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parser of orcid publication data from xml original dump

This commit is contained in:
Enrico Ottonello 2020-06-24 16:29:32 +02:00
parent 52f62d5d8c
commit fcbb4c1489
13 changed files with 1102 additions and 1 deletions

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@ -84,6 +84,12 @@
<artifactId>spark-sql_2.11</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
<version>1.8</version>
</dependency>
</dependencies>

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@ -9,6 +9,7 @@ public class AuthorData implements Serializable {
private String name;
private String surname;
private String creditName;
private String otherName;
private String errorCode;
public String getErrorCode() {
@ -50,4 +51,12 @@ public class AuthorData implements Serializable {
public void setOid(String oid) {
this.oid = oid;
}
public String getOtherName() {
return otherName;
}
public void setOtherName(String otherName) {
this.otherName = otherName;
}
}

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@ -0,0 +1,54 @@
package eu.dnetlib.doiboost.orcidnodoi.model;
import java.io.Serializable;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
public class Contributor extends AuthorData implements Serializable {
private String sequence;
private String role;
private boolean simpleMatch = false;
private Double score = 0.0;
private boolean bestMatch = false;
public String getSequence() {
return sequence;
}
public void setSequence(String sequence) {
this.sequence = sequence;
}
public String getRole() {
return role;
}
public void setRole(String role) {
this.role = role;
}
public boolean isSimpleMatch() {
return simpleMatch;
}
public void setSimpleMatch(boolean simpleMatch) {
this.simpleMatch = simpleMatch;
}
public Double getScore() {
return score;
}
public void setScore(Double score) {
this.score = score;
}
public boolean isBestMatch() {
return bestMatch;
}
public void setBestMatch(boolean bestMatch) {
this.bestMatch = bestMatch;
}
}

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@ -0,0 +1,32 @@
package eu.dnetlib.doiboost.orcidnodoi.model;
public class ExternalId {
private String type;
private String value;
private String relationShip;
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public String getValue() {
return value;
}
public void setValue(String value) {
this.value = value;
}
public String getRelationShip() {
return relationShip;
}
public void setRelationShip(String relationShip) {
this.relationShip = relationShip;
}
}

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@ -0,0 +1,32 @@
package eu.dnetlib.doiboost.orcidnodoi.model;
public class PublicationDate {
private String year;
private String month;
private String day;
public String getYear() {
return year;
}
public void setYear(String year) {
this.year = year;
}
public String getMonth() {
return month;
}
public void setMonth(String month) {
this.month = month;
}
public String getDay() {
return day;
}
public void setDay(String day) {
this.day = day;
}
}

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@ -0,0 +1,101 @@
package eu.dnetlib.doiboost.orcidnodoi.model;
import java.io.Serializable;
import java.util.List;
public class WorkDataNoDoi implements Serializable {
private String oid;
private String id;
private String sourceName;
private String type;
private List<String> titles;
private List<String> urls;
List<ExternalId> extIds;
List<PublicationDate> publicationDates;
List<Contributor> contributors;
public String getOid() {
return oid;
}
public void setOid(String oid) {
this.oid = oid;
}
public String getErrorCode() {
return errorCode;
}
public void setErrorCode(String errorCode) {
this.errorCode = errorCode;
}
private String errorCode;
public String getId() {
return id;
}
public void setId(String id) {
this.id = id;
}
public List<String> getTitles() {
return titles;
}
public void setTitles(List<String> titles) {
this.titles = titles;
}
public String getSourceName() {
return sourceName;
}
public void setSourceName(String sourceName) {
this.sourceName = sourceName;
}
public String getType() {
return type;
}
public void setType(String type) {
this.type = type;
}
public List<String> getUrls() {
return urls;
}
public void setUrls(List<String> urls) {
this.urls = urls;
}
public List<ExternalId> getExtIds() {
return extIds;
}
public void setExtIds(List<ExternalId> extIds) {
this.extIds = extIds;
}
public List<PublicationDate> getPublicationDates() {
return publicationDates;
}
public void setPublicationDates(List<PublicationDate> publicationDates) {
this.publicationDates = publicationDates;
}
public List<Contributor> getContributors() {
return contributors;
}
public void setContributors(List<Contributor> contributors) {
this.contributors = contributors;
}
}

