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Enhance Dedup authors matching with algorithms used for ORCID enhancements (task 9690) #419

Merged
giambattista.bloisi merged 1 commits from dedup_authorsmatch_bytoken into beta 2024-04-16 10:24:12 +02:00
Conversation 0 Commits 1 Files Changed 6 +169 -94
6 changed files with 169 additions and 94 deletions
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7
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/MergeUtils.java
View File

@ -497,9 +497,14 @@ public class MergeUtils {
}
private static Field<String> selectOldestDate(Field<String> d1, Field<String> d2) {
if (d1 == null || StringUtils.isBlank(d1.getValue())) {
return d2;
} else if (d2 == null || StringUtils.isBlank(d2.getValue())) {
return d1;
}
return Stream
.of(d1, d2)
.filter(Objects::nonNull)
.min(
Comparator
.comparing(

45
dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/AuthorsMatch.java
View File

@ -1,16 +1,18 @@
package eu.dnetlib.pace.tree;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import com.wcohen.ss.AbstractStringDistance;
import eu.dnetlib.pace.config.Config;
import eu.dnetlib.pace.model.Person;
import eu.dnetlib.pace.tree.support.AbstractListComparator;
import eu.dnetlib.pace.tree.support.ComparatorClass;
import eu.dnetlib.pace.util.AuthorMatchers;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import java.util.function.BiFunction;
import java.util.stream.Collectors;
@ComparatorClass("authorsMatch")
public class AuthorsMatch extends AbstractListComparator {
@ -41,24 +43,36 @@ public class AuthorsMatch extends AbstractListComparator {
}
@Override
public double compare(final List<String> a, final List<String> b, final Config conf) {
if (a.isEmpty() || b.isEmpty())
public double compare(final List<String> left, final List<String> right, final Config conf) {
if (left.isEmpty() || right.isEmpty())
return -1;
if (a.size() > SIZE_THRESHOLD || b.size() > SIZE_THRESHOLD)
if (left.size() > SIZE_THRESHOLD || right.size() > SIZE_THRESHOLD)
return 1.0;
int maxMiss = Integer.MAX_VALUE;
List<Person> bList = b.stream().map(author -> new Person(author, false)).collect(Collectors.toList());
Double threshold = getDoubleParam("threshold");
int maxMiss = Integer.MAX_VALUE;
if (threshold != null && threshold >= 0.0 && threshold <= 1.0 && a.size() == b.size()) {
maxMiss = (int) Math.floor((1 - threshold) * Math.max(a.size(), b.size()));
if (threshold != null && threshold >= 0.0 && threshold <= 1.0 && left.size() == right.size()) {
maxMiss = (int) Math.floor((1 - threshold) * Math.max(left.size(), right.size()));
}
int common = 0;
List<String> a = new ArrayList<>(left);
List<String> b = new ArrayList<>(right);
common += AuthorMatchers
.removeMatches(a, b, (BiFunction<String, String, Object>) AuthorMatchers::matchEqualsIgnoreCase)
.size() / 2;
common += AuthorMatchers
.removeMatches(a, b, (BiFunction<String, String, Object>) AuthorMatchers::matchOrderedTokenAndAbbreviations)
.size() / 2;
List<Person> bList = b.stream().map(author -> new Person(author, false)).collect(Collectors.toList());
// compare each element of List1 with each element of List2
int alreadyMatched = common;
for (int i = 0; i < a.size(); i++) {
Person p1 = new Person(a.get(i), false);
@ -123,13 +137,13 @@ public class AuthorsMatch extends AbstractListComparator {
}
}
if (i - common > maxMiss) {
if (i - common - alreadyMatched > maxMiss) {
return 0.0;
}
}
// normalization factor to compute the score
int normFactor = a.size() == b.size() ? a.size() : (a.size() + b.size() - common);
int normFactor = left.size() == right.size() ? left.size() : (left.size() + right.size() - common);
if (TYPE.equals("percentage")) {
return (double) common / normFactor;
@ -160,5 +174,4 @@ public class AuthorsMatch extends AbstractListComparator {
public String normalization(String s) {
return normalize(utf8(cleanup(s)));
}
}

53
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchers.scala → dhp-pace-core/src/main/java/eu/dnetlib/pace/util/AuthorMatchers.scala
View File

@ -1,9 +1,10 @@
package eu.dnetlib.dhp.enrich.orcid
package eu.dnetlib.pace.util
import java.util.Locale
import java.util.regex.Pattern
import scala.util.control.Breaks.{break, breakable}
object ORCIDAuthorMatchers {
object AuthorMatchers {
val SPLIT_REGEX = Pattern.compile("[\\s,\\.]+")
val WORD_DIFF = 2
@ -45,7 +46,8 @@ object ORCIDAuthorMatchers {
var res: Boolean = false
if (e1.length != 1 && e2.length != 1) {
res = e1 == e2
longMatches += 1
if (res)
longMatches += 1
} else {
res = true
shortMatches += 1
@ -62,4 +64,49 @@ object ORCIDAuthorMatchers {
}
longMatches > 0 && (shortMatches + longMatches) == Math.min(p1.length, p2.length)
}
def removeMatches(
graph_authors: java.util.List[String],
orcid_authors: java.util.List[String],
matchingFunc: java.util.function.BiFunction[String,String,Boolean]
) : java.util.List[String] = {
removeMatches(graph_authors, orcid_authors, (a, b) => matchingFunc(a,b))
}
def removeMatches(
graph_authors: java.util.List[String],
orcid_authors: java.util.List[String],
matchingFunc: (String, String) => Boolean
) : java.util.List[String] = {
val matched = new java.util.ArrayList[String]()
if (graph_authors != null && !graph_authors.isEmpty) {
val ait = graph_authors.iterator
while (ait.hasNext) {
val author = ait.next()
val oit = orcid_authors.iterator
breakable {
while (oit.hasNext) {
val orcid = oit.next()
if (matchingFunc(author, orcid)) {
ait.remove()
oit.remove()
matched.add(author)
matched.add(orcid)
break()
}
}
}
}
}
matched
}
}

145
dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkDedupTest.java
View File

