WIP: graph cleaner implementation
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parent
c4d9f1837f
commit
bed65a1be6
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@ -2,16 +2,13 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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import java.util.Map;
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import java.util.Objects;
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import java.util.function.Function;
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import java.util.function.Consumer;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.spark.api.java.function.MapFunction;
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import com.google.common.collect.Maps;
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import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
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import eu.dnetlib.dhp.schema.oaf.Field;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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@ -20,54 +17,47 @@ public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
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private VocabularyGroup vocabularies;
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private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap();
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private Map<Class, Consumer<Object>> mapping = Maps.newHashMap();
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public CleaningRule(VocabularyGroup vocabularies) {
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this.vocabularies = vocabularies;
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mapping.put(Qualifier.class, o -> patchQualifier(o));
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mapping.put(StructuredProperty.class, o -> patchSp(o));
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mapping.put(Field.class, o -> patchStringField(o));
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setMappings(vocabularies);
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}
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@Override
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public T call(T value) throws Exception {
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OafNavigator2.apply(value, mapping);
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OafNavigator.apply(value, mapping);
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return value;
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}
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private Object patchQualifier(Object o) {
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Qualifier q = (Qualifier) o;
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if (vocabularies.vocabularyExists(q.getSchemeid())) {
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return vocabularies.lookup(q.getSchemeid(), q.getClassid());
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}
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return o;
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}
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private Object patchSp(Object o) {
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StructuredProperty sp = (StructuredProperty) o;
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if (StringUtils.isBlank(sp.getValue())) {
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return null;
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}
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return o;
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}
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private Object patchStringField(Object o) {
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Field f = (Field) o;
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try {
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if (StringUtils.isBlank((String) f.getValue())) {
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return null;
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/**
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* Populates the mapping for the Oaf types subject to cleaning
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*
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* @param vocabularies
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*/
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private void setMappings(VocabularyGroup vocabularies) {
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mapping.put(Qualifier.class, o -> {
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Qualifier q = (Qualifier) o;
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if (vocabularies.vocabularyExists(q.getSchemeid())) {
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Qualifier newValue = vocabularies.lookup(q.getSchemeid(), q.getClassid());
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q.setClassid(newValue.getClassid());
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q.setClassname(newValue.getClassname());
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}
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} catch (ClassCastException e) {
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// ignored on purpose
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}
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return o;
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});
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mapping.put(StructuredProperty.class, o -> {
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StructuredProperty sp = (StructuredProperty) o;
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// TODO implement a policy
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/*
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* if (StringUtils.isBlank(sp.getValue())) { sp.setValue(null); sp.setQualifier(null); sp.setDataInfo(null);
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* }
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*/
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});
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}
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public VocabularyGroup getVocabularies() {
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return vocabularies;
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}
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}
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@ -1,132 +1,56 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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import java.beans.BeanInfo;
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import java.beans.IntrospectionException;
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import java.beans.Introspector;
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import java.beans.PropertyDescriptor;
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import java.lang.reflect.Field;
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import java.lang.reflect.InvocationTargetException;
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import java.util.*;
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import java.util.function.Function;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.common.collect.Lists;
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import java.util.function.Consumer;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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import scala.Tuple2;
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public class OafNavigator {
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public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
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reflect(oaf, mapping);
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public static <E extends Oaf> E apply(E oaf, Map<Class, Consumer<Object>> mapping) {
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try {
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navigate(oaf, mapping);
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} catch (IllegalAccessException e) {
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throw new RuntimeException(e);
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}
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return oaf;
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}
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public static void reflect(Object o, Map<Class, Function<Object, Object>> mapping) {
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visit(o, mapping);
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}
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public static void visit(final Object thingy, Map<Class, Function<Object, Object>> mapping) {
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try {
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final Class<?> clazz = thingy.getClass();
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if (!isPrimitive(thingy) && clazz.getPackage().equals(Oaf.class.getPackage())) {
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final BeanInfo beanInfo = Introspector.getBeanInfo(clazz);
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for (final PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) {
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try {
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final Object value = descriptor.getReadMethod().invoke(thingy);
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if (value != null && !isPrimitive(value)) {
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System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType());
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if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) {
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for (Object vi : (Iterable) value) {
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visit(vi, mapping);
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}
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} else {
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if (mapping.keySet().contains(value.getClass())) {
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final Object newValue = mapping.get(value.getClass()).apply(value);
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System.out
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.println(
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"PATCHING " + descriptor.getName() + " " + descriptor.getPropertyType());
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System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
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System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
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descriptor.getWriteMethod().invoke(newValue);
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}
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visit(value, mapping);
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}
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}
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} catch (final IllegalArgumentException e) {
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// handle this please
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} catch (final IllegalAccessException e) {
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// and this also
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} catch (final InvocationTargetException e) {
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// and this, too
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} catch (JsonProcessingException e) {
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e.printStackTrace();
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}
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}
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}
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} catch (final IntrospectionException e) {
