code formatting

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java

@@ -255,7 +255,6 @@ public class PMArticle implements Serializable {
 		return grants;
 	}
 
-
 	public String getPmcId() {
 		return pmcId;
 	}

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

@@ -56,13 +56,11 @@ object PubMedToOaf {
     null
   }
 
-
+  def createOriginalOpenaireId(article: PMArticle): String = {
-  def createOriginalOpenaireId(article:PMArticle) :String =  {
     if (StringUtils.isNotEmpty(article.getPmcId)) {
-      val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC","")}")
+      val md5 = DHPUtils.md5(s"$OAI_HEADER${article.getPmcId.replace("PMC", "")}")
       s"$OLD_PMC_PREFIX$md5"
-    }
+    } else
-    else
       null
 
   }
@@ -142,26 +140,24 @@ object PubMedToOaf {
     val pidList = ListBuffer[StructuredProperty]()
 
     pidList += OafMapperUtils.structuredProperty(
-        article.getPmid,
+      article.getPmid,
-        PidType.pmid.toString,
+      PidType.pmid.toString,
-        PidType.pmid.toString,
+      PidType.pmid.toString,
+      ModelConstants.DNET_PID_TYPES,
+      ModelConstants.DNET_PID_TYPES,
+      dataInfo
+    )
+
+    if (StringUtils.isNotBlank(article.getPmcId)) {
+      pidList += OafMapperUtils.structuredProperty(
+        article.getPmcId,
+        PidType.pmc.toString,
+        PidType.pmc.toString,
         ModelConstants.DNET_PID_TYPES,
         ModelConstants.DNET_PID_TYPES,
         dataInfo
       )
-
+    }
-
-    if (StringUtils.isNotBlank(article.getPmcId))
-      {
-        pidList += OafMapperUtils.structuredProperty(
-          article.getPmcId,
-          PidType.pmc.toString,
-          PidType.pmc.toString,
-          ModelConstants.DNET_PID_TYPES,
-          ModelConstants.DNET_PID_TYPES,
-          dataInfo
-        )
-      }
     if (pidList == null)
       return null
 
@@ -297,7 +293,7 @@ object PubMedToOaf {
     if (StringUtils.isNotEmpty(article.getPmcId)) {
       val originalIDS = ListBuffer[String]()
       originalIDS += createOriginalOpenaireId(article)
-      pidList.map(s => s.getValue).foreach(p =>originalIDS +=  p)
+      pidList.map(s => s.getValue).foreach(p => originalIDS += p)
       result.setOriginalId(originalIDS.asJava)
     } else
       result.setOriginalId(pidList.map(s => s.getValue).asJava)

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala

@@ -48,9 +48,6 @@ class DataciteToOAFTest extends AbstractVocabularyTest {
 
   }
 
-
-
-
   @Test
   def testConvert(): Unit = {
 
@@ -76,11 +73,8 @@ class DataciteToOAFTest extends AbstractVocabularyTest {
 
     assertEquals(100, nativeSize)
 
-    val result: Dataset[String] = spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING)
+    val result: Dataset[String] =
-
+      spark.read.text(targetPath).as[String].map(DataciteUtilityTest.convertToOAF)(Encoders.STRING)
-
-
-
 
     result
       .groupBy(col("value").alias("class"))

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteUtilityTest.scala

@@ -6,25 +6,24 @@ import org.json4s.jackson.JsonMethods.parse
 
 object DataciteUtilityTest {
 
-  def convertToOAF(input:String) : String = {
+  def convertToOAF(input: String): String = {
     implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
     lazy val json = parse(input)
 
-
+    val isRelation: String = (json \\ "source").extractOrElse("NULL")
-    val isRelation:String = (json \\ "source").extractOrElse("NULL")
 
     if (isRelation != "NULL") {
       return "Relation"
     }
 
     val iType: List[String] = for {
-      JObject(instance)                     <- json \\ "instance"
+      JObject(instance)                             <- json \\ "instance"
       JField("instancetype", JObject(instancetype)) <- instance
-      JField("classname", JString(classname)) <- instancetype
+      JField("classname", JString(classname))       <- instancetype
 
     } yield classname
 
-    val l:String =iType.head.toLowerCase()
+    val l: String = iType.head.toLowerCase()
     l
   }
 

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

@@ -76,12 +76,11 @@ class BioScholixTest extends AbstractVocabularyTest {
 
   }
 
-
+  private def checkPMArticle(article: PMArticle): Unit = {
-  private def checkPMArticle(article:PMArticle): Unit = {
     assertNotNull(article.getPmid)
     assertNotNull(article.getTitle)
     assertNotNull(article.getAuthors)
-    article.getAuthors.asScala.foreach{a =>
+    article.getAuthors.asScala.foreach { a =>
       assertNotNull(a)
       assertNotNull(a.getFullName)
     }
@@ -89,20 +88,21 @@ class BioScholixTest extends AbstractVocabularyTest {
   }
 
