code formatting
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@ -4,318 +4,319 @@ package eu.dnetlib.dhp.oa.merge;
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import java.text.Normalizer;
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import java.text.Normalizer;
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import java.util.*;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.StringUtils;
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import com.wcohen.ss.JaroWinkler;
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import com.wcohen.ss.JaroWinkler;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.Author;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.pace.model.Person;
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import eu.dnetlib.pace.model.Person;
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import scala.Tuple2;
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import scala.Tuple2;
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public class AuthorMerger {
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public class AuthorMerger {
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private static final Double THRESHOLD = 0.95;
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private static final Double THRESHOLD = 0.95;
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private AuthorMerger() {
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private AuthorMerger() {
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}
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}
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public static List<Author> merge(List<List<Author>> authors) {
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public static List<Author> merge(List<List<Author>> authors) {
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authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)));
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authors.sort((o1, o2) -> -Integer.compare(countAuthorsPids(o1), countAuthorsPids(o2)));
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List<Author> author = new ArrayList<>();
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List<Author> author = new ArrayList<>();
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for (List<Author> a : authors) {
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for (List<Author> a : authors) {
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author = mergeAuthor(author, a);
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author = mergeAuthor(author, a);
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}
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}
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return author;
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return author;
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}
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}
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public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
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public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b, Double threshold) {
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int pa = countAuthorsPids(a);
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int pa = countAuthorsPids(a);
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int pb = countAuthorsPids(b);
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int pb = countAuthorsPids(b);
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List<Author> base;
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List<Author> base;
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List<Author> enrich;
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List<Author> enrich;
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int sa = authorsSize(a);
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int sa = authorsSize(a);
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int sb = authorsSize(b);
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int sb = authorsSize(b);
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if (sa == sb) {
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if (sa == sb) {
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base = pa > pb ? a : b;
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base = pa > pb ? a : b;
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enrich = pa > pb ? b : a;
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enrich = pa > pb ? b : a;
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} else {
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} else {
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base = sa > sb ? a : b;
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base = sa > sb ? a : b;
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enrich = sa > sb ? b : a;
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enrich = sa > sb ? b : a;
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}
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}
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enrichPidFromList(base, enrich, threshold);
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enrichPidFromList(base, enrich, threshold);
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return base;
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return base;
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}
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}
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public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
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public static List<Author> mergeAuthor(final List<Author> a, final List<Author> b) {
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return mergeAuthor(a, b, THRESHOLD);
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return mergeAuthor(a, b, THRESHOLD);
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}
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}
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private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
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private static void enrichPidFromList(List<Author> base, List<Author> enrich, Double threshold) {
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if (base == null || enrich == null)
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if (base == null || enrich == null)
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return;
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return;
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// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
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// <pidComparableString, Author> (if an Author has more than 1 pid, it appears 2 times in the list)
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final Map<String, Author> basePidAuthorMap = base
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final Map<String, Author> basePidAuthorMap = base
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.stream()
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.flatMap(
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.flatMap(
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a -> a
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a -> a
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.getPid()
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.getPid()
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.stream()
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.stream()
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.filter(Objects::nonNull)
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.filter(Objects::nonNull)
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.map(p -> new Tuple2<>(pidToComparableString(p), a)))
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.map(p -> new Tuple2<>(pidToComparableString(p), a)))
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.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
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.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
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// <pid, Author> (list of pid that are missing in the other list)
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// <pid, Author> (list of pid that are missing in the other list)
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final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
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final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
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.stream()
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.stream()
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.filter(a -> a.getPid() != null && !a.getPid().isEmpty())
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.flatMap(
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.flatMap(
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a -> a
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a -> a
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.getPid()
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.getPid()
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.stream()
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.stream()
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.filter(Objects::nonNull)
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.filter(Objects::nonNull)
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.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
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.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
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.map(p -> new Tuple2<>(p, a)))
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.map(p -> new Tuple2<>(p, a)))
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.collect(Collectors.toList());
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.collect(Collectors.toList());
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pidToEnrich
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pidToEnrich
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.forEach(
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.forEach(
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a -> {
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a -> {
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Optional<Tuple2<Double, Author>> simAuthor = base
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Optional<Tuple2<Double, Author>> simAuthor = base
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.stream()
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.stream()
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.map(ba -> new Tuple2<>(sim(ba, a._2()), ba))
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.map(ba -> new Tuple2<>(sim(ba, a._2()), ba))
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.max(Comparator.comparing(Tuple2::_1));
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.max(Comparator.comparing(Tuple2::_1));
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if (simAuthor.isPresent()) {
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if (simAuthor.isPresent()) {
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double th = threshold;
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double th = threshold;
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// increase the threshold if the surname is too short
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// increase the threshold if the surname is too short
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if (simAuthor.get()._2().getSurname() != null
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if (simAuthor.get()._2().getSurname() != null
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&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
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&& simAuthor.get()._2().getSurname().length() <= 3 && threshold > 0.0)
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th = 0.99;
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th = 0.99;
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if (simAuthor.get()._1() > th) {
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if (simAuthor.get()._1() > th) {
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Author r = simAuthor.get()._2();
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Author r = simAuthor.get()._2();
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if (r.getPid() == null) {
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if (r.getPid() == null) {
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r.setPid(new ArrayList<>());
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r.setPid(new ArrayList<>());
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}
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}
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// TERRIBLE HACK but for some reason when we create and Array with Arrays.asList,
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// TERRIBLE HACK but for some reason when we create and Array with Arrays.asList,
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// it creates of fixed size, and the add method raise UnsupportedOperationException at
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// it creates of fixed size, and the add method raise UnsupportedOperationException at
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// java.util.AbstractList.add
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// java.util.AbstractList.add
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final List<StructuredProperty> tmp = new ArrayList<>(r.getPid());
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final List<StructuredProperty> tmp = new ArrayList<>(r.getPid());
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tmp.add(a._1());
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tmp.add(a._1());
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r.setPid(tmp);
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r.setPid(tmp);
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}
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}
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}
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}
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});
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});
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}
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}
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public static String normalizeFullName(final String fullname) {
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public static String normalizeFullName(final String fullname) {
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return nfd(fullname)
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return nfd(fullname)
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.toLowerCase()
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.toLowerCase()
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// do not compact the regexes in a single expression, would cause StackOverflowError
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// do not compact the regexes in a single expression, would cause StackOverflowError
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// in case
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// in case
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// of large input strings
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// of large input strings
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.replaceAll("(\\W)+", " ")
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.replaceAll("(\\W)+", " ")
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.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
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.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
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.replaceAll("(\\p{Punct})+", " ")
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.replaceAll("(\\p{Punct})+", " ")
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.replaceAll("(\\d)+", " ")
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.replaceAll("(\\d)+", " ")
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.replaceAll("(\\n)+", " ")
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.replaceAll("(\\n)+", " ")
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.trim();
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.trim();
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}
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}
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private static String authorFieldToBeCompared(Author author) {
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if (StringUtils.isNotBlank(author.getSurname())) {
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return author.getSurname();
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private static String authorFieldToBeCompared(Author author) {
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}
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if (StringUtils.isNotBlank(author.getSurname())) {
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if (StringUtils.isNotBlank(author.getFullname())) {
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return author.getSurname();
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return author.getFullname();
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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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if (StringUtils.isNotBlank(author.getFullname())) {
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* This method tries to figure out when two author are the same in the contest
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return author.getFullname();
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* of ORCID enrichment
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}
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*
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return null;
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* @param left Author in the OAF entity
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}
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* @param right Author ORCID
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* @return based on a heuristic on the names of the authors if they are the same.
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*/
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public static boolean checkORCIDSimilarity(final Author left, final Author right) {
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final Person pl = parse(left);
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final Person pr = parse(right);
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/**
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// If one of them didn't have a surname we verify if they have the fullName not empty
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* This method tries to figure out when two author are the same in the contest
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// and verify if the normalized version is equal
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* of ORCID enrichment
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if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) &&
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*
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pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) {
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* @param left Author in the OAF entity
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* @param right Author ORCID
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* @return based on a heuristic on the names of the authors if they are the same.
