partial implementation of the ROR->actionset workflow
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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.utils.OafMapperUtils.dataInfo;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
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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.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.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.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.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 String COUNTRIES_VOC = "dnet:countries";
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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 List<KeyValue> ROR_COLLECTED_FROM = listKeyValues("10|openaire____::993a7ae7a863813cf95028b50708e222", "ROR");
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private static final DataInfo ROR_DATA_INFO = dataInfo(false, "", false, false, ENTITYREGISTRY_PROVENANCE_ACTION, "0.92");
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private static final Qualifier ROR_PID_TYPE = qualifier("ROR", "ROR", "dnet:pid_types", "dnet:pid_types");
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private static final Qualifier GRID_PID_TYPE = qualifier("GRID", "GRID", "dnet:pid_types", "dnet:pid_types");
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private static final Qualifier WIKIDATA_PID_TYPE = qualifier("Wikidata", "Wikidata", "dnet:pid_types", "dnet:pid_types");
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private static final Qualifier ORGREF_PID_TYPE = qualifier("OrgRef", "OrgRef", "dnet:pid_types", "dnet:pid_types");
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private static final Qualifier ISNI_PID_TYPE = qualifier("ISNI", "ISNI", "dnet:pid_types", "dnet:pid_types");
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private static final Qualifier FUNDREF_PID_TYPE = qualifier("FundRef", "FundRef", "dnet:pid_types", "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(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) {
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readInputPath(spark, inputPath)
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.map(GenerateRorActionSetJob::convertRorOrg, 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(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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private 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|ror_________::%s", DHPUtils.md5(r.getId())));
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o.setOriginalId(Arrays.asList(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.setCountry(qualifier(r.getCountry().getCountryCode(), r.getCountry().getCountryName(), COUNTRIES_VOC, COUNTRIES_VOC));
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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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pids.add(structuredProperty(r.getExternalIds().getGrid().getAll(), GRID_PID_TYPE, ROR_DATA_INFO));
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pids.addAll(pids(r.getExternalIds().getFundRef().getAll(), FUNDREF_PID_TYPE));
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pids.addAll(pids(r.getExternalIds().getIsni().getAll(), ISNI_PID_TYPE));
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pids.addAll(pids(r.getExternalIds().getOrgRef().getAll(), ORGREF_PID_TYPE));
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pids.addAll(pids(r.getExternalIds().getWikidata().getAll(), WIKIDATA_PID_TYPE));
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return pids;
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}
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private static List<StructuredProperty> pids(final List<String> list, final Qualifier pidType) {
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if (list == null) { return new ArrayList<>(); }
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return list.stream()
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.filter(StringUtils::isNotBlank)
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.distinct()
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.map(s -> structuredProperty(s, pidType, ROR_DATA_INFO))
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.collect(Collectors.toList());
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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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return names.stream().filter(StringUtils::isNotBlank).map(s -> field(s, ROR_DATA_INFO)).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 inputPath) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, RorOrganization>) value -> OBJECT_MAPPER.readValue(value, RorOrganization.class), Encoders.bean(RorOrganization.class));
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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public class Address implements Serializable {
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private Float lat;
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private String stateCode;
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private Integer countryGeonamesId;
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private Float lng;
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private String state;
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private String city;
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private GeonamesCity geonamesCity;
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private String postcode;
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private Boolean primary;
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private String line;
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private final static long serialVersionUID = 2444635485253443195L;
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public Float getLat() {
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return lat;
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}
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public void setLat(final Float lat) {
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this.lat = lat;
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}
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public String getStateCode() {
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return stateCode;
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}
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public void setStateCode(final String stateCode) {
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this.stateCode = stateCode;
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}
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public Integer getCountryGeonamesId() {
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return countryGeonamesId;
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}
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public void setCountryGeonamesId(final Integer countryGeonamesId) {
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this.countryGeonamesId = countryGeonamesId;
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}
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public Float getLng() {
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return lng;
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}
