forked from D-Net/dnet-hadoop
Implemented new method for update baseline inside scala node
This commit is contained in:
parent
b84e0cabeb
commit
2557bb41f5
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@ -6,18 +6,130 @@ import eu.dnetlib.dhp.schema.oaf.Result
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import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf}
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import eu.dnetlib.dhp.utils.ISLookupClientFactory
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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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val buffer = Array.fill[Byte](1024)(0)
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while(i.read(buffer)>0) {
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fsDataOutputStream.write(buffer)
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}
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i.close()
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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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@ -51,6 +163,10 @@ object SparkCreateBaselineDataFrame {
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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 isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
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val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
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val spark: SparkSession =
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@ -61,16 +177,15 @@ object SparkCreateBaselineDataFrame {
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.master(parser.get("master")).getOrCreate()
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import spark.implicits._
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val sc = spark.sparkContext
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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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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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@ -87,7 +202,5 @@ object SparkCreateBaselineDataFrame {
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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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//s"$workingPath/oaf/baseline_oaf"
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}
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}
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@ -4,20 +4,16 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem
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import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal}
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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.{FileSystem, Path}
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import org.apache.http.client.config.RequestConfig
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import org.apache.http.client.methods.{HttpGet, HttpUriRequest}
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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.sql.expressions.Aggregator
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import org.apache.spark.sql.functions.max
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import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.apache.spark.sql._
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import org.slf4j.{Logger, LoggerFactory}
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object SparkDownloadEBILinks {
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def createEBILinks(pmid:Long):EBILinkItem = {
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val res = requestLinks(pmid)
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@ -26,7 +22,6 @@ object SparkDownloadEBILinks {
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null
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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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@ -61,42 +56,6 @@ object SparkDownloadEBILinks {
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}
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}
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def requestBaseLineUpdatePage():List[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") ).map(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 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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while (files.hasNext) {
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val c = files.next()
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c.getPath
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}
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}
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def requestLinks(PMID:Long):String = {
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requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
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@ -1,6 +1,7 @@
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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":"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":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
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]
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@ -1,5 +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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{"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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@ -25,7 +25,6 @@
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="GenerateBaselineDataset">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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@ -43,6 +42,7 @@
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</spark-opts>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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<arg>--hdfsServerUri</arg><arg>${nameNode}</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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@ -1,59 +1,67 @@
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<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>workingPath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>sourcePath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>workingPath</name>
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<description>the Working Path</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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</parameters>
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<start to="DownloadEBILinks"/>
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<start to="DownloadEBILinks"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="DownloadEBILinks">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Incremental Download EBI Links</name>
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<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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</spark>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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<action name="DownloadEBILinks">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Incremental Download EBI Links</name>
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<class>eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks</class>
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<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.shuffle.partitions=2000
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${sourcePath}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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<arg>--master</arg><arg>yarn</arg>
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</spark>
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<ok to="OverrideFolders"/>
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<error to="Kill"/>
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</action>
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<action name="OverrideFolders">
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<fs>
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<delete path="${sourcePath}/ebi_links_dataset_old"/>
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<move source="${sourcePath}/ebi_links_dataset" target="${sourcePath}/ebi_links_dataset_old"/>
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<move source="${workingPath}/links_final" target="${sourcePath}/ebi_links_dataset"/>
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</fs>
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<ok to="End"/>
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<error to="Kill"/>
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</action>
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<end name="End"/>
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</workflow-app>
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@ -51,11 +51,6 @@ class BioScholixTest extends AbstractVocabularyTest{
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}
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@Test
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def testDownloadEBIUpdate() = {
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val data = SparkDownloadEBILinks.requestBaseLineUpdatePage()
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println(data)
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}
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@Test
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