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*/
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public static boolean checkORCIDSimilarity(final Author left, final Author right) {
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final Person pl = parse(left);
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final Person pr = parse(right);
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// If one of them didn't have a surname we verify if they have the fullName not empty
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if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
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// and verify if the normalized version is equal
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&& !pr.getFullname().isEmpty()) {
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if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) &&
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return pl
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pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) {
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.getFullname()
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.stream()
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.anyMatch(
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fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
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} else {
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return false;
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}
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}
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// The Authors have one surname in common
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if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
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if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null
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// If one of them has only a surname and is the same we can say that they are the same author
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&& !pr.getFullname().isEmpty()) {
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if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
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return pl
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(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
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.getFullname()
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return true;
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.stream()
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// The authors have the same initials of Name in common
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.anyMatch(
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if (pl
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fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr))));
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.getName()
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} else {
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.stream()
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return false;
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.anyMatch(
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}
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nl -> pr
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}
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.getName()
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// The Authors have one surname in common
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.stream()
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if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) {
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.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
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return true;
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}
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// If one of them has only a surname and is the same we can say that they are the same author
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// Sometimes we noticed that publication have author wrote in inverse order Surname, Name
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if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) ||
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// We verify if we have an exact match between name and surname
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(pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank)))
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if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) &&
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return true;
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pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl))))
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// The authors have the same initials of Name in common
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return true;
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if (pl
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else
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.getName()
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return false;
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.stream()
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}
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.anyMatch(
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//
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nl -> pr
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.getName()
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.stream()
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.anyMatch(nr -> nr.equalsIgnoreCase(nl))))
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return true;
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}
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// Sometimes we noticed that publication have author wrote in inverse order Surname, Name
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/**
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// We verify if we have an exact match between name and surname
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* Method to enrich ORCID information in one list of authors based on another list
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if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) &&
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*
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pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl))))
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* @param baseAuthor the Author List in the OAF Entity
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return true;
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* @param orcidAuthor The list of ORCID Author intersected
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else
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* @return The Author List of the OAF Entity enriched with the orcid Author
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return false;
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*/
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}
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public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
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//
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/**
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if (baseAuthor == null || baseAuthor.isEmpty())
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* Method to enrich ORCID information in one list of authors based on another list
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return orcidAuthor;
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*
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* @param baseAuthor the Author List in the OAF Entity
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* @param orcidAuthor The list of ORCID Author intersected
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* @return The Author List of the OAF Entity enriched with the orcid Author
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*/
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public static List<Author> enrichOrcid(List<Author> baseAuthor, List<Author> orcidAuthor) {
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if (baseAuthor == null || baseAuthor.isEmpty())
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if (orcidAuthor == null || orcidAuthor.isEmpty())
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return orcidAuthor;
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return baseAuthor;
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if (orcidAuthor == null || orcidAuthor.isEmpty())
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if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
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return baseAuthor;
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return baseAuthor;
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if (baseAuthor.size() == 1 && orcidAuthor.size() > 10)
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final List<Author> oAuthor = new ArrayList<>();
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return baseAuthor;
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oAuthor.addAll(orcidAuthor);
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final List<Author> oAuthor = new ArrayList<>();
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baseAuthor.forEach(ba -> {
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oAuthor.addAll(orcidAuthor);
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Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
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if (aMatch.isPresent()) {
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final Author sameAuthor = aMatch.get();
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addPid(ba, sameAuthor.getPid());
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oAuthor.remove(sameAuthor);
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}
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});
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return baseAuthor;
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}
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baseAuthor.forEach(ba -> {
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private static void addPid(final Author a, final List<StructuredProperty> pids) {
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Optional<Author> aMatch = oAuthor.stream().filter(oa -> checkORCIDSimilarity(ba, oa)).findFirst();
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if (aMatch.isPresent()) {
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final Author sameAuthor = aMatch.get();
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addPid(ba, sameAuthor.getPid());
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oAuthor.remove(sameAuthor);
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}
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});
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return baseAuthor;
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}
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private static void addPid(final Author a, final List<StructuredProperty> pids) {
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if (a.getPid() == null) {
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a.setPid(new ArrayList<>());
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}
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if (a.getPid() == null) {
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a.getPid().addAll(pids);
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a.setPid(new ArrayList<>());
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}
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a.getPid().addAll(pids);
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}
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}
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public static String pidToComparableString(StructuredProperty pid) {
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final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
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: "";
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return (pid.getQualifier() != null ? classid : "")
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+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
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}
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||||||
public static String pidToComparableString(StructuredProperty pid) {
|
public static int countAuthorsPids(List<Author> authors) {
|
||||||
final String classid = pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase()
|
if (authors == null)
|
||||||
: "";
|
return 0;
|
||||||
return (pid.getQualifier() != null ? classid : "")
|
|
||||||
+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
|
|
||||||
}
|
|
||||||
|
|
||||||
public static int countAuthorsPids(List<Author> authors) {
|
return (int) authors.stream().filter(AuthorMerger::hasPid).count();
|
||||||
if (authors == null)
|
}
|
||||||
return 0;
|
|
||||||
|
|
||||||
return (int) authors.stream().filter(AuthorMerger::hasPid).count();
|
private static int authorsSize(List<Author> authors) {
|
||||||
}
|
if (authors == null)
|
||||||
|
return 0;
|
||||||
|
return authors.size();
|
||||||
|
}
|
||||||
|
|
||||||
private static int authorsSize(List<Author> authors) {
|
private static Double sim(Author a, Author b) {
|
||||||
if (authors == null)
|
|
||||||
return 0;
|
|
||||||
return authors.size();
|
|
||||||
}
|
|
||||||
|
|
||||||
private static Double sim(Author a, Author b) {
|
final Person pa = parse(a);
|
||||||
|
final Person pb = parse(b);
|
||||||
|
|
||||||
final Person pa = parse(a);
|
// if both are accurate (e.g. they have name and surname)
|
||||||
final Person pb = parse(b);
|
if (pa.isAccurate() & pb.isAccurate()) {
|
||||||
|
return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5
|
||||||
|
+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5;
|
||||||
|
} else {
|
||||||
|
return new JaroWinkler()
|
||||||
|
.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
// if both are accurate (e.g. they have name and surname)
|
private static boolean hasPid(Author a) {
|
||||||
if (pa.isAccurate() & pb.isAccurate()) {
|
if (a == null || a.getPid() == null || a.getPid().isEmpty())
|
||||||
return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5
|
return false;
|
||||||
+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5;
|
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
|
||||||
} else {
|
}
|
||||||
return new JaroWinkler()
|
|
||||||
.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
private static boolean hasPid(Author a) {
|
private static Person parse(Author author) {
|
||||||
if (a == null || a.getPid() == null || a.getPid().isEmpty())
|
if (StringUtils.isNotBlank(author.getSurname())) {
|
||||||
return false;
|
return new Person(author.getSurname() + ", " + author.getName(), false);
|
||||||
return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
|
} else {
|
||||||
}
|
if (StringUtils.isNotBlank(author.getFullname()))
|
||||||
|
return new Person(author.getFullname(), false);
|
||||||
|
else
|
||||||
|
return new Person("", false);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
private static Person parse(Author author) {
|
public static String normalize(final String s) {
|
||||||
if (StringUtils.isNotBlank(author.getSurname())) {
|
String[] normalized = nfd(s)
|
||||||
return new Person(author.getSurname() + ", " + author.getName(), false);
|
.toLowerCase()
|
||||||
} else {
|
// do not compact the regexes in a single expression, would cause StackOverflowError
|
||||||
if (StringUtils.isNotBlank(author.getFullname()))
|
// in case
|
||||||
return new Person(author.getFullname(), false);
|
// of large input strings
|
||||||
else
|
.replaceAll("(\\W)+", " ")
|
||||||
return new Person("", false);
|
.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
|
||||||
}
|
.replaceAll("(\\p{Punct})+", " ")
|
||||||
}
|
.replaceAll("(\\d)+", " ")
|
||||||
|
.replaceAll("(\\n)+", " ")
|
||||||
|
.trim()
|
||||||
|
.split(" ");
|
||||||
|
|
||||||
public static String normalize(final String s) {
|
Arrays.sort(normalized);
|
||||||
String[] normalized = 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()
|
|
||||||
.split(" ");
|
|
||||||
|
|
||||||
Arrays.sort(normalized);
|
return String.join(" ", normalized);
|
||||||
|
}
|
||||||
|
|
||||||
return String.join(" ", normalized);
|
private static String nfd(final String s) {
|
||||||
}
|
return Normalizer.normalize(s, Normalizer.Form.NFD);
|
||||||
|
}
|
||||||
private static String nfd(final String s) {
|
|
||||||
return Normalizer.normalize(s, Normalizer.Form.NFD);
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue