orcid-no-doi #98
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@ -3,7 +3,7 @@ package eu.dnetlib.dhp.schema.orcid;
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import java.io.Serializable;
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import java.io.Serializable;
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public class Summary implements Serializable {
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public class AuthorHistory implements Serializable {
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private String creationMethod;
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private String creationMethod;
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private String completionDate;
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private String completionDate;
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private String submissionDate;
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private String submissionDate;
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@ -0,0 +1,23 @@
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package eu.dnetlib.dhp.schema.orcid;
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public class AuthorSummary extends OrcidData {
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AuthorData authorData;
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AuthorHistory authorHistory;
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public AuthorData getAuthorData() {
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return authorData;
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}
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public void setAuthorData(AuthorData authorData) {
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this.authorData = authorData;
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}
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public AuthorHistory getAuthorHistory() {
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return authorHistory;
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}
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public void setAuthorHistory(AuthorHistory authorHistory) {
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this.authorHistory = authorHistory;
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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package eu.dnetlib.dhp.schema.orcid;
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import java.io.Serializable;
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import java.io.Serializable;
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@ -12,9 +12,9 @@ import eu.dnetlib.dhp.schema.orcid.AuthorData;
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public class Contributor extends AuthorData implements Serializable {
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public class Contributor extends AuthorData implements Serializable {
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private String sequence;
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private String sequence;
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private String role;
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private String role;
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private transient boolean simpleMatch = false;
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private transient boolean simpleMatch;
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private transient Double score = 0.0;
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private transient Double score;
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private transient boolean bestMatch = false;
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private transient boolean bestMatch;
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public String getSequence() {
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public String getSequence() {
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return sequence;
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return sequence;
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@ -1,5 +1,5 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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package eu.dnetlib.dhp.schema.orcid;
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/**
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/**
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* This class models the data related to external id, that are retrieved from an orcid publication
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* This class models the data related to external id, that are retrieved from an orcid publication
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@ -0,0 +1,14 @@
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package eu.dnetlib.dhp.schema.orcid;
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public class OrcidData {
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protected String base64CompressData;
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public String getBase64CompressData() {
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return base64CompressData;
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}
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public void setBase64CompressData(String base64CompressData) {
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this.base64CompressData = base64CompressData;
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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package eu.dnetlib.dhp.schema.orcid;
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/**
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/**
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* This class models the data related to a publication date, that are retrieved from an orcid publication
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* This class models the data related to a publication date, that are retrieved from an orcid publication
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@ -0,0 +1,14 @@
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package eu.dnetlib.dhp.schema.orcid;
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public class Work extends OrcidData {
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WorkDetail workDetail;
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public WorkDetail getWorkDetail() {
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return workDetail;
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}
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public void setWorkDetail(WorkDetail workDetail) {
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this.workDetail = workDetail;
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}
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}
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@ -1,14 +1,19 @@
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package eu.dnetlib.doiboost.orcidnodoi.model;
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package eu.dnetlib.dhp.schema.orcid;
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import java.io.Serializable;
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import java.io.Serializable;
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import java.util.List;
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import java.util.List;
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import eu.dnetlib.dhp.schema.orcid.Contributor;
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import eu.dnetlib.dhp.schema.orcid.ExternalId;
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import eu.dnetlib.dhp.schema.orcid.OrcidData;
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import eu.dnetlib.dhp.schema.orcid.PublicationDate;
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/**
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/**
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* This class models the data that are retrieved from orcid publication
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* This class models the data that are retrieved from orcid publication
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*/
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*/
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public class WorkDataNoDoi implements Serializable {
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public class WorkDetail implements Serializable {
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private String oid;
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private String oid;
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private String id;
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private String id;
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@ -4,44 +4,27 @@ package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.io.IOException;
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import java.util.*;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.io.IOUtils;
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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.io.Text;
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import org.apache.hadoop.mapreduce.lib.output.SequenceFileOutputFormat;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaPairRDD;
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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.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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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.slf4j.Logger;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.slf4j.LoggerFactory;
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import com.esotericsoftware.minlog.Log;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.orcid.Work;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
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import scala.Tuple2;
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public class SparkUpdateOrcidDatasets {
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public class SparkUpdateOrcidDatasets {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws IOException, Exception {
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidDatasets.class);
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logger.info("[ SparkUpdateOrcidDatasets STARTED]");
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logger.info("[ SparkUpdateOrcidDatasets STARTED]");
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@ -70,71 +53,35 @@ public class SparkUpdateOrcidDatasets {
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spark -> {
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spark -> {
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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sc.hadoopConfiguration().set("mapreduce.output.fileoutputformat.compress", "true");
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JavaPairRDD<Text, Text> xmlSummariesRDD = sc
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JavaPairRDD<Text, Text> xmlSummariesRDD = sc
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.sequenceFile(workingPath.concat("xml/authors/xml_authors.seq"), Text.class, Text.class);
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.sequenceFile(workingPath.concat("xml/authors/xml_authors.seq"), Text.class, Text.class);
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xmlSummariesRDD
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xmlSummariesRDD
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.repartition(5)
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.map(seq -> {
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.map(seq -> XMLRecordParser.VTDParseAuthorData(seq._2().toString().getBytes()))
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AuthorSummary authorSummary = XMLRecordParser
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.filter(summary -> summary != null)
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.VTDParseAuthorSummary(seq._2().toString().getBytes());
