code formatting

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java

@@ -7,7 +7,6 @@ import java.io.IOException;
 import java.util.Optional;
 import java.util.concurrent.atomic.AtomicInteger;
 
-import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin;
 import org.apache.hadoop.fs.FileSystem;
 import org.apache.hadoop.fs.Path;
 import org.apache.hadoop.io.IntWritable;
@@ -29,6 +28,7 @@ import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.osf.OsfPreprintsCollectorPlugin;
 import eu.dnetlib.dhp.collection.plugin.rest.RestCollectorPlugin;
+import eu.dnetlib.dhp.collection.plugin.zenodo.CollectZenodoDumpCollectorPlugin;
 import eu.dnetlib.dhp.common.aggregation.AggregatorReport;
 import eu.dnetlib.dhp.common.collection.CollectorException;
 import eu.dnetlib.dhp.common.collection.HttpClientParams;

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

@@ -503,7 +503,6 @@ case object Crossref2Oaf {
       )
     }
 
-
     if (doi.startsWith("10.3410") || doi.startsWith("10.12703"))
       instance.setHostedby(
         OafMapperUtils.keyValue(OafMapperUtils.createOpenaireId(10, "openaire____::H1Connect", true), "H1Connect")
@@ -556,14 +555,18 @@ case object Crossref2Oaf {
       result
   }
 
-
-
   def generateIdentifier(oaf: Result, doi: String): String = {
     val id = DHPUtils.md5(doi.toLowerCase)
     s"50|doiboost____|$id"
   }
 
-  private def generateAuthor(given: String, family: String, orcid: String, index: Int, affiliation: Option[List[mappingAffiliation]]): Author = {
+  private def generateAuthor(
+    given: String,
+    family: String,
+    orcid: String,
+    index: Int,
+    affiliation: Option[List[mappingAffiliation]]
+  ): Author = {
     val a = new Author
     a.setName(given)
     a.setSurname(family)
@@ -700,7 +703,6 @@ case object Crossref2Oaf {
     if (objectType == null)
       return resultList
 
-
     // If the item has a relations is-review-of, then we force it to a peer-review
     val is_review = json \ "relation" \ "is-review-of" \ "id"
     var force_to_review = false
@@ -713,7 +715,6 @@ case object Crossref2Oaf {
     if (typology == null)
       return List()
 
-
     val result = generateItemFromType(typology._2)
     if (result == null)
       return List()

dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/collection/crossref/CrossrefMappingTest.scala

@@ -28,17 +28,21 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
     val input =
       IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/issn_pub.json"), "utf-8")
 
-    Crossref2Oaf.convert(input, vocabularies, TransformationType.All).foreach(record => {
+    Crossref2Oaf
-      Assertions.assertNotNull(record)
+      .convert(input, vocabularies, TransformationType.All)
-    })
+      .foreach(record => {
+        Assertions.assertNotNull(record)
+      })
 
   }
 
-
   @Test
   def mappingAffiliation(): Unit = {
     val input =
-      IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"), "utf-8")
+      IOUtils.toString(
+        getClass.getResourceAsStream("/eu/dnetlib/dhp/collection/crossref/affiliationTest.json"),
+        "utf-8"
+      )
     val data = Crossref2Oaf.convert(input, vocabularies, TransformationType.OnlyResult)
     data.foreach(record => {
       Assertions.assertNotNull(record)
@@ -46,10 +50,10 @@ class CrossrefMappingTest extends AbstractVocabularyTest {
       val publication = record.asInstanceOf[Publication]
       publication.getAuthor.asScala.foreach(author => {
         Assertions.assertNotNull(author.getRawAffiliationString)
-        Assertions.assertTrue(author.getRawAffiliationString.size()>0)
+        Assertions.assertTrue(author.getRawAffiliationString.size() > 0)
 
-        })
       })
+    })
     println(mapper.writerWithDefaultPrettyPrinter().writeValueAsString(data.head))
   }
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep1.java

@@ -1,16 +1,16 @@
 
 package eu.dnetlib.dhp.resulttocommunityfromsemrel;
 
+import static java.lang.String.join;
+
 import static eu.dnetlib.dhp.PropagationConstant.*;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
-import static java.lang.String.join;
 
 import java.io.IOException;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
-import eu.dnetlib.dhp.schema.common.ModelConstants;
 import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.sql.*;
@@ -22,6 +22,7 @@ import com.google.gson.Gson;
 import eu.dnetlib.dhp.api.Utils;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
+import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.oaf.Relation;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
@@ -37,8 +38,7 @@ public class PrepareResultCommunitySetStep1 {
 	 * relation
 	 */
 	// TODO
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE =
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE = "select target resultId, community_context  "
-			"select target resultId, community_context  "
 		+ "from (select id, collect_set(co.id) community_context "
 		+ "       from  result "
 		+ "       lateral view explode (context) c as co "
@@ -60,26 +60,26 @@ public class PrepareResultCommunitySetStep1 {
 		+ "where length(co) > 0 "
 		+ "group by resultId";
 
