DoiBoostAuthorMerger - first implementation and test class for the specific Author Merger for doiboost. First change: crossref as base to be enriched. If crossref is empty, the longest from all the merging providers is taken. Modified the normalization function to remove accents from words. Added class to store the most similar author list to be enriched w.r.t. one enriching author (related to DoiBoostAuthorMerger)

This commit is contained in:
Miriam Baglioni 2021-08-11 15:51:48 +02:00
parent 577f3b1ac8
commit 6a4af4abfc
4 changed files with 699 additions and 6 deletions

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@ -0,0 +1,47 @@
package eu.dnetlib.doiboost;
import eu.dnetlib.dhp.schema.oaf.Author;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
public class AuthorAssoc implements Serializable {
private Double score ;
private List<Author> to_be_enriched;
private Author with_enricheing_content;
public Double getScore() {
return score;
}
public void setScore(Double score) {
this.score = score;
}
public List<Author> getTo_be_enriched() {
return to_be_enriched;
}
public void setTo_be_enriched(List<Author> to_be_enriched) {
this.to_be_enriched = to_be_enriched;
}
public Author getWith_enricheing_content() {
return with_enricheing_content;
}
public void setWith_enricheing_content(Author with_enricheing_content) {
this.with_enricheing_content = with_enricheing_content;
}
public static AuthorAssoc newInstance(Author a){
AuthorAssoc ret = new AuthorAssoc();
ret.score = 0.0;
ret.to_be_enriched = new ArrayList<>();
ret.with_enricheing_content = a;
return ret;
}
}

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@ -0,0 +1,236 @@
package eu.dnetlib.doiboost;
import java.text.Normalizer;
import java.util.*;
import java.util.stream.Collectors;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.utils.DHPUtils;
import com.wcohen.ss.JaroWinkler;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import scala.Tuple2;
/**
* This is a version of the AuthorMerger specific for DoiBoost.
* Here we suppose a match must exist for the authors. We compare via JaroWrinkler similarity measure each author in the list
* that should be enriched with each author in the enriching list. For each enriching author we select the best match that is
* the author with the highest similarity score.
* The association is done from the enriching author to the enriched because in this way only one match per enriching author can be found
* One enriching author can have the same maximum similarity score with more than one
*
*
*
*
* The idea is to enrich the most similar authors having at least one
* word of the name in
* common
* Quello che faccio e abbastanza semplice: ho una struttura dati che mantine linformazione di associazione fra il record che puo possibilmente arricchire e quello che deve essere arricchito.
* 6:22
* Questa struttura ha la lista di autori che possono essere arricchiti, lautore che arricchisce e lo score di similarita fra lautore che arricchisce e gli autori arricchiti. E il valore di una mappa che per chiave la il fullname dellautore che arricchisce
* 6:23
* per ogni autore che puo essere arricchito verifico se la entri nella mappa di quello che arricchisce e associata ad un autore con score di similarita piu basso. Se cosi e modifico lassociazione nella mappa per lautore che arricchisce, sostituendo lautore arricchito a cui era associato prima con quello nuovo che ha score piu alto. Se lo score e lo stesso, aggiungo il nuovo autore da arricchire alla lista degli autori associata allautore che arricchisce
* 6:25
* Alla fine caso facile: ogni entry e associata ad un unico autore da arricchire => verifico che almeno una delle parole che sono nei due nomi sia in comune fra i due insiemi Se e cosi, aggiungo i pid mancanti allautore da arricchire dellautore che arricchisce
* 6:26
* caso brutto: ci sono piu autori da arricchire con la stessa similarita: arricchisco quello che ha il maggior numero di parole del fullname uguali a quelle dellautore che arricchisce. In caso di parita non si arricchisce
* 6:28
* ricordiamoci che si parte dal presupposto che un match debba esistere visto che abbiamo lo stesso doi
* 6:29
* di conseguenza lautore che ha lo score di similarita piu alto fra quelli presenti ed anche una parola in comune del nome dovrebbe essere sufficiente per poterlo arricchire.