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.mapToPair(
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authorSummary
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summary -> new Tuple2<>(summary.getOid(),
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.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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OBJECT_MAPPER.writeValueAsString(summary)))
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return authorSummary;
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.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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})
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.saveAsNewAPIHadoopFile(
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.filter(authorSummary -> authorSummary != null)
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workingPath.concat("orcid_dataset/authors"),
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.map(authorSummary -> JsonWriter.create(authorSummary))
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Text.class,
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.saveAsTextFile(workingPath.concat("orcid_dataset/authors"), GzipCodec.class);
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Text.class,
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SequenceFileOutputFormat.class,
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sc.hadoopConfiguration());
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JavaPairRDD<Text, Text> xmlWorksRDD = sc
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JavaPairRDD<Text, Text> xmlWorksRDD = sc
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.sequenceFile(workingPath.concat("xml/works/*"), Text.class, Text.class);
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.sequenceFile(workingPath.concat("xml/works/*"), Text.class, Text.class);
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xmlWorksRDD
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xmlWorksRDD
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.map(seq -> XMLRecordParserNoDoi.VTDParseWorkData(seq._2().toString().getBytes()))
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.map(seq -> {
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WorkDetail workDetail = XMLRecordParserNoDoi.VTDParseWorkData(seq._2().toString().getBytes());
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Work work = new Work();
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work.setWorkDetail(workDetail);
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work.setBase64CompressData(ArgumentApplicationParser.compressArgument(seq._2().toString()));
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return work;
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})
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.filter(work -> work != null)
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.filter(work -> work != null)
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.mapToPair(
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.map(work -> JsonWriter.create(work))
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work -> new Tuple2<>(work.getOid().concat("_").concat(work.getId()),
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.saveAsTextFile(workingPath.concat("orcid_dataset/works"), GzipCodec.class);
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OBJECT_MAPPER.writeValueAsString(work)))
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.mapToPair(t -> new Tuple2(new Text(t._1()), new Text(t._2())))
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.saveAsNewAPIHadoopFile(
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workingPath.concat("orcid_dataset/works"),
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Text.class,
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Text.class,
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SequenceFileOutputFormat.class,
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sc.hadoopConfiguration());
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});
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});
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}
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}
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private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
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AuthorData authorData = new AuthorData();
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authorData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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authorData.setName(getJsonValue(jElement, "name"));
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authorData.setSurname(getJsonValue(jElement, "surname"));
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authorData.setCreditName(getJsonValue(jElement, "creditname"));
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return authorData;
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}
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private static WorkData loadWorkFromJson(Text orcidId, Text json) {
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WorkData workData = new WorkData();
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workData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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workData.setDoi(getJsonValue(jElement, "doi"));
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return workData;
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return null;
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}
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}
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}
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@ -3,11 +3,11 @@ package eu.dnetlib.doiboost.orcid.json;
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import com.google.gson.Gson;
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import com.google.gson.Gson;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.dhp.schema.orcid.WorkDetail;
