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Implemented new method for update baseline inside scala node

This commit is contained in:
Sandro La Bruzzo 2021-10-06 16:41:08 +02:00
parent b84e0cabeb
commit 2557bb41f5
8 changed files with 1625 additions and 116 deletions
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123
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala
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@ -6,18 +6,130 @@ 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.hadoop.conf.Configuration
import org.apache.hadoop.fs.{FSDataOutputStream, FileSystem, Path}
import org.apache.http.client.config.RequestConfig
import org.apache.http.client.methods.HttpGet
import org.apache.http.impl.client.HttpClientBuilder
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 java.io.InputStream
import scala.io.Source
import scala.xml.pull.XMLEventReader
object SparkCreateBaselineDataFrame {
def requestBaseLineUpdatePage(maxFile:String):List[(String,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") ).filter(s => s > maxFile).map(s => (s,s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList
result
}
def downloadBaselinePart(url:String):InputStream = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
response.getEntity.getContent
}
def requestPage(url:String):String = {
val r = new HttpGet(url)
val timeout = 60; // seconds
val config = RequestConfig.custom()
.setConnectTimeout(timeout * 1000)
.setConnectionRequestTimeout(timeout * 1000)
.setSocketTimeout(timeout * 1000).build()
val client = HttpClientBuilder.create().setDefaultRequestConfig(config).build()
try {
var tries = 4
while (tries > 0) {
println(s"requesting ${r.getURI}")
try {
val response = client.execute(r)
println(s"get response with status${response.getStatusLine.getStatusCode}")
if (response.getStatusLine.getStatusCode > 400) {
tries -= 1
}
else
return IOUtils.toString(response.getEntity.getContent)
} catch {
case e: Throwable =>
println(s"Error on requesting ${r.getURI}")
e.printStackTrace()
tries -= 1
}
}
""
} finally {
if (client != null)
client.close()
}
}
def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = {
val conf = new Configuration
conf.set("fs.defaultFS", hdfsServerUri)
val fs = FileSystem.get(conf)
val p = new Path(baselinePath)
val files = fs.listFiles(p,false)
var max_file = ""
while (files.hasNext) {
val c = files.next()
val data = c.getPath.toString
val fileName = data.substring(data.lastIndexOf("/")+1)
if (fileName> max_file)
max_file = fileName
}
val files_to_download = requestBaseLineUpdatePage(max_file)
files_to_download.foreach { u =>
val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}")
val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true)
val i = downloadBaselinePart(u._2)
val buffer = Array.fill[Byte](1024)(0)
while(i.read(buffer)>0) {
fsDataOutputStream.write(buffer)
}
i.close()
println(s"Downloaded ${u._2} into $baselinePath/${u._1}")
fsDataOutputStream.close()
}
}
val pmArticleAggregator: Aggregator[(String, PMArticle), PMArticle, PMArticle] = new Aggregator[(String, PMArticle), PMArticle, PMArticle] with Serializable {
override def zero: PMArticle = new PMArticle
@ -51,6 +163,10 @@ object SparkCreateBaselineDataFrame {
val targetPath = parser.get("targetPath")
log.info("targetPath: {}", targetPath)
val hdfsServerUri = parser.get("hdfsServerUri")
log.info("hdfsServerUri: {}", targetPath)
val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl)
val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService)
val spark: SparkSession =
@ -61,16 +177,15 @@ object SparkCreateBaselineDataFrame {
.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])
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()))
@ -87,7 +202,5 @@ object SparkCreateBaselineDataFrame {
.map(a => PubMedToOaf.convert(a, vocabularies)).as[Result]
.filter(p => p!= null)
.write.mode(SaveMode.Overwrite).save(targetPath)
//s"$workingPath/oaf/baseline_oaf"
}
}

45
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala
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@ -4,20 +4,16 @@ 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 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
@ -61,42 +56,6 @@ 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")

7
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json
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@ -1,6 +1,7 @@
[
{"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":"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":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true}
]

4
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json
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@ -1,5 +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}
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the working path ", "paramRequired": true}
]

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml
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@ -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"/>

14
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml
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@ -1,4 +1,4 @@
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
<workflow-app name="Create EBI Dataset" xmlns="uri:oozie:workflow:0.5">
<parameters>
<property>
<name>sourcePath</name>
@ -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>
</workflow-app>

5
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala
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@ -51,11 +51,6 @@ class BioScholixTest extends AbstractVocabularyTest{
}
@Test
def testDownloadEBIUpdate() = {
val data = SparkDownloadEBILinks.requestBaseLineUpdatePage()
println(data)
}
@Test

1433
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result Normal file
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