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public void setLng(final Float lng) {
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this.lng = lng;
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}
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public String getState() {
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return state;
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}
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public void setState(final String state) {
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this.state = state;
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}
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public String getCity() {
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return city;
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}
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public void setCity(final String city) {
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this.city = city;
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}
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public GeonamesCity getGeonamesCity() {
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return geonamesCity;
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}
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public void setGeonamesCity(final GeonamesCity geonamesCity) {
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this.geonamesCity = geonamesCity;
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}
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public String getPostcode() {
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return postcode;
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}
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public void setPostcode(final String postcode) {
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this.postcode = postcode;
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}
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public Boolean getPrimary() {
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return primary;
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}
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public void setPrimary(final Boolean primary) {
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this.primary = primary;
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}
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public String getLine() {
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return line;
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}
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public void setLine(final String line) {
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this.line = line;
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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public class Country implements Serializable {
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private String countryCode;
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private String countryName;
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private final static long serialVersionUID = 4357848706229493627L;
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public String getCountryCode() {
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return countryCode;
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}
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public void setCountryCode(final String countryCode) {
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this.countryCode = countryCode;
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}
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public String getCountryName() {
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return countryName;
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}
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public void setCountryName(final String countryName) {
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this.countryName = countryName;
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.List;
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public class ExternalIdType implements Serializable {
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private List<String> all = new ArrayList<>();
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private String preferred;
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private final static long serialVersionUID = 2616688352998387611L;
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public List<String> getAll() {
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return all;
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}
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public void setAll(final List<String> all) {
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this.all = all;
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}
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public String getPreferred() {
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return preferred;
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}
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public void setPreferred(final String preferred) {
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this.preferred = preferred;
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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public class ExternalIds implements Serializable {
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private ExternalIdType wikidata;
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private ExternalIdType orgRef;
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private ExternalIdType isni;
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private ExternalIdType fundRef;
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private GridType grid;
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private final static long serialVersionUID = 686536347353680869L;
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public ExternalIdType getWikidata() {
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return wikidata;
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}
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public void setWikidata(final ExternalIdType wikidata) {
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this.wikidata = wikidata;
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}
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public ExternalIdType getOrgRef() {
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return orgRef;
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}
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public void setOrgRef(final ExternalIdType orgRef) {
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this.orgRef = orgRef;
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}
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public ExternalIdType getIsni() {
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return isni;
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}
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public void setIsni(final ExternalIdType isni) {
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this.isni = isni;
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}
