forked from D-Net/dnet-hadoop
[personEntity] added relations with projects extracting the info from the database
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ce4ee1189f
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09a2c93fc7
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@ -2,13 +2,18 @@
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package eu.dnetlib.dhp.actionmanager.personentity;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static org.apache.spark.sql.functions.*;
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import java.io.BufferedWriter;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.*;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.common.DbClient;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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@ -22,6 +27,7 @@ import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.spark_project.jetty.util.StringUtil;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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@ -43,9 +49,14 @@ import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import scala.Tuple2;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataOutputStream;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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public class ExtractPerson implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
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private static final String QUERY = "SELECT * FROM project_person WHERE pid_type = 'ORCID'";
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String OPENAIRE_PREFIX = "openaire____";
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private static final String SEPARATOR = "::";
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@ -62,6 +73,12 @@ public class ExtractPerson implements Serializable {
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private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
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public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
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public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
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public static final String OPENAIRE_DATASOURCE_ID = "10|infrastruct_::f66f1bd369679b5b077dcdf006089556";
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public static final String OPENAIRE_DATASOURCE_NAME = "OpenAIRE";
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public static List<KeyValue> collectedfromOpenAIRE = OafMapperUtils
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.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
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public static final DataInfo DATAINFO = OafMapperUtils
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.dataInfo(
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@ -106,19 +123,130 @@ public class ExtractPerson implements Serializable {
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final String workingDir = parser.get("workingDir");
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log.info("workingDir {}", workingDir);
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final String dbUrl = parser.get("postgresUrl");
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final String dbUser = parser.get("postgresUser");
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final String dbPassword = parser.get("postgresPassword");
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final String hdfsNameNode = parser.get("hdfsNameNode");
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration());
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createActionSet(spark, inputPath, outputPath, workingDir);
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extractInfoForActionSetFromORCID(spark, inputPath, workingDir);
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extractInfoForActionSetFromProjects(spark, inputPath, workingDir, dbUrl, dbUser, dbPassword, workingDir + "/project", hdfsNameNode);
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createActionSet(spark, outputPath, workingDir);
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});
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}
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private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
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private static void extractInfoForActionSetFromProjects(SparkSession spark, String inputPath, String workingDir,
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String dbUrl, String dbUser, String dbPassword, String hdfsPath, String hdfsNameNode) throws IOException {
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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Path hdfsWritePath = new Path(hdfsPath);
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FSDataOutputStream fos = fileSystem.create(hdfsWritePath);
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try (DbClient dbClient = new DbClient(dbUrl, dbUser, dbPassword)) {
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try (BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fos, StandardCharsets.UTF_8))) {
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dbClient.processResults(QUERY, rs -> writeRelation(getRelationWithProject(rs), writer));
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}
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} catch (IOException e) {
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e.printStackTrace();
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}
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}
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public static Relation getRelationWithProject(ResultSet rs) {
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try {
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return getProjectRelation(rs.getString("project"), rs.getString("pid"),
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rs.getString("role"));
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} catch (final SQLException e) {
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throw new RuntimeException(e);
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}
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}
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private static Relation getProjectRelation(String project, String orcid, String role) {
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String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
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String target = project.substring(0,14)
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+ IdentifierFactory.md5(project.substring(15));
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List<KeyValue> properties = new ArrayList<>();
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Relation relation = OafMapperUtils
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.getRelation(
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source, target, ModelConstants.PROJECT_PERSON_RELTYPE, ModelConstants.PROJECT_PERSON_SUBRELTYPE,
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ModelConstants.PROJECT_PERSON_PARTICIPATES,
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collectedfromOpenAIRE,
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DATAINFO,
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null);
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relation.setValidated(true);
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if (StringUtil.isNotBlank(role)) {
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KeyValue kv = new KeyValue();
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kv.setKey("role");
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kv.setValue(role);
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properties.add(kv);
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}
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if (!properties.isEmpty())
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relation.setProperties(properties);
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return relation;
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}
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protected static void writeRelation(final Relation relation, BufferedWriter writer) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(relation));
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writer.newLine();
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} catch (final IOException e) {
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throw new RuntimeException(e);
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}
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}
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private static void createActionSet(SparkSession spark,String outputPath, String workingDir) {
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Dataset<Person> people;
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people = spark
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.read()
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.textFile(workingDir + "/people")
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.map(
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(MapFunction<String, Person>) value -> OBJECT_MAPPER
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.readValue(value, Person.class),
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Encoders.bean(Person.class));
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people
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.union(
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getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
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.union(
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getRelations(spark, workingDir + "/coauthorship")
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.toJavaRDD()
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.map(r -> new AtomicAction(r.getClass(), r)))
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.union(
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getRelations(spark, workingDir + "/affiliation")
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.toJavaRDD()
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.map(r -> new AtomicAction(r.getClass(), r)))
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.union(
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getRelations(spark, workingDir + "/project")
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.toJavaRDD()
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.map(r -> new AtomicAction(r.getClass(), r)))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
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}
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private static void extractInfoForActionSetFromORCID(SparkSession spark, String inputPath, String workingDir) {
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Dataset<Author> authors = spark
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.read()
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.parquet(inputPath + "Authors")
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@ -149,7 +277,7 @@ public class ExtractPerson implements Serializable {
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.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
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//Mapping all the orcid profiles even if the profile has no visible works
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Dataset<Person> people;
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authors.map((MapFunction<Author, Person>) op -> {
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Person person = new Person();
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person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
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@ -257,34 +385,6 @@ public class ExtractPerson implements Serializable {
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(workingDir + "/affiliation");
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people = spark
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.read()
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.textFile(workingDir + "/people")
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.map(
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(MapFunction<String, Person>) value -> OBJECT_MAPPER
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.readValue(value, Person.class),
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Encoders.bean(Person.class));
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people.show(false);
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people
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.union(
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getRelations(spark, workingDir + "/authorship").toJavaRDD().map(r -> new AtomicAction(r.getClass(), r)))
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.union(
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getRelations(spark, workingDir + "/coauthorship")
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.toJavaRDD()
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.map(r -> new AtomicAction(r.getClass(), r)))
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.union(
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getRelations(spark, workingDir + "/affiliation")
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.toJavaRDD()
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.map(r -> new AtomicAction(r.getClass(), r)))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
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}
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private static Dataset<Relation> getRelations(SparkSession spark, String path) {
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