used javax.xml.stream.XMLEventReader instead of deprecated scala.xml.pull.XMLEventReader

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala

@@ -3,7 +3,7 @@ package eu.dnetlib.dhp.sx.bio.ebi
 import eu.dnetlib.dhp.application.ArgumentApplicationParser
 import eu.dnetlib.dhp.collection.CollectionUtils
 import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup
-import eu.dnetlib.dhp.schema.oaf.{Oaf, Result}
+import eu.dnetlib.dhp.schema.oaf.Oaf
 import eu.dnetlib.dhp.sx.bio.pubmed._
 import eu.dnetlib.dhp.utils.ISLookupClientFactory
 import org.apache.commons.io.IOUtils
@@ -14,13 +14,13 @@ 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.apache.spark.sql.expressions.Aggregator
 import org.slf4j.{Logger, LoggerFactory}
 
-import java.io.InputStream
-import scala.io.Source
-import scala.xml.pull.XMLEventReader
+import java.io.{ByteArrayInputStream, InputStream}
+import java.nio.charset.Charset
+import javax.xml.stream.XMLInputFactory
 
 object SparkCreateBaselineDataFrame {
 
@@ -83,7 +83,7 @@ object SparkCreateBaselineDataFrame {
           if (response.getStatusLine.getStatusCode > 400) {
             tries -= 1
           } else
-            return IOUtils.toString(response.getEntity.getContent)
+            return IOUtils.toString(response.getEntity.getContent, Charset.defaultCharset())
         } catch {
           case e: Throwable =>
             println(s"Error on requesting ${r.getURI}")
@@ -155,7 +155,7 @@ object SparkCreateBaselineDataFrame {
       IOUtils.toString(
         SparkEBILinksToOaf.getClass.getResourceAsStream(
           "/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"
-        )
+        ),Charset.defaultCharset()
       )
     )
     parser.parseArgument(args)
@@ -194,10 +194,11 @@ object SparkCreateBaselineDataFrame {
     if (!"true".equalsIgnoreCase(skipUpdate)) {
       downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri)
       val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000)
+      val inputFactory = XMLInputFactory.newInstance
       val ds: Dataset[PMArticle] = spark.createDataset(
         k.filter(i => i._1.endsWith(".gz"))
           .flatMap(i => {
-            val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes()))
+            val xml =inputFactory.createXMLEventReader(new ByteArrayInputStream(i._2.getBytes()))
             new PMParser(xml)
           })
       )

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala

@@ -1,7 +1,8 @@
 package eu.dnetlib.dhp.sx.bio.pubmed
 
 import scala.xml.MetaData
-import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader}
+import javax.xml.stream.XMLEventReader
+import scala.xml.pull.{EvElemEnd, EvElemStart, EvText}
 
 /** @param xml
   */

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala

@@ -16,6 +16,7 @@ import org.mockito.junit.jupiter.MockitoExtension
 
 import java.io.{BufferedReader, InputStream, InputStreamReader}
 import java.util.zip.GZIPInputStream
+import javax.xml.stream.XMLInputFactory
 import scala.collection.JavaConverters._
 import scala.collection.mutable.ListBuffer
 import scala.io.Source
@@ -49,10 +50,8 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testEBIData() = {
-    val inputXML = Source
-      .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-      .mkString
-    val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes()))
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
     new PMParser(xml).foreach(s => println(mapper.writeValueAsString(s)))
   }
 
@@ -91,9 +90,10 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   @Test
   def testParsingPubmedXML(): Unit = {
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     parser.foreach(checkPMArticle)
   }
@@ -156,9 +156,9 @@ class BioScholixTest extends AbstractVocabularyTest {
   @Test
   def testPubmedMapping(): Unit = {
 
-    val xml = new XMLEventReader(
-      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
-    )
+    val inputFactory = XMLInputFactory.newInstance
+    val xml = inputFactory.createXMLEventReader(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+
     val parser = new PMParser(xml)
     val results = ListBuffer[Oaf]()
     parser.foreach(x => results += PubMedToOaf.convert(x, vocabularies))