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subjects cleaning #239

Merged
claudio.atzori merged 15 commits from clean_subjects into beta 2022-09-09 15:17:09 +02:00
Conversation 6 Commits 15 Files Changed 29 +320 -119
29 changed files with 320 additions and 119 deletions
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6
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/Vocabulary.java
View File

@ -83,4 +83,10 @@ public class Vocabulary implements Serializable {
.orElse(null);
}
public Qualifier lookup(String id) {
return Optional
.ofNullable(getSynonymAsQualifier(id))
.orElse(getTermAsQualifier(id));
}
}

7
dhp-common/src/main/java/eu/dnetlib/dhp/common/vocabulary/VocabularyGroup.java
View File

@ -81,6 +81,13 @@ public class VocabularyGroup implements Serializable {
vocs.put(id.toLowerCase(), new Vocabulary(id, name));
}
public Optional<Vocabulary> find(final String vocId) {
return Optional
.ofNullable(vocId)
.map(String::toLowerCase)
.map(vocs::get);
}
public void addTerm(final String vocId, final String id, final String name) {
if (vocabularyExists(vocId)) {
vocs.get(vocId.toLowerCase()).addTerm(id, name);

34
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -1,6 +1,8 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
import java.time.LocalDate;
import java.time.ZoneId;
import java.time.format.DateTimeFormatter;
@ -16,7 +18,6 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
@ -191,8 +192,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
}
if (Objects.nonNull(r.getSubject())) {
r
.setSubject(
List<Subject> subjects = Lists
.newArrayList(
r
.getSubject()
.stream()
@ -201,7 +202,18 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(sp -> Objects.nonNull(sp.getQualifier()))
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
.map(GraphCleaningFunctions::cleanValue)
.collect(Collectors.toList()));
.collect(
Collectors
.toMap(
s -> Optional
.ofNullable(s.getQualifier())
.map(q -> q.getClassid() + s.getValue())
.orElse(s.getValue()),
Function.identity(),
(s1, s2) -> Collections
.min(Lists.newArrayList(s1, s1), new SubjectProvenanceComparator())))
.values());
r.setSubject(subjects);
}
if (Objects.nonNull(r.getTitle())) {
r
@ -382,14 +394,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(p -> StringUtils.isNotBlank(p.getValue()))
.map(p -> {
// hack to distinguish orcid from orcid_pending
String pidProvenance = Optional
.ofNullable(p.getDataInfo())
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
String pidProvenance = getProvenance(p.getDataInfo());
if (p
.getQualifier()
.getClassid()
@ -520,6 +525,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return s;
}
protected static Subject cleanValue(Subject s) {
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
return s;
}
protected static Field<String> cleanValue(Field<String> s) {
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
return s;

39
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -14,6 +14,7 @@ import java.util.stream.Collectors;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.*;
@ -141,7 +142,7 @@ public class OafMapperUtils {
}
public static Qualifier unknown(final String schemeid, final String schemename) {
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
return qualifier(UNKNOWN, "Unknown", schemeid, schemename);
}
public static AccessRight accessRight(
@ -189,6 +190,17 @@ public class OafMapperUtils {
return q;
}
public static Subject subject(
final String value,
final String classid,
final String classname,
final String schemeid,
final String schemename,
final DataInfo dataInfo) {
return subject(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
}
public static StructuredProperty structuredProperty(
final String value,
final String classid,
@ -200,6 +212,20 @@ public class OafMapperUtils {
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
}
public static Subject subject(
final String value,
final Qualifier qualifier,
final DataInfo dataInfo) {
if (value == null) {
return null;
}
final Subject s = new Subject();
s.setValue(value);
s.setQualifier(qualifier);
s.setDataInfo(dataInfo);
return s;
}
public static StructuredProperty structuredProperty(
final String value,
final Qualifier qualifier,
@ -477,4 +503,15 @@ public class OafMapperUtils {
rel.setProperties(properties);
return rel;
}
public static String getProvenance(DataInfo dataInfo) {
return Optional
.ofNullable(dataInfo)
.map(
d -> Optional
.ofNullable(d.getProvenanceaction())
.map(Qualifier::getClassid)
.orElse(""))
.orElse("");
}
}

