diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java index b745584ee..c275ac838 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/HttpConnector2.java @@ -142,18 +142,9 @@ public class HttpConnector2 { } return attemptDownload(newUrl, retryNumber + 1, report); } - if (is4xx(urlConn.getResponseCode())) { - // CLIENT ERROR, DO NOT RETRY - report - .put( - REPORT_PREFIX + urlConn.getResponseCode(), - String - .format( - "%s error: %s", requestUrl, urlConn.getResponseMessage())); - throw new CollectorException("4xx error: request will not be repeated. " + report); - } - if (is5xx(urlConn.getResponseCode())) { + if (is4xx(urlConn.getResponseCode()) || is5xx(urlConn.getResponseCode())) { switch (urlConn.getResponseCode()) { + case HttpURLConnection.HTTP_NOT_FOUND: case HttpURLConnection.HTTP_BAD_GATEWAY: case HttpURLConnection.HTTP_UNAVAILABLE: case HttpURLConnection.HTTP_GATEWAY_TIMEOUT: diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java index 5434bed1b..cc4b10fb8 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiCollectorPlugin.java @@ -21,6 +21,9 @@ import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; public class OaiCollectorPlugin implements CollectorPlugin { + public static final String DATE_REGEX = "\\d{4}-\\d{2}-\\d{2}"; + public static final String UTC_DATETIME_REGEX = "\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z"; + private static final String FORMAT_PARAM = "format"; private static final String OAI_SET_PARAM = "set"; private static final Object OAI_FROM_DATE_PARAM = "fromDate"; @@ -62,13 +65,11 @@ public class OaiCollectorPlugin implements CollectorPlugin { throw new CollectorException("Param 'mdFormat' is null or empty"); } - if (fromDate != null && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}") - && !fromDate.matches("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z")) { + if (fromDate != null && !fromDate.matches(DATE_REGEX) && !fromDate.matches(UTC_DATETIME_REGEX)) { throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + fromDate); } - if (untilDate != null && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}") - && !untilDate.matches("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z")) { + if (untilDate != null && !untilDate.matches(DATE_REGEX) && !untilDate.matches(UTC_DATETIME_REGEX)) { throw new CollectorException("Invalid date (YYYY-MM-DD or YYYY-MM-DDT00:00:00Z): " + untilDate); } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index 392311765..75dd746ea 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -107,12 +107,12 @@ public class OaiIterator implements Iterator { if (set != null && !set.isEmpty()) { url += "&set=" + URLEncoder.encode(set, "UTF-8"); } - if (fromDate != null && (fromDate.matches("\\d{4}-\\d{2}-\\d{2}") - || fromDate.matches("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z"))) { + if (fromDate != null && (fromDate.matches(OaiCollectorPlugin.DATE_REGEX) + || fromDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) { url += "&from=" + URLEncoder.encode(fromDate, "UTF-8"); } - if (untilDate != null && (untilDate.matches("\\d{4}-\\d{2}-\\d{2}") - || untilDate.matches("\\d{4}-\\d{2}-\\d{2}T\\d{2}:\\d{2}:\\d{2}Z"))) { + if (untilDate != null && (untilDate.matches(OaiCollectorPlugin.DATE_REGEX) + || untilDate.matches(OaiCollectorPlugin.UTC_DATETIME_REGEX))) { url += "&until=" + URLEncoder.encode(untilDate, "UTF-8"); } log.info("Start harvesting using url: " + url); diff --git a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java index a4fb20b1c..9927d6560 100644 --- a/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java +++ b/dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/GenerateStatsJob.java @@ -80,6 +80,7 @@ public class GenerateStatsJob { .map( (MapFunction, DatasourceStats>) t -> t._2, Encoders.bean(DatasourceStats.class)) + .coalesce(1) .write() .mode(SaveMode.Overwrite) .jdbc(dbUrl, "oa_datasource_stats_temp", connectionProperties); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/AuthorAssoc.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/AuthorAssoc.java new file mode 100644 index 000000000..807567fba --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/AuthorAssoc.java @@ -0,0 +1,47 @@ +package eu.dnetlib.doiboost; + +import eu.dnetlib.dhp.schema.oaf.Author; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +public class AuthorAssoc implements Serializable { + private Double score ; + private List to_be_enriched; + private Author with_enricheing_content; + + public Double getScore() { + return score; + } + + public void setScore(Double score) { + this.score = score; + } + + public List getTo_be_enriched() { + return to_be_enriched; + } + + public void setTo_be_enriched(List to_be_enriched) { + this.to_be_enriched = to_be_enriched; + } + + public Author getWith_enricheing_content() { + return with_enricheing_content; + } + + public void setWith_enricheing_content(Author with_enricheing_content) { + this.with_enricheing_content = with_enricheing_content; + } + + public static AuthorAssoc newInstance(Author a){ + AuthorAssoc ret = new AuthorAssoc(); + ret.score = 0.0; + ret.to_be_enriched = new ArrayList<>(); + ret.with_enricheing_content = a; + + return ret; + + } +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostAuthorMerger.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostAuthorMerger.java new file mode 100644 index 000000000..70032097e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostAuthorMerger.java @@ -0,0 +1,236 @@ + +package eu.dnetlib.doiboost; + +import java.text.Normalizer; +import java.util.