changed logic for save in s3 directly

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java

@@ -24,7 +24,7 @@ import eu.dnetlib.dhp.schema.oaf.*;
 
 public class DumpProducts implements Serializable {
 
-	public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, CommunityMap communityMap,
+	public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, String communityMapPath,
 		Class<? extends OafEntity> inputClazz,
 		Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> outputClazz,
 		boolean graph) {
@@ -36,19 +36,60 @@ public class DumpProducts implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Utils.removeOutputDir(spark, outputPath);
-				execDump(spark, inputPath, outputPath, communityMap, inputClazz, outputClazz, graph);// , dumpClazz);
+				execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, graph);// ,
-
+																											// dumpClazz);
 			});
 	}
 
+//	public void run(Boolean isSparkSessionManaged, String inputPath, String outputPath, CommunityMap communityMap,
+//		Class<? extends OafEntity> inputClazz,
+//		Class<? extends eu.dnetlib.dhp.schema.dump.oaf.Result> outputClazz,
+//		boolean graph) {
+//
+//		SparkConf conf = new SparkConf();
+//
+//		runWithSparkSession(
+//			conf,
+//			isSparkSessionManaged,
+//			spark -> {
+//				Utils.removeOutputDir(spark, outputPath);
+//				execDump(spark, inputPath, outputPath, communityMap, inputClazz, outputClazz, graph);// ,
+//				// dumpClazz);
+//			});
+//	}
+
+//	public static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> void execDump(
+//		SparkSession spark,
+//		String inputPath,
+//		String outputPath,
+//		CommunityMap communityMap,
+//		Class<I> inputClazz,
+//		Class<O> outputClazz,
+//		boolean graph) {
+//
+//		// CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
+//
+//		Utils
+//			.readPath(spark, inputPath, inputClazz)
+//			.map(value -> execMap(value, communityMap, graph), Encoders.bean(outputClazz))
+//			.filter(Objects::nonNull)
+//			.write()
+//			.mode(SaveMode.Overwrite)
+//			.option("compression", "gzip")
+//			.json(outputPath);
+//
+//	}
+
 	public static <I extends OafEntity, O extends eu.dnetlib.dhp.schema.dump.oaf.Result> void execDump(
 		SparkSession spark,
 		String inputPath,
 		String outputPath,
-		CommunityMap communityMap,
+		String communityMapPath,
 		Class<I> inputClazz,
 		Class<O> outputClazz,
-		boolean graph) throws ClassNotFoundException {
+		boolean graph) {
+
+		CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath);
 
 		Utils
 			.readPath(spark, inputPath, inputClazz)

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Utils.java

@@ -7,8 +7,10 @@ import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SparkSession;
 
 import com.fasterxml.jackson.databind.ObjectMapper;
+import com.google.gson.Gson;
 
 import eu.dnetlib.dhp.common.HdfsSupport;
+import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
 import eu.dnetlib.dhp.oa.graph.dump.graph.Constants;
 import eu.dnetlib.dhp.utils.DHPUtils;
 import eu.dnetlib.dhp.utils.ISLookupClientFactory;
@@ -40,4 +42,10 @@ public class Utils {
 				"%s|%s::%s", Constants.CONTEXT_ID, Constants.CONTEXT_NS_PREFIX,
 				DHPUtils.md5(id));
 	}
+
+	public static CommunityMap getCommunityMap(SparkSession spark, String communityMapPath) {
+
+		return new Gson().fromJson(spark.read().textFile(communityMapPath).collectAsList().get(0), CommunityMap.class);
+
+	}
 }

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/CreateContextEntities.java

@@ -100,7 +100,7 @@ public class CreateContextEntities implements Serializable {
 	protected <R extends ResearchInitiative> void writeEntity(final R r) {
 		try {
 			writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r));
-			//log.info("writing context : {}", new Gson().toJson(r));
+			// log.info("writing context : {}", new Gson().toJson(r));
 			writer.newLine();
 		} catch (final Exception e) {
 			throw new RuntimeException(e);

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/DumpGraphEntities.java

@@ -35,13 +35,19 @@ public class DumpGraphEntities implements Serializable {
 		String inputPath,
 		String outputPath,
 		Class<? extends OafEntity> inputClazz,
-		CommunityMap communityMap) {
+		String communityMapPath) {
+		// CommunityMap communityMap) {
 
 		SparkConf conf = new SparkConf();
+
 		switch (ModelSupport.idPrefixMap.get(inputClazz)) {
 			case "50":
 				DumpProducts d = new DumpProducts();
-				d.run(isSparkSessionManaged, inputPath, outputPath, communityMap, inputClazz, Result.class, true);
+				d
+					.run(
+						isSparkSessionManaged, inputPath, outputPath, communityMapPath, inputClazz, Result.class,
+						true);
+				// d.run(isSparkSessionManaged, inputPath, outputPath, communityMap, inputClazz, Result.class, true);
 				break;
 			case "40":
 				runWithSparkSession(

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Extractor.java

@@ -8,13 +8,17 @@ import java.util.*;
 
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.function.FlatMapFunction;
+import org.apache.spark.sql.Dataset;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.SaveMode;
 import org.apache.spark.sql.SparkSession;
 
+import com.google.gson.Gson;
+
 import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
 import eu.dnetlib.dhp.oa.graph.dump.Utils;
 import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
+import eu.dnetlib.dhp.oa.graph.dump.zenodo.Community;
 import eu.dnetlib.dhp.schema.common.ModelConstants;
 import eu.dnetlib.dhp.schema.common.ModelSupport;
 import eu.dnetlib.dhp.schema.dump.oaf.Provenance;
@@ -28,6 +32,24 @@ import eu.dnetlib.dhp.schema.oaf.Result;
 
 public class Extractor implements Serializable {
 
+//	public void run(Boolean isSparkSessionManaged,
+//		String inputPath,
+//		String outputPath,
+//		Class<? extends Result> inputClazz,
+//		String communityMapPath) {
+//
+//		SparkConf conf = new SparkConf();
+//
+//		runWithSparkSession(
+//			conf,
+//			isSparkSessionManaged,
+//			spark -> {
+//				Utils.removeOutputDir(spark, outputPath);
+//				extractRelationResult(
+//					spark, inputPath, outputPath, inputClazz, Utils.getCommunityMap(spark, communityMapPath));
+//			});
+//	}
+
 	public void run(Boolean isSparkSessionManaged,
 		String inputPath,
 		String outputPath,
@@ -41,7 +63,8 @@ public class Extractor implements Serializable {
 			isSparkSessionManaged,
 			spark -> {
 				Utils.removeOutputDir(spark, outputPath);
-				extractRelationResult(spark, inputPath, outputPath, inputClazz, communityMap);
+				extractRelationResult(
+					spark, inputPath, outputPath, inputClazz, communityMap);
 			});
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/Process.java

@@ -56,24 +56,33 @@ public class Process implements Serializable {
 					String nodeType = ModelSupport.idPrefixEntity.get(ds.substring(0, 2));
 
 					String contextId = Utils.getContextId(ci.getId());
-					relationList.add(Relation.newInstance(
+					relationList
-							Node.newInstance(contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
+						.add(
+							Relation
+								.newInstance(
+									Node
+										.newInstance(
+											contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
 									Node.newInstance(ds, nodeType),
 									RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
 									Provenance
 										.newInstance(
 											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.USER_CLAIM,
-											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.DEFAULT_TRUST)
+											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.DEFAULT_TRUST)));
-					));
 
-					relationList.add(Relation.newInstance(Node.newInstance(ds, nodeType),
+					relationList
-							Node.newInstance(contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
+						.add(
+							Relation
+								.newInstance(
+									Node.newInstance(ds, nodeType),
+									Node
+										.newInstance(
+											contextId, eu.dnetlib.dhp.schema.dump.oaf.graph.Constants.CONTEXT_ENTITY),
 									RelType.newInstance(ModelConstants.IS_RELATED_TO, ModelConstants.RELATIONSHIP),
 									Provenance
 										.newInstance(
 											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.USER_CLAIM,
-											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.DEFAULT_TRUST)
+											eu.dnetlib.dhp.oa.graph.dump.graph.Constants.DEFAULT_TRUST)));
-							));
 
 				});
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkDumpEntitiesJob.java

@@ -42,6 +42,8 @@ public class SparkDumpEntitiesJob implements Serializable {
 		final String resultClassName = parser.get("resultTableName");
 		log.info("resultTableName: {}", resultClassName);
 
+		final String communityMapPath = parser.get("communityMapPath");
+
 		final String isLookUpUrl = parser.get("isLookUpUrl");
 		log.info("isLookUpUrl: {}", isLookUpUrl);
 
@@ -52,7 +54,8 @@ public class SparkDumpEntitiesJob implements Serializable {
 		CommunityMap communityMap = queryInformationSystem.getCommunityMap();
 
 		DumpGraphEntities dg = new DumpGraphEntities();
-		dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
+		dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath);
+		// dg.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
 
 	}
 

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/graph/SparkExtractRelationFromEntities.java

@@ -42,6 +42,8 @@ public class SparkExtractRelationFromEntities implements Serializable {
 		final String resultClassName = parser.get("resultTableName");
 		log.info("resultTableName: {}", resultClassName);
 
+//		final String communityMapPath = parser.get("communityMapPath");
+
 		final String isLookUpUrl = parser.get("isLookUpUrl");
 		log.info("isLookUpUrl: {}", isLookUpUrl);
 
@@ -52,6 +54,7 @@ public class SparkExtractRelationFromEntities implements Serializable {
 		CommunityMap communityMap = queryInformationSystem.getCommunityMap();
 
 		Extractor extractor = new Extractor();
+		// extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMapPath);
 		extractor.run(isSparkSessionManaged, inputPath, outputPath, inputClazz, communityMap);
 
 	}