* 6:30
* I casi di omonimia che potrebbero portare problemi con i rank degli autori non si mappano
*/
public class DoiBoostAuthorMerger {
public static List<Author> merge(List<List<Author>> authors, Boolean crossref) {
Iterator<List<Author>> it = authors.iterator();
List<Author> author = it.next();
while (it.hasNext()){
List<Author> autList = it.next();
Tuple2<List<Author>, Boolean> tmp = mergeAuthor(author, autList, crossref);
author = tmp._1();
crossref = tmp._2();
}
return author;
}
public static Tuple2<List<Author>, Boolean> mergeAuthor(final List<Author> baseAuthor, final List<Author> otherAuthor,
final Boolean crossref) {
if(baseAuthor == null || baseAuthor.size() == 0)
return new Tuple2<>(otherAuthor, false);
if(otherAuthor == null || otherAuthor.size() == 0)
return new Tuple2<>(baseAuthor, crossref);
if(crossref) {
enrichPidFromList(baseAuthor, otherAuthor);
return new Tuple2<>(baseAuthor, true);
}
else
if (baseAuthor.size() > otherAuthor.size()){
enrichPidFromList(baseAuthor, otherAuthor);
return new Tuple2<>(baseAuthor, false);
}else{
enrichPidFromList(otherAuthor, baseAuthor);
return new Tuple2<>(otherAuthor, false);
}
}
private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
//search authors having identifiers in the enrich list
final List<Author> authorsWithPids = enrich
.stream()
.filter(a -> a.getPid() != null && a.getPid().size() > 0)
.collect(Collectors.toList());
Map<String, AuthorAssoc> assocMap = authorsWithPids
.stream()
.map(
a -> new Tuple2<>(DHPUtils.md5(a.getFullname()), AuthorAssoc.newInstance(a)))
.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
//for each author in the base list, we search the best enriched match
base.stream()
.map(a -> new Tuple2<>(a, authorsWithPids.stream()
.map(e -> new Tuple2<>(e, sim(a, e))).collect(Collectors.toList())))
.forEach(t2 -> {
for (Tuple2<Author, Double> t : t2._2()) {
String mapEntry = DHPUtils.md5(t._1().getFullname());
AuthorAssoc aa = assocMap.get(mapEntry);
if(aa.getScore() < t._2() && aa.getScore() < 0.9){
aa.setScore(t._2());
aa.setTo_be_enriched(new ArrayList<>());
aa.getTo_be_enriched().add(t2._1());
}else if(t._2() > 0.9){
aa.getTo_be_enriched().add(t2._1());
}
}
});
assocMap.keySet().forEach(k -> enrichAuthor(assocMap.get(k)));
}
private static long getCommonWords(List<String> fullEnrich, List<String> fullEnriching){
return fullEnrich.stream().filter( w -> fullEnriching.contains(w)).count();
}
private static void enrichAuthor(Author enrich, Author enriching){
//verify if some of the words in the fullname are contained in the other
//get normalized fullname
long commonWords = getCommonWords(normalize(enrich.getFullname()),
normalize(enriching.getFullname()));
if(commonWords > 0 ){
if(enrich.getPid() == null){
enrich.setPid(new ArrayList<>());
}
Set<String> aPids = enrich.getPid().stream().map(p -> pidToComparableString(p)).collect(Collectors.toSet());
enriching.getPid().forEach(p -> {
if (!aPids.contains(pidToComparableString(p))){
enrich.getPid().add(p);
}
});
if (enrich.getAffiliation() == null){
if (enriching.getAffiliation() != null){
enrich.setAffiliation(enriching.getAffiliation());
}
}
}
}
//Verify the number of words in common. The one that has more, wins. If the number of words in common are the same we
//enrich no author
private static void enrichAuthor(AuthorAssoc authorAssoc) {
if (authorAssoc.getTo_be_enriched().size() == 1){
enrichAuthor(authorAssoc.getTo_be_enriched().get(0), authorAssoc.getWith_enricheing_content());
}else{
long common = 0;
List<Author> selected = new ArrayList<>() ;
for(Author a : authorAssoc.getTo_be_enriched()){
long current_common = getCommonWords(normalize(a.getFullname()),
normalize(authorAssoc.getWith_enricheing_content().getFullname()));
if (current_common > common){
common = current_common;
selected = new ArrayList<>();
selected.add(a);
}else if(current_common == common){
selected.add(a);
}
}
if (selected.size() == 1){
enrichAuthor(selected.get(0), authorAssoc.getWith_enricheing_content());
}
}
}
public static String pidToComparableString(StructuredProperty pid) {
return (pid.getQualifier() != null
? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
: "")
+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
}
private static Double sim(Author a, Author b) {
return new JaroWinkler()
.score(normalizeString(a.getFullname()), normalizeString(b.getFullname()));
}
private static String normalizeString(String fullname) {
return String.join(" ", normalize(fullname));
}
private static List<String> normalize(final String s) {
String[] normalized = nfd(s)
.replaceAll("[^\\p{ASCII}]", "")