@ -43,15 +43,13 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.schema.sx.OafUtils;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
import scala.Tuple2;
@ExtendWith(MockitoExtension.class)
@TestMethodOrder(MethodOrderer.OrderAnnotation.class)
public class SparkDedupTest implements Serializable {
static final boolean CHECK_CARDINALITIES = true;
@Mock(serializable = true)
ISLookUpService isLookUpService;
@ -191,12 +189,13 @@ public class SparkDedupTest implements Serializable {
System.out.println("ds_simrel = " + ds_simrel);
System.out.println("orp_simrel = " + orp_simrel);
assertEquals(751, orgs_simrel);
assertEquals(546, pubs_simrel);
assertEquals(113, sw_simrel);
assertEquals(148, ds_simrel);
assertEquals(280, orp_simrel);
if (CHECK_CARDINALITIES) {
assertEquals(751, orgs_simrel);
assertEquals(566, pubs_simrel);
assertEquals(113, sw_simrel);
assertEquals(148, ds_simrel);
assertEquals(280, orp_simrel);
}
}
@Test
@ -239,21 +238,27 @@ public class SparkDedupTest implements Serializable {
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "otherresearchproduct"))
.count();
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
assertEquals(751, orgs_simrel);
assertEquals(546, pubs_simrel);
assertEquals(148, ds_simrel);
assertEquals(280, orp_simrel);
// System.out.println("orgs_simrel = " + orgs_simrel);
// System.out.println("pubs_simrel = " + pubs_simrel);
// System.out.println("ds_simrel = " + ds_simrel);
// System.out.println("orp_simrel = " + orp_simrel);
// entities simrels to be different from the number of previous step (new simrels in the whitelist)
Dataset<Row> sw_simrel = spark
.read()
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"));
System.out.println("orgs_simrel = " + orgs_simrel);
System.out.println("pubs_simrel = " + pubs_simrel);
System.out.println("ds_simrel = " + ds_simrel);
System.out.println("orp_simrel = " + orp_simrel);
System.out.println("sw_simrel = " + sw_simrel.count());
// entities simrels supposed to be equal to the number of previous step (no rels in whitelist)
if (CHECK_CARDINALITIES) {
assertEquals(751, orgs_simrel);
assertEquals(566, pubs_simrel);
assertEquals(148, ds_simrel);
assertEquals(280, orp_simrel);
assertEquals(115, sw_simrel.count());
}
// check if the first relation in the whitelist exists
assertTrue(
sw_simrel
@ -272,10 +277,6 @@ public class SparkDedupTest implements Serializable {
rel -> rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0])
&& rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1]))
.count() > 0);
assertEquals(115, sw_simrel.count());
// System.out.println("sw_simrel = " + sw_simrel.count());
}
@Test
@ -466,17 +467,19 @@ public class SparkDedupTest implements Serializable {
assertTrue(dups.contains(r.getSource()));
});
assertEquals(1268, orgs_mergerel);
assertEquals(1112, pubs.count());
assertEquals(292, sw_mergerel);
assertEquals(476, ds_mergerel);
assertEquals(742, orp_mergerel);
// System.out.println("orgs_mergerel = " + orgs_mergerel);
// System.out.println("pubs_mergerel = " + pubs_mergerel);
// System.out.println("sw_mergerel = " + sw_mergerel);
// System.out.println("ds_mergerel = " + ds_mergerel);
// System.out.println("orp_mergerel = " + orp_mergerel);
System.out.println("orgs_mergerel = " + orgs_mergerel);
System.out.println("pubs_mergerel = " + pubs.count());
System.out.println("sw_mergerel = " + sw_mergerel);
System.out.println("ds_mergerel = " + ds_mergerel);
System.out.println("orp_mergerel = " + orp_mergerel);
if (CHECK_CARDINALITIES) {
assertEquals(1268, orgs_mergerel);
assertEquals(1156, pubs.count());
assertEquals(292, sw_mergerel);
assertEquals(476, ds_mergerel);
assertEquals(742, orp_mergerel);
}
}
@Test
@ -552,17 +555,19 @@ public class SparkDedupTest implements Serializable {
assertTrue(dups.contains(r.getSource()));
});
assertEquals(1268, orgs_mergerel);
assertEquals(1112, pubs.count());
assertEquals(292, sw_mergerel);
assertEquals(476, ds_mergerel);
assertEquals(742, orp_mergerel);
// System.out.println("orgs_mergerel = " + orgs_mergerel);
// System.out.println("pubs_mergerel = " + pubs_mergerel);
// System.out.println("sw_mergerel = " + sw_mergerel);
// System.out.println("ds_mergerel = " + ds_mergerel);
// System.out.println("orp_mergerel = " + orp_mergerel);
System.out.println("orgs_mergerel = " + orgs_mergerel);
System.out.println("pubs_mergerel = " + pubs.count());
System.out.println("sw_mergerel = " + sw_mergerel);
System.out.println("ds_mergerel = " + ds_mergerel);
System.out.println("orp_mergerel = " + orp_mergerel);
if (CHECK_CARDINALITIES) {
assertEquals(1268, orgs_mergerel);
assertEquals(1156, pubs.count());
assertEquals(292, sw_mergerel);
assertEquals(476, ds_mergerel);
assertEquals(742, orp_mergerel);
}
}
@Test
@ -607,19 +612,21 @@ public class SparkDedupTest implements Serializable {
testOutputBasePath + "/" + testActionSetId + "/otherresearchproduct_deduprecord")
.count();
assertEquals(86, orgs_deduprecord);
assertEquals(91, pubs.count());
assertEquals(47, sw_deduprecord);
assertEquals(97, ds_deduprecord);
assertEquals(92, orp_deduprecord);
System.out.println("orgs_deduprecord = " + orgs_deduprecord);
System.out.println("pubs_deduprecord = " + pubs.count());
System.out.println("sw_deduprecord = " + sw_deduprecord);
System.out.println("ds_deduprecord = " + ds_deduprecord);
System.out.println("orp_deduprecord = " + orp_deduprecord);
if (CHECK_CARDINALITIES) {
assertEquals(86, orgs_deduprecord);
assertEquals(96, pubs.count());
assertEquals(47, sw_deduprecord);
assertEquals(97, ds_deduprecord);
assertEquals(92, orp_deduprecord);
}
verifyRoot_1(mapper, pubs);
// System.out.println("orgs_deduprecord = " + orgs_deduprecord);
// System.out.println("pubs_deduprecord = " + pubs_deduprecord);
// System.out.println("sw_deduprecord = " + sw_deduprecord);
// System.out.println("ds_deduprecord = " + ds_deduprecord);
// System.out.println("orp_deduprecord = " + orp_deduprecord);
}
private static void verifyRoot_1(ObjectMapper mapper, Dataset<Publication> pubs) {
@ -745,21 +752,23 @@ public class SparkDedupTest implements Serializable {
.distinct()
.count();
assertEquals(925, publications);
assertEquals(839, organizations);
assertEquals(100, projects);
assertEquals(100, datasource);
assertEquals(196, softwares);
assertEquals(389, dataset);
assertEquals(520, otherresearchproduct);
System.out.println("publications = " + publications);
System.out.println("organizations = " + organizations);
System.out.println("projects = " + projects);
System.out.println("datasource = " + datasource);
System.out.println("software = " + softwares);
System.out.println("dataset = " + dataset);
System.out.println("otherresearchproduct = " + otherresearchproduct);
// System.out.println("publications = " + publications);
// System.out.println("organizations = " + organizations);
// System.out.println("projects = " + projects);
// System.out.println("datasource = " + datasource);
// System.out.println("software = " + softwares);
// System.out.println("dataset = " + dataset);
// System.out.println("otherresearchproduct = " + otherresearchproduct);
if (CHECK_CARDINALITIES) {
assertEquals(930, publications);
assertEquals(839, organizations);
assertEquals(100, projects);
assertEquals(100, datasource);
assertEquals(196, softwares);
assertEquals(389, dataset);
assertEquals(520, otherresearchproduct);
}
long deletedOrgs = jsc
.textFile(testDedupGraphBasePath + "/organization")

