Implemented new method for update baseline

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala

@@ -4,6 +4,8 @@ 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.impl.client.HttpClientBuilder
@@ -25,8 +27,8 @@ object SparkDownloadEBILinks {
   }
 
 
-  def requestLinks(PMID:Long):String = {
+  def requestPage(url:String):String = {
-    val r = new HttpGet(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
+    val r = new HttpGet(url)
     val timeout = 60; // seconds
     val config = RequestConfig.custom()
       .setConnectTimeout(timeout * 1000)
@@ -57,6 +59,46 @@ object SparkDownloadEBILinks {
       if (client != null)
         client.close()
     }
+  }
+
+
+  def requestBaseLineUpdatePage():List[String] = {
+    val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/")
+
+    val result =data.lines.filter(l => l.startsWith("<a href=")).map{l =>
+      val end = l.lastIndexOf("\">")
+      val start = l.indexOf("<a href=\"")
+
+      if (start>= 0 && end >start)
+        l.substring(start+9, (end-start))
+      else
+        ""
+    }.filter(s =>s.endsWith(".gz") ).map(s => s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s").toList
+
+    result
+  }
+
+  def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = {
+
+
+    val conf = new Configuration
+    conf.set("fs.defaultFS", hdfsServerUri)
+    val fs =  FileSystem.get(conf)
+    val p = new Path((baselinePath))
+    val files = fs.listFiles(p,false)
+
+    while (files.hasNext) {
+      val c = files.next()
+      c.getPath
+
+    }
+
+
+  }
+
+
+  def requestLinks(PMID:Long):String = {
+    requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json")
 
   }
   def main(args: Array[String]): Unit = {

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala

@@ -7,6 +7,7 @@ import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
 import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved
 import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF
 import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo
+import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks
 import org.json4s.DefaultFormats
 import org.json4s.JsonAST.{JField, JObject, JString}
 import org.json4s.jackson.JsonMethods.parse
@@ -50,6 +51,13 @@ class BioScholixTest extends AbstractVocabularyTest{
   }
 
 
+  @Test
+  def testDownloadEBIUpdate() = {
+    val data = SparkDownloadEBILinks.requestBaseLineUpdatePage()
+    println(data)
+  }
+
+
   @Test
   def testEBIData() = {
     val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString