code formatted

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

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 /**
@@ -7,31 +8,32 @@ package eu.dnetlib.dhp.sx.bio.pubmed;
  */
 public class PMAffiliation {
 
-    private  String name;
+	private String name;
 
-    private PMIdentifier identifier;
+	private PMIdentifier identifier;
 
-    public PMAffiliation() {
+	public PMAffiliation() {
 
-    }
+	}
-    public PMAffiliation(String name, PMIdentifier identifier) {
-        this.name = name;
-        this.identifier = identifier;
-    }
 
-    public String getName() {
+	public PMAffiliation(String name, PMIdentifier identifier) {
-        return name;
+		this.name = name;
-    }
+		this.identifier = identifier;
+	}
 
-    public void setName(String name) {
+	public String getName() {
-        this.name = name;
+		return name;
-    }
+	}
 
-    public PMIdentifier getIdentifier() {
+	public void setName(String name) {
-        return identifier;
+		this.name = name;
-    }
+	}
 
-    public void setIdentifier(PMIdentifier identifier) {
+	public PMIdentifier getIdentifier() {
-        this.identifier = identifier;
+		return identifier;
-    }
+	}
+
+	public void setIdentifier(PMIdentifier identifier) {
+		this.identifier = identifier;
+	}
 }

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

@@ -97,5 +97,4 @@ public class PMAuthor implements Serializable {
 		this.affiliation = affiliation;
 	}
 
-
 }

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

@@ -1,53 +1,53 @@
+
 package eu.dnetlib.dhp.sx.bio.pubmed;
 
 public class PMIdentifier {
 
-    private String pid;
+	private String pid;
-    private String type;
+	private String type;
 
+	public PMIdentifier(String pid, String type) {
+		this.pid = cleanPid(pid);
+		this.type = type;
+	}
 
-    public PMIdentifier(String pid, String type) {
+	public PMIdentifier() {
-        this.pid = cleanPid(pid);
-        this.type = type;
-    }
 
-    public PMIdentifier() {
+	}
 
-    }
+	private String cleanPid(String pid) {
 
-    private String cleanPid(String pid) {
+		if (pid == null) {
+			return null;
+		}
 
-        if (pid == null) {
+		// clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
-            return null;
+		if (pid.matches("[0-9]{15}[0-9X]")) {
-        }
+			return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
+		}
 
-        // clean ORCID ID in the form 0000000163025705 to 0000-0001-6302-5705
+		// clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
-        if (pid.matches("[0-9]{15}[0-9X]")) {
+		if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
-            return pid.replaceAll("(.{4})(.{4})(.{4})(.{4})", "$1-$2-$3-$4");
+			return pid.replaceAll("http://orcid.org/", "");
-        }
+		}
+		return pid;
+	}
 
-        // clean ORCID in the form http://orcid.org/0000-0001-8567-3543 to 0000-0001-8567-3543
+	public String getPid() {
-        if (pid.matches("http://orcid.org/[0-9]{4}-[0-9]{4}-[0-9]{4}-[0-9]{4}")) {
+		return pid;
-            return pid.replaceAll("http://orcid.org/", "");
+	}
-        }
-        return pid;
-    }
 
-    public String getPid() {
+	public PMIdentifier setPid(String pid) {
-        return pid;
+		this.pid = cleanPid(pid);
-    }
+		return this;
+	}
 
-    public PMIdentifier setPid(String pid) {
+	public String getType() {
-        this.pid = cleanPid(pid);
+		return type;
-        return this;
+	}
-    }
 
-    public String getType() {
+	public PMIdentifier setType(String type) {
-        return type;
+		this.type = type;
-    }
+		return this;
-
+	}
-    public PMIdentifier setType(String type) {
-        this.type = type;
-        return this;
-    }
 }

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/collection/crossref/Crossref2Oaf.scala

@@ -673,7 +673,6 @@ case object Crossref2Oaf {
     val doi = input.getString(0)
     val rorId = input.getString(1)
 
-
     val pubId = IdentifierFactory.idFromPid("50", "doi", DoiCleaningRule.clean(doi), true)
     val affId = GenerateRorActionSetJob.calculateOpenaireId(rorId)
 

dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PMParser2.scala

@@ -82,21 +82,22 @@ class PMParser2 {
         a.setLastName((author \ "LastName").text)
         a.setForeName((author \ "ForeName").text)
         val id = (author \ "Identifier").text
-        val idType =(author \ "Identifier" \ "@Source").text
+        val idType = (author \ "Identifier" \ "@Source").text
 
-        if(id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
+        if (id != null && id.nonEmpty && idType != null && idType.nonEmpty) {
           a.setIdentifier(new PMIdentifier(id, idType))
         }
 
-
         val affiliation = (author \ "AffiliationInfo" \ "Affiliation").text
-        val affiliationId  = (author \ "AffiliationInfo" \ "Identifier").text
+        val affiliationId = (author \ "AffiliationInfo" \ "Identifier").text
         val affiliationIdType = (author \ "AffiliationInfo" \ "Identifier" \ "@Source").text
 
-        if(affiliation != null && affiliation.nonEmpty) {
+        if (affiliation != null && affiliation.nonEmpty) {
           val aff = new PMAffiliation()
           aff.setName(affiliation)
-          if(affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty) {
+          if (
+            affiliationId != null && affiliationId.nonEmpty && affiliationIdType != null && affiliationIdType.nonEmpty
+          ) {
             aff.setIdentifier(new PMIdentifier(affiliationId, affiliationIdType))
           }
           a.setAffiliation(aff)

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

@@ -294,11 +294,23 @@ object PubMedToOaf {
       author.setName(a.getForeName)
       author.setSurname(a.getLastName)
       author.setFullname(a.getFullName)
-      if(a.getIdentifier != null) {
+      if (a.getIdentifier != null) {
-        author.setPid(List(OafMapperUtils.structuredProperty(a.getIdentifier.getPid,
+        author.setPid(
-          OafMapperUtils.qualifier(a.getIdentifier.getType,a.getIdentifier.getType,ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES), dataInfo)).asJava)
+          List(
+            OafMapperUtils.structuredProperty(
+              a.getIdentifier.getPid,
+              OafMapperUtils.qualifier(
+                a.getIdentifier.getType,
+                a.getIdentifier.getType,
+                ModelConstants.DNET_PID_TYPES,
+                ModelConstants.DNET_PID_TYPES
+              ),
+              dataInfo
+            )
+          ).asJava
+        )
       }
-      if (a.getAffiliation!= null)
+      if (a.getAffiliation != null)
         author.setRawAffiliationString(List(a.getAffiliation.getName).asJava)
       author.setRank(index + 1)
       author

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

@@ -63,7 +63,6 @@ class BioScholixTest extends AbstractVocabularyTest {
       "0000000333457333",
       "0000000335964515",
       "0000000302921949",
-
       "http://orcid.org/0000-0001-8567-3543",
       "http://orcid.org/0000-0001-7868-8528",
       "0000-0001-9189-1440",