46
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/SubjectProvenanceComparator.java Normal file
View File

@ -0,0 +1,46 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
import static org.apache.commons.lang3.StringUtils.isBlank;
import java.util.Comparator;
import eu.dnetlib.dhp.schema.oaf.Subject;
public class SubjectProvenanceComparator implements Comparator<Subject> {
@Override
public int compare(Subject left, Subject right) {
String lProv = getProvenance(left.getDataInfo());
String rProv = getProvenance(right.getDataInfo());
if (isBlank(lProv) && isBlank(rProv))
return 0;
if (isBlank(lProv))
return 1;
if (isBlank(rProv))
return -1;
if (lProv.equals(rProv))
return 0;
if (lProv.toLowerCase().contains("crosswalk"))
return -1;
if (rProv.toLowerCase().contains("crosswalk"))
return 1;
if (lProv.toLowerCase().contains("user"))
return -1;
if (rProv.toLowerCase().contains("user"))
return 1;
if (lProv.toLowerCase().contains("propagation"))
return -1;
if (rProv.toLowerCase().contains("propagation"))
return 1;
if (lProv.toLowerCase().contains("iis"))
return -1;
if (rProv.toLowerCase().contains("iis"))
return 1;
return 0;
}
}

13
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/Constants.java
View File

@ -13,6 +13,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
public class Constants {
@ -58,13 +59,13 @@ public class Constants {
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
}
public static StructuredProperty getSubject(String sbj, String classid, String classname,
public static Subject getSubject(String sbj, String classid, String classname,
String diqualifierclassid) {
if (sbj.equals(NULL))
return null;
StructuredProperty sp = new StructuredProperty();
sp.setValue(sbj);
sp
Subject s = new Subject();
s.setValue(sbj);
s
.setQualifier(
OafMapperUtils
.qualifier(
@ -72,7 +73,7 @@ public class Constants {
classname,
ModelConstants.DNET_SUBJECT_TYPOLOGIES,
ModelConstants.DNET_SUBJECT_TYPOLOGIES));
sp
s
.setDataInfo(
OafMapperUtils
.dataInfo(
@ -88,7 +89,7 @@ public class Constants {
ModelConstants.DNET_PROVENANCE_ACTIONS),
""));
return sp;
return s;
}
}

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java
View File

@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
@ -79,7 +80,7 @@ public class PrepareFOSSparkJob implements Serializable {
HashSet<String> level3 = new HashSet<>();
addLevels(level1, level2, level3, first);
it.forEachRemaining(v -> addLevels(level1, level2, level3, v));
List<StructuredProperty> sbjs = new ArrayList<>();
List<Subject> sbjs = new ArrayList<>();
level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));

3
dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareSDGSparkJob.java
View File

@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.Subject;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
import eu.dnetlib.dhp.utils.DHPUtils;
@ -73,7 +74,7 @@ public class PrepareSDGSparkJob implements Serializable {
Result r = new Result();
r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
SDGDataModel first = it.next();
List<StructuredProperty> sbjs = new ArrayList<>();
List<Subject> sbjs = new ArrayList<>();
sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
it
.forEachRemaining(

6
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala
View File

@ -19,7 +19,7 @@ import java.time.chrono.ThaiBuddhistDate
import java.time.format.DateTimeFormatter
import java.util.{Date, Locale}
import scala.collection.JavaConverters._
import scala.io.{Codec, Source}
import scala.io.Source
object DataciteToOAFTransformation {
@ -252,7 +252,7 @@ object DataciteToOAFTransformation {
.exists(i => i.getHostedby != null && "figshare".equalsIgnoreCase(i.getHostedby.getValue))
if (hosted_by_figshare) {
r.getInstance().asScala.foreach(i => i.setAccessright(ModelConstants.OPEN_ACCESS_RIGHT()))
val l: List[StructuredProperty] = List()
val l: List[Subject] = List()
r.setSubject(l.asJava)
}
}
@ -492,7 +492,7 @@ object DataciteToOAFTransformation {
subjects
.filter(s => s.subject.nonEmpty)
.map(s =>
OafMapperUtils.structuredProperty(
OafMapperUtils.subject(
s.subject.get,
SUBJ_CLASS,
SUBJ_CLASS,

