mergin with branch beta

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

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

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

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

dhp-workflows/dhp-aggregation/pom.xml

@@ -29,6 +29,13 @@
                             <goal>testCompile</goal>
                         </goals>
                     </execution>
+                    <execution>
+                        <id>scala-doc</id>
+                        <phase>process-resources</phase> <!-- or wherever -->
+                        <goals>
+                            <goal>doc</goal>
+                        </goals>
+                    </execution>
                 </executions>
                 <configuration>
                     <scalaVersion>${scala.version}</scalaVersion>

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java

@@ -5,94 +5,249 @@ import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
+/**
+ * This class represent an instance of Pubmed Article extracted from the native XML
+ *
+ * @author Sandro La Bruzzo
+ */
+
 public class PMArticle implements Serializable {
 
+	/**
+	 * the Pubmed Identifier
+	 */
 	private String pmid;
+	/**
+	 * the DOI
+	 */
 	private String doi;
+	/**
+	 * the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
+	 * All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
+	 */
 	private String date;
+	/**
+	 * This is an 'envelop' element that contains various elements describing the journal cited; i.e., ISSN, Volume, Issue, and PubDate and author name(s), however, it does not contain data itself.
+	 */
 	private PMJournal journal;
+	/**
+	 * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. The NLM journal title abbreviation is exported in the <MedlineTA> element.
+	 */
 	private String title;
+	/**
+	 * English-language abstracts are taken directly from the published article.
+	 * If the article does not have a published abstract, the National Library of Medicine does not create one,
+	 * thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
+	 * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
+	 */
 	private String description;
+	/**
+	 * the language in which an article was published is recorded in <Language>.
+	 * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
+	 * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
+	 *  Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
+	 */
 	private String language;
+
+	/**
+	 * NLM controlled vocabulary, Medical Subject Headings (MeSH®), is used to characterize the content of the articles represented by MEDLINE citations.	 *
+	 */
 	private final List<PMSubject> subjects = new ArrayList<>();
+	/**
+	 * This element is used to identify the type of article indexed for MEDLINE;
+	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
+	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
+	 */
 	private final List<PMSubject> publicationTypes = new ArrayList<>();
+	/**
+	 * Personal and collective (corporate) author names published with the article are found in <AuthorList>.
+	 */
 	private List<PMAuthor> authors = new ArrayList<>();
 
-	public List<PMSubject> getPublicationTypes() {
+	/**
-		return publicationTypes;
+	 * <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
-	}
+	 * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
-
+	 */
 	private final List<PMGrant> grants = new ArrayList<>();
 
-	public List<PMGrant> getGrants() {
+	/**
-		return grants;
+	 * get the DOI
-	}
+	 * @return a DOI
-
+	 */
 	public String getDoi() {
 		return doi;
 	}
 
+	/**
+	 * Set the DOI
+	 * @param doi a DOI
+	 */
 	public void setDoi(String doi) {
 		this.doi = doi;
 	}
 
+	/**
+	 * get the Pubmed Identifier
+	 * @return the PMID
+	 */
 	public String getPmid() {
 		return pmid;
 	}
 
+	/**
+	 * set the Pubmed Identifier
+	 * @param pmid the Pubmed Identifier
+	 */
 	public void setPmid(String pmid) {
 		this.pmid = pmid;
 	}
 
+	/**
+	 * the Pubmed Date extracted from <PubmedPubDate> Specifies a date significant to either the article's history or the citation's processing.
+	 * All <History> dates will have a <Year>, <Month>, and <Day> elements. Some may have an <Hour>, <Minute>, and <Second> element(s).
+	 *
+	 * @return the Pubmed Date
+	 */
 	public String getDate() {
 		return date;
 	}
 
+	/**
+	 * Set the pubmed Date
+	 * @param date
+	 */
 	public void setDate(String date) {
 		this.date = date;
 	}
 
+	/**
+	 * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element.
+		 * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles.
+	 * The NLM journal title abbreviation is exported in the <MedlineTA> element.
+	 *
+	 * @return the pubmed Journal Extracted
+	 */
 	public PMJournal getJournal() {
 		return journal;
 	}
 
+	/**
+	 * Set the mapped pubmed Journal
+	 * @param journal
+	 */
 	public void setJournal(PMJournal journal) {
 		this.journal = journal;
 	}
 
+	/**
+	 * English-language abstracts are taken directly from the published article.
+	 * If the article does not have a published abstract, the National Library of Medicine does not create one,
+	 * thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
+	 * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
+	 *
+	 *  @return the extracted pubmed Title
+	 */
 	public String getTitle() {
 		return title;
 	}
 
+	/**
+	 * set the pubmed title
+	 * @param title
+	 */
 	public void setTitle(String title) {
 		this.title = title;
 	}
 
+	/**
+	 * English-language abstracts are taken directly from the published article.
+	 * If the article does not have a published abstract, the National Library of Medicine does not create one,
+	 * thus the record lacks the <Abstract> and <AbstractText> elements. However, in the absence of a formally
+	 * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used.
+	 *
+	 * @return the Mapped Pubmed Article Abstracts
+	 */
 	public String getDescription() {
 		return description;
 	}
 
+	/**
+	 * Set the Mapped Pubmed Article Abstracts
+	 * @param description
+	 */
 	public void setDescription(String description) {
 		this.description = description;
 	}
 
+	/**
+	 * Personal and collective (corporate) author names published with the article are found in <AuthorList>.
+	 *
+	 * @return get the Mapped Authors lists
+	 */
 	public List<PMAuthor> getAuthors() {
 		return authors;
 	}
 
+	/**
+	 * Set the Mapped Authors lists
+	 * @param authors
+	 */
 	public void setAuthors(List<PMAuthor> authors) {
 		this.authors = authors;
 	}
 
+	/**
+	 * This element is used to identify the type of article indexed for MEDLINE;
+	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
+	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
+	 *
+	 * @return the mapped Subjects
+	 */
 	public List<PMSubject> getSubjects() {
 		return subjects;
 	}
 
+	/**
+	 *
+	 * the language in which an article was published is recorded in <Language>.
+	 * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single
+	 * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value.
+	 *  Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined.
+	 *
+	 * @return The mapped Language
+	 */
 	public String getLanguage() {
 		return language;
 	}
 
