dhp-pace-core/src/main/java/eu/dnetlib/pace/tree/CountryMatch.java

@@ -1,3 +1,4 @@
+
 package eu.dnetlib.pace.tree;
 
 import java.util.Map;
@@ -11,37 +12,37 @@ import eu.dnetlib.pace.tree.support.ComparatorClass;
 @ComparatorClass("countryMatch")
 public class CountryMatch extends AbstractStringComparator {
 
-    public CountryMatch(Map<String, String> params) {
+	public CountryMatch(Map<String, String> params) {
-        super(params, new com.wcohen.ss.JaroWinkler());
+		super(params, new com.wcohen.ss.JaroWinkler());
-    }
+	}
 
-    public CountryMatch(final double weight) {
+	public CountryMatch(final double weight) {
-        super(weight, new com.wcohen.ss.JaroWinkler());
+		super(weight, new com.wcohen.ss.JaroWinkler());
-    }
+	}
 
-    protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
+	protected CountryMatch(final double weight, final AbstractStringDistance ssalgo) {
-        super(weight, ssalgo);
+		super(weight, ssalgo);
-    }
+	}
 
-    @Override
+	@Override
-    public double distance(final String a, final String b, final Config conf) {
+	public double distance(final String a, final String b, final Config conf) {
-        if (a.isEmpty() || b.isEmpty()) {
+		if (a.isEmpty() || b.isEmpty()) {
-            return -1.0; // return -1 if a field is missing
+			return -1.0; // return -1 if a field is missing
-        }
+		}
-        if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
+		if (a.equalsIgnoreCase("unknown") || b.equalsIgnoreCase("unknown")) {
-            return -1.0; // return -1 if a country is UNKNOWN
+			return -1.0; // return -1 if a country is UNKNOWN
-        }
+		}
 
-        return a.equals(b) ? 1.0 : 0;
+		return a.equals(b) ? 1.0 : 0;
-    }
+	}
 
-    @Override
+	@Override
-    public double getWeight() {
+	public double getWeight() {
-        return super.weight;
+		return super.weight;
-    }
+	}
 
-    @Override
+	@Override
-    protected double normalize(final double d) {
+	protected double normalize(final double d) {
-        return d;
+		return d;
-    }
+	}
 }

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkBulkTagJob.java

@@ -33,10 +33,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.bulktag.community.*;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
-import eu.dnetlib.dhp.schema.oaf.Context;
+import eu.dnetlib.dhp.schema.oaf.*;
-import eu.dnetlib.dhp.schema.oaf.Datasource;
-import eu.dnetlib.dhp.schema.oaf.Project;
-import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
 import scala.Tuple2;
 
@@ -114,27 +111,35 @@ public class SparkBulkTagJob {
 				extendCommunityConfigurationForEOSC(spark, inputPath, cc);
 				execBulkTag(
 					spark, inputPath, outputPath, protoMap, cc);
+				execEntityTag(
+					spark, inputPath + "organization", outputPath + "organization",
+					Utils.getCommunityOrganization(baseURL), Organization.class, TaggingConstants.CLASS_ID_ORGANIZATION,
+					TaggingConstants.CLASS_NAME_BULKTAG_ORGANIZATION);
+				execEntityTag(
+					spark, inputPath + "project", outputPath + "project", Utils.getCommunityProjects(baseURL),
+					Project.class, TaggingConstants.CLASS_ID_PROJECT, TaggingConstants.CLASS_NAME_BULKTAG_PROJECT);
 				execDatasourceTag(spark, inputPath, outputPath, Utils.getDatasourceCommunities(baseURL));
-				execProjectTag(spark, inputPath, outputPath, Utils.getCommunityProjects(baseURL));
+
 			});
 	}
 
-	private static void execProjectTag(SparkSession spark, String inputPath, String outputPath,
+	private static <E extends OafEntity> void execEntityTag(SparkSession spark, String inputPath, String outputPath,
-		CommunityEntityMap communityProjects) {
+		CommunityEntityMap communityEntity, Class<E> entityClass,
-		Dataset<Project> projects = readPath(spark, inputPath + "project", Project.class);
+		String classID, String calssName) {
+		Dataset<E> entity = readPath(spark, inputPath, entityClass);
 		Dataset<EntityCommunities> pc = spark
 			.createDataset(
-				communityProjects
+				communityEntity
 					.keySet()
 					.stream()
-					.map(k -> EntityCommunities.newInstance(k, communityProjects.get(k)))
+					.map(k -> EntityCommunities.newInstance(k, communityEntity.get(k)))
 					.collect(Collectors.toList()),
 				Encoders.bean(EntityCommunities.class));
 
-		projects
+		entity
-			.joinWith(pc, projects.col("id").equalTo(pc.col("entityId")), "left")
+			.joinWith(pc, entity.col("id").equalTo(pc.col("entityId")), "left")
-			.map((MapFunction<Tuple2<Project, EntityCommunities>, Project>) t2 -> {
+			.map((MapFunction<Tuple2<E, EntityCommunities>, E>) t2 -> {
-				Project ds = t2._1();
+				E ds = t2._1();
 				if (t2._2() != null) {
 					List<String> context = Optional
 						.ofNullable(ds.getContext())
@@ -156,8 +161,8 @@ public class SparkBulkTagJob {
 													false, TaggingConstants.BULKTAG_DATA_INFO_TYPE, true, false,
 													OafMapperUtils
 														.qualifier(
-															TaggingConstants.CLASS_ID_DATASOURCE,
+															classID,
-															TaggingConstants.CLASS_NAME_BULKTAG_DATASOURCE,
+															calssName,
 															ModelConstants.DNET_PROVENANCE_ACTIONS,
 															ModelConstants.DNET_PROVENANCE_ACTIONS),
 													"1")));
@@ -166,17 +171,17 @@ public class SparkBulkTagJob {
 					});
 				}
 				return ds;
-			}, Encoders.bean(Project.class))
+			}, Encoders.bean(entityClass))
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(outputPath + "project");
+			.json(outputPath);
 
-		readPath(spark, outputPath + "project", Project.class)
+		readPath(spark, outputPath, entityClass)
 			.write()
 			.mode(SaveMode.Overwrite)
 			.option("compression", "gzip")
-			.json(inputPath + "project");
+			.json(inputPath);
 	}
 
 	private static void execDatasourceTag(SparkSession spark, String inputPath, String outputPath,

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/TaggingConstants.java

@@ -13,6 +13,9 @@ public class TaggingConstants {
 	public static final String CLASS_ID_CZENODO = "community:zenodocommunity";
 	public static final String CLASS_ID_ADVANCED_CONSTRAINT = "community:advconstraint";
 
+	public static final String CLASS_ID_PROJECT = "community:project";
+	public static final String CLASS_ID_ORGANIZATION = "community:organization";
+
 	public static final String ZENODO_COMMUNITY_INDICATOR = "zenodo.org/communities/";
 
 	public static final String CLASS_NAME_BULKTAG_SUBJECT = "Bulktagging for Community - Subject";
@@ -20,5 +23,8 @@ public class TaggingConstants {
 	public static final String CLASS_NAME_BULKTAG_ZENODO = "Bulktagging for Community - Zenodo";
 	public static final String CLASS_NAME_BULKTAG_ADVANCED_CONSTRAINT = "Bulktagging for Community - Advanced Constraints";
 
+	public static final String CLASS_NAME_BULKTAG_PROJECT = "Bulktagging for Community - Project";
+	public static final String CLASS_NAME_BULKTAG_ORGANIZATION = "Bulktagging for Community - Organization";
+
 	public static final String TAGGING_TRUST = "0.8";
 }

