ -200,7 +200,7 @@ case object Crossref2Oaf {
     a.setSurname(family)
     a.setFullname(s"$given $family")
     if (StringUtils.isNotBlank(orcid))
-      a.setPid(List(createSP(orcid, ORCID, PID_TYPES, generateDataInfo())).asJava)
+      a.setPid(List(createSP(orcid, ORCID_PENDING, PID_TYPES, generateDataInfo())).asJava)
 
     a
   }

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefImporter.java

@@ -2,18 +2,16 @@
 package eu.dnetlib.doiboost.crossref;
 
 import java.io.ByteArrayOutputStream;
+import java.util.Optional;
 import java.util.zip.Inflater;
 
 import org.apache.commons.codec.binary.Base64;
 import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang3.StringUtils;
 import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.IntWritable;
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 
@@ -30,34 +28,45 @@ public class CrossrefImporter {
 
 		parser.parseArgument(args);
 
-		final String hdfsuri = parser.get("namenode");
+		final String namenode = parser.get("namenode");
-		System.out.println("HDFS URI" + hdfsuri);
+		System.out.println("namenode: " + namenode);
-		Path hdfswritepath = new Path(parser.get("targetPath"));
-		System.out.println("TargetPath: " + hdfsuri);
 
-		final Long timestamp = StringUtils.isNotBlank(parser.get("timestamp"))
+		Path targetPath = new Path(parser.get("targetPath"));
-			? Long.parseLong(parser.get("timestamp"))
+		System.out.println("targetPath: " + targetPath);
-			: -1;
 
-		if (timestamp > 0)
+		final Long timestamp = Optional
-			System.out.println("Timestamp added " + timestamp);
+			.ofNullable(parser.get("timestamp"))
+			.map(s -> {
+				try {
+					return Long.parseLong(s);
+				} catch (NumberFormatException e) {
+					return -1L;
+				}
+			})
+			.orElse(-1L);
+		System.out.println("timestamp: " + timestamp);
+
+		final String esServer = parser.get("esServer");
+		System.out.println("esServer: " + esServer);
+
+		final String esIndex = parser.get("esIndex");
+		System.out.println("esIndex: " + esIndex);
 
 		// ====== Init HDFS File System Object
 		Configuration conf = new Configuration();
 		// Set FileSystem URI
-		conf.set("fs.defaultFS", hdfsuri);
+		conf.set("fs.defaultFS", namenode);
 		// Because of Maven
 		conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
 		conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
 
-		ESClient client = timestamp > 0
+		// "ip-90-147-167-25.ct1.garrservices.it", "crossref"
-			? new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref", timestamp)
+		final ESClient client = new ESClient(esServer, esIndex, timestamp);
-			: new ESClient("ip-90-147-167-25.ct1.garrservices.it", "crossref");
 
 		try (SequenceFile.Writer writer = SequenceFile
 			.createWriter(
 				conf,
-				SequenceFile.Writer.file(hdfswritepath),
+				SequenceFile.Writer.file(targetPath),
 				SequenceFile.Writer.keyClass(IntWritable.class),
 				SequenceFile.Writer.valueClass(Text.class))) {
 
@@ -74,8 +83,7 @@ public class CrossrefImporter {
 					end = System.currentTimeMillis();
 					final float time = (end - start) / 1000.0F;
 					System.out
-						.println(
+						.println(String.format("Imported %s records last 100000 imported in %s seconds", i, time));
-							String.format("Imported %d records last 100000 imported in %f seconds", i, time));
 					start = System.currentTimeMillis();
 				}
 			}

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/ESClient.java

@@ -1,11 +1,11 @@
 
 package eu.dnetlib.doiboost.crossref;
 
-import java.io.IOException;
 import java.util.Iterator;
 import java.util.List;
 
 import org.apache.commons.io.IOUtils;
+import org.apache.http.HttpHeaders;
 import org.apache.http.client.methods.CloseableHttpResponse;
 import org.apache.http.client.methods.HttpPost;
 import org.apache.http.entity.StringEntity;
@@ -17,13 +17,17 @@ import org.slf4j.LoggerFactory;
 import com.jayway.jsonpath.JsonPath;
 
 public class ESClient implements Iterator<String> {
-	private static final Logger logger = LoggerFactory.getLogger(ESClient.class);
 
-	static final String blobPath = "$.hits[*].hits[*]._source.blob";
+	private static final String BLOB_PATH = "$.hits.hits[*]._source.blob";
-	static final String scrollIdPath = "$._scroll_id";
+	private static final String SCROLL_ID_PATH = "$._scroll_id";
-	static final String JSON_NO_TS = "{\"size\":1000}";
+	private static final String JSON_NO_TS = "{\"size\":1000}";
-	static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
+	private static final String JSON_WITH_TS = "{\"size\":1000, \"query\":{\"range\":{\"timestamp\":{\"gte\":%d}}}}";
-	static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
+	private static final String JSON_SCROLL = "{\"scroll_id\":\"%s\",\"scroll\" : \"1m\"}";
+
+	public static final String APPLICATION_JSON = "application/json";
+
+	public static final String ES_SEARCH_URL = "http://%s:9200/%s/_search?scroll=1m";
+	public static final String ES_SCROLL_URL = "http://%s:9200/_search/scroll";
 
 	private final String scrollId;
 
@@ -31,47 +35,30 @@ public class ESClient implements Iterator<String> {
 
 	private final String esHost;
 
-	public ESClient(final String esHost, final String esIndex) throws IOException {
+	public ESClient(final String esHost, final String esIndex, final long timestamp) {
-
 		this.esHost = esHost;
-		final String body = getResponse(
-			String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex), JSON_NO_TS);
-		scrollId = getJPathString(scrollIdPath, body);
-		buffer = getBlobs(body);
-	}
 