.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()
.split(" ");
Arrays.sort(normalized);
return Arrays.asList(normalized);
}
private static String nfd(final String s) {
return Normalizer.normalize(s, Normalizer.Form.NFD);
}
}

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@ -3,7 +3,7 @@ package eu.dnetlib.doiboost
import eu.dnetlib.dhp.application.ArgumentApplicationParser
import eu.dnetlib.dhp.oa.merge.AuthorMerger
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.dhp.schema.oaf.{Author, Organization, Publication, Relation, Dataset => OafDataset}
import eu.dnetlib.doiboost.mag.ConversionUtil
import org.apache.commons.io.IOUtils
import org.apache.spark.SparkConf
@ -25,6 +25,7 @@ object SparkGenerateDoiBoost {
val conf: SparkConf = new SparkConf()
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json")))
parser.parseArgument(args)
var crossref : Boolean = true
val spark: SparkSession =
SparkSession
.builder()
@ -52,8 +53,8 @@ object SparkGenerateDoiBoost {
if (a != null && a._2 != null) {
b.mergeFrom(a._2)
b.setId(a._1)
val authors =AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor)
b.setAuthor(authors)
val authors =DoiBoostAuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor, true)
b.setAuthor(authors._1)
return b
}
}
@ -68,8 +69,8 @@ object SparkGenerateDoiBoost {
else {
if (b2 != null ) {
b1.mergeFrom(b2)
val authors =AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor)
b1.setAuthor(authors)
val authors = DoiBoostAuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor, true)
b1.setAuthor(authors._1)
if (b2.getId!= null && b2.getId.nonEmpty)
b1.setId(b2.getId)
return b1
@ -104,7 +105,10 @@ object SparkGenerateDoiBoost {
val otherPub = item._2._2
if (otherPub != null) {
crossrefPub.mergeFrom(otherPub)
crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor))
val mergeRes : (java.util.List[Author], java.lang.Boolean) = DoiBoostAuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor, crossref)
crossrefPub.setAuthor(mergeRes._1)
crossref = mergeRes._2
}
}
crossrefPub

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@ -0,0 +1,406 @@
package eu.dnetlib.dhp.doiboost;
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
import java.util.stream.Collectors;
import org.apache.neethi.Assertion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.doiboost.DoiBoostAuthorMerger;
import eu.dnetlib.pace.util.MapDocumentUtil;
import scala.Tuple2;
public class DoiBoostAuthorMergerTest {
private String publicationsBasePath;
private List<List<Author>> authors;
@BeforeEach
public void setUp() throws Exception {
publicationsBasePath = Paths
.get(DoiBoostAuthorMergerTest.class.getResource("/eu/dnetlib/dhp/doiboost").toURI())
.toFile()
.getAbsolutePath();
}
@Test
public void mergeTestOrcid() {
authors = readSample(publicationsBasePath + "/matching_authors_first.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(10, merge.size());
Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count());
merge
.stream()
.filter(a -> a.getPid() != null)
.forEach(
a -> Assertions
.assertTrue(
a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))));
merge.stream().filter(a -> a.getPid() != null).forEach(a -> {
try {
System.out.println(new ObjectMapper().writeValueAsString(a));
} catch (JsonProcessingException e) {
e.printStackTrace();
}
});
}
public <T> List<Tuple2<String, T>> readSample(String path, Class<T> clazz) {
List<Tuple2<String, T>> res = new ArrayList<>();
BufferedReader reader;
try {
reader = new BufferedReader(new FileReader(path));
String line = reader.readLine();
while (line != null) {
res
.add(
new Tuple2<>(
MapDocumentUtil.getJPathString("$.id", line),
new ObjectMapper().readValue(line, clazz)));
// read next line
line = reader.readLine();
}
reader.close();
} catch (IOException e) {
e.printStackTrace();
}
return res;
}
public String authorToString(Author a) {
String print = "Fullname = ";
print += a.getFullname() + " pid = [";
if (a.getPid() != null)
for (StructuredProperty sp : a.getPid()) {
print += sp.toComparableString() + " ";
}
print += "]";
return print;
}
@Test
public void mergeTestMAG() {
authors = readSample(publicationsBasePath + "/matching_authors_second", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
for (List<Author> authors1 : authors) {
System.out.println("List " + (authors.indexOf(authors1) + 1));
for (Author author : authors1) {
System.out.println(authorToString(author));
}
}
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(10, merge.size());
Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count());
merge
.stream()
.filter(a -> a.getPid() != null)
