[AffiliationFromPublisher]refactoring after compilation

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelations.java

@@ -89,64 +89,66 @@ public class PrepareAffiliationRelations implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Constants.removeOutputDir(spark, outputPath);
-				createActionSet(spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath, publisherInputPath, outputPath);
+				createActionSet(
+					spark, crossrefInputPath, pubmedInputPath, openapcInputPath, dataciteInputPath, webcrawlInputPath,
+					publisherInputPath, outputPath);
 			});
 	}
 
-	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath, String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath, String outputPath) {
+	private static void createActionSet(SparkSession spark, String crossrefInputPath, String pubmedInputPath,
+		String openapcInputPath, String dataciteInputPath, String webcrawlInputPath, String publisherlInputPath,
+		String outputPath) {
 		List<KeyValue> collectedFromCrossref = OafMapperUtils
 			.listKeyValues(ModelConstants.CROSSREF_ID, "Crossref");
 		JavaPairRDD<Text, Text> crossrefRelations = prepareAffiliationRelations(
-				spark, crossrefInputPath, collectedFromCrossref);
+			spark, crossrefInputPath, collectedFromCrossref);
 
 		List<KeyValue> collectedFromPubmed = OafMapperUtils
 			.listKeyValues(ModelConstants.PUBMED_CENTRAL_ID, "Pubmed");
 		JavaPairRDD<Text, Text> pubmedRelations = prepareAffiliationRelations(
-				spark, pubmedInputPath, collectedFromPubmed);
+			spark, pubmedInputPath, collectedFromPubmed);
 
 		List<KeyValue> collectedFromOpenAPC = OafMapperUtils
 			.listKeyValues(ModelConstants.OPEN_APC_ID, "OpenAPC");
 		JavaPairRDD<Text, Text> openAPCRelations = prepareAffiliationRelations(
-				spark, openapcInputPath, collectedFromOpenAPC);
+			spark, openapcInputPath, collectedFromOpenAPC);
 
 		List<KeyValue> collectedFromDatacite = OafMapperUtils
 			.listKeyValues(ModelConstants.DATACITE_ID, "Datacite");
 		JavaPairRDD<Text, Text> dataciteRelations = prepareAffiliationRelations(
-				spark, dataciteInputPath, collectedFromDatacite);
+			spark, dataciteInputPath, collectedFromDatacite);
 
 		List<KeyValue> collectedFromWebCrawl = OafMapperUtils
 			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 		JavaPairRDD<Text, Text> webCrawlRelations = prepareAffiliationRelations(
-				spark, webcrawlInputPath, collectedFromWebCrawl);
+			spark, webcrawlInputPath, collectedFromWebCrawl);
 
 		List<KeyValue> collectedfromPublisher = OafMapperUtils
-				.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
+			.listKeyValues(OPENAIRE_DATASOURCE_ID, OPENAIRE_DATASOURCE_NAME);
 		JavaPairRDD<Text, Text> publisherRelations = prepareAffiliationRelationFromPublisher(
-				spark, publisherlInputPath, collectedfromPublisher);
+			spark, publisherlInputPath, collectedfromPublisher);
 
 		crossrefRelations
 			.union(pubmedRelations)
 			.union(openAPCRelations)
 			.union(dataciteRelations)
 			.union(webCrawlRelations)
-				.union(publisherRelations)
+			.union(publisherRelations)
 			.saveAsHadoopFile(
-					outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
+				outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, BZip2Codec.class);
 	}
 
-	private static JavaPairRDD<Text,Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
+	private static JavaPairRDD<Text, Text> prepareAffiliationRelationFromPublisher(SparkSession spark, String inputPath,
-																				  List<KeyValue> collectedfrom){
+		List<KeyValue> collectedfrom) {
-
 
 		Dataset<Row> df = spark
-				.read()
+			.read()
-				.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
+			.schema("`DOI` STRING, `Organizations` ARRAY<STRUCT<`RORid`:STRING,`Confidence`:DOUBLE>>")
-				.json(inputPath)
+			.json(inputPath)
-				.where("DOI is not null");
+			.where("DOI is not null");
 
 		return getTextTextJavaPairRDD(collectedfrom, df.selectExpr("DOI", "Organizations as Matchings"));
 
-
 	}
 
 	private static <I extends Result> JavaPairRDD<Text, Text> prepareAffiliationRelations(SparkSession spark,
@@ -174,41 +176,41 @@ public class PrepareAffiliationRelations implements Serializable {
 
 		// prepare action sets for affiliation relations
 		return df
-				.toJavaRDD()
+			.toJavaRDD()
-				.flatMap((FlatMapFunction<Row, Relation>) row -> {
+			.flatMap((FlatMapFunction<Row, Relation>) row -> {
 
-					// DOI to OpenAIRE id
+				// DOI to OpenAIRE id
-					final String paperId = ID_PREFIX
+				final String paperId = ID_PREFIX
-							+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
+					+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", row.getAs("doi")));
 
-					// ROR id to OpenAIRE id
+				// ROR id to OpenAIRE id
-					final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
+				final String affId = GenerateRorActionSetJob.calculateOpenaireId(row.getAs("rorid"));
 
-					Qualifier qualifier = OafMapperUtils
+				Qualifier qualifier = OafMapperUtils
-							.qualifier(
+					.qualifier(
-									BIP_AFFILIATIONS_CLASSID,
+						BIP_AFFILIATIONS_CLASSID,
-									BIP_AFFILIATIONS_CLASSNAME,
+						BIP_AFFILIATIONS_CLASSNAME,
-									ModelConstants.DNET_PROVENANCE_ACTIONS,
+						ModelConstants.DNET_PROVENANCE_ACTIONS,
-									ModelConstants.DNET_PROVENANCE_ACTIONS);
+						ModelConstants.DNET_PROVENANCE_ACTIONS);
 
-					// format data info; setting `confidence` into relation's `trust`
+				// format data info; setting `confidence` into relation's `trust`
-					DataInfo dataInfo = OafMapperUtils
+				DataInfo dataInfo = OafMapperUtils
-							.dataInfo(
+					.dataInfo(
-									false,
+						false,
-									BIP_INFERENCE_PROVENANCE,
+						BIP_INFERENCE_PROVENANCE,
-									true,
+						true,
-									false,
+						false,
-									qualifier,
+						qualifier,
-									Double.toString(row.getAs("confidence")));
+						Double.toString(row.getAs("confidence")));
 
-					// return bi-directional relations
+				// return bi-directional relations
-					return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
+				return getAffiliationRelationPair(paperId, affId, collectedfrom, dataInfo).iterator();
 
-				})
+			})
-				.map(p -> new AtomicAction(Relation.class, p))
+			.map(p -> new AtomicAction(Relation.class, p))
-				.mapToPair(
+			.mapToPair(
-						aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
+				aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
-								new Text(OBJECT_MAPPER.writeValueAsString(aa))));
+					new Text(OBJECT_MAPPER.writeValueAsString(aa))));
 	}
 
 	private static List<Relation> getAffiliationRelationPair(String paperId, String affId, List<KeyValue> collectedfrom,

dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/bipaffiliations/PrepareAffiliationRelationsTest.java

@@ -79,8 +79,8 @@ public class PrepareAffiliationRelationsTest {
 			.getPath();
 
 		String publisherAffiliationRelationPath = getClass()
-				.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
+			.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/publishers")
-				.getPath();
+			.getPath();
 
 		String outputPath = workingDir.toString() + "/actionSet";
 
@@ -93,7 +93,7 @@ public class PrepareAffiliationRelationsTest {
 					"-openapcInputPath", crossrefAffiliationRelationPath,
 					"-dataciteInputPath", crossrefAffiliationRelationPath,
 					"-webCrawlInputPath", crossrefAffiliationRelationPath,
-						"-publisherInputPath", publisherAffiliationRelationPath,
+					"-publisherInputPath", publisherAffiliationRelationPath,
 					"-outputPath", outputPath
 				});
 

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingAuthorOrcidTest.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.broker.oa.matchers.simple;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
@@ -16,7 +17,8 @@ class EnrichMissingAuthorOrcidTest {
 	final EnrichMissingAuthorOrcid matcher = new EnrichMissingAuthorOrcid();
 
 	@BeforeEach
-	void setUp() throws Exception {}
+	void setUp() throws Exception {
+	}
 
 	@Test
 	void testFindDifferences_1() {

dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtilsTest.java

@@ -23,7 +23,8 @@ import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 public class ConversionUtilsTest {
 
 	@BeforeEach
-	public void setUp() throws Exception {}
+	public void setUp() throws Exception {
+	}
 
 	@Test
 	public void testAllResultPids() {

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java

@@ -20,7 +20,6 @@ import javax.xml.transform.*;
 import javax.xml.transform.dom.DOMSource;
 import javax.xml.transform.stream.StreamResult;
 
-import eu.dnetlib.dhp.oa.provision.model.*;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.ImmutablePair;
 import org.apache.commons.lang3.tuple.Pair;
@@ -42,6 +41,7 @@ import com.google.common.collect.Sets;
 import com.mycila.xmltool.XMLDoc;
 import com.mycila.xmltool.XMLTag;
 
+import eu.dnetlib.dhp.oa.provision.model.*;
 import eu.dnetlib.dhp.schema.common.*;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.Result;