-	public ESClient(final String esHost, final String esIndex, final long timestamp)
+		final String body = timestamp > 0
-		throws IOException {
+			? getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), String.format(JSON_WITH_TS, timestamp))
-		this.esHost = esHost;
+			: getResponse(String.format(ES_SEARCH_URL, esHost, esIndex), JSON_NO_TS);
-		final String body = getResponse(
+		scrollId = getJPathString(SCROLL_ID_PATH, body);
-			String.format("http://%s:9200/%s/_search?scroll=1m", esHost, esIndex),
-			String.format(JSON_WITH_TS, timestamp));
-		scrollId = getJPathString(scrollIdPath, body);
 		buffer = getBlobs(body);
 	}
 
 	private String getResponse(final String url, final String json) {
-		CloseableHttpClient client = HttpClients.createDefault();
+		try (CloseableHttpClient client = HttpClients.createDefault()) {
-		try {
-
 			HttpPost httpPost = new HttpPost(url);
 			if (json != null) {
 				StringEntity entity = new StringEntity(json);
 				httpPost.setEntity(entity);
-				httpPost.setHeader("Accept", "application/json");
+				httpPost.setHeader(HttpHeaders.ACCEPT, APPLICATION_JSON);
-				httpPost.setHeader("Content-type", "application/json");
+				httpPost.setHeader(HttpHeaders.CONTENT_TYPE, APPLICATION_JSON);
 			}
-			CloseableHttpResponse response = client.execute(httpPost);
+			try (CloseableHttpResponse response = client.execute(httpPost)) {
-
 				return IOUtils.toString(response.getEntity().getContent());
+			}
 		} catch (Throwable e) {
 			throw new RuntimeException("Error on executing request ", e);
-		} finally {
-			try {
-				client.close();
-			} catch (IOException e) {
-				throw new RuntimeException("Unable to close client ", e);
-			}
 		}
 	}
 
@@ -87,7 +74,7 @@ public class ESClient implements Iterator<String> {
 	}
 
 	private List<String> getBlobs(final String body) {
-		final List<String> res = JsonPath.read(body, "$.hits.hits[*]._source.blob");
+		final List<String> res = JsonPath.read(body, BLOB_PATH);
 		return res;
 	}
 
@@ -102,11 +89,11 @@ public class ESClient implements Iterator<String> {
 		if (buffer.isEmpty()) {
 
 			final String json_param = String.format(JSON_SCROLL, scrollId);
-			final String body = getResponse(String.format("http://%s:9200/_search/scroll", esHost), json_param);
+			final String body = getResponse(String.format(ES_SCROLL_URL, esHost), json_param);
 			try {
 				buffer = getBlobs(body);
 			} catch (Throwable e) {
-				logger.error("Error on  get next page: body:" + body);
+				System.out.println("Error on  get next page: body:" + body);
 			}
 		}
 		return nextItem;

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala

@@ -11,7 +11,7 @@ import org.slf4j.{Logger, LoggerFactory}
 
 import scala.collection.JavaConverters._
 
-object SparkPreProcessMAG {
+object SparkProcessMAG {
   def main(args: Array[String]): Unit = {
 
     val logger: Logger = LoggerFactory.getLogger(getClass)

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala

@@ -1,11 +1,11 @@
 package eu.dnetlib.doiboost.orcid
 
+import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Publication}
 import eu.dnetlib.dhp.schema.orcid.OrcidDOI
 import eu.dnetlib.doiboost.DoiBoostMappingUtil
 import eu.dnetlib.doiboost.DoiBoostMappingUtil.{ORCID, PID_TYPES, createSP, generateDataInfo, generateIdentifier}
 import org.apache.commons.lang.StringUtils
-import org.codehaus.jackson.map.ObjectMapper
 import org.slf4j.{Logger, LoggerFactory}
 
 import scala.collection.JavaConverters._
@@ -18,7 +18,7 @@ case class ORCIDItem(oid:String,name:String,surname:String,creditName:String,err
 case class ORCIDElement(doi:String, authors:List[ORCIDItem]) {}
 object ORCIDToOAF {
   val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass)
-  val mapper = new ObjectMapper
+  val mapper = new ObjectMapper()
 
   def isJsonValid(inputStr: String): Boolean = {
     import java.io.IOException

dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/SparkDownloadOrcidAuthors.java

@@ -3,10 +3,8 @@ package eu.dnetlib.doiboost.orcid;
 
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
-import java.io.IOException;
 import java.text.SimpleDateFormat;
 import java.util.Date;
-import java.util.List;
 import java.util.Optional;
 
 import org.apache.commons.io.IOUtils;
@@ -18,11 +16,9 @@ import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaPairRDD;
-import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.Function;
 import org.apache.spark.util.LongAccumulator;
-import org.mortbay.log.Log;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -36,7 +32,7 @@ public class SparkDownloadOrcidAuthors {
 	static final String DATE_FORMAT = "yyyy-MM-dd HH:mm:ss";
 	static final String lastUpdate = "2020-09-29 00:00:00";
 
-	public static void main(String[] args) throws IOException, Exception {
+	public static void main(String[] args) throws Exception {
 
 		final ArgumentApplicationParser parser = new ArgumentApplicationParser(
 			IOUtils
@@ -51,12 +47,12 @@ public class SparkDownloadOrcidAuthors {
 			.orElse(Boolean.TRUE);
 		logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
 		final String workingPath = parser.get("workingPath");
-		logger.info("workingPath: ", workingPath);
+		logger.info("workingPath: {}", workingPath);
 		final String outputPath = parser.get("outputPath");
-		logger.info("outputPath: ", outputPath);
+		logger.info("outputPath: {}", outputPath);
 		final String token = parser.get("token");
 		final String lambdaFileName = parser.get("lambdaFileName");
-		logger.info("lambdaFileName: ", lambdaFileName);
+		logger.info("lambdaFileName: {}", lambdaFileName);
 
