forked from D-Net/dnet-hadoop
merge branch with master
This commit is contained in:
commit
fcaedac980
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@ -341,13 +341,7 @@ object DoiBoostMappingUtil {
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def generateIdentifier (oaf: Result, doi: String): String = {
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val id = DHPUtils.md5 (doi.toLowerCase)
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return s"50|${
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doiBoostNSPREFIX
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}${
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SEPARATOR
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}${
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id
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}"
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s"50|${doiBoostNSPREFIX}${SEPARATOR}${id}"
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}
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@ -93,7 +93,7 @@ case object Crossref2Oaf {
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result.setOriginalId(tmp.filter(id => id != null).asJava)
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//Set identifier as {50|60} | doiboost____::md5(DOI)
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//Set identifier as 50 | doiboost____::md5(DOI)
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result.setId(generateIdentifier(result, doi))
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// Add DataInfo
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@ -267,7 +267,7 @@ case object Crossref2Oaf {
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val r = new Relation
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r.setSource(sourceId)
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r.setTarget(s"$nsPrefix::$targetId")
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r.setTarget(s"40|$nsPrefix::$targetId")
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r.setRelType("resultProject")
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r.setRelClass("isProducedBy")
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r.setSubRelType("outcome")
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@ -0,0 +1,54 @@
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package eu.dnetlib.dhp.doiboost
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import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, StructuredProperty, Dataset => OafDataset}
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import org.apache.spark.sql.functions.{col, sum}
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession}
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import scala.::
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import scala.collection.JavaConverters._
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class QueryTest {
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def extractLicense(p:Publication):Tuple2[String,String] = {
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val tmp = p.getInstance().asScala.map(i => i.getLicense.getValue).distinct.mkString(",")
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(p.getId,tmp)
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}
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def hasDOI(publication: Publication, doi:String):Boolean = {
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val s = publication.getOriginalId.asScala.filter(i => i.equalsIgnoreCase(doi))
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s.nonEmpty
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}
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def hasNullHostedBy(publication: Publication):Boolean = {
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publication.getInstance().asScala.exists(i => i.getHostedby == null || i.getHostedby.getValue == null)
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}
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def myQuery(spark:SparkSession): Unit = {
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implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication]
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implicit val mapEncoderDat: Encoder[OafDataset] = Encoders.kryo[OafDataset]
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implicit val mapEncoderRel: Encoder[Relation] = Encoders.kryo[Relation]
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val doiboostPubs:Dataset[Publication] = spark.read.load("/data/doiboost/process/doiBoostPublicationFiltered").as[Publication]
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val relFunder: Dataset[Relation] = spark.read.format("org.apache.spark.sql.parquet").load("/data/doiboost/process/crossrefRelation").as[Relation]
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doiboostPubs.filter(p => p.getDateofacceptance != null && p.getDateofacceptance.getValue!= null && p.getDateofacceptance.getValue.length > 0 )
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doiboostPubs.filter(p=>hasDOI(p, "10.1016/j.is.2020.101522")).collect()(0).getDescription.get(0).getValue
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doiboostPubs.filter(p=> hasNullHostedBy(p)).count()
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doiboostPubs.map(p=> (p.getId, p.getBestaccessright.getClassname))(Encoders.tuple(Encoders.STRING,Encoders.STRING))
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}
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}
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@ -90,169 +90,15 @@ public class CleanGraphSparkJob {
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final CleaningRuleMap mapping = CleaningRuleMap.create(vocs);
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readTableFromPath(spark, inputPath, clazz)
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.map((MapFunction<T, T>) value -> fixVocabularyNames(value), Encoders.bean(clazz))
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.map((MapFunction<T, T>) value -> CleaningFunctions.fixVocabularyNames(value), Encoders.bean(clazz))
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.map((MapFunction<T, T>) value -> OafCleaner.apply(value, mapping), Encoders.bean(clazz))
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.map((MapFunction<T, T>) value -> fixDefaults(value), Encoders.bean(clazz))
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.map((MapFunction<T, T>) value -> CleaningFunctions.fixDefaults(value), Encoders.bean(clazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath);
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}
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protected static <T extends Oaf> T fixVocabularyNames(T value) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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// nothing to clean here
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} else if (value instanceof Organization) {
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Organization o = (Organization) value;
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if (Objects.nonNull(o.getCountry())) {
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fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
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}
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES);
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fixVocabName(r.getResourcetype(), ModelConstants.DNET_DATA_CITE_RESOURCE);
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fixVocabName(r.getBestaccessright(), ModelConstants.DNET_ACCESS_MODES);
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if (Objects.nonNull(r.getSubject())) {
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r.getSubject().forEach(s -> fixVocabName(s.getQualifier(), ModelConstants.DNET_SUBJECT_TYPOLOGIES));
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}
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES);
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fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS);
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
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r.getAuthor().forEach(a -> {
