resolving conflicts for PR#134
This commit is contained in:
commit
a45b95ccc1
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@ -67,6 +67,7 @@ public class AuthorMerger {
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a -> a
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.map(p -> new Tuple2<>(pidToComparableString(p), a)))
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.collect(Collectors.toMap(Tuple2::_1, Tuple2::_2, (x1, x2) -> x1));
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@ -78,6 +79,7 @@ public class AuthorMerger {
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a -> a
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.filter(p -> !basePidAuthorMap.containsKey(pidToComparableString(p)))
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.map(p -> new Tuple2<>(p, a)))
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.collect(Collectors.toList());
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@ -150,7 +152,7 @@ public class AuthorMerger {
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}
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private static boolean hasPid(Author a) {
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if (a == null || a.getPid() == null || a.getPid().size() == 0)
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if (a == null || a.getPid() == null || a.getPid().isEmpty())
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return false;
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return a.getPid().stream().anyMatch(p -> p != null && StringUtils.isNotBlank(p.getValue()));
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}
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@ -159,7 +161,10 @@ public class AuthorMerger {
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if (StringUtils.isNotBlank(author.getSurname())) {
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return new Person(author.getSurname() + ", " + author.getName(), false);
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} else {
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if (StringUtils.isNotBlank(author.getFullname()))
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return new Person(author.getFullname(), false);
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else
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return new Person("", false);
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}
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}
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@ -1,9 +1,10 @@
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package eu.dnetlib.dhp.actionmanager.datacite
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import org.apache.commons.io.IOUtils
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest}
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import org.apache.http.entity.StringEntity
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import org.apache.http.impl.client.HttpClients
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import org.apache.http.impl.client.{HttpClientBuilder, HttpClients}
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import java.io.IOException
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@ -56,12 +57,16 @@ abstract class AbstractRestClient extends Iterator[String]{
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private def doHTTPRequest[A <: HttpUriRequest](r: A) :String ={
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val client = HttpClients.createDefault
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val timeout = 60; // seconds
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val config = RequestConfig.custom()
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.setConnectTimeout(timeout * 1000)
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.setConnectionRequestTimeout(timeout * 1000)
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.setSocketTimeout(timeout * 1000).build()
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val client =HttpClientBuilder.create().setDefaultRequestConfig(config).build()
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var tries = 4
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try {
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while (tries > 0) {
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println(s"requesting ${r.getURI}")
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try {
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val response = client.execute(r)
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println(s"get response with status${response.getStatusLine.getStatusCode}")
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if (response.getStatusLine.getStatusCode > 400) {
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@ -69,18 +74,14 @@ abstract class AbstractRestClient extends Iterator[String]{
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}
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else
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return IOUtils.toString(response.getEntity.getContent)
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}
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""
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} catch {
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case e: Throwable =>
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throw new RuntimeException("Error on executing request ", e)
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} finally try client.close()
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catch {
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case e: IOException =>
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throw new RuntimeException("Unable to close client ", e)
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println(s"Error on requesting ${r.getURI}")
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e.printStackTrace()
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tries-=1
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}
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}
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""
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}
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getBufferData()
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}
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@ -367,7 +367,7 @@ object DataciteToOAFTransformation {
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result.setDateofcollection(ISO8601FORMAT.format(d))
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result.setDateoftransformation(ISO8601FORMAT.format(ts))
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result.setDateoftransformation(ISO8601FORMAT.format(d))
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result.setDataInfo(dataInfo)
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val creators = (json \\ "creators").extractOrElse[List[CreatorType]](List())
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@ -140,7 +140,7 @@ object ImportDatacite {
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private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = {
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var from:Long = timestamp * 1000
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val delta:Long = 50000000L
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val delta:Long = 100000000L
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var client: DataciteAPIImporter = null
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val now :Long =System.currentTimeMillis()
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var i = 0
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@ -0,0 +1,73 @@
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package eu.dnetlib.dhp.actionmanager.scholix
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
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import org.apache.spark.SparkConf
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object SparkCreateActionset {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/generate_actionset.json")).mkString)
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val workingDirFolder = parser.get("workingDirFolder")
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log.info(s"workingDirFolder -> $workingDirFolder")
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implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val resultEncoders: Encoder[Result] = Encoders.kryo[Result]
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implicit val relationEncoders: Encoder[Relation] = Encoders.kryo[Relation]
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import spark.implicits._
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val relation = spark.read.load(s"$sourcePath/relation").as[Relation]
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relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.flatMap(r => List(r.getSource, r.getTarget)).distinct().write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/id_relation")
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val idRelation = spark.read.load(s"$workingDirFolder/id_relation").as[String]
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log.info("extract source and target Identifier involved in relations")
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log.info("save relation filtered")
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relation.filter(r => (r.getDataInfo == null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
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.write.mode(SaveMode.Overwrite).save(s"$workingDirFolder/actionSetOaf")
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log.info("saving entities")
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val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders))
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entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result])
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entities
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.joinWith(idRelation, entities("_1").equalTo(idRelation("value")))
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.map(p => p._1._2)
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.write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf")
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}
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}
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@ -0,0 +1,86 @@
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package eu.dnetlib.dhp.actionmanager.scholix
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import com.fasterxml.jackson.databind.ObjectMapper
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.action.AtomicAction
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Dataset => OafDataset,Publication, Software, OtherResearchProduct, Relation}
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import org.apache.hadoop.io.Text
