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code formatting

This commit is contained in:
Claudio Atzori 2020-06-12 12:03:25 +02:00
parent 4bcad1c9c3
commit 463489f59f
9 changed files with 79 additions and 76 deletions
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29
dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java
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@ -17,12 +17,11 @@ import com.google.common.collect.Lists;
import com.google.common.hash.Hashing; import com.google.common.hash.Hashing;
/** /**
* PacePerson tries to derive information from the fullname string of an author. * PacePerson tries to derive information from the fullname string of an author. Such informations are Names, Surnames
* Such informations are Names, Surnames an Fullname split into terms. It provides also an additional field for * an Fullname split into terms. It provides also an additional field for the original data. The calculation of the
* the original data. * names and the surnames is not always possible. When it is impossible to assert which are the names and the surnames,
* The calculation of the names and the surnames is not always possible. When it is impossible to assert which are the * the lists are empty.
* names and the surnames, the lists are empty. */
* */
public class PacePerson { public class PacePerson {
private static final String UTF8 = "UTF-8"; private static final String UTF8 = "UTF-8";
@ -38,14 +37,14 @@ public class PacePerson {
* *
* @param s the string to capitalize * @param s the string to capitalize
* @return the input string with capital letter * @return the input string with capital letter
* */ */
public static final String capitalize(final String s) { public static final String capitalize(final String s) {
return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); return WordUtils.capitalize(s.toLowerCase(), ' ', '-');
} }
/** /**
* Adds a dot to a string with length equals to 1 * Adds a dot to a string with length equals to 1
* */ */
public static final String dotAbbreviations(final String s) { public static final String dotAbbreviations(final String s) {
return s.length() == 1 ? s + "." : s; return s.length() == 1 ? s + "." : s;
} }
@ -67,7 +66,7 @@ public class PacePerson {
* *
* @param s the input string (fullname of the author) * @param s the input string (fullname of the author)
* @param aggressive set the string normalization type * @param aggressive set the string normalization type
* */ */
public PacePerson(String s, final boolean aggressive) { public PacePerson(String s, final boolean aggressive) {
original = s; original = s;
s = Normalizer.normalize(s, Normalizer.Form.NFD); s = Normalizer.normalize(s, Normalizer.Form.NFD);
@ -86,7 +85,7 @@ public class PacePerson {
// s = s.replaceAll("[\\W&&[^,-]]", ""); // s = s.replaceAll("[\\W&&[^,-]]", "");
} }
//if the string contains a comma, it can derive surname and name by splitting on it // if the string contains a comma, it can derive surname and name by splitting on it
if (s.contains(",")) { if (s.contains(",")) {
final String[] arr = s.split(","); final String[] arr = s.split(",");
if (arr.length == 1) { if (arr.length == 1) {
@ -97,23 +96,23 @@ public class PacePerson {
fullname.addAll(surname); fullname.addAll(surname);
fullname.addAll(name); fullname.addAll(name);
} }
} else { //otherwise, it should rely on CAPS terms and short terms } else { // otherwise, it should rely on CAPS terms and short terms
fullname = splitTerms(s); fullname = splitTerms(s);
int lastInitialPosition = fullname.size(); int lastInitialPosition = fullname.size();
boolean hasSurnameInUpperCase = false; boolean hasSurnameInUpperCase = false;
//computes lastInitialPosition and hasSurnameInUpperCase // computes lastInitialPosition and hasSurnameInUpperCase
for (int i = 0; i < fullname.size(); i++) { for (int i = 0; i < fullname.size(); i++) {
final String term = fullname.get(i); final String term = fullname.get(i);
if (term.length() == 1) { if (term.length() == 1) {
lastInitialPosition = i; //first word in the name longer than 1 (to avoid name with dots) lastInitialPosition = i; // first word in the name longer than 1 (to avoid name with dots)
} else if (term.equals(term.toUpperCase())) { } else if (term.equals(term.toUpperCase())) {
hasSurnameInUpperCase = true; //if one of the words is CAPS hasSurnameInUpperCase = true; // if one of the words is CAPS
} }
} }
//manages particular cases of fullnames // manages particular cases of fullnames
if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini if (lastInitialPosition < fullname.size() - 1) { // Case: Michele G. Artini
name = fullname.subList(0, lastInitialPosition + 1); name = fullname.subList(0, lastInitialPosition + 1);
surname = fullname.subList(lastInitialPosition + 1, fullname.size()); surname = fullname.subList(lastInitialPosition + 1, fullname.size());