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@ -0,0 +1,216 @@
package eu.dnetlib.doiboost.orcidnodoi.xml;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.ximpleware.*;
import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.dhp.parser.utility.VtdUtilityParser;
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
import eu.dnetlib.doiboost.orcidnodoi.model.ExternalId;
import eu.dnetlib.doiboost.orcidnodoi.model.PublicationDate;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
public class XMLRecordParserNoDoi {
private static final Logger logger = LoggerFactory.getLogger(XMLRecordParserNoDoi.class);
private static final String NS_COMMON_URL = "http://www.orcid.org/ns/common";
private static final String NS_COMMON = "common";
private static final String NS_PERSON_URL = "http://www.orcid.org/ns/person";
private static final String NS_PERSON = "person";
private static final String NS_DETAILS_URL = "http://www.orcid.org/ns/personal-details";
private static final String NS_DETAILS = "personal-details";
private static final String NS_OTHER_URL = "http://www.orcid.org/ns/other-name";
private static final String NS_OTHER = "other-name";
private static final String NS_RECORD_URL = "http://www.orcid.org/ns/record";
private static final String NS_RECORD = "record";
private static final String NS_ERROR_URL = "http://www.orcid.org/ns/error";
private static final String NS_WORK = "work";
private static final String NS_WORK_URL = "http://www.orcid.org/ns/work";
private static final String NS_ERROR = "error";
public static WorkDataNoDoi VTDParseWorkData(byte[] bytes)
throws VtdException, EncodingException, EOFException, EntityException, ParseException, XPathParseException,
NavException, XPathEvalException {
logger.info("parsing xml ...");
final VTDGen vg = new VTDGen();
vg.setDoc(bytes);
vg.parse(true);
final VTDNav vn = vg.getNav();
final AutoPilot ap = new AutoPilot(vn);
ap.declareXPathNameSpace(NS_COMMON, NS_COMMON_URL);
ap.declareXPathNameSpace(NS_WORK, NS_WORK_URL);
ap.declareXPathNameSpace(NS_ERROR, NS_ERROR_URL);
WorkDataNoDoi workData = new WorkDataNoDoi();
final List<String> errors = VtdUtilityParser.getTextValue(ap, vn, "//error:response-code");
if (!errors.isEmpty()) {
workData.setErrorCode(errors.get(0));
return workData;
}
List<VtdUtilityParser.Node> workNodes = VtdUtilityParser
.getTextValuesWithAttributes(ap, vn, "//work:work", Arrays.asList("path", "put-code"));
if (!workNodes.isEmpty()) {
final String oid = (workNodes.get(0).getAttributes().get("path")).split("/")[1];
workData.setOid(oid);
final String id = (workNodes.get(0).getAttributes().get("put-code"));
workData.setId(id);
} else {
return null;
}
final List<String> titles = VtdUtilityParser
.getTextValue(
ap, vn, "//common:title");
if (!titles.isEmpty()) {
workData.setTitles(titles);
}
final List<String> sourceNames = VtdUtilityParser
.getTextValue(
ap, vn, "//common:source-name");
if (!sourceNames.isEmpty()) {
workData.setSourceName(sourceNames.get(0));
}
final List<String> types = VtdUtilityParser
.getTextValue(
ap, vn, "//work:type");
if (!types.isEmpty()) {
workData.setType(types.get(0));
}
final List<String> urls = VtdUtilityParser
.getTextValue(
ap, vn, "//common:url");
if (!urls.isEmpty()) {
workData.setUrls(urls);
}
workData.setPublicationDates(getPublicationDates(vg, vn, ap));
workData.setExtIds(getExternalIds(vg, vn, ap));
workData.setContributors(getContributors(vg, vn, ap));
return workData;
}
private static List<PublicationDate> getPublicationDates(VTDGen vg, VTDNav vn, AutoPilot ap)
throws XPathParseException, NavException, XPathEvalException {
List<PublicationDate> publicationDates = new ArrayList<PublicationDate>();
int yearIndex = 0;
ap.selectXPath("//common:publication-date/common:year");
while (ap.evalXPath() != -1) {
PublicationDate publicationDate = new PublicationDate();
int t = vn.getText();
if (t >= 0) {
publicationDate.setYear(vn.toNormalizedString(t));
publicationDates.add(yearIndex, publicationDate);
yearIndex++;
}
}
int monthIndex = 0;
ap.selectXPath("//common:publication-date/common:month");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
publicationDates.get(monthIndex).setMonth(vn.toNormalizedString(t));
monthIndex++;
}
}
int dayIndex = 0;
ap.selectXPath("//common:publication-date/common:day");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
publicationDates.get(dayIndex).setDay(vn.toNormalizedString(t));
dayIndex++;
}
}
return publicationDates;
}
private static List<ExternalId> getExternalIds(VTDGen vg, VTDNav vn, AutoPilot ap)
throws XPathParseException, NavException, XPathEvalException {
List<ExternalId> extIds = new ArrayList<ExternalId>();
int typeIndex = 0;
ap.selectXPath("//common:external-id/common:external-id-type");
while (ap.evalXPath() != -1) {
ExternalId extId = new ExternalId();
int t = vn.getText();
if (t >= 0) {
extId.setType(vn.toNormalizedString(t));
extIds.add(typeIndex, extId);
typeIndex++;
}
}
int valueIndex = 0;
ap.selectXPath("//common:external-id/common:external-id-value");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
extIds.get(valueIndex).setValue(vn.toNormalizedString(t));
valueIndex++;
}
}
int relationshipIndex = 0;
ap.selectXPath("//common:external-id/common:external-id-relationship");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
extIds.get(relationshipIndex).setRelationShip(vn.toNormalizedString(t));
relationshipIndex++;
}
}
if (typeIndex == valueIndex) {
return extIds;
}
return new ArrayList<ExternalId>();
}
private static List<Contributor> getContributors(VTDGen vg, VTDNav vn, AutoPilot ap)
throws XPathParseException, NavException, XPathEvalException {
List<Contributor> contributors = new ArrayList<Contributor>();
int nameIndex = 0;
ap.selectXPath("//work:contributor/work:credit-name");
while (ap.evalXPath() != -1) {
Contributor contributor = new Contributor();
int t = vn.getText();
if (t >= 0) {
contributor.setCreditName(vn.toNormalizedString(t));
contributors.add(nameIndex, contributor);
nameIndex++;
}
}
int sequenceIndex = 0;
ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-sequence");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
contributors.get(sequenceIndex).setSequence(vn.toNormalizedString(t));
sequenceIndex++;
}
}
int roleIndex = 0;
ap.selectXPath("//work:contributor/work:contributor-attributes/work:contributor-role");
while (ap.evalXPath() != -1) {
int t = vn.getText();
if (t >= 0) {
contributors.get(roleIndex).setRole(vn.toNormalizedString(t));
roleIndex++;
}
}
return contributors;
}
}

