Indentation fixes

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

@@ -3,7 +3,6 @@ package eu.dnetlib.dhp.actionmanager;
 
 import java.util.Optional;
 
-import eu.dnetlib.dhp.common.HdfsSupport;
 import org.apache.spark.api.java.function.MapFunction;
 import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
@@ -12,6 +11,7 @@ import org.apache.spark.sql.SparkSession;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.common.HdfsSupport;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.Subject;
@@ -94,6 +94,7 @@ public class Constants {
 		return s;
 
 	}
+
 	public static void removeOutputDir(SparkSession spark, String path) {
 		HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
 	}

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

@@ -8,12 +8,6 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.actionmanager.Constants;
-import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
-import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
-import eu.dnetlib.dhp.schema.action.AtomicAction;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import org.apache.commons.io.IOUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.hadoop.mapred.SequenceFileOutputFormat;
@@ -22,17 +16,23 @@ import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
 import org.apache.spark.api.java.function.FlatMapFunction;
 import org.apache.spark.api.java.function.MapFunction;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import org.apache.spark.sql.Dataset;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.actionmanager.Constants;
+import eu.dnetlib.dhp.actionmanager.bipaffiliations.model.*;
+import eu.dnetlib.dhp.actionmanager.ror.GenerateRorActionSetJob;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
+import eu.dnetlib.dhp.schema.action.AtomicAction;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.*;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
@@ -79,7 +79,8 @@ public class PrepareAffiliationRelations implements Serializable {
 			});
 	}
 
-    private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath, String outputPath) {
+	private static <I extends Result> void prepareAffiliationRelations(SparkSession spark, String inputPath,
+		String outputPath) {
 
 		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
 
@@ -89,15 +90,23 @@ public class PrepareAffiliationRelations implements Serializable {
 			.map(item -> OBJECT_MAPPER.readValue(item, AffiliationRelationDeserializer.class));
 
 		// convert affiliation to an internal representation
-        Dataset<AffiliationRelationModel> affiliationRelations =
+		Dataset<AffiliationRelationModel> affiliationRelations = spark
-            spark.createDataset(
+			.createDataset(
-                affiliationRelationsDeserializeRDD.flatMap(entry ->
+				affiliationRelationsDeserializeRDD
-                    entry.getMatchings().stream().flatMap(matching ->
+					.flatMap(
-                    matching.getRorId().stream().map( rorId -> new AffiliationRelationModel(
+						entry -> entry
+							.getMatchings()
+							.stream()
+							.flatMap(
+								matching -> matching
+									.getRorId()
+									.stream()
+									.map(
+										rorId -> new AffiliationRelationModel(
 											entry.getDoi(),
 											rorId,
-                        matching.getConfidence()
+											matching.getConfidence())))
-                    ))).collect(Collectors.toList())
+							.collect(Collectors.toList())
 							.iterator())
 					.rdd(),
 				Encoders.bean(AffiliationRelationModel.class));
@@ -107,19 +116,22 @@ public class PrepareAffiliationRelations implements Serializable {
 			.flatMap((FlatMapFunction<AffiliationRelationModel, Relation>) affRel -> {
 
 				// DOI to OpenAIRE id
-                final String paperId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
+				final String paperId = ID_PREFIX
+					+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", affRel.getDoi()));
 
 				// ROR id to OpenAIRE id
 				final String affId = GenerateRorActionSetJob.calculateOpenaireId(affRel.getRorId());
 
-                Qualifier qualifier = OafMapperUtils.qualifier(
+				Qualifier qualifier = OafMapperUtils
+					.qualifier(
 						BIP_AFFILIATIONS_CLASSID,
 						BIP_AFFILIATIONS_CLASSNAME,
 						ModelConstants.DNET_PROVENANCE_ACTIONS,
 						ModelConstants.DNET_PROVENANCE_ACTIONS);
 
 				// format data info; setting `confidence` into relation's `trust`
-                DataInfo dataInfo = OafMapperUtils.dataInfo(
+				DataInfo dataInfo = OafMapperUtils
+					.dataInfo(
 						false,
 						BIP_INFERENCE_PROVENANCE,
 						true,
@@ -141,8 +153,10 @@ public class PrepareAffiliationRelations implements Serializable {
 	}
 
 	private static List<Relation> getAffiliationRelationPair(String paperId, String affId, DataInfo dataInfo) {
-        return Arrays.asList(
+		return Arrays
-            OafMapperUtils.getRelation(
+			.asList(
+				OafMapperUtils
+					.getRelation(
 						paperId,
 						affId,
 						ModelConstants.RESULT_ORGANIZATION,
@@ -151,7 +165,8 @@ public class PrepareAffiliationRelations implements Serializable {
 						null,
 						dataInfo,
 						null),
-            OafMapperUtils.getRelation(
+				OafMapperUtils
+					.getRelation(
 						affId,
 						paperId,
 						ModelConstants.RESULT_ORGANIZATION,
@@ -159,7 +174,6 @@ public class PrepareAffiliationRelations implements Serializable {
 						ModelConstants.IS_AUTHOR_INSTITUTION_OF,
 						null,
 						dataInfo,
-                null)
+						null));
-        );
 	}
 }

