From 5818abaab4402ac508c4ab1a3a9e44249eeb9594 Mon Sep 17 00:00:00 2001 From: Sandro La Bruzzo Date: Wed, 20 May 2020 17:05:46 +0200 Subject: [PATCH] fixed Crossref Mapping --- .../doiboost/crossref/Crossref2Oaf.scala | 15 +- .../doiboost/mag/SparkPreProcessMAG.scala | 182 +++++++++--------- .../doiboost/CrossrefMappingTest.scala | 4 +- .../eu/dnetlib/doiboost/awardTest.json | 9 +- 4 files changed, 111 insertions(+), 99 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index ece5d123f..b515a7330 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -137,6 +137,9 @@ case object Crossref2Oaf { if (StringUtils.isNotBlank(issuedDate)) { result.setDateofacceptance(asField(issuedDate)) } + else { + result.setDateofacceptance(asField(createdDate.getValue)) + } result.setRelevantdate(List(createdDate, postedDate, acceptedDate, publishedOnlineDate, publishedPrintDate).filter(p => p != null).asJava) @@ -233,6 +236,16 @@ case object Crossref2Oaf { val queue = new mutable.Queue[Relation] + def snfRule(award:String): String = { + var tmp1 = StringUtils.substringAfter(award,"_") + val tmp2 = StringUtils.substringBefore(tmp1,"/") + logger.debug(s"From $award to $tmp2") + tmp2 + + + } + + def extractECAward(award: String): String = { val awardECRegex: Regex = "[0-9]{4,9}".r if (awardECRegex.findAllIn(award).hasNext) @@ -298,7 +311,7 @@ case object Crossref2Oaf { case "10.13039/501100006588" | "10.13039/501100004488" => generateSimpleRelationFromAward(funder, "irb_hr______", a=>a.replaceAll("Project No.", "").replaceAll("HRZZ-","") ) case "10.13039/501100006769"=> generateSimpleRelationFromAward(funder, "rsf_________", a=>a) - case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", extractECAward) + case "10.13039/501100001711"=> generateSimpleRelationFromAward(funder, "snsf________", snfRule) case "10.13039/501100004410"=> generateSimpleRelationFromAward(funder, "tubitakf____", a =>a) case "10.10.13039/100004440"=> generateSimpleRelationFromAward(funder, "wt__________", a =>a) case "10.13039/100004440"=> queue += generateRelation(sourceId,"1e5e62235d094afd01cd56e65112fc63", "wt__________" ) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala index 56ab91d62..0001c83c6 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkPreProcessMAG.scala @@ -31,100 +31,99 @@ object SparkPreProcessMAG { implicit val mapEncoderPubs: Encoder[Publication] = org.apache.spark.sql.Encoders.kryo[Publication] implicit val tupleForJoinEncoder: Encoder[(String, Publication)] = Encoders.tuple(Encoders.STRING, mapEncoderPubs) -// logger.info("Phase 1) make uninque DOI in Papers:") -// val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers] -// -// -// // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one -// val result: RDD[MagPapers] = d.where(col("Doi").isNotNull).rdd.map { p: MagPapers => Tuple2(p.Doi, p) }.reduceByKey { case (p1: MagPapers, p2: MagPapers) => -// var r = if (p1 == null) p2 else p1 -// if (p1 != null && p2 != null) { -// if (p1.CreatedDate != null && p2.CreatedDate != null) { -// if (p1.CreatedDate.before(p2.CreatedDate)) -// r = p1 -// else -// r = p2 -// } else { -// r = if (p1.CreatedDate == null) p2 else p1 -// } -// } -// r -// }.map(_._2) -// -// val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) -// distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct") -// logger.info(s"Total number of element: ${result.count()}") -// -// logger.info("Phase 3) Group Author by PaperId") -// val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor] -// -// val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation] -// -// val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation] -// -// -// paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId"))) -// .map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null)) } -// .joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left") -// .map(s => { -// val mpa = s._1._2 -// val af = s._2 -// if (af != null) { -// MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName) -// } else -// mpa -// }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors")) -// .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors") -// -// logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors") -// -// val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal] -// -// val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers] -// -// val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList] -// -// val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left") -// firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left") -// .map { a: ((MagPapers, MagJournal), MagPaperWithAuthorList) => ConversionUtil.createOAFFromJournalAuthorPaper(a) }.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2") -// -// -// var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] -// -// val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] -// -// -// logger.info("Phase 5) enrich publication with URL and Instances") -// -// magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") -// .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } -// .write.mode(SaveMode.Overwrite) -// .save(s"${parser.get("targetPath")}/merge_step_3") -// -// -// logger.info("Phase 6) Enrich Publication with description") -// val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] -// pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") -// -// val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract] -// -// -// magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] -// -// magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left").map(p => { -// val pub = p._1._2 -// val abst = p._2 -// if (abst != null) { -// pub.setDescription(List(asField(abst.IndexedAbstract)).asJava) -// } -// pub -// } -// ).