196 lines
7.8 KiB
Java
196 lines
7.8 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.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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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|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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r.getLabels().forEach(l -> names.add(l.getLabel()));
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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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