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java

@@ -465,6 +465,138 @@ public class BulkTagJobTest {
 
 	}
 
+	@Test
+	void organizationTag() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
+			.getPath();
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+		SparkBulkTagJob
+			.main(
+				new String[] {
+
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", sourcePath,
+					"-taggingConf", taggingConf,
+
+					"-outputPath", workingDir.toString() + "/",
+					"-baseURL", "https://services.openaire.eu/openaire/community/",
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-nameNode", "local"
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Organization> tmp = sc
+			.textFile(workingDir.toString() + "/organization")
+			.map(item -> OBJECT_MAPPER.readValue(item, Organization.class));
+
+		Assertions.assertEquals(4, tmp.count());
+		org.apache.spark.sql.Dataset<Organization> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(Organization.class));
+
+		verificationDataset.createOrReplaceTempView("organization");
+
+		String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+			+ "from organization "
+			+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
+
+		org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
+
+		idExplodeCommunity.show(false);
+
+		Assertions.assertEquals(3, idExplodeCommunity.count());
+		Assertions
+			.assertEquals(
+				3, idExplodeCommunity.filter("provenance = 'community:organization'").count());
+		Assertions
+			.assertEquals(
+				3,
+				idExplodeCommunity
+					.filter("name = 'Bulktagging for Community - Organization'")
+					.count());
+
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'netherlands'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'beopen'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
+
+	}
+
+	@Test
+	void projectTag() throws Exception {
+		final String sourcePath = getClass()
+			.getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource/")
+			.getPath();
+		LocalFileSystem fs = FileSystem.getLocal(new Configuration());
+		fs
+			.copyFromLocalFile(
+				false, new org.apache.hadoop.fs.Path(getClass()
+					.getResource("/eu/dnetlib/dhp/bulktag/pathMap/")
+					.getPath()),
+				new org.apache.hadoop.fs.Path(workingDir.toString() + "/data/bulktagging/protoMap"));
+		SparkBulkTagJob
+			.main(
+				new String[] {
+
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath", sourcePath,
+					"-taggingConf", taggingConf,
+
+					"-outputPath", workingDir.toString() + "/",
+					"-baseURL", "https://services.openaire.eu/openaire/community/",
+
+					"-pathMap", workingDir.toString() + "/data/bulktagging/protoMap/pathMap",
+					"-nameNode", "local"
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Project> tmp = sc
+			.textFile(workingDir.toString() + "/project")
+			.map(item -> OBJECT_MAPPER.readValue(item, Project.class));
+
+		Assertions.assertEquals(4, tmp.count());
+		org.apache.spark.sql.Dataset<Project> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(Project.class));
+
+		verificationDataset.createOrReplaceTempView("project");
+
+		String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
+			+ "from project "
+			+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
+
+		org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
+
+		idExplodeCommunity.show(false);
+
+		Assertions.assertEquals(4, idExplodeCommunity.count());
+		Assertions
+			.assertEquals(
+				4, idExplodeCommunity.filter("provenance = 'community:project'").count());
+		Assertions
+			.assertEquals(
+				4,
+				idExplodeCommunity
+					.filter("name = 'Bulktagging for Community - Project'")
+					.count());
+
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'enermaps'").count());
+		Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'clarin'").count());
+		Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'dh-ch'").count());
+
+	}
+
 	@Test
 	void bulktagByZenodoCommunityTest() throws Exception {
 		final String sourcePath = getClass()

dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/model/ProvisionModelSupport.java

@@ -5,7 +5,6 @@ import java.io.StringReader;
 import java.util.*;
 import java.util.stream.Collectors;
 
-import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import org.apache.commons.lang3.StringUtils;
 import org.dom4j.Document;
 import org.dom4j.DocumentException;
@@ -31,6 +30,7 @@ import eu.dnetlib.dhp.schema.solr.Context;
 import eu.dnetlib.dhp.schema.solr.Country;
 import eu.dnetlib.dhp.schema.solr.Datasource;
 import eu.dnetlib.dhp.schema.solr.EoscIfGuidelines;
+import eu.dnetlib.dhp.schema.solr.ExternalReference;
 import eu.dnetlib.dhp.schema.solr.Instance;
 import eu.dnetlib.dhp.schema.solr.Journal;
 import eu.dnetlib.dhp.schema.solr.Measure;
@@ -562,10 +562,16 @@ public class ProvisionModelSupport {
 			.orElse(null);
 	}
 
-	private static List<ExternalReference> mapExternalReference(List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
+	private static List<ExternalReference> mapExternalReference(
-		return Optional.ofNullable(externalReference)
+		List<eu.dnetlib.dhp.schema.oaf.ExternalReference> externalReference) {
-				.map(ext -> ext.stream()
+		return Optional
-						.map(e -> ExternalReference.newInstance(
+			.ofNullable(externalReference)
+			.map(
+				ext -> ext
+					.stream()
+					.map(
+						e -> ExternalReference
+							.newInstance(
 								e.getSitename(),
 								e.getLabel(),
 								e.getAlternateLabel(),
@@ -573,8 +579,8 @@ public class ProvisionModelSupport {
 								mapCodeLabel(e.getQualifier()),
 								e.getRefidentifier(),
 								e.getQuery()))
-						.collect(Collectors.toList()))
+					.collect(Collectors.toList()))
-				.orElse(Lists.newArrayList());
+			.orElse(Lists.newArrayList());
 	}
 
 	private static List<Context> asContext(List<eu.dnetlib.dhp.schema.oaf.Context> ctxList,

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java

@@ -1,12 +1,13 @@
 
 package eu.dnetlib.dhp.oa.provision;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
+
 import java.io.File;
 import java.io.IOException;
 import java.net.URI;
 import java.nio.file.Path;
 