 		SparkConf conf = new SparkConf();
 		runWithSparkSession(
@@ -171,8 +167,8 @@ public class SparkDownloadOrcidAuthors {
 	}
 
 	private static boolean isModified(String orcidId, String modifiedDate) {
-		Date modifiedDateDt = null;
+		Date modifiedDateDt;
-		Date lastUpdateDt = null;
+		Date lastUpdateDt;
 		try {
 			if (modifiedDate.length() != 19) {
 				modifiedDate = modifiedDate.substring(0, 19);

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_as_params.json

@@ -5,5 +5,6 @@
   {"paramName": "cr",   "paramLongName":"crossRefRelation",                 "paramDescription": "the UnpayWall Publication Path",  "paramRequired": true},
   {"paramName": "da",   "paramLongName":"dbaffiliationRelationPath",        "paramDescription": "the MAG Publication Path",        "paramRequired": true},
   {"paramName": "do",   "paramLongName":"dbOrganizationPath",               "paramDescription": "the MAG Publication Path",        "paramRequired": true},
-  {"paramName": "w",    "paramLongName":"targetPath",                       "paramDescription": "the Working Path",                "paramRequired": true}
+  {"paramName": "w",    "paramLongName":"targetPath",                       "paramDescription": "the Working Path",                "paramRequired": true},
+  {"paramName": "sp",    "paramLongName":"sFilePath",                       "paramDescription": "the Sequence file Path",          "paramRequired": true}
 ]

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json

@@ -3,5 +3,5 @@
   {"paramName": "hb",   "paramLongName":"hostedByMapPath",            "paramDescription": "the hosted By Map Path",         "paramRequired": true},
   {"paramName": "ap",   "paramLongName":"affiliationPath",            "paramDescription": "the Affliation Path",            "paramRequired": true},
   {"paramName": "pa",   "paramLongName":"paperAffiliationPath",      "paramDescription": "the paperAffiliation Path",       "paramRequired": true},
-  {"paramName": "w",    "paramLongName":"workingDirPath",            "paramDescription": "the Working Path",                "paramRequired": true}
+  {"paramName": "w",    "paramLongName":"workingPath",                "paramDescription": "the Working Path",                "paramRequired": true}
 ]

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/import_from_es.json

@@ -1,5 +1,7 @@
 [
   {"paramName":"t",   "paramLongName":"targetPath",    "paramDescription": "the path of the sequencial file to write",   "paramRequired": true},
   {"paramName":"n",   "paramLongName":"namenode",      "paramDescription": "the hive metastore uris",                    "paramRequired": true},
-  {"paramName":"ts",   "paramLongName":"timestamp",         "paramDescription": "timestamp",                                  "paramRequired": false}
+  {"paramName":"ts",  "paramLongName":"timestamp",     "paramDescription": "timestamp",                                  "paramRequired": false},
+  {"paramName":"ess", "paramLongName":"esServer",     "paramDescription": "elasticsearch server url",                   "paramRequired": true},
+  {"paramName":"esi", "paramLongName":"esIndex",      "paramDescription": "elasticsearch index name",                   "paramRequired": true}
 ]

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/config-default.xml

@@ -0,0 +1,42 @@
+<configuration>
+    <property>
+        <name>jobTracker</name>
+        <value>yarnRM</value>
+    </property>
+    <property>
+        <name>nameNode</name>
+        <value>hdfs://nameservice1</value>
+    </property>
+    <property>
+        <name>oozie.use.system.libpath</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>oozie.action.sharelib.for.spark</name>
+        <value>spark2</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>hive_metastore_uris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>spark2YarnHistoryServerAddress</name>
+        <value>http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>spark2ExtraListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorAppListener"</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>"com.cloudera.spark.lineage.NavigatorQueryListener"</value>
+    </property>
+</configuration>

dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml

@@ -0,0 +1,335 @@
+<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorIntersectionMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+
+
+        <!-- Itersection Parameters -->
+        <property>
+            <name>workingPath</name>
+            <description>the working Path</description>
+        </property>
+
+        <property>
+            <name>hostedByMapPath</name>
+            <description>the hostedByMap Path</description>
+        </property>
+        <property>
+            <name>outputPath</name>
+            <description>the Path of the sequence file action set</description>
+        </property>
+
+
+        <!-- Crossref Parameters -->
+        <property>
+            <name>inputPathCrossref</name>
+            <description>the Crossref input path</description>
+        </property>
+        <property>
+            <name>crossrefTimestamp</name>
+            <description>Timestamp for the Crossref incremental Harvesting</description>
+        </property>
+        <property>
+            <name>esServer</name>
+            <description>elasticsearch server url for the Crossref Harvesting</description>
+        </property>
+        <property>
+            <name>esIndex</name>
+            <description>elasticsearch index name for the Crossref Harvesting</description>
+        </property>
+
+        <!--    MAG Parameters    -->
+        <property>
+            <name>inputPathMAG</name>
+            <description>the MAG working path</description>
+        </property>
+
+
+        <!--    UnpayWall Parameters    -->
+        <property>
+            <name>inputPathUnpayWall</name>
+            <description>the UnpayWall working path</description>
+        </property>
+
+        <!--    ORCID Parameters    -->
+        <property>
+            <name>inputPathOrcid</name>
+            <description>the ORCID working path</description>
+        </property>
+
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+        </configuration>
+    </global>
+
+    <start to="resume_from"/>
+
+    <decision name="resume_from">
+        <switch>
+            <case to="ConvertCrossrefToOAF">${wf:conf('resumeFrom') eq 'ConvertCrossrefToOAF'}</case>
+            <case to="ResetMagWorkingPath">${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'}</case>
+            <case to="ProcessMAG">${wf:conf('resumeFrom') eq 'PreprocessMag'}</case>
+            <case to="ProcessUW">${wf:conf('resumeFrom') eq 'PreprocessUW'}</case>
+            <case to="ProcessORCID">${wf:conf('resumeFrom') eq 'PreprocessORCID'}</case>
+            <case to="CreateDOIBoost">${wf:conf('resumeFrom') eq 'CreateDOIBoost'}</case>
+            <case to="GenerateActionSet">${wf:conf('resumeFrom') eq 'GenerateActionSet'}</case>
+            <default to="ImportCrossRef"/>
+        </switch>
+    </decision>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+    <action name="ImportCrossRef">
+        <java>
+            <main-class>eu.dnetlib.doiboost.crossref.CrossrefImporter</main-class>
+            <arg>--targetPath</arg><arg>${inputPathCrossref}/index_update</arg>
+            <arg>--namenode</arg><arg>${nameNode}</arg>
+            <arg>--esServer</arg><arg>${esServer}</arg>
+            <arg>--esIndex</arg><arg>${esIndex}</arg>
+            <arg>--timestamp</arg><arg>${crossrefTimestamp}</arg>
+        </java>
+        <ok to="GenerateCrossrefDataset"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <!-- CROSSREF SECTION -->
+
+    <action name="GenerateCrossrefDataset">
+            <spark xmlns="uri:oozie:spark-action:0.2">
+                <master>yarn-cluster</master>
+                <mode>cluster</mode>
+                <name>GenerateCrossrefDataset</name>
+                <class>eu.dnetlib.doiboost.crossref.CrossrefDataset</class>
+                <jar>dhp-doiboost-${projectVersion}.jar</jar>
+                <spark-opts>
+                    --executor-memory=${sparkExecutorMemory}
+                    --executor-cores=${sparkExecutorCores}
+                    --driver-memory=${sparkDriverMemory}
+                    --conf spark.sql.shuffle.partitions=3840
+                    ${sparkExtraOPT}
+                </spark-opts>
+                <arg>--workingPath</arg><arg>${inputPathCrossref}</arg>
+                <arg>--master</arg><arg>yarn-cluster</arg>
+            </spark>
+            <ok to="RenameDataset"/>
+            <error to="Kill"/>
+    </action>
+
+    <action name="RenameDataset">
+        <fs>
+            <delete path="${inputPathCrossref}/crossref_ds"/>
+            <move source="${inputPathCrossref}/crossref_ds_updated"
+                  target="${inputPathCrossref}/crossref_ds"/>
+        </fs>
+        <ok to="ConvertCrossrefToOAF"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="ConvertCrossrefToOAF">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>ConvertCrossrefToOAF</name>
+            <class>eu.dnetlib.doiboost.crossref.SparkMapDumpIntoOAF</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${inputPathCrossref}/crossref_ds</arg>
+            <arg>--targetPath</arg><arg>${workingPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="ResetMagWorkingPath"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <!-- MAG SECTION -->
+    <action name="ResetMagWorkingPath">
+        <fs>
+            <delete path="${inputPathMAG}/dataset"/>
+            <delete path="${inputPathMAG}/process"/>
+            <delete path="${inputPathMAG}/dataset"/>
+        </fs>
+        <ok to="ConvertMagToDataset"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ConvertMagToDataset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert Mag to Dataset</name>
+            <class>eu.dnetlib.doiboost.mag.SparkImportMagIntoDataset</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${inputPathMAG}/input</arg>
+            <arg>--targetPath</arg><arg>${inputPathMAG}/dataset</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="ProcessMAG"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="ProcessMAG">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert Mag to OAF Dataset</name>
+            <class>eu.dnetlib.doiboost.mag.SparkProcessMAG</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
+            <arg>--workingPath</arg><arg>${inputPathMAG}/process</arg>
+            <arg>--targetPath</arg><arg>${workingPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="ProcessUW"/>
+        <error to="Kill"/>
+    </action>
+
+    <!--  UnpayWall  SECTION -->
+
+    <action name="ProcessUW">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert UnpayWall to Dataset</name>
+            <class>eu.dnetlib.doiboost.uw.SparkMapUnpayWallToOAF</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${inputPathUnpayWall}/uw_extracted</arg>
+            <arg>--targetPath</arg><arg>${workingPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="ProcessORCID"/>
+        <error to="Kill"/>
+    </action>
+
+    <!--  ORCID  SECTION -->
+    <action name="ProcessORCID">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Convert ORCID to Dataset</name>
+            <class>eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${inputPathOrcid}</arg>
+            <arg>--targetPath</arg><arg>${workingPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="CreateDOIBoost"/>
+        <error to="Kill"/>
+    </action>
+
+    <!-- INTERSECTION SECTION-->
+    <action name="CreateDOIBoost">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Create DOIBoost Infospace</name>
+            <class>eu.dnetlib.doiboost.SparkGenerateDoiBoost</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorIntersectionMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--hostedByMapPath</arg><arg>${hostedByMapPath}</arg>
+            <arg>--affiliationPath</arg><arg>${inputPathMAG}/process/Affiliations</arg>
+            <arg>--paperAffiliationPath</arg><arg>${inputPathMAG}/process/PaperAuthorAffiliations</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="GenerateActionSet"/>
+        <error to="Kill"/>
+    </action>
+
+
+    <action name="GenerateActionSet">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn-cluster</master>
+            <mode>cluster</mode>
+            <name>Generate DOIBoost ActionSet</name>
+            <class>eu.dnetlib.doiboost.SparkGenerateDOIBoostActionSet</class>
+            <jar>dhp-doiboost-${projectVersion}.jar</jar>
+            <spark-opts>
+                --executor-memory=${sparkExecutorMemory}
+                --executor-cores=${sparkExecutorCores}
+                --driver-memory=${sparkDriverMemory}
+                --conf spark.sql.shuffle.partitions=3840
+                ${sparkExtraOPT}
+            </spark-opts>
+            <arg>--dbPublicationPath</arg><arg>${workingPath}/doiBoostPublicationFiltered</arg>
+            <arg>--dbDatasetPath</arg><arg>${workingPath}/crossrefDataset</arg>
+            <arg>--crossRefRelation</arg><arg>${workingPath}/crossrefRelation</arg>
+            <arg>--dbaffiliationRelationPath</arg><arg>${workingPath}/doiBoostPublicationAffiliation</arg>
+            <arg>--dbOrganizationPath</arg><arg>${workingPath}/doiBoostOrganization</arg>
+            <arg>--targetPath</arg><arg>${workingPath}/actionDataSet</arg>
+            <arg>--sFilePath</arg><arg>${outputPath}</arg>
+            <arg>--master</arg><arg>yarn-cluster</arg>
+        </spark>
+        <ok to="End"/>
+        <error to="Kill"/>
+    </action>
+
+    <end name="End"/>
+</workflow-app>

dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala

@@ -1,9 +1,9 @@
 package eu.dnetlib.doiboost.orcid
 
+import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.schema.oaf.Publication
 import eu.dnetlib.doiboost.orcid.SparkConvertORCIDToOAF.getClass
 import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
-import org.codehaus.jackson.map.ObjectMapper
 import org.junit.jupiter.api.Assertions._
 import org.junit.jupiter.api.Test
 import org.slf4j.{Logger, LoggerFactory}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/orcidtoresultfromsemrel/PrepareResultOrcidAssociationStep1.java

@@ -104,7 +104,7 @@ public class PrepareResultOrcidAssociationStep1 {
 			+ "               LATERAL VIEW EXPLODE (author) a AS MyT "
 			+ "               LATERAL VIEW EXPLODE (MyT.pid) p AS MyP "
 			+ "               WHERE lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID + "' or "
-			+ "                       lower(MyP.qalifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
+			+ "                       lower(MyP.qualifier.classid) = '" + ModelConstants.ORCID_PENDING + "') tmp "
 			+ "               GROUP BY id) r_t "
 			+ " JOIN ("
 			+ "        SELECT source, target "

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningFunctions.java

@@ -16,7 +16,10 @@ import eu.dnetlib.dhp.schema.oaf.*;
 public class CleaningFunctions {
 
 	public static final String DOI_URL_PREFIX_REGEX = "(^http(s?):\\/\\/)(((dx\\.)?doi\\.org)|(handle\\.test\\.datacite\\.org))\\/";
-	public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
+
+	public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
+	public static final int ORCID_LEN = 19;
+
 	public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
 
 	public static final Set<String> PID_BLACKLIST = new HashSet<>();
@@ -86,7 +89,7 @@ public class CleaningFunctions {
 		} else if (value instanceof Organization) {
 			Organization o = (Organization) value;
 			if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
-				o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
+				o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
 			}
 		} else if (value instanceof Relation) {
 			// nothing to clean here
@@ -153,12 +156,14 @@ public class CleaningFunctions {
 			if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
 				r
 					.setResourcetype(
-						qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
+						qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
 			}
 			if (Objects.nonNull(r.getInstance())) {
 				for (Instance i : r.getInstance()) {
 					if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
-						i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
+						i
+							.setAccessright(
+								qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
 					}
 					if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
 						i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
@@ -173,7 +178,7 @@ public class CleaningFunctions {
 				if (Objects.isNull(bestaccessrights)) {
 					r
 						.setBestaccessright(
-							qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
+							qualifier(ModelConstants.UNKNOWN, "not available", ModelConstants.DNET_ACCESS_MODES));
 				} else {
 					r.setBestaccessright(bestaccessrights);
 				}
@@ -211,14 +216,31 @@ public class CleaningFunctions {
 													.map(Qualifier::getClassid)
 													.orElse(""))
 											.orElse("");
-										if (pidProvenance.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
+										if (p
+											.getQualifier()
+											.getClassid()
+											.toLowerCase()
+											.contains(ModelConstants.ORCID)) {
+											if (pidProvenance
+												.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
 												p.getQualifier().setClassid(ModelConstants.ORCID);
 											} else {
 												p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
 											}
-										p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
+											final String orcid = p
+												.getValue()
+												.trim()
+												.toLowerCase()
+												.replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4");
+											if (orcid.length() == ORCID_LEN) {
+												p.setValue(orcid);
+											} else {
+												p.setValue("");
+											}
+										}
 										return p;
 									})
+									.filter(p -> StringUtils.isNotBlank(p.getValue()))
 									.collect(
 										Collectors
 											.toMap(

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/GroupEntitiesAndRelationsSparkJob.java

@@ -21,6 +21,7 @@ import org.apache.spark.sql.expressions.Aggregator;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import com.fasterxml.jackson.databind.DeserializationFeature;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import com.jayway.jsonpath.Configuration;
 import com.jayway.jsonpath.DocumentContext;
@@ -44,7 +45,8 @@ public class GroupEntitiesAndRelationsSparkJob {
 
 	private final static String SOURCE_JPATH = "$.source";
 