11
dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorEnricher.scala
View File

@ -3,6 +3,7 @@ package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.{Author, StructuredProperty}
import eu.dnetlib.dhp.schema.sx.OafUtils
import eu.dnetlib.pace.util.AuthorMatchers
import java.util
import scala.beans.BeanProperty
@ -39,7 +40,7 @@ object ORCIDAuthorEnricher extends Serializable {
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.givenName + " " + orcid.familyName),
AuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.givenName + " " + orcid.familyName),
"fullName"
) ++
// Look after exact reversed fullname match, reconstruct ORCID fullname as familyName + givenName
@ -47,7 +48,7 @@ object ORCIDAuthorEnricher extends Serializable {
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.familyName + " " + orcid.givenName),
AuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.familyName + " " + orcid.givenName),
"reversedFullName"
) ++
// split author names in tokens, order the tokens, then check for matches of full tokens or abbreviations
@ -55,7 +56,7 @@ object ORCIDAuthorEnricher extends Serializable {
unmatched_authors,
orcid_authors,
(author, orcid) =>
ORCIDAuthorMatchers
AuthorMatchers
.matchOrderedTokenAndAbbreviations(author.getFullname, orcid.givenName + " " + orcid.familyName),
"orderedTokens"
) ++
@ -63,7 +64,7 @@ object ORCIDAuthorEnricher extends Serializable {
extractAndEnrichMatches(
unmatched_authors,
orcid_authors,
(author, orcid) => ORCIDAuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.creditName),
(author, orcid) => AuthorMatchers.matchEqualsIgnoreCase(author.getFullname, orcid.creditName),
"creditName"
) ++
// look after exact matches in ORCID otherNames
@ -71,7 +72,7 @@ object ORCIDAuthorEnricher extends Serializable {
unmatched_authors,
orcid_authors,
(author, orcid) =>
orcid.otherNames != null && ORCIDAuthorMatchers.matchOtherNames(author.getFullname, orcid.otherNames.asScala),
orcid.otherNames != null && AuthorMatchers.matchOtherNames(author.getFullname, orcid.otherNames.asScala),
"otherNames"
)
}

2
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/enrich/orcid/ORCIDAuthorMatchersTest.scala
View File

@ -1,6 +1,6 @@
package eu.dnetlib.dhp.enrich.orcid
import eu.dnetlib.dhp.enrich.orcid.ORCIDAuthorMatchers.matchOrderedTokenAndAbbreviations
import eu.dnetlib.pace.util.AuthorMatchers.matchOrderedTokenAndAbbreviations
import org.junit.jupiter.api.Assertions.{assertFalse, assertTrue}
import org.junit.jupiter.api.Test