-import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.apache.solr.client.solrj.SolrQuery;
@@ -32,14 +33,13 @@ import org.junit.jupiter.api.io.TempDir;
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.junit.jupiter.MockitoExtension;
-
-import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
-import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import static org.junit.jupiter.api.Assertions.assertEquals;
+import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument;
+import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
+import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
 
 @ExtendWith(MockitoExtension.class)
 public class SolrConfigExploreTest {
@@ -91,7 +91,7 @@ public class SolrConfigExploreTest {
 		SparkConf conf = new SparkConf();
 		conf.setAppName(XmlIndexingJobTest.class.getSimpleName());
 		conf.registerKryoClasses(new Class[] {
-				SerializableSolrInputDocument.class
+			SerializableSolrInputDocument.class
 		});
 
 		conf.setMaster("local[1]");
@@ -101,10 +101,10 @@ public class SolrConfigExploreTest {
 		conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString());
 
 		spark = SparkSession
-				.builder()
+			.builder()
-				.appName(SolrConfigExploreTest.class.getSimpleName())
+			.appName(SolrConfigExploreTest.class.getSimpleName())
-				.config(conf)
+			.config(conf)
-				.getOrCreate();
+			.getOrCreate();
 
 		// random unassigned HTTP port
 		final int jettyPort = 0;
@@ -134,35 +134,35 @@ public class SolrConfigExploreTest {
 
 		log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString());
 		log
-				.info(
+			.info(
-						CollectionAdminRequest.ClusterStatus
+				CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
+					.getClusterStatus()
-								.process(miniCluster.getSolrClient())
+					.process(miniCluster.getSolrClient())
-								.toString());
+					.toString());
 
 		NamedList<Object> res = createCollection(
-				miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), SHADOW_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		// miniCluster.getSolrClient().setDefaultCollection(SHADOW_COLLECTION);
 
 		res = createCollection(
-				miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
+			miniCluster.getSolrClient(), PUBLIC_COLLECTION, 4, 2, 20, CONFIG_NAME);
 		res.forEach(o -> log.info(o.toString()));
 
 		admin = new SolrAdminApplication(miniCluster.getZkClient().getZkServerAddress());
 		CollectionAdminResponse rsp = (CollectionAdminResponse) admin
-				.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
+			.createAlias(ProvisionConstants.PUBLIC_ALIAS_NAME, PUBLIC_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 		rsp = (CollectionAdminResponse) admin.createAlias(ProvisionConstants.SHADOW_ALIAS_NAME, SHADOW_COLLECTION);
 		assertEquals(0, rsp.getStatus());
 
 		log
-				.info(
+			.info(
-						CollectionAdminRequest.ClusterStatus
+				CollectionAdminRequest.ClusterStatus
-								.getClusterStatus()
+					.getClusterStatus()
-								.process(miniCluster.getSolrClient())
+					.process(miniCluster.getSolrClient())
-								.toString());
+					.toString());
 
 	}
 
@@ -180,7 +180,8 @@ public class SolrConfigExploreTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",
@@ -200,7 +201,8 @@ public class SolrConfigExploreTest {
 //            System.out.println(rsp.getExplainMap());
 
 			for (SolrDocument doc : rsp.getResults()) {
-				log.info(
+				log
+					.info(
 						doc.get("score") + "\t" +
 							doc.get("__indexrecordidentifier") + "\t" +
 							doc.get("resultidentifier") + "\t" +
@@ -216,7 +218,7 @@ public class SolrConfigExploreTest {
 	}
 
 	protected static NamedList<Object> createCollection(CloudSolrClient client, String name, int numShards,
-														int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
+		int replicationFactor, int maxShardsPerNode, String configName) throws Exception {
 		ModifiableSolrParams modParams = new ModifiableSolrParams();
 		modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name());
 		modParams.set("name", name);

dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java

@@ -85,7 +85,8 @@ public class SolrConfigTest extends SolrTest {
 
 		new XmlIndexingJob(spark, inputPath, SHADOW_FORMAT, ProvisionConstants.SHADOW_ALIAS_NAME, batchSize)
 			.run(isLookupClient);
-		Assertions.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
+		Assertions
+			.assertEquals(0, miniCluster.getSolrClient().commit(ProvisionConstants.SHADOW_ALIAS_NAME).getStatus());
 
 		String[] queryStrings = {
 			"cancer",