.forEach(
a -> Assertions
.assertTrue(
a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL"))));
merge.stream().filter(a -> a.getPid() != null).forEach(a -> {
try {
System.out.println(new ObjectMapper().writeValueAsString(a));
} catch (JsonProcessingException e) {
e.printStackTrace();
}
});
}
@Test
public void mergeTestCrossrefEmpty1() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/empty_crossref_authors_first.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(3, merge.size());
Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count());
merge
.stream()
.filter(a -> a.getPid() != null)
.forEach(
a -> Assertions
.assertTrue(
a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))));
merge.stream().filter(a -> a.getPid() != null).forEach(a -> {
try {
System.out.println(new ObjectMapper().writeValueAsString(a));
} catch (JsonProcessingException e) {
e.printStackTrace();
}
});
System.out.println(new ObjectMapper().writeValueAsString(merge));
}
@Test
public void mergeTestCrossrefEmpty2() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/empty_crossref_authors_second.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, false);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(10, merge.size());
Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count());
merge
.stream()
.filter(a -> a.getPid() != null)
.forEach(
a -> Assertions
.assertTrue(
a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL"))));
merge.stream().filter(a -> a.getPid() != null).forEach(a -> {
try {
System.out.println(new ObjectMapper().writeValueAsString(a));
} catch (JsonProcessingException e) {
e.printStackTrace();
}
});
Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
}
@Test
public void mergeTestCrossrefEmpty3() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/empty_crossref_author_third.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(10, merge.size());
Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count());
merge
.stream()
.filter(a -> a.getPid() != null)
.forEach(
a -> Assertions
.assertTrue(
a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL"))));
Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
}
@Test
public void mergeTestCrossrefEmpty4() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/empty_crossref_author_fourth.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
Assertions.assertEquals(3, merge.size());
Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count());
Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
}
@Test
public void shouldMergeTest1() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/should_appear_author1.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
Assertions.assertTrue(6 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count());
merge.stream().filter(a -> a.getRank() == 26)
.forEach(a ->
Assertions.assertTrue(a.getPid()
.stream()
.anyMatch(pid -> pid.getValue().equals("0000-0002-2445-5275")
&& pid.getQualifier().getClassid().equals(ModelConstants.ORCID)
)
)
);
}
@Test
public void shouldMergeTest2() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/should_appear_author2.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
Assertions.assertTrue(5 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null)
.filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count());
merge.stream().filter(a -> a.getFullname().equals("da luz geraldo eduardo"))
.forEach(a ->
Assertions.assertTrue(a.getPid()
.stream()
.anyMatch(pid -> pid.getValue().equals("http://orcid.org/0000-0003-2434-0387")
&& pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)
)
)
);
}
@Test
public void shouldNotMergeTest1() throws JsonProcessingException {
authors = readSample(publicationsBasePath + "/should_appear_author3.json", Publication.class)
.stream()
.map(p -> p._2().getAuthor())
.collect(Collectors.toList());
List<Author> merge = DoiBoostAuthorMerger.merge(authors, true);
System.out.println("Merge ");
for (Author author : merge) {
System.out.println(authorToString(author));
}
// Assertions.assertTrue(5 == merge.stream().filter(a -> a.getPid() !=null)
// .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count());
//
// Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null)
// .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count());
//
// merge.stream().filter(a -> a.getFullname().equals("da luz geraldo eduardo"))
// .forEach(a ->
// Assertions.assertTrue(a.getPid()
// .stream()
// .anyMatch(pid -> pid.getValue().equals("http://orcid.org/0000-0003-2434-0387")
// && pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING)
// )
// )
// );
}
}