345 lines
12 KiB
Java
345 lines
12 KiB
Java
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package eu.dnetlib.dhp.bulktag;
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import static eu.dnetlib.dhp.PropagationConstant.removeOutputDir;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.BufferedOutputStream;
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import java.io.IOException;
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import java.nio.charset.StandardCharsets;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.zip.GZIPOutputStream;
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import org.apache.avro.TestAnnotation;
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import org.apache.commons.compress.archivers.tar.TarArchiveEntry;
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import org.apache.commons.compress.archivers.tar.TarArchiveInputStream;
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import org.apache.commons.compress.compressors.gzip.GzipCompressorInputStream;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FSDataInputStream;
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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 org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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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 com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import com.sun.media.sound.ModelInstrumentComparator;
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import eu.dnetlib.dhp.api.Utils;
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import eu.dnetlib.dhp.api.model.CommunityEntityMap;
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import eu.dnetlib.dhp.api.model.EntityCommunities;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.bulktag.community.*;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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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.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Project;
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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 scala.Tuple2;
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public class SparkBulkTagJob {
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private static String OPENAIRE_3 = "openaire3.0";
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private static String OPENAIRE_4 = "openaire-pub_4.0";
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private static String OPENAIRE_CRIS = "openaire-cris_1.1";
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private static String OPENAIRE_DATA = "openaire2.0_data";
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private static String EOSC = "10|openaire____::2e06c1122c7df43765fdcf91080824fa";
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private static final Logger log = LoggerFactory.getLogger(SparkBulkTagJob.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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SparkBulkTagJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/wf/subworkflows/bulktag/input_bulkTag_parameters.json"));
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log.info(args.toString());
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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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final String baseURL = parser.get("baseURL");
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log.info("baseURL: {}", baseURL);
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log.info("pathMap: {}", parser.get("pathMap"));
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String protoMappingPath = parser.get("pathMap");
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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Configuration configuration = new Configuration();
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configuration.set("fs.defaultFS", hdfsNameNode);
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FileSystem fs = FileSystem.get(configuration);
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String temp = IOUtils.toString(fs.open(new Path(protoMappingPath)), StandardCharsets.UTF_8);
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log.info("protoMap: {}", temp);
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ProtoMap protoMap = new Gson().fromJson(temp, ProtoMap.class);
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log.info("pathMap: {}", new Gson().toJson(protoMap));
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SparkConf conf = new SparkConf();
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CommunityConfiguration cc;
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String taggingConf = Optional
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.ofNullable(parser.get("taggingConf"))
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.map(String::valueOf)
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.orElse(null);
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if (taggingConf != null) {
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cc = CommunityConfigurationFactory.newInstance(taggingConf);
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} else {
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cc = Utils.getCommunityConfiguration(baseURL);
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log.info(OBJECT_MAPPER.writeValueAsString(cc));
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}
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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extendCommunityConfigurationForEOSC(spark, inputPath, cc);
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execBulkTag(
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spark, inputPath, outputPath, protoMap, cc);
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execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL));
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execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL));
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});
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}
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private static void execProjectTag(SparkSession spark, String inputPath, String outputPath,
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CommunityEntityMap communityProjects) {
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Dataset<Project> projects = readPath(spark, inputPath + "project", Project.class);
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Dataset<EntityCommunities> pc = spark
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.createDataset(
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communityProjects
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.keySet()
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.stream()
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.map(k -> EntityCommunities.newInstance(k, communityProjects.get(k)))
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.collect(Collectors.toList()),
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Encoders.bean(EntityCommunities.class));
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projects
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.joinWith(pc, projects.col("id").equalTo(pc.col("entityId")), "left")
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.map((MapFunction<Tuple2<Project, EntityCommunities>, Project>) t2 -> {
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Project ds = t2._1();
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if (t2._2() != null) {
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List<String> context = Optional
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.ofNullable(ds.getContext())
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.map(v -> v.stream().map(c -> c.getId()).collect(Collectors.toList()))
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.orElse(new ArrayList<>());
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if (!Optional.ofNullable(ds.getContext()).isPresent())
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ds.setContext(new ArrayList<>());
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t2._2().getCommunitiesId().forEach(c -> {
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if (!context.contains(c)) {
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Context con = new Context();
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con.setId(c);
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con
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.setDataInfo(
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Arrays
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.asList(
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OafMapperUtils
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.dataInfo(
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false, TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
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OafMapperUtils
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.qualifier(
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TaggingConstants.CLASS_ID_DATASOURCE,
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TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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"1")));
