forked from D-Net/dnet-hadoop
148 lines
6.1 KiB
Java
148 lines
6.1 KiB
Java
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package eu.dnetlib.dhp.actionmanager.bipaffiliations;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.actionmanager.Constants;
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import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
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import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import org.apache.commons.io.IOUtils;
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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.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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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 org.apache.spark.sql.Dataset;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import scala.Tuple2;
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/**
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* Creates action sets for Crossref affiliation relations inferred by BIP!
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*/
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public class PrepareAffiliationRelations implements Serializable {
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private static final String DOI = "doi";
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private static final Logger log = LoggerFactory.getLogger(PrepareAffiliationRelations.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ID_PREFIX = "50|doi_________::";
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public static final String BIP_AFFILIATIONS_CLASSID = "result:organization:bipinference";
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public static final String BIP_AFFILIATIONS_CLASSNAME = "Affiliation relation inferred by BIP!";
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public static final String BIP_INFERENCE_PROVENANCE = "bip_affiliation";
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public static <I extends Result> void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareAffiliationRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/bipaffiliations/input_actionset_parameter.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Constants.isSparkSessionManaged(parser);
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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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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Constants.removeOutputDir(spark, outputPath);
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prepareAffiliationRelations(spark, inputPath, outputPath);
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});
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}
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private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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// load and parse affiliation relations from HDFS
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JavaRDD<AffiliationRelationDeserializer> affiliationRelationsDeserializeRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
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// convert affiliation to an internal representation
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Dataset<AffiliationRelationModel> affiliationRelations =
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spark.createDataset(
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affiliationRelationsDeserializeRDD.flatMap(entry ->
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entry.getMatchings().stream().flatMap(matching ->
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matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
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entry.getDoi(),
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rorId,
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matching.getConfidence()
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))).collect(Collectors.toList())
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.iterator())
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.rdd(),
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Encoders.bean(AffiliationRelationModel.class));
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// prepare action sets for affiliation relations
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affiliationRelations
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.map((MapFunction<AffiliationRelationModel, Relation>) affRel -> {
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// DOI to OpenAIRE id
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final String paperId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
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// ROR id to OpenAIRE id
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final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
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Qualifier qualifier = OafMapperUtils.qualifier(
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BIP_AFFILIATIONS_CLASSID,
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BIP_AFFILIATIONS_CLASSNAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS);
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// format data info; setting `confidence` into relation's `trust`
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DataInfo dataInfo = OafMapperUtils.dataInfo(
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false,
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BIP_INFERENCE_PROVENANCE,
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true,
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false,
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qualifier,
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Double.toString(affRel.getConfidence()));
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return OafMapperUtils.getRelation(
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paperId,
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affId,
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ModelConstants.RESULT_ORGANIZATION,
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ModelConstants.AFFILIATION,
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ModelConstants.HAS_AUTHOR_INSTITUTION,
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null,
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dataInfo,
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null);
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}, Encoders.bean(Relation.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Relation.class, p))
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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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}
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