From 2408083566923dc2f9af86d6228da4417b077131 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Sat, 23 May 2020 08:46:49 +0200 Subject: [PATCH] implemented filtering step --- .../eu/dnetlib/dhp/oa/dedup/AuthorMerger.java | 25 +- .../dhp/oa/dedup/EntityMergerTest.java | 2 +- .../doiboost/DoiBoostMappingUtil.scala | 301 +++++++++++++----- .../doiboost/SparkGenerateDoiBoost.scala | 15 +- .../eu/dnetlib/dhp/doiboost/hbMap.json | 1 + .../doiboost/DoiBoostHostedByMapTest.scala | 16 + 6 files changed, 254 insertions(+), 106 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/hbMap.json create mode 100644 dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostHostedByMapTest.scala diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java index 5e63c4b65..ee5fd5165 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AuthorMerger.java @@ -82,10 +82,11 @@ public class AuthorMerger { .map(ba -> new Tuple2<>(sim(ba, a._2()), ba)) .max(Comparator.comparing(Tuple2::_1)); - if(simAuthor.isPresent()) { + if (simAuthor.isPresent()) { double th = THRESHOLD; - //increase the threshold if the surname is too short - if (simAuthor.get()._2().getSurname() != null && simAuthor.get()._2().getSurname().length()<=3) + // increase the threshold if the surname is too short + if (simAuthor.get()._2().getSurname() != null + && simAuthor.get()._2().getSurname().length() <= 3) th = 0.99; if (simAuthor.get()._1() > th) { @@ -100,9 +101,10 @@ public class AuthorMerger { } public static String pidToComparableString(StructuredProperty pid) { - return (pid.getQualifier() != null ? - pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" : "") - + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + return (pid.getQualifier() != null + ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" + : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); } public static int countAuthorsPids(List authors) { @@ -123,14 +125,13 @@ public class AuthorMerger { final Person pa = parse(a); final Person pb = parse(b); - //if both are accurate (e.g. they have name and surname) + // if both are accurate (e.g. they have name and surname) 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; + 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())); + return new JaroWinkler() + .score(normalize(pa.getNormalisedFullname()), normalize(pb.getNormalisedFullname())); } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java index 55879030b..144d5d49a 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/EntityMergerTest.java @@ -96,7 +96,7 @@ public class EntityMergerTest implements Serializable { public void publicationMergerTest2() throws InstantiationException, IllegalAccessException, IOException { Publication pub_merged = DedupRecordFactory - .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); + .entityMerger(dedupId, publications2.iterator(), 0, dataInfo, Publication.class); assertEquals(pub_merged.getAuthor().size(), 27); // insert assertions here diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 60ad790a7..d16a549d3 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -1,13 +1,22 @@ package eu.dnetlib.doiboost -import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, KeyValue, Qualifier, Result, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf.{DataInfo, Dataset, Field, Instance, KeyValue, Publication, Qualifier, Result, StructuredProperty} import eu.dnetlib.dhp.utils.DHPUtils +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse + +import scala.collection.JavaConverters._ +import scala.io.Source + + +case class HostedByItemType(id: String, officialName: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} object DoiBoostMappingUtil { //STATIC STRING val MAG = "microsoft" - val MAG_NAME= "Microsoft Academic Graph" + val MAG_NAME = "Microsoft Academic Graph" val ORCID = "ORCID" val CROSSREF = "Crossref" val UNPAYWALL = "UnpayWall" @@ -19,112 +28,234 @@ object DoiBoostMappingUtil { val DNET_LANGUAGES = "dnet:languages" val PID_TYPES = "dnet:pid_types" + val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;") - def generateDataInfo(): DataInfo = { - generateDataInfo("0.9") + def retrieveHostedByMap(): Map[String, HostedByItemType] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + val jsonMap = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/hbMap.json")).mkString + lazy val json: json4s.JValue = parse(jsonMap) + json.extract[Map[String, HostedByItemType]] } - def generateDataInfo(trust:String): DataInfo = { - val di = new DataInfo - di.setDeletedbyinference(false) - di.setInferred(false) - di.setInvisible(false) - di.setTrust(trust) - di.setProvenanceaction(createQualifier("sysimport:actionset", "dnet:provenanceActions")) - di - } + def retrieveHostedByItem(issn: String, eissn: String, lissn: String, hostedByMap: Map[String, HostedByItemType]): HostedByItemType = { + if (issn != null && issn.nonEmpty && hostedByMap.contains(issn)) + return hostedByMap(issn) + if (eissn != null && eissn.nonEmpty && hostedByMap.contains(eissn)) + return hostedByMap(eissn) - def createSP(value: String, classId: String, schemeId: String): StructuredProperty = { - val sp = new StructuredProperty - sp.setQualifier(createQualifier(classId, schemeId)) - sp.setValue(value) - sp + if (lissn != null && lissn.nonEmpty && hostedByMap.contains(lissn)) + return hostedByMap(lissn) - } - - def createSP(value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = { - val sp = new StructuredProperty - sp.setQualifier(createQualifier(classId, schemeId)) - sp.setValue(value) - sp.setDataInfo(dataInfo) - sp - - } - - def createCrossrefCollectedFrom(): KeyValue = { - - val cf = new KeyValue - cf.setValue(CROSSREF) - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(CROSSREF.toLowerCase)) - cf - - } - - - def createUnpayWallCollectedFrom(): KeyValue = { - - val cf = new KeyValue - cf.setValue(UNPAYWALL) - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(UNPAYWALL.toLowerCase)) - cf - - } - - def createORIDCollectedFrom(): KeyValue = { - - val cf = new KeyValue - cf.setValue(ORCID) - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ORCID.toLowerCase)) - cf + null } - def generateIdentifier(oaf: Result, doi: String): String = { - val id = DHPUtils.md5(doi.toLowerCase) - if (oaf.isInstanceOf[Dataset]) - return s"60|${doiBoostNSPREFIX}${SEPARATOR}${id}" - s"50|${doiBoostNSPREFIX}${SEPARATOR}${id}" - } + + def fixPublication(publication: Publication, hostedByMap: Map[String, HostedByItemType]): Publication = { + if (publication.getJournal == null) + return publication + + val issn = publication.getJournal.getIssnPrinted + val eissn = publication.getJournal.getIssnOnline + val lissn = publication.getJournal.getIssnLinking + + val item = retrieveHostedByItem(issn, eissn, lissn, hostedByMap) + if (item!= null) { + val l = publication.getInstance().asScala.map(i =>{ + val hb = new KeyValue + hb.setValue (item.officialName) + hb.setKey (s"10|${item.id}" ) + i.setHostedby(hb) + if(item.openAccess) + i.setAccessright(createQualifier("Open", "dnet:access_modes")) + i + }).asJava + + publication.setInstance(l) + } + publication +} +def generateDataInfo (): DataInfo = { + generateDataInfo ("0.9") +} + def filterPublication (publication: Publication): Boolean = { - def createMAGCollectedFrom(): KeyValue = { + //Case empty publication + if (publication == null) + return false - val cf = new KeyValue - cf.setValue(MAG) - cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(MAG)) - cf - - } - - def createQualifier(clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = { - val q = new Qualifier - q.setClassid(clsName) - q.setClassname(clsValue) - q.setSchemeid(schName) - q.setSchemename(schValue) - q - } - - def createQualifier(cls: String, sch: String): Qualifier = { - createQualifier(cls, cls, sch, sch) - } + //Case publication with no title + if (publication.getTitle == null || publication.getTitle.size == 0) + return false - def asField[T](value: T): Field[T] = { - val tmp = new Field[T] - tmp.setValue(value) - tmp + val s = publication.getTitle.asScala.count (p => p.getValue != null + && p.getValue.nonEmpty && ! p.getValue.equalsIgnoreCase ("[NO TITLE AVAILABLE]") ) + + if (s == 0) + return false + + // fixes #4360 (test publisher) + val publisher = if (publication.getPublisher != null) publication.getPublisher.getValue else null + + if (publisher != null && (publisher.equalsIgnoreCase ("Test accounts") || publisher.equalsIgnoreCase ("CrossRef Test Account") ) ) { + return false; +} + + //Publication with no Author + if (publication.getAuthor == null || publication.getAuthor.size () == 0) + return false - } + //filter invalid author + val authors = publication.getAuthor.asScala.map (s => { + if (s.getFullname.nonEmpty) { + s.getFullname +} + else + s"${ + s.getName +} ${ + s.getSurname +}" +}) + val c = authors.count (isValidAuthorName) + if (c == 0) + return false + + // fixes #4368 + if (authors.count (s => s.equalsIgnoreCase ("Addie Jackson") ) > 0 && "Elsevier BV".equalsIgnoreCase (publication.getPublisher.getValue) ) + return false + + true +} + + + def isValidAuthorName (fullName: String): Boolean = { + if (fullName == null || fullName.isEmpty) + return false + if (invalidName.contains (fullName.toLowerCase.trim) ) + return false + true +} + + + def generateDataInfo (trust: String): DataInfo = { + val di = new DataInfo + di.setDeletedbyinference (false) + di.setInferred (false) + di.setInvisible (false) + di.setTrust (trust) + di.setProvenanceaction (createQualifier ("sysimport:actionset", "dnet:provenanceActions") ) + di +} + + + def createSP (value: String, classId: String, schemeId: String): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier (createQualifier (classId, schemeId) ) + sp.setValue (value) + sp + +} + + def createSP (value: String, classId: String, schemeId: String, dataInfo: DataInfo): StructuredProperty = { + val sp = new StructuredProperty + sp.setQualifier (createQualifier (classId, schemeId) ) + sp.setValue (value) + sp.setDataInfo (dataInfo) + sp + +} + + def createCrossrefCollectedFrom (): KeyValue = { + + val cf = new KeyValue + cf.setValue (CROSSREF) + cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (CROSSREF.toLowerCase) ) + cf + +} + + + def createUnpayWallCollectedFrom (): KeyValue = { + + val cf = new KeyValue + cf.setValue (UNPAYWALL) + cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (UNPAYWALL.toLowerCase) ) + cf + +} + + def createORIDCollectedFrom (): KeyValue = { + + val cf = new KeyValue + cf.setValue (ORCID) + cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (ORCID.toLowerCase) ) + cf + +} + + + def generateIdentifier (oaf: Result, doi: String): String = { + val id = DHPUtils.md5 (doi.toLowerCase) + if (oaf.isInstanceOf[Dataset] ) + return s"60|${ + doiBoostNSPREFIX +}${ + SEPARATOR +}${ + id +}" + s"50|${ + doiBoostNSPREFIX +}${ + SEPARATOR +}${ + id +}" +} + + + def createMAGCollectedFrom (): KeyValue = { + + val cf = new KeyValue + cf.setValue (MAG) + cf.setKey ("10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5 (MAG) ) + cf + +} + + def createQualifier (clsName: String, clsValue: String, schName: String, schValue: String): Qualifier = { + val q = new Qualifier + q.setClassid (clsName) + q.setClassname (clsValue) + q.setSchemeid (schName) + q.setSchemename (schValue) + q +} + + def createQualifier (cls: String, sch: String): Qualifier = { + createQualifier (cls, cls, sch, sch) +} + + + def asField[T] (value: T): Field[T] = { + val tmp = new Field[T] + tmp.setValue (value) + tmp + + +} } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 4d8c4a342..2efa3aa5e 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -32,11 +32,11 @@ object SparkGenerateDoiBoost { logger.info("Phase 1) repartition and move all the dataset in a same working folder") - spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication") - spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s => s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset") - spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication") - spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication") - spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication") +// spark.read.load(crossrefPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefPublication") +// spark.read.load(crossrefDatasetPath).as(Encoders.bean(classOf[OafDataset])).map(s => s)(Encoders.kryo[OafDataset]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/crossrefDataset") +// spark.read.load(uwPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/uwPublication") +// spark.read.load(orcidPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/orcidPublication") +// spark.read.load(magPublicationPath).as(Encoders.bean(classOf[Publication])).map(s => s)(Encoders.kryo[Publication]).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/magPublication") implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] @@ -67,14 +67,13 @@ object SparkGenerateDoiBoost { logger.info("Phase 3) Join Result with MAG") val sj: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/secondJoin").as[Publication].map(p => (p.getId, p)) - sj.where(sj("_1").like()) - val magPublication: Dataset[(String, Publication)] = spark.read.load(s"$workingDirPath/magPublication").as[Publication].map(p => (p.getId, p)) sj.joinWith(magPublication, sj("_1").equalTo(magPublication("_1")), "left").map(applyMerge).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublication") + val doiBoostPublication: Dataset[Publication] = spark.read.load(s"$workingDirPath/doiBoostPublication").as[Publication] - + doiBoostPublication.filter(p=>DoiBoostMappingUtil.filterPublication(p)).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationFiltered") diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/hbMap.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/hbMap.json new file mode 100644 index 000000000..b4c7b3a05 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/hbMap.json @@ -0,0 +1 @@ +{"19718357": {"id": "openaire____::issn19718357", "officialName": "Argomenti. Rivista di economia, cultura e ricerca sociale", "issn": "19718357", "eissn": "19718357", "lissn": "", "openAccess": false}, "1234123X": {"id": "openaire____::issn1234123X", "officialName": "Testing The Journal Registration Again", "issn": "1234123X", "eissn": "1234123X", "lissn": "12341234", "openAccess": false}, "12341234": {"id": "openaire____::issn12341234", "officialName": "test", "issn": "12341234", "eissn": "", "lissn": "", "openAccess": false}, "1300-4050": {"id": "doajarticles::1300-4050", "officialName": "Marmara \u0130leti\u015fim Dergisi", "issn": "1300-4050", "eissn": "2529-0053", "lissn": "", "openAccess": true}, "12341233": {"id": "openaire____::issn12341233", "officialName": "One More Journal", "issn": "12341233", "eissn": "", "lissn": "", "openAccess": false}, "23639075": {"id": "openaire____::issn23639075", "officialName": "Future Cities and Environment ", "issn": "23639075", "eissn": "", "lissn": "", "openAccess": false}, "2611657X": {"id": "openaire____::issn2611657X", "officialName": "Whatever. A Transdisciplinary Journal of Queer Theories and Studies", "issn": "2611657X", "eissn": "", "lissn": "", "openAccess": false}, "20476930": {"id": "openaire____::issn20476930", "officialName": "Bulletin of the History of Archaeology", "issn": "20476930", "eissn": "", "lissn": "", "openAccess": false}, "20565542": {"id": "openaire____::issn20565542", "officialName": "Open Journal of Bioresources", "issn": "20565542", "eissn": "", "lissn": "", "openAccess": false}, "20536712": {"id": "openaire____::issn20536712", "officialName": "Secularism and Nonreligion", "issn": "20536712", "eissn": "", "lissn": "", "openAccess": false}, "20499647": {"id": "openaire____::issn20499647", "officialName": "Journal of Open Research Software", "issn": "20499647", "eissn": "", "lissn": "", "openAccess": false}, "1450-7226": {"id": "doajarticles::1450-7226", "officialName": "The University Thought: Publication in Natural Sciences", "issn": "1450-7226", "eissn": "2560-3094", "lissn": "", "openAccess": true}, "2560-3094": {"id": "doajarticles::1450-7226", "officialName": "The University Thought: Publication in Natural Sciences", "issn": "1450-7226", "eissn": "2560-3094", "lissn": "", "openAccess": true}, "20498128": {"id": "openaire____::issn20498128", "officialName": "Opticon1826", "issn": "20498128", "eissn": "", "lissn": "", "openAccess": false}, "1303-1414": {"id": "tubitakulakb::1303-1414", "officialName": "Spor Bilimleri Dergisi", "issn": "1303-1414", "eissn": "", "lissn": "", "openAccess": false}, "1308-951X": {"id": "tubitakulakb::1308-951X", "officialName": "The International Journal of Research in Teacher Education", "issn": "1308-951X", "eissn": "", "lissn": "", "openAccess": false}, "1300-0853": {"id": "tubitakulakb::1300-0853", "officialName": "STED / S\u00fcrekli T\u0131p E\u011fitimi Dergisi", "issn": "1300-0853", "eissn": "", "lissn": "", "openAccess": false}, "13001337": {"id": "openaire____::issn13001337", "officialName": "E\u011e\u0130T\u0130M VE B\u0130L\u0130M", "issn": 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