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public class JsonHelper {
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public class JsonHelper {
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public static String createOidWork(WorkDataNoDoi workData) {
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public static String createOidWork(WorkDetail workData) {
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return new Gson().toJson(workData);
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return new Gson().toJson(workData);
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}
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}
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}
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}
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@ -12,8 +12,9 @@ import com.ximpleware.*;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.parser.utility.VtdException;
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import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
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import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.AuthorHistory;
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import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
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public class XMLRecordParser {
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public class XMLRecordParser {
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@ -234,4 +235,114 @@ public class XMLRecordParser {
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}
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}
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return workIdLastModifiedDate;
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return workIdLastModifiedDate;
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}
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}
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public static AuthorSummary VTDParseAuthorSummary(byte[] bytes)
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throws VtdException, ParseException {
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final VTDGen vg = new VTDGen();
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vg.setDoc(bytes);
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vg.parse(true);
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final VTDNav vn = vg.getNav();
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final AutoPilot ap = new AutoPilot(vn);
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ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
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ap.declareXPathNameSpace(NS_PERSON, NS_PERSON_URL);
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ap.declareXPathNameSpace(NS_DETAILS, NS_DETAILS_URL);
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ap.declareXPathNameSpace(NS_OTHER, NS_OTHER_URL);
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ap.declareXPathNameSpace(NS_RECORD, NS_RECORD_URL);
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ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
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ap.declareXPathNameSpace(NS_HISTORY, NS_HISTORY_URL);
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AuthorData authorData = retrieveAuthorData(ap, vn, bytes);
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AuthorHistory authorHistory = retrieveAuthorHistory(ap, vn, bytes);
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AuthorSummary authorSummary = new AuthorSummary();
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authorSummary.setAuthorData(authorData);
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authorSummary.setAuthorHistory(authorHistory);
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return authorSummary;
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}
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private static AuthorData retrieveAuthorData(AutoPilot ap, VTDNav vn, byte[] bytes)
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throws VtdException {
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AuthorData authorData = new AuthorData();
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final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
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if (!errors.isEmpty()) {
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authorData.setErrorCode(errors.get(0));
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return authorData;
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}
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|
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List<VtdUtilityParser.Node> recordNodes = VtdUtilityParser
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.getTextValuesWithAttributes(
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ap, vn, "//record:record", Arrays.asList("path"));
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if (!recordNodes.isEmpty()) {
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final String oid = (recordNodes.get(0).getAttributes().get("path")).substring(1);
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authorData.setOid(oid);
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} else {
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return null;
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}
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|
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final List<String> names = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:given-names");
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if (!names.isEmpty()) {
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authorData.setName(names.get(0));
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}
|
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|
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final List<String> surnames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:family-name");
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if (!surnames.isEmpty()) {
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authorData.setSurname(surnames.get(0));
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}
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|
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final List<String> creditNames = VtdUtilityParser.getTextValue(ap, vn, "//personal-details:credit-name");
|
||||||
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if (!creditNames.isEmpty()) {
|
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authorData.setCreditName(creditNames.get(0));
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}
|
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|
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final List<String> otherNames = VtdUtilityParser.getTextValue(ap, vn, "//other-name:content");
|
||||||
|
if (!otherNames.isEmpty()) {
|
||||||
|
authorData.setOtherNames(otherNames);
|
||||||
|
}
|
||||||
|
return authorData;
|
||||||
|
}
|
||||||
|
|
||||||
|
private static AuthorHistory retrieveAuthorHistory(AutoPilot ap, VTDNav vn, byte[] bytes)
|
||||||
|
throws VtdException {
|
||||||
|
AuthorHistory authorHistory = new AuthorHistory();
|
||||||
|
final String creationMethod = VtdUtilityParser.getSingleValue(ap, vn, "//history:creation-method");
|
||||||
|
if (StringUtils.isNoneBlank(creationMethod)) {
|
||||||
|
authorHistory.setCreationMethod(creationMethod);
|
||||||
|
}
|
||||||
|
|
||||||
|
final String completionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:completion-date");
|
||||||
|
if (StringUtils.isNoneBlank(completionDate)) {
|
||||||
|
authorHistory.setCompletionDate(completionDate);
|
||||||
|
}
|
||||||
|
|
||||||
|
final String submissionDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:submission-date");
|
||||||
|
if (StringUtils.isNoneBlank(submissionDate)) {
|
||||||
|
authorHistory.setSubmissionDate(submissionDate);
|
||||||
|
}
|
||||||
|
|
||||||
|
final String claimed = VtdUtilityParser.getSingleValue(ap, vn, "//history:claimed");
|
||||||
|
if (StringUtils.isNoneBlank(claimed)) {
|
||||||
|
authorHistory.setClaimed(Boolean.parseBoolean(claimed));
|
||||||
|
}
|
||||||
|
|
||||||
|
final String verifiedEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-email");
|
||||||
|
if (StringUtils.isNoneBlank(verifiedEmail)) {
|
||||||
|
authorHistory.setVerifiedEmail(Boolean.parseBoolean(verifiedEmail));
|
||||||
|
}
|
||||||
|
|
||||||
|
final String verifiedPrimaryEmail = VtdUtilityParser.getSingleValue(ap, vn, "//history:verified-primary-email");
|
||||||
|
if (StringUtils.isNoneBlank(verifiedPrimaryEmail)) {
|
||||||
|
authorHistory.setVerifiedPrimaryEmail(Boolean.parseBoolean(verifiedPrimaryEmail));
|
||||||
|
}
|
||||||
|
|
||||||
|
final String deactivationDate = VtdUtilityParser.getSingleValue(ap, vn, "//history:deactivation-date");
|
||||||
|
if (StringUtils.isNoneBlank(deactivationDate)) {
|
||||||
|
authorHistory.setDeactivationDate(deactivationDate);
|
||||||
|
}
|
||||||
|
|
||||||
|
final String lastModifiedDate = VtdUtilityParser
|
||||||
|
.getSingleValue(ap, vn, "//history:history/common:last-modified-date");
|
||||||
|
if (StringUtils.isNoneBlank(lastModifiedDate)) {
|
||||||
|
authorHistory.setLastModifiedDate(lastModifiedDate);
|
||||||
|
}
|
||||||
|
return authorHistory;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
@ -19,8 +19,8 @@ import org.apache.hadoop.io.compress.CompressionCodec;
|
||||||
import org.apache.hadoop.io.compress.CompressionCodecFactory;
|
import org.apache.hadoop.io.compress.CompressionCodecFactory;
|
||||||
import org.mortbay.log.Log;
|
import org.mortbay.log.Log;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
import eu.dnetlib.doiboost.orcid.json.JsonHelper;
|
import eu.dnetlib.doiboost.orcid.json.JsonHelper;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
|
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
|
import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
@ -87,29 +87,29 @@ public class ActivitiesDumpReader {
|
||||||
while ((line = br.readLine()) != null) {
|
while ((line = br.readLine()) != null) {
|
||||||
buffer.append(line);
|
buffer.append(line);
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workDataNoDoi = XMLRecordParserNoDoi
|
WorkDetail workDetail = XMLRecordParserNoDoi
|
||||||
.VTDParseWorkData(buffer.toString().getBytes());
|
.VTDParseWorkData(buffer.toString().getBytes());
|
||||||
if (workDataNoDoi != null) {
|
if (workDetail != null) {
|
||||||
if (workDataNoDoi.getErrorCode() != null) {
|
if (workDetail.getErrorCode() != null) {
|
||||||
errorFromOrcidFound += 1;
|
errorFromOrcidFound += 1;
|
||||||
Log
|
Log
|
||||||
.debug(
|
.debug(
|
||||||
"error from Orcid with code "
|
"error from Orcid with code "
|
||||||
+ workDataNoDoi.getErrorCode()
|
+ workDetail.getErrorCode()
|
||||||
+ " for entry "
|
+ " for entry "
|
||||||
+ entry.getName());
|
+ entry.getName());
|
||||||
continue;
|
continue;
|
||||||
}
|
}
|
||||||
boolean isDoiFound = workDataNoDoi
|
boolean isDoiFound = workDetail
|
||||||
.getExtIds()
|
.getExtIds()
|
||||||
.stream()
|
.stream()
|
||||||
.filter(e -> e.getType() != null)
|
.filter(e -> e.getType() != null)
|
||||||
.anyMatch(e -> e.getType().equals("doi"));
|
.anyMatch(e -> e.getType().equals("doi"));
|
||||||
if (!isDoiFound) {
|
if (!isDoiFound) {
|
||||||
String jsonData = JsonHelper.createOidWork(workDataNoDoi);
|
String jsonData = JsonHelper.createOidWork(workDetail);
|
||||||
Log.debug("oid: " + workDataNoDoi.getOid() + " data: " + jsonData);
|
Log.debug("oid: " + workDetail.getOid() + " data: " + jsonData);
|
||||||
|
|
||||||
final Text key = new Text(workDataNoDoi.getOid());
|
final Text key = new Text(workDetail.getOid());
|
||||||
final Text value = new Text(jsonData);
|
final Text value = new Text(jsonData);
|
||||||
|
|
||||||
try {
|
try {
|
||||||
|
|
|
@ -30,8 +30,8 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||||
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
import eu.dnetlib.doiboost.orcid.json.JsonHelper;
|
import eu.dnetlib.doiboost.orcid.json.JsonHelper;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
|
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
|
import eu.dnetlib.doiboost.orcidnodoi.oaf.PublicationToOaf;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
|
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
|
||||||
import scala.Tuple2;
|
import scala.Tuple2;
|
||||||
|
@ -81,10 +81,10 @@ public class SparkGenEnrichedOrcidWorks {
|
||||||
|
|
||||||
JavaPairRDD<Text, Text> activitiesRDD = sc
|
JavaPairRDD<Text, Text> activitiesRDD = sc
|
||||||
.sequenceFile(workingPath + outputWorksPath + "*.seq", Text.class, Text.class);
|
.sequenceFile(workingPath + outputWorksPath + "*.seq", Text.class, Text.class);
|
||||||
Dataset<WorkDataNoDoi> activitiesDataset = spark
|
Dataset<WorkDetail> activitiesDataset = spark
|
||||||
.createDataset(
|
.createDataset(
|
||||||
activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
|
activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
|
||||||
Encoders.bean(WorkDataNoDoi.class));
|
Encoders.bean(WorkDetail.class));
|
||||||
logger.info("Works data loaded: " + activitiesDataset.count());
|
logger.info("Works data loaded: " + activitiesDataset.count());
|
||||||
|
|
||||||
JavaRDD<Tuple2<String, String>> enrichedWorksRDD = activitiesDataset
|
JavaRDD<Tuple2<String, String>> enrichedWorksRDD = activitiesDataset
|
||||||
|
@ -92,8 +92,8 @@ public class SparkGenEnrichedOrcidWorks {
|
||||||
summariesDataset,
|
summariesDataset,
|
||||||
activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
|
activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
|
||||||
.map(
|
.map(
|
||||||
(MapFunction<Tuple2<WorkDataNoDoi, AuthorData>, Tuple2<String, String>>) value -> {
|
(MapFunction<Tuple2<WorkDetail, AuthorData>, Tuple2<String, String>>) value -> {
|
||||||
WorkDataNoDoi w = value._1;
|
WorkDetail w = value._1;
|
||||||
AuthorData a = value._2;
|
AuthorData a = value._2;
|
||||||
AuthorMatcher.match(a, w.getContributors());
|
AuthorMatcher.match(a, w.getContributors());
|
||||||
return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w));
|
return new Tuple2<>(a.getOid(), JsonHelper.createOidWork(w));
|
||||||
|
@ -161,9 +161,9 @@ public class SparkGenEnrichedOrcidWorks {
|
||||||
return authorData;
|
return authorData;
|
||||||
}
|
}
|
||||||
|
|
||||||
private static WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) {
|
private static WorkDetail loadWorkFromJson(Text orcidId, Text json) {
|
||||||
|
|
||||||
WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class);
|
WorkDetail workData = new Gson().fromJson(json.toString(), WorkDetail.class);
|
||||||
return workData;
|
return workData;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
@ -19,8 +19,8 @@ import com.ximpleware.XPathParseException;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.parser.utility.VtdException;
|
import eu.dnetlib.dhp.parser.utility.VtdException;
|
||||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
|
import eu.dnetlib.dhp.schema.orcid.Contributor;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This class is used for searching from a list of publication contributors a
|
* This class is used for searching from a list of publication contributors a
|
||||||
|
@ -209,7 +209,7 @@ public class AuthorMatcher {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
private static String toJson(WorkDataNoDoi work) {
|
private static String toJson(WorkDetail work) {
|
||||||
GsonBuilder builder = new GsonBuilder();
|
GsonBuilder builder = new GsonBuilder();
|
||||||
Gson gson = builder.create();
|
Gson gson = builder.create();
|
||||||
return gson.toJson(work);
|
return gson.toJson(work);
|
||||||
|
|
|
@ -12,10 +12,10 @@ import com.ximpleware.*;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.parser.utility.VtdException;
|
import eu.dnetlib.dhp.parser.utility.VtdException;
|
||||||
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
|
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
|
import eu.dnetlib.dhp.schema.orcid.Contributor;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId;
|
import eu.dnetlib.dhp.schema.orcid.ExternalId;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate;
|
import eu.dnetlib.dhp.schema.orcid.PublicationDate;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* This class is used for parsing xml data with vtd parser
|
* This class is used for parsing xml data with vtd parser
|
||||||
|
@ -42,7 +42,7 @@ public class XMLRecordParserNoDoi {
|
||||||
|
|
||||||
private static final String NS_ERROR = "error";
|
private static final String NS_ERROR = "error";
|
||||||
|
|
||||||
public static WorkDataNoDoi VTDParseWorkData(byte[] bytes)
|
public static WorkDetail VTDParseWorkData(byte[] bytes)
|
||||||
throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException,
|
throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException,
|
||||||
NavException, XPathEvalException {
|
NavException, XPathEvalException {
|
||||||
final VTDGen vg = new VTDGen();
|
final VTDGen vg = new VTDGen();
|
||||||
|
@ -54,7 +54,7 @@ public class XMLRecordParserNoDoi {
|
||||||
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
|
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
|
||||||
ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
|
ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
|
||||||
|
|
||||||
WorkDataNoDoi workData = new WorkDataNoDoi();
|
WorkDetail workData = new WorkDetail();
|
||||||
final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
|
final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
|
||||||
if (!errors.isEmpty()) {
|
if (!errors.isEmpty()) {
|
||||||
workData.setErrorCode(errors.get(0));
|
workData.setErrorCode(errors.get(0));
|
||||||
|
|
|
@ -2,7 +2,7 @@
|
||||||
<parameters>
|
<parameters>
|
||||||
<property>
|
<property>
|
||||||
<name>spark2MaxExecutors</name>
|
<name>spark2MaxExecutors</name>
|
||||||
<value>5</value>
|
<value>40</value>
|
||||||
</property>
|
</property>
|
||||||
<property>
|
<property>
|
||||||
<name>sparkDriverMemory</name>
|
<name>sparkDriverMemory</name>
|
||||||
|
|
|
@ -5,21 +5,23 @@ import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||||