2
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala
View File

@ -281,7 +281,7 @@ object BioDBToOAF {
d.setSubject(
subjects
.map(s =>
OafMapperUtils.structuredProperty(
OafMapperUtils.subject(
s,
SUBJ_CLASS,
SUBJ_CLASS,

4
dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala
View File

@ -265,8 +265,8 @@ object PubMedToOaf {
result.setLanguage(term)
}
val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s =>
OafMapperUtils.structuredProperty(
val subjects: List[Subject] = article.getSubjects.asScala.map(s =>
OafMapperUtils.subject(
s.getValue,
SUBJ_CLASS,
SUBJ_CLASS,

10
dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java
View File

@ -72,7 +72,7 @@ public class ProduceTest {
JavaRDD<Result> tmp = getResultJavaRDD();
List<StructuredProperty> sbjs = tmp
List<Subject> sbjs = tmp
.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
.flatMap(row -> row.getSubject().iterator())
.collect();
@ -169,7 +169,7 @@ public class ProduceTest {
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
List<Subject> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
@ -396,7 +396,7 @@ public class ProduceTest {
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
List<Subject> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
@ -508,7 +508,7 @@ public class ProduceTest {
.getSubject()
.size());
List<StructuredProperty> sbjs = tmp
List<Subject> sbjs = tmp
.filter(row -> row.getId().equals(doi))
.flatMap(row -> row.getSubject().iterator())
.collect();
@ -537,7 +537,7 @@ public class ProduceTest {
JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
List<StructuredProperty> sbjs_sdg = tmp
List<Subject> sbjs_sdg = tmp
.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
.flatMap(row -> row.getSubject().iterator())
.filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID))

33
dhp-workflows/dhp-broker-events/src/main/java/eu/dnetlib/dhp/broker/oa/util/ConversionUtils.java
View File

@ -26,20 +26,7 @@ import eu.dnetlib.broker.objects.OaBrokerRelatedPublication;
import eu.dnetlib.broker.objects.OaBrokerRelatedSoftware;
import eu.dnetlib.broker.objects.OaBrokerTypedValue;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Datasource;
import eu.dnetlib.dhp.schema.oaf.ExternalReference;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.*;
public class ConversionUtils {
@ -71,6 +58,10 @@ public class ConversionUtils {
return sp != null ? new OaBrokerTypedValue(classId(sp.getQualifier()), sp.getValue()) : null;
}
public static OaBrokerTypedValue oafSubjectToBrokerTypedValue(final Subject sp) {
return sp != null ? new OaBrokerTypedValue(classId(sp.getQualifier()), sp.getValue()) : null;
}
public static OaBrokerRelatedDataset oafDatasetToBrokerDataset(final Dataset d) {
if (d == null) {
return null;
@ -115,7 +106,7 @@ public class ConversionUtils {
res.setTitles(structPropList(result.getTitle()));
res.setAbstracts(fieldList(result.getDescription()));
res.setLanguage(classId(result.getLanguage()));
res.setSubjects(structPropTypedList(result.getSubject()));
res.setSubjects(subjectList(result.getSubject()));
res.setCreators(mappedList(result.getAuthor(), ConversionUtils::oafAuthorToBrokerAuthor));
res.setPublicationdate(fieldValue(result.getDateofacceptance()));
res.setPublisher(fieldValue(result.getPublisher()));
@ -304,6 +295,18 @@ public class ConversionUtils {
.collect(Collectors.toList());
}
private static List<OaBrokerTypedValue> subjectList(final List<Subject> list) {
if (list == null) {
return new ArrayList<>();
}
return list
.stream()
.map(ConversionUtils::oafSubjectToBrokerTypedValue)
.filter(Objects::nonNull)
.collect(Collectors.toList());
}
private static <F, T> List<T> mappedList(final List<F> list, final Function<F, T> func) {
if (list == null) {
return new ArrayList<>();