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

@@ -1,11 +1,13 @@
-package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
 
-import com.fasterxml.jackson.annotation.JsonProperty;
+package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
-import lombok.Data;
 
 import java.io.Serializable;
 import java.util.List;
 
+import com.fasterxml.jackson.annotation.JsonProperty;
+
+import lombok.Data;
+
 @Data
 public class AffiliationRelationDeserializer implements Serializable {
 	@JsonProperty("DOI")
@@ -23,4 +25,3 @@ public class AffiliationRelationDeserializer implements Serializable {
 	}
 
 }
-

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

@@ -1,11 +1,12 @@
+
 package eu.dnetlib.dhp.actionmanager.bipaffiliations.model;
 
+import java.io.Serializable;
+
 import lombok.AllArgsConstructor;
 import lombok.Data;
 import lombok.NoArgsConstructor;
 
-import java.io.Serializable;
-
 @Data
 @AllArgsConstructor
 public class AffiliationRelationModel implements Serializable {

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/job.properties

@@ -28,15 +28,8 @@ oozie.use.system.libpath=true
 spark2ExtraListeners=com.cloudera.spark.lineage.NavigatorAppListener
 spark2SqlQueryExecutionListeners=com.cloudera.spark.lineage.NavigatorQueryListener
 
-# I think this should be the oozie workflow directory
-# oozieWorkflowPath=/user/ilias.kanellos/workflow_example/
-
-
-# The workflow application path
-wfAppPath=${oozieTopWfApplicationPath}
-
 # The following is needed as a property of a workflow
 oozie.wf.application.path=${oozieTopWfApplicationPath}
 
-inputPath=/user/schatz/affiliations/data-v3.json
+inputPath=/user/schatz/affiliations/data-v3.1.json
-outputPath=/tmp/crossref-affiliations-output-v3
+outputPath=/tmp/crossref-affiliations-output-v3.1

dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/bipaffiliations/oozie_app/workflow.xml

@@ -1,4 +1,4 @@
-<workflow-app name="BipFinderScore" xmlns="uri:oozie:workflow:0.5">
+<workflow-app name="BipAffiliations" xmlns="uri:oozie:workflow:0.5">
     <parameters>
 
         <property>
@@ -84,7 +84,7 @@
             <master>yarn</master>
             <mode>cluster</mode>
             <name>Produces the atomic action with the inferred by BIP! affiliation relations from Crossref</name>
-            <class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations/class>
+            <class>eu.dnetlib.dhp.actionmanager.bipaffiliations.PrepareAffiliationRelations</class>
             <jar>dhp-aggregation-${projectVersion}.jar</jar>
             <spark-opts>
                 --executor-memory=${sparkExecutorMemory}

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

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.dhp.actionmanager.bipaffiliations;
 
 import static org.junit.jupiter.api.Assertions.*;
@@ -6,10 +7,6 @@ import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 
-import eu.dnetlib.dhp.schema.common.ModelConstants;
-import eu.dnetlib.dhp.schema.oaf.Relation;
-import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
-import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 import org.apache.commons.io.FileUtils;
 import org.apache.hadoop.io.Text;
 import org.apache.spark.SparkConf;
@@ -29,6 +26,10 @@ import org.slf4j.LoggerFactory;
 import com.fasterxml.jackson.databind.ObjectMapper;
 
 import eu.dnetlib.dhp.schema.action.AtomicAction;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
+import eu.dnetlib.dhp.schema.oaf.Relation;
+import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
+import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
 
 public class PrepareAffiliationRelationsTest {
 
@@ -105,31 +106,40 @@ public class PrepareAffiliationRelationsTest {
 		Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
 		dataset.createOrReplaceTempView("result");
 
-        Dataset<Row> execVerification = spark.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
+		Dataset<Row> execVerification = spark
+			.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
 
 		// verify that we have equal number of bi-directional relations
-        Assertions.assertEquals(8, execVerification
+		Assertions
+			.assertEquals(
+				8, execVerification
 					.filter(
-                    "relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION +"'")
+						"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
 					.collectAsList()
 					.size());
 
-        Assertions.assertEquals(8, execVerification
+		Assertions
+			.assertEquals(
+				8, execVerification
 					.filter(
-                    "relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF +"'")
+						"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
 					.collectAsList()
 					.size());
 
 		// check confidence value of a specific relation
 		String sourceDOI = "10.1105/tpc.8.3.343";
 
-        final String sourceOpenaireId = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
+		final String sourceOpenaireId = ID_PREFIX
+			+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
 
-        Assertions.assertEquals("0.7071067812", execVerification
+		Assertions
+			.assertEquals(
+				"0.7071067812", execVerification
 					.filter(
-                    "source='" + sourceOpenaireId +"'")
+						"source='" + sourceOpenaireId + "'")
-            .collectAsList().get(0).getString(4));
+					.collectAsList()
+					.get(0)
+					.getString(4));
 
 	}
 }
-