Merge pull request '[BulkTag]added tagging for the organization relevant for the community.' (#461) from tagOrganization into beta

Reviewed-on: #461

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()