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if (Objects.nonNull(a.getPid())) {
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a.getPid().forEach(p -> {
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fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES);
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});
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}
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});
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}
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if (value instanceof Publication) {
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} else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return value;
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}
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private static void fixVocabName(Qualifier q, String vocabularyName) {
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if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
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q.setSchemeid(vocabularyName);
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q.setSchemename(vocabularyName);
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}
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}
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protected static <T extends Oaf> T fixDefaults(T value) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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// nothing to clean here
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} else if (value instanceof Organization) {
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Organization o = (Organization) value;
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if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
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o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
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}
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
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r.setPublisher(null);
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}
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if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
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r
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.setLanguage(
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qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
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}
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if (Objects.nonNull(r.getSubject())) {
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r
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.setSubject(
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r
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.getSubject()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.filter(sp -> Objects.nonNull(sp.getQualifier()))
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.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
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.collect(Collectors.toList()));
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}
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if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
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r
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.setResourcetype(
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qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
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}
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
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i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
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}
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if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
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i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
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}
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if (Objects.isNull(i.getRefereed())) {
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i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
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}
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}
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}
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if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
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Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance());
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if (Objects.isNull(bestaccessrights)) {
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r
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.setBestaccessright(
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qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
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} else {
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r.setBestaccessright(bestaccessrights);
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
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boolean nullRank = r
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.getAuthor()
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.stream()
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.anyMatch(a -> Objects.isNull(a.getRank()));
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if (nullRank) {
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int i = 1;
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for (Author author : r.getAuthor()) {
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author.setRank(i++);
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}
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}
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}
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if (value instanceof Publication) {
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} else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return value;
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}
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private static Qualifier qualifier(String classid, String classname, String scheme) {
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return OafMapperUtils
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.qualifier(
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classid, classname, scheme, scheme);
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}
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private static <T extends Oaf> Dataset<T> readTableFromPath(
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SparkSession spark, String inputEntityPath, Class<T> clazz) {
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|
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@ -0,0 +1,196 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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import java.util.LinkedHashMap;
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import java.util.Objects;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import com.clearspring.analytics.util.Lists;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.oa.graph.raw.AbstractMdRecordToOafMapper;
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import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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public class CleaningFunctions {
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public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
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public static <T extends Oaf> T fixVocabularyNames(T value) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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// nothing to clean here
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} else if (value instanceof Organization) {
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Organization o = (Organization) value;
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if (Objects.nonNull(o.getCountry())) {