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import org.apache.hadoop.io.compress.GzipCodec
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import org.apache.hadoop.mapred.SequenceFileOutputFormat
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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import scala.io.Source
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object SparkSaveActionSet {
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def toActionSet(item: Oaf): (String, String) = {
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val mapper = new ObjectMapper()
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item match {
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case dataset: OafDataset =>
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val a: AtomicAction[OafDataset] = new AtomicAction[OafDataset]
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a.setClazz(classOf[OafDataset])
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a.setPayload(dataset)
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(dataset.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case publication: Publication =>
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val a: AtomicAction[Publication] = new AtomicAction[Publication]
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a.setClazz(classOf[Publication])
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a.setPayload(publication)
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(publication.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case software: Software =>
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val a: AtomicAction[Software] = new AtomicAction[Software]
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a.setClazz(classOf[Software])
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a.setPayload(software)
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(software.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case orp: OtherResearchProduct =>
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val a: AtomicAction[OtherResearchProduct] = new AtomicAction[OtherResearchProduct]
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a.setClazz(classOf[OtherResearchProduct])
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a.setPayload(orp)
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(orp.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case relation: Relation =>
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val a: AtomicAction[Relation] = new AtomicAction[Relation]
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a.setClazz(classOf[Relation])
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a.setPayload(relation)
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(relation.getClass.getCanonicalName, mapper.writeValueAsString(a))
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case _ =>
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null
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}
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}
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/actionset/save_actionset.json")).mkString)
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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implicit val oafEncoders: Encoder[Oaf] = Encoders.kryo[Oaf]
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implicit val tEncoder: Encoder[(String, String)] = Encoders.tuple(Encoders.STRING, Encoders.STRING)
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spark.read.load(sourcePath).as[Oaf]
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.map(o => toActionSet(o))
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.filter(o => o != null)
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.rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text, Text]], classOf[GzipCodec])
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}
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}
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@ -0,0 +1,6 @@
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[
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{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
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{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingDirFolder","paramDescription": "the working Dir Folder", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
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]
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@ -0,0 +1,23 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>spark2</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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|
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@ -0,0 +1,76 @@
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<workflow-app name="Scholexplorer_to_ActionSet_Workflow" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the path of the consistent graph</description>
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</property>
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<property>
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<name>workingDirFolder</name>
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<description>the path of working dir ActionSet</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the path of Scholexplorer ActionSet</description>
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</property>
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</parameters>
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<start to="createActionSet"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="createActionSet">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Create Action Set</name>
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<class>eu.dnetlib.dhp.actionmanager.scholix.SparkCreateActionset</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.sql.shuffle.partitions=3840
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--targetPath</arg><arg>${outputPath}</arg>
|
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<arg>--workingDirFolder</arg><arg>${workingDirFolder}</arg>
|
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<arg>--master</arg><arg>yarn-cluster</arg>
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</spark>
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<ok to="SaveActionSet"/>
|
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<error to="Kill"/>
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</action>
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|
||||
|
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<action name="SaveActionSet">
|
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<spark xmlns="uri:oozie:spark-action:0.2">
|
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<master>yarn-cluster</master>
|
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<mode>cluster</mode>
|
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<name>Save Action Set</name>
|
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<class>eu.dnetlib.dhp.actionmanager.scholix.SparkSaveActionSet</class>
|
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
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<spark-opts>
|
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--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=3840
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDirFolder}/actionSetOaf</arg>
|
||||
<arg>--targetPath</arg><arg>${outputPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,5 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "source path", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the target path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -3,13 +3,14 @@ package eu.dnetlib.dhp.actionmanager.datacite
|
|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import com.fasterxml.jackson.databind.SerializationFeature
|
||||
|
||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import org.junit.jupiter.api.extension.ExtendWith
|
||||
import org.junit.jupiter.api.{BeforeEach, Test}
|
||||
import org.mockito.junit.jupiter.MockitoExtension
|
||||
|
||||
import java.text.SimpleDateFormat
|
||||
import java.util.Locale
|
||||
import scala.io.Source
|
||||
|
||||
@ExtendWith(Array(classOf[MockitoExtension]))
|
||||
|
|
@ -22,6 +23,18 @@ class DataciteToOAFTest extends AbstractVocabularyTest{
|
|||
super.setUpVocabulary()
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testDateMapping:Unit = {
|
||||
val inputDate = "2021-07-14T11:52:54+0000"
|
||||
val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US)
|
||||
val dt = ISO8601FORMAT.parse(inputDate)
|
||||
println(dt.getTime)
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testMapping() :Unit = {
|
||||
val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDataset {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsReferencedBy extends AbstractEnrichMissingDat
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isReferencedBy");
|
||||
return relType.equals(ModelConstants.IS_REFERENCED_BY);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDataset {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsRelatedTo extends AbstractEnrichMissingDatase
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isRelatedTo");
|
||||
return relType.equals(ModelConstants.IS_RELATED_TO);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingDataset {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedBy extends AbstractEnrichMissingD
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isSupplementedBy");
|
||||
return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingDataset {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingDatasetIsSupplementedTo extends AbstractEnrichMissingD
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isSupplementedTo");
|
||||
return relType.equals(ModelConstants.IS_SUPPLEMENT_TO);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedDatasets;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingDatasetReferences extends AbstractEnrichMissingDataset
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("references");
|
||||
return relType.equals(ModelConstants.REFERENCES);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissingPublication {
|
||||
|
||||
|
|
@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsReferencedBy extends AbstractEnrichMissin
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isReferencedBy");
|
||||
return relType.equals(ModelConstants.IS_REFERENCED_BY);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPublication {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsRelatedTo extends AbstractEnrichMissingPu
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isRelatedTo");
|
||||
return relType.equals(ModelConstants.IS_RELATED_TO);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMissingPublication {
|
||||
|
||||
|
|
@ -11,6 +12,6 @@ public class EnrichMissingPublicationIsSupplementedBy extends AbstractEnrichMiss
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isSupplementedBy");
|
||||
return relType.equals(ModelConstants.IS_SUPPLEMENTED_BY);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMissingPublication {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingPublicationIsSupplementedTo extends AbstractEnrichMiss
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("isSupplementedTo");
|
||||
return relType.equals(ModelConstants.IS_SUPPLEMENT_TO);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,6 +2,7 @@
|
|||
package eu.dnetlib.dhp.broker.oa.matchers.relatedPublications;
|
||||
|
||||
import eu.dnetlib.dhp.broker.model.Topic;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
|
||||
public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPublication {
|
||||
|
||||
|
|
@ -11,7 +12,7 @@ public class EnrichMissingPublicationReferences extends AbstractEnrichMissingPub
|
|||
|
||||
@Override
|
||||
protected boolean filterByType(final String relType) {
|
||||
return relType.equals("references");
|
||||
return relType.equals(ModelConstants.REFERENCES);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -17,6 +17,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
|
||||
public class ClusterUtils {
|
||||
|
|
@ -52,15 +53,15 @@ public class ClusterUtils {
|
|||
}
|
||||
|
||||
public static boolean isDedupRoot(final String id) {
|
||||
return id.contains("dedup_wf_");
|
||||
return id.contains("dedup");
|
||||
}
|
||||
|
||||
public static final boolean isValidResultResultClass(final String s) {
|
||||
return s.equals("isReferencedBy")
|
||||
|| s.equals("isRelatedTo")
|
||||
|| s.equals("references")
|
||||
|| s.equals("isSupplementedBy")
|
||||
|| s.equals("isSupplementedTo");
|
||||
return s.equals(ModelConstants.IS_REFERENCED_BY)
|
||||
|| s.equals(ModelConstants.IS_RELATED_TO)
|
||||
|| s.equals(ModelConstants.REFERENCES)
|
||||
|| s.equals(ModelConstants.IS_SUPPLEMENTED_BY)
|
||||
|| s.equals(ModelConstants.IS_SUPPLEMENT_TO);
|
||||
}
|
||||
|
||||
public static <T> T incrementAccumulator(final T o, final LongAccumulator acc) {
|
||||
|
|
|
|||
|
|
@ -23,6 +23,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.common.HdfsSupport;
|
||||
import eu.dnetlib.dhp.schema.common.EntityType;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
|
@ -77,17 +78,22 @@ public class SparkUpdateEntity extends AbstractSparkAction {
|
|||
(type, clazz) -> {
|
||||
final String outputPath = dedupGraphPath + "/" + type;
|
||||
removeOutputDir(spark, outputPath);
|
||||
|
||||
final String ip = DedupUtility.createEntityPath(graphBasePath, type.toString());
|
||||
if (HdfsSupport.exists(ip, sc.hadoopConfiguration())) {
|
||||
JavaRDD<String> sourceEntity = sc
|
||||
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
|
||||
|
||||
if (mergeRelExists(workingPath, type.toString())) {
|
||||
|
||||
final String mergeRelPath = DedupUtility.createMergeRelPath(workingPath, "*", type.toString());
|
||||
final String mergeRelPath = DedupUtility
|
||||
.createMergeRelPath(workingPath, "*", type.toString());
|
||||
final String dedupRecordPath = DedupUtility
|
||||
.createDedupRecordPath(workingPath, "*", type.toString());
|
||||
|
||||
final Dataset<Relation> rel = spark.read().load(mergeRelPath).as(Encoders.bean(Relation.class));
|
||||
final Dataset<Relation> rel = spark
|
||||
.read()
|
||||
.load(mergeRelPath)
|
||||
.as(Encoders.bean(Relation.class));
|
||||
|
||||
final JavaPairRDD<String, String> mergedIds = rel
|
||||
.where("relClass == 'merges'")
|
||||
|
|
@ -119,6 +125,7 @@ public class SparkUpdateEntity extends AbstractSparkAction {
|
|||
}
|
||||
|
||||
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,12 +1,16 @@
|
|||
package eu.dnetlib.doiboost
|
||||
|
||||
import java.time.LocalDate
|
||||
import java.time.format.DateTimeFormatter
|
||||
|
||||
import eu.dnetlib.dhp.schema.action.AtomicAction
|
||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.oaf.{AccessRight, DataInfo, Dataset, Field, Instance, KeyValue, Oaf, OpenAccessRoute, Organization, Publication, Qualifier, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.commons.lang3.StringUtils
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{getClosedAccessQualifier, getEmbargoedAccessQualifier, getUnknownQualifier}
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -118,10 +122,74 @@ object DoiBoostMappingUtil {
|
|||
}
|
||||
|
||||
|
||||
def decideAccessRight(lic : Field[String], date:String) : AccessRight = {
|
||||
if(lic == null){
|
||||
//Default value Unknown
|
||||
return getUnknownQualifier()
|
||||
}
|
||||
val license : String = lic.getValue
|
||||
//CC licenses
|
||||
if(license.startsWith("cc") ||
|
||||
license.startsWith("http://creativecommons.org/licenses") ||
|
||||
license.startsWith("https://creativecommons.org/licenses") ||
|
||||
|
||||
//ACS Publications Author choice licenses (considered OPEN also by Unpaywall)
|
||||
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html") ||
|
||||
license.equals("http://pubs.acs.org/page/policy/authorchoice_termsofuse.html") ||
|
||||
license.equals("http://pubs.acs.org/page/policy/authorchoice_ccbyncnd_termsofuse.html") ||
|
||||
|
||||
//APA (considered OPEN also by Unpaywall)
|
||||
license.equals("http://www.apa.org/pubs/journals/resources/open-access.aspx")){
|
||||
|
||||
val oaq : AccessRight = getOpenAccessQualifier()
|
||||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||||
return oaq
|
||||
}
|
||||
|
||||
//OUP (BUT ONLY AFTER 12 MONTHS FROM THE PUBLICATION DATE, OTHERWISE THEY ARE EMBARGOED)
|
||||
if(license.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")){
|
||||
val now = java.time.LocalDate.now
|
||||
|
||||
try{
|
||||
val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd"))
|
||||
if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){
|
||||
val oaq : AccessRight = getOpenAccessQualifier()
|
||||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||||
return oaq
|
||||
}
|
||||
else{
|
||||
return getEmbargoedAccessQualifier()
|
||||
}
|
||||
}catch {
|
||||
case e: Exception => {
|
||||
try{
|
||||
val pub_date = LocalDate.parse(date, DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'"))
|
||||
if (((now.toEpochDay - pub_date.toEpochDay)/365.0) > 1){
|
||||
val oaq : AccessRight = getOpenAccessQualifier()
|
||||
oaq.setOpenAccessRoute(OpenAccessRoute.hybrid)
|
||||
return oaq
|
||||
}
|
||||
else{
|
||||
return getEmbargoedAccessQualifier()
|
||||
}
|
||||
}catch{
|
||||
case ex: Exception => return getClosedAccessQualifier()
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
return getClosedAccessQualifier()
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
def getOpenAccessQualifier():AccessRight = {
|
||||
OafMapperUtils.accessRight("OPEN","Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||
|
||||
OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN,"Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||
}
|
||||
|
||||
def getRestrictedQualifier():AccessRight = {
|
||||
|
|
@ -129,6 +197,20 @@ object DoiBoostMappingUtil {
|
|||
}
|
||||
|
||||
|
||||
def getUnknownQualifier():AccessRight = {
|
||||
OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||
}
|
||||
|
||||
|
||||
def getEmbargoedAccessQualifier():AccessRight = {
|
||||
OafMapperUtils.accessRight("EMBARGO","Embargo",ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||
}
|
||||
|
||||
def getClosedAccessQualifier():AccessRight = {
|
||||
OafMapperUtils.accessRight("CLOSED","Closed Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)
|
||||
}
|
||||
|
||||
|
||||
def extractInstance(r:Result):Option[Instance] = {
|
||||
r.getInstance().asScala.find(i => i.getInstancetype != null && i.getInstancetype.getClassid.nonEmpty)
|
||||
}
|
||||
|
|
@ -150,10 +232,11 @@ object DoiBoostMappingUtil {
|
|||
if (item != null) {
|
||||
hb.setValue(item.officialname)
|
||||
hb.setKey(generateDSId(item.id))
|
||||
if (item.openAccess)
|
||||
if (item.openAccess) {
|
||||
i.setAccessright(getOpenAccessQualifier())
|
||||
val ar = getOpenAccessQualifier()
|
||||
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename))
|
||||
i.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold)
|
||||
}
|
||||
|
||||
}
|
||||
else {
|
||||
hb = ModelConstants.UNKNOWN_REPOSITORY
|
||||
|
|
@ -161,17 +244,8 @@ object DoiBoostMappingUtil {
|
|||
i.setHostedby(hb)
|
||||
})
|
||||
|
||||
val ar = publication.getInstance().asScala.filter(i => i.getInstancetype != null && i.getAccessright!= null && i.getAccessright.getClassid!= null).map(f=> f.getAccessright.getClassid)
|
||||
if (ar.nonEmpty) {
|
||||
if(ar.contains(ModelConstants.ACCESS_RIGHT_OPEN)){
|
||||
val ar = getOpenAccessQualifier()
|
||||
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename))
|
||||
}
|
||||
else {
|
||||
val ar = getRestrictedQualifier()
|
||||
publication.setBestaccessright(OafMapperUtils.qualifier(ar.getClassid, ar.getClassname, ar.getSchemeid, ar.getSchemename))
|
||||
}
|
||||
}
|
||||
publication.setBestaccessright(OafMapperUtils.createBestAccessRights(publication.getInstance()))
|
||||
|
||||
publication
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,7 +4,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
|||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil.{decideAccessRight, _}
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
|
|
@ -168,12 +168,22 @@ case object Crossref2Oaf {
|
|||
// Mapping instance
|
||||
val instance = new Instance()
|
||||
val license = for {
|
||||
JString(lic) <- json \ "license" \ "URL"
|
||||
} yield asField(lic)
|
||||
val l = license.filter(d => StringUtils.isNotBlank(d.getValue))
|
||||
if (l.nonEmpty)
|
||||
instance.setLicense(l.head)
|
||||
|
||||
JObject(license) <- json \ "license"
|
||||
JField("URL", JString(lic)) <- license
|
||||
JField("content-version", JString(content_version)) <- license
|
||||
} yield (asField(lic), content_version)
|
||||
val l = license.filter(d => StringUtils.isNotBlank(d._1.getValue))
|
||||
if (l.nonEmpty){
|
||||
if (l exists (d => d._2.equals("vor"))){
|
||||
for(d <- l){
|
||||
if (d._2.equals("vor")){
|
||||
instance.setLicense(d._1)
|
||||
}
|
||||
}
|
||||
}
|
||||
else{
|
||||
instance.setLicense(l.head._1)}
|
||||
}
|
||||
|
||||
// Ticket #6281 added pid to Instance
|
||||
instance.setPid(result.getPid)
|
||||
|
|
@ -185,7 +195,7 @@ case object Crossref2Oaf {
|
|||
OafMapperUtils.qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS, ModelConstants.DNET_REVIEW_LEVELS))
|
||||
}
|
||||
|
||||
instance.setAccessright(getRestrictedQualifier())
|
||||
instance.setAccessright(decideAccessRight(instance.getLicense, result.getDateofacceptance.getValue))
|
||||
instance.setInstancetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
|
||||
result.setResourcetype(OafMapperUtils.qualifier(cobjCategory.substring(0, 4), cobjCategory.substring(5), ModelConstants.DNET_PUBLICATION_RESOURCE, ModelConstants.DNET_PUBLICATION_RESOURCE))
|
||||
|
||||
|
|
|
|||
|
|
@ -11,6 +11,7 @@ import org.slf4j.{Logger, LoggerFactory}
|
|||
|
||||
import scala.collection.JavaConverters._
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
import eu.dnetlib.doiboost.uw.UnpayWallToOAF.get_unpaywall_color
|
||||
|
||||
|
||||
|
||||
|
|
@ -23,6 +24,21 @@ case class OALocation(evidence:Option[String], host_type:Option[String], is_best