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ds.getContext().add(con);
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}
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});
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}
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return ds;
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}, Encoders.bean(Project.class))
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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 + "project");
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readPath(spark, outputPath + "project", Datasource.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + "project");
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}
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private static void execDatasourceTag(SparkSession spark, String inputPath, String outputPath,
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List<EntityCommunities> datasourceCommunities) {
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Dataset<Datasource> datasource = readPath(spark, inputPath + "datasource", Datasource.class);
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Dataset<EntityCommunities> dc = spark
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.createDataset(datasourceCommunities, Encoders.bean(EntityCommunities.class));
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datasource
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.joinWith(dc, datasource.col("id").equalTo(dc.col("entityId")), "left")
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.map((MapFunction<Tuple2<Datasource, EntityCommunities>, Datasource>) t2 -> {
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Datasource ds = t2._1();
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if (t2._2() != null) {
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List<String> context = Optional
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.ofNullable(ds.getContext())
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.map(v -> v.stream().map(c -> c.getId()).collect(Collectors.toList()))
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.orElse(new ArrayList<>());
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if (!Optional.ofNullable(ds.getContext()).isPresent())
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ds.setContext(new ArrayList<>());
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t2._2().getCommunitiesId().forEach(c -> {
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if (!context.contains(c)) {
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Context con = new Context();
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con.setId(c);
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con
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.setDataInfo(
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Arrays
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.asList(
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OafMapperUtils
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.dataInfo(
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false, TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
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OafMapperUtils
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.qualifier(
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TaggingConstants.CLASS_ID_DATASOURCE,
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TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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"1")));
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ds.getContext().add(con);
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}
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});
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}
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return ds;
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}, Encoders.bean(Datasource.class))
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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 + "datasource");
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readPath(spark, outputPath + "datasource", Datasource.class)
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + "datasource");
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}
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private static void extendCommunityConfigurationForEOSC(SparkSession spark, String inputPath,
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CommunityConfiguration cc) {
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Dataset<String> datasources = readPath(
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spark, inputPath
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+ "datasource",
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Datasource.class)
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.filter((FilterFunction<Datasource>) ds -> isOKDatasource(ds))
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.map((MapFunction<Datasource, String>) ds -> ds.getId(), Encoders.STRING());
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Map<String, List<Pair<String, SelectionConstraints>>> dsm = cc.getEoscDatasourceMap();
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for (String ds : datasources.collectAsList()) {
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if (!dsm.containsKey(ds)) {
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ArrayList<Pair<String, SelectionConstraints>> eoscList = new ArrayList<>();
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dsm.put(ds, eoscList);
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}
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}
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}
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private static boolean isOKDatasource(Datasource ds) {
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final String compatibility = ds.getOpenairecompatibility().getClassid();
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return (compatibility.equalsIgnoreCase(OPENAIRE_3) ||
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compatibility.equalsIgnoreCase(OPENAIRE_4) ||
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compatibility.equalsIgnoreCase(OPENAIRE_CRIS) ||
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compatibility.equalsIgnoreCase(OPENAIRE_DATA)) &&
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ds.getCollectedfrom().stream().anyMatch(cf -> cf.getKey().equals(EOSC));
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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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ProtoMap protoMappingParams,
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CommunityConfiguration communityConfiguration) {
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try {
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System.out.println(new ObjectMapper().writeValueAsString(protoMappingParams));
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} catch (JsonProcessingException e) {
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throw new RuntimeException(e);
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}
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ModelSupport.entityTypes
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.keySet()
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.parallelStream()
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.filter(ModelSupport::isResult)
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.forEach(e -> {
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removeOutputDir(spark, outputPath + e.name());
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ResultTagger resultTagger = new ResultTagger();
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Class<R> resultClazz = ModelSupport.entityTypes.get(e);
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readPath(spark, inputPath + e.name(), 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 -> resultTagger
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.enrichContextCriteria(
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value, communityConfiguration, protoMappingParams),
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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 + e.name());// writing the tagging in the working dir for entity
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readPath(spark, outputPath + e.name(), resultClazz) // copy the tagging in the actual result output path
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath + e.name());
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});
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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 (Objects.isNull(r.getDataInfo())) {
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r.setDataInfo(OafMapperUtils.dataInfo(false, "", false, false, OafMapperUtils.unknown("", ""), ""));
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} else if (r.getDataInfo().getDeletedbyinference() == null) {
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r.getDataInfo().setDeletedbyinference(false);
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}
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if (Objects.isNull(r.getContext())) {
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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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