|
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.time.LocalDate;
|
|
||||||
import java.util.HashMap;
|
|
||||||
import java.util.Map;
|
import java.util.Map;
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
import org.apache.commons.io.IOUtils;
|
||||||
import org.junit.jupiter.api.Test;
|
import org.junit.jupiter.api.Test;
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
import com.ximpleware.*;
|
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||||
|
import eu.dnetlib.dhp.schema.orcid.AuthorSummary;
|
||||||
|
import eu.dnetlib.dhp.schema.orcid.Work;
|
||||||
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
import eu.dnetlib.doiboost.orcid.OrcidClientTest;
|
import eu.dnetlib.doiboost.orcid.OrcidClientTest;
|
||||||
import eu.dnetlib.doiboost.orcid.SparkDownloadOrcidWorks;
|
import eu.dnetlib.doiboost.orcid.SparkDownloadOrcidWorks;
|
||||||
import eu.dnetlib.doiboost.orcid.model.WorkData;
|
import eu.dnetlib.doiboost.orcid.model.WorkData;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
|
import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
|
||||||
|
import eu.dnetlib.doiboost.orcidnodoi.xml.XMLRecordParserNoDoi;
|
||||||
|
|
||||||
public class XMLRecordParserTest {
|
public class XMLRecordParserTest {
|
||||||
private static final String NS_WORK = "work";
|
private static final String NS_WORK = "work";
|
||||||
|
@ -29,7 +31,7 @@ public class XMLRecordParserTest {
|
||||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
@Test
|
@Test
|
||||||
public void testOrcidAuthorDataXMLParser() throws Exception {
|
private void testOrcidAuthorDataXMLParser() throws Exception {
|
||||||
|
|
||||||
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
|
String xml = IOUtils.toString(this.getClass().getResourceAsStream("summary_0000-0001-6828-479X.xml"));
|
||||||
|
|
||||||
|
@ -104,4 +106,26 @@ public class XMLRecordParserTest {
|
||||||
}
|
}
|
||||||
});
|
});
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testAuthorSummaryXMLParser() throws Exception {
|
||||||
|
String xml = IOUtils
|
||||||
|
.toString(
|
||||||
|
this.getClass().getResourceAsStream("record_0000-0001-5004-5918.xml"));
|
||||||
|
AuthorSummary authorSummary = XMLRecordParser.VTDParseAuthorSummary(xml.getBytes());
|
||||||
|
authorSummary.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
|
||||||
|
OrcidClientTest.logToFile(JsonWriter.create(authorSummary));
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void testWorkDataXMLParser() throws Exception {
|
||||||
|
String xml = IOUtils
|
||||||
|
.toString(
|
||||||
|
this.getClass().getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
|
||||||
|
WorkDetail workDetail = XMLRecordParserNoDoi.VTDParseWorkData(xml.getBytes());
|
||||||
|
Work work = new Work();
|
||||||
|
work.setWorkDetail(workDetail);
|
||||||
|
work.setBase64CompressData(ArgumentApplicationParser.compressArgument(xml));
|
||||||
|
OrcidClientTest.logToFile(JsonWriter.create(work));
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
@ -21,8 +21,8 @@ import com.ximpleware.XPathParseException;
|
||||||
|
|
||||||
import eu.dnetlib.dhp.parser.utility.VtdException;
|
import eu.dnetlib.dhp.parser.utility.VtdException;
|
||||||
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
import eu.dnetlib.dhp.schema.orcid.AuthorData;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
|
import eu.dnetlib.dhp.schema.orcid.Contributor;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
|
import eu.dnetlib.dhp.schema.orcid.WorkDetail;
|
||||||
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
|
import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
|
||||||
|
|
||||||
public class OrcidNoDoiTest {
|
public class OrcidNoDoiTest {
|
||||||
|
@ -48,7 +48,7 @@ public class OrcidNoDoiTest {
|
||||||
if (p == null) {
|
if (p == null) {
|
||||||
logger.info("XMLRecordParserNoDoi null");
|
logger.info("XMLRecordParserNoDoi null");
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workData = null;
|
WorkDetail workData = null;
|
||||||
try {
|
try {
|
||||||
workData = p.VTDParseWorkData(xml.getBytes());
|
workData = p.VTDParseWorkData(xml.getBytes());
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
|
@ -105,7 +105,7 @@ public class OrcidNoDoiTest {
|
||||||
if (p == null) {
|
if (p == null) {
|
||||||
logger.info("XMLRecordParserNoDoi null");
|
logger.info("XMLRecordParserNoDoi null");
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workData = null;
|
WorkDetail workData = null;
|
||||||
try {
|
try {
|
||||||
workData = p.VTDParseWorkData(xml.getBytes());
|
workData = p.VTDParseWorkData(xml.getBytes());
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
|
@ -136,7 +136,7 @@ public class OrcidNoDoiTest {
|
||||||
if (p == null) {
|
if (p == null) {
|
||||||
logger.info("XMLRecordParserNoDoi null");
|
logger.info("XMLRecordParserNoDoi null");
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workData = null;
|
WorkDetail workData = null;
|
||||||
try {
|
try {
|
||||||
workData = p.VTDParseWorkData(xml.getBytes());
|
workData = p.VTDParseWorkData(xml.getBytes());
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
|
@ -179,7 +179,7 @@ public class OrcidNoDoiTest {
|
||||||
if (p == null) {
|
if (p == null) {
|
||||||
logger.info("XMLRecordParserNoDoi null");
|
logger.info("XMLRecordParserNoDoi null");
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workData = null;
|
WorkDetail workData = null;
|
||||||
try {
|
try {
|
||||||
workData = p.VTDParseWorkData(xml.getBytes());
|
workData = p.VTDParseWorkData(xml.getBytes());
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
|
@ -308,7 +308,7 @@ public class OrcidNoDoiTest {
|
||||||
if (p == null) {
|
if (p == null) {
|
||||||
logger.info("XMLRecordParserNoDoi null");
|
logger.info("XMLRecordParserNoDoi null");
|
||||||
}
|
}
|
||||||
WorkDataNoDoi workData = null;
|
WorkDetail workData = null;
|
||||||
try {
|
try {
|
||||||
workData = p.VTDParseWorkData(xml.getBytes());
|
workData = p.VTDParseWorkData(xml.getBytes());
|
||||||
} catch (Exception e) {
|
} catch (Exception e) {
|
||||||
|
|
Loading…
Reference in New Issue