WIP: graph cleaner implementation

dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java

@@ -0,0 +1,94 @@
+
+package eu.dnetlib.dhp.oa.graph.clean;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import eu.dnetlib.dhp.schema.oaf.Oaf;
+
+import java.lang.reflect.Field;
+import java.util.*;
+import java.util.function.Function;
+
+public class OafNavigator2 {
+
+	public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
+		navigate(oaf, mapping);
+		return oaf;
+	}
+
+	private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
+		if (Objects.isNull(o) || isPrimitive(o)) {
+			return;
+		} else {
+			try {
+				for (Field field : getAllFields(o.getClass())) {
+					System.out.println("VISITING " + field.getName() + " in " + o.getClass());
+					field.setAccessible(true);
+					Object value = field.get(o);
+
+					if (Objects.nonNull(value)) {
+						final Class<?> fieldType = field.getType();
+						if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
+							Object[] fs = (Object[]) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} if (Iterable.class.isAssignableFrom(fieldType)) {
+							Iterable fs = (Iterable) value;
+							for (Object fi : fs) {
+								navigate(fi, mapping);
+							}
+						} else {
+							final Function<Object, Object> cleaningFn = mapping.get(value.getClass());
+							if (Objects.nonNull(cleaningFn)) {
+								final Object newValue = cleaningFn.apply(value);
+								if (!Objects.equals(value, newValue)) {
+									System.out.println("PATCHING " + field.getName()+ " " + value.getClass());
+									System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
+									System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
+									field.set(o, newValue);
+								}
+							}
+						}
+					}
+				}
+
+			} catch (IllegalAccessException | IllegalArgumentException | JsonProcessingException e) {
+				throw new RuntimeException(e);
+			}
+		}
+	}
+
+	private static ObjectMapper getObjectMapper() {
+		final ObjectMapper mapper = new ObjectMapper();
+		return mapper;
+	}
+
+	private static boolean isPrimitive(Object o) {
+		return o.getClass().isPrimitive()
+			|| o instanceof Class
+			|| o instanceof Integer
+			|| o instanceof Double
+			|| o instanceof Float
+			|| o instanceof Long
+			|| o instanceof Boolean
+			|| o instanceof String
+			|| o instanceof Byte;
+	}
+
+	private static List<Field> getAllFields(Class<?> clazz) {
+		return getAllFields(new LinkedList<>(), clazz);
+	}
+
+	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;
+	}
+
+}