forked from D-Net/dnet-hadoop
moved AuthoreMerger into dhp-common
This commit is contained in:
parent
fe0a7870e6
commit
eec418cd26
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@ -92,6 +92,17 @@
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<groupId>com.squareup.okhttp3</groupId>
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<artifactId>okhttp</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib</groupId>
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<artifactId>dnet-pace-core</artifactId>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-schemas</artifactId>
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<version>${project.version}</version>
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</dependency>
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</dependencies>
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</project>
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@ -0,0 +1,168 @@
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package eu.dnetlib.dhp.oa.merge;
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import java.text.Normalizer;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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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.StructuredProperty;
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import eu.dnetlib.pace.model.Person;
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import scala.Tuple2;
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public class AuthorMerger {
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private static final Double THRESHOLD = 0.95;
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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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List<Author> author = new ArrayList<>();
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for (List<Author> a : authors) {
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author = mergeAuthor(author, a);
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}
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return author;
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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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int pa = countAuthorsPids(a);
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int pb = countAuthorsPids(b);
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List<Author> base, enrich;
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int sa = authorsSize(a);
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int sb = authorsSize(b);
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if (pa == pb) {
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base = sa > sb ? a : b;
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enrich = sa > sb ? b : a;
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} else {
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base = pa > pb ? a : b;
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enrich = pa > pb ? b : a;
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}
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enrichPidFromList(base, enrich);
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return base;
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}
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private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
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if (base == null || enrich == null)
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return;
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final Map<String, Author> basePidAuthorMap = base
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.stream()
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.filter(a -> a.getPid() != null && a.getPid().size() > 0)
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.flatMap(
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a -> a
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.getPid()
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.stream()
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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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final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
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.stream()
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.filter(a -> a.getPid() != null && a.getPid().size() > 0)
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.flatMap(
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a -> a
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.getPid()
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.stream()
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.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
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.map(p -> new Tuple2<>(p, a)))
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.collect(Collectors.toList());
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pidToEnrich
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.forEach(
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a -> {
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Optional<Tuple2<Double, Author>> simAuthor = base
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.stream()
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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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if (simAuthor.isPresent()) {
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double th = THRESHOLD;
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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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&& simAuthor.get()._2().getSurname().length() <= 3)
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th = 0.99;
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if (simAuthor.get()._1() > th) {
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Author r = simAuthor.get()._2();
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if (r.getPid() == null) {
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r.setPid(new ArrayList<>());
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}
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r.getPid().add(a._1());
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}
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}
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});
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}
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public static String pidToComparableString(StructuredProperty pid) {
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return (pid.getQualifier() != null
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? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
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: "")
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+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
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}
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public static int countAuthorsPids(List<Author> authors) {
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if (authors == null)
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return 0;
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return (int) authors.stream().filter(AuthorMerger::hasPid).count();
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}
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private static int authorsSize(List<Author> authors) {
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if (authors == null)
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return 0;
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return authors.size();
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}
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private static Double sim(Author a, Author b) {
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final Person pa = parse(a);
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final Person pb = parse(b);
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// if both are accurate (e.g. they have name and surname)
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if (pa.isAccurate() & pb.isAccurate()) {
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return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5
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+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5;
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} else {
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return new JaroWinkler()
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.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
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}
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}
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private static boolean hasPid(Author a) {
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if (a == null || a.getPid() == null || a.getPid().size() == 0)
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return false;
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return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
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}
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private static Person parse(Author author) {
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if (StringUtils.isNotBlank(author.getSurname())) {
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return new Person(author.getSurname() + ", " + author.getName(), false);
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} else {
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return new Person(author.getFullname(), false);
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}
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}
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private static String normalize(final String s) {
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return nfd(s)
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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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// in case
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// of large input strings
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.replaceAll("(\\W)+", " ")
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.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
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.replaceAll("(\\p{Punct})+", " ")
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.replaceAll("(\\d)+", " ")
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.replaceAll("(\\n)+", " ")
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.trim();
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}
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private static String nfd(final String s) {
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return Normalizer.normalize(s, Normalizer.Form.NFD);
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}
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}
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@ -1,170 +0,0 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.text.Normalizer;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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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.StructuredProperty;
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import eu.dnetlib.pace.model.Person;
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import scala.Tuple2;
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public class AuthorMerger {
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private static final Double THRESHOLD = 0.95;
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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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List<Author> author = new ArrayList<>();
