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WIP: graph cleaner implementation

This commit is contained in:
Claudio Atzori 2020-06-12 10:45:18 +02:00
parent ba8a024af9
commit 97b1c4057c
5 changed files with 217 additions and 54 deletions
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90
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java
View File

@ -1,86 +1,70 @@
package eu.dnetlib.dhp.oa.graph.clean;
import java.lang.reflect.Field;
import java.util.Arrays;
import java.util.LinkedList;
import java.util.List;
import java.util.Objects;
import com.google.common.collect.Maps;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import eu.dnetlib.dhp.oa.graph.raw.common.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import java.util.Map;
import java.util.Objects;
import java.util.function.Function;
public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
private VocabularyGroup vocabularies;
private Map<Class, Function<Object, 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));
}
@Override
public T call(T value) throws Exception {
doClean(value);
OafNavigator.apply(value, mapping);
return value;
}
private void doClean(Object o) {
if (Objects.isNull(o)) {
return;
}
if (o instanceof Iterable) {
for (Object oi : (Iterable) o) {
doClean(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) {
Qualifier q = (Qualifier) value;
if (vocabularies.vocabularyExists(q.getSchemeid())) {
field.set(o, vocabularies.lookup(q.getSchemeid(), q.getClassid()));
}
} else {
doClean(value);
}
}
} catch (IllegalAccessException | IllegalArgumentException e) {
throw new RuntimeException(e);
}
}
private Object patchQualifier(Object o) {
Qualifier q = (Qualifier) o;
if (vocabularies.vocabularyExists(q.getSchemeid())) {
return vocabularies.lookup(q.getSchemeid(), q.getClassid());
}
return o;
}
private static List<Field> getAllFields(List<Field> fields, Class<?> clazz) {
fields.addAll(Arrays.asList(clazz.getDeclaredFields()));
private Object patchSp(Object o) {
StructuredProperty sp = (StructuredProperty) o;
if (StringUtils.isBlank(sp.getValue())) {
return null;
}
return o;
}
final Class<?> superclass = clazz.getSuperclass();
if (Objects.nonNull(superclass) && superclass.getPackage().equals(Oaf.class.getPackage())) {
getAllFields(fields, superclass);
private Object patchStringField(Object o) {
Field f = (Field) o;
try {
if (StringUtils.isBlank((String) f.getValue())) {
return null;
}
} catch (ClassCastException e) {
// ignored on purpose
}
return fields;
return o;
}
public VocabularyGroup getVocabularies() {

147
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java
View File

@ -1,4 +1,151 @@
package eu.dnetlib.dhp.oa.graph.clean;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.collect.Lists;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import scala.Tuple2;
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;
public class OafNavigator {
public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
reflect(oaf, mapping);
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)) {
return;
} 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));
}
}
}
}
} catch (IllegalAccessException | IllegalArgumentException e) {
throw new RuntimeException(e);
}
}
}
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;
}
}

5
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/VocabularyGroup.java
View File

@ -105,7 +105,10 @@ public class VocabularyGroup implements Serializable {
}
public Qualifier getTermAsQualifier(final String vocId, final String id) {
return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
if (vocabularyExists(vocId)) {
return vocs.get(vocId.toLowerCase()).getTermAsQualifier(id);
}
return OafMapperUtils.qualifier(id, id, "", "");
}
public Qualifier getSynonymAsQualifier(final String vocId, final String syn) {

7
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java
View File

@ -7,6 +7,7 @@ import static org.mockito.Mockito.lenient;
import java.io.IOException;
import java.util.HashSet;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.stream.Collectors;
import java.util.stream.Stream;
@ -15,6 +16,7 @@ import org.apache.commons.io.IOUtils;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.api.extension.ExtendWith;
import org.junit.platform.commons.util.StringUtils;
import org.mockito.Mock;
import org.mockito.junit.jupiter.MockitoExtension;
@ -82,6 +84,11 @@ public class CleaningRuleTest {
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_out));
assertTrue(
p_out
.getPid()
.stream()
.allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
}
private Stream<Qualifier> getAuthorPidTypes(Publication pub) {

22
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -380,6 +380,28 @@
"schemename": "dnet:pid_types"
},
"value": "10.1007/s109090161569x"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "sysimport:crosswalk:datasetarchive",
"classname": "sysimport:crosswalk:datasetarchive",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "doi",
"classname": "doi",
"schemeid": "dnet:pid_types",
"schemename": "dnet:pid_types"
},
"value": ""
}
],
"relevantdate": [