forked from D-Net/dnet-hadoop
Merge branch 'beta' into beta_solr_config
This commit is contained in:
commit
14fbf92ad6
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@ -60,14 +60,10 @@ object SparkCreateActionset {
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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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|
|
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@ -1,14 +1,12 @@
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package eu.dnetlib.dhp.sx.graph.bio
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package eu.dnetllib.dhp.sx.bio
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import eu.dnetlib.dhp.schema.common.ModelConstants
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import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils}
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import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty}
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import eu.dnetlib.dhp.schema.oaf._
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import org.json4s.DefaultFormats
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import org.json4s.JsonAST.{JField, JObject, JString}
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import org.json4s.jackson.JsonMethods.{compact, parse, render}
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import scala.collection.JavaConverters._
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import collection.JavaConverters._
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object BioDBToOAF {
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case class EBILinkItem(id: Long, links: String) {}
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@ -231,7 +229,6 @@ object BioDBToOAF {
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}
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def generate_unresolved_id(pid: String, pidType: String): String = {
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s"unresolved::$pid::$pidType"
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}
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@ -1,8 +1,8 @@
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package eu.dnetlib.dhp.sx.graph.bio
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package eu.dnetllib.dhp.sx.bio
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
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import BioDBToOAF.ScholixResolved
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import eu.dnetlib.dhp.schema.oaf.Oaf
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import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
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import org.apache.commons.io.IOUtils
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import org.apache.spark.SparkConf
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import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
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@ -33,7 +33,6 @@ object SparkTransformBioDatabaseToOAF {
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implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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import spark.implicits._
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database.toUpperCase() match {
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case "UNIPROT" =>
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spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath)
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@ -0,0 +1,200 @@
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package eu.dnetllib.dhp.sx.bio.ebi
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
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import eu.dnetlib.dhp.schema.oaf.Result
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
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import org.apache.commons.io.IOUtils
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import org.apache.hadoop.conf.Configuration
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import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.HttpGet
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import org.apache.http.impl.client.HttpClientBuilder
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import org.apache.spark.SparkConf
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import org.apache.spark.rdd.RDD
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import org.apache.spark.sql.expressions.Aggregator
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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import java.io.InputStream
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import scala.io.Source
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import scala.xml.pull.XMLEventReader
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object SparkCreateBaselineDataFrame {
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def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = {
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val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
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|
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val result = data.lines.filter(l => l.startsWith("<a href=")).map { l =>
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val end = l.lastIndexOf("\">")
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val start = l.indexOf("<a href=\"")
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|
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if (start >= 0 && end > start)
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l.substring(start + 9, end - start)
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else
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""
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}.filter(s => s.endsWith(".gz")).filter(s => s > maxFile).map(s => (s, s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList
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result
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}
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def downloadBaselinePart(url: String): InputStream = {
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val r = new HttpGet(url)
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val timeout = 60; // seconds
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val config = RequestConfig.custom()
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.setConnectTimeout(timeout * 1000)
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.setConnectionRequestTimeout(timeout * 1000)
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.setSocketTimeout(timeout * 1000).build()
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val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
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val response = client.execute(r)
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println(s"get response with status${response.getStatusLine.getStatusCode}")
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response.getEntity.getContent
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}
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def requestPage(url: String): String = {
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val r = new HttpGet(url)
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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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try {
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var tries = 4
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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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tries -= 1
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}
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else
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return IOUtils.toString(response.getEntity.getContent)
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} catch {
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case e: Throwable =>
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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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} finally {
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if (client != null)
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client.close()
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||||
}
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||||
}
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def downloadBaseLineUpdate(baselinePath: String, hdfsServerUri: String): Unit = {
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val conf = new Configuration
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conf.set("fs.defaultFS", hdfsServerUri)
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val fs = FileSystem.get(conf)
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val p = new Path(baselinePath)
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val files = fs.listFiles(p, false)
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var max_file = ""
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while (files.hasNext) {
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val c = files.next()
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val data = c.getPath.toString
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val fileName = data.substring(data.lastIndexOf("/") + 1)
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||||
|
||||
if (fileName > max_file)
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max_file = fileName
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}
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val files_to_download = requestBaseLineUpdatePage(max_file)
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||||
|
||||
files_to_download.foreach { u =>
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val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}")
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val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true)
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val i = downloadBaselinePart(u._2)
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IOUtils.copy(i, fsDataOutputStream)
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println(s"Downloaded ${u._2} into $baselinePath/${u._1}")
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fsDataOutputStream.close()
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}
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||||
|
||||
}
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||||
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val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
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override def zero: PMArticle = new PMArticle
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override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
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if (b != null && b.getPmid != null) b else a._2
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}
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override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
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if (b1 != null && b1.getPmid != null) b1 else b2
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}
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override def finish(reduction: PMArticle): PMArticle = reduction
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override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
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override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
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}
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def main(args: Array[String]): Unit = {
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val conf: SparkConf = new SparkConf()
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val log: Logger = LoggerFactory.getLogger(getClass)
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val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json")))
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parser.parseArgument(args)
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val isLookupUrl: String = parser.get("isLookupUrl")
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log.info("isLookupUrl: {}", isLookupUrl)
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val workingPath = parser.get("workingPath")
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log.info("workingPath: {}", workingPath)
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val targetPath = parser.get("targetPath")
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log.info("targetPath: {}", targetPath)
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val hdfsServerUri = parser.get("hdfsServerUri")
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log.info("hdfsServerUri: {}", targetPath)
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|
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val skipUpdate = parser.get("skipUpdate")
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log.info("skipUpdate: {}", skipUpdate)
|
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|
||||
|
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val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
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val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
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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(SparkEBILinksToOaf.getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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|
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val sc = spark.sparkContext
|
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import spark.implicits._
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|
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implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
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implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
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implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
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implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
|
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if (!"true".equalsIgnoreCase(skipUpdate)) {
|
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downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
|
||||
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
|
||||
val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => {
|
||||
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
|
||||
new PMParser(xml)
|
||||
}))
|
||||
ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
|
||||
.agg(pmArticleAggregator.toColumn)
|
||||
.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
|
||||
}
|
||||
|
||||
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
|
||||
exported_dataset
|
||||
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
|
||||
.filter(p => p != null)
|
||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
}
|
||||
}
|
||||
|
|
@ -1,23 +1,19 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
package eu.dnetllib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.hadoop.conf.Configuration
|
||||
import org.apache.hadoop.fs.{FileSystem, Path}
|
||||
import org.apache.http.client.config.RequestConfig
|
||||
import org.apache.http.client.methods.{HttpGet, HttpUriRequest}
|
||||
import org.apache.http.client.methods.HttpGet
|
||||
import org.apache.http.impl.client.HttpClientBuilder
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql.functions.max
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkDownloadEBILinks {
|
||||
|
||||
|
||||
def createEBILinks(pmid: Long): EBILinkItem = {
|
||||
|
||||
val res = requestLinks(pmid)
|
||||
|
|
@ -26,7 +22,6 @@ object SparkDownloadEBILinks {
|
|||
null
|
||||
}
|
||||
|
||||
|
||||
def requestPage(url: String): String = {
|
||||
val r = new HttpGet(url)
|
||||
val timeout = 60; // seconds
|
||||
|
|
@ -61,46 +56,11 @@ object SparkDownloadEBILinks {
|
|||
}
|
||||
}
|
||||
|
||||
|
||||
def requestBaseLineUpdatePage():List[String] = {
|
||||
val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
|
||||
|
||||
val result =data.lines.filter(l => l.startsWith("<a href=")).map{l =>
|
||||
val end = l.lastIndexOf("\">")
|
||||
val start = l.indexOf("<a href=\"")
|
||||
|
||||
if (start>= 0 && end >start)
|
||||
l.substring(start+9, (end-start))
|
||||
else
|
||||
""
|
||||
}.filter(s =>s.endsWith(".gz") ).map(s => s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s").toList
|
||||
|
||||
result
|
||||
}
|
||||
|
||||
def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = {
|
||||
|
||||
|
||||
val conf = new Configuration
|
||||
conf.set("fs.defaultFS", hdfsServerUri)
|
||||
val fs = FileSystem.get(conf)
|
||||
val p = new Path((baselinePath))
|
||||
val files = fs.listFiles(p,false)
|
||||
|
||||
while (files.hasNext) {
|
||||
val c = files.next()
|
||||
c.getPath
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
def requestLinks(PMID: Long): String = {
|
||||
requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
|
||||
|
||||
}
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
|
|
@ -1,15 +1,14 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
package eu.dnetllib.dhp.sx.bio.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.schema.oaf.Oaf
|
||||
import eu.dnetlib.dhp.sx.graph.bio
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.EBILinkItem
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
object SparkEBILinksToOaf {
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
|
|
@ -24,12 +23,12 @@ object SparkEBILinksToOaf {
|
|||
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
|
||||
|
||||
import spark.implicits._
|
||||
val sourcePath = parser.get("sourcePath")
|
||||
log.info(s"sourcePath -> $sourcePath")
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info(s"targetPath -> $targetPath")
|
||||
|
||||
import spark.implicits._
|
||||
implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
|
||||
|
||||
val ebLinks: Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links != null)
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
import java.util.ArrayList;
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
public class PMGrant {
|
||||
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
import java.io.Serializable;
|
||||
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed
|
||||
|
||||
import scala.xml.MetaData
|
||||
import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
|
||||
|
|
@ -1,5 +1,5 @@
|
|||
|
||||
package eu.dnetlib.dhp.sx.graph.bio.pubmed;
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed;
|
||||
|
||||
public class PMSubject {
|
||||
private String value;
|
||||
|
|
@ -1,11 +1,12 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio.pubmed
|
||||
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
import java.util.regex.Pattern
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
object PubMedToOaf {
|
||||
|
||||
|
|
@ -71,7 +72,7 @@ object PubMedToOaf {
|
|||
if (article.getPublicationTypes == null)
|
||||
return null
|
||||
val i = new Instance
|
||||
var pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
|
||||
val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo))
|
||||
if (pidList == null)
|
||||
return null
|
||||
|
||||
|
|
@ -105,7 +106,7 @@ object PubMedToOaf {
|
|||
if (alternateIdentifier != null)
|
||||
i.setAlternateIdentifier(List(alternateIdentifier).asJava)
|
||||
result.setInstance(List(i).asJava)
|
||||
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection breakOut)
|
||||
i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut)
|
||||
val urlLists: List[String] = pidList
|
||||
.map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue))
|
||||
.filter(t => t._1.nonEmpty)
|
||||
|
|
@ -136,7 +137,7 @@ object PubMedToOaf {
|
|||
}
|
||||
|
||||
|
||||
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection breakOut)
|
||||
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection.breakOut)
|
||||
if (subjects != null)
|
||||
result.setSubject(subjects.asJava)
|
||||
|
||||
|
|
@ -148,7 +149,7 @@ object PubMedToOaf {
|
|||
author.setFullname(a.getFullName)
|
||||
author.setRank(index + 1)
|
||||
author
|
||||
}(collection breakOut)
|
||||
}(collection.breakOut)
|
||||
|
||||
|
||||
if (authors != null && authors.nonEmpty)
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false},
|
||||
{"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -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":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,17 +1,22 @@
|
|||
<workflow-app name="Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<workflow-app name="Download_Transform_Pubmed_Workflow" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>baselineWorkingPath</name>
|
||||
<description>the Baseline Working Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>the Target Path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>isLookupUrl</name>
|
||||
<description>The IS lookUp service endopoint</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>targetPath</name>
|
||||
<description>The target path</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>skipUpdate</name>
|
||||
<value>false</value>
|
||||
<description>The request block size</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="ConvertDataset"/>
|
||||
|
|
@ -24,9 +29,9 @@
|
|||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Convert Baseline to Dataset</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkCreateBaselineDataFrame</class>
|
||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||
<name>Convert Baseline to OAF Dataset</name>
|
||||
<class>eu.dnetllib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -41,6 +46,8 @@
|
|||
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
<arg>--skipUpdate</arg><arg>${skipUpdate}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -1,13 +1,10 @@
|
|||
package eu.dnetlib.dhp.sx.graph.bio.pubmed
|
||||
package eu.dnetllib.dhp.sx.bio
|
||||
|
||||
import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature}
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{CleaningFunctions, OafMapperUtils, PidType}
|
||||
import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest
|
||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
|
||||
import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo
|
||||
import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks
|
||||
import eu.dnetllib.dhp.sx.bio.BioDBToOAF.ScholixResolved
|
||||
import eu.dnetllib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf}
|
||||
import org.json4s.DefaultFormats
|
||||
import org.json4s.JsonAST.{JField, JObject, JString}
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
|
|
@ -51,16 +48,11 @@ class BioScholixTest extends AbstractVocabularyTest{
|
|||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testDownloadEBIUpdate() = {
|
||||
val data = SparkDownloadEBILinks.requestBaseLineUpdatePage()
|
||||
println(data)
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
def testEBIData() = {
|
||||
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString
|
||||
val inputXML = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")).mkString
|
||||
val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
|
||||
new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s)))
|
||||
}
|
||||
|
|
@ -70,7 +62,7 @@ class BioScholixTest extends AbstractVocabularyTest{
|
|||
def testPubmedToOaf(): Unit = {
|
||||
assertNotNull(vocabularies)
|
||||
assertTrue(vocabularies.vocabularyExists("dnet:publication_resource"))
|
||||
val records:String =Source.fromInputStream(getClass.getResourceAsStream("pubmed_dump")).mkString
|
||||
val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")).mkString
|
||||
val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies))
|
||||
assertEquals(10, r.size)
|
||||
assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p)))
|
||||
File diff suppressed because it is too large
Load Diff
|
|
@ -1,3 +1,4 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.io.IOException;
|
||||
|
|
@ -5,10 +6,7 @@ import java.util.Optional;
|
|||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaPairRDD;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.api.java.function.FilterFunction;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
import org.apache.spark.api.java.function.PairFunction;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
|
|
@ -21,7 +19,6 @@ import org.slf4j.LoggerFactory;
|
|||
import org.xml.sax.SAXException;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.oa.dedup.model.Block;
|
||||
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
||||
|
|
@ -31,7 +28,6 @@ import eu.dnetlib.pace.config.DedupConfig;
|
|||
import eu.dnetlib.pace.model.MapDocument;
|
||||
import eu.dnetlib.pace.util.MapDocumentUtil;
|
||||
import scala.Tuple2;
|
||||
import scala.Tuple3;
|
||||
|
||||
public class SparkWhitelistSimRels extends AbstractSparkAction {
|
||||
|
||||
|
|
@ -82,7 +78,9 @@ public class SparkWhitelistSimRels extends AbstractSparkAction {
|
|||
JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
// file format: source####target
|
||||
Dataset<Tuple2<String, String>> whiteListRels = spark.createDataset(sc
|
||||
Dataset<Tuple2<String, String>> whiteListRels = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(whiteListPath)
|
||||
// check if the line is in the correct format: id1####id2
|
||||
.filter(s -> s.contains(WHITELIST_SEPARATOR) && s.split(WHITELIST_SEPARATOR).length == 2)
|
||||
|
|
@ -99,7 +97,9 @@ public class SparkWhitelistSimRels extends AbstractSparkAction {
|
|||
|
||||
final String outputPath = DedupUtility.createSimRelPath(workingPath, actionSetId, subEntity);
|
||||
|
||||
Dataset<Tuple2<String, String>> entities = spark.createDataset(sc
|
||||
Dataset<Tuple2<String, String>> entities = spark
|
||||
.createDataset(
|
||||
sc
|
||||
.textFile(DedupUtility.createEntityPath(graphBasePath, subEntity))
|
||||
.repartition(numPartitions)
|
||||
.mapToPair(
|
||||
|
|
@ -112,17 +112,20 @@ public class SparkWhitelistSimRels extends AbstractSparkAction {
|
|||
|
||||
Dataset<Tuple2<String, String>> whiteListRels1 = whiteListRels
|
||||
.joinWith(entities, whiteListRels.col("_1").equalTo(entities.col("_1")), "inner")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Tuple2<String, String>> whiteListRels2 = whiteListRels1
|
||||
.joinWith(entities, whiteListRels1.col("_2").equalTo(entities.col("_1")), "inner")
|
||||
.map((MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1, Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
.map(
|
||||
(MapFunction<Tuple2<Tuple2<String, String>, Tuple2<String, String>>, Tuple2<String, String>>) Tuple2::_1,
|
||||
Encoders.tuple(Encoders.STRING(), Encoders.STRING()));
|
||||
|
||||
Dataset<Relation> whiteListSimRels = whiteListRels2
|
||||
.map((MapFunction<Tuple2<String, String>, Relation>)
|
||||
r -> createSimRel(r._1(), r._2(), entity),
|
||||
Encoders.bean(Relation.class)
|
||||
);
|
||||
.map(
|
||||
(MapFunction<Tuple2<String, String>, Relation>) r -> createSimRel(r._1(), r._2(), entity),
|
||||
Encoders.bean(Relation.class));
|
||||
|
||||
saveParquet(whiteListSimRels, outputPath, SaveMode.Append);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,117 @@
|
|||
|
||||
package eu.dnetlib.dhp.oa.dedup;
|
||||
|
||||
import java.util.concurrent.TimeUnit;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.http.client.methods.CloseableHttpResponse;
|
||||
import org.apache.http.client.methods.HttpGet;
|
||||
import org.apache.http.impl.client.CloseableHttpClient;
|
||||
import org.apache.http.impl.client.HttpClients;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
|
||||
public class UpdateOpenorgsJob {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(UpdateOpenorgsJob.class);
|
||||
|
||||
public static void main(String[] args) throws Exception {
|
||||
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
||||
IOUtils
|
||||
.toString(
|
||||
SparkCreateSimRels.class
|
||||
.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateOpenorgsJob_parameters.json")));
|
||||
parser.parseArgument(args);
|
||||
|
||||
final String apiUrl = parser.get("apiUrl");
|
||||
final int delay = Integer.parseInt(parser.get("delay"));
|
||||
|
||||
log.info("apiUrl: '{}'", apiUrl);
|
||||
log.info("delay: '{}'", delay);
|
||||
|
||||
APIResponse res = httpCall(apiUrl);
|
||||
while (res != null && res.getStatus().equals(ImportStatus.RUNNING)) {
|
||||
TimeUnit.MINUTES.sleep(delay);
|
||||
res = httpCall(apiUrl + "/status");
|
||||
}
|
||||
|
||||
if (res == null) {
|
||||
log.error("Openorgs Update FAILED: No response");
|
||||
throw new RuntimeException("Openorgs Update FAILED: No response");
|
||||
}
|
||||
|
||||
if (res.getStatus() == null || !res.getStatus().equals(ImportStatus.SUCCESS)) {
|
||||
log.error("Openorgs Update FAILED: '{}' - '{}'", res.getStatus(), res.getMessage());
|
||||
throw new RuntimeException(res.getMessage());
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
private static APIResponse httpCall(final String url) throws Exception {
|
||||
final HttpGet req = new HttpGet(url);
|
||||
|
||||
try (final CloseableHttpClient client = HttpClients.createDefault()) {
|
||||
try (final CloseableHttpResponse response = client.execute(req)) {
|
||||
final String s = IOUtils.toString(response.getEntity().getContent());
|
||||
return (new ObjectMapper()).readValue(s, APIResponse.class);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
class APIResponse {
|
||||
private String id;
|
||||
private Long dateStart;
|
||||
private Long dateEnd;
|
||||
private ImportStatus status;
|
||||
private String message;
|
||||
|
||||
public String getId() {
|
||||
return id;
|
||||
}
|
||||
|
||||
public void setId(String id) {
|
||||
this.id = id;
|
||||
}
|
||||
|
||||
public Long getDateStart() {
|
||||
return dateStart;
|
||||
}
|
||||
|
||||
public void setDateStart(Long dateStart) {
|
||||
this.dateStart = dateStart;
|
||||
}
|
||||
|
||||
public Long getDateEnd() {
|
||||
return dateEnd;
|
||||
}
|
||||
|
||||
public void setDateEnd(Long dateEnd) {
|
||||
this.dateEnd = dateEnd;
|
||||
}
|
||||
|
||||
public ImportStatus getStatus() {
|
||||
return status;
|
||||
}
|
||||
|
||||
public void setStatus(ImportStatus status) {
|
||||
this.status = status;
|
||||
}
|
||||
|
||||
public String getMessage() {
|
||||
return message;
|
||||
}
|
||||
|
||||
public void setMessage(String message) {
|
||||
this.message = message;
|
||||
}
|
||||
}
|
||||
|
||||
enum ImportStatus {
|
||||
SUCCESS, FAILED, RUNNING, NOT_LAUNCHED, NOT_YET_STARTED
|
||||
}
|
||||
|
|
@ -28,6 +28,11 @@
|
|||
<name>dbPwd</name>
|
||||
<description>password to access the OpenOrgs database</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>dbConnections</name>
|
||||
<value>10</value>
|
||||
<description>number of connections to the postgres db</description>
|
||||
</property>
|
||||
<property>
|
||||
<name>workingPath</name>
|
||||
<description>path for the working directory</description>
|
||||
|
|
@ -223,7 +228,7 @@
|
|||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
<arg>--numConnections</arg><arg>${dbConnections}</arg>
|
||||
</spark>
|
||||
<ok to="PrepareNewOrgs"/>
|
||||
<error to="Kill"/>
|
||||
|
|
@ -254,19 +259,24 @@
|
|||
<arg>--dbTable</arg><arg>${dbTable}</arg>
|
||||
<arg>--dbUser</arg><arg>${dbUser}</arg>
|
||||
<arg>--dbPwd</arg><arg>${dbPwd}</arg>
|
||||
<arg>--numConnections</arg><arg>20</arg>
|
||||
<arg>--numConnections</arg><arg>${dbConnections}</arg>
|
||||
</spark>
|
||||
<ok to="update_openorgs"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<action name="update_openorgs">
|
||||
<shell xmlns="uri:oozie:shell-action:0.1">
|
||||
<job-tracker>${jobTracker}</job-tracker>
|
||||
<name-node>${nameNode}</name-node>
|
||||
<exec>/usr/bin/curl</exec>
|
||||
<argument>${apiUrl}</argument>
|
||||
</shell>
|
||||
<java>
|
||||
<configuration>
|
||||
<property>
|
||||
<name>oozie.launcher.mapreduce.user.classpath.first</name>
|
||||
<value>true</value>
|
||||
</property>
|
||||
</configuration>
|
||||
<main-class>eu.dnetlib.dhp.oa.dedup.UpdateOpenorgsJob</main-class>
|
||||
<arg>--apiUrl</arg><arg>${apiUrl}</arg>
|
||||
<arg>--delay</arg><arg>5</arg>
|
||||
</java>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,14 @@
|
|||
[
|
||||
{
|
||||
"paramName": "api",
|
||||
"paramLongName": "apiUrl",
|
||||
"paramDescription": "the url of the API",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "d",
|
||||
"paramLongName": "delay",
|
||||
"paramDescription": "delay for the HTTP call in minutes",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
|
|
@ -269,17 +269,23 @@ public class SparkDedupTest implements Serializable {
|
|||
.load(DedupUtility.createSimRelPath(testOutputBasePath, testActionSetId, "software"));
|
||||
|
||||
// check if the first relation in the whitelist exists
|
||||
assertTrue(sw_simrel
|
||||
assertTrue(
|
||||
sw_simrel
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(rel ->
|
||||
rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1])).count() > 0);
|
||||
.filter(
|
||||
rel -> rel.getSource().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[0])
|
||||
&& rel.getTarget().equalsIgnoreCase(whiteList.get(0).split(WHITELIST_SEPARATOR)[1]))
|
||||
.count() > 0);
|
||||
// check if the second relation in the whitelist exists
|
||||
assertTrue(sw_simrel
|
||||
assertTrue(
|
||||
sw_simrel
|
||||
.as(Encoders.bean(Relation.class))
|
||||
.toJavaRDD()
|
||||
.filter(rel ->
|
||||
rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0]) && rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1])).count() > 0);
|
||||
.filter(
|
||||
rel -> rel.getSource().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[0])
|
||||
&& rel.getTarget().equalsIgnoreCase(whiteList.get(1).split(WHITELIST_SEPARATOR)[1]))
|
||||
.count() > 0);
|
||||
|
||||
assertEquals(338, sw_simrel.count());
|
||||
|
||||
|
|
|
|||
|
|
@ -208,7 +208,7 @@ object SparkGenerateDoiBoost {
|
|||
(r.getTarget,r)
|
||||
else
|
||||
("resolved", r)
|
||||
})
|
||||
})(Encoders.tuple(Encoders.STRING, mapEncoderRel))
|
||||
|
||||
val openaireOrganization:Dataset[(String,String)] = spark.read.text(openaireOrganizationPath).as[String].flatMap(s => extractIdGRID(s)).groupByKey(_._2).reduceGroups((x,y) => if (x != null) x else y ).map(_._2)
|
||||
|
||||
|
|
@ -222,7 +222,7 @@ object SparkGenerateDoiBoost {
|
|||
else
|
||||
currentRels.setTarget(currentOrgs._1)
|
||||
currentRels
|
||||
}.write.save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
||||
}.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation")
|
||||
|
||||
magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => {
|
||||
val affiliation = item._2
|
||||
|
|
|
|||
|
|
@ -48,7 +48,7 @@
|
|||
<!-- MAG Parameters -->
|
||||
<property>
|
||||
<name>inputPathMAG</name>
|
||||
<description>the MAG working path</description>
|
||||
<description>the MAG input path</description>
|
||||
</property>
|
||||
|
||||
|
||||
|
|
@ -138,7 +138,7 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${inputPathMAG}/dataset</arg>
|
||||
<arg>--workingPath</arg><arg>${inputPathMAG}/process_p</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}/MAG</arg>
|
||||
<arg>--targetPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn-cluster</arg>
|
||||
</spark>
|
||||
|
|
|
|||
|
|
@ -84,7 +84,8 @@ public class PropagationConstant {
|
|||
return di;
|
||||
}
|
||||
|
||||
public static Qualifier getQualifier(String inference_class_id, String inference_class_name, String qualifierSchema) {
|
||||
public static Qualifier getQualifier(String inference_class_id, String inference_class_name,
|
||||
String qualifierSchema) {
|
||||
Qualifier pa = new Qualifier();
|
||||
pa.setClassid(inference_class_id);
|
||||
pa.setClassname(inference_class_name);
|
||||
|
|
@ -108,7 +109,11 @@ public class PropagationConstant {
|
|||
r.setRelClass(rel_class);
|
||||
r.setRelType(rel_type);
|
||||
r.setSubRelType(subrel_type);
|
||||
r.setDataInfo(getDataInfo(inference_provenance, inference_class_id, inference_class_name, ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
r
|
||||
.setDataInfo(
|
||||
getDataInfo(
|
||||
inference_provenance, inference_class_id, inference_class_name,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS));
|
||||
return r;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -173,7 +173,10 @@ public class SparkOrcidToResultFromSemRelJob {
|
|||
if (toaddpid) {
|
||||
StructuredProperty p = new StructuredProperty();
|
||||
p.setValue(autoritative_author.getOrcid());
|
||||
p.setQualifier(getQualifier(ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
|
||||
p
|
||||
.setQualifier(
|
||||
getQualifier(
|
||||
ModelConstants.ORCID_PENDING, ModelConstants.ORCID_CLASSNAME, ModelConstants.DNET_PID_TYPES));
|
||||
p
|
||||
.setDataInfo(
|
||||
getDataInfo(
|
||||
|
|
|
|||
|
|
@ -10,7 +10,6 @@ import java.util.List;
|
|||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -22,6 +21,7 @@ import org.slf4j.Logger;
|
|||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Context;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import scala.Tuple2;
|
||||
|
|
|
|||
|
|
@ -7,7 +7,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
|||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.function.MapFunction;
|
||||
|
|
@ -20,6 +19,7 @@ import org.slf4j.LoggerFactory;
|
|||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import scala.Tuple2;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,93 +0,0 @@
|
|||
package eu.dnetlib.dhp.sx.graph.ebi
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
|
||||
import eu.dnetlib.dhp.schema.oaf.Result
|
||||
import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
|
||||
import eu.dnetlib.dhp.utils.ISLookupClientFactory
|
||||
import org.apache.commons.io.IOUtils
|
||||
import org.apache.spark.SparkConf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.sql.expressions.Aggregator
|
||||
import org.apache.spark.sql._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import scala.io.Source
|
||||
import scala.xml.pull.XMLEventReader
|
||||
|
||||
object SparkCreateBaselineDataFrame {
|
||||
|
||||
|
||||
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
|
||||
override def zero: PMArticle = new PMArticle
|
||||
|
||||
override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = {
|
||||
if (b != null && b.getPmid!= null) b else a._2
|
||||
}
|
||||
|
||||
override def merge(b1: PMArticle, b2: PMArticle): PMArticle = {
|
||||
if (b1 != null && b1.getPmid!= null) b1 else b2
|
||||
|
||||
}
|
||||
|
||||
override def finish(reduction: PMArticle): PMArticle = reduction
|
||||
|
||||
override def bufferEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
|
||||
override def outputEncoder: Encoder[PMArticle] = Encoders.kryo[PMArticle]
|
||||
}
|
||||
|
||||
|
||||
def main(args: Array[String]): Unit = {
|
||||
val conf: SparkConf = new SparkConf()
|
||||
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json")))
|
||||
parser.parseArgument(args)
|
||||
val isLookupUrl: String = parser.get("isLookupUrl")
|
||||
log.info("isLookupUrl: {}", isLookupUrl)
|
||||
val workingPath = parser.get("workingPath")
|
||||
log.info("workingPath: {}", workingPath)
|
||||
|
||||
val targetPath = parser.get("targetPath")
|
||||
log.info("targetPath: {}", targetPath)
|
||||
|
||||
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
|
||||
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
|
||||
val spark: SparkSession =
|
||||
SparkSession
|
||||
.builder()
|
||||
.config(conf)
|
||||
.appName(SparkEBILinksToOaf.getClass.getSimpleName)
|
||||
.master(parser.get("master")).getOrCreate()
|
||||
import spark.implicits._
|
||||
|
||||
|
||||
val sc = spark.sparkContext
|
||||
|
||||
|
||||
|
||||
implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle])
|
||||
implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal])
|
||||
implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor])
|
||||
implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||
|
||||
val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000)
|
||||
val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{
|
||||
val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
|
||||
new PMParser(xml)
|
||||
|
||||
} ))
|
||||
|
||||
ds.map(p => (p.getPmid,p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
|
||||
.agg(pmArticleAggregator.toColumn)
|
||||
.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
|
||||
|
||||
val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
|
||||
exported_dataset
|
||||
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
|
||||
.filter(p => p!= null)
|
||||
.write.mode(SaveMode.Overwrite).save(targetPath)
|
||||
|
||||
//s"$workingPath/oaf/baseline_oaf"
|
||||
}
|
||||
}
|
||||
|
|
@ -1,7 +1,6 @@
|
|||
package eu.dnetlib.dhp.sx.graph.pangaea
|
||||
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||
import eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf
|
||||
import org.apache.spark.rdd.RDD
|
||||
import org.apache.spark.{SparkConf, SparkContext}
|
||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
||||
|
|
|
|||
|
|
@ -1,6 +0,0 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"i", "paramLongName":"isLookupUrl","paramDescription": "isLookupUrl", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the path of the sequencial file to read", "paramRequired": true},
|
||||
{"paramName":"t", "paramLongName":"targetPath","paramDescription": "the oaf path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
[
|
||||
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||
{"paramName":"s", "paramLongName":"sourcePath","paramDescription": "the source Path", "paramRequired": true},
|
||||
{"paramName":"w", "paramLongName":"workingPath","paramDescription": "the working path ", "paramRequired": true}
|
||||
]
|
||||
|
|
@ -25,7 +25,6 @@
|
|||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="GenerateBaselineDataset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
|
|
@ -43,6 +42,7 @@
|
|||
</spark-opts>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
|
|
|
|||
|
|
@ -51,9 +51,17 @@
|
|||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="OverrideFolders"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
<action name="OverrideFolders">
|
||||
<fs>
|
||||
<delete path="${sourcePath}/ebi_links_dataset_old"/>
|
||||
<move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
|
||||
<move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
|
||||
</fs>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -84,7 +84,28 @@ public class IndexRecordTransformerTest {
|
|||
|
||||
@Test
|
||||
public void testForEOSCFutureTraining() throws IOException, TransformerException {
|
||||
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/training-notebooks-seadatanet.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureAirQualityCopernicus() throws IOException, TransformerException {
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/air-quality-copernicus.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureB2SharePlotSw() throws IOException, TransformerException {
|
||||
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-sw.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testForEOSCFutureB2SharePlotRelatedORP() throws IOException, TransformerException {
|
||||
final String record = IOUtils
|
||||
.toString(getClass().getResourceAsStream("eosc-future/b2share-plot-related-orp.xml"));
|
||||
testRecordTransformation(record);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,114 @@
|
|||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>r37b0ad08687::a8df7db30ae0e4e0b875a098df7b652f</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2021-10-07T01:56:56Z</dri:dateOfCollection>
|
||||
<dri:status>under curation</dri:status>
|
||||
<counters/>
|
||||
</header>
|
||||
<metadata>
|
||||
<oaf:entity xmlns:oaf="http://namespace.openaire.eu/oaf"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
|
||||
xsi:schemaLocation="http://namespace.openaire.eu/oaf http://namespace.openaire.eu/oaf http://www.openaire.eu/schema/0.2/oaf-0.2.xsd">
|
||||
|
||||
<oaf:result>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
|
||||
schemename="dnet:dataCite_title">Using CAMS European air quality analysis from Copernicus
|
||||
Atmosphere Monitoring with RELIANCE services
|
||||
</title>
|
||||
<creator rank="1" name="Simone" surname="Mantovani" orcid_pending="0000-0003-3979-3645">Simone Mantovani</creator>
|
||||
<dateofacceptance>2021-10-07</dateofacceptance>
|
||||
<resulttype classid="software" classname="software" schemeid="dnet:result_typologies"
|
||||
schemename="dnet:result_typologies"/>
|
||||
<language classid="" classname="" schemeid="dnet:languages" schemename="dnet:languages"/>
|
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|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types" schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset" trust="0.9">10.5281/zenodo.3475785</pid>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes" schemename="dnet:access_modes" />
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
|
|
|
|||
|
|
@ -11,9 +11,13 @@ TARGET_DB=$2
|
|||
|
||||
TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 </dev/urandom | head -c 6`
|
||||
|
||||
echo "Downloading context data"
|
||||
echo "Downloading context ids"
|
||||
curl -L ${CONTEXT_API}/contexts/?type=ri,community -H "accept: application/json" | /usr/local/sbin/jq -r '.[] | "\(.id),\(.label)"' > contexts.csv
|
||||
|
||||
echo "Downloading categories data"
|
||||
cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv
|
||||
|
||||
echo "Downloading concepts data"
|
||||
cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv
|
||||
cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv
|
||||
cat categories.csv | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -753,7 +753,7 @@
|
|||
<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>[2.7.18]</dhp-schemas.version>
|
||||
<dhp-schemas.version>[2.8.20]</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