   @Test
-  def  testParsingPubmedXML():Unit = {
+  def testParsingPubmedXML(): Unit = {
-    val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")))
+    val xml = new XMLEventReader(
+      Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml"))
+    )
     val parser = new PMParser(xml)
     parser.foreach(checkPMArticle)
   }
 
-
+  private def checkPubmedPublication(o: Oaf): Unit = {
-  private def checkPubmedPublication(o:Oaf): Unit = {
     assertTrue(o.isInstanceOf[Publication])
-    val p:Publication = o.asInstanceOf[Publication]
+    val p: Publication = o.asInstanceOf[Publication]
     assertNotNull(p.getId)
     assertNotNull(p.getTitle)
-    p.getTitle.asScala.foreach(t =>assertNotNull(t.getValue))
+    p.getTitle.asScala.foreach(t => assertNotNull(t.getValue))
-    p.getAuthor.asScala.foreach(a =>assertNotNull(a.getFullname))
+    p.getAuthor.asScala.foreach(a => assertNotNull(a.getFullname))
     assertNotNull(p.getInstance())
     p.getInstance().asScala.foreach { i =>
       assertNotNull(i.getCollectedfrom)
@@ -112,28 +112,26 @@ class BioScholixTest extends AbstractVocabularyTest {
     assertNotNull(p.getOriginalId)
     p.getOriginalId.asScala.foreach(oId => assertNotNull(oId))
 
-
+    val hasPMC = p
-    val hasPMC = p.getInstance().asScala.exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString)))
+      .getInstance()
-
+      .asScala
-
+      .exists(i => i.getPid.asScala.exists(pid => pid.getQualifier.getClassid.equalsIgnoreCase(PidType.pmc.toString)))
 
     if (hasPMC) {
       assertTrue(p.getOriginalId.asScala.exists(oId => oId.startsWith("od_______267::")))
     }
   }
 
-
   @Test
-  def testPubmedOriginalID():Unit = {
+  def testPubmedOriginalID(): Unit = {
-    val article:PMArticle  = new PMArticle
+    val article: PMArticle = new PMArticle
-
 
     article.setPmid("1234")
 
     article.setTitle("a Title")
 
     // VERIFY PUBLICATION IS NOT NULL
-    article.getPublicationTypes.add( new PMSubject("article",null, null))
+    article.getPublicationTypes.add(new PMSubject("article", null, null))
     var publication = PubMedToOaf.convert(article, vocabularies).asInstanceOf[Publication]
     assertNotNull(publication)
     assertEquals("50|pmid________::81dc9bdb52d04dc20036dbd8313ed055", publication.getId)
@@ -146,30 +144,25 @@ class BioScholixTest extends AbstractVocabularyTest {
 
     // VERIFY ORIGINAL ID GENERATE IN OLD WAY USING PMC IDENTIFIER EXISTS
 
-
+    val oldOpenaireID = "od_______267::0000072375bc0e68fa09d4e6b7658248"
-    val oldOpenaireID ="od_______267::0000072375bc0e68fa09d4e6b7658248"
 
     val hasOldOpenAIREID = publication.getOriginalId.asScala.exists(o => o.equalsIgnoreCase(oldOpenaireID))
 
     assertTrue(hasOldOpenAIREID)
   }
 
-
   @Test
-  def testPubmedMapping() :Unit = {
+  def testPubmedMapping(): Unit = {
 
-    val xml = new XMLEventReader(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")))
+    val xml = new XMLEventReader(
+      Source.fromInputStream(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))
 
-
-
-
     results.foreach(checkPubmedPublication)
 
-
-
   }
 
   @Test

dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java

@@ -162,7 +162,7 @@ class MigrateDbEntitiesApplicationTest {
 			.stream()
 			.map(Qualifier::getSchemeid)
 			.collect(Collectors.toCollection(HashSet::new));
-		assertEquals(1,cpSchemeId.size());
+		assertEquals(1, cpSchemeId.size());
 		assertTrue(cpSchemeId.contains("eosc:contentpolicies"));
 		HashSet<String> cpSchemeName = ds
 			.getContentpolicies()
@@ -289,16 +289,16 @@ class MigrateDbEntitiesApplicationTest {
 		checkProperty(r1, "contribution", "436754.0");
 		checkProperty(r2, "contribution", "436754.0");
 
-		checkProperty(r1, "currency","EUR");
+		checkProperty(r1, "currency", "EUR");
 		checkProperty(r2, "currency", "EUR");
 	}
 
 	private void checkProperty(Relation r, String property, String value) {
 		final List<KeyValue> p = r
-				.getProperties()
+			.getProperties()
-				.stream()
+			.stream()
-				.filter(kv -> kv.getKey().equals(property))
+			.filter(kv -> kv.getKey().equals(property))
-				.collect(Collectors.toList());
+			.collect(Collectors.toList());
 		assertFalse(p.isEmpty());
 		assertEquals(1, p.size());
 		assertEquals(value, p.get(0).getValue());