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@ -44,7 +44,7 @@ public class XMLRecordParserTest {
String xml = IOUtils
.toString(
this.getClass().getResourceAsStream("activity_work_0000-0002-5982-8983.xml"));
this.getClass().getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
XMLRecordParser p = new XMLRecordParser();

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@ -0,0 +1,326 @@
package eu.dnetlib.doiboost.orcidnodoi.xml;
import com.ximpleware.NavException;
import com.ximpleware.ParseException;
import com.ximpleware.XPathEvalException;
import com.ximpleware.XPathParseException;
import eu.dnetlib.dhp.parser.utility.VtdException;
import eu.dnetlib.doiboost.orcid.model.AuthorData;
import eu.dnetlib.doiboost.orcidnodoi.model.Contributor;
import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
import jdk.nashorn.internal.ir.annotations.Ignore;
import org.apache.commons.io.IOUtils;
import org.apache.commons.text.similarity.JaccardSimilarity;
import org.apache.commons.text.similarity.JaroWinklerSimilarity;
import org.junit.jupiter.api.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.text.Normalizer;
import java.util.*;
import static org.junit.jupiter.api.Assertions.assertNotNull;
public class OrcidNoDoiTest {
private static final Logger logger = LoggerFactory.getLogger(OrcidNoDoiTest.class);
String nameA = "Khairy";
String surnameA = "Abdel Dayem";
String otherNameA = "Dayem MKA";
String nameB = "K";
String surnameB = "Abdel-Dayem";
String orcidIdA = "0000-0003-2760-1191";
Double threshold = 0.8;
@Test
@Ignore
private void similarityTest() throws Exception {
logger.info("running testSimilarity ....");
logger
.info(
"JaroWinklerSimilarity: "
+ Double.toString(similarityJaroWinkler(nameA, surnameA, nameB, surnameB)));
logger
.info(
"JaccardSimilarity: " + Double.toString(similarityJaccard(nameA, surnameA, nameB, surnameB)));
}
@Test
@Ignore
private void bestMatchTest() throws Exception {
logger.info("running bestMatchTest ....");
String contributor = surnameB + ", " + nameB;
logger.info("score: " + Double.toString(bestMatch(surnameA, nameA, contributor)));
}
private static Double bestMatch(String authorSurname, String authorName, String contributor) {
logger.debug(authorSurname + " " + authorName + " vs " + contributor);
String[] contributorSplitted = contributor.split(" ");
if (contributorSplitted.length == 0) {
return 0.0;
}
final String contributorName = contributorSplitted[contributorSplitted.length - 1];
String contributorSurname = "";
if (contributorSplitted.length > 1) {
StringJoiner joiner = new StringJoiner(" ");
for (int i = 0; i < contributorSplitted.length - 1; i++) {
joiner.add(contributorSplitted[i]);
}
contributorSurname = joiner.toString();
}
logger
.debug(
"contributorName: " + contributorName +
" contributorSurname: " + contributorSurname);
String authorNameNrm = normalize(authorName);
String authorSurnameNrm = normalize(authorSurname);
String contributorNameNrm = normalize(contributorName);
String contributorSurnameNrm = normalize(contributorSurname);
Double sm1 = similarity(authorNameNrm, authorSurnameNrm, contributorNameNrm, contributorSurnameNrm);
Double sm2 = similarity(authorNameNrm, authorSurnameNrm, contributorSurnameNrm, contributorNameNrm);
if (sm1.compareTo(sm2) >= 0) {
return sm1;
}
return sm2;
}
private static Double similarity(String nameA, String surnameA, String nameB, String surnameB) {
Double score = similarityJaroWinkler(nameA, surnameA, nameB, surnameB);
logger
.debug(nameA + ", " + surnameA + " <> " + nameB + ", " + surnameB + " score: " + Double.toString(score));
return score;
}
private static Double similarityJaccard(String nameA, String surnameA, String nameB, String surnameB) {