-	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
+		.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
 
 	public static void main(String[] args) throws Exception {
 

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

@@ -23,7 +23,15 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
-import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.*;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.asString;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.createOpenaireId;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.journal;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listFields;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
+import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
 
 import java.io.Closeable;
 import java.io.IOException;
@@ -462,44 +470,48 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
 
 				return Arrays.asList(r);
 			} else {
+				final String validationDate = rs.getString("curation_date");
+
 				final String sourceId = createOpenaireId(rs.getString(SOURCE_TYPE), rs.getString("source_id"), false);
 				final String targetId = createOpenaireId(rs.getString(TARGET_TYPE), rs.getString("target_id"), false);
 
 				final Relation r1 = new Relation();
 				final Relation r2 = new Relation();
 
-				if (rs.getString(SOURCE_TYPE).equals("project")) {
+				r1.setValidated(true);
+				r1.setValidationDate(validationDate);
 				r1.setCollectedfrom(collectedFrom);
-					r1.setRelType(RESULT_PROJECT);
-					r1.setSubRelType(OUTCOME);
-					r1.setRelClass(PRODUCES);
-
-					r2.setCollectedfrom(collectedFrom);
-					r2.setRelType(RESULT_PROJECT);
-					r2.setSubRelType(OUTCOME);
-					r2.setRelClass(IS_PRODUCED_BY);
-				} else {
-					r1.setCollectedfrom(collectedFrom);
-					r1.setRelType(RESULT_RESULT);
-					r1.setSubRelType(RELATIONSHIP);
-					r1.setRelClass(IS_RELATED_TO);
-
-					r2.setCollectedfrom(collectedFrom);
-					r2.setRelType(RESULT_RESULT);
-					r2.setSubRelType(RELATIONSHIP);
-					r2.setRelClass(IS_RELATED_TO);
-				}
-
 				r1.setSource(sourceId);
 				r1.setTarget(targetId);
 				r1.setDataInfo(info);
 				r1.setLastupdatetimestamp(lastUpdateTimestamp);
 
+				r2.setValidationDate(validationDate);
+				r2.setValidated(true);
+				r2.setCollectedfrom(collectedFrom);
 				r2.setSource(targetId);
 				r2.setTarget(sourceId);
 				r2.setDataInfo(info);
 				r2.setLastupdatetimestamp(lastUpdateTimestamp);
 
+				if (rs.getString(SOURCE_TYPE).equals("project")) {
+					r1.setRelType(RESULT_PROJECT);
+					r1.setSubRelType(OUTCOME);
+					r1.setRelClass(PRODUCES);
+
+					r2.setRelType(RESULT_PROJECT);
+					r2.setSubRelType(OUTCOME);
+					r2.setRelClass(IS_PRODUCED_BY);
+				} else {
+					r1.setRelType(RESULT_RESULT);
+					r1.setSubRelType(RELATIONSHIP);
+					r1.setRelClass(IS_RELATED_TO);
+
+					r2.setRelType(RESULT_RESULT);
+					r2.setSubRelType(RELATIONSHIP);
+					r2.setRelClass(IS_RELATED_TO);
+				}
+
 				return Arrays.asList(r1, r2);
 			}
 

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

@@ -11,7 +11,8 @@ import org.apache.hadoop.conf.Configuration;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.SequenceFile;
 import org.apache.hadoop.io.Text;
-import org.codehaus.jackson.map.ObjectMapper;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.oaf.Oaf;
 

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryClaims.sql

@@ -1 +1 @@
-SELECT source_type, source_id, target_type, target_id, semantics FROM claim WHERE approved=TRUE;
+SELECT source_type, source_id, target_type, target_id, semantics, curation_date::text FROM claim WHERE approved=TRUE;

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java

@@ -35,7 +35,7 @@ public class MigrateDbEntitiesApplicationTest {
 
 	private MigrateDbEntitiesApplication app;
 
-	@Mock
+	@Mock(lenient = true)
 	private ResultSet rs;
 