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public ExternalIdType getFundRef() {
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return fundRef;
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}
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public void setFundRef(final ExternalIdType fundRef) {
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this.fundRef = fundRef;
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}
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public GridType getGrid() {
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return grid;
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}
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public void setGrid(final GridType grid) {
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this.grid = grid;
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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public class GeonamesAdmin implements Serializable {
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private String asciiName;
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private Integer id;
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private String name;
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private String code;
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private final static long serialVersionUID = 7294958526269195673L;
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public String getAsciiName() {
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return asciiName;
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}
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public void setAsciiName(final String asciiName) {
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this.asciiName = asciiName;
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}
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public Integer getId() {
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return id;
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}
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public void setId(final Integer id) {
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this.id = id;
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}
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public String getName() {
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return name;
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}
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public void setName(final String name) {
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this.name = name;
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}
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public String getCode() {
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return code;
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}
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public void setCode(final String code) {
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this.code = code;
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}
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}
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package eu.dnetlib.dhp.actionmanager.ror.model;
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import java.io.Serializable;
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public class GeonamesCity implements Serializable {
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private GeonamesAdmin geonamesAdmin1;
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private GeonamesAdmin geonamesAdmin2;
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private String city;
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private Integer id;
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private NameAndCode nutsLevel1;
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private NameAndCode nutsLevel2;
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private NameAndCode nutsLevel3;
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private License license;
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private final static long serialVersionUID = -8389480201526252955L;
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public NameAndCode getNutsLevel2() {
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return nutsLevel2;
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}
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public void setNutsLevel2(final NameAndCode nutsLevel2) {
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this.nutsLevel2 = nutsLevel2;
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}
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public GeonamesAdmin getGeonamesAdmin2() {
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return geonamesAdmin2;
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}
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public void setGeonamesAdmin2(final GeonamesAdmin geonamesAdmin2) {
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this.geonamesAdmin2 = geonamesAdmin2;
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}
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public GeonamesAdmin getGeonamesAdmin1() {
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return geonamesAdmin1;
|
||||
}
|
||||
|
||||
public void setGeonamesAdmin1(final GeonamesAdmin geonamesAdmin1) {
|
||||
this.geonamesAdmin1 = geonamesAdmin1;
|
||||
}
|
||||
|
||||
public String getCity() {
|
||||
return city;
|
||||
}
|
||||
|
||||
public void setCity(final String city) {
|
||||
this.city = city;
|
||||
}
|
||||
|
||||
public Integer getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(final Integer id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public NameAndCode getNutsLevel1() {
|
||||
return nutsLevel1;
|
||||
}
|
||||
|
||||
public void setNutsLevel1(final NameAndCode nutsLevel1) {
|
||||
this.nutsLevel1 = nutsLevel1;
|
||||
}
|
||||
|
||||
public NameAndCode getNutsLevel3() {
|
||||
return nutsLevel3;
|
||||
}
|
||||
|
||||
public void setNutsLevel3(final NameAndCode nutsLevel3) {
|
||||
this.nutsLevel3 = nutsLevel3;
|
||||
}
|
||||
|
||||
public License getLicense() {
|
||||
return license;
|
||||
}
|
||||
|
||||
public void setLicense(final License license) {
|
||||
this.license = license;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,32 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class GridType implements Serializable {
|
||||
|
||||
/**
|
||||
*
|
||||
*/
|
||||
private static final long serialVersionUID = -5605887658267581353L;
|
||||
|
||||
private String all;
|
||||
private String preferred;
|
||||
|
||||
public String getAll() {
|
||||
return all;
|
||||
}
|
||||
|
||||
public void setAll(final String all) {
|
||||
this.all = all;
|
||||
}
|
||||
|
||||
public String getPreferred() {
|
||||
return preferred;
|
||||
}
|
||||
|
||||
public void setPreferred(final String preferred) {
|
||||
this.preferred = preferred;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class Label implements Serializable {
|
||||
|
||||
private String iso639;
|
||||
private String label;
|
||||
private final static long serialVersionUID = -6576156103297850809L;
|
||||
|
||||
public String getIso639() {
|
||||
return iso639;
|
||||
}
|
||||
|
||||
public void setIso639(final String iso639) {
|
||||
this.iso639 = iso639;
|
||||
}
|
||||
|
||||
public String getLabel() {
|
||||
return label;
|