11
dhp-common/src/test/java/eu/dnetlib/dhp/common/PacePersonTest.java
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@ -1,22 +1,23 @@
package eu.dnetlib.dhp.common; package eu.dnetlib.dhp.common;
import org.junit.jupiter.api.Test;
import static org.junit.jupiter.api.Assertions.*; import static org.junit.jupiter.api.Assertions.*;
import org.junit.jupiter.api.Test;
public class PacePersonTest { public class PacePersonTest {
@Test @Test
public void pacePersonTest1(){ public void pacePersonTest1() {
PacePerson p = new PacePerson("Artini, Michele", false); PacePerson p = new PacePerson("Artini, Michele", false);
assertEquals("Artini",p.getSurnameString()); assertEquals("Artini", p.getSurnameString());
assertEquals("Michele", p.getNameString()); assertEquals("Michele", p.getNameString());
assertEquals("Artini, Michele", p.getNormalisedFullname()); assertEquals("Artini, Michele", p.getNormalisedFullname());
} }
@Test @Test
public void pacePersonTest2(){ public void pacePersonTest2() {
PacePerson p = new PacePerson("Michele G. Artini", false); PacePerson p = new PacePerson("Michele G. Artini", false);
assertEquals("Artini, Michele G.", p.getNormalisedFullname()); assertEquals("Artini, Michele G.", p.getNormalisedFullname());
assertEquals("Michele G", p.getNameString()); assertEquals("Michele G", p.getNameString());

4
dhp-schemas/src/main/java/eu/dnetlib/dhp/schema/common/ModelConstants.java
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@ -27,8 +27,7 @@ public class ModelConstants {
public static final String RESULT_RESULT = "resultResult"; public static final String RESULT_RESULT = "resultResult";
/** /**
* @deprecated * @deprecated Use {@link ModelConstants#RELATIONSHIP} instead.
* Use {@link ModelConstants#RELATIONSHIP} instead.
*/ */
@Deprecated @Deprecated
public static final String PUBLICATION_DATASET = "publicationDataset"; public static final String PUBLICATION_DATASET = "publicationDataset";
@ -47,7 +46,6 @@ public class ModelConstants {
public static final String REVIEWS = "reviews"; public static final String REVIEWS = "reviews";
public static final String IS_REVIEWED_BY = "IsReviewedBy"; public static final String IS_REVIEWED_BY = "IsReviewedBy";
public static final String RESULT_PROJECT = "resultProject"; public static final String RESULT_PROJECT = "resultProject";
public static final String OUTCOME = "outcome"; public static final String OUTCOME = "outcome";
public static final String IS_PRODUCED_BY = "isProducedBy"; public static final String IS_PRODUCED_BY = "isProducedBy";

24
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRule.java
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@ -1,27 +1,27 @@
package eu.dnetlib.dhp.oa.graph.clean; package eu.dnetlib.dhp.oa.graph.clean;
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.Map;
import java.util.Objects; import java.util.Objects;
import java.util.function.Function; import java.util.function.Function;
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;
public class CleaningRule<T extends Oaf> implements MapFunction<T, T> { public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
private VocabularyGroup vocabularies; private VocabularyGroup vocabularies;
private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap(); private Map<Class, Function<Object, Object>> mapping = Maps.newHashMap();
public CleaningRule(VocabularyGroup vocabularies) { public CleaningRule(VocabularyGroup vocabularies) {
this.vocabularies = vocabularies; this.vocabularies = vocabularies;
@ -33,7 +33,7 @@ public class CleaningRule<T extends Oaf> implements MapFunction<T, T> {
@Override @Override
public T call(T value) throws Exception { public T call(T value) throws Exception {
OafNavigator.apply(value, mapping); OafNavigator2.apply(value, mapping);
return value; return value;
} }

22
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator.java
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@ -1,12 +1,6 @@
package eu.dnetlib.dhp.oa.graph.clean; 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.BeanInfo;
import java.beans.IntrospectionException; import java.beans.IntrospectionException;
import java.beans.Introspector; import java.beans.Introspector;
@ -16,6 +10,13 @@ import java.lang.reflect.InvocationTargetException;
import java.util.*; import java.util.*;
import java.util.function.Function; import java.util.function.Function;
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;
public class OafNavigator { public class OafNavigator {
public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) { public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
@ -45,7 +46,7 @@ public class OafNavigator {
System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType()); System.out.println("VISITING " + descriptor.getName() + " " + descriptor.getPropertyType());
if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) { if (Iterable.class.isAssignableFrom(descriptor.getPropertyType())) {
for(Object vi : (Iterable) value) { for (Object vi : (Iterable) value) {
visit(vi, mapping); visit(vi, mapping);
} }
@ -53,7 +54,9 @@ public class OafNavigator {
if (mapping.keySet().contains(value.getClass())) { if (mapping.keySet().contains(value.getClass())) {
final Object newValue = mapping.get(value.getClass()).apply(value); final Object newValue = mapping.get(value.getClass()).apply(value);
System.out.println("PATCHING " + descriptor.getName()+ " " + descriptor.getPropertyType()); System.out
.println(
"PATCHING " + descriptor.getName() + " " + descriptor.getPropertyType());
System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value)); System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue)); System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
descriptor.getWriteMethod().invoke(newValue); descriptor.getWriteMethod().invoke(newValue);
@ -101,7 +104,8 @@ public class OafNavigator {
for (Object fi : fs) { for (Object fi : fs) {
navigate(fi, mapping); navigate(fi, mapping);
} }
} if (Iterable.class.isAssignableFrom(fieldType)) { }
if (Iterable.class.isAssignableFrom(fieldType)) {
Iterable fs = (Iterable) value; Iterable fs = (Iterable) value;
for (Object fi : fs) { for (Object fi : fs) {
navigate(fi, mapping); navigate(fi, mapping);

22
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/OafNavigator2.java
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@ -1,14 +1,15 @@
package eu.dnetlib.dhp.oa.graph.clean; 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.lang.reflect.Field;
import java.util.*; import java.util.*;
import java.util.function.Function; 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 class OafNavigator2 {
public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) { public static <E extends Oaf> E apply(E oaf, Map<Class, Function<Object, Object>> mapping) {
@ -22,7 +23,7 @@ public class OafNavigator2 {
} else { } else {
try { try {
for (Field field : getAllFields(o.getClass())) { for (Field field : getAllFields(o.getClass())) {
System.out.println("VISITING " + field.getName() + " in " + o.getClass()); //System.out.println("VISITING " + field.getName() + " in " + o.getClass());
field.setAccessible(true); field.setAccessible(true);
Object value = field.get(o); Object value = field.get(o);
@ -33,7 +34,8 @@ public class OafNavigator2 {
for (Object fi : fs) { for (Object fi : fs) {
navigate(fi, mapping); navigate(fi, mapping);
} }
} if (Iterable.class.isAssignableFrom(fieldType)) { }
if (Iterable.class.isAssignableFrom(fieldType)) {
Iterable fs = (Iterable) value; Iterable fs = (Iterable) value;
for (Object fi : fs) { for (Object fi : fs) {
navigate(fi, mapping); navigate(fi, mapping);
@ -43,9 +45,9 @@ public class OafNavigator2 {
if (Objects.nonNull(cleaningFn)) { if (Objects.nonNull(cleaningFn)) {
final Object newValue = cleaningFn.apply(value); final Object newValue = cleaningFn.apply(value);
if (!Objects.equals(value, newValue)) { if (!Objects.equals(value, newValue)) {
System.out.println("PATCHING " + field.getName()+ " " + value.getClass()); //System.out.println("PATCHING " + field.getName() + " " + value.getClass());
System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value)); //System.out.println("OLD VALUE " + getObjectMapper().writeValueAsString(value));
System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue)); //System.out.println("NEW VALUE " + getObjectMapper().writeValueAsString(newValue));
field.set(o, newValue); field.set(o, newValue);
} }
} }
@ -53,7 +55,7 @@ public class OafNavigator2 {
} }
} }
} catch (IllegalAccessException | IllegalArgumentException | JsonProcessingException e) { } catch (IllegalAccessException | IllegalArgumentException /*| JsonProcessingException*/ e) {
throw new RuntimeException(e); throw new RuntimeException(e);
} }
} }

2
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/GenerateEntitiesApplication.java
View File

@ -140,11 +140,9 @@ public class GenerateEntitiesApplication {
final String type = StringUtils.substringAfter(id, ":"); final String type = StringUtils.substringAfter(id, ":");
switch (type.toLowerCase()) { switch (type.toLowerCase()) {
case "oaf-store-claim":
case "oaf-store-cleaned": case "oaf-store-cleaned":
case "oaf-store-claim": case "oaf-store-claim":
return new OafToOafMapper(vocs, false).processMdRecord(s); return new OafToOafMapper(vocs, false).processMdRecord(s);
case "odf-store-claim":
case "odf-store-cleaned": case "odf-store-cleaned":
case "odf-store-claim": case "odf-store-claim":
return new OdfToOafMapper(vocs, false).processMdRecord(s); return new OdfToOafMapper(vocs, false).processMdRecord(s);

8
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleTest.java
View File

@ -84,11 +84,9 @@ public class CleaningRuleTest {
// TODO add more assertions to verity the cleaned values // TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_out)); System.out.println(MAPPER.writeValueAsString(p_out));
assertTrue( /*
p_out * assertTrue( p_out .getPid() .stream() .allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
.getPid() */
.stream()
.allMatch(sp -> StringUtils.isNotBlank(sp.getValue())));
} }
private Stream<Qualifier> getAuthorPidTypes(Publication pub) { private Stream<Qualifier> getAuthorPidTypes(Publication pub) {

5
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -897,7 +897,10 @@ public class XmlRecordFactory implements Serializable {
metadata.add(XmlSerializationUtils.mapQualifier("contracttype", p.getContracttype())); metadata.add(XmlSerializationUtils.mapQualifier("contracttype", p.getContracttype()));
} }
if (p.getOamandatepublications() != null) { if (p.getOamandatepublications() != null) {
metadata.add(XmlSerializationUtils.asXmlElement("oamandatepublications", p.getOamandatepublications().getValue())); metadata
.add(
XmlSerializationUtils
.asXmlElement("oamandatepublications", p.getOamandatepublications().getValue()));
} }
if (p.getEcsc39() != null) { if (p.getEcsc39() != null) {
metadata.add(XmlSerializationUtils.asXmlElement("ecsc39", p.getEcsc39().getValue())); metadata.add(XmlSerializationUtils.asXmlElement("ecsc39", p.getEcsc39().getValue()));