return new JaccardSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
}
private static Double similarityJaroWinkler(String nameA, String surnameA, String nameB, String surnameB) {
return new JaroWinklerSimilarity().apply(normalize(parse(nameA, surnameA)), normalize(parse(nameB, surnameB)));
}
private static String parse(String name, String surname) {
return surname + " " + name;
}
private static String normalize(final String s) {
return nfd(s)
.toLowerCase()
// do not compact the regexes in a single expression, would cause StackOverflowError
// in case
// of large input strings
.replaceAll("(\\W)+", " ")
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
.replaceAll("(\\p{Punct})+", " ")
.replaceAll("(\\d)+", " ")
.replaceAll("(\\n)+", " ")
.trim();
}
private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
@Test
@Ignore
public void readPublicationFieldsTest()
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
logger.info("running loadPublicationFieldsTest ....");
String xml = IOUtils
.toString(
OrcidNoDoiTest.class.getResourceAsStream("activity_work_0000-0003-2760-1191.xml"));
if (xml == null) {
logger.info("Resource not found");
}
XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
if (p == null) {
logger.info("XMLRecordParserNoDoi null");
}
WorkDataNoDoi workData = null;
try {
workData = p.VTDParseWorkData(xml.getBytes());
} catch (Exception e) {
logger.error("parsing xml", e);
}
assertNotNull(workData);
assertNotNull(workData.getOid());
logger.info("oid: " + workData.getOid());
assertNotNull(workData.getTitles());
logger.info("titles: ");
workData.getTitles().forEach(t -> {
logger.info(t);
});
logger.info("source: " + workData.getSourceName());
logger.info("type: " + workData.getType());
logger.info("urls: ");
workData.getUrls().forEach(u -> {
logger.info(u);
});
logger.info("publication date: ");
workData.getPublicationDates().forEach(d -> {
logger.info(d.getYear() + " - " + d.getMonth() + " - " + d.getDay());
});
logger.info("external id: ");
workData.getExtIds().removeIf(e -> e.getRelationShip() != null && !e.getRelationShip().equals("self"));
workData.getExtIds().forEach(e -> {
logger.info(e.getType() + " - " + e.getValue() + " - " + e.getRelationShip());
});
logger.info("contributors: ");
workData.getContributors().forEach(c -> {
logger
.info(
c.getName() + " - " + c.getRole() + " - " + c.getSequence());
});
}
private void updateRanks(List<Contributor> contributors) {
boolean seqFound = false;
if (contributors
.stream()
.filter(
c -> c.getRole() != null && c.getSequence() != null &&
c.getRole().equals("author") && (c.getSequence().equals("first") ||
c.getSequence().equals("additional")))
.count() > 0) {
seqFound = true;
logger.info("sequence data found");
}
if (!seqFound) {
List<Integer> seqIds = Arrays.asList(0);
contributors.forEach(c -> {
int currentSeq = seqIds.get(0) + 1;
seqIds.set(0, currentSeq);
c.setSequence(Integer.toString(seqIds.get(0)));
});
}
}
private void updateAuthorsSimpleMatch(List<Contributor> contributors, AuthorData author) {
contributors.forEach(c -> {
if (c.isSimpleMatch()) {
logger.info("simple match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
}
});
updateRanks(contributors);
}
private void updateAuthorsSimilarityMatch(List<Contributor> contributors, AuthorData author) {
logger.info("inside updateAuthorsSimilarityMatch ...");
contributors.forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence() + " - best: " + c.isBestMatch() + " - simpe: "
+ c.isSimpleMatch());
});
contributors
.stream()
.filter(c -> c.isBestMatch())
.forEach(c -> {
logger.info("similarity match on : " + c.getCreditName());
