[cleaning] country cleaning must use both PID and AlternateIdentifier fields

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/country/CleanCountrySparkJob.java

@@ -4,9 +4,12 @@ package eu.dnetlib.dhp.oa.graph.clean.country;
 import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
 
 import java.io.Serializable;
+import java.util.Collection;
 import java.util.List;
 import java.util.Optional;
+import java.util.function.Function;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import javax.swing.text.html.Option;
 
@@ -30,6 +33,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 import eu.dnetlib.dhp.application.ArgumentApplicationParser;
 import eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob;
 import eu.dnetlib.dhp.schema.oaf.Country;
+import eu.dnetlib.dhp.schema.oaf.Instance;
 import eu.dnetlib.dhp.schema.oaf.Result;
 import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
 import eu.dnetlib.dhp.schema.oaf.utils.PidType;
@@ -110,8 +114,8 @@ public class CleanCountrySparkJob implements Serializable {
 				return r;
 			}
 
-			if (r
-				.getPid()
+			List<StructuredProperty> ids = getPidsAndAltIds(r).collect(Collectors.toList());
+			if (ids
 				.stream()
 				.anyMatch(
 					p -> p
@@ -148,6 +152,42 @@ public class CleanCountrySparkJob implements Serializable {
 			.json(inputPath);
 	}
 
+	private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
+		final Stream<StructuredProperty> resultPids = Optional
+			.ofNullable(r.getPid())
+			.map(Collection::stream)
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instancePids = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getPid())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		final Stream<StructuredProperty> instanceAltIds = Optional
+			.ofNullable(r.getInstance())
+			.map(
+				instance -> instance
+					.stream()
+					.flatMap(
+						i -> Optional
+							.ofNullable(i.getAlternateIdentifier())
+							.map(Collection::stream)
+							.orElse(Stream.empty())))
+			.orElse(Stream.empty());
+
+		return Stream
+			.concat(
+				Stream.concat(resultPids, instancePids),
+				instanceAltIds);
+	}
+
 	private static boolean pidInParam(String value, String[] verifyParam) {
 		for (String s : verifyParam)
 			if (value.startsWith(s))