22
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala
View File

@ -391,6 +391,28 @@ object DoiBoostMappingUtil {
di
}
def createSubject(value: String, classId: String, schemeId: String): Subject = {
val s = new Subject
s.setQualifier(OafMapperUtils.qualifier(classId, classId, schemeId, schemeId))
s.setValue(value)
s
}
def createSubject(
value: String,
classId: String,
className: String,
schemeId: String,
schemeName: String
): Subject = {
val s = new Subject
s.setQualifier(OafMapperUtils.qualifier(classId, className, schemeId, schemeName))
s.setValue(value)
s
}
def createSP(
value: String,
classId: String,

2
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -201,7 +201,7 @@ case object Crossref2Oaf {
if (subjectList.nonEmpty) {
result.setSubject(
subjectList.map(s => createSP(s, "keywords", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava
subjectList.map(s => createSubject(s, "keyword", ModelConstants.DNET_SUBJECT_TYPOLOGIES)).asJava
)
}

12
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/mag/MagDataModel.scala
View File

@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.mag
import eu.dnetlib.dhp.schema.common.ModelConstants
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty}
import eu.dnetlib.dhp.schema.oaf.{Instance, Journal, Publication, StructuredProperty, Subject}
import eu.dnetlib.doiboost.DoiBoostMappingUtil
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
import org.json4s
@ -210,8 +210,8 @@ case object ConversionUtil {
val className = "Microsoft Academic Graph classification"
val classid = "MAG"
val p: List[StructuredProperty] = fieldOfStudy.subjects.flatMap(s => {
val s1 = createSP(
val p: List[Subject] = fieldOfStudy.subjects.flatMap(s => {
val s1 = createSubject(
s.DisplayName,
classid,
className,
@ -219,10 +219,10 @@ case object ConversionUtil {
ModelConstants.DNET_SUBJECT_TYPOLOGIES
)
val di = DoiBoostMappingUtil.generateDataInfo(s.Score.toString)
var resList: List[StructuredProperty] = List(s1)
var resList: List[Subject] = List(s1)
if (s.MainType.isDefined) {
val maintp = s.MainType.get
val s2 = createSP(
val s2 = createSubject(
s.MainType.get,
classid,
className,
@ -232,7 +232,7 @@ case object ConversionUtil {
s2.setDataInfo(di)
resList = resList ::: List(s2)
if (maintp.contains(".")) {
val s3 = createSP(
val s3 = createSubject(
maintp.split("\\.").head,
classid,
className,

2
dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java
View File

@ -290,7 +290,7 @@ public class EOSCTagJobTest {
.stream()
.anyMatch(s -> s.getCode().equals("EOSC::Jupyter Notebook")));
List<StructuredProperty> subjects = tmp
List<Subject> subjects = tmp
.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244"))
.collect()
.get(0)

34
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/clean/CleaningRuleMap.java
View File

@ -3,16 +3,15 @@ package eu.dnetlib.dhp.oa.graph.clean;
import java.io.Serializable;
import java.util.HashMap;
import java.util.concurrent.atomic.AtomicReference;
import org.apache.commons.lang3.SerializationUtils;
import org.apache.commons.lang3.StringUtils;
import eu.dnetlib.dhp.common.FunctionalInterfaceSupport.SerializableConsumer;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.Country;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.*;
public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Object>> implements Serializable {
@ -27,9 +26,36 @@ public class CleaningRuleMap extends HashMap<Class<?>, SerializableConsumer<Obje
mapping.put(AccessRight.class, o -> cleanQualifier(vocabularies, (AccessRight) o));
mapping.put(Country.class, o -> cleanCountry(vocabularies, (Country) o));
mapping.put(Relation.class, o -> cleanRelation(vocabularies, (Relation) o));
mapping.put(Subject.class, o -> cleanSubject(vocabularies, (Subject) o));
return mapping;
}
private static void cleanSubject(VocabularyGroup vocabularies, Subject subject) {
if (cleanSubjectForVocabulary(ModelConstants.DNET_SUBJECT_FOS_CLASSID, vocabularies, subject)) {
return;
} else {
// TODO cleaning based on different subject vocabs can be added here
}
}
private static boolean cleanSubjectForVocabulary(String vocabularyId, VocabularyGroup vocabularies,
Subject subject) {
AtomicReference<Boolean> modified = new AtomicReference<>(false);
vocabularies.find(vocabularyId).ifPresent(vocabulary -> {
if (!ModelConstants.DNET_SUBJECT_KEYWORD.equalsIgnoreCase(subject.getQualifier().getClassid())) {
return;
}
Qualifier newValue = vocabulary.lookup(subject.getValue());
if (!ModelConstants.UNKNOWN.equals(newValue.getClassid())) {
miriam.baglioni commented 2022-08-08 10:52:28 +02:00
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I do not understand why you compare subject.value and newValue.classid

I do not understand why you compare subject.value and newValue.classid
miriam.baglioni commented 2022-08-08 11:00:57 +02:00
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I saw by myself. It is ok.

One thing: you will not change the classId of the subject if the value provided is equal to the term in the vocabulary.

I saw by myself. It is ok. One thing: you will not change the classId of the subject if the value provided is equal to the term in the vocabulary.
claudio.atzori commented 2022-08-08 12:41:34 +02:00
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You are right. However, the vocabulary.lookup method already tryes to find match a synonym and in case it can't then it looks for a matching equivalent term:

public Qualifier lookup(String id) {
	return Optional
		.ofNullable(getSynonymAsQualifier(id))
		.orElse(getTermAsQualifier(id));
}

Then, in case a matching term cannot be found, the method returns a qualifier set to UNKNOWN

public Qualifier getTermAsQualifier(final String termId) {
	if (StringUtils.isBlank(termId)) {
		return OafMapperUtils.unknown(getId(), getName());
	} else if (termExists(termId)) {
		final VocabularyTerm t = getTerm(termId);
		return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName());
	} else {
		return OafMapperUtils.qualifier(termId, termId, getId(), getName());
	}
}

hence I could just exploit this to decide what to do when the value provided is equal to the term in the vocabulary.

You are right. However, the `vocabulary.lookup` method already tryes to find match a synonym and in case it can't then it looks for a matching equivalent term: ``` public Qualifier lookup(String id) { return Optional .ofNullable(getSynonymAsQualifier(id)) .orElse(getTermAsQualifier(id)); } ``` Then, in case a matching term cannot be found, the method returns a qualifier set to UNKNOWN ``` public Qualifier getTermAsQualifier(final String termId) { if (StringUtils.isBlank(termId)) { return OafMapperUtils.unknown(getId(), getName()); } else if (termExists(termId)) { final VocabularyTerm t = getTerm(termId); return OafMapperUtils.qualifier(t.getId(), t.getName(), getId(), getName()); } else { return OafMapperUtils.qualifier(termId, termId, getId(), getName()); } } ``` hence I could just exploit this to decide what to do when the value provided is equal to the term in the vocabulary.
miriam.baglioni commented 2022-08-08 14:12:32 +02:00
Outdated
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Yes, I do agree

Yes, I do agree
subject.setValue(newValue.getClassid());
subject.getQualifier().setClassid(vocabularyId);
subject.getQualifier().setClassname(vocabulary.getName());
modified.set(true);
}
});
return modified.get();
}
private static void cleanRelation(VocabularyGroup vocabularies, Relation r) {
if (vocabularies.vocabularyExists(ModelConstants.DNET_RELATION_SUBRELTYPE)) {
Qualifier newValue = vocabularies.lookup(ModelConstants.DNET_RELATION_SUBRELTYPE, r.getSubRelType());