|
|||
object UnpayWallToOAF {
|
||||
val logger: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
||||
|
||||
def get_unpaywall_color(input:String):Option[OpenAccessRoute] = {
|
||||
if(input == null || input.equalsIgnoreCase("close"))
|
||||
return None
|
||||
if(input.equalsIgnoreCase("green"))
|
||||
return Some(OpenAccessRoute.green)
|
||||
if(input.equalsIgnoreCase("bronze"))
|
||||
return Some(OpenAccessRoute.bronze)
|
||||
if(input.equalsIgnoreCase("hybrid"))
|
||||
return Some(OpenAccessRoute.hybrid)
|
||||
else
|
||||
return Some(OpenAccessRoute.gold)
|
||||
|
||||
}
|
||||
|
||||
def get_color(is_oa:Boolean, location: OALocation, journal_is_oa:Boolean):Option[OpenAccessRoute] = {
|
||||
if (is_oa) {
|
||||
if (location.host_type.isDefined) {
|
||||
|
|
@ -65,7 +81,7 @@ object UnpayWallToOAF {
|
|||
|
||||
val oaLocation:OALocation = (json \ "best_oa_location").extractOrElse[OALocation](null)
|
||||
|
||||
val colour = get_color(is_oa, oaLocation, journal_is_oa)
|
||||
val colour = get_unpaywall_color((json \ "oa_status").extractOrElse[String](null))
|
||||
|
||||
pub.setCollectedfrom(List(createUnpayWallCollectedFrom()).asJava)
|
||||
pub.setDataInfo(generateDataInfo())
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="Generate DOIBoost ActionSet" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Generate DOIBoost ActionSet - PREPROCESS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="Generate DOIBoost ActionSet for PROD" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Generate DOIBoost ActionSet - PROCESS" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
|
|
@ -99,7 +99,7 @@
|
|||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${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}
|
||||
|
|
@ -124,7 +124,7 @@
|
|||
--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}
|
||||
|
|
|
|||
|
|
@ -492,6 +492,124 @@ class CrossrefMappingTest {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testLicenseVorClosed() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_vor.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
|
||||
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
println(mapper.writeValueAsString(item))
|
||||
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://www.springer.com/vor")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("CLOSED")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testLicenseOpen() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_open.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
|
||||
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid))
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
println(mapper.writeValueAsString(item))
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testLicenseEmbargoOpen() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_open.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
|
||||
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("OPEN")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == OpenAccessRoute.hybrid))
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
println(mapper.writeValueAsString(item))
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
def testLicenseEmbargo() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
|
||||
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
println(mapper.writeValueAsString(item))
|
||||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testLicenseEmbargoDateTime() :Unit = {
|
||||
val json = Source.fromInputStream(getClass.getResourceAsStream("publication_license_embargo_datetime.json")).mkString
|
||||
|
||||
|
||||
assertNotNull(json)
|
||||
assertFalse(json.isEmpty);
|
||||
|
||||
val resultList: List[Oaf] = Crossref2Oaf.convert(json)
|
||||
|
||||
assertTrue(resultList.nonEmpty)
|
||||
|
||||
|
||||
val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result]
|
||||
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getLicense.getValue.equals("https://academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getClassid.equals("EMBARGO")))
|
||||
assertTrue(item.getInstance().asScala exists (i => i.getAccessright.getOpenAccessRoute == null))
|
||||
mapper.getSerializationConfig.enable(SerializationConfig.Feature.INDENT_OUTPUT)
|
||||
println(mapper.writeValueAsString(item))
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,42 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkConvertDatasetToJsonRDD {
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info(s"targetPath -> $targetPath")
|
||||
|
||||
val resultObject = List("publication","dataset","software", "otherResearchProduct")
|
||||
val mapper = new ObjectMapper()
|
||||
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
|
||||
|
||||
resultObject.foreach{item =>
|
||||
spark.read.load(s"$sourcePath/$item").as[Result].map(r=> mapper.writeValueAsString(r))(Encoders.STRING).rdd.saveAsTextFile(s"$targetPath/${item.toLowerCase}", classOf[GzipCodec])
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
object SparkConvertRDDtoDataset {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/convert_dataset_json_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
val t = parser.get("targetPath")
|
||||
log.info(s"targetPath -> $t")
|
||||
|
||||
val entityPath = s"$t/entities"
|
||||
val relPath = s"$t/relation"
|
||||
val mapper = new ObjectMapper()
|
||||
implicit val datasetEncoder: Encoder[OafDataset] = Encoders.kryo(classOf[OafDataset])
|
||||
implicit val publicationEncoder: Encoder[Publication] = Encoders.kryo(classOf[Publication])
|
||||
implicit val relationEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
implicit val orpEncoder: Encoder[OtherResearchProduct] = Encoders.kryo(classOf[OtherResearchProduct])
|
||||
implicit val softwareEncoder: Encoder[Software] = Encoders.kryo(classOf[Software])
|
||||
|
||||
|
||||
log.info("Converting dataset")
|
||||
val rddDataset =spark.sparkContext.textFile(s"$sourcePath/dataset").map(s => mapper.readValue(s, classOf[OafDataset]))
|
||||
spark.createDataset(rddDataset).as[OafDataset].write.mode(SaveMode.Overwrite).save(s"$entityPath/dataset")
|
||||
|
||||
|
||||
log.info("Converting publication")
|
||||
val rddPublication =spark.sparkContext.textFile(s"$sourcePath/publication").map(s => mapper.readValue(s, classOf[Publication]))
|
||||
spark.createDataset(rddPublication).as[Publication].write.mode(SaveMode.Overwrite).save(s"$entityPath/publication")
|
||||
|
||||
log.info("Converting software")
|
||||
val rddSoftware =spark.sparkContext.textFile(s"$sourcePath/software").map(s => mapper.readValue(s, classOf[Software]))
|
||||
spark.createDataset(rddSoftware).as[Software].write.mode(SaveMode.Overwrite).save(s"$entityPath/software")
|
||||
|
||||
log.info("Converting otherresearchproduct")
|
||||
val rddOtherResearchProduct =spark.sparkContext.textFile(s"$sourcePath/otherresearchproduct").map(s => mapper.readValue(s, classOf[OtherResearchProduct]))
|
||||
spark.createDataset(rddOtherResearchProduct).as[OtherResearchProduct].write.mode(SaveMode.Overwrite).save(s"$entityPath/otherresearchproduct")
|
||||
|
||||
|
||||
log.info("Converting Relation")
|
||||
|
||||
|
||||
val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation]))
|
||||
spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath")
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
@ -70,7 +70,7 @@ object SparkCreateInputGraph {
|
|||
|
||||
resultObject.foreach { r =>
|
||||
log.info(s"Make ${r._1} unique")
|
||||
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/dedup/${r._1}",spark, r._2)
|
||||
makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/preprocess/${r._1}",spark, r._2)
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -42,6 +42,7 @@ object SparkCreateScholix {
|
|||
|
||||
|
||||
val relationDS: Dataset[(String, Relation)] = spark.read.load(relationPath).as[Relation]
|
||||
.filter(r => (r.getDataInfo== null || r.getDataInfo.getDeletedbyinference == false) && !r.getRelClass.toLowerCase.contains("merge"))
|
||||
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
|
||||
val summaryDS: Dataset[(String, ScholixSummary)] = spark.read.load(summaryPath).as[ScholixSummary]
|
||||
|
|
|
|||
|
|
@ -1,7 +1,7 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
|
||||
import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary
|
||||
import eu.dnetlib.dhp.sx.graph.scholix.ScholixUtils
|
||||
import org.apache.commons.io.IOUtils
|
||||
|
|
@ -29,11 +29,12 @@ object SparkCreateSummaryObject {
|
|||
log.info(s"targetPath -> $targetPath")
|
||||
|
||||
implicit val resultEncoder:Encoder[Result] = Encoders.kryo[Result]
|
||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
||||
|
||||
implicit val summaryEncoder:Encoder[ScholixSummary] = Encoders.kryo[ScholixSummary]
|
||||
|
||||
|
||||
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result]
|
||||
val ds:Dataset[Result] = spark.read.load(s"$sourcePath/*").as[Result].filter(r=>r.getDataInfo== null || r.getDataInfo.getDeletedbyinference== false)
|
||||
|
||||
ds.repartition(6000).map(r => ScholixUtils.resultToSummary(r)).filter(s => s!= null).write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
|
||||
|
|
|
|||
|
|
@ -1,10 +1,17 @@
|
|||
package eu.dnetlib.dhp.sx.graph
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.io.compress.GzipCodec
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql._
|
||||
import org.json4s
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.collection.JavaConverters._
|
||||
|
|
@ -25,16 +32,97 @@ object SparkResolveRelation {
|
|||
val relationPath = parser.get("relationPath")
|
||||
log.info(s"sourcePath -> $relationPath")
|
||||
val entityPath = parser.get("entityPath")
|
||||
log.info(s"targetPath -> $entityPath")
|
||||
log.info(s"entityPath -> $entityPath")
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info(s"workingPath -> $workingPath")
|
||||
|
||||
|
||||
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||
import spark.implicits._
|
||||
val entities:Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
|
||||
|
||||
|
||||
extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath)
|
||||
|
||||
val mappper = new ObjectMapper()
|
||||
|
||||
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)]
|
||||
|
||||
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
|
||||
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{
|
||||
m =>
|
||||
val sourceResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty)
|
||||
currentRelation.setSource(sourceResolved._1)
|
||||
currentRelation
|
||||
}.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedSource")
|
||||
|
||||
|
||||
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{
|
||||
m =>
|
||||
val targetResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (targetResolved!=null && targetResolved._1.nonEmpty)
|
||||
currentRelation.setTarget(targetResolved._1)
|
||||
currentRelation
|
||||
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relation_resolved")
|
||||
|
||||
spark.read.load(s"$workingPath/relation_resolved").as[Relation]
|
||||
.map(r => mappper.writeValueAsString(r))
|
||||
.rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec])
|
||||
|
||||
}
|
||||
|
||||
|
||||
private def extractPidsFromRecord(input:String):(String,List[(String,String)]) = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
lazy val json: json4s.JValue = parse(input)
|
||||
val id:String = (json \ "id").extract[String]
|
||||
val result: List[(String,String)] = for {
|
||||
JObject(pids) <- json \ "pid"
|
||||
JField("value", JString(pidValue)) <- pids
|
||||
JField("qualifier", JObject(qualifier)) <- pids
|
||||
JField("classname", JString(pidType)) <- qualifier
|
||||
} yield (pidValue, pidType)
|
||||
(id,result)
|
||||
}
|
||||
|
||||
private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = {
|
||||
import spark.implicits._
|
||||
|
||||
val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*")
|
||||
.map(i => extractPidsFromRecord(i))
|
||||
.filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty)
|
||||
.flatMap{ p =>
|
||||
p._2.map(pid =>
|
||||
(p._1, convertPidToDNETIdentifier(pid._1, pid._2))
|
||||
)
|
||||
}.filter(r =>r._1 != null || r._2 != null)
|
||||
|
||||
spark.createDataset(d)
|
||||
.groupByKey(_._2)
|
||||
.reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y)
|
||||
.map(s => s._2)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/relationResolvedPid")
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
This method should be used once we finally convert everythings in Kryo dataset
|
||||
instead of using rdd of json
|
||||
*/
|
||||
private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = {
|
||||
import spark.implicits._
|
||||
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
|
||||
entities.flatMap(e => e.getPid.asScala
|
||||
.map(p =>
|
||||
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
|
||||
|
|
@ -45,41 +133,9 @@ object SparkResolveRelation {
|
|||
.map(s => s._2)
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/resolvedPid")
|
||||
|
||||
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/resolvedPid").as[(String,String)]
|
||||
|
||||
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
|
||||
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_1")), "left").map{
|
||||
m =>
|
||||
val sourceResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (sourceResolved!=null && sourceResolved._2.nonEmpty)
|
||||
currentRelation.setSource(sourceResolved._2)
|
||||
currentRelation
|
||||
}.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/resolvedSource")
|
||||
|
||||
|
||||
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/resolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_1")), "left").map{
|
||||
m =>
|
||||
val targetResolved = m._2
|
||||
val currentRelation = m._1._2
|
||||
if (targetResolved!=null && targetResolved._2.nonEmpty)
|
||||
currentRelation.setTarget(targetResolved._2)
|
||||
currentRelation
|
||||
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
|
||||
.write
|
||||
.mode(SaveMode.Overwrite)
|
||||
.save(s"$workingPath/resolvedRelation")
|
||||
.save(s"$workingPath/relationResolvedPid")
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
def convertPidToDNETIdentifier(pid:String, pidType: String):String = {
|
||||
if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty)
|
||||
null
|
||||
|
|
|
|||
|
|
@ -199,7 +199,7 @@ object BioDBToOAF {
|
|||
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
|
||||
}
|
||||
val relevant_dates: List[StructuredProperty] = dates.filter(d => !d.date_info.contains("entry version"))
|
||||
.map(date => OafMapperUtils.structuredProperty(date.date, "UNKNOWN", "UNKNOWN", ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
|
||||
.map(date => OafMapperUtils.structuredProperty(date.date, ModelConstants.UNKNOWN, ModelConstants.UNKNOWN, ModelConstants.DNET_DATACITE_DATE, ModelConstants.DNET_DATACITE_DATE, DATA_INFO))
|
||||
if (relevant_dates != null && relevant_dates.nonEmpty)
|
||||
d.setRelevantdate(relevant_dates.asJava)
|
||||
d.setDateofacceptance(OafMapperUtils.field(i_date.get.date, DATA_INFO))
|
||||
|
|
@ -218,12 +218,12 @@ object BioDBToOAF {
|
|||
|
||||
|
||||
if (references_pmid != null && references_pmid.nonEmpty) {
|
||||
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
|
||||
val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
|
||||
rel.getCollectedfrom
|
||||
List(d, rel)
|
||||
}
|
||||
else if (references_doi != null && references_doi.nonEmpty) {
|
||||
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), "relationship", "isRelatedTo", if (i_date.isDefined) i_date.get.date else null)
|
||||
val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null)
|
||||
List(d, rel)
|
||||
}
|
||||
else
|
||||
|
|
@ -243,7 +243,7 @@ object BioDBToOAF {
|
|||
rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava)
|
||||
rel.setDataInfo(DATA_INFO)
|
||||
|
||||
rel.setRelType("resultResult")
|
||||
rel.setRelType(ModelConstants.RESULT_RESULT)
|
||||
rel.setSubRelType(subRelType)
|
||||
rel.setRelClass(relClass)
|
||||
|
||||
|
|
@ -263,7 +263,7 @@ object BioDBToOAF {
|
|||
|
||||
|
||||
def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = {
|
||||
createRelation(pid,pidType,sourceId,collectedFrom, "supplement","IsSupplementTo", date)
|
||||
createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date)
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -392,6 +392,6 @@ object BioDBToOAF {
|
|||
i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
|
||||
d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(input.date), DATA_INFO))
|
||||
|
||||
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"),"relationship", "isRelatedTo", GraphCleaningFunctions.cleanDate(input.date)))
|
||||
List(d, createRelation(input.pmid, "pmid", d.getId, collectedFromMap("ebi"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, GraphCleaningFunctions.cleanDate(input.date)))
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ object PubMedToOaf {
|
|||
)
|
||||
|
||||
def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = {
|
||||
val result_typologies = getVocabularyTerm("dnet:result_typologies", vocabularies, cobjQualifier.getClassid)
|
||||
val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid)
|
||||
result_typologies.getClassid match {
|
||||
case "dataset" => new Dataset
|
||||
case "publication" => new Publication
|
||||
|
|
@ -68,11 +68,11 @@ object PubMedToOaf {
|
|||
//else We have to find a terms that match the vocabulary otherwise we discard it
|
||||
val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue))
|
||||
if (ja.isDefined) {
|
||||
val cojbCategory = getVocabularyTerm("dnet:publication_resource", vocabularies, ja.get.getValue)
|
||||
val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue)
|
||||
i.setInstancetype(cojbCategory)
|
||||
} else {
|
||||
val i_type = article.getPublicationTypes.asScala
|
||||
.map(s => getVocabularyTerm("dnet:publication_resource", vocabularies, s.getValue))
|
||||
.map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue))
|
||||
.find(q => q != null)
|
||||
if (i_type.isDefined)
|
||||
i.setInstancetype(i_type.get)
|
||||
|
|
@ -112,7 +112,7 @@ object PubMedToOaf {
|
|||
|
||||
if (article.getLanguage != null) {
|
||||
|
||||
val term = vocabularies.getSynonymAsQualifier("dnet:languages", article.getLanguage)
|
||||
val term = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_LANGUAGES, article.getLanguage)
|
||||
if (term != null)
|
||||
result.setLanguage(term)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,11 +1,10 @@
|
|||
package eu.dnetlib.dhp.sx.graph.scholix
|
||||
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.{Dataset, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.sx.scholix.{Scholix, ScholixCollectedFrom, ScholixEntityId, ScholixIdentifier, ScholixRelationship, ScholixResource}
|
||||
import eu.dnetlib.dhp.schema.oaf.{Publication, Relation, Result, StructuredProperty}
|
||||
import eu.dnetlib.dhp.schema.sx.scholix._
|
||||
import eu.dnetlib.dhp.schema.sx.summary.{CollectedFromType, SchemeValue, ScholixSummary, Typology}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import org.apache.spark.sql.Encoders.bean
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.{Encoder, Encoders}
|
||||
import org.json4s
|
||||
|
|
@ -301,14 +300,14 @@ object ScholixUtils {
|
|||
if (r.getPid == null || r.getPid.isEmpty)
|
||||
return null
|
||||
|
||||
val pids:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
|
||||
if (pids.isEmpty)
|
||||
val persistentIdentifiers:List[ScholixIdentifier] = extractTypedIdentifierFromInstance(r)
|
||||
if (persistentIdentifiers.isEmpty)
|
||||
return null
|
||||
s.setLocalIdentifier(pids.asJava)
|
||||
if (r.isInstanceOf[Dataset])
|
||||
s.setTypology(Typology.dataset)
|
||||
else
|
||||
s.setLocalIdentifier(persistentIdentifiers.asJava)
|
||||
if (r.isInstanceOf[Publication] )
|
||||
s.setTypology(Typology.publication)
|
||||
else
|
||||
s.setTypology(Typology.dataset)
|
||||
|
||||
s.setSubType(r.getInstance().get(0).getInstancetype.getClassname)
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,5 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the working dir base path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the graph Raw base path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ExtractEntities"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ExtractEntities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract entities in raw graph</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=2000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
</spark>
|
||||
<ok to="DropDedupPath"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="DropDedupPath">
|
||||
<fs>
|
||||
<delete path='${targetPath}/dedup'/>
|
||||
<mkdir path='${targetPath}/dedup/'/>
|
||||
</fs>
|
||||
<ok to="GenerateInputGraphForDedup"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="GenerateInputGraphForDedup">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Generate Input Graph for deduplication</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertDatasetToJsonRDD</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/preprocess</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/dedup</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Create Scholix final Graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
|
|
@ -6,48 +6,22 @@
|
|||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the graph Raw base path</description>
|
||||
<description>the final graph path</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ExtractEntities"/>
|
||||
<start to="ImportDatasetEntities"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ExtractEntities">
|
||||
<action name="ImportDatasetEntities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract entities in raw graph</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=2000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
</spark>
|
||||
<ok to="ResolveRelations"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
<action name="ResolveRelations">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Resolve Relations in raw graph</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
|
||||
