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WIP: graph cleaner implementation

This commit is contained in:
Claudio Atzori 2020-06-12 18:25:47 +02:00
parent c4d9f1837f
commit bed65a1be6
3 changed files with 58 additions and 240 deletions
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62
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java
View File

@ -2,16 +2,13 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.util.Map;
import java.util.Objects;
import java.util.function.Function;
import java.util.function.Consumer;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
@ -20,54 +17,47 @@ public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
private VocabularyGroup vocabularies;
private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap();
private Map<Class, Consumer<Object>> mapping = Maps.newHashMap();
public CleaningRule(VocabularyGroup vocabularies) {
this.vocabularies = vocabularies;
mapping.put(Qualifier.class, o -> patchQualifier(o));
mapping.put(StructuredProperty.class, o -> patchSp(o));
mapping.put(Field.class, o -> patchStringField(o));
setMappings(vocabularies);
}
@Override
public T call(T value) throws Exception {
OafNavigator2.apply(value, mapping);
OafNavigator.apply(value, mapping);
return value;
}
private Object patchQualifier(Object o) {
Qualifier q = (Qualifier) o;
if (vocabularies.vocabularyExists(q.getSchemeid())) {
return vocabularies.lookup(q.getSchemeid(), q.getClassid());
}
return o;
}
private Object patchSp(Object o) {
StructuredProperty sp = (StructuredProperty) o;
if (StringUtils.isBlank(sp.getValue())) {
return null;
}
return o;
}
private Object patchStringField(Object o) {
Field f = (Field) o;
try {
if (StringUtils.isBlank((String) f.getValue())) {
return null;
/**
* Populates the mapping for the Oaf types subject to cleaning
*
* @param vocabularies
*/
private void setMappings(VocabularyGroup vocabularies) {
mapping.put(Qualifier.class, o -> {
Qualifier q = (Qualifier) o;
if (vocabularies.vocabularyExists(q.getSchemeid())) {
Qualifier newValue = vocabularies.lookup(q.getSchemeid(), q.getClassid());
q.setClassid(newValue.getClassid());
q.setClassname(newValue.getClassname());
}
} catch (ClassCastException e) {
// ignored on purpose
}
return o;
});
mapping.put(StructuredProperty.class, o -> {
StructuredProperty sp = (StructuredProperty) o;
// TODO implement a policy
/*
* if (StringUtils.isBlank(sp.getValue())) { sp.setValue(null); sp.setQualifier(null); sp.setDataInfo(null);
* }
*/
});
}
public VocabularyGroup getVocabularies() {
return vocabularies;
}
}

140
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java
View File

@ -1,132 +1,56 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.beans.BeanInfo;
import java.beans.IntrospectionException;
import java.beans.Introspector;
import java.beans.PropertyDescriptor;
import java.lang.reflect.Field;
import java.lang.reflect.InvocationTargetException;
import java.util.*;
import java.util.function.Function;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import java.util.function.Consumer;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import scala.Tuple2;
public class OafNavigator {
public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
reflect(oaf, mapping);
public static <E extends Oaf> E apply(E oaf, Map<Class, Consumer<Object>> mapping) {
try {
navigate(oaf, mapping);
} catch (IllegalAccessException e) {
throw new RuntimeException(e);
}
return oaf;
}
public static void reflect(Object o, Map<Class, Function<Object, Object>> mapping) {
visit(o, mapping);
}
public static void visit(final Object thingy, Map<Class, Function<Object, Object>> mapping) {
try {
final Class<?> clazz = thingy.getClass();
if (!isPrimitive(thingy) && clazz.getPackage().equals(Oaf.class.getPackage())) {
final BeanInfo beanInfo = Introspector.getBeanInfo(clazz);
for (final PropertyDescriptor descriptor : beanInfo.getPropertyDescriptors()) {
try {
final Object value = descriptor.getReadMethod().invoke(thingy);
if (value != null && !isPrimitive(value)) {
System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType());
if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) {
for (Object vi : (Iterable) value) {
visit(vi, mapping);
}
} else {
if (mapping.keySet().contains(value.getClass())) {
final Object newValue = mapping.get(value.getClass()).apply(value);
System.out
.println(
"PATCHING " + descriptor.getName() + " " + descriptor.getPropertyType());
System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
descriptor.getWriteMethod().invoke(newValue);
}
visit(value, mapping);
}
}
} catch (final IllegalArgumentException e) {
// handle this please
} catch (final IllegalAccessException e) {
// and this also
} catch (final InvocationTargetException e) {
// and this, too
} catch (JsonProcessingException e) {
e.printStackTrace();
}
}
}
} catch (final IntrospectionException e) {
// do something sensible here
}
}
private static ObjectMapper getObjectMapper() {
final ObjectMapper mapper = new ObjectMapper();
return mapper;
}
private static void navigate(Object o, Map<Class, Function<Object, Object>> mapping) {
if (Objects.isNull(o) || isPrimitive(o)) {
private static void navigate(Object o, Map<Class, Consumer<Object>> mapping) throws IllegalAccessException {
if (isPrimitive(o)) {
return;
} else if (isIterable(o.getClass())) {
for (final Object elem : (Iterable<?>) o) {
navigate(elem, mapping);
}
} else if (hasMapping(o, mapping)) {
mapping.get(o.getClass()).accept(o);
} else {
try {
for (Field field : getAllFields(o.getClass())) {
System.out.println(field.getName());
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 {
if (mapping.keySet().contains(value.getClass())) {
System.out.println("PATCHING " + field.getName());
field.set(o, mapping.get(value.getClass()).apply(value));
}
}
}
for (final Field f : getAllFields(o.getClass())) {
f.setAccessible(true);
final Object val = f.get(o);
if (!isPrimitive(val) && hasMapping(val, mapping)) {
mapping.get(val.getClass()).accept(val);
} else {
navigate(f.get(o), mapping);
}
} catch (IllegalAccessException | IllegalArgumentException e) {
throw new RuntimeException(e);
}
}
}
private static boolean hasMapping(Object o, Map<Class, Consumer<Object>> mapping) {
return mapping.containsKey(o.getClass());
}
private static boolean isIterable(final Class<?> cl) {
return Iterable.class.isAssignableFrom(cl);
}
private static boolean isPrimitive(Object o) {
return o.getClass().isPrimitive()
return Objects.isNull(o)
|| o.getClass().isPrimitive()
|| o instanceof Class
|| o instanceof Integer
|| o instanceof Double

96
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java
View File

@ -1,96 +0,0 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.lang.reflect.Field;
import java.util.*;
import java.util.function.Function;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.schema.oaf.Oaf;
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;
}
}