 	@Mock

dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/textgrid.xml

@@ -6,29 +6,29 @@
                 xmlns:dc="http://purl.org/dc/elements/1.1/"
                 xmlns:dri="http://www.driver-repository.eu/namespace/dri"
                 xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-        <dri:objIdentifier>r3f52792889d::000051aa1f61d77d2c0b340091f8024e</dri:objIdentifier>
+        <dri:objIdentifier>r3f52792889d::00002412cb25f2f3047712d00ab2c8eb</dri:objIdentifier>
-        <dri:recordIdentifier>textgrid:q9cv.0</dri:recordIdentifier>
+        <dri:recordIdentifier>hdl:11858/00-1734-0000-0003-EE73-2</dri:recordIdentifier>
-        <dri:dateOfCollection>2020-11-17T09:34:11.128+01:00</dri:dateOfCollection>
+        <dri:dateOfCollection>2020-12-16T10:04:03.148Z</dri:dateOfCollection>
         <oaf:datasourceprefix>r3f52792889d</oaf:datasourceprefix>
-        <identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</identifier>
+        <identifier xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</identifier>
-        <datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-21T13:35:20Z</datestamp>
+        <datestamp xmlns="http://www.openarchives.org/OAI/2.0/">2012-01-29T20:54:12Z</datestamp>
-        <dr:dateOfTransformation>2020-11-17T19:08:56.703+01:00</dr:dateOfTransformation>
+        <dr:dateOfTransformation>2020-12-16T16:02:37.562Z</dr:dateOfTransformation>
     </oai:header>
     <metadata>
         <datacite:resource xmlns="http://www.openarchives.org/OAI/2.0/"
                            xmlns:dc="http://purl.org/dc/elements/1.1/"
                            xmlns:dri="http://www.driver-repository.eu/namespace/dri"
                            xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-            <datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-7664-F</datacite:identifier>
+            <datacite:identifier identifierType="Handle">hdl:11858/00-1734-0000-0003-EE73-2</datacite:identifier>
             <datacite:creators>
                 <datacite:creator>
-                    <datacite:creatorName>Hoffmann von Fallersleben, August Heinrich</datacite:creatorName>
+                    <datacite:creatorName>Liliencron, Detlev von</datacite:creatorName>
-                    <datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://de.dariah.eu/pnd-service">118552589</datacite:nameIdentifier>
+                    <datacite:nameIdentifier nameIdentifierScheme="pnd" schemeURI="https://ref.de.dariah.eu/pndsearch/pndquery.xql?id=">118572954</datacite:nameIdentifier>
                 </datacite:creator>
             </datacite:creators>
             <datacite:titles>
-                <datacite:title titleType="Other">Mailied</datacite:title>
+                <datacite:title titleType="Other">Auf dem Trocknen</datacite:title>
-                <datacite:title titleType="Other">August Heinrich Hoffmann von Fallersleben: Unpolitische Lieder von Hoffmann von Fallersleben, 1. + 2. Theil, 1. Theil, Hamburg: Hoffmann und Campe, 1841.</datacite:title>
+                <datacite:title titleType="Other">Detlev von Liliencron: Gute Nacht. Hinterlassene Gedichte, Berlin: Schuster &amp; Loeffler, 1909.</datacite:title>
             </datacite:titles>
             <datacite:publisher>TextGrid</datacite:publisher>
             <datacite:publicationYear>2012</datacite:publicationYear>
@@ -38,21 +38,21 @@
                 </datacite:contributor>
                 <datacite:contributor contributorType="Other">
                     <datacite:contributorName>Digitale Bibliothek</datacite:contributorName>
-                    <datacite:nameIdentifier nameIdentifierScheme="textgrid">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
+                    <datacite:nameIdentifier nameIdentifierScheme="textgrid" schemeURI="http://www.textgridlab.org/schema/textgrid-metadata_2010.xsd">TGPR-372fe6dc-57f2-6cd4-01b5-2c4bbefcfd3c</datacite:nameIdentifier>
                 </datacite:contributor>
             </datacite:contributors>
             <datacite:dates>
-                <datacite:date dateType="Created">2012-01-21T13:35:20Z</datacite:date>
+                <datacite:date dateType="Created">2012-01-29T20:54:12Z</datacite:date>
-                <datacite:date dateType="Issued">2012-01-21T13:35:20Z</datacite:date>
+                <datacite:date dateType="Issued">2012-01-29T20:54:12Z</datacite:date>
-                <datacite:date dateType="Updated">2012-01-21T13:35:20Z</datacite:date>
+                <datacite:date dateType="Updated">2012-01-29T20:54:12Z</datacite:date>
             </datacite:dates>
             <datacite:resourceType resourceTypeGeneral="Dataset"/>
             <alternateIdentifiers xmlns="http://datacite.org/schema/kernel-3">
-                <datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:q9cv.0</datacite:alternateIdentifier>
+                <datacite:alternateIdentifier alternateIdentifierType="URI" xmlns="http://www.openarchives.org/OAI/2.0/">textgrid:rn8z.0</datacite:alternateIdentifier>
-                <alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-7664-F</alternateIdentifier>
+                <alternateIdentifier alternateIdentifierType="URL">http://hdl.handle.net/hdl:11858/00-1734-0000-0003-EE73-2</alternateIdentifier>
             </alternateIdentifiers>
             <datacite:relatedIdentifiers>
-                <datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-7666-B</datacite:relatedIdentifier>
+                <datacite:relatedIdentifier relatedIdentifierType="Handle" relationType="IsPartOf">hdl:11858/00-1734-0000-0003-EE72-4</datacite:relatedIdentifier>
             </datacite:relatedIdentifiers>
             <datacite:sizes>
                 <datacite:size>527 Bytes</datacite:size>
@@ -77,17 +77,18 @@
             <datacite:geoLocations>
                 <datacite:geoLocation>
                     <datacite:geoLocationPlace
-                            xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Hamburg</datacite:geoLocationPlace>
+                            xmlns:xs="http://www.w3.org/2001/XMLSchema" xsi:type="xs:string">Berlin</datacite:geoLocationPlace>
                 </datacite:geoLocation>
             </datacite:geoLocations>
         </datacite:resource>
-        <oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-7664-F</oaf:identifier>
+        <oaf:identifier identifierType="handle">hdl:11858/00-1734-0000-0003-EE73-2</oaf:identifier>
         <dr:CobjCategory type="dataset">0021</dr:CobjCategory>
         <oaf:refereed>0002</oaf:refereed>
-        <oaf:dateAccepted>2012-01-21</oaf:dateAccepted>
+        <oaf:dateAccepted>2012-01-29</oaf:dateAccepted>
         <oaf:accessrights>OPEN</oaf:accessrights>
         <oaf:license>http://creativecommons.org/licenses/by/3.0/de/legalcode</oaf:license>
         <oaf:language>und</oaf:language>
+        <oaf:country>DE</oaf:country>
         <oaf:hostedBy id="re3data_____::r3d100011365" name="TextGrid Repository"/>
         <oaf:collectedFrom id="re3data_____::r3d100011365" name="TextGrid Repository"/>
     </metadata>
@@ -95,11 +96,11 @@
            xmlns:dri="http://www.driver-repository.eu/namespace/dri"
            xmlns:prov="http://www.openarchives.org/OAI/2.0/provenance" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
         <provenance xmlns="http://www.openarchives.org/OAI/2.0/provenance" xsi:schemaLocation="http://www.openarchives.org/OAI/2.0/provenance http://www.openarchives.org/OAI/2.0/provenance.xsd">
-            <originDescription altered="true" harvestDate="2020-11-17T09:34:11.128+01:00">
+            <originDescription altered="true" harvestDate="2020-12-16T10:04:03.148Z">
                 <baseURL>https%3A%2F%2Fdev.textgridlab.org%2F1.0%2Ftgoaipmh%2Foai</baseURL>
-                <identifier>textgrid:q9cv.0</identifier>
+                <identifier>textgrid:rn8z.0</identifier>
-                <datestamp>2012-01-21T13:35:20Z</datestamp>
+                <datestamp>2012-01-29T20:54:12Z</datestamp>
-                <metadataNamespace>http://schema.datacite.org/oai/oai-1.0/</metadataNamespace>
+                <metadataNamespace/>
             </originDescription>
         </provenance>
         <oaf:datainfo>
@@ -107,9 +108,10 @@
             <oaf:deletedbyinference>false</oaf:deletedbyinference>
             <oaf:trust>0.9</oaf:trust>
             <oaf:inferenceprovenance/>
-            <oaf:provenanceaction classid="sysimport:crosswalk"
+            <oaf:provenanceaction classid="sysimport:crosswalk:datasetarchive"
-                                  classname="sysimport:crosswalk"
+                                  classname="sysimport:crosswalk:datasetarchive"
                                   schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
         </oaf:datainfo>
     </about>
 </record>
+

