From 6f4d0c05eae2965d5b2afde1d78627cbf2ebbd63 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Tue, 28 Nov 2023 08:43:56 +0100 Subject: [PATCH] Implemented Author MErger for ORCID that takes in account the case when name and surname are swapped --- .../eu/dnetlib/dhp/oa/merge/AuthorMerger.java | 114 ++++-------------- .../eu/dnetlib/oa/merge/AuthorMergerTest.java | 33 ++--- .../dhp/oa/merge/authors_orcid_sample.json | 3 + .../oa/merge/authors_publication_sample.json | 2 + .../SparkEnrichGraphWithOrcidAuthors.scala | 15 ++- 5 files changed, 51 insertions(+), 116 deletions(-) create mode 100644 dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json create mode 100644 dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java index 6c3058303..852ee163d 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/oa/merge/AuthorMerger.java @@ -159,17 +159,11 @@ public class AuthorMerger { .replaceAll("(\\p{Punct})+", " ") .replaceAll("(\\d)+", " ") .replaceAll("(\\n)+", " ") + .trim(); // return Arrays.stream(fullname.split("[\\s | , | ;]+")).map(String::toLowerCase).sorted().collect(Collectors.joining()); } - private static String generateAuthorkey(final Author a) { - if (a.getSurname() == null) - return "NOSURNAME"; - - return normalize(a.getSurname()); - } - // // public static List enrichOrcid2(List baseAuthor, List orcidAuthor) { // if (baseAuthor == null || baseAuthor.isEmpty()) @@ -226,54 +220,26 @@ public class AuthorMerger { return null; } - public static boolean checkSimilarity3(final Author left, final Author right) { - - if (StringUtils.isNotBlank(left.getSurname()) && StringUtils.isNotBlank(left.getName()) - && - StringUtils.isNotBlank(right.getSurname()) && StringUtils.isNotBlank(right.getName()) - - ) - return left.getSurname().equalsIgnoreCase(right.getSurname()) - && left.getName().substring(0, 1).equalsIgnoreCase(right.getName().substring(0, 1)); - - final Person pl = parse(left); - final Person pr = parse(right); - - // If one of them didn't have a surname the match is false - if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && - pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) - return false; - - // The Authors have one surname in common - if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { - - // If one of them has only a surname and is the same we can say that they are the same author - if ((pl.getName() == null || pl.getName().stream().allMatch(StringUtils::isBlank)) || - (pr.getName() == null || pr.getName().stream().allMatch(StringUtils::isBlank))) - return true; - // The authors have the same initials of Name in common - if (pl - .getName() - .stream() - .anyMatch( - nl -> pr - .getName() - .stream() - .anyMatch(nr -> nr.substring(0, 1).equalsIgnoreCase(nl.substring(0, 1))))) - return true; - } - return false; - } - public static boolean checkSimilarity2(final Author left, final Author right) { final Person pl = parse(left); final Person pr = parse(right); - // If one of them didn't have a surname the match is false + // If one of them didn't have a surname we verify if they have the fullName not empty + // and verify if the normalized version is equal if (!(pl.getSurname() != null && pl.getSurname().stream().anyMatch(StringUtils::isNotBlank) && - pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) - return false; + pr.getSurname() != null && pr.getSurname().stream().anyMatch(StringUtils::isNotBlank))) { + if (pl.getFullname() != null && !pl.getFullname().isEmpty() && pr.getFullname() != null + && !pr.getFullname().isEmpty()) { + return pl + .getFullname() + .stream() + .anyMatch( + fl -> pr.getFullname().stream().anyMatch(fr -> normalize(fl).equalsIgnoreCase(normalize(fr)))); + } else { + return false; + } + } // The Authors have one surname in common if (pl.getSurname().stream().anyMatch(sl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(sl)))) { @@ -292,56 +258,18 @@ public class AuthorMerger { .anyMatch(nr -> nr.substring(0, 1).equalsIgnoreCase(nl.substring(0, 1))))) return true; } - return false; - } - public static boolean checkSimilarity(final Author left, final Author right) { - - if (left.getSurname() == null && left.getFullname() == null) + // Sometimes we noticed that publication have author wrote in inverse order Surname, Name + // We verify if we have an exact match between name and surname + if (pl.getSurname().stream().anyMatch(sl -> pr.getName().stream().anyMatch(nr -> nr.equalsIgnoreCase(sl))) && + pl.getName().stream().anyMatch(nl -> pr.getSurname().stream().anyMatch(sr -> sr.equalsIgnoreCase(nl)))) + return true; + else return false; - if (right.getSurname() == null && right.getFullname() == null) - return false; - - // The Authors have the same surname, or we are tolerant from 1 different char(lets say 1 Typo) - if (StringUtils.isNotBlank(left.getSurname()) && StringUtils.isNotBlank(right.getSurname())) { - if (left.getSurname().equalsIgnoreCase(right.getSurname()) - || hammingDist(left.getSurname().toLowerCase(), right.getSurname().toLowerCase()) < 2) { - // IN case on of the two Authors has no given Name the match is true - if (StringUtils.isBlank(left.getName()) || StringUtils.isBlank(right.getName())) - return true; - // If the surname is correct, and they have the same name or the name starts with the same Letter we can - // say is the same author - if (left.getName().equalsIgnoreCase(right.getName()) - || left.getName().substring(0, 1).equalsIgnoreCase(right.getName().substring(0, 1))) - return true; - } - // Different SURNAME - else { - return false; - } - } else { - // This is the case where the two authors have or the surname or the fullname - // get the first not null of the surname or fullname of both - final String l = authorFieldToBeCompared(left); - final String r = authorFieldToBeCompared(right); - if (l == null || r == null) - return false; - // The same length means they are the same field - if (l.length() == r.length()) { - return normalize(l).equals(normalize(r)); - } - // In this case probably l contains the surname and r contains the fullname - if (l.length() < r.length()) - return normalize(r).contains(normalize(l)); - // In this case probably l contains the fullname and r contains the surname - return normalize(l).contains(normalize(r)); - } - return false; } public static List enrichOrcid2(List baseAuthor, List orcidAuthor) { - final Integer match_itm = 0; if (baseAuthor == null || baseAuthor.isEmpty()) return orcidAuthor; diff --git a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java index 7f8d673d1..9eccab5f1 100644 --- a/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/oa/merge/AuthorMergerTest.java @@ -9,6 +9,7 @@ import java.io.IOException; import java.io.InputStreamReader; import java.util.Arrays; import java.util.List; +import java.util.Objects; import java.util.stream.Collectors; import org.junit.jupiter.api.Test; @@ -22,22 +23,15 @@ import eu.dnetlib.dhp.schema.oaf.Author; public class AuthorMergerTest { + @Test - public void testNormalization() { - - assertEquals("bruzzolasandro", AuthorMerger.normalizeFullName("Sandro, La Bruzzo")); - assertEquals("baglionimiriam", AuthorMerger.normalizeFullName("Miriam Baglioni")); - assertEquals("baglionimiriam", AuthorMerger.normalizeFullName("Miriam ;Baglioni,")); - - } - public void testEnrcichAuthor() throws Exception { final ObjectMapper mapper = new ObjectMapper(); BufferedReader pr = new BufferedReader(new InputStreamReader( - AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication.json"))); + Objects.requireNonNull(AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_publication_sample.json")))); BufferedReader or = new BufferedReader(new InputStreamReader( - AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid.json"))); + Objects.requireNonNull(AuthorMergerTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json")))); TypeReference> aclass = new TypeReference>() { }; @@ -93,32 +87,27 @@ public class AuthorMergerTest { enrichedAuthorWithPid); System.out.println("================="); - - if (++i > 30) - break; } - } - } @Test public void checkSimilarityTest() { final Author left = new Author(); - left.setSurname("Wu"); - left.setName("M."); - left.setFullname("Wu, M."); + left.setName("Anand"); + left.setSurname("Rachna"); + left.setFullname("Anand, Rachna"); System.out.println(AuthorMerger.normalizeFullName(left.getFullname())); final Author right = new Author(); - right.setName("Xin"); - right.setSurname("Wu"); - right.setFullname("Xin Wu"); + right.setName("Rachna"); + right.setSurname("Anand"); + right.setFullname("Rachna, Anand"); // System.out.println(AuthorMerger.normalize(right.getFullname())); boolean same = AuthorMerger.checkSimilarity2(left, right); - assertFalse(same); + assertTrue(same); } diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json new file mode 100644 index 000000000..ec521b3b7 --- /dev/null +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/oa/merge/authors_orcid_sample.json @@ -0,0 +1,3 @@ +WrappedArray(arXiv1507.08202) +50|arXiv_dedup_::34e03f2336b8b28286550425e65634ea +[{"fullname":"Liron Barak","name":"Liron","surname":"Barak","rank":null,"pid":[{"value":"0000-0002-3436-2726","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Giuseppe Avolio","name":"Giuseppe","surname":"Avolio","rank":null,"pid":[{"value":"0000-0003-2664-3437","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Tobias Golling","name":"Tobias","surname":"Golling","rank":null,"pid":[{"value":"0000-0001-8535-6687","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Ivan Sykora","name":"Ivan","surname":"Sykora","rank":null,"pid":[{"value":"0000-0003-3447-5621","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Joao Carvalho","name":"Joao","surname":"Carvalho","rank":null,"pid":[{"value":"0000-0002-3015-7821","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Jonathan David Long","name":"Jonathan David","surname":"Long","rank":null,"pid":[{"value":"0000-0002-2115-9382","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Heather Russell","name":"Heather","surname":"Russell","rank":null,"pid":[{"value":"0000-0003-4181-0678","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Alison Lister","name":"Alison","surname":"Lister","rank":null,"pid":[{"value":"0000-0002-1552-3651","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Malte Backhaus","name":"Malte","surname":"Backhaus","rank":null,"pid":[{"value":"0000-0002-5888-2304","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Xin Wu","name":"Xin","surname":"Wu","rank":null,"pid":[{"value":"0000-0001-7655-389X","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Luke Lambourne","name":"Luke","surname":"Lambourne","rank":null,"pid":[{"value":"0000-0002-7001-7575","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Kazunori Hanagaki","name":"Kazunori","surname":"Hanagaki","rank":null,"pid":[{"value":"0000-0003-0676-0441","qualifier":{"classid":"ORCID","classname":"ORCID","schemeid":"ORCID","schemename":"ORCID"},"dataInfo":null}],"affiliation":null},{"fullname":"Krzysztof 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Romano","surname":"Saez","rank":115,"pid":[],"affiliation":null},{"fullname":"Santoni, C.","name":"C.","surname":"Santoni","rank":116,"pid":[],"affiliation":null},{"fullname":"Simon, D.","name":"D.","surname":"Simon","rank":117,"pid":[],"affiliation":null},{"fullname":"Theveneaux-Pelzer, Timothée","name":"Timothée","surname":"Theveneaux-Pelzer","rank":118,"pid":[],"affiliation":null},{"fullname":"Vazeille, F.","name":"F.","surname":"Vazeille","rank":119,"pid":[],"affiliation":null},{"fullname":"Yatsenko, E.","name":"E.","surname":"Yatsenko","rank":120,"pid":[],"affiliation":null}] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala index e190b2b33..9b85ba4f2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/enrich/orcid/SparkEnrichGraphWithOrcidAuthors.scala @@ -27,6 +27,8 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] def enrichResult(spark: SparkSession, graphPath: String, orcidPath: String, outputPath: String): Unit = { val orcidPublication = generateOrcidTable(spark, orcidPath) + + implicit val publicationEncoder = Encoders.bean(classOf[Publication]) val aschema = new StructType() @@ -68,6 +70,16 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] .select("dnet_id", "orcid_authors") .cache() + + orcidPublication + .join( + entities, + lower(col("schema")).equalTo(lower(col("pid_schema"))) && + lower(col("value")).equalTo(lower(col("pid_value"))), + "inner" + ) + .groupBy(col("dnet_id")).agg(collect_set(struct(col("pid_schema"), col("pid_value")))).write.mode("Overwrite").save("/user/sandro.labruzzo/enrich_pub") + val publication = spark.read.schema(publicationEncoder.schema).json(graphPath).as[Publication] publication @@ -95,13 +107,14 @@ class SparkEnrichGraphWithOrcidAuthors(propertyPath: String, args: Array[String] .where( "identifier.schema = 'doi' or identifier.schema ='pmid' or identifier.schema ='pmc' or identifier.schema ='arxiv' or identifier.schema ='handle'" ) - orcidAuthors + val orcidPublication =orcidAuthors .join(orcidWorks, orcidAuthors("orcid").equalTo(orcidWorks("orcid"))) .select( col("identifier.schema").alias("schema"), col("identifier.value").alias("value"), struct(orcidAuthors("orcid").alias("orcid"), col("givenName"), col("familyName")).alias("author") ) + orcidPublication } }