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fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
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}
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES);
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fixVocabName(r.getResourcetype(), ModelConstants.DNET_DATA_CITE_RESOURCE);
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fixVocabName(r.getBestaccessright(), ModelConstants.DNET_ACCESS_MODES);
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if (Objects.nonNull(r.getSubject())) {
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r.getSubject().forEach(s -> fixVocabName(s.getQualifier(), ModelConstants.DNET_SUBJECT_TYPOLOGIES));
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}
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES);
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fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS);
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
|
||||
r.getAuthor().forEach(a -> {
|
||||
if (Objects.nonNull(a.getPid())) {
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a.getPid().forEach(p -> {
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fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES);
|
||||
});
|
||||
}
|
||||
});
|
||||
}
|
||||
if (value instanceof Publication) {
|
||||
|
||||
} else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) {
|
||||
|
||||
} else if (value instanceof OtherResearchProduct) {
|
||||
|
||||
} else if (value instanceof Software) {
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
return value;
|
||||
}
|
||||
|
||||
protected static <T extends Oaf> T fixDefaults(T value) {
|
||||
if (value instanceof Datasource) {
|
||||
// nothing to clean here
|
||||
} else if (value instanceof Project) {
|
||||
// nothing to clean here
|
||||
} else if (value instanceof Organization) {
|
||||
Organization o = (Organization) value;
|
||||
if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
|
||||
o.setCountry(qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_COUNTRY_TYPE));
|
||||
}
|
||||
} else if (value instanceof Relation) {
|
||||
// nothing to clean here
|
||||
} else if (value instanceof Result) {
|
||||
|
||||
Result r = (Result) value;
|
||||
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
|
||||
r.setPublisher(null);
|
||||
}
|
||||
if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
|
||||
r
|
||||
.setLanguage(
|
||||
qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
|
||||
}
|
||||
if (Objects.nonNull(r.getSubject())) {
|
||||
r
|
||||
.setSubject(
|
||||
r
|
||||
.getSubject()
|
||||
.stream()
|
||||
.filter(Objects::nonNull)
|
||||
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
|
||||
.filter(sp -> Objects.nonNull(sp.getQualifier()))
|
||||
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
|
||||
r
|
||||
.setResourcetype(
|
||||
qualifier("UNKNOWN", "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
|
||||
}
|
||||
if (Objects.nonNull(r.getInstance())) {
|
||||
for (Instance i : r.getInstance()) {
|
||||
if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
|
||||
i.setAccessright(qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
|
||||
}
|
||||
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
|
||||
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
|
||||
}
|
||||
if (Objects.isNull(i.getRefereed())) {
|
||||
i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
|
||||
}
|
||||
}
|
||||
}
|
||||
if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
|
||||
Qualifier bestaccessrights = AbstractMdRecordToOafMapper.createBestAccessRights(r.getInstance());
|
||||
if (Objects.isNull(bestaccessrights)) {
|
||||
r
|
||||
.setBestaccessright(
|
||||
qualifier("UNKNOWN", "not available", ModelConstants.DNET_ACCESS_MODES));
|
||||
} else {
|
||||
r.setBestaccessright(bestaccessrights);
|
||||
}
|
||||
}
|
||||
if (Objects.nonNull(r.getAuthor())) {
|
||||
boolean nullRank = r
|
||||
.getAuthor()
|
||||
.stream()
|
||||
.anyMatch(a -> Objects.isNull(a.getRank()));
|
||||
if (nullRank) {
|
||||
int i = 1;
|
||||
for (Author author : r.getAuthor()) {
|
||||
author.setRank(i++);
|
||||
}
|
||||
}
|
||||
for(Author a : r.getAuthor()) {
|
||||
if (Objects.isNull(a.getPid())) {
|
||||
a.setPid(Lists.newArrayList());
|
||||
} else {
|
||||
a.setPid(
|
||||
a.getPid().stream()
|
||||
.filter(p -> Objects.nonNull(p.getQualifier()))
|
||||
.filter(p -> StringUtils.isNotBlank(p.getValue()))
|
||||
.map(p -> {
|
||||
p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
|
||||
return p;
|
||||
})
|
||||
.collect(Collectors.toMap(StructuredProperty::getValue, Function.identity(), (p1, p2) -> p1, LinkedHashMap::new))
|
||||
.values()
|
||||
.stream()
|
||||
.collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
if (value instanceof Publication) {
|
||||
|
||||
} else if (value instanceof eu.dnetlib.dhp.schema.oaf.Dataset) {
|
||||
|
||||
} else if (value instanceof OtherResearchProduct) {
|
||||
|
||||
} else if (value instanceof Software) {
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
return value;
|
||||
}
|
||||
|
||||
// HELPERS
|
||||
|
||||
private static void fixVocabName(Qualifier q, String vocabularyName) {
|
||||
if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
|
||||
q.setSchemeid(vocabularyName);
|
||||
q.setSchemename(vocabularyName);
|
||||
}
|
||||
}
|
||||
|
||||
private static Qualifier qualifier(String classid, String classname, String scheme) {
|
||||
return OafMapperUtils
|
||||
.qualifier(
|
||||
classid, classname, scheme, scheme);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -1,10 +1,10 @@
|
|||
DROP VIEW IF EXISTS ${hiveDbName}.result;
|
||||
|
||||
CREATE VIEW IF NOT EXISTS result as
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.publication p
|
||||
CREATE VIEW IF NOT EXISTS ${hiveDbName}.result as
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.publication p
|
||||
union all
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.dataset d
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.dataset d
|
||||
union all
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.software s
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.software s
|
||||
union all
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.otherresearchproduct o;
|
||||
select id, dateofcollection, title, publisher, bestaccessright, datainfo, collectedfrom, pid, author, resulttype, language, country, subject, description, dateofacceptance, relevantdate, embargoenddate, resourcetype, context, externalreference, instance from ${hiveDbName}.otherresearchproduct o;
|
||||
|
|
|
|||
|
|
@ -62,7 +62,7 @@ public class CleaningFunctionTest {
|
|||
assertTrue(p_in instanceof Result);
|
||||
assertTrue(p_in instanceof Publication);
|
||||
|
||||
Publication p_out = OafCleaner.apply(CleanGraphSparkJob.fixVocabularyNames(p_in), mapping);
|
||||
Publication p_out = OafCleaner.apply(CleaningFunctions.fixVocabularyNames(p_in), mapping);
|
||||
|
||||
assertNotNull(p_out);
|
||||
|
||||
|
|
@ -88,7 +88,7 @@ public class CleaningFunctionTest {
|
|||
.map(p -> p.getQualifier())
|
||||
.allMatch(q -> pidTerms.contains(q.getClassid())));
|
||||
|
||||
Publication p_defaults = CleanGraphSparkJob.fixDefaults(p_out);
|
||||
Publication p_defaults = CleaningFunctions.fixDefaults(p_out);
|
||||
assertEquals("CLOSED", p_defaults.getBestaccessright().getClassid());
|
||||
assertNull(p_out.getPublisher());
|
||||
|
||||
|
|
|
|||
|
|
@ -27,6 +27,28 @@
|
|||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "0000-0001-9613-6639"
|
||||
},
|
||||
{
|
||||
"dataInfo": {
|
||||
"deletedbyinference": false,
|
||||
"inferenceprovenance": "",
|
||||
"inferred": false,
|
||||
"invisible": false,
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "sysimport:crosswalk:datasetarchive",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "ORCID12",
|
||||
"classname": "ORCID12",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "https://orcid.org/0000-0001-9613-6639"
|
||||
}
|
||||
],
|
||||
"rank": 1,
|
||||
|
|
@ -91,8 +113,7 @@
|
|||
],
|
||||
"fullname": "Barry, Peter S.",
|
||||
"name": "Peter S.",
|
||||
"pid": [
|
||||
],
|
||||
"pid": null,
|
||||
"rank": 3,
|
||||
"surname": "Barry"
|
||||
},
|
||||
|
|
|
|||
Loading…
Reference in New Issue