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// do something sensible here
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}
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}
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private static ObjectMapper getObjectMapper() {
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final ObjectMapper mapper = new ObjectMapper();
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return mapper;
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}
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private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
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if (Objects.isNull(o) || isPrimitive(o)) {
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private static void navigate(Object o, Map<Class, Consumer<Object>> mapping) throws IllegalAccessException {
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if (isPrimitive(o)) {
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return;
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} else if (isIterable(o.getClass())) {
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for (final Object elem : (Iterable<?>) o) {
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navigate(elem, mapping);
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}
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} else if (hasMapping(o, mapping)) {
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mapping.get(o.getClass()).accept(o);
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} else {
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try {
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for (Field field : getAllFields(o.getClass())) {
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System.out.println(field.getName());
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field.setAccessible(true);
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Object value = field.get(o);
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if (Objects.nonNull(value)) {
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final Class<?> fieldType = field.getType();
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if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
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Object[] fs = (Object[]) value;
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for (Object fi : fs) {
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navigate(fi, mapping);
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}
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}
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if (Iterable.class.isAssignableFrom(fieldType)) {
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Iterable fs = (Iterable) value;
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for (Object fi : fs) {
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navigate(fi, mapping);
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}
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} else {
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if (mapping.keySet().contains(value.getClass())) {
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System.out.println("PATCHING " + field.getName());
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field.set(o, mapping.get(value.getClass()).apply(value));
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}
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}
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}
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for (final Field f : getAllFields(o.getClass())) {
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f.setAccessible(true);
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final Object val = f.get(o);
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if (!isPrimitive(val) && hasMapping(val, mapping)) {
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mapping.get(val.getClass()).accept(val);
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} else {
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navigate(f.get(o), mapping);
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}
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} catch (IllegalAccessException | IllegalArgumentException e) {
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throw new RuntimeException(e);
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}
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}
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}
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private static boolean hasMapping(Object o, Map<Class, Consumer<Object>> mapping) {
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return mapping.containsKey(o.getClass());
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}
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private static boolean isIterable(final Class<?> cl) {
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return Iterable.class.isAssignableFrom(cl);
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}
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private static boolean isPrimitive(Object o) {
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return o.getClass().isPrimitive()
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return Objects.isNull(o)
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|| o.getClass().isPrimitive()
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|| o instanceof Class
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|| o instanceof Integer
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|| o instanceof Double
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@ -1,96 +0,0 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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import java.lang.reflect.Field;
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import java.util.*;
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import java.util.function.Function;
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import com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.Oaf;
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public class OafNavigator2 {
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public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
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navigate(oaf, mapping);
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return oaf;
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}
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private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
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if (Objects.isNull(o) || isPrimitive(o)) {
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return;
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} else {
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try {
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for (Field field : getAllFields(o.getClass())) {
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//System.out.println("VISITING " + field.getName() + " in " + o.getClass());
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field.setAccessible(true);
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Object value = field.get(o);
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if (Objects.nonNull(value)) {
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final Class<?> fieldType = field.getType();
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if ((fieldType.isArray() && !fieldType.getComponentType().isPrimitive())) {
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Object[] fs = (Object[]) value;
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for (Object fi : fs) {
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navigate(fi, mapping);
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}
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}
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if (Iterable.class.isAssignableFrom(fieldType)) {
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Iterable fs = (Iterable) value;
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for (Object fi : fs) {
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navigate(fi, mapping);
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}
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} else {
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final Function<Object, Object> cleaningFn = mapping.get(value.getClass());
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if (Objects.nonNull(cleaningFn)) {
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final Object newValue = cleaningFn.apply(value);
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if (!Objects.equals(value, newValue)) {
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//System.out.println("PATCHING " + field.getName() + " " + value.getClass());
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//System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
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//System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
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field.set(o, newValue);
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}
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}
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}
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}
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}
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} catch (IllegalAccessException | IllegalArgumentException /*| JsonProcessingException*/ e) {
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throw new RuntimeException(e);
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}
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}
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}
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private static ObjectMapper getObjectMapper() {
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final ObjectMapper mapper = new ObjectMapper();
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return mapper;
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}
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private static boolean isPrimitive(Object o) {
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return o.getClass().isPrimitive()
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|| o instanceof Class
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|| o instanceof Integer
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|| o instanceof Double
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|| o instanceof Float
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|| o instanceof Long
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|| o instanceof Boolean
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|| o instanceof String
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|| o instanceof Byte;
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}
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private static List<Field> getAllFields(Class<?> clazz) {
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return getAllFields(new LinkedList<>(), clazz);
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}
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private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
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fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
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final Class<?> superclass = clazz.getSuperclass();
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if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
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getAllFields(fields, superclass);
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}
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return fields;
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}
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}
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