[EOSC context TAG] first implementation of the logic to tag results imported from datasources registered in the EOSC
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package eu.dnetlib.dhp.bulktag.eosc;
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import java.io.Serializable;
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/**
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* @author miriam.baglioni
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* @Date 21/07/22
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*/
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public class DatasourceMaster implements Serializable {
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private String datasource;
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private String master;
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public String getDatasource() {
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return datasource;
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}
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public void setDatasource(String datasource) {
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this.datasource = datasource;
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}
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public String getMaster() {
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return master;
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}
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public void setMaster(String master) {
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this.master = master;
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}
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}
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package eu.dnetlib.dhp.bulktag.eosc;
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/**
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* @author miriam.baglioni
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* @Date 21/07/22
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*/
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.DbClient;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.common.RelationInverse;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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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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import java.io.BufferedWriter;
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import java.io.Closeable;
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import java.io.IOException;
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import java.io.OutputStreamWriter;
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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.Arrays;
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import java.util.List;
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import java.util.function.Consumer;
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import java.util.function.Function;
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public class ReadMasterDatasourceFromDB implements Closeable {
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private final DbClient dbClient;
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private static final Log log = LogFactory.getLog(ReadMasterDatasourceFromDB.class);
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private final BufferedWriter writer;
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private final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String QUERY = "SELECT dso.id datasource, d.id master FROM " +
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"(SELECT id FROM dsm_services WHERE id like 'eosc%') dso " +
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"FULL JOIN " +
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"(SELECT id, duplicate FROM dsm_dedup_services WHERE duplicate like 'eosc%')d " +
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"ON dso.id = d.duplicate";
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public static void main(final String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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ReadMasterDatasourceFromDB.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/blacklist/blacklist_parameters.json")));
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parser.parseArgument(args);
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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 hdfsPath = parser.get("hdfsPath") + "/datasourceMasters";
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final String hdfsNameNode = parser.get("hdfsNameNode");
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try (final ReadMasterDatasourceFromDB rmd = new ReadMasterDatasourceFromDB(hdfsPath, hdfsNameNode, dbUrl, dbUser,
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dbPassword)) {
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log.info("Processing datasources...");
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rmd.execute(QUERY, rmd::datasourceMasterMap);
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}
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}
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public void execute(final String sql, final Function<ResultSet, DatasourceMaster> producer) {
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dbClient.processResults(sql, rs -> writeMap(producer.apply(rs)));
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}
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public DatasourceMaster datasourceMasterMap(ResultSet rs) {
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try {
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DatasourceMaster dm = new DatasourceMaster();
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String datasource = rs.getString("datasource");
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dm.setDatasource(datasource);
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String master = rs.getString("master");
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if (StringUtils.isNotBlank(master))
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dm.setMaster(OafMapperUtils.createOpenaireId(10, master, true));
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else
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dm.setMaster(OafMapperUtils.createOpenaireId(10, datasource, true));
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return dm;
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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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@Override
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public void close() throws IOException {
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dbClient.close();
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writer.close();
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}
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public ReadMasterDatasourceFromDB(
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final String hdfsPath, String hdfsNameNode, final String dbUrl, final String dbUser, final String dbPassword)
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throws IOException {
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this.dbClient = new DbClient(dbUrl, dbUser, dbPassword);
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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 fsDataOutputStream = null;
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if (fileSystem.exists(hdfsWritePath)) {
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fsDataOutputStream = fileSystem.append(hdfsWritePath);
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} else {
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fsDataOutputStream = fileSystem.create(hdfsWritePath);
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}
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this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8));
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}
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protected void writeMap(final DatasourceMaster dm) {
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try {
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writer.write(OBJECT_MAPPER.writeValueAsString(dm));
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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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}
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@ -0,0 +1,145 @@
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package eu.dnetlib.dhp.bulktag.eosc;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bulktag.SparkBulkTagJob;
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import eu.dnetlib.dhp.bulktag.community.*;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.Context;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import javax.print.attribute.DocAttributeSet;
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import java.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
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import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
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import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.TAGGING_TRUST;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.DNET_PROVENANCE_ACTIONS;
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/**
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* @author miriam.baglioni
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* @Date 21/07/22
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*/
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public class SparkEoscBulkTag implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkEoscBulkTag.class);
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public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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SparkEoscBulkTag.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/bulktag/input_bulkTag_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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String datasourceMapPath = parser.get("datasourceMapPath");
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log.info("datasourceMapPath: {}", datasourceMapPath);
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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CommunityConfiguration cc;
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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execBulkTag(spark, inputPath, outputPath, datasourceMapPath, resultClazz);
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});
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}
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private static <R extends Result> void execBulkTag(
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SparkSession spark,
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String inputPath,
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String outputPath,
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String datasourceMapPath,
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Class<R> resultClazz) {
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final List<String> hostedByList = Arrays.asList(readPath(spark, datasourceMapPath, DatasourceMaster.class)
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.map((MapFunction<DatasourceMaster, String>) dm -> dm.getMaster(), Encoders.STRING())
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.collect());
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readPath(spark, inputPath, resultClazz)
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.map(patchResult(), Encoders.bean(resultClazz))
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.filter(Objects::nonNull)
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.map(
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(MapFunction<R, R>) value -> enrich(value, hostedByList),
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Encoders.bean(resultClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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private static <R extends Result> R enrich(R value, List<String> hostedByList) {
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if(value.getInstance().stream().anyMatch(i -> hostedByList.contains(i.getHostedby().getKey())) ||
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(value.getEoscifguidelines() != null && value.getEoscifguidelines().size() > 0)){
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Context context = new Context();
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context.setId("eosc");
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OafMapperUtils.dataInfo(false, BULKTAG_DATA_INFO_TYPE,true,false,
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OafMapperUtils.qualifier(CLASS_ID_DATASOURCE, CLASS_NAME_BULKTAG_DATASOURCE,
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DNET_PROVENANCE_ACTIONS, DNET_PROVENANCE_ACTIONS), TAGGING_TRUST);
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value.getContext().add(context);
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}
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return value;
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}
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public static <R> Dataset<R> readPath(
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SparkSession spark, String inputPath, Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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// TODO remove this hack as soon as the values fixed by this method will be provided as NON null
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private static <R extends Result> MapFunction<R, R> patchResult() {
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return r -> {
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if (r.getDataInfo().getDeletedbyinference() == null) {
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r.getDataInfo().setDeletedbyinference(false);
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}
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if (r.getContext() == null) {
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r.setContext(new ArrayList<>());
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}
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return r;
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};
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}
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}
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