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for (List<Author> a : authors) {
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author = mergeAuthor(author, a);
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}
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return author;
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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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int pa = countAuthorsPids(a);
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int pb = countAuthorsPids(b);
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List<Author> base, enrich;
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int sa = authorsSize(a);
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int sb = authorsSize(b);
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if (pa == pb) {
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base = sa > sb ? a : b;
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enrich = sa > sb ? b : a;
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} else {
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base = pa > pb ? a : b;
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enrich = pa > pb ? b : a;
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}
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enrichPidFromList(base, enrich);
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return base;
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}
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private static void enrichPidFromList(List<Author> base, List<Author> enrich) {
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if (base == null || enrich == null)
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return;
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final Map<String, Author> basePidAuthorMap = base
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.stream()
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.filter(a -> a.getPid() != null && a.getPid().size() > 0)
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.flatMap(
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a -> a
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.getPid()
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.stream()
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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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final List<Tuple2<StructuredProperty, Author>> pidToEnrich = enrich
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.stream()
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.filter(a -> a.getPid() != null && a.getPid().size() > 0)
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.flatMap(
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a -> a
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.getPid()
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.stream()
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.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
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.map(p -> new Tuple2<>(p, a)))
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.collect(Collectors.toList());
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pidToEnrich
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.forEach(
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a -> {
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Optional<Tuple2<Double, Author>> simAuthor = base
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.stream()
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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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if (simAuthor.isPresent()) {
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double th = THRESHOLD;
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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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&& simAuthor.get()._2().getSurname().length() <= 3)
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th = 0.99;
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if (simAuthor.get()._1() > th) {
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Author r = simAuthor.get()._2();
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if (r.getPid() == null) {
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r.setPid(new ArrayList<>());
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}
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r.getPid().add(a._1());
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}
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}
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});
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}
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public static String pidToComparableString(StructuredProperty pid) {
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return (pid.getQualifier() != null
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? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : ""
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: "")
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+ (pid.getValue() != null ? pid.getValue().toLowerCase() : "");
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}
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public static int countAuthorsPids(List<Author> authors) {
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if (authors == null)
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return 0;
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return (int) authors.stream().filter(AuthorMerger::hasPid).count();
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}
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private static int authorsSize(List<Author> authors) {
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if (authors == null)
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return 0;
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return authors.size();
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}
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private static Double sim(Author a, Author b) {
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final Person pa = parse(a);
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final Person pb = parse(b);
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// if both are accurate (e.g. they have name and surname)
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if (pa.isAccurate() & pb.isAccurate()) {
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return new JaroWinkler().score(normalize(pa.getSurnameString()), normalize(pb.getSurnameString())) * 0.5
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+ new JaroWinkler().score(normalize(pa.getNameString()), normalize(pb.getNameString())) * 0.5;
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} else {
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return new JaroWinkler()
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.score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname()));
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}
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}
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private static boolean hasPid(Author a) {
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if (a == null || a.getPid() == null || a.getPid().size() == 0)
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return false;
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return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
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}
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private static Person parse(Author author) {
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if (StringUtils.isNotBlank(author.getSurname())) {
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return new Person(author.getSurname() + ", " + author.getName(), false);
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} else {
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return new Person(author.getFullname(), false);
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}
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}
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private static String normalize(final String s) {
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return nfd(s)
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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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// in case
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// of large input strings
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.replaceAll("(\\W)+", " ")
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.replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ")
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.replaceAll("(\\p{Punct})+", " ")
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.replaceAll("(\\d)+", " ")
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.replaceAll("(\\n)+", " ")
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.trim();
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}
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private static String nfd(final String s) {
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return Normalizer.normalize(s, Normalizer.Form.NFD);
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}
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}
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@ -1,11 +1,12 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.io.Serializable;
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import java.util.Collection;
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import java.util.Iterator;
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import java.util.List;
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import eu.dnetlib.dhp.oa.merge.AuthorMerger;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.api.java.function.MapGroupsFunction;
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import org.apache.spark.sql.Dataset;
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@ -10,6 +10,7 @@ import java.io.Serializable;
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import java.nio.file.Paths;
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import java.util.*;
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import eu.dnetlib.dhp.oa.merge.AuthorMerger;
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import org.codehaus.jackson.map.ObjectMapper;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Test;
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@ -83,13 +83,6 @@
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<artifactId>dhp-schemas</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>eu.dnetlib.dhp</groupId>
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<artifactId>dhp-dedup-openaire</artifactId>
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<version>${project.version}</version>
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</dependency>
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<dependency>
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<groupId>com.jayway.jsonpath</groupId>
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<artifactId>json-path</artifactId>
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.ebi
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import eu.dnetlib.dhp.oa.dedup.AuthorMerger
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import eu.dnetlib.dhp.oa.merge.AuthorMerger
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Dataset => OafDataset}
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import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
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import org.apache.spark.sql.{Encoder, Encoders}
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