<name>Import JSONRDD to Dataset kryo</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkConvertRDDtoDataset</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
|
|
@ -60,9 +34,8 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--relationPath</arg><arg>${targetPath}/extracted/relation</arg>
|
||||
<arg>--workingPath</arg><arg>${targetPath}/resolved/</arg>
|
||||
<arg>--entityPath</arg><arg>${targetPath}/dedup</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
</spark>
|
||||
<ok to="CreateSummaries"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -87,7 +60,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/dedup</arg>
|
||||
<arg>--sourcePath</arg><arg>${targetPath}/entities</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/provision/summaries</arg>
|
||||
</spark>
|
||||
<ok to="CreateScholix"/>
|
||||
|
|
@ -114,7 +87,7 @@
|
|||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--summaryPath</arg><arg>${targetPath}/provision/summaries</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/provision/scholix</arg>
|
||||
<arg>--relationPath</arg><arg>${targetPath}/resolved/resolvedRelation</arg>
|
||||
<arg>--relationPath</arg><arg>${targetPath}/relation</arg>
|
||||
|
||||
</spark>
|
||||
<ok to="DropJSONPath"/>
|
||||
|
|
@ -182,9 +155,5 @@
|
|||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,62 @@
|
|||
<workflow-app name="Resolve Relation" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>entityPath</name>
|
||||
<description>the path of deduplicate Entities</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>relationPath</name>
|
||||
<description>the path of relation unresolved</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the path of relation unresolved</description>
|
||||
</property>
|
||||
|
||||
</parameters>
|
||||
|
||||
<start to="DropRelFolder"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DropRelFolder">
|
||||
<fs>
|
||||
<delete path='${targetPath}/relation'/>
|
||||
<delete path='${targetPath}/relation_resolved'/>
|
||||
<delete path='${targetPath}/resolvedSource'/>
|
||||
<delete path='${targetPath}/resolvedPid'/>
|
||||
|
||||
</fs>
|
||||
<ok to="ResolveRelations"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="ResolveRelations">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Resolve Relations in raw graph</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.shuffle.partitions=3000
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--relationPath</arg><arg>${relationPath}</arg>
|
||||
<arg>--workingPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--entityPath</arg><arg>${entityPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,120 +0,0 @@
|
|||
<workflow-app name="Create Raw Graph Step 2: Map XML to OAF Entities" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>the working path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ExtractDLIPublication"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="ExtractDLIPublication">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract DLI Entities (Publication)</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=5000
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>-e</arg><arg>publication</arg>
|
||||
</spark>
|
||||
<ok to="ExtractDLIDataset"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ExtractDLIDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract DLI Entities (Dataset)</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=5000
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>-e</arg><arg>dataset</arg>
|
||||
</spark>
|
||||
<ok to="ExtractDLIUnknown"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ExtractDLIUnknown">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract DLI Entities (Unknown)</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=5000
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>-e</arg><arg>unknown</arg>
|
||||
</spark>
|
||||
<ok to="ExtractDLIRelation"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="ExtractDLIRelation">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Extract DLI Entities (Relation)</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkSplitOafTODLIEntities</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory ${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.sql.shuffle.partitions=5000
|
||||
${sparkExtraOPT}
|
||||
</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>-e</arg><arg>relation</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -1,61 +0,0 @@
|
|||
<workflow-app name="Create Raw Graph Final Step: Construct the Scholexplorer Raw Graph" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the source path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkDriverMemory</name>
|
||||
<description>memory for driver process</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>sparkExecutorMemory</name>
|
||||
<description>memory for individual executor</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>entity</name>
|
||||
<description>the entity to be merged</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="DeleteTargetPath"/>
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<action name="DeleteTargetPath">
|
||||
<fs>
|
||||
<mkdir path="${targetPath}"/>
|
||||
|
||||
<delete path='${targetPath}/${entity}'/>
|
||||
</fs>
|
||||
<ok to="MergeDLIEntities"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="MergeDLIEntities">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Merge ${entity}</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.SparkScholexplorerCreateRawGraphJob</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<spark-opts> --executor-memory ${sparkExecutorMemory} --driver-memory=${sparkDriverMemory} ${sparkExtraOPT}</spark-opts>
|
||||
<arg>-mt</arg> <arg>yarn-cluster</arg>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}/${entity}</arg>
|
||||
<arg>--targetPath</arg><arg>${targetPath}/${entity}</arg>
|
||||
<arg>--entity</arg><arg>${entity}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -24,6 +24,7 @@ import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
|
|||
import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.PidType;
|
||||
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
||||
|
||||
|
|
@ -250,7 +251,24 @@ public class MappersTest {
|
|||
final Relation r1 = (Relation) list.get(1);
|
||||
final Relation r2 = (Relation) list.get(2);
|
||||
|
||||
assertEquals(d.getId(), r1.getSource());
|
||||
assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r1.getTarget());
|
||||
assertEquals(ModelConstants.RESULT_PROJECT, r1.getRelType());
|
||||
assertEquals(ModelConstants.OUTCOME, r1.getSubRelType());
|
||||
assertEquals(ModelConstants.IS_PRODUCED_BY, r1.getRelClass());
|
||||
assertTrue(r1.getValidated());
|
||||
assertEquals("2020-01-01", r1.getValidationDate());
|
||||
|
||||
assertEquals(d.getId(), r2.getTarget());
|
||||
assertEquals("40|corda_______::e06332dee33bec6c2ba4c98601053229", r2.getSource());
|
||||
assertEquals(ModelConstants.RESULT_PROJECT, r2.getRelType());
|
||||
assertEquals(ModelConstants.OUTCOME, r2.getSubRelType());
|
||||
assertEquals(ModelConstants.PRODUCES, r2.getRelClass());
|
||||
assertTrue(r2.getValidated());
|
||||
assertEquals("2020-01-01", r2.getValidationDate());
|
||||
|
||||
assertValidId(d.getId());
|
||||
assertEquals("50|doi_________::000374d100a9db469bd42b69dbb40b36", d.getId());
|
||||
assertEquals(2, d.getOriginalId().size());
|
||||
assertTrue(d.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:zenodo.org:3234526")));
|
||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
|
|
@ -304,10 +322,12 @@ public class MappersTest {
|
|||
});
|
||||
assertEquals("0001", d.getInstance().get(0).getRefereed().getClassid());
|
||||
assertNotNull(d.getInstance().get(0).getPid());
|
||||
assertTrue(d.getInstance().get(0).getPid().isEmpty());
|
||||
assertFalse(d.getInstance().get(0).getPid().isEmpty());
|
||||
|
||||
assertEquals("doi", d.getInstance().get(0).getAlternateIdentifier().get(0).getQualifier().getClassid());
|
||||
assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getAlternateIdentifier().get(0).getValue());
|
||||
assertEquals("doi", d.getInstance().get(0).getPid().get(0).getQualifier().getClassid());
|
||||
assertEquals("10.5281/zenodo.3234526", d.getInstance().get(0).getPid().get(0).getValue());
|
||||
|
||||
assertTrue(d.getInstance().get(0).getAlternateIdentifier().isEmpty());
|
||||
|
||||
assertValidId(r1.getSource());
|
||||
assertValidId(r1.getTarget());
|
||||
|
|
@ -561,6 +581,31 @@ public class MappersTest {
|
|||
assertNotNull(d.getInstance().get(0).getUrl());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testEnermaps() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("enermaps.xml"));
|
||||
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
|
||||
|
||||
System.out.println("***************");
|
||||
System.out.println(new ObjectMapper().writeValueAsString(list));
|
||||
System.out.println("***************");
|
||||
|
||||
assertEquals(1, list.size());
|
||||
assertTrue(list.get(0) instanceof Dataset);
|
||||
|
||||
final Dataset d = (Dataset) list.get(0);
|
||||
|
||||
assertValidId(d.getId());
|
||||
assertValidId(d.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(StringUtils.isNotBlank(d.getTitle().get(0).getValue()));
|
||||
assertEquals(1, d.getAuthor().size());
|
||||
assertEquals(1, d.getInstance().size());
|
||||
assertNotNull(d.getInstance().get(0).getUrl());
|
||||
assertNotNull(d.getContext());
|
||||
assertTrue(StringUtils.isNotBlank(d.getContext().get(0).getId()));
|
||||
assertEquals("enermaps::selection::tgs00004", d.getContext().get(0).getId());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testClaimFromCrossref() throws IOException {
|
||||
final String xml = IOUtils.toString(getClass().getResourceAsStream("oaf_claim_crossref.xml"));
|
||||
|
|
@ -681,8 +726,8 @@ public class MappersTest {
|
|||
final Dataset p = (Dataset) list.get(0);
|
||||
|
||||
assertValidId(p.getId());
|
||||
assertEquals(2, p.getOriginalId().size());
|
||||
assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("df76e73f-0483-49a4-a9bb-63f2f985574a")));
|
||||
assertTrue(p.getOriginalId().size() == 1);
|
||||
assertEquals("df76e73f-0483-49a4-a9bb-63f2f985574a", p.getOriginalId().get(0));
|
||||
assertValidId(p.getCollectedfrom().get(0).getKey());
|
||||
assertTrue(p.getAuthor().size() > 0);
|
||||
|
||||
|
|
@ -713,12 +758,11 @@ public class MappersTest {
|
|||
}
|
||||
|
||||
private void assertValidId(final String id) {
|
||||
System.out.println(id);
|
||||
// System.out.println(id);
|
||||
|
||||
assertEquals(49, id.length());
|
||||
assertEquals('|', id.charAt(2));
|
||||
assertEquals(':', id.charAt(15));
|
||||
assertEquals(':', id.charAt(16));
|
||||
assertEquals(IdentifierFactory.ID_PREFIX_SEPARATOR, id.substring(2, 3));
|
||||
assertEquals(IdentifierFactory.ID_SEPARATOR, id.substring(15, 17));
|
||||
}
|
||||
|
||||
private List<String> vocs() throws IOException {
|
||||
|
|
|
|||
|
|
@ -9,6 +9,41 @@
|
|||
|
||||
<artifactId>dhp-graph-provision</artifactId>
|
||||
|
||||
<build>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>net.alchim31.maven</groupId>
|
||||
<artifactId>scala-maven-plugin</artifactId>
