[orcidenrichment] fixing issue
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227e84be99
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@ -1,5 +1,16 @@
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.author.SparkEnrichWithOrcidAuthors;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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@ -8,98 +19,125 @@ import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.utils.OrcidAuthor;
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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.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.util.List;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.stream.Collectors;
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public class SparkPropagateOrcidAuthor extends SparkEnrichWithOrcidAuthors {
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private static final Logger log = LoggerFactory.getLogger(SparkPropagateOrcidAuthor.class);
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private static final Logger log = LoggerFactory.getLogger(SparkPropagateOrcidAuthor.class);
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public SparkPropagateOrcidAuthor(String propertyPath, String[] args, Logger log) {
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super(propertyPath, args, log);
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}
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public SparkPropagateOrcidAuthor(String propertyPath, String[] args, Logger log) {
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super(propertyPath, args, log);
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}
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public static void main(String[] args) throws Exception {
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public static void main(String[] args) throws Exception {
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// Create instance and run the Spark application
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SparkPropagateOrcidAuthor app = new SparkPropagateOrcidAuthor("/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json", args, log);
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app.initialize().run();
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// Create instance and run the Spark application
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SparkPropagateOrcidAuthor app = new SparkPropagateOrcidAuthor(
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"/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/input_orcidtoresult_parameters.json", args, log);
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app.initialize().run();
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}
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}
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private static OrcidAuthors getOrcidAuthorsList(List<Author> authors) {
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OrcidAuthors oas = new OrcidAuthors();
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List<OrcidAuthor> tmp = authors.stream().map(SparkPropagateOrcidAuthor::getOrcidAuthor)
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.filter(Objects::nonNull).collect(Collectors.toList());
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oas.setOrcidAuthorList(tmp);
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return oas;
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}
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private static OrcidAuthors getOrcidAuthorsList(List<Author> authors) {
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OrcidAuthors oas = new OrcidAuthors();
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List<OrcidAuthor> tmp = authors
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.stream()
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.map(SparkPropagateOrcidAuthor::getOrcidAuthor)
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.filter(Objects::nonNull)
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.collect(Collectors.toList());
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oas.setOrcidAuthorList(tmp);
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return oas;
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}
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private static OrcidAuthor getOrcidAuthor(Author a){
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return Optional.ofNullable(getOrcid(a))
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.map(orcid -> new OrcidAuthor(orcid,a.getSurname(), a.getName(), a.getFullname(), null))
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.orElse(null);
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private static OrcidAuthor getOrcidAuthor(Author a) {
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return Optional
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.ofNullable(getOrcid(a))
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.map(orcid -> new OrcidAuthor(orcid, a.getSurname(), a.getName(), a.getFullname(), null))
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.orElse(null);
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}
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}
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private static String getOrcid(Author a){
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if (a.getPid().stream().anyMatch(p->p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID)))
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return a.getPid().stream().filter(p->p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID)).findFirst().get().getValue();
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if (a.getPid().stream().anyMatch(p->p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID_PENDING)))
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return a.getPid().stream().filter(p->p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID_PENDING)).findFirst().get().getValue();
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return null;
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private static String getOrcid(Author a) {
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if (a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID)))
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return a
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.getPid()
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.stream()
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.filter(p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID))
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.findFirst()
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.get()
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.getValue();
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if (a
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.getPid()
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.stream()
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.anyMatch(p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID_PENDING)))
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return a
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.getPid()
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.stream()
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.filter(p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID_PENDING))
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.findFirst()
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.get()
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.getValue();
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return null;
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}
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}
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@Override
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public void createTemporaryData(SparkSession spark, String graphPath, String orcidPath, String targetPath) {
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ModelSupport.entityTypes
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.keySet().stream().filter(ModelSupport::isResult)
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.forEach(e -> {
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Dataset<Row> orcidDnet = spark.read().schema(Encoders.bean(Result.class).schema())
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.json(graphPath + "/"+ e.name())
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.as(Encoders.bean(Result.class))
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.filter((FilterFunction<Result>) r -> r.getAuthor().stream()
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.anyMatch(a -> a.getPid()
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.stream()
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.anyMatch(p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID) ||
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p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID_PENDING))))
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.map((MapFunction<Result, Tuple2<String, OrcidAuthors>>) r ->
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new Tuple2<>(r.getId(), getOrcidAuthorsList(r.getAuthor()))
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, Encoders.tuple(Encoders.STRING(), Encoders.bean(OrcidAuthors.class)))
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.selectExpr("_1 as target", "_2 as orcid_authors");
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@Override
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public void createTemporaryData(SparkSession spark, String graphPath, String orcidPath, String targetPath) {
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ModelSupport.entityTypes
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.keySet()
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.stream()
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.filter(ModelSupport::isResult)
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.forEach(e -> {
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Dataset<Row> orcidDnet = spark
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.read()
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.schema(Encoders.bean(Result.class).schema())
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.json(graphPath + "/" + e.name())
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.as(Encoders.bean(Result.class))
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.filter(
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(FilterFunction<Result>) r -> r.getAuthor() != null &&
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r
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getPid() != null && a
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.getPid()
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.stream()
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.anyMatch(
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p -> p.getQualifier().getClassid().equalsIgnoreCase(ModelConstants.ORCID) ||
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p
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.getQualifier()
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.getClassid()
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.equalsIgnoreCase(ModelConstants.ORCID_PENDING))))
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.map(
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(MapFunction<Result, Tuple2<String, OrcidAuthors>>) r -> new Tuple2<>(r.getId(),
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getOrcidAuthorsList(r.getAuthor())),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(OrcidAuthors.class)))
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.selectExpr("_1 as target", "_2.orcidAuthorList as orcid_authors");
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Dataset<Row> result = spark.read().schema(Encoders.bean(Result.class).schema())
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.json(graphPath + "/"+ e.name())
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.as(Encoders.bean(Result.class))
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.selectExpr("id", "author as graph_authors");
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Dataset<Row> result = spark
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.read()
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.schema(Encoders.bean(Result.class).schema())
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.json(graphPath + "/" + e.name())
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.as(Encoders.bean(Result.class))
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.selectExpr("id", "author as graph_authors");
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Dataset<Row> supplements = spark.read()
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.schema(Encoders.bean(Relation.class).schema())
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.json(graphPath + "/"+ "relation")
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.where("relclass IN('" + ModelConstants.IS_SUPPLEMENT_TO + "', '" +
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ModelConstants.IS_SUPPLEMENTED_BY + "')")
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.selectExpr("source as id", "target");
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Dataset<Row> supplements = spark
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.read()
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.schema(Encoders.bean(Relation.class).schema())
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.json(graphPath + "/" + "relation")
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.where(
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"relclass IN('" + ModelConstants.IS_SUPPLEMENT_TO + "', '" +
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ModelConstants.IS_SUPPLEMENTED_BY + "')")
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.selectExpr("source as id", "target");
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result
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.join(supplements, "id")
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.join(orcidDnet, "target")
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.drop("target")
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(targetPath + "/"+ e.name() + "_unmatched");
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result
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.join(supplements, "id")
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.join(orcidDnet, "target")
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.drop("target")
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(targetPath + "/" + e.name() + "_unmatched");
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});
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}
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});
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}
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}
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