WIP: graph cleaner implementation

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

@@ -0,0 +1,88 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import eu.dnetlib.dhp.oa.graph.raw.common.OafMapperUtils;
+import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+import eu.dnetlib.dhp.schema.oaf.Qualifier;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.spark.api.java.function.MapFunction;
+
+import java.lang.reflect.Field;
+import java.util.Arrays;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Objects;
+
+public class NormalizeEmptyFields<T extends Oaf> implements MapFunction<T, T> {
+
+	private VocabularyGroup vocabularies;
+
+	public NormalizeEmptyFields(VocabularyGroup vocabularies) {
+		this.vocabularies = vocabularies;
+	}
+
+	@Override
+	public T call(T value) throws Exception {
+
+		doNormalize(value);
+
+		return value;
+	}
+
+	private void doNormalize(Object o) {
+		if (Objects.isNull(o)) {
+			return;
+		}
+
+		if (o instanceof Iterable) {
+			for (Object oi : (Iterable) o) {
+				doNormalize(oi);
+			}
+		} else {
+
+			Class clazz = o.getClass();
+
+			if (clazz.isPrimitive()
+				|| o instanceof Integer
+				|| o instanceof Double
+				|| o instanceof Float
+				|| o instanceof Long
+				|| o instanceof Boolean
+				|| o instanceof String) {
+				return;
+			} else {
+				try {
+					for (Field field : getAllFields(new LinkedList<>(), clazz)) {
+						field.setAccessible(true);
+						Object value = field.get(o);
+						if (value instanceof Qualifier && Objects.isNull(value)) {
+							field.set(o, OafMapperUtils.unknown("", ""));
+						} else if (value instanceof Field && Objects.isNull(value)) {
+
+						} else {
+							doNormalize(value);
+						}
+					}
+				} catch (IllegalAccessException | IllegalArgumentException e) {
+					throw new RuntimeException(e);
+				}
+			}
+		}
+	}
+
+	private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
+		fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
+
+		final Class<?> superclass = clazz.getSuperclass();
+		if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
+			getAllFields(fields, superclass);
+		}
+
+		return fields;
+	}
+
+	public VocabularyGroup getVocabularies() {
+		return vocabularies;
+	}
+}