*; +import java.util.stream.Collectors; + +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.DHPUtils; + +import com.wcohen.ss.JaroWinkler; + +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +import scala.Tuple2; + +/** + * This is a version of the AuthorMerger specific for DoiBoost. + * Here we suppose a match must exist for the authors. We compare via JaroWrinkler similarity measure each author in the list + * that should be enriched with each author in the enriching list. For each enriching author we select the best match that is + * the author with the highest similarity score. + * The association is done from the enriching author to the enriched because in this way only one match per enriching author can be found + * One enriching author can have the same maximum similarity score with more than one + * + * + * + * + * The idea is to enrich the most similar authors having at least one + * word of the name in + * common + * Quello che faccio e’ abbastanza semplice: ho una struttura dati che mantine l’informazione di associazione fra il record che puo’ possibilmente arricchire e quello che deve essere arricchito. + * 6:22 + * Questa struttura ha la lista di autori che possono essere arricchiti, l’autore che arricchisce e lo score di similarita fra l’autore che arricchisce e gli autori arricchiti. E’ il valore di una mappa che per chiave la il fullname dell’autore che arricchisce + * 6:23 + * per ogni autore che puo’ essere arricchito verifico se la entri nella mappa di quello che arricchisce e’ associata ad un autore con score di similarita’ piu’ basso. Se cosi’ e’ modifico l’associazione nella mappa per l’autore che arricchisce, sostituendo l’autore arricchito a cui era associato prima con quello nuovo che ha score piu’ alto. Se lo score e’ lo stesso, aggiungo il nuovo autore da arricchire alla lista degli autori associata all’autore che arricchisce + * 6:25 + * Alla fine caso facile: ogni entry e’ associata ad un unico autore da arricchire => verifico che almeno una delle parole che sono nei due nomi sia in comune fra i due insiemi Se e’ cosi’, aggiungo i pid mancanti all’autore da arricchire dell’autore che arricchisce + * 6:26 + * caso brutto: ci sono piu’ autori da arricchire con la stessa similarita: arricchisco quello che ha il maggior numero di parole del fullname uguali a quelle dell’autore che arricchisce. In caso di parita’ non si arricchisce + * 6:28 + * ricordiamoci che si parte dal presupposto che un match debba esistere visto che abbiamo lo stesso doi + * 6:29 + * di conseguenza l’autore che ha lo score di similarita’ piu’ alto fra quelli presenti ed anche una parola in comune del nome dovrebbe essere sufficiente per poterlo arricchire. + * 6:30 + * I casi di omonimia che potrebbero portare problemi con i rank degli autori non si mappano + */ + +public class DoiBoostAuthorMerger { + + + public static List merge(List> authors, Boolean crossref) { + + Iterator> it = authors.iterator(); + List author = it.next(); + + while (it.hasNext()){ + List autList = it.next(); + Tuple2, Boolean> tmp = mergeAuthor(author, autList, crossref); + author = tmp._1(); + crossref = tmp._2(); + } + + return author; + + } + + public static Tuple2, Boolean> mergeAuthor(final List baseAuthor, final List otherAuthor, + final Boolean crossref) { + + if(baseAuthor == null || baseAuthor.size() == 0) + return new Tuple2<>(otherAuthor, false); + if(otherAuthor == null || otherAuthor.size() == 0) + return new Tuple2<>(baseAuthor, crossref); + + if(crossref) { + enrichPidFromList(baseAuthor, otherAuthor); + return new Tuple2<>(baseAuthor, true); + } + else + if (baseAuthor.size() > otherAuthor.size()){ + enrichPidFromList(baseAuthor, otherAuthor); + return new Tuple2<>(baseAuthor, false); + }else{ + enrichPidFromList(otherAuthor, baseAuthor); + return new Tuple2<>(otherAuthor, false); + } + + } + + + private static void enrichPidFromList(List base, List enrich) { + + //search authors having identifiers in the enrich list + final List authorsWithPids = enrich + .stream() + .filter(a -> a.getPid() != null && a.getPid().size() > 0) + .collect(Collectors.toList()); + + Map assocMap = authorsWithPids + .stream() + .map( + a -> new Tuple2<>(DHPUtils.md5(a.getFullname()), AuthorAssoc.newInstance(a))) + .collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1)); + + + //for each author in the base list, we search the best enriched match + base.stream() + .map(a -> new Tuple2<>(a, authorsWithPids.stream() + .map(e -> new Tuple2<>(e, sim(a, e))).collect(Collectors.toList()))) + .forEach(t2 -> { + + for (Tuple2 t : t2._2()) { + String mapEntry = DHPUtils.md5(t._1().getFullname()); + AuthorAssoc aa = assocMap.get(mapEntry); + if(aa.getScore() < t._2() && aa.getScore() < 0.9){ + aa.setScore(t._2()); + aa.setTo_be_enriched(new ArrayList<>()); + aa.getTo_be_enriched().add(t2._1()); + }else if(t._2() > 0.9){ + aa.getTo_be_enriched().add(t2._1()); + } + } + + }); + + assocMap.keySet().forEach(k -> enrichAuthor(assocMap.get(k))); + + + } + + private static long getCommonWords(List fullEnrich, List fullEnriching){ + return fullEnrich.stream().filter( w -> fullEnriching.contains(w)).count(); + } + + + private static void enrichAuthor(Author enrich, Author enriching){ + //verify if some of the words in the fullname are contained in the other + //get normalized fullname + + long commonWords = getCommonWords(normalize(enrich.getFullname()), + normalize(enriching.getFullname())); + if(commonWords > 0 ){ + if(enrich.getPid() == null){ + enrich.setPid(new ArrayList<>()); + } + Set aPids = enrich.getPid().stream().map(p -> pidToComparableString(p)).collect(Collectors.toSet()); + enriching.getPid().forEach(p -> { + if (!aPids.contains(pidToComparableString(p))){ + enrich.getPid().add(p); + } + }); + if (enrich.getAffiliation() == null){ + if (enriching.getAffiliation() != null){ + enrich.setAffiliation(enriching.getAffiliation()); + } + } + } + + + } + + //Verify the number of words in common. The one that has more, wins. If the number of words in common are the same we + //enrich no author + private static void enrichAuthor(AuthorAssoc authorAssoc) { + if (authorAssoc.getTo_be_enriched().size() == 1){ + enrichAuthor(authorAssoc.getTo_be_enriched().get(0), authorAssoc.getWith_enricheing_content()); + }else{ + long common = 0; + List selected = new ArrayList<>() ; + for(Author a : authorAssoc.getTo_be_enriched()){ + long current_common = getCommonWords(normalize(a.getFullname()), + normalize(authorAssoc.getWith_enricheing_content().getFullname())); + if (current_common > common){ + common = current_common; + selected = new ArrayList<>(); + selected.add(a); + }else if(current_common == common){ + selected.add(a); + } + } + if (selected.size() == 1){ + enrichAuthor(selected.get(0), authorAssoc.getWith_enricheing_content()); + } + } + + } + + + public static String pidToComparableString(StructuredProperty pid) { + return (pid.getQualifier() != null + ? pid.getQualifier().getClassid() != null ? pid.getQualifier().getClassid().toLowerCase() : "" + : "") + + (pid.getValue() != null ? pid.getValue().toLowerCase() : ""); + } + + + + + private static Double sim(Author a, Author b) { + return new JaroWinkler() + .score(normalizeString(a.getFullname()), normalizeString(b.getFullname())); + + } + + private static String normalizeString(String fullname) { + return String.join(" ", normalize(fullname)); + } + + + private static List normalize(final String s) { + String[] normalized = nfd(s) + .replaceAll("[^\\p{ASCII}]", "") + .toLowerCase() + // do not compact the regexes in a single expression, would cause StackOverflowError + // in case + // of large input strings + .replaceAll("(\\W)+", " ") + .replaceAll("(\\p{InCombiningDiacriticalMarks})+", " ") + .replaceAll("(\\p{Punct})+", " ") + .replaceAll("(\\d)+", " ") + .replaceAll("(\\n)+", " ") + .trim() + .split(" "); + + Arrays.sort(normalized); + + return Arrays.asList(normalized); + + + } + + private static String nfd(final String s) { + return Normalizer.normalize(s, Normalizer.Form.NFD); + } +} 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 a6101c07e..12e4ac379 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 @@ -38,6 +38,9 @@ object DoiBoostMappingUtil { val OPENAIRE_PREFIX = "openaire____" val SEPARATOR = "::" + val DOI_PREFIX_REGEX = "(^10\\.|\\/10.)" + val DOI_PREFIX = "10." + val invalidName = List(",", "none none", "none, none", "none &na;", "(:null)", "test test test", "test test", "test", "&na; &na;") def toActionSet(item:Oaf) :(String, String) = { @@ -352,5 +355,28 @@ object DoiBoostMappingUtil { } + def isEmpty(x: String) = x == null || x.trim.isEmpty + + def normalizeDoi(input : String) :String ={ + if(input == null) + return null + val replaced = input.replaceAll("(?:\\n|\\r|\\t|\\s)", "").toLowerCase.replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX) + if (isEmpty(replaced)) + return null + + if(replaced.indexOf("10.") < 0) + return null + + val ret = replaced.substring(replaced.indexOf("10.")) + + if (!ret.startsWith(DOI_PREFIX)) + return null + + return ret + + + } + + } 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 b77de13b9..deda8c987 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 @@ -3,7 +3,7 @@ package eu.dnetlib.doiboost import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.merge.AuthorMerger import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.{Organization, Publication, Relation, Dataset => OafDataset} +import eu.dnetlib.dhp.schema.oaf.{Author, Organization, Publication, Relation, Dataset => OafDataset} import eu.dnetlib.doiboost.mag.ConversionUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf @@ -25,6 +25,7 @@ object SparkGenerateDoiBoost { val conf: SparkConf = new SparkConf() val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/doiboost/generate_doiboost_params.json"))) parser.parseArgument(args) + var crossref : Boolean = true val spark: SparkSession = SparkSession .builder() @@ -104,7 +105,10 @@ object SparkGenerateDoiBoost { val otherPub = item._2._2 if (otherPub != null) { crossrefPub.mergeFrom(otherPub) - crossrefPub.setAuthor(AuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor)) + val mergeRes : (java.util.List[Author], java.lang.Boolean) = DoiBoostAuthorMerger.mergeAuthor(crossrefPub.getAuthor, otherPub.getAuthor, crossref) + crossrefPub.setAuthor(mergeRes._1) + crossref = mergeRes._2 + } } crossrefPub 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 3f6a26c46..15a321431 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 @@ -16,9 +16,10 @@ import scala.collection.JavaConverters._ import scala.collection.mutable import scala.util.matching.Regex import eu.dnetlib.dhp.schema.scholexplorer.OafUtils - import java.util +import eu.dnetlib.doiboost.DoiBoostMappingUtil + case class CrossrefDT(doi: String, json:String, timestamp: Long) {} case class mappingAffiliation(name: String) {} @@ -89,7 +90,7 @@ case object Crossref2Oaf { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats //MAPPING Crossref DOI into PID - val doi: String = (json \ "DOI").extract[String] + val doi: String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String]) result.setPid(List(createSP(doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava) //MAPPING Crossref DOI into OriginalId @@ -101,6 +102,7 @@ case object Crossref2Oaf { val originalIds = new util.ArrayList(tmp.filter(id => id != null).asJava) result.setOriginalId(originalIds) + // Add DataInfo result.setDataInfo(generateDataInfo()) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala index 4a39a2987..159b817c7 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/CrossrefDataset.scala @@ -1,6 +1,7 @@ package eu.dnetlib.doiboost.crossref import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.doiboost.DoiBoostMappingUtil import org.apache.commons.io.IOUtils import org.apache.hadoop.io.{IntWritable, Text} import org.apache.spark.SparkConf @@ -21,7 +22,7 @@ object CrossrefDataset { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = parse(input) val ts:Long = (json \ "indexed" \ "timestamp").extract[Long] - val doi:String = (json \ "DOI").extract[String] + val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String]) CrossrefDT(doi, input, ts) } diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala index b11e2d8de..526ff7b3a 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/GenerateCrossrefDataset.scala @@ -1,6 +1,7 @@ package eu.dnetlib.doiboost.crossref import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.crossref.CrossrefDataset.to_item import eu.dnetlib.doiboost.crossref.UnpackCrtossrefEntries.getClass import org.apache.hadoop.io.{IntWritable, Text} @@ -27,7 +28,7 @@ object GenerateCrossrefDataset { def crossrefElement(meta: String): CrossrefDT = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = parse(meta) - val doi:String = (json \ "DOI").extract[String] + val doi:String = DoiBoostMappingUtil.normalizeDoi((json \ "DOI").extract[String]) val timestamp: Long = (json \ "indexed" \ "timestamp").extract[Long] CrossrefDT(doi, meta, timestamp) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala index e8c283a7a..fd9629024 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/MagDataModel.scala @@ -196,8 +196,8 @@ case object ConversionUtil { val authors = inputParams._2 val pub = new Publication - pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava) - pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava) + pub.setPid(List(createSP(paper.Doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava) + pub.setOriginalId(List(paper.PaperId.toString, paper.Doi).asJava) //IMPORTANT //The old method result.setId(generateIdentifier(result, doi)) @@ -258,11 +258,14 @@ case object ConversionUtil { val description = inputParams._2 val pub = new Publication - pub.setPid(List(createSP(paper.Doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava) - pub.setOriginalId(List(paper.PaperId.toString, paper.Doi.toLowerCase).asJava) + pub.setPid(List(createSP(paper.Doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava) + pub.setOriginalId(List(paper.PaperId.toString, paper.Doi).asJava) - //Set identifier as 50 | doiboost____::md5(DOI) - pub.setId(generateIdentifier(pub, paper.Doi.toLowerCase)) + //IMPORTANT + //The old method result.setId(generateIdentifier(result, doi)) + //will be replaced using IdentifierFactory + + pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub)) val mainTitles = createSP(paper.PaperTitle, "main title", ModelConstants.DNET_DATACITE_TITLE) val originalTitles = createSP(paper.OriginalTitle, "alternative title", ModelConstants.DNET_DATACITE_TITLE) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala index 173e33360..ecb389af8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala @@ -2,6 +2,7 @@ package eu.dnetlib.doiboost.mag import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.Publication +import eu.dnetlib.doiboost.DoiBoostMappingUtil import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.rdd.RDD @@ -12,6 +13,23 @@ import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ object SparkProcessMAG { + + def getDistinctResults (d:Dataset[MagPapers]):Dataset[MagPapers]={ + d.where(col("Doi").isNotNull) + .groupByKey(mp => DoiBoostMappingUtil.normalizeDoi(mp.Doi))(Encoders.STRING) + .reduceGroups((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2)) + .map(_._2)(Encoders.product[MagPapers]) + .map(mp => { + new MagPapers(mp.PaperId, mp.Rank, DoiBoostMappingUtil.normalizeDoi(mp.Doi), + mp.DocType, mp.PaperTitle, mp.OriginalTitle, + mp.BookTitle, mp.Year, mp.Date, mp.Publisher: String, + mp.JournalId, mp.ConferenceSeriesId, mp.ConferenceInstanceId, + mp.Volume, mp.Issue, mp.FirstPage, mp.LastPage, + mp.ReferenceCount, mp.CitationCount, mp.EstimatedCitation, + mp.OriginalVenue, mp.FamilyId, mp.CreatedDate) + })(Encoders.product[MagPapers]) + } + def main(args: Array[String]): Unit = { val logger: Logger = LoggerFactory.getLogger(getClass) @@ -33,17 +51,11 @@ object SparkProcessMAG { 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:") + logger.info("Phase 1) make uninue DOI in Papers:") val d: Dataset[MagPapers] = spark.read.load(s"$sourcePath/Papers").as[MagPapers] // Filtering Papers with DOI, and since for the same DOI we have multiple version of item with different PapersId we get the last one - val result: RDD[MagPapers] = d.where(col("Doi").isNotNull) - .rdd - .map{ p: MagPapers => Tuple2(p.Doi, p) } - .reduceByKey((p1:MagPapers,p2:MagPapers) => ConversionUtil.choiceLatestMagArtitcle(p1,p2)) - .map(_._2) - - val distinctPaper: Dataset[MagPapers] = spark.createDataset(result) + val distinctPaper: Dataset[MagPapers] = getDistinctResults(d) distinctPaper.write.mode(SaveMode.Overwrite).save(s"$workingPath/Papers_distinct") diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala index 0b5edfb19..1cd3f7028 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcid/ORCIDToOAF.scala @@ -84,7 +84,7 @@ object ORCIDToOAF { JField("type", JString(typeValue)) <- extIds JField("value", JString(value)) <- extIds if "doi".equalsIgnoreCase(typeValue) - } yield (typeValue, value) + } yield (typeValue, DoiBoostMappingUtil.normalizeDoi(value)) if (doi.nonEmpty) { return doi.map(l =>OrcidWork(oid, l._2)) } @@ -102,7 +102,7 @@ object ORCIDToOAF { def convertTOOAF(input:ORCIDItem) :Publication = { val doi = input.doi val pub:Publication = new Publication - pub.setPid(List(createSP(doi.toLowerCase, "doi", ModelConstants.DNET_PID_TYPES)).asJava) + pub.setPid(List(createSP(doi, "doi", ModelConstants.DNET_PID_TYPES)).asJava) pub.setDataInfo(generateDataInfo()) pub.setId(IdentifierFactory.createDOIBoostIdentifier(pub)) diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala index a7f97aaf8..cc758bcae 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/uw/UnpayWallToOAF.scala @@ -3,6 +3,7 @@ package eu.dnetlib.doiboost.uw import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory import eu.dnetlib.dhp.schema.oaf.{AccessRight, Instance, OpenAccessRoute, Publication} +import eu.dnetlib.doiboost.DoiBoostMappingUtil import org.json4s import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse @@ -53,7 +54,10 @@ object UnpayWallToOAF { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = parse(input) - val doi = (json \"doi").extract[String] + val doi = DoiBoostMappingUtil.normalizeDoi((json \"doi").extract[String]) + + if(doi == null) + return null val is_oa = (json\ "is_oa").extract[Boolean] diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml index fa47e142d..1ac17dff9 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/oozie_app/workflow.xml @@ -111,7 +111,7 @@ ${wf:conf('resumeFrom') eq 'CreateDOIBoost'} ${wf:conf('resumeFrom') eq 'GenerateActionSet'} ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} - + @@ -319,7 +319,7 @@ --executor-memory=${sparkExecutorIntersectionMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 + --conf spark.sql.shuffle.partitions=7680 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostAuthorMergerTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostAuthorMergerTest.java new file mode 100644 index 000000000..0cad167ae --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/DoiBoostAuthorMergerTest.java @@ -0,0 +1,406 @@ + +package eu.dnetlib.dhp.doiboost; + +import java.io.BufferedReader; +import java.io.FileReader; +import java.io.IOException; +import java.nio.file.Paths; +import java.util.ArrayList; +import java.util.List; +import java.util.stream.Collectors; + +import org.apache.neethi.Assertion; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Author; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.doiboost.DoiBoostAuthorMerger; +import eu.dnetlib.pace.util.MapDocumentUtil; +import scala.Tuple2; + +public class DoiBoostAuthorMergerTest { + + private String publicationsBasePath; + + private List> authors; + + + @BeforeEach + public void setUp() throws Exception { + + publicationsBasePath = Paths + .get(DoiBoostAuthorMergerTest.class.getResource("/eu/dnetlib/dhp/doiboost").toURI()) + .toFile() + .getAbsolutePath(); + + } + + @Test + public void mergeTestOrcid() { + + authors = readSample(publicationsBasePath + "/matching_authors_first.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + for (List authors1 : authors) { + System.out.println("List " + (authors.indexOf(authors1) + 1)); + for (Author author : authors1) { + System.out.println(authorToString(author)); + } + } + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(10, merge.size()); + + Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count()); + + merge + .stream() + .filter(a -> a.getPid() != null) + .forEach( + a -> Assertions + .assertTrue( + a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID)))); + merge.stream().filter(a -> a.getPid() != null).forEach(a -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(a)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + } + + public List> readSample(String path, Class clazz) { + List> res = new ArrayList<>(); + BufferedReader reader; + try { + reader = new BufferedReader(new FileReader(path)); + String line = reader.readLine(); + while (line != null) { + res + .add( + new Tuple2<>( + MapDocumentUtil.getJPathString("$.id", line), + new ObjectMapper().readValue(line, clazz))); + // read next line + line = reader.readLine(); + } + reader.close(); + } catch (IOException e) { + e.printStackTrace(); + } + + return res; + } + + public String authorToString(Author a) { + + String print = "Fullname = "; + print += a.getFullname() + " pid = ["; + if (a.getPid() != null) + for (StructuredProperty sp : a.getPid()) { + print += sp.toComparableString() + " "; + } + print += "]"; + return print; + } + + @Test + public void mergeTestMAG() { + + authors = readSample(publicationsBasePath + "/matching_authors_second", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + for (List authors1 : authors) { + System.out.println("List " + (authors.indexOf(authors1) + 1)); + for (Author author : authors1) { + System.out.println(authorToString(author)); + } + } + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(10, merge.size()); + + Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count()); + + merge + .stream() + .filter(a -> a.getPid() != null) + .forEach( + a -> Assertions + .assertTrue( + a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL")))); + merge.stream().filter(a -> a.getPid() != null).forEach(a -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(a)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + } + + + @Test + public void mergeTestCrossrefEmpty1() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/empty_crossref_authors_first.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(3, merge.size()); + + Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count()); + + merge + .stream() + .filter(a -> a.getPid() != null) + .forEach( + a -> Assertions + .assertTrue( + a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID)))); + merge.stream().filter(a -> a.getPid() != null).forEach(a -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(a)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + System.out.println(new ObjectMapper().writeValueAsString(merge)); + + } + + + @Test + public void mergeTestCrossrefEmpty2() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/empty_crossref_authors_second.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + + List merge = DoiBoostAuthorMerger.merge(authors, false); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(10, merge.size()); + + Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count()); + + merge + .stream() + .filter(a -> a.getPid() != null) + .forEach( + a -> Assertions + .assertTrue( + a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL")))); + merge.stream().filter(a -> a.getPid() != null).forEach(a -> { + try { + System.out.println(new ObjectMapper().writeValueAsString(a)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); + + } + + @Test + public void mergeTestCrossrefEmpty3() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/empty_crossref_author_third.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(10, merge.size()); + + Assertions.assertEquals(10, merge.stream().filter(a -> a.getPid() != null).count()); + + merge + .stream() + .filter(a -> a.getPid() != null) + .forEach( + a -> Assertions + .assertTrue( + a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals("URL")))); + + Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); + + + } + + + @Test + public void mergeTestCrossrefEmpty4() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/empty_crossref_author_fourth.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + + Assertions.assertEquals(3, merge.size()); + + Assertions.assertEquals(3, merge.stream().filter(a -> a.getPid() != null).count()); + + + Assertions.assertTrue(3 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); + + + } + + @Test + public void shouldMergeTest1() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/should_appear_author1.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + Assertions.assertTrue(6 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); + + Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count()); + + merge.stream().filter(a -> a.getRank() == 26) + .forEach(a -> + Assertions.assertTrue(a.getPid() + .stream() + .anyMatch(pid -> pid.getValue().equals("0000-0002-2445-5275") + && pid.getQualifier().getClassid().equals(ModelConstants.ORCID) + ) + ) + ); + + + } + + @Test + public void shouldMergeTest2() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/should_appear_author2.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + + + Assertions.assertTrue(5 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); + + Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null) + .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count()); + + merge.stream().filter(a -> a.getFullname().equals("da luz geraldo eduardo")) + .forEach(a -> + Assertions.assertTrue(a.getPid() + .stream() + .anyMatch(pid -> pid.getValue().equals("http://orcid.org/0000-0003-2434-0387") + && pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING) + ) + ) + ); + + + } + + @Test + public void shouldNotMergeTest1() throws JsonProcessingException { + + authors = readSample(publicationsBasePath + "/should_appear_author3.json", Publication.class) + .stream() + .map(p -> p._2().getAuthor()) + .collect(Collectors.toList()); + + + List merge = DoiBoostAuthorMerger.merge(authors, true); + + System.out.println("Merge "); + for (Author author : merge) { + System.out.println(authorToString(author)); + } + +// Assertions.assertTrue(5 == merge.stream().filter(a -> a.getPid() !=null) +// .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID))).count()); +// +// Assertions.assertTrue(34 == merge.stream().filter(a -> a.getPid() !=null) +// .filter(a -> a.getPid().stream().anyMatch(p -> p.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))).count()); +// +// merge.stream().filter(a -> a.getFullname().equals("da luz geraldo eduardo")) +// .forEach(a -> +// Assertions.assertTrue(a.getPid() +// .stream() +// .anyMatch(pid -> pid.getValue().equals("http://orcid.org/0000-0003-2434-0387") +// && pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING) +// ) +// ) +// ); + + + } +} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/NormalizeDoiTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/NormalizeDoiTest.scala new file mode 100644 index 000000000..a9a841ee9 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/NormalizeDoiTest.scala @@ -0,0 +1,46 @@ +package eu.dnetlib.dhp.doiboost + +import eu.dnetlib.doiboost.DoiBoostMappingUtil +import org.junit.jupiter.api.Test + +class NormalizeDOITest { + + @Test + def doiDSLowerCase():Unit = { + val doi ="10.1042/BCJ20160876" + + assert(DoiBoostMappingUtil.normalizeDoi(doi).equals(doi.toLowerCase())) + + } + + + @Test + def doiFiltered():Unit = { + val doi = "0.1042/BCJ20160876" + + assert(DoiBoostMappingUtil.normalizeDoi(doi) == null) + } + + @Test + def doiFiltered2():Unit = { + val doi = "https://doi.org/0.1042/BCJ20160876" + + assert(DoiBoostMappingUtil.normalizeDoi(doi) == null) + } + + + @Test + def doiCleaned():Unit = { + val doi = "https://doi.org/10.1042/BCJ20160876" + + assert(DoiBoostMappingUtil.normalizeDoi(doi).equals("10.1042/BCJ20160876".toLowerCase())) + } + + @Test + def doiCleaned1():Unit = { + val doi = "https://doi.org/10.1042/ BCJ20160876" + + assert(DoiBoostMappingUtil.normalizeDoi(doi).equals("10.1042/BCJ20160876".toLowerCase())) + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala index cb543b4d7..0fa34d88e 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -461,5 +461,37 @@ class CrossrefMappingTest { // }) } + @Test + def testNormalizeDOI(): Unit = { + val template = Source.fromInputStream(getClass.getResourceAsStream("article_funder_template.json")).mkString + val line :String = "\"funder\": [{\"name\": \"Wellcome Trust Masters Fellowship\",\"award\": [\"090633\"]}]," + val json = template.replace("%s", line) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + val items = resultList.filter(p => p.isInstanceOf[Publication]) + val result: Result = items.head.asInstanceOf[Publication] + + result.getPid.asScala.foreach(pid => assertTrue(pid.getQualifier.getClassid.equals("doi"))) + assertTrue(result.getPid.size() == 1) + result.getPid.asScala.foreach(pid => assertTrue(pid.getValue.equals("10.26850/1678-4618EQJ.v35.1.2010.p41-46".toLowerCase()))) + + } + + @Test + def testNormalizeDOI2(): Unit = { + val template = Source.fromInputStream(getClass.getResourceAsStream("article.json")).mkString + + val resultList: List[Oaf] = Crossref2Oaf.convert(template) + assertTrue(resultList.nonEmpty) + val items = resultList.filter(p => p.isInstanceOf[Publication]) + val result: Result = items.head.asInstanceOf[Publication] + + result.getPid.asScala.foreach(pid => assertTrue(pid.getQualifier.getClassid.equals("doi"))) + assertTrue(result.getPid.size() == 1) + result.getPid.asScala.foreach(pid => assertTrue(pid.getValue.equals("10.26850/1678-4618EQJ.v35.1.2010.p41-46".toLowerCase()))) + + } + + } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala index 88b1669f4..7eb50665e 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/mag/MAGMappingTest.scala @@ -4,7 +4,7 @@ import java.sql.Timestamp import eu.dnetlib.dhp.schema.oaf.Publication import org.apache.htrace.fasterxml.jackson.databind.SerializationFeature -import org.apache.spark.SparkConf +import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.api.java.function.MapFunction import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} import org.codehaus.jackson.map.{ObjectMapper, SerializationConfig} @@ -62,6 +62,55 @@ class MAGMappingTest { logger.debug(description) } + @Test + def normalizeDoiTest():Unit = { + + import org.json4s.jackson.Serialization.write + import org.json4s.DefaultFormats + + implicit val formats = DefaultFormats + + val conf = new SparkConf().setAppName("test").setMaster("local[2]") + val sc = new SparkContext(conf) + val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + val path = getClass.getResource("magPapers.json").getPath + + import org.apache.spark.sql.Encoders + val schema = Encoders.product[MagPapers].schema + + import spark.implicits._ + val magPapers :Dataset[MagPapers] = spark.read.option("multiline",true).schema(schema).json(path).as[MagPapers] + val ret :Dataset[MagPapers] = SparkProcessMAG.getDistinctResults(magPapers) + assertTrue(ret.count == 10) + ret.take(10).foreach(mp => assertTrue(mp.Doi.equals(mp.Doi.toLowerCase()))) + + spark.close() + } + + @Test + def normalizeDoiTest2():Unit = { + + import org.json4s.jackson.Serialization.write + import org.json4s.DefaultFormats + + implicit val formats = DefaultFormats + + val conf = new SparkConf().setAppName("test").setMaster("local[2]") + val sc = new SparkContext(conf) + val spark = SparkSession.builder.config(sc.getConf).getOrCreate() + val path = getClass.getResource("duplicatedMagPapers.json").getPath + + import org.apache.spark.sql.Encoders + val schema = Encoders.product[MagPapers].schema + + import spark.implicits._ + val magPapers :Dataset[MagPapers] = spark.read.option("multiline",true).schema(schema).json(path).as[MagPapers] + val ret :Dataset[MagPapers] = SparkProcessMAG.getDistinctResults(magPapers) + assertTrue(ret.count == 8) + ret.take(8).foreach(mp => assertTrue(mp.Doi.equals(mp.Doi.toLowerCase()))) + spark.close() + //ret.take(8).foreach(mp => println(write(mp))) + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala index cdda3b2af..69985dae2 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcid/MappingORCIDToOAFTest.scala @@ -12,6 +12,8 @@ import org.slf4j.{Logger, LoggerFactory} import java.nio.file.Path import scala.io.Source +import scala.collection.JavaConversions._ + class MappingORCIDToOAFTest { val logger: Logger = LoggerFactory.getLogger(ORCIDToOAF.getClass) val mapper = new ObjectMapper() @@ -59,13 +61,30 @@ class MappingORCIDToOAFTest { assertTrue(oA == p.count()) println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(p.first())) + spark.close() + } + + + @Test + def testExtractDat1():Unit ={ + + + + val aList: List[OrcidAuthor] = List(OrcidAuthor("0000-0002-4335-5309", Some("Lucrecia"), Some("Curto"), null, null, null ), + OrcidAuthor("0000-0001-7501-3330", Some("Emilio"), Some("Malchiodi"), null, null, null ), OrcidAuthor("0000-0002-5490-9186", Some("Sofia"), Some("Noli Truant"), null, null, null )) + + val orcid:ORCIDItem = ORCIDItem("10.1042/BCJ20160876", aList) + + val oaf = ORCIDToOAF.convertTOOAF(orcid) + assert(oaf.getPid.size() == 1) + oaf.getPid.toList.foreach(pid => assert(pid.getQualifier.getClassid.equals("doi"))) + oaf.getPid.toList.foreach(pid => assert(pid.getValue.equals("10.1042/BCJ20160876"))) + //println(mapper.writeValueAsString(oaf)) + } - - - } diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala index 6688fc616..fa696fffc 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/uw/UnpayWallMappingTest.scala @@ -20,16 +20,26 @@ class UnpayWallMappingTest { val Ilist = Source.fromInputStream(getClass.getResourceAsStream("input.json")).mkString - + var i:Int = 0 for (line <-Ilist.lines) { val p = UnpayWallToOAF.convertToOAF(line) if(p!= null) { assertTrue(p.getInstance().size()==1) + if (i== 0){ + assertTrue(p.getPid.get(0).getValue.equals("10.1038/2211089b0")) + } + if (i== 1){ + assertTrue(p.getPid.get(0).getValue.equals("10.1021/acs.bioconjchem.8b00058.s001")) + } + if (i== 2){ + assertTrue(p.getPid.get(0).getValue.equals("10.1021/acs.bioconjchem.8b00086.s001")) + } logger.info(s"ID : ${p.getId}") } assertNotNull(line) assertTrue(line.nonEmpty) + i = i+1 } @@ -39,7 +49,9 @@ class UnpayWallMappingTest { val item = UnpayWallToOAF.convertToOAF(l) assertEquals(item.getInstance().get(0).getAccessright.getOpenAccessRoute, OpenAccessRoute.bronze) + logger.info(mapper.writeValueAsString(item)) + } } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/empty_crossref_author_fourth.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/empty_crossref_author_fourth.json new file mode 100644 index 000000000..0cabcaf21 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/empty_crossref_author_fourth.json @@ -0,0 +1,3 @@ +{"collectedfrom":[{"key":"10|openaire____::081b82f96300b6a6e3d282bad31cb6e2","value":"Crossref","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:actionset","classname":"sysimport:actionset","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585329822470,"id":"50|doi_________::f248499c5e0b967ce27df8ed45bffe53","originalId":["10.1042/bcj20160876","50|doiboost____::f248499c5e0b967ce27df8ed45bffe53"],"pid":[{"value":"10.1042/bcj20160876","qualifier":{"classid":"doi","classname":"doi","schemeid":"dnet:pid_types","schemename":"dnet:pid_types"},"dataInfo":null}],"dateofcollection":"2020-03-27T17:23:42Z","dateoftransformation":null,"extraInfo":null,"oaiprovenance":null,"measures":null,"author":null,"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":null,"country":null,"subject":null,"title":[{"value":"Kinetic 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Combining surface plasmon resonance, fluorescence anisotropy and far-UV circular dichroism (CD), we determined that the best model to describe both inhibitory and activating Ly49/MHC-I interactions is one in which the two MHC-I binding sites of the Ly49 homodimer present similar binding constants for the two sites (∼106 M–1) with a slightly positive co-operativity in some cases, and without far-UV CD observable conformational changes. Furthermore, Ly49/MHC-I interactions are diffusion-controlled and enthalpy-driven. These features stand in marked contrast with the activation-controlled and entropy-driven interaction of Ly49s with the viral immunoevasin m157, which is characterized by strong positive co-operativity and conformational selection. These differences are explained by the distinct structures of Ly49/MHC-I and Ly49/m157 complexes. 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classification","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"dataInfo":null}],"title":[{"value":"kinetic and thermodynamic studies of the interaction between activating and inhibitory ly49 natural killer receptors and mhc class i molecules","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":null},{"value":"Kinetic and thermodynamic studies of the interaction between activating and inhibitory Ly49 natural killer receptors and MHC class I molecules","qualifier":{"classid":"alternative title","classname":"alternative title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":null}],"relevantdate":null,"description":[{"value":"Natural killer (NK) cells are lymphocytes of the innate immune system that eliminate virally infected or malignantly transformed cells. 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Combining surface plasmon resonance, fluorescence anisotropy and far-UV circular dichroism (CD), we determined that the best model to describe both inhibitory and activating Ly49/MHC-I interactions is one in which the two MHC-I binding sites of the Ly49 homodimer present similar binding constants for the two sites (∼10 6  M –1 ) with a slightly positive co-operativity in some cases, and without far-UV CD observable conformational changes. Furthermore, Ly49/MHC-I interactions are diffusion-controlled and enthalpy-driven. These features stand in marked contrast with the activation-controlled and entropy-driven interaction of Ly49s with the viral immunoevasin m157, which is characterized by strong positive co-operativity and conformational selection. These differences are explained by the distinct structures of Ly49/MHC-I and Ly49/m157 complexes. 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"1049-2275", "published_date": "2010-09-01", "best_oa_location": null, "journal_is_in_doaj": false, "has_repository_copy": false} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java index 9b99097ce..d5c310c1b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MergeClaimsApplication.java @@ -3,8 +3,12 @@ package eu.dnetlib.dhp.oa.graph.raw; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; +import java.util.ArrayList; +import java.util.List; import java.util.Objects; import java.util.Optional; +import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -98,14 +102,9 @@ public class MergeClaimsApplication { raw .joinWith(claim, raw.col("_1").equalTo(claim.col("_1")), "full_outer") .map( - (MapFunction, Tuple2>, T>) value -> { - Optional> opRaw = Optional.ofNullable(value._1()); - Optional> opClaim = Optional.ofNullable(value._2()); - - return opRaw.isPresent() - ? opRaw.get()._2() - : opClaim.isPresent() ? opClaim.get()._2() : null; - }, + (MapFunction, Tuple2>, T>) value -> processClaims( + Optional.ofNullable(value._1()), + Optional.ofNullable(value._2())), Encoders.bean(clazz)) .filter(Objects::nonNull) .map( @@ -117,6 +116,78 @@ public class MergeClaimsApplication { .text(outPath); } + private static T processClaims(Optional> opRaw, + Optional> opClaim) { + + // when both are present + if (opClaim.isPresent() && opRaw.isPresent()) { + T oafClaim = opClaim.get()._2(); + if (oafClaim instanceof Result) { + T oafRaw = opRaw.get()._2(); + + // merge the context lists from both oaf objects ... + final List context = mergeContexts((Result) oafClaim, (Result) oafRaw); + + // ... and set it on the result from the aggregator + ((Result) oafRaw).setContext(context); + return oafRaw; + } + } + + // otherwise prefer the result from the aggregator + return opRaw.isPresent() + ? opRaw.get()._2() + : opClaim.map(Tuple2::_2).orElse(null); + } + + private static List mergeContexts(Result oafClaim, Result oafRaw) { + return new ArrayList<>( + Stream + .concat( + Optional + .ofNullable(oafClaim.getContext()) + .map(List::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(oafRaw.getContext()) + .map(List::stream) + .orElse(Stream.empty())) + .collect( + Collectors + .toMap( + Context::getId, + c -> c, + (c1, c2) -> { + Context c = new Context(); + c.setId(c1.getId()); + c + .setDataInfo( + new ArrayList<>( + Stream + .concat( + Optional + .ofNullable(c1.getDataInfo()) + .map(List::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(c2.getDataInfo()) + .map(List::stream) + .orElse(Stream.empty())) + .collect( + Collectors + .toMap( + d -> Optional + .ofNullable(d.getProvenanceaction()) + .map(Qualifier::getClassid) + .orElse(""), + d -> d, + (d1, d2) -> d1)) + .values())); + return c; + })) + .values()); + } + private static Dataset readFromPath( SparkSession spark, String path, Class clazz) { return spark diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 1a55499c1..a9d3e05fe 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -480,38 +480,15 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i final String sourceId = createOpenaireId(sourceType, rs.getString("source_id"), false); final String targetId = createOpenaireId(targetType, rs.getString("target_id"), false); - final Relation r1 = new Relation(); - final Relation r2 = new Relation(); - - if (StringUtils.isNotBlank(validationDate)) { - r1.setValidated(true); - r1.setValidationDate(validationDate); - r2.setValidated(true); - r2.setValidationDate(validationDate); - } - r1.setCollectedfrom(COLLECTED_FROM_CLAIM); - r1.setSource(sourceId); - r1.setTarget(targetId); - r1.setDataInfo(DATA_INFO_CLAIM); - r1.setLastupdatetimestamp(lastUpdateTimestamp); - - r2.setCollectedfrom(COLLECTED_FROM_CLAIM); - r2.setSource(targetId); - r2.setTarget(sourceId); - r2.setDataInfo(DATA_INFO_CLAIM); - r2.setLastupdatetimestamp(lastUpdateTimestamp); + Relation r1 = prepareRelation(sourceId, targetId, validationDate); + Relation r2 = prepareRelation(targetId, sourceId, validationDate); final String semantics = rs.getString("semantics"); switch (semantics) { case "resultResult_relationship_isRelatedTo": - r1.setRelType(RESULT_RESULT); - r1.setSubRelType(RELATIONSHIP); - r1.setRelClass(IS_RELATED_TO); - - r2.setRelType(RESULT_RESULT); - r2.setSubRelType(RELATIONSHIP); - r2.setRelClass(IS_RELATED_TO); + r1 = setRelationSemantic(r1, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO); + r2 = setRelationSemantic(r2, RESULT_RESULT, RELATIONSHIP, IS_RELATED_TO); break; case "resultProject_outcome_produces": if (!"project".equals(sourceType)) { @@ -521,13 +498,12 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i "invalid claim, sourceId: %s, targetId: %s, semantics: %s", sourceId, targetId, semantics)); } - r1.setRelType(RESULT_PROJECT); - r1.setSubRelType(OUTCOME); - r1.setRelClass(PRODUCES); - - r2.setRelType(RESULT_PROJECT); - r2.setSubRelType(OUTCOME); - r2.setRelClass(IS_PRODUCED_BY); + r1 = setRelationSemantic(r1, RESULT_PROJECT, OUTCOME, PRODUCES); + r2 = setRelationSemantic(r2, RESULT_PROJECT, OUTCOME, IS_PRODUCED_BY); + break; + case "resultResult_publicationDataset_isRelatedTo": + r1 = setRelationSemantic(r1, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO); + r2 = setRelationSemantic(r2, RESULT_RESULT, PUBLICATION_DATASET, IS_RELATED_TO); break; default: throw new IllegalArgumentException("claim semantics not managed: " + semantics); @@ -540,6 +516,27 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } + private Relation prepareRelation(String sourceId, String targetId, String validationDate) { + Relation r = new Relation(); + if (StringUtils.isNotBlank(validationDate)) { + r.setValidated(true); + r.setValidationDate(validationDate); + } + r.setCollectedfrom(COLLECTED_FROM_CLAIM); + r.setSource(sourceId); + r.setTarget(targetId); + r.setDataInfo(DATA_INFO_CLAIM); + r.setLastupdatetimestamp(lastUpdateTimestamp); + return r; + } + + private Relation setRelationSemantic(Relation r, String relType, String subRelType, String relClass) { + r.setRelType(relType); + r.setSubRelType(subRelType); + r.setRelClass(relClass); + return r; + } + private List prepareContext(final String id, final DataInfo dataInfo) { final Context context = new Context(); context.setId(id);