forked from D-Net/dnet-hadoop
216 lines
7.5 KiB
Java
216 lines
7.5 KiB
Java
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package eu.dnetlib.dhp.actionmanager.ror;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.ENTITYREGISTRY_PROVENANCE_ACTION;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.dataInfo;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.field;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.listKeyValues;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.qualifier;
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import static eu.dnetlib.dhp.schema.oaf.OafMapperUtils.structuredProperty;
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import java.io.InputStream;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Date;
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import java.util.LinkedHashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Optional;
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import java.util.Set;
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import java.util.stream.Collectors;
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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.hadoop.conf.Configuration;
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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.hadoop.io.Text;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.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.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.project.SparkAtomicActionJob;
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import eu.dnetlib.dhp.actionmanager.ror.model.ExternalIdType;
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import eu.dnetlib.dhp.actionmanager.ror.model.RorOrganization;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.DataInfo;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import scala.Tuple2;
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public class GenerateRorActionSetJob {
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private static final Logger log = LoggerFactory.getLogger(GenerateRorActionSetJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ROR_NS_PREFIX = "ror_________";
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private static final List<KeyValue> ROR_COLLECTED_FROM = listKeyValues(
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"10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR");
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private static final DataInfo ROR_DATA_INFO = dataInfo(
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false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92");
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private static final Qualifier ROR_PID_TYPE = qualifier(
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"ROR", "ROR", ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES);
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public static void main(final String[] args) throws Exception {
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final String jsonConfiguration = IOUtils
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.toString(
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SparkAtomicActionJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/ror/action_set_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final 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("inputPath");
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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 SparkConf conf = new SparkConf();
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runWithSparkSession(conf, isSparkSessionManaged, spark -> {
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removeOutputDir(spark, outputPath);
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processRorOrganizations(spark, inputPath, outputPath);
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});
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}
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private static void removeOutputDir(final SparkSession spark, final String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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private static void processRorOrganizations(final SparkSession spark,
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final String inputPath,
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final String outputPath) throws Exception {
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readInputPath(spark, inputPath)
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.map(
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(MapFunction<RorOrganization, Organization>) GenerateRorActionSetJob::convertRorOrg,
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Encoders.bean(Organization.class))
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.toJavaRDD()
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.map(o -> new AtomicAction<>(Organization.class, o))
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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(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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}
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protected static Organization convertRorOrg(final RorOrganization r) {
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final Date now = new Date();
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final Organization o = new Organization();
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o.setId(String.format("20|%s::%s", ROR_NS_PREFIX, DHPUtils.md5(r.getId())));
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o.setOriginalId(Arrays.asList(String.format("%s::%s", ROR_NS_PREFIX, r.getId())));
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o.setCollectedfrom(ROR_COLLECTED_FROM);
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o.setPid(pids(r));
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o.setDateofcollection(now.toString());
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o.setDateoftransformation(now.toString());
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o.setExtraInfo(new ArrayList<>()); // Values not present in the file
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o.setOaiprovenance(null); // Values not present in the file
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o.setLegalshortname(field(r.getAcronyms().stream().findFirst().orElse(r.getName()), ROR_DATA_INFO));
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o.setLegalname(field(r.getName(), ROR_DATA_INFO));
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o.setAlternativeNames(alternativeNames(r));
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o.setWebsiteurl(field(r.getLinks().stream().findFirst().orElse(null), ROR_DATA_INFO));
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o.setLogourl(null);
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o.setEclegalbody(null);
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o.setEclegalperson(null);
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o.setEcnonprofit(null);
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o.setEcresearchorganization(null);
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o.setEchighereducation(null);
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o.setEcinternationalorganizationeurinterests(null);
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o.setEcinternationalorganization(null);
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o.setEcenterprise(null);
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o.setEcsmevalidated(null);
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o.setEcnutscode(null);
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if (r.getCountry() != null) {
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o
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.setCountry(
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qualifier(
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r.getCountry().getCountryCode(), r
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.getCountry()
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.getCountryName(),
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ModelConstants.DNET_COUNTRY_TYPE, ModelConstants.DNET_COUNTRY_TYPE));
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} else {
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o.setCountry(null);
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}
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o.setDataInfo(ROR_DATA_INFO);
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o.setLastupdatetimestamp(now.getTime());
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return o;
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}
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private static List<StructuredProperty> pids(final RorOrganization r) {
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final List<StructuredProperty> pids = new ArrayList<>();
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pids.add(structuredProperty(r.getId(), ROR_PID_TYPE, ROR_DATA_INFO));
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for (final Map.Entry<String, ExternalIdType> e : r.getExternalIds().entrySet()) {
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final String type = e.getKey();
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final List<String> all = e.getValue().getAll();
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if (all != null) {
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final Qualifier qualifier = qualifier(
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type, type, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES);
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for (final String pid : all) {
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pids
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.add(structuredProperty(pid, qualifier, ROR_DATA_INFO));
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}
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}
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}
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return pids;
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}
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private static List<Field<String>> alternativeNames(final RorOrganization r) {
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final Set<String> names = new LinkedHashSet<>();
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names.addAll(r.getAliases());
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names.addAll(r.getAcronyms());
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r.getLabels().forEach(l -> names.add(l.getLabel()));
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return names
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.stream()
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.filter(StringUtils::isNotBlank)
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.map(s -> field(s, ROR_DATA_INFO))
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.collect(Collectors.toList());
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}
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private static Dataset<RorOrganization> readInputPath(
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final SparkSession spark,
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final String path) throws Exception {
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try (final FileSystem fileSystem = FileSystem.get(new Configuration());
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final InputStream is = fileSystem.open(new Path(path))) {
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final RorOrganization[] arr = OBJECT_MAPPER.readValue(is, RorOrganization[].class);
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return spark.createDataset(Arrays.asList(arr), Encoders.bean(RorOrganization.class));
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}
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}
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}
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