||||
}
|
||||
|
||||
public void setLabel(final String label) {
|
||||
this.label = label;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class License implements Serializable {
|
||||
|
||||
private String attribution;
|
||||
private String license;
|
||||
private final static long serialVersionUID = -194308261058176439L;
|
||||
|
||||
public String getAttribution() {
|
||||
return attribution;
|
||||
}
|
||||
|
||||
public void setAttribution(final String attribution) {
|
||||
this.attribution = attribution;
|
||||
}
|
||||
|
||||
public String getLicense() {
|
||||
return license;
|
||||
}
|
||||
|
||||
public void setLicense(final String license) {
|
||||
this.license = license;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,28 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class NameAndCode implements Serializable {
|
||||
|
||||
private String name;
|
||||
private String code;
|
||||
private final static long serialVersionUID = 5459836979206140843L;
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setName(final String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getCode() {
|
||||
return code;
|
||||
}
|
||||
|
||||
public void setCode(final String code) {
|
||||
this.code = code;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
public class Relationship implements Serializable {
|
||||
|
||||
private String type;
|
||||
private String id;
|
||||
private String label;
|
||||
private final static long serialVersionUID = 7847399503395576960L;
|
||||
|
||||
public String getType() {
|
||||
return type;
|
||||
}
|
||||
|
||||
public void setType(final String type) {
|
||||
this.type = type;
|
||||
}
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(final String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public String getLabel() {
|
||||
return label;
|
||||
}
|
||||
|
||||
public void setLabel(final String label) {
|
||||
this.label = label;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,156 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.ror.model;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
|
||||
public class RorOrganization implements Serializable {
|
||||
|
||||
private List<String> ipAddresses = new ArrayList<>();
|
||||
private List<String> aliases = new ArrayList<>();
|
||||
private List<String> acronyms = new ArrayList<>();
|
||||
private List<String> links = new ArrayList<>();
|
||||
private Country country;
|
||||
private String name;
|
||||
private String wikipediaUrl;
|
||||
private List<Address> addresses = new ArrayList<>();
|
||||
private List<String> types = new ArrayList<>();
|
||||
private Integer established;
|
||||
private List<Relationship> relationships = new ArrayList<>();
|
||||
private String emailAddress;
|
||||
private ExternalIds externalIds;
|
||||
private String id;
|
||||
private List<Label> labels = new ArrayList<>();
|
||||
private String status;
|
||||
private final static long serialVersionUID = -2658312087616043225L;
|
||||
|
||||
public List<String> getIpAddresses() {
|
||||
return ipAddresses;
|
||||
}
|
||||
|
||||
public void setIpAddresses(final List<String> ipAddresses) {
|
||||
this.ipAddresses = ipAddresses;
|
||||
}
|
||||
|
||||
public List<String> getAliases() {
|
||||
return aliases;
|
||||
}
|
||||
|
||||
public void setAliases(final List<String> aliases) {
|
||||
this.aliases = aliases;
|
||||
}
|
||||
|
||||
public List<String> getAcronyms() {
|
||||
return acronyms;
|
||||
}
|
||||
|
||||
public void setAcronyms(final List<String> acronyms) {
|
||||
this.acronyms = acronyms;
|
||||
}
|
||||
|
||||
public List<String> getLinks() {
|
||||
return links;
|
||||
}
|
||||
|
||||
public void setLinks(final List<String> links) {
|
||||
this.links = links;
|
||||
}
|
||||
|
||||
public Country getCountry() {
|
||||
return country;
|
||||
}
|
||||
|
||||
public void setCountry(final Country country) {
|
||||
this.country = country;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setName(final String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getWikipediaUrl() {
|
||||
return wikipediaUrl;
|
||||
}
|
||||
|
||||
public void setWikipediaUrl(final String wikipediaUrl) {
|
||||
this.wikipediaUrl = wikipediaUrl;
|
||||
}
|
||||
|
||||
public List<Address> getAddresses() {
|
||||
return addresses;
|
||||
}
|
||||
|
||||
public void setAddresses(final List<Address> addresses) {
|
||||
this.addresses = addresses;
|
||||
}
|
||||
|
||||
public List<String> getTypes() {
|
||||
return types;
|
||||
}
|
||||
|
||||
public void setTypes(final List<String> types) {
|
||||
this.types = types;
|
||||
}
|
||||
|
||||
public Integer getEstablished() {
|
||||
return established;
|
||||
}
|
||||
|
||||
public void setEstablished(final Integer established) {
|
||||
this.established = established;
|
||||
}
|
||||
|
||||
public List<Relationship> getRelationships() {
|
||||
return relationships;
|
||||
}
|
||||
|
||||
public void setRelationships(final List<Relationship> relationships) {
|
||||
this.relationships = relationships;
|
||||
}
|
||||
|
||||
public String getEmailAddress() {
|
||||
return emailAddress;
|
||||
}
|
||||
|
||||
public void setEmailAddress(final String emailAddress) {
|
||||
this.emailAddress = emailAddress;
|
||||
}
|
||||
|
||||
public ExternalIds getExternalIds() {
|
||||
return externalIds;
|
||||
}
|
||||
|
||||
public void setExternalIds(final ExternalIds externalIds) {
|
||||
this.externalIds = externalIds;
|
||||
}
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(final String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public List<Label> getLabels() {
|
||||
return labels;
|
||||
}
|
||||
|
||||
public void setLabels(final List<Label> labels) {
|
||||
this.labels = labels;
|
||||
}
|
||||
|
||||
public String getStatus() {
|
||||
return status;
|
||||
}
|
||||
|
||||
public void setStatus(final String status) {
|
||||
this.status = status;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,14 @@
|
|||
[
|
||||
{
|
||||
"paramName": "i",
|
||||
"paramLongName": "inputPath",
|
||||
"paramDescription": "the path of the input json",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "o",
|
||||
"paramLongName": "outputPath",
|
||||
"paramDescription": "the path of the new ActionSet",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -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>
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
<workflow-app name="Update_ROR_action_set" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>inputPath</name>
|
||||
<description>the path of the json</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>outputPath</name>
|
||||
<description>path where to store the action set</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="deleteoutputpath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="deleteoutputpath">
|
||||
<fs>
|
||||
<delete path='${outputPath}'/>
|
||||
<mkdir path='${outputPath}'/>
|
||||
<delete path='${workingDir}'/>
|
||||
<mkdir path='${workingDir}'/>
|
||||
</fs>
|
||||
<ok to="processRorFile"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="processRorFile">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>ProcessRorFile</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--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.shuffle.partitions=3840
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${inputPath}</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
Loading…
Reference in New Issue