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4") -// + logger.info("Phase 1) make uninque DOI in Papers:") + val d: Dataset[MagPapers] = spark.read.load(s"${parser.get("sourcePath")}/Papers").as[MagPapers] + + // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one + val result: RDD[MagPapers] = d.where(col("Doi").isNotNull).rdd.map { p: MagPapers => Tuple2(p.Doi, p) }.reduceByKey { case (p1: MagPapers, p2: MagPapers) => + var r = if (p1 == null) p2 else p1 + if (p1 != null && p2 != null) { + if (p1.CreatedDate != null && p2.CreatedDate != null) { + if (p1.CreatedDate.before(p2.CreatedDate)) + r = p1 + else + r = p2 + } else { + r = if (p1.CreatedDate == null) p2 else p1 + } + } + r + }.map(_._2) + + + + val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) + distinctPaper.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/Papers_distinct") + logger.info(s"Total number of element: ${result.count()}") + + logger.info("Phase 3) Group Author by PaperId") + val authors = spark.read.load(s"$sourcePath/Authors").as[MagAuthor] + + val affiliation = spark.read.load(s"$sourcePath/Affiliations").as[MagAffiliation] + val paperAuthorAffiliation = spark.read.load(s"$sourcePath/PaperAuthorAffiliations").as[MagPaperAuthorAffiliation] + + paperAuthorAffiliation.joinWith(authors, paperAuthorAffiliation("AuthorId").equalTo(authors("AuthorId"))) + .map { case (a: MagPaperAuthorAffiliation, b: MagAuthor) => (a.AffiliationId, MagPaperAuthorDenormalized(a.PaperId, b, null)) } + .joinWith(affiliation, affiliation("AffiliationId").equalTo(col("_1")), "left") + .map(s => { + val mpa = s._1._2 + val af = s._2 + if (af != null) { + MagPaperAuthorDenormalized(mpa.PaperId, mpa.author, af.DisplayName) + } else + mpa + }).groupBy("PaperId").agg(collect_list(struct($"author", $"affiliation")).as("authors")) + .write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_1_paper_authors") + + logger.info("Phase 4) create First Version of publication Entity with Paper Journal and Authors") + + val journals = spark.read.load(s"$sourcePath/Journals").as[MagJournal] + + val papers = spark.read.load((s"${parser.get("targetPath")}/Papers_distinct")).as[MagPapers] + + val paperWithAuthors = spark.read.load(s"${parser.get("targetPath")}/merge_step_1_paper_authors").as[MagPaperWithAuthorList] + + val firstJoin = papers.joinWith(journals, papers("JournalId").equalTo(journals("JournalId")), "left") + firstJoin.joinWith(paperWithAuthors, firstJoin("_1.PaperId").equalTo(paperWithAuthors("PaperId")), "left") + .map { a: ((MagPapers, MagJournal), MagPaperWithAuthorList) => ConversionUtil.createOAFFromJournalAuthorPaper(a) }.write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_2") + + + var magPubs: Dataset[(String, Publication)] = spark.read.load(s"${parser.get("targetPath")}/merge_step_2").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] + + + logger.info("Phase 5) enrich publication with URL and Instances") + + magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") + .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } + .write.mode(SaveMode.Overwrite) + .save(s"${parser.get("targetPath")}/merge_step_3") + + + logger.info("Phase 6) Enrich Publication with description") + val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] + pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") + + val paperAbstract = spark.read.load((s"${parser.get("targetPath")}/PaperAbstract")).as[MagPaperAbstract] + + + magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_3").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + + magPubs.joinWith(paperAbstract, col("_1").equalTo(paperAbstract("PaperId")), "left").map(p => { + val pub = p._1._2 + val abst = p._2 + if (abst != null) { + pub.setDescription(List(asField(abst.IndexedAbstract)).asJava) + } + pub + } + ).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/merge_step_4") + logger.info("Phase 7) Enrich Publication with FieldOfStudy") - val magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] + magPubs = spark.read.load(s"${parser.get("targetPath")}/merge_step_4").as[Publication].map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] val fos = spark.read.load(s"$sourcePath/FieldsOfStudy").select($"FieldOfStudyId".alias("fos"), $"DisplayName", $"MainType") @@ -135,7 +134,6 @@ object SparkPreProcessMAG { .groupBy($"PaperId").agg(collect_list(struct($"FieldOfStudyId", $"DisplayName", $"MainType", $"Score")).as("subjects")) .as[MagFieldOfStudy] - magPubs.joinWith(paperField, col("_1").equalTo(paperField("PaperId")), "left"). map(item => { val publication = item._1._2 diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala index 2d7cf4216..0f9a3f8fb 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/CrossrefMappingTest.scala @@ -90,9 +90,9 @@ class CrossrefMappingTest { val rels:List[Relation] = resultList.filter(p => p.isInstanceOf[Relation]).map(r=> r.asInstanceOf[Relation]) - assertEquals(rels.size, 4) - rels.foreach(s => logger.info(s.getTarget)) + rels.foreach(s => logger.info(s.getTarget)) + assertEquals(rels.size, 3 ) } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json index f570b3bdb..7c6e7beb9 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/awardTest.json @@ -179,12 +179,13 @@ ], "funder": [ { + "DOI": "10.13039/501100001711", + "name": "Swiss National Science Foundation (Schweizerische Nationalfonds)", "doi-asserted-by": "publisher", - "DOI": "10.13039/501100000781", - "name": "European Research Council", "award": [ - "284236-REPCOLLAB", - "FP7/2007-2013" + "CR32I3_156724", + "31003A_173281/1", + "200021_165850" ] } ],