|
||||
<version>4.0.1</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>scala-compile-first</id>
|
||||
<phase>initialize</phase>
|
||||
<goals>
|
||||
<goal>add-source</goal>
|
||||
<goal>compile</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
<execution>
|
||||
<id>scala-test-compile</id>
|
||||
<phase>process-test-resources</phase>
|
||||
<goals>
|
||||
<goal>testCompile</goal>
|
||||
</goals>
|
||||
</execution>
|
||||
</executions>
|
||||
<configuration>
|
||||
<args>
|
||||
<arg>-Xmax-classfile-name</arg>
|
||||
<arg>200</arg>
|
||||
</args>
|
||||
<scalaVersion>${scala.version}</scalaVersion>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
|
||||
</build>
|
||||
|
||||
<dependencies>
|
||||
|
||||
<dependency>
|
||||
|
|
|
|||
|
|
@ -71,6 +71,9 @@ public class DropAndCreateESIndex {
|
|||
log.info(STATUS_CODE_TEXT, response.getStatusLine());
|
||||
}
|
||||
|
||||
log.info("Sleeping 60 seconds to avoid to lost the creation of index request");
|
||||
Thread.sleep(60000);
|
||||
|
||||
try (CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
|
||||
final String summaryConf = IOUtils
|
||||
|
|
|
|||
|
|
@ -21,6 +21,7 @@ import com.google.common.collect.Lists;
|
|||
import eu.dnetlib.dhp.oa.provision.model.JoinedEntity;
|
||||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntity;
|
||||
import eu.dnetlib.dhp.oa.provision.model.RelatedEntityWrapper;
|
||||
import eu.dnetlib.dhp.oa.provision.utils.ContextDef;
|
||||
import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
|
||||
import eu.dnetlib.dhp.oa.provision.utils.XmlRecordFactory;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ echo "Getting file from " $SCRIPT_PATH
|
|||
hdfs dfs -copyToLocal $SCRIPT_PATH
|
||||
|
||||
echo "Creating indicators"
|
||||
impala-shell -d ${TARGET} -q "invalidate metadata"
|
||||
impala-shell -q "invalidate metadata"
|
||||
impala-shell -d ${TARGET} -q "show tables" --delimited | sed "s/^\(.*\)/compute stats ${TARGET}.\1;/" | impala-shell -c -f -
|
||||
cat step16_7-createIndicatorsTables.sql | impala-shell -d $TARGET -f -
|
||||
echo "Indicators created"
|
||||
|
|
@ -57,12 +57,14 @@ UNION ALL
|
|||
SELECT * FROM ${stats_db_name}.software_sources
|
||||
UNION ALL
|
||||
SELECT * FROM ${stats_db_name}.otherresearchproduct_sources;
|
||||
--
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_sources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_sources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_sources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_sources COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
||||
|
||||
create table ${stats_db_name}.result_orcid as
|
||||
select distinct res.id, regexp_replace(res.orcid, 'http://orcid.org/' ,'') as orcid
|
||||
from (
|
||||
SELECT substr(res.id, 4) as id, auth_pid.value as orcid
|
||||
FROM ${openaire_db_name}.result res
|
||||
LATERAL VIEW explode(author) a as auth
|
||||
LATERAL VIEW explode(auth.pid) ap as auth_pid
|
||||
LATERAL VIEW explode(auth.pid.qualifier.classid) apt as author_pid_type
|
||||
WHERE res.datainfo.deletedbyinference = FALSE and res.datainfo.invisible = FALSE and author_pid_type = 'orcid') as res
|
||||
|
|
@ -34,12 +34,3 @@ union all
|
|||
select * from ${stats_db_name}.software_refereed
|
||||
union all
|
||||
select * from ${stats_db_name}.otherresearchproduct_refereed;
|
||||
--
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_refereed COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_refereed COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_refereed COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_refereed COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -40,3 +40,197 @@ join result_instance ri on ri.id = p.id
|
|||
join datasource on datasource.id = ri.hostedby
|
||||
where datasource.id like '%doajarticles%') tmp
|
||||
on p.id= tmp.id;
|
||||
|
||||
create table indi_project_pubs_count stored as parquet as
|
||||
select pr.id id, count(p.id) total_pubs from project_results pr
|
||||
join publication p on p.id=pr.result
|
||||
group by pr.id;
|
||||
|
||||
create table indi_project_datasets_count stored as parquet as
|
||||
select pr.id id, count(d.id) total_datasets from project_results pr
|
||||
join dataset d on d.id=pr.result
|
||||
group by pr.id;
|
||||
|
||||
create table indi_project_software_count stored as parquet as
|
||||
select pr.id id, count(s.id) total_software from project_results pr
|
||||
join software s on s.id=pr.result
|
||||
group by pr.id;
|
||||
|
||||
create table indi_project_otherresearch_count stored as parquet as
|
||||
select pr.id id, count(o.id) total_other from project_results pr
|
||||
join otherresearchproduct o on o.id=pr.result
|
||||
group by pr.id;
|
||||
|
||||
create table indi_pub_avg_year_country_oa stored as parquet as
|
||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||
from
|
||||
(SELECT year, country, SUM(CASE
|
||||
WHEN bestlicence='Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS OpenAccess, SUM(CASE
|
||||
WHEN bestlicence<>'Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS NonOpenAccess
|
||||
FROM publication p
|
||||
join result_organization ro on p.id=ro.id
|
||||
join organization o on o.id=ro.organization
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by year, country) tmp;
|
||||
|
||||
create table indi_dataset_avg_year_country_oa stored as parquet as
|
||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||
from
|
||||
(SELECT year, country, SUM(CASE
|
||||
WHEN bestlicence='Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS OpenAccess, SUM(CASE
|
||||
WHEN bestlicence<>'Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS NonOpenAccess
|
||||
FROM dataset d
|
||||
join result_organization ro on d.id=ro.id
|
||||
join organization o on o.id=ro.organization
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by year, country) tmp;
|
||||
|
||||
create table indi_software_avg_year_country_oa stored as parquet as
|
||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||
from
|
||||
(SELECT year, country, SUM(CASE
|
||||
WHEN bestlicence='Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS OpenAccess, SUM(CASE
|
||||
WHEN bestlicence<>'Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS NonOpenAccess
|
||||
FROM software s
|
||||
join result_organization ro on s.id=ro.id
|
||||
join organization o on o.id=ro.organization
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by year, country) tmp;
|
||||
|
||||
|
||||
create table indi_other_avg_year_country_oa stored as parquet as
|
||||
select year, country, round(OpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageOA,
|
||||
round(NonOpenAccess/(OpenAccess+NonOpenAccess)*100,3) as averageNonOA
|
||||
from
|
||||
(SELECT year, country, SUM(CASE
|
||||
WHEN bestlicence='Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS OpenAccess, SUM(CASE
|
||||
WHEN bestlicence<>'Open Access' THEN 1
|
||||
ELSE 0
|
||||
END) AS NonOpenAccess
|
||||
FROM otherresearchproduct orp
|
||||
join result_organization ro on orp.id=ro.id
|
||||
join organization o on o.id=ro.organization
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by year, country) tmp;
|
||||
|
||||
create table indi_pub_avg_year_context_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from publication_concepts pc
|
||||
join context c on pc.concept like concat('%',c.id,'%')
|
||||
join publication p on p.id=pc.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by c.name, year )
|
||||
select year, name, round(no_of_pubs/total*100,3) averageofpubs
|
||||
from total;
|
||||
|
||||
create table indi_dataset_avg_year_context_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from dataset_concepts pc
|
||||
join context c on pc.concept like concat('%',c.id,'%')
|
||||
join dataset p on p.id=pc.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by c.name, year )
|
||||
select year, name, round(no_of_pubs/total*100,3) averageofdataset
|
||||
from total;
|
||||
|
||||
create table indi_software_avg_year_context_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from software_concepts pc
|
||||
join context c on pc.concept like concat('%',c.id,'%')
|
||||
join software p on p.id=pc.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by c.name, year )
|
||||
select year, name, round(no_of_pubs/total*100,3) averageofsoftware
|
||||
from total;
|
||||
|
||||
create table indi_other_avg_year_context_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pc.id) no_of_pubs, year, c.name name, sum(count(distinct pc.id)) over(PARTITION by year) as total from otherresearchproduct_concepts pc
|
||||
join context c on pc.concept like concat('%',c.id,'%')
|
||||
join otherresearchproduct p on p.id=pc.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by c.name, year )
|
||||
select year, name, round(no_of_pubs/total*100,3) averageofother
|
||||
from total;
|
||||
|
||||
create table indi_other_avg_year_content_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||
from otherresearchproduct_datasources pd
|
||||
join datasource d on datasource=d.id
|
||||
join otherresearchproduct p on p.id=pd.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by d.type, year)
|
||||
select year, type, round(no_of_pubs/total*100,3) averageOfOtherresearchproduct
|
||||
from total;
|
||||
|
||||
create table indi_software_avg_year_content_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||
from software_datasources pd
|
||||
join datasource d on datasource=d.id
|
||||
join software p on p.id=pd.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by d.type, year)
|
||||
select year, type, round(no_of_pubs/total*100,3) averageOfSoftware
|
||||
from total;
|
||||
|
||||
create table indi_dataset_avg_year_content_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||
from dataset_datasources pd
|
||||
join datasource d on datasource=d.id
|
||||
join dataset p on p.id=pd.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by d.type, year)
|
||||
select year, type, round(no_of_pubs/total*100,3) averageOfDatasets
|
||||
from total;
|
||||
|
||||
create table indi_pub_avg_year_content_oa stored as parquet as
|
||||
with total as
|
||||
(select count(distinct pd.id) no_of_pubs, year, d.type type, sum(count(distinct pd.id)) over(PARTITION by year) as total
|
||||
from publication_datasources pd
|
||||
join datasource d on datasource=d.id
|
||||
join publication p on p.id=pd.id
|
||||
where cast(year as int)>=2003 and cast(year as int)<=2021
|
||||
group by d.type, year)
|
||||
select year, type, round(no_of_pubs/total*100,3) averageOfPubs
|
||||
from total;
|
||||
|
||||
create table indi_pub_has_cc_licence stored as parquet as
|
||||
select distinct p.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license
|
||||
from publication p
|
||||
left outer join (select p.id, license.type as lic from publication p
|
||||
join publication_licenses as license on license.id = p.id
|
||||
where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp
|
||||
on p.id= tmp.id;
|
||||
|
||||
create table indi_pub_has_cc_licence_url stored as parquet as
|
||||
select distinct p.id, (case when lic_host='' or lic_host is null then 0 else 1 end) as has_cc_license_url