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/DLIToOAF.scala

@@ -1,15 +1,15 @@
 package eu.dnetlib.dhp.export
 
+import com.fasterxml.jackson.databind.ObjectMapper
+
 import java.time.LocalDateTime
 import java.time.format.DateTimeFormatter
-
 import eu.dnetlib.dhp.common.PacePerson
 import eu.dnetlib.dhp.schema.action.AtomicAction
 import eu.dnetlib.dhp.schema.oaf.{Author, Dataset, ExternalReference, Field, Instance, KeyValue, Oaf, Publication, Qualifier, Relation, Result, StructuredProperty}
 import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
 import eu.dnetlib.dhp.utils.DHPUtils
 import org.apache.commons.lang3.StringUtils
-import org.codehaus.jackson.map.ObjectMapper
 import eu.dnetlib.dhp.schema.scholexplorer.OafUtils._
 
 import scala.collection.JavaConverters._

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/export/SparkExportContentForOpenAire.scala

@@ -1,27 +1,21 @@
 package eu.dnetlib.dhp.`export`
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
-import eu.dnetlib.dhp.schema.oaf.{Instance, Publication, Relation, Dataset => OafDataset}
+import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
 import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
 import org.apache.commons.io.IOUtils
 import org.apache.hadoop.io.Text
 import org.apache.hadoop.io.compress.GzipCodec
 import org.apache.hadoop.mapred.SequenceFileOutputFormat
-import org.apache.spark.rdd.RDD
 import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
 import org.apache.spark.sql.functions._
 import org.apache.spark.sql.expressions.Window
-import org.apache.spark.{SparkConf, SparkContext}
+import org.apache.spark.SparkConf
-import org.codehaus.jackson.map.ObjectMapper
 
 import scala.collection.mutable.ArrayBuffer
-import scala.collection.JavaConverters._
 
 object SparkExportContentForOpenAire {
 
-
-
-
   def main(args: Array[String]): Unit = {
     val conf: SparkConf = new SparkConf()
     val parser = new ArgumentApplicationParser(IOUtils.toString(SparkExportContentForOpenAire.getClass.getResourceAsStream("input_export_content_parameters.json")))
@@ -178,11 +172,4 @@ object SparkExportContentForOpenAire {
     fRels.union(fpubs).union(fdats).rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$workingPath/export/rawset", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec])
   }
 
-
-
-
-
-
-
-
 }

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

@@ -10,7 +10,8 @@ import org.apache.http.client.methods.HttpPut;
 import org.apache.http.entity.StringEntity;
 import org.apache.http.impl.client.CloseableHttpClient;
 import org.apache.http.impl.client.HttpClients;
-import org.codehaus.jackson.map.ObjectMapper;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 

dhp-workflows/dhp-graph-provision-scholexplorer/src/main/java/eu/dnetlib/dhp/provision/SparkConvertDatasetToJson.scala

@@ -1,5 +1,6 @@
 package eu.dnetlib.dhp.provision
 
+import com.fasterxml.jackson.databind.ObjectMapper
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.provision.scholix.Scholix
 import eu.dnetlib.dhp.provision.scholix.summary.ScholixSummary
@@ -7,7 +8,6 @@ import org.apache.commons.io.IOUtils
 import org.apache.hadoop.io.compress.GzipCodec
 import org.apache.spark.SparkConf
 import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
-import org.codehaus.jackson.map.ObjectMapper
 
 object SparkConvertDatasetToJson {
 

dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/workflow.xml

@@ -259,7 +259,7 @@
     <action name="Step17">
         <hive2 xmlns="uri:oozie:hive2-action:0.1">
             <jdbc-url>${hive_jdbc_url}</jdbc-url>
-            <script>scripts/updateProductionViews.sql</script>
+            <script>scripts/step17.sql</script>
 			<param>stats_db_name=${stats_db_name}</param>
 			<param>stats_db_shadow_name=${stats_db_shadow_name}</param>
         </hive2>
@@ -287,8 +287,8 @@
             <name-node>${nameNode}</name-node>
             <exec>impala-shell.sh</exec>
             <argument>${stats_db_shadow_name}</argument>
-            <argument>computeProductionStats.sql</argument>
+            <argument>step19.sql</argument>
-            <argument>${wf:appPath()}/scripts/computeProductionStats.sql</argument>
+            <argument>${wf:appPath()}/scripts/step19.sql</argument>
             <file>impala-shell.sh</file>
         </shell>
         <ok to="Step20"/>