c.setName(author.getName());
c.setSurname(author.getSurname());
c.setOid(author.getOid());
});
updateRanks(contributors);
}
@Test
@Ignore
public void authorSimilarityMatchTest() throws Exception {
logger.info("running authorSimilarityMatchTest ....");
authorMatchTest("activity_work_0000-0003-2760-1191-similarity.xml");
}
@Test
private void authorSimpleMatchTest() throws Exception {
logger.info("running authorSimpleMatchTest ....");
authorMatchTest("activity_work_0000-0003-2760-1191.xml");
}
private void authorMatchTest(String orcidWork)
throws IOException, XPathEvalException, XPathParseException, NavException, VtdException, ParseException {
AuthorData author = new AuthorData();
author.setName(nameA);
author.setSurname(surnameA);
author.setOid(orcidIdA);
String xml = IOUtils
.toString(
OrcidNoDoiTest.class.getResourceAsStream(orcidWork));
if (xml == null) {
logger.info("Resource not found");
}
XMLRecordParserNoDoi p = new XMLRecordParserNoDoi();
if (p == null) {
logger.info("XMLRecordParserNoDoi null");
}
WorkDataNoDoi workData = null;
try {
workData = p.VTDParseWorkData(xml.getBytes());
} catch (Exception e) {
logger.error("parsing xml", e);
}
assertNotNull(workData);
int matchCounter = 0;
List<Integer> matchCounters = Arrays.asList(matchCounter);
Contributor contributor = null;
workData.getContributors().forEach(c -> {
if (normalize(c.getCreditName()).contains(normalize(author.getName())) ||
normalize(c.getCreditName()).contains(normalize(author.getSurname())) ||
((author.getOtherName() != null)
&& normalize(c.getCreditName()).contains(normalize(author.getOtherName())))) {
matchCounters.set(0, matchCounters.get(0) + 1);
c.setSimpleMatch(true);
}
});
logger.info("match counter: " + Integer.toString(matchCounters.get(0)));
if (matchCounters.get(0) == 1) {
updateAuthorsSimpleMatch(workData.getContributors(), author);
} else if (matchCounters.get(0) > 1) {
Optional<Contributor> optCon = workData
.getContributors()
.stream()
.filter(c -> c.isSimpleMatch())
.map(c -> {
c.setScore(bestMatch(nameA, surnameA, c.getCreditName()));
logger.debug("nella map: " + c.getCreditName() + " score: " + c.getScore());
return c;
})
.filter(c -> c.getScore() >= threshold)
.max(Comparator.comparing(c -> c.getScore()));
Contributor bestMatchContributor = null;
if (optCon.isPresent()) {
bestMatchContributor = optCon.get();
bestMatchContributor.setBestMatch(true);
logger.info("best match: " + bestMatchContributor.getCreditName());
updateAuthorsSimilarityMatch(workData.getContributors(), author);
}
}
logger.info("UPDATED contributors: ");
workData.getContributors().forEach(c -> {
logger
.info(
c.getOid() + " - " + c.getCreditName() + " - " +
c.getName() + " - " + c.getSurname() + " - " +
c.getRole() + " - " + c.getSequence());
});
}
}
//
// orcid_RDD = sc.textFile(ORCID_DUMP_PATH)
// no_doi_works_RDD = orcid_RDD.map(orcid_map).filter(lambda x:x is not None).map(lambda x: json.dumps(x)).saveAsTextFile(path=ORCID_OPENAIRE_PATH,compressionCodecClass="org.apache.hadoop.io.compress.GzipCodec")
//

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@ -0,0 +1,106 @@
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<work:work xmlns:address="http://www.orcid.org/ns/address"
xmlns:email="http://www.orcid.org/ns/email" xmlns:history="http://www.orcid.org/ns/history"
xmlns:employment="http://www.orcid.org/ns/employment"
xmlns:education="http://www.orcid.org/ns/education"
xmlns:other-name="http://www.orcid.org/ns/other-name"
xmlns:deprecated="http://www.orcid.org/ns/deprecated"
xmlns:funding="http://www.orcid.org/ns/funding"
xmlns:research-resource="http://www.orcid.org/ns/research-resource"
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