|
||||
from publication p
|
||||
left outer join (select p.id, lower(parse_url(license.type, "HOST")) as lic_host
|
||||
from publication p
|
||||
join publication_licenses as license on license.id = p.id
|
||||
WHERE lower(parse_url(license.type, 'HOST')) = 'creativecommons.org') tmp
|
||||
on p.id= tmp.id;
|
||||
|
||||
create table indi_pub_has_abstract stored as parquet as
|
||||
select distinct publication.id, coalesce(abstract, 1) has_abstract
|
||||
from publication;
|
||||
|
|
@ -90,27 +90,8 @@ FROM ${openaire_db_name}.publication p
|
|||
where p.datainfo.deletedbyinference = false;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.publication_citations AS
|
||||
SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result
|
||||
SELECT substr(p.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
|
||||
FROM ${openaire_db_name}.publication p
|
||||
lateral view explode(p.extrainfo) citations AS citation
|
||||
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
|
||||
and p.datainfo.deletedbyinference = false;
|
||||
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_tmp COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_classifications COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_concepts COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_datasources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_languages COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_oids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_pids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_topics COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.publication_citations COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -116,6 +116,13 @@ compute stats TARGET.indi_pub_doi_from_crossref;
|
|||
create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id);
|
||||
compute stats TARGET.indi_pub_gold_oa;
|
||||
|
||||
create view TARGET.indi_dataset_avg_year_country_oa as select * from SOURCE.indi_dataset_avg_year_country_oa orig;
|
||||
create view TARGET.indi_project_datasets_count as select * from SOURCE.indi_project_datasets_count orig;
|
||||
create view TARGET.indi_project_otherresearch_count as select * from SOURCE.indi_project_otherresearch_count orig;
|
||||
create view TARGET.indi_project_pubs_count as select * from SOURCE.indi_project_pubs_count orig;
|
||||
create view TARGET.indi_project_software_count as select * from SOURCE.indi_project_software_count orig;
|
||||
create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig;
|
||||
|
||||
--denorm
|
||||
alter table TARGET.result rename to TARGET.res_tmp;
|
||||
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ FROM ${openaire_db_name}.dataset d
|
|||
WHERE d.datainfo.deletedbyinference = FALSE;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.dataset_citations AS
|
||||
SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS result
|
||||
SELECT substr(d.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
|
||||
FROM ${openaire_db_name}.dataset d
|
||||
LATERAL VIEW explode(d.extrainfo) citations AS citation
|
||||
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
|
||||
|
|
@ -96,20 +96,3 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj
|
|||
FROM ${openaire_db_name}.dataset p
|
||||
LATERAL VIEW explode(p.subject) subjects AS subject
|
||||
where p.datainfo.deletedbyinference = false;
|
||||
--
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_tmp COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_classifications COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_concepts COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_datasources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_languages COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_oids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_pids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.dataset_topics COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -41,7 +41,7 @@ from ${openaire_db_name}.software s
|
|||
where s.datainfo.deletedbyinference = false;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.software_citations AS
|
||||
SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT
|
||||
SELECT substr(s.id, 4) as id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
|
||||
FROM ${openaire_db_name}.software s
|
||||
LATERAL VIEW explode(s.extrainfo) citations as citation
|
||||
where xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
|
||||
|
|
@ -96,20 +96,3 @@ SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subj
|
|||
FROM ${openaire_db_name}.software p
|
||||
LATERAL VIEW explode(p.subject) subjects AS subject
|
||||
where p.datainfo.deletedbyinference = false;
|
||||
--
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_tmp COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_classifications COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_concepts COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_datasources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_languages COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_oids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_pids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.software_topics COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -41,7 +41,7 @@ WHERE o.datainfo.deletedbyinference = FALSE;
|
|||
|
||||
-- Otherresearchproduct_citations
|
||||
CREATE TABLE ${stats_db_name}.otherresearchproduct_citations AS
|
||||
SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS RESULT
|
||||
SELECT substr(o.id, 4) AS id, xpath_string(citation.value, "//citation/id[@type='openaire']/@value") AS cites
|
||||
FROM ${openaire_db_name}.otherresearchproduct o LATERAL VIEW explode(o.extrainfo) citations AS citation
|
||||
WHERE xpath_string(citation.value, "//citation/id[@type='openaire']/@value") != ""
|
||||
and o.datainfo.deletedbyinference = false;
|
||||
|
|
@ -87,20 +87,3 @@ CREATE TABLE ${stats_db_name}.otherresearchproduct_topics AS
|
|||
SELECT substr(p.id, 4) AS id, subjects.subject.qualifier.classname AS type, subjects.subject.value AS topic
|
||||
FROM ${openaire_db_name}.otherresearchproduct p LATERAL VIEW explode(p.subject) subjects AS subject
|
||||
where p.datainfo.deletedbyinference = false;
|
||||
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_tmp COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_classifications COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_concepts COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_datasources COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_languages COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_oids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_pids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.otherresearchproduct_topics COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -13,11 +13,17 @@ WHERE r.reltype = 'projectOrganization'
|
|||
and r.datainfo.deletedbyinference = false;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.project_results AS
|
||||
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result
|
||||
SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS result, r.datainfo.provenanceaction.classname as provenance
|
||||
FROM ${openaire_db_name}.relation r
|
||||
WHERE r.reltype = 'resultProject'
|
||||
and r.datainfo.deletedbyinference = false;
|
||||
|
||||
create table ${stats_db_name}.project_classification as
|
||||
select substr(p.id, 4) as id, class.h2020programme.code, class.level1, class.level2, class.level3
|
||||
from ${openaire_db_name}.project p
|
||||
lateral view explode(p.h2020classification) classifs as class
|
||||
where p.datainfo.deletedbyinference=false and class.h2020programme is not null;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.project_tmp
|
||||
(
|
||||
id STRING,
|
||||
|
|
|
|||
|
|
@ -130,12 +130,7 @@ WHERE r.reltype = 'resultOrganization'
|
|||
and r.datainfo.deletedbyinference = false;
|
||||
|
||||
CREATE TABLE ${stats_db_name}.result_projects AS
|
||||
select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend
|
||||
select pr.result AS id, pr.id AS project, datediff(p.enddate, p.startdate) AS daysfromend, pr.provenance as provenance
|
||||
FROM ${stats_db_name}.result r
|
||||
JOIN ${stats_db_name}.project_results pr ON r.id = pr.result
|
||||
JOIN ${stats_db_name}.project_tmp p ON p.id = pr.id;
|
||||
|
||||
-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.result_organization COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.result_projects COMPUTE STATISTICS FOR COLUMNS;
|
||||
|
|
@ -17,7 +17,9 @@ CREATE TABLE ${stats_db_name}.datasource_tmp
|
|||
`latitude` STRING,
|
||||
`longitude` STRING,
|
||||
`websiteurl` STRING,
|
||||
`compatibility` STRING
|
||||
`compatibility` STRING,
|
||||
issn_printed STRING,
|
||||
issn_online STRING
|
||||
) CLUSTERED BY (id) INTO 100 buckets stored AS orc tblproperties ('transactional' = 'true');
|
||||
|
||||
-- Insert statement that takes into account the piwik_id of the openAIRE graph
|
||||
|
|
@ -32,7 +34,9 @@ SELECT substr(d1.id, 4) AS id,
|
|||
d1.latitude.value AS latitude,
|
||||
d1.longitude.value AS longitude,
|
||||
d1.websiteurl.value AS websiteurl,
|
||||
d1.openairecompatibility.classid AS compatibility
|
||||
d1.openairecompatibility.classid AS compatibility,
|
||||
d1.journal.issnprinted AS issn_printed,
|
||||
d1.journal.issnonline AS issn_online
|
||||
FROM ${openaire_db_name}.datasource d1
|
||||
LEFT OUTER JOIN
|
||||
(SELECT id, split(originalidd, '\\:')[1] as piwik_id
|
||||
|
|
@ -51,7 +55,7 @@ CREATE TABLE ${stats_db_name}.dual
|
|||
INSERT INTO ${stats_db_name}.dual
|
||||
VALUES ('X');
|
||||
INSERT INTO ${stats_db_name}.datasource_tmp (`id`, `name`, `type`, `dateofvalidation`, `yearofvalidation`, `harvested`,
|
||||
`piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`)
|
||||
`piwik_id`, `latitude`, `longitude`, `websiteurl`, `compatibility`, `issn_printed`, `issn_online`)
|
||||
SELECT 'other',
|
||||
'Other',
|
||||
'Repository',
|
||||
|
|
@ -62,7 +66,9 @@ SELECT 'other',
|
|||
NULL,
|
||||
NULL,
|
||||
NULL,
|
||||
'unknown'
|
||||
'unknown',
|
||||
null,
|
||||
null
|
||||
FROM ${stats_db_name}.dual
|
||||
WHERE 'other' not in (SELECT id FROM ${stats_db_name}.datasource_tmp WHERE name = 'Unknown Repository');
|
||||
DROP TABLE ${stats_db_name}.dual;
|
||||
|
|
@ -98,12 +104,3 @@ where d.datainfo.deletedbyinference = false;
|
|||
CREATE OR REPLACE VIEW ${stats_db_name}.datasource_results AS
|
||||
SELECT datasource AS id, id AS result
|
||||
FROM ${stats_db_name}.result_datasources;
|
||||
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_tmp COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_languages COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_oids COMPUTE STATISTICS FOR COLUMNS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS;
|
||||
-- ANALYZE TABLE ${stats_db_name}.datasource_organizations COMPUTE STATISTICS FOR COLUMNS;
|
||||
2
pom.xml
2
pom.xml
|
|
@ -741,7 +741,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[2.6.14]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[2.7.15]</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue