Merge branch 'beta' into beta_solr_config
commit
14fbf92ad6
@ -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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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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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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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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val skipUpdate = parser.get("skipUpdate")
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log.info("skipUpdate: {}", skipUpdate)
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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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val sc = spark.sparkContext
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import spark.implicits._
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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"$workingPath/baseline", hdfsServerUri)
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val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
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val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => {
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val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
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new PMParser(xml)
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}))
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ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1)
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.agg(pmArticleAggregator.toColumn)
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.map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset")
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}
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val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle]
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exported_dataset
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.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
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.filter(p => p != null)
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.write.mode(SaveMode.Overwrite).save(targetPath)
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}
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}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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import java.util.ArrayList;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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public class PMGrant {
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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import java.io.Serializable;
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@ -1,4 +1,4 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed
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package eu.dnetllib.dhp.sx.bio.pubmed
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import scala.xml.MetaData
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import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
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@ -1,5 +1,5 @@
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package eu.dnetlib.dhp.sx.graph.bio.pubmed;
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package eu.dnetllib.dhp.sx.bio.pubmed;
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public class PMSubject {
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private String value;
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@ -0,0 +1,8 @@
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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":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true},
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{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true},
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{"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false},
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{"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
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]
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@ -0,0 +1,5 @@
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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": "the source Path", "paramRequired": true},
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{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true}
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]
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File diff suppressed because it is too large
Load Diff
@ -0,0 +1,117 @@
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package eu.dnetlib.dhp.oa.dedup;
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import java.util.concurrent.TimeUnit;
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import org.apache.commons.io.IOUtils;
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import org.apache.http.client.methods.CloseableHttpResponse;
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import org.apache.http.client.methods.HttpGet;
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import org.apache.http.impl.client.CloseableHttpClient;
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import org.apache.http.impl.client.HttpClients;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class UpdateOpenorgsJob {
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private static final Logger log = LoggerFactory.getLogger(UpdateOpenorgsJob.class);
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public static void main(String[] args) throws Exception {
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ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkCreateSimRels.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/dedup/updateOpenorgsJob_parameters.json")));
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parser.parseArgument(args);
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final String apiUrl = parser.get("apiUrl");
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final int delay = Integer.parseInt(parser.get("delay"));
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log.info("apiUrl: '{}'", apiUrl);
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log.info("delay: '{}'", delay);
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APIResponse res = httpCall(apiUrl);
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while (res != null && res.getStatus().equals(ImportStatus.RUNNING)) {
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TimeUnit.MINUTES.sleep(delay);
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res = httpCall(apiUrl + "/status");
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}
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if (res == null) {
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log.error("Openorgs Update FAILED: No response");
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throw new RuntimeException("Openorgs Update FAILED: No response");
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}
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if (res.getStatus() == null || !res.getStatus().equals(ImportStatus.SUCCESS)) {
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log.error("Openorgs Update FAILED: '{}' - '{}'", res.getStatus(), res.getMessage());
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throw new RuntimeException(res.getMessage());
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}
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}
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private static APIResponse httpCall(final String url) throws Exception {
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final HttpGet req = new HttpGet(url);
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try (final CloseableHttpClient client = HttpClients.createDefault()) {
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try (final CloseableHttpResponse response = client.execute(req)) {
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final String s = IOUtils.toString(response.getEntity().getContent());
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return (new ObjectMapper()).readValue(s, APIResponse.class);
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}
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}
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}
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}
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class APIResponse {
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private String id;
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private Long dateStart;
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private Long dateEnd;
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private ImportStatus status;
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private String message;
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public String getId() {
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return id;
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}
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|
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public void setId(String id) {
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this.id = id;
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}
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|
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public Long getDateStart() {
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return dateStart;
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}
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public void setDateStart(Long dateStart) {
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this.dateStart = dateStart;
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}
|
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|
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public Long getDateEnd() {
|
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return dateEnd;
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}
|
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|
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public void setDateEnd(Long dateEnd) {
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this.dateEnd = dateEnd;
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}
|
||||
|
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public ImportStatus getStatus() {
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return status;
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||||
}
|
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|
||||
public void setStatus(ImportStatus status) {
|
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this.status = status;
|
||||
}
|
||||
|
||||
public String getMessage() {
|
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return message;
|
||||
}
|
||||
|
||||
public void setMessage(String message) {
|
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this.message = message;
|
||||
}
|
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}
|
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|
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enum ImportStatus {
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SUCCESS, FAILED, RUNNING, NOT_LAUNCHED, NOT_YET_STARTED
|
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}
|
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@ -0,0 +1,14 @@
|
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[
|
||||
{
|
||||
"paramName": "api",
|
||||
"paramLongName": "apiUrl",
|
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"paramDescription": "the url of the API",
|
||||
"paramRequired": true
|
||||
},
|
||||
{
|
||||
"paramName": "d",
|
||||
"paramLongName": "delay",
|
||||
"paramDescription": "delay for the HTTP call in minutes",
|
||||
"paramRequired": true
|
||||
}
|
||||
]
|
||||
File diff suppressed because it is too large
Load Diff
@ -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"
|
||||
}
|
||||
}
|
||||
@ -1,6 +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}
|
||||
]
|
||||
@ -1,59 +1,67 @@
|
||||
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<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>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
|
||||
<parameters>
|
||||
<property>
|
||||
<name>sourcePath</name>
|
||||
<description>the Working Path</description>
|
||||
</property>
|
||||
<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>
|
||||
<property>
|
||||
<name>sparkExecutorCores</name>
|
||||
<description>number of cores used by single executor</description>
|
||||
</property>
|
||||
</parameters>
|
||||
|
||||
<start to="DownloadEBILinks"/>
|
||||
<start to="DownloadEBILinks"/>
|
||||
|
||||
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
<kill name="Kill">
|
||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
|
||||
<action name="DownloadEBILinks">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Incremental Download EBI Links</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</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}${spark2EventLogDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${workingPath}</arg>
|
||||
<arg>--master</arg><arg>yarn</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
<action name="DownloadEBILinks">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Incremental Download EBI Links</name>
|
||||
<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
|
||||
<jar>dhp-graph-mapper-${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>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||
<arg>--workingPath</arg><arg>${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>
|
||||
@ -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"/>
|
||||
<description>
|
||||
This notebook shows how to discover and access the Copernicus Atmosphere Monitoring products available in the RELIANCE datacube resources.
|
||||
The process is structured in 6 steps, including example of data analysis and visualization with the Python libraries installed in the Jupyter environment
|
||||
</description>
|
||||
<country classid="" classname="" schemeid="" schemename=""/>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">EOSC Jupyter Notebook
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">RELIANCE
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">Copernicus
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">Air quality
|
||||
</subject>
|
||||
|
||||
<relevantdate classid="" classname="" schemeid="" schemename=""/>
|
||||
<publisher>Zenodo</publisher>
|
||||
<embargoenddate/>
|
||||
<journal issn="" eissn="" lissn="" ep="" iss="" sp="" vol=""/>
|
||||
<source/>
|
||||
<fulltext/>
|
||||
<format/>
|
||||
<storagedate/>
|
||||
<resourcetype classid="" classname="" schemeid="" schemename=""/>
|
||||
<device/>
|
||||
<size/>
|
||||
<version/>
|
||||
<lastmetadataupdate/>
|
||||
<metadataversionnumber/>
|
||||
<documentationUrl/>
|
||||
<codeRepositoryUrl/>
|
||||
<programmingLanguage classid="" classname="" schemeid="" schemename=""/>
|
||||
<contactperson/>
|
||||
<contactgroup/>
|
||||
<tool/>
|
||||
<originalId>oai:zenodo.org:5554786</originalId>
|
||||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<pid classid="oai" classname="Open Archives Initiative" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types">oai:zenodo.org:5554786
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types">10.5281/zenodo.5554786
|
||||
</pid>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<datainfo>
|
||||
<inferred>false</inferred>
|
||||
<deletedbyinference>false</deletedbyinference>
|
||||
<trust>0.9</trust>
|
||||
<inferenceprovenance/>
|
||||
<provenanceaction classid="user:insert" classname="user:insert"
|
||||
schemeid="dnet:provenanceActions" schemename="dnet:provenanceActions"/>
|
||||
</datainfo>
|
||||
<rels>
|
||||
<rel inferred="false" trust="0.9" inferenceprovenance="" provenanceaction="user:claim">
|
||||
<to class="isProducedBy" scheme="dnet:result_project_relations" type="project">
|
||||
corda__h2020::8771f523c34e38902d4921037d545ef8
|
||||
</to>
|
||||
<title>REsearch LIfecycle mAnagemeNt for Earth Science Communities and CopErnicus users in EOSC</title>
|
||||
<code>101017501</code>
|
||||
<acronym>RELIANCE</acronym>
|
||||
<funding>
|
||||
<funder id="ec__________::EC" shortname="EC" name="European Commission" jurisdiction="EU" />
|
||||
<funding_level_0 name="H2020">ec__________::EC::H2020</funding_level_0>
|
||||
<funding_level_1 name="RIA">ec__________::EC::H2020::RIA</funding_level_1>
|
||||
</funding>
|
||||
</rel>
|
||||
</rels>
|
||||
<children>
|
||||
<instance id="r37b0ad08687::a8df7db30ae0e4e0b875a098df7b652f">
|
||||
<instancetype classid="0029" classname="Software" schemeid="dnet:publication_resource"
|
||||
schemename="dnet:publication_resource"/>
|
||||
<collectedfrom name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<hostedby name="Zenodo" id="re3data_____::7b0ad08687b2c960d5aeef06f811d5e6"/>
|
||||
<accessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<dateofacceptance/>
|
||||
<webresource>
|
||||
<url>https://zenodo.org/record/5554786</url>
|
||||
</webresource>
|
||||
</instance>
|
||||
</children>
|
||||
</oaf:result>
|
||||
</oaf:entity>
|
||||
</metadata>
|
||||
</result>
|
||||
</record>
|
||||
@ -0,0 +1,288 @@
|
||||
<record>
|
||||
<result xmlns:dri="http://www.driver-repository.eu/namespace/dri"
|
||||
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
|
||||
<header>
|
||||
<dri:objIdentifier>doi_dedup___::44fd8a9b5b79adb0783ac245b21e3127</dri:objIdentifier>
|
||||
<dri:dateOfCollection>2019-09-19T07:43:31+0000</dri:dateOfCollection>
|
||||
<dri:dateOfTransformation>2019-09-19T07:43:31+0000</dri:dateOfTransformation>
|
||||
</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>
|
||||
<collectedfrom name="Datacite" id="openaire____::9e3be59865b2c1c335d32dae2fe7b254"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
<originalId>10.23728/b2share.ebcd2972c5fb44199f8b3fdf9f6413c6</originalId>
|
||||
<originalId>10.23728/b2share.a69a7b2dcc22449e8734552dde4d3906</originalId>
|
||||
<originalId>6a93c069-a167-44cb-bfe8-74c275637347</originalId>
|
||||
<originalId>50|r3730f562f9e::9b434fedc00d568b8e00611a7fa19f41</originalId>
|
||||
<originalId>10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016</originalId>
|
||||
<originalId>ada23067-496a-494f-bd82-6ffe3cf4f0fb</originalId>
|
||||
<originalId>50|r3730f562f9e::b9cd774e8126b6902d56f9a4aa03e1dc</originalId>
|
||||
<originalId>f3bd1041-422c-439d-8e68-c1d0711d130d</originalId>
|
||||
<originalId>50|r3730f562f9e::b847821a0ca5365b0d971dd89dea6bf1</originalId>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.ebcd2972c5fb44199f8b3fdf9f6413c6
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.a69a7b2dcc22449e8734552dde4d3906
|
||||
</pid>
|
||||
<pid classid="doi" classname="Digital Object Identifier" schemeid="dnet:pid_types"
|
||||
schemename="dnet:pid_types" inferred="false" provenanceaction="sysimport:actionset"
|
||||
trust="0.9">10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016
|
||||
</pid>
|
||||
<title classid="main title" classname="main title" schemeid="dnet:dataCite_title"
|
||||
schemename="dnet:dataCite_title">HCG16 L-band VLA C+D array final data
|
||||
</title>
|
||||
<bestaccessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<creator rank="1" name="Michael G." surname="Jones">Jones, Michael G.</creator>
|
||||
<dateofacceptance>2019-01-01</dateofacceptance>
|
||||
<description>These are the reduced final data associated with the paper Jones et al. 2019 submitted
|
||||
to Astronomy & Astrophysics. They are used by a mybinder (https://gke.mybinder.org/)
|
||||
executable environment to generate the final plots of that paper. The link for this environment
|
||||
is https://mybinder.org/v2/gh/AMIGA-IAA/hcg-16/master. The raw VLA D and C array data of HCG 16
|
||||
were collected by the Very Large Array (http://www.vla.nrao.edu/) in 1989 and 1999, under PI
|
||||
projects of Barbara Williams. The project numbers are AW234 and AW500 respectively. The file
|
||||
also includes a grz colour image and r-band image from DECaLS DR8
|
||||
(http://legacysurvey.org/decamls/), a GBT HI spectrum published in Borthakur et al. 2010 (ApJ
|
||||
710, 385), an HI data cube from HIPASS (https://www.atnf.csiro.au/research/multibeam/release/),
|
||||
and a source mask (and associated parameters file) for the HIPASS cube generated using SoFiA
|
||||
(https://github.com/SoFiA-Admin/SoFiA-2).
|
||||
</description>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">3.5.2.1.1 → Observational astronomy →
|
||||
Radio astronomy
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">HI
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">VLA
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies">HCG16
|
||||
</subject>
|
||||
<subject classid="keyword" classname="keyword" schemeid="dnet:subject_classification_typologies"
|
||||
schemename="dnet:subject_classification_typologies" inferred="false"
|
||||
provenanceaction="sysimport:crosswalk:repository" trust="0.9">Various
|
||||
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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">10.23728/b2share.7c8655b6f25348358b4e6fece7ab6016
|
||||
</pid>
|
||||
<collectedfrom name="Datacite" id="openaire____::9e3be59865b2c1c335d32dae2fe7b254"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
</rel>
|
||||
</rels>
|
||||
<children>
|
||||
<instance id="userclaim___::ee29372a239b79db3ac4c5debe44d6e6">
|
||||
<instancetype classid="0029" classname="Software" schemeid="dnet:publication_resource"
|
||||
schemename="dnet:publication_resource"/>
|
||||
<collectedfrom name="B2FIND" id="re3data_____::730f562f9efe8a3b3742d2da510d4335"/>
|
||||
<hostedby name="B2SHARE" id="re3data_____::ad3609c351bd520edf6f10f5e0d9b877"/>
|
||||
<accessright classid="OPEN" classname="Open Access" schemeid="dnet:access_modes"
|
||||
schemename="dnet:access_modes"/>
|
||||
<dateofacceptance>2021-09-30</dateofacceptance>
|
||||
<webresource>
|
||||
<url>http://dx.doi.org/10.23728/b2share.adf6e2e942b04561a8640c449b48c14a</url>
|
||||
</webresource>
|
||||
</instance>
|
||||
</children>
|
||||
</oaf:result>
|
||||
</oaf:entity>
|
||||
</metadata>
|
||||
</result>
|
||||
</record>
|
||||
Loading…
Reference in New Issue