-	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO =
+	private static final String RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO = "select target as resultId, community_context "
-			"select target as resultId, community_context " +
+		+
-			"from resultWithContext rwc " +
+		"from resultWithContext rwc " +
-			"join relatedToRelations r " +
+		"join relatedToRelations r " +
-			"join patents p  " +
+		"join patents p  " +
-			"on rwc.id = r.source and r.target = p.id";
+		"on rwc.id = r.source and r.target = p.id";
 
 	private static final String RESULT_WITH_CONTEXT = "select id, collect_set(co.id) community_context        \n" +
-			"    from  result        " +
+		"    from  result        " +
-			"    lateral view explode (context) c as co     " +
+		"    lateral view explode (context) c as co     " +
-			"    where  lower(co.id) IN %s" +
+		"    where  lower(co.id) IN %s" +
-			"    group by id";
+		"    group by id";
 
 	private static final String RESULT_PATENT = "select id " +
-			"    from result " +
+		"    from result " +
-			"    where array_contains(instance.instancetype.classname, 'Patent')";
+		"    where array_contains(instance.instancetype.classname, 'Patent')";
 
 	private static final String IS_RELATED_TO_RELATIONS = "select source, target " +
-			"    from relation " +
+		"    from relation " +
-			"    where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
+		"    where lower(relClass) = 'isrelatedto' and datainfo.deletedbyinference = false";
 
 	public static void main(String[] args) throws Exception {
 		String jsonConfiguration = IOUtils
@@ -107,17 +107,25 @@ public class PrepareResultCommunitySetStep1 {
 		SparkConf conf = new SparkConf();
 		conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
 
-		final String allowedsemrel ="(" + join(",",
+		final String allowedsemrel = "(" + join(
-				Arrays.asList(parser.get("allowedsemrels").split(";")).stream().map(value -> "'" + value.toLowerCase() + "'")
+			",",
-						.toArray(String[]::new)) + ")";
+			Arrays
+				.asList(parser.get("allowedsemrels").split(";"))
+				.stream()
+				.map(value -> "'" + value.toLowerCase() + "'")
+				.toArray(String[]::new))
+			+ ")";
 		log.info("allowedSemRel: {}", allowedsemrel);
 
 		final String baseURL = parser.get("baseURL");
 		log.info("baseURL: {}", baseURL);
 
-		final String communityIdList = "(" + join(",", getCommunityList(baseURL).stream()
+		final String communityIdList = "(" + join(
+			",", getCommunityList(baseURL)
+				.stream()
 				.map(value -> "'" + value.toLowerCase() + "'")
-				.toArray(String[]::new)) + ")";
+				.toArray(String[]::new))
+			+ ")";
 
 		final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
 		log.info("resultType: {}", resultType);
@@ -161,18 +169,17 @@ public class PrepareResultCommunitySetStep1 {
 		relation.createOrReplaceTempView("relation");
 
 		Dataset<R> result = readPath(spark, inputResultPath, resultClazz)
-				.where("datainfo.deletedbyinference != true AND datainfo.invisible != true");
+			.where("datainfo.deletedbyinference != true AND datainfo.invisible != true");
 		result.createOrReplaceTempView("result");
 
 		final String outputResultPath = outputPath + "/" + resultType;
 		log.info("writing output results to: {}", outputResultPath);
 
-
 		String resultContextQuery = String
 			.format(
 				RESULT_CONTEXT_QUERY_TEMPLATE,
-					"AND  lower(co.id) IN " + communityIdList,
+				"AND  lower(co.id) IN " + communityIdList,
-					"AND lower(relClass) IN " + allowedsemrel);
+				"AND lower(relClass) IN " + allowedsemrel);
 		Dataset<Row> result_context = spark.sql(resultContextQuery);
 
 		Dataset<Row> rwc = spark.sql(String.format(RESULT_WITH_CONTEXT, communityIdList));
@@ -183,18 +190,17 @@ public class PrepareResultCommunitySetStep1 {
 		patents.createOrReplaceTempView("patents");
 		relatedToRelations.createOrReplaceTempView("relatedTorelations");
 
-
+		result_context = result_context.unionAll(spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
-		result_context = result_context.unionAll( spark.sql(RESULT_CONTEXT_QUERY_TEMPLATE_IS_RELATED_TO));
 
 		result_context.createOrReplaceTempView("result_context");
 
 		spark
-				.sql(RESULT_COMMUNITY_LIST_QUERY)
+			.sql(RESULT_COMMUNITY_LIST_QUERY)
-				.as(Encoders.bean(ResultCommunityList.class))
+			.as(Encoders.bean(ResultCommunityList.class))
-				.write()
+			.write()
-				.option("compression", "gzip")
+			.option("compression", "gzip")
-				.mode(SaveMode.Append)
+			.mode(SaveMode.Append)
-				.json(outputResultPath);
+			.json(outputResultPath);
 
 	}
 

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/PrepareResultCommunitySetStep2.java

@@ -77,7 +77,7 @@ public class PrepareResultCommunitySetStep2 {
 					if (b == null) {
 						return a;
 					}
-                    Set<String> community_set = new HashSet<>(a.getCommunityList());
+					Set<String> community_set = new HashSet<>(a.getCommunityList());
 					community_set.addAll(b.getCommunityList());
 					a.setCommunityList(new ArrayList<>(community_set));
 					return a;

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/resulttocommunityfromsemrel/ResultToCommunityJobTest.java

@@ -10,7 +10,6 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
 import org.apache.commons.io.FileUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
@@ -27,6 +26,7 @@ import org.slf4j.LoggerFactory;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 
+import eu.dnetlib.dhp.resulttocommunityfromorganization.ResultCommunityList;
 import eu.dnetlib.dhp.schema.oaf.Dataset;
 import scala.collection.Seq;
 
@@ -279,53 +279,55 @@ public class ResultToCommunityJobTest {
 	@Test
 	public void prepareStep1Test() throws Exception {
 		/*
-
+		 * final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";")) .map(value ->
-
+		 * "'" + value.toLowerCase() + "'") .toArray(String[]::new)); log.info("allowedSemRel: {}", new
-		final String allowedsemrel = join(",", Arrays.stream(parser.get("allowedsemrels").split(";"))
+		 * Gson().toJson(allowedsemrel)); final String baseURL = parser.get("baseURL"); log.info("baseURL: {}",
-				.map(value -> "'" + value.toLowerCase() + "'")
+		 * baseURL);
-				.toArray(String[]::new));
-
-		log.info("allowedSemRel: {}", new Gson().toJson(allowedsemrel));
-
-		final String baseURL = parser.get("baseURL");
-		log.info("baseURL: {}", baseURL);
 		 */
 		PrepareResultCommunitySetStep1
-				.main(
+			.main(
-						new String[] {
+				new String[] {
-								"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
-								"-sourcePath", getClass()
+					"-sourcePath", getClass()
-								.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
+						.getResource("/eu/dnetlib/dhp/resulttocommunityfromsemrel/graph")
-								.getPath(),
+						.getPath(),
-								"-hive_metastore_uris", "",
+					"-hive_metastore_uris", "",
-								"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
+					"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
-								"-outputPath", workingDir.toString() + "/preparedInfo",
+					"-outputPath", workingDir.toString() + "/preparedInfo",
-								"-allowedsemrels","issupplementto;issupplementedby",
+					"-allowedsemrels", "issupplementto;issupplementedby",
-								"-baseURL","https://dev-openaire.d4science.org/openaire/community/"
+					"-baseURL", "https://dev-openaire.d4science.org/openaire/community/"
-						});
+				});
 
-
+		org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark
-		org.apache.spark.sql.Dataset<ResultCommunityList> resultCommunityList = spark.read().schema(Encoders.bean(ResultCommunityList.class).schema())
+			.read()
-				.json(workingDir.toString() + "/preparedInfo/publication")
+			.schema(Encoders.bean(ResultCommunityList.class).schema())
-				.as(Encoders.bean(ResultCommunityList.class));
+			.json(workingDir.toString() + "/preparedInfo/publication")
+			.as(Encoders.bean(ResultCommunityList.class));
 
 		Assertions.assertEquals(2, resultCommunityList.count());
-		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
+		Assertions
-		Assertions.assertEquals(1,resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
+			.assertEquals(
+				1,
+				resultCommunityList.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'").count());
+		Assertions
+			.assertEquals(
+				1,
+				resultCommunityList.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'").count());
 
 		ArrayList<String> communities = resultCommunityList
-				.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
+			.filter("resultId = '50|dedup_wf_001::06e51d2bf295531b2d2e7a1b55500783'")
-				.first().getCommunityList();
+			.first()
+			.getCommunityList();
 		Assertions.assertEquals(2, communities.size());
 		Assertions.assertTrue(communities.stream().anyMatch(cid -> "beopen".equals(cid)));
 		Assertions.assertTrue(communities.stream().anyMatch(cid -> "dh-ch".equals(cid)));
 
 		communities = resultCommunityList
-				.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
+			.filter("resultId = '50|pending_org_::82f63b2d21ae88596b9d8991780e9888'")
-				.first().getCommunityList();
+			.first()
+			.getCommunityList();
 		Assertions.assertEquals(1, communities.size());
 		Assertions.assertEquals("dh-ch", communities.get(0));
 	}
 
-
 }