+	/**
+	 *
+	 *  Set The mapped Language
+	 *
+	 * @param language the mapped Language
+	 */
 	public void setLanguage(String language) {
 		this.language = language;
 	}
+
+	/**
+	 *  This element is used to identify the type of article indexed for MEDLINE;
+	 * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of
+	 * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural).
+	 *
+	 * @return the mapped Publication Type
+	 */
+	public List<PMSubject> getPublicationTypes() {
+		return publicationTypes;
+	}
+
+	/**
+	 * <GrantID> contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service
+	 * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations.
+	 * @return the mapped grants
+	 */
+
+	public List<PMGrant> getGrants() {
+		return grants;
+	}
 }

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java

@@ -3,27 +3,57 @@ package eu.dnetlib.dhp.sx.bio.pubmed;
 
 import java.io.Serializable;
 
+/**
+ * The type Pubmed author.
+ *
+ * @author Sandro La Bruzzo
+ */
 public class PMAuthor implements Serializable {
 
 	private String lastName;
 	private String foreName;
 
+	/**
+	 * Gets last name.
+	 *
+	 * @return the last name
+	 */
 	public String getLastName() {
 		return lastName;
 	}
 
+	/**
+	 * Sets last name.
+	 *
+	 * @param lastName the last name
+	 */
 	public void setLastName(String lastName) {
 		this.lastName = lastName;
 	}
 
+	/**
+	 * Gets fore name.
+	 *
+	 * @return the fore name
+	 */
 	public String getForeName() {
 		return foreName;
 	}
 
+	/**
+	 * Sets fore name.
+	 *
+	 * @param foreName the fore name
+	 */
 	public void setForeName(String foreName) {
 		this.foreName = foreName;
 	}
 
+	/**
+	 * Gets full name.
+	 *
+	 * @return the full name
+	 */
 	public String getFullName() {
 		return String
 			.format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : "");

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java

@@ -1,41 +1,86 @@
 
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
+/**
+ * The type Pm grant.
+ *
+ * @author Sandro La Bruzzo
+ */
 public class PMGrant {
 
 	private String grantID;
 	private String agency;
 	private String country;
 
+	/**
+	 * Instantiates a new Pm grant.
+	 */
 	public PMGrant() {
 	}
 
+	/**
+	 * Instantiates a new Pm grant.
+	 *
+	 * @param grantID the grant id
+	 * @param agency  the agency
+	 * @param country the country
+	 */
 	public PMGrant(String grantID, String agency, String country) {
 		this.grantID = grantID;
 		this.agency = agency;
 		this.country = country;
 	}
 
+	/**
+	 * Gets grant id.
+	 *
+	 * @return the grant id
+	 */
 	public String getGrantID() {
 		return grantID;
 	}
 
+	/**
+	 * Sets grant id.
+	 *
+	 * @param grantID the grant id
+	 */
 	public void setGrantID(String grantID) {
 		this.grantID = grantID;
 	}
 
+	/**
+	 * Gets agency.
+	 *
+	 * @return the agency
+	 */
 	public String getAgency() {
 		return agency;
 	}
 
+	/**
+	 * Sets agency.
+	 *
+	 * @param agency the agency
+	 */
 	public void setAgency(String agency) {
 		this.agency = agency;
 	}
 
+	/**
+	 * Gets country.
+	 *
+	 * @return the country
+	 */
 	public String getCountry() {
 		return country;
 	}
 
+	/**
+	 * Sets country.
+	 *
+	 * @param country the country
+	 */
 	public void setCountry(String country) {
 		this.country = country;
 	}

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java

@@ -3,6 +3,11 @@ package eu.dnetlib.dhp.sx.bio.pubmed;
 
 import java.io.Serializable;
 
+/**
+ * The type Pm journal.
+ *
+ * @author  Sandro La Bruzzo
+ */
 public class PMJournal implements Serializable {
 
 	private String issn;
@@ -11,42 +16,92 @@ public class PMJournal implements Serializable {
 	private String date;
 	private String title;
 
+	/**
+	 * Gets issn.
+	 *
+	 * @return the issn
+	 */
 	public String getIssn() {
 		return issn;
 	}
 
+	/**
+	 * Sets issn.
+	 *
+	 * @param issn the issn
+	 */
 	public void setIssn(String issn) {
 		this.issn = issn;
 	}
 
+	/**
+	 * Gets volume.
+	 *
+	 * @return the volume
+	 */
 	public String getVolume() {
 		return volume;
 	}
 
+	/**
+	 * Sets volume.
+	 *
+	 * @param volume the volume
+	 */
 	public void setVolume(String volume) {
 		this.volume = volume;
 	}
 
+	/**
+	 * Gets issue.
+	 *
+	 * @return the issue
+	 */
 	public String getIssue() {
 		return issue;
 	}
 
+	/**
+	 * Sets issue.
+	 *
+	 * @param issue the issue
+	 */
 	public void setIssue(String issue) {
 		this.issue = issue;
 	}
 
+	/**
+	 * Gets date.
+	 *
+	 * @return the date
+	 */
 	public String getDate() {
 		return date;
 	}
 
+	/**
+	 * Sets date.
+	 *
+	 * @param date the date
+	 */
 	public void setDate(String date) {
 		this.date = date;
 	}
 
+	/**
+	 * Gets title.
+	 *
+	 * @return the title
+	 */
 	public String getTitle() {
 		return title;
 	}
 
+	/**
+	 * Sets title.
+	 *
+	 * @param title the title
+	 */
 	public void setTitle(String title) {
 		this.title = title;
 	}

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

@@ -2,6 +2,12 @@ package eu.dnetlib.dhp.sx.bio.pubmed
 
 import scala.xml.MetaData
 import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
+
+
+/**
+ *
+ * @param xml
+ */
 class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] {
 
   var currentArticle:PMArticle = generateNextArticle()

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java

@@ -1,40 +1,83 @@
 
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
+/**
+ * The type Pubmed subject.
+ */
 public class PMSubject {
 	private String value;
 	private String meshId;
 	private String registryNumber;
 
+	/**
+	 * Instantiates a new Pm subject.
+	 */
 	public PMSubject() {
 	}
 
+	/**
+	 * Instantiates a new Pm subject.
+	 *
+	 * @param value          the value
+	 * @param meshId         the mesh id
+	 * @param registryNumber the registry number
+	 */
 	public PMSubject(String value, String meshId, String registryNumber) {
 		this.value = value;
 		this.meshId = meshId;
 		this.registryNumber = registryNumber;
 	}
 
+	/**
+	 * Gets value.
+	 *
+	 * @return the value
+	 */
 	public String getValue() {
 		return value;
 	}
 
+	/**
+	 * Sets value.
+	 *
+	 * @param value the value
+	 */
 	public void setValue(String value) {
 		this.value = value;
 	}
 
+	/**
+	 * Gets mesh id.
+	 *
+	 * @return the mesh id
+	 */
 	public String getMeshId() {
 		return meshId;
 	}
 
+	/**
+	 * Sets mesh id.
+	 *
+	 * @param meshId the mesh id
+	 */
 	public void setMeshId(String meshId) {
 		this.meshId = meshId;
 	}
 
+	/**
+	 * Gets registry number.
+	 *
+	 * @return the registry number
+	 */
 	public String getRegistryNumber() {
 		return registryNumber;
 	}
 
+	/**
+	 * Sets registry number.
+	 *
+	 * @param registryNumber the registry number
+	 */
 	public void setRegistryNumber(String registryNumber) {
 		this.registryNumber = registryNumber;
 	}

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

@@ -8,6 +8,9 @@ import scala.collection.JavaConverters._
 
 import java.util.regex.Pattern
 
+/**
+ *
+ */
 object PubMedToOaf {
 
   val SUBJ_CLASS = "keywords"
@@ -15,7 +18,17 @@ object PubMedToOaf {
     "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/",
     "doi" -> "https://dx.doi.org/"
   )
+  val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
+  val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
 
+
+
+  /**
+   * Cleaning the DOI Applying regex in order to
+   * remove doi starting with URL
+   * @param doi input DOI
+   * @return cleaned DOI
+   */
   def cleanDoi(doi: String): String = {
 
     val regex = "^10.\\d{4,9}\\/[\\[\\]\\-\\<\\>._;()\\/:A-Z0-9]+$"
@@ -30,6 +43,15 @@ object PubMedToOaf {
     null
   }
 
+  /**
+   *
+   * Create an instance of class extends Result
+   * starting from OAF instanceType value
+   *
+   * @param cobjQualifier OAF instance type
+   * @param vocabularies All dnet vocabularies
+   * @return the correct instance
+   */
   def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
     val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid)
     result_typologies.getClassid match {
@@ -42,6 +64,12 @@ object PubMedToOaf {
     }
   }
 
+  /**
+   *  Mapping the Pubmedjournal info into the OAF Journale
+   *
+   * @param j the pubmedJournal
+   * @return the OAF Journal
+   */
   def mapJournal(j: PMJournal): Journal = {
     if (j == null)
       return null
@@ -49,6 +77,7 @@ object PubMedToOaf {
 
     journal.setDataInfo(dataInfo)
     journal.setName(j.getTitle)
+    journal.setConferencedate(j.getDate)
     journal.setVol(j.getVolume)
     journal.setIssnPrinted(j.getIssn)
     journal.setIss(j.getIssue)
@@ -57,25 +86,43 @@ object PubMedToOaf {
 
   }
 
-
+  /**
+   *
+   * Find vocabulary term into synonyms and term in the vocabulary
+   *
+   * @param vocabularyName the input vocabulary name
+   * @param vocabularies all the vocabularies
+   * @param term the term to find
+   *
+   * @return the cleaned term value
+   */
   def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = {
     val a = vocabularies.getSynonymAsQualifier(vocabularyName, term)
     val b = vocabularies.getTermAsQualifier(vocabularyName, term)
     if (a == null) b else a
   }
 
-  val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9")
-  val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central")
 
+  /**
+   *  Map the Pubmed Article into the OAF instance
+   *
+   *
+   * @param article the pubmed articles
+   * @param vocabularies the vocabularies
+   * @return The OAF instance if the mapping did not fail
+   */
   def convert(article: PMArticle, vocabularies: VocabularyGroup): Result = {
 
     if (article.getPublicationTypes == null)
       return null
-    val i = new Instance
+
+
+    // MAP PMID into  pid with  classid = classname = pmid
     val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
     if (pidList == null)
       return null
 
+    // MAP //ArticleId[./@IdType="doi"]   into  alternateIdentifier with classid = classname = doi
     var alternateIdentifier: StructuredProperty = null
     if (article.getDoi != null) {
       val normalizedPid = cleanDoi(article.getDoi)
@@ -83,43 +130,64 @@ object PubMedToOaf {
         alternateIdentifier = OafMapperUtils.structuredProperty(normalizedPid, PidType.doi.toString, PidType.doi.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo)
     }
 
+    // INSTANCE MAPPING
+    //--------------------------------------------------------------------------------------
+
     // If the article contains the typology Journal Article then we apply this type
     //else We have to find a terms that match the vocabulary otherwise we discard it
     val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
+    val pubmedInstance = new Instance
     if (ja.isDefined) {
       val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue)
-      i.setInstancetype(cojbCategory)
+      pubmedInstance.setInstancetype(cojbCategory)
     } else {
       val i_type = article.getPublicationTypes.asScala
         .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))
         .find(q => q != null)
       if (i_type.isDefined)
-        i.setInstancetype(i_type.get)
+        pubmedInstance.setInstancetype(i_type.get)
       else
         return null
     }
-    val result = createResult(i.getInstancetype, vocabularies)
+    val result = createResult(pubmedInstance.getInstancetype, vocabularies)
     if (result == null)
       return result
     result.setDataInfo(dataInfo)
-    i.setPid(pidList.asJava)
+    pubmedInstance.setPid(pidList.asJava)
     if (alternateIdentifier != null)
-      i.setAlternateIdentifier(List(alternateIdentifier).asJava)
+      pubmedInstance.setAlternateIdentifier(List(alternateIdentifier).asJava)
-    result.setInstance(List(i).asJava)
+    result.setInstance(List(pubmedInstance).asJava)
-    i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
+    pubmedInstance.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
+    //CREATE URL From pmid
     val urlLists: List[String] = pidList
       .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
       .filter(t => t._1.nonEmpty)
       .map(t => t._1 + t._2)
     if (urlLists != null)
-      i.setUrl(urlLists.asJava)
+      pubmedInstance.setUrl(urlLists.asJava)
-    i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
+
-    i.setCollectedfrom(collectedFrom)
+    //ASSIGN DateofAcceptance
+    pubmedInstance.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
+    //ASSIGN COLLECTEDFROM
+    pubmedInstance.setCollectedfrom(collectedFrom)
     result.setPid(pidList.asJava)
+
+    //END INSTANCE MAPPING
+    //--------------------------------------------------------------------------------------
+
+
+    // JOURNAL MAPPING
+    //--------------------------------------------------------------------------------------
     if (article.getJournal != null && result.isInstanceOf[Publication])
       result.asInstanceOf[Publication].setJournal(mapJournal(article.getJournal))
     result.setCollectedfrom(List(collectedFrom).asJava)
+    //END JOURNAL MAPPING
+    //--------------------------------------------------------------------------------------
 
+
+
+    // RESULT MAPPING
+    //--------------------------------------------------------------------------------------
     result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo))
 
     if (article.getTitle == null || article.getTitle.isEmpty)
@@ -159,6 +227,9 @@ object PubMedToOaf {
 
     result.setId(article.getPmid)
 
+
+    // END RESULT MAPPING
+    //--------------------------------------------------------------------------------------
     val id = IdentifierFactory.createIdentifier(result)
     if (article.getPmid.equalsIgnoreCase(id))
       return null

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json

@@ -0,0 +1,33 @@
+[
+  {
+    "paramName":"s",
+    "paramLongName":"sourcePath",
+    "paramDescription": "the path of the sequencial file to read",
+    "paramRequired": true
+  },
+  {
+    "paramName":"out",
+    "paramLongName":"outputPath",
+    "paramDescription": "the output path",
+    "paramRequired": true
+  },
+
+  {
+    "paramName": "ssm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "true if the spark session is managed, false otherwise",
+    "paramRequired": false
+  },
+  {
+    "paramName": "hnn",
+    "paramLongName": "hdfsNameNode",
+    "paramDescription": "the path used to store the HostedByMap",
+    "paramRequired": true
+  },
+  {
+    "paramName": "cfn",
+    "paramLongName": "classForName",
+    "paramDescription": "the path used to store the HostedByMap",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/config-default.xml

@@ -0,0 +1,30 @@
+<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>hiveMetastoreUris</name>
+        <value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
+    </property>
+    <property>
+        <name>hiveJdbcUrl</name>
+        <value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
+    </property>
+    <property>
+        <name>hiveDbName</name>
+        <value>openaire</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+</configuration>

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

@@ -0,0 +1,174 @@
+
+<workflow-app name="UnresolvedEntities" xmlns="uri:oozie:workflow:0.5">
+    <parameters>
+        <property>
+            <name>fosPath</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>
+        <property>
+            <name>sparkDriverMemory</name>
+            <description>memory for driver process</description>
+        </property>
+        <property>
+            <name>sparkExecutorMemory</name>
+            <description>memory for individual executor</description>
+        </property>
+        <property>
+            <name>sparkExecutorCores</name>
+            <description>number of cores used by single executor</description>
+        </property>
+        <property>
+            <name>oozieActionShareLibForSpark2</name>
+            <description>oozie action sharelib for spark 2.*</description>
+        </property>
+        <property>
+            <name>spark2ExtraListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+            <description>spark 2.* extra listeners classname</description>
+        </property>
+        <property>
+            <name>spark2SqlQueryExecutionListeners</name>
+            <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+            <description>spark 2.* sql query execution listeners classname</description>
+        </property>
+        <property>
+            <name>spark2YarnHistoryServerAddress</name>
+            <description>spark 2.* yarn history server address</description>
+        </property>
+        <property>
+            <name>spark2EventLogDir</name>
+            <description>spark 2.* event log dir location</description>
+        </property>
+    </parameters>
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+    <start to="prepareInfo"/>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+
+
+    <fork name="prepareInfo">
+        <path start="prepareBip"/>
+        <path start="getFOS"/>
+    </fork>
+
+    <action name="prepareBip">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the unresolved from bip finder!</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder</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>--sourcePath</arg><arg>${bipScorePath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
+        </spark>
+        <ok to="join"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="getFOS">
+        <java>
+            <main-class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSData</main-class>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--sourcePath</arg><arg>${fosPath}</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
+            <arg>--classForName</arg><arg>eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel</arg>
+        </java>
+        <ok to="prepareFos"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="prepareFos">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the unresolved from FOS!</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/input/fos</arg>
+            <arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
+
+        </spark>
+        <ok to="join"/>
+        <error to="Kill"/>
+    </action>
+
+
+
+    <join name="join" to="produceUnresolved"/>
+
+    <action name="produceUnresolved">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Saves the result produced for bip and fos by grouping results with the same id</name>
+            <class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.SparkSaveUnresolved</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--sourcePath</arg><arg>${workingDir}/prepared</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/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "sp",
+    "paramLongName": "sourcePath",
+    "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/createunresolvedentities/produce_unresolved_parameters.json

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "when true will stop SparkSession after job execution",
+    "paramRequired": false
+  },
+  {
+    "paramName": "sp",
+    "paramLongName": "sourcePath",
+    "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/opencitations/as_parameters.json

@@ -0,0 +1,25 @@
+[
+  {
+    "paramName": "ip",
+    "paramLongName": "inputPath",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "op",
+    "paramLongName": "outputPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "issm",
+    "paramLongName": "isSparkSessionManaged",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": false
+  },  {
+  "paramName": "sdr",
+  "paramLongName": "shouldDuplicateRels",
+  "paramDescription": "the hdfs name node",
+  "paramRequired": false
+}
+]

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

@@ -0,0 +1,20 @@
+[
+  {
+    "paramName": "if",
+    "paramLongName": "inputFile",
+    "paramDescription": "the zipped opencitations file",
+    "paramRequired": true
+  },
+  {
+    "paramName": "wp",
+    "paramLongName": "workingPath",
+    "paramDescription": "the working path",
+    "paramRequired": true
+  },
+  {
+    "paramName": "hnn",
+    "paramLongName": "hdfsNameNode",
+    "paramDescription": "the hdfs name node",
+    "paramRequired": true
+  }
+]

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/config-default.xml

@@ -0,0 +1,58 @@
+<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>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>spark2ExtraListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorAppListener</value>
+    </property>
+    <property>
+        <name>spark2SqlQueryExecutionListeners</name>
+        <value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
+    </property>
+    <property>
+        <name>oozie.launcher.mapreduce.user.classpath.first</name>
+        <value>true</value>
+    </property>
+    <property>
+        <name>sparkExecutorNumber</name>
+        <value>4</value>
+    </property>
+    <property>
+        <name>spark2EventLogDir</name>
+        <value>/user/spark/spark2ApplicationHistory</value>
+    </property>
+    <property>
+        <name>sparkDriverMemory</name>
+        <value>15G</value>
+    </property>
+    <property>
+        <name>sparkExecutorMemory</name>
+        <value>6G</value>
+    </property>
+    <property>
+        <name>sparkExecutorCores</name>
+        <value>1</value>
+    </property>
+</configuration>

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/download.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+for file in $(echo $1 | tr ";" "\n"); do curl -L $(echo $file | cut -d '@' -f 1 ) | hdfs dfs -put - $2/$(echo $file | cut -d '@' -f 2)  ; done;

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

@@ -0,0 +1,91 @@
+<workflow-app name="OpenCitations Integration" xmlns="uri:oozie:workflow:0.5">
+
+    <global>
+        <job-tracker>${jobTracker}</job-tracker>
+        <name-node>${nameNode}</name-node>
+        <configuration>
+            <property>
+                <name>mapreduce.job.queuename</name>
+                <value>${queueName}</value>
+            </property>
+            <property>
+                <name>oozie.launcher.mapred.job.queue.name</name>
+                <value>${oozieLauncherQueueName}</value>
+            </property>
+            <property>
+                <name>oozie.action.sharelib.for.spark</name>
+                <value>${oozieActionShareLibForSpark2}</value>
+            </property>
+
+        </configuration>
+    </global>
+
+    <start to="resume_from"/>
+
+    <decision name="resume_from">
+        <switch>
+            <case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
+            <case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
+            <default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
+        </switch>
+    </decision>
+
+    <kill name="Kill">
+        <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
+    </kill>
+    <action name="download">
+        <shell xmlns="uri:oozie:shell-action:0.2">
+            <job-tracker>${jobTracker}</job-tracker>
+            <name-node>${nameNode}</name-node>
+            <configuration>
+                <property>
+                    <name>mapred.job.queue.name</name>
+                    <value>${queueName}</value>
+                </property>
+            </configuration>
+            <exec>download.sh</exec>
+            <argument>${filelist}</argument>
+            <argument>${workingPath}/Original</argument>
+            <env-var>HADOOP_USER_NAME=${wf:user()}</env-var>
+            <file>download.sh</file>
+            <capture-output/>
+        </shell>
+        <ok to="extract"/>
+        <error to="Kill"/>
+    </action>
+    <action name="extract">
+        <java>
+            <main-class>eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs</main-class>
+            <arg>--hdfsNameNode</arg><arg>${nameNode}</arg>
+            <arg>--inputFile</arg><arg>${inputFile}</arg>
+            <arg>--workingPath</arg><arg>${workingPath}</arg>
+        </java>
+        <ok to="create_actionset"/>
+        <error to="Kill"/>
+    </action>
+
+    <action name="create_actionset">
+        <spark xmlns="uri:oozie:spark-action:0.2">
+            <master>yarn</master>
+            <mode>cluster</mode>
+            <name>Produces the AS for OC</name>
+            <class>eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob</class>
+            <jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
+            </spark-opts>
+            <arg>--inputPath</arg><arg>${workingPath}/COCI</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/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/opencitations_parameters.json

@@ -0,0 +1,8 @@
+[
+  {"paramName":"n",   "paramLongName":"hdfsServerUri",	"paramDescription": "the server uri",   "paramRequired": true},
+  {"paramName":"w",   "paramLongName":"workingPath",	"paramDescription": "the default work path",	"paramRequired": true},
+  {"paramName":"f",   "paramLongName":"opencitationFile",	"paramDescription": "the name of the file",	"paramRequired": true},
+  {"paramName":"issm",   "paramLongName":"isSparkSessionManaged",	"paramDescription": "the name of the activities orcid file",	"paramRequired": false},
+  {"paramName":"o",   "paramLongName":"outputPath",	"paramDescription": "the name of the activities orcid file",	"paramRequired": true}
+
+]

dhp-workflows/dhp-aggregation/src/site/markdown/index.md

@@ -0,0 +1,9 @@
+##DHP-Aggregation
+
+This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
+
+Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
+the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
+of each MDStore.
+
+It defines [mappings](mappings.md) for transformation of different datasource (See mapping section).

dhp-workflows/dhp-aggregation/src/site/markdown/introduction.md

@@ -0,0 +1,7 @@
+##DHP-Aggregation
+
+This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records.
+
+Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure
+the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping
+of each MDStore.

dhp-workflows/dhp-aggregation/src/site/markdown/mappings.md

@@ -0,0 +1,18 @@
+DHP Aggregation
+===============
+
+DHP-Aggregations contains different mappings from original data format into OAF Data Format, 
+which converge in the graph in different ways:
+
+- Via Action Manager
+- Direct in the MdStore on Hadoop
+
+Below the list of the implemented mapping
+
+
+Mappings
+=======
+
+1. [PubMed](pubmed.md)
+2. [Datacite](datacite.md)
+

dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md

@@ -0,0 +1,62 @@
+#Pubmed Mapping
+This section describes the mapping implemented for [MEDLINE/PubMed](https://pubmed.ncbi.nlm.nih.gov/).
+
+Collection
+---------
+The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with 
+the following [shcema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html) 
+
+
+Parsing
+-------
+The resposible class of parsing is [PMParser](./scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates 
+an intermediate mapping of PubMed Article defined [here](/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html)
+
+
+Mapping
+-------
+
+The table below describes the mapping from the XML Native to the OAF mapping
+
+
+
+
+
+| Xpath Source | Oaf Field  | Notes       |
+| ----------- | ----------- | ----------- |
+| //PMID      | pid         | classid = classname = pmid
+|  | **Instance Mapping** |      |
+|//PublicationType | InstanceType  | If the article contains the typology **Journal Article** then we apply this type else We have to find a terms that match the vocabulary otherwise we discard it
+|//PMID | instance/PID | Map the pmid also in the pid in the instance |
+| //ArticleId[./@IdType="doi"   | instance/alternateIdentifier  |classid = classname = doi
+|//PMID | instance/URL | prepend to the PMId the base url https://pubmed.ncbi.nlm.nih.gov/
+| //PubmedPubDate | instance/Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it
+|  FOR ALL INSTANCE | CollectedFrom | datasourceName: *Europe PubMed Central* DatasourceId:   
+|  | **Journal Mapping** |      |
+|//Journal/PubDate| Journal/Conferencedate | map the date of the Journal
+|//Journal/Title| Journal/Name | |
+|//Journal/Volume| Journal/Vol | |
+|//Journal/ISSN| Journal/issPrinted | |
+|//Journal/Issue| Journal/Iss | |
+|  | **Publication Mapping** |      |
+| //PubmedPubDate | Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it
+| //Title | title | with qualifier ModelConstants.MAIN_TITLE_QUALIFIER
+| //AbstractText | Description ||
+|//Language| Language| cleaning vocabulary -> dnet:languages
+|//DescriptorName| Subject | classId, className = keyword
+|  | **Author Mapping** |      |
+|//Author/LastName| author.Surname| |
+|//Author/ForeName| author.Forename| |
+|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist |
+|FOR ALL AUTHOR | author.rank| sequential number starting from 1|
+
+
+
+
+
+
+
+
+
+
+

dhp-workflows/dhp-aggregation/src/site/site.xml

@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="ISO-8859-1"?>
+<project xmlns="http://maven.apache.org/DECORATION/1.8.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xsi:schemaLocation="http://maven.apache.org/DECORATION/1.8.0 https://maven.apache.org/xsd/decoration-1.8.0.xsd"
+         name="DHP-Aggregation">
+    <skin>
+        <groupId>org.apache.maven.skins</groupId>
+        <artifactId>maven-fluido-skin</artifactId>
+        <version>1.8</version>
+    </skin>
+    <poweredBy>
+        <logo name="OpenAIRE Research Graph" href="https://graph.openaire.eu/"
+              img="https://graph.openaire.eu/assets/common-assets/logo-large-graph.png"/>
+    </poweredBy>
+    <body>
+        <links>
+            <item name="Code" href="https://code-repo.d4science.org/" />
+        </links>
+        <menu name="Documentation">
+            <item name="Mappings" href="mappings.html" collapse="true">
+                <item name="Pubmed" href="pubmed.html"/>
+                <item name="Datacite" href="datacite.html"/>
+            </item>
+            <item name="Release Notes" href="release-notes.html" />
+            <item name="General Information" href="about.html"/>
+
+            <item name="JavaDoc" href="apidocs/" />
+            <item name="ScalaDoc" href="scaladocs/" />
+
+        </menu>
+        <menu ref="reports"/>
+    </body>
+</project>

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java

@@ -0,0 +1,250 @@
+
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+import java.io.BufferedReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+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.actionmanager.createunresolvedentities.model.FOSDataModel;
+import eu.dnetlib.dhp.common.collection.CollectorException;
+import eu.dnetlib.dhp.schema.oaf.Result;
+
+public class PrepareTest {
+
+	private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
+
+	private static Path workingDir;
+	private static SparkSession spark;
+	private static LocalFileSystem fs;
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
+
+		fs = FileSystem.getLocal(new Configuration());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void bipPrepareTest() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
+			.getPath();
+
+		PrepareBipFinder
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+					"--outputPath", workingDir.toString() + "/work"
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/work/bip")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+
+		Assertions.assertEquals(86, tmp.count());
+
+		String doi1 = "unresolved::10.0000/096020199389707::doi";
+
+		Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
+		Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size());
+		Assertions
+			.assertEquals(
+				"6.34596412687e-09", tmp
+					.filter(r -> r.getId().equals(doi1))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(sl -> sl.getId().equals("influence"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"0.641151896994", tmp
+					.filter(r -> r.getId().equals(doi1))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(sl -> sl.getId().equals("popularity_alt"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+		Assertions
+			.assertEquals(
+				"2.33375102921e-09", tmp
+					.filter(r -> r.getId().equals(doi1))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.stream()
+					.filter(sl -> sl.getId().equals("popularity"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+	}
+
+	@Test
+	void getFOSFileTest() throws IOException, ClassNotFoundException {
+
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/h2020_fos_sbs.csv")
+			.getPath();
+		final String outputPath = workingDir.toString() + "/fos.json";
+
+		new GetFOSData()
+			.doRewrite(
+				sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel",
+				'\t', fs);
+
+		BufferedReader in = new BufferedReader(
+			new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
+
+		String line;
+		int count = 0;
+		while ((line = in.readLine()) != null) {
+			FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
+
+			System.out.println(new ObjectMapper().writeValueAsString(fos));
+			count += 1;
+		}
+
+		assertEquals(38, count);
+
+	}
+
+	@Test
+	void fosPrepareTest() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
+			.getPath();
+
+		PrepareFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", sourcePath,
+
+					"-outputPath", workingDir.toString() + "/work"
+
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/work/fos")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+
+		String doi1 = "unresolved::10.3390/s18072310::doi";
+
+		assertEquals(50, tmp.count());
+		assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
+		assertTrue(
+			tmp
+				.filter(r -> r.getId().equals(doi1))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("engineering and technology"));
+
+		assertTrue(
+			tmp
+				.filter(r -> r.getId().equals(doi1))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("nano-technology"));
+		assertTrue(
+			tmp
+				.filter(r -> r.getId().equals(doi1))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("nanoscience & nanotechnology"));
+
+		String doi = "unresolved::10.1111/1365-2656.12831::doi";
+		assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
+		assertTrue(
+			tmp
+				.filter(r -> r.getId().equals(doi))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("psychology and cognitive sciences"));
+
+		assertTrue(
+			tmp
+				.filter(r -> r.getId().equals(doi))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("social sciences"));
+		assertFalse(
+			tmp
+				.filter(r -> r.getId().equals(doi))
+				.flatMap(r -> r.getSubject().iterator())
+				.map(sbj -> sbj.getValue())
+				.collect()
+				.contains("NULL"));
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java

@@ -0,0 +1,234 @@
+
+package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.hadoop.conf.Configuration;
+import org.apache.hadoop.fs.FileSystem;
+import org.apache.hadoop.fs.LocalFileSystem;
+import org.apache.spark.SparkConf;
+import org.apache.spark.api.java.JavaRDD;
+import org.apache.spark.api.java.JavaSparkContext;
+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.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.*;
+
+public class ProduceTest {
+	private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
+
+	private static Path workingDir;
+	private static SparkSession spark;
+	private static LocalFileSystem fs;
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+	private static final String ID_PREFIX = "50|doi_________";
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files.createTempDirectory(ProduceTest.class.getSimpleName());
+
+		fs = FileSystem.getLocal(new Configuration());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(ProduceTest.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(ProduceTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void produceTest() throws Exception {
+
+		final String bipPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
+			.getPath();
+
+		PrepareBipFinder
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", bipPath,
+					"--outputPath", workingDir.toString() + "/work"
+
+				});
+		final String fosPath = getClass()
+			.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json")
+			.getPath();
+
+		PrepareFOSSparkJob
+			.main(
+				new String[] {
+					"--isSparkSessionManaged", Boolean.FALSE.toString(),
+					"--sourcePath", fosPath,
+					"-outputPath", workingDir.toString() + "/work"
+				});
+
+		SparkSaveUnresolved.main(new String[] {
+			"--isSparkSessionManaged", Boolean.FALSE.toString(),
+			"--sourcePath", workingDir.toString() + "/work",
+
+			"-outputPath", workingDir.toString() + "/unresolved"
+
+		});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Result> tmp = sc
+			.textFile(workingDir.toString() + "/unresolved")
+			.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
+
+		Assertions.assertEquals(135, tmp.count());
+
+		Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")).count());
+
+		Assertions
+			.assertEquals(
+				3, tmp
+					.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
+					.collect()
+					.get(0)
+					.getSubject()
+					.size());
+
+		Assertions
+			.assertEquals(
+				3, tmp
+					.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
+					.collect()
+					.get(0)
+					.getMeasures()
+					.size());
+
+		List<StructuredProperty> sbjs = tmp
+			.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
+			.flatMap(row -> row.getSubject().iterator())
+			.collect();
+
+		sbjs.forEach(sbj -> Assertions.assertEquals("FOS", sbj.getQualifier().getClassid()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals(
+						"Fields of Science and Technology classification", sbj.getQualifier().getClassname()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
+
+		sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
+		sbjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
+		sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
+		sbjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
+		sbjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
+		sbjs
+			.forEach(
+				sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals(
+						ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
+		sbjs
+			.forEach(
+				sbj -> Assertions
+					.assertEquals(
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
+						sbj.getDataInfo().getProvenanceaction().getSchemename()));
+
+		sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("engineering and technology"));
+		sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nano-technology"));
+		sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nanoscience & nanotechnology"));
+
+		List<Measure> measures = tmp
+			.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi"))
+			.flatMap(row -> row.getMeasures().iterator())
+			.collect();
+		Assertions
+			.assertEquals(
+				"7.5597134689e-09", measures
+					.stream()
+					.filter(mes -> mes.getId().equals("influence"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"4.903880192", measures
+					.stream()
+					.filter(mes -> mes.getId().equals("popularity_alt"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				"1.17977512835e-08", measures
+					.stream()
+					.filter(mes -> mes.getId().equals("popularity"))
+					.collect(Collectors.toList())
+					.get(0)
+					.getUnit()
+					.get(0)
+					.getValue());
+
+		Assertions
+			.assertEquals(
+				49, tmp
+					.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
+					.filter(row -> row.getSubject() != null)
+					.count());
+
+		Assertions
+			.assertEquals(
+				85,
+				tmp
+					.filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi"))
+					.filter(r -> r.getMeasures() != null)
+					.count());
+
+	}
+
+}

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java

@@ -0,0 +1,335 @@
+
+package eu.dnetlib.dhp.actionmanager.opencitations;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+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.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Publication;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
+
+public class CreateOpenCitationsASTest {
+
+	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
+
+	private static SparkSession spark;
+
+	private static Path workingDir;
+	private static final Logger log = LoggerFactory
+		.getLogger(CreateOpenCitationsASTest.class);
+
+	@BeforeAll
+	public static void beforeAll() throws IOException {
+		workingDir = Files
+			.createTempDirectory(CreateOpenCitationsASTest.class.getSimpleName());
+		log.info("using work dir {}", workingDir);
+
+		SparkConf conf = new SparkConf();
+		conf.setAppName(CreateOpenCitationsASTest.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(CreateOpenCitationsASTest.class.getSimpleName())
+			.config(conf)
+			.getOrCreate();
+	}
+
+	@AfterAll
+	public static void afterAll() throws IOException {
+		FileUtils.deleteDirectory(workingDir.toFile());
+		spark.stop();
+	}
+
+	@Test
+	void testNumberofRelations() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-shouldDuplicateRels",
+					Boolean.TRUE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		assertEquals(60, tmp.count());
+
+		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+
+	}
+
+	@Test
+	void testNumberofRelations2() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		assertEquals(44, tmp.count());
+
+		// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
+
+	}
+
+	@Test
+	void testRelationsCollectedFrom() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
+			assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
+		});
+
+	}
+
+	@Test
+	void testRelationsDataInfo() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals(false, r.getDataInfo().getInferred());
+			assertEquals(false, r.getDataInfo().getDeletedbyinference());
+			assertEquals("0.91", r.getDataInfo().getTrust());
+			assertEquals(
+				CreateActionSetSparkJob.OPENCITATIONS_CLASSID, r.getDataInfo().getProvenanceaction().getClassid());
+			assertEquals(
+				CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, r.getDataInfo().getProvenanceaction().getClassname());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
+			assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
+		});
+
+	}
+
+	@Test
+	void testRelationsSemantics() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("citation", r.getSubRelType());
+			assertEquals("resultResult", r.getRelType());
+		});
+		assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
+		assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
+
+	}
+
+	@Test
+	void testRelationsSourceTargetPrefix() throws Exception {
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		tmp.foreach(r -> {
+			assertEquals("50|doi_________::", r.getSource().substring(0, 17));
+			assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
+		});
+
+	}
+
+	@Test
+	void testRelationsSourceTargetCouple() throws Exception {
+		final String doi1 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
+		final String doi2 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
+		final String doi3 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
+		final String doi4 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
+		final String doi5 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
+		final String doi6 = "50|doi_________::"
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
+
+		String inputPath = getClass()
+			.getResource(
+				"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
+			.getPath();
+
+		CreateActionSetSparkJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged",
+					Boolean.FALSE.toString(),
+					"-inputPath",
+					inputPath,
+					"-outputPath",
+					workingDir.toString() + "/actionSet"
+				});
+
+		final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
+
+		JavaRDD<Relation> tmp = sc
+			.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
+			.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
+			.map(aa -> ((Relation) aa.getPayload()));
+
+		JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
+
+		assertEquals(10, check.count());
+
+		check.foreach(r -> {
+			if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
+				r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
+				assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
+				assertEquals(doi1, r.getTarget());
+			}
+		});
+
+		assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
+		check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
+
+	}
+}

dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json

@@ -0,0 +1,86 @@
+{"10.3390/s18072310": [{"id": "influence", "unit": [{"value": "7.5597134689e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "4.903880192", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.17977512835e-08", "key": "score"}]}]}
+{"10.0000/096020199389707": [{"id": "influence", "unit": [{"value": "6.34596412687e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.641151896994", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "2.33375102921e-09", "key": "score"}]}]}
+{"10.00000/jpmc.2017.106": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "5.39172290649e-09", "key": "score"}]}]}
+{"10.0000/9781845416881": [{"id": "influence", "unit": [{"value": "5.96492048955e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "1.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.12641925838e-08", "key": "score"}]}]}
+{"10.0000/anziamj.v0i0.266": [{"id": "influence", "unit": [{"value": "5.91019644836e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.0", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.76260934675e-10", "key": "score"}]}]}
+{"10.0000/anziamj.v48i0.79": [{"id": "influence", "unit": [{"value": "6.93311506443e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.002176782336", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "1.7668105708e-09", "key": "score"}]}]}
+{"10.0000/anziamj.v50i0.1472": [{"id": "influence", "unit": [{"value": "6.26777280882e-09", "key": "score"}]}, {"id": "popularity_alt", "unit": [{"value": "0.406656", "key": "score"}]}, {"id": "popularity", "unit": [{"value": "3.39745193285e-09", "key": "score"}]}]}
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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/h2020_fos_sbs.csv

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input1

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2

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dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3

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dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml

@@ -89,7 +89,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
             <arg>--o</arg><arg>${graphOutputPath}</arg>
@@ -114,7 +114,7 @@
                 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
                 --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
                 --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
-                --conf spark.sql.shuffle.partitions=7680
+                --conf spark.sql.shuffle.partitions=15000
             </spark-opts>
             <arg>--graphInputPath</arg><arg>${graphBasePath}</arg>
             <arg>--outputPath</arg><arg>${workingPath}/grouped_entities</arg>

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java

@@ -25,6 +25,24 @@ public class PropagationConstant {
 	private PropagationConstant() {
 	}
 
+	public static final String DOI = "doi";
+	public static final String REF_DOI = ".refs";
+
+	public static final String UPDATE_DATA_INFO_TYPE = "update";
+	public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos";
+	public static final String UPDATE_CLASS_NAME = "Inferred  by OpenAIRE";
+	public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip";
+
+	public static final String FOS_CLASS_ID = "FOS";
+	public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification";
+
+	public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations";
+	public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations";
+	public static final String ID_PREFIX = "50|doi_________::";
+	public static final String OC_TRUST = "0.91";
+
+	public final static String NULL = "NULL";
+
 	public static final String INSTITUTIONAL_REPO_TYPE = "pubsrepository::institutional";
 
 	public static final String PROPAGATION_DATA_INFO_TYPE = "propagation";
@@ -75,10 +93,25 @@ public class PropagationConstant {
 
 	public static DataInfo getDataInfo(
 		String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema) {
+
+		return getDataInfo(inference_provenance, inference_class_id, inference_class_name, qualifierSchema, "0.85");
+	}
+
+	public static DataInfo getDataInfo(
+		String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
+		String trust) {
+		return getDataInfo(
+			inference_provenance, inference_class_id, inference_class_name, qualifierSchema, trust, true);
+
+	}
+
+	public static DataInfo getDataInfo(
+		String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema,
+		String trust, boolean inferred) {
 		DataInfo di = new DataInfo();
-		di.setInferred(true);
+		di.setInferred(inferred);
 		di.setDeletedbyinference(false);
-		di.setTrust("0.85");
+		di.setTrust(trust);
 		di.setInferenceprovenance(inference_provenance);
 		di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name, qualifierSchema));
 		return di;

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala

@@ -19,7 +19,7 @@ object SparkResolveEntities {
   def main(args: Array[String]): Unit = {
     val log: Logger = LoggerFactory.getLogger(getClass)
     val conf: SparkConf = new SparkConf()
-    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/resolution/resolve_params.json")))
+    val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json")))
     parser.parseArgument(args)
     val spark: SparkSession =
       SparkSession

dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml

@@ -1,4 +1,4 @@
-<workflow-app name="Resolve Relation" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="Resolve relation and entities" xmlns="uri:oozie:workflow:0.5">
     <parameters>
         <property>
             <name>graphBasePath</name>
@@ -37,7 +37,7 @@
             <arg>--graphBasePath</arg><arg>${graphBasePath}</arg>
             <arg>--workingPath</arg><arg>${workingDir}</arg>
         </spark>
-        <ok to="End"/>
+        <ok to="ResolveEntities"/>
         <error to="Kill"/>
     </action>
 
@@ -45,7 +45,7 @@
         <spark xmlns="uri:oozie:spark-action:0.2">
             <master>yarn</master>
             <mode>cluster</mode>
-            <name>Resolve Relations in raw graph</name>
+            <name>Resolve Entities in raw graph</name>
             <class>eu.dnetlib.dhp.oa.graph.resolution.SparkResolveEntities</class>
             <jar>dhp-graph-mapper-${projectVersion}.jar</jar>
             <spark-opts>
@@ -67,6 +67,6 @@
         <error to="Kill"/>
     </action>
 
-
     <end name="End"/>
+
 </workflow-app>

pom.xml

@@ -550,7 +550,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-site-plugin</artifactId>
-					<version>3.7.1</version>
+					<version>3.9.1</version>
 				</plugin>
 
 				<plugin>