49
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java
View File

@ -8,15 +8,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.PRODUCES;
import static eu.dnetlib.dhp.schema.common.ModelConstants.REPOSITORY_PROVENANCE_ACTIONS;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.UNKNOWN;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.keyValue;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.oaiIProvenance;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
import java.util.*;
@ -29,26 +21,7 @@ import com.google.common.collect.Sets;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.common.ModelSupport;
import eu.dnetlib.dhp.schema.oaf.AccessRight;
import eu.dnetlib.dhp.schema.oaf.Author;
import eu.dnetlib.dhp.schema.oaf.Context;
import eu.dnetlib.dhp.schema.oaf.DataInfo;
import eu.dnetlib.dhp.schema.oaf.Dataset;
import eu.dnetlib.dhp.schema.oaf.Field;
import eu.dnetlib.dhp.schema.oaf.GeoLocation;
import eu.dnetlib.dhp.schema.oaf.Instance;
import eu.dnetlib.dhp.schema.oaf.Journal;
import eu.dnetlib.dhp.schema.oaf.KeyValue;
import eu.dnetlib.dhp.schema.oaf.OAIProvenance;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.OafEntity;
import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
import eu.dnetlib.dhp.schema.oaf.Publication;
import eu.dnetlib.dhp.schema.oaf.Qualifier;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.Software;
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ -411,7 +384,7 @@ public abstract class AbstractMdRecordToOafMapper {
protected abstract List<StructuredProperty> prepareTitles(Document doc, DataInfo info);
protected abstract List<StructuredProperty> prepareSubjects(Document doc, DataInfo info);
protected abstract List<Subject> prepareSubjects(Document doc, DataInfo info);
protected abstract Qualifier prepareLanguages(Document doc);
@ -559,6 +532,22 @@ public abstract class AbstractMdRecordToOafMapper {
return res;
}
protected List<Subject> prepareSubjectList(
final Node node,
final String xpath,
final DataInfo info) {
final List<Subject> res = new ArrayList<>();
for (final Object o : node.selectNodes(xpath)) {
final Node n = (Node) o;
res
.add(
subject(
n.getText(), n.valueOf("@classid"), n.valueOf("@classname"), n.valueOf("@schemeid"),
n.valueOf("@schemename"), info));
}
return res;
}
protected OAIProvenance prepareOAIprovenance(final Document doc) {
final Node n = doc.selectSingleNode("//*[local-name()='provenance']/*[local-name()='originDescription']");

4
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OafToOafMapper.java
View File

@ -84,8 +84,8 @@ public class OafToOafMapper extends AbstractMdRecordToOafMapper {
}
@Override
protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
return prepareListStructProps(doc, "//dc:subject", info);
protected List<Subject> prepareSubjects(final Document doc, final DataInfo info) {
return prepareSubjectList(doc, "//dc:subject", info);
}
@Override

6
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/OdfToOafMapper.java
View File

@ -179,7 +179,7 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
url.add(HTTP_DOI_PREIFX + ((Node) o).getText().trim());
}
for (final Object o : doc
.selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) {
.selectNodes("//*[local-name()='alternateIdentifier' and ./@alternateIdentifierType='Handle']")) {
url.add(HTTP_HANDLE_PREIFX + ((Node) o).getText().trim());
}
for (final Object o : doc.selectNodes("//*[local-name()='identifier' and ./@identifierType='Handle']")) {
@ -257,8 +257,8 @@ public class OdfToOafMapper extends AbstractMdRecordToOafMapper {
}
@Override
protected List<StructuredProperty> prepareSubjects(final Document doc, final DataInfo info) {
return prepareListStructProps(doc, "//*[local-name()='subject']", info);
protected List<Subject> prepareSubjects(final Document doc, final DataInfo info) {
return prepareSubjectList(doc, "//*[local-name()='subject']", info);
}
@Override

27
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
View File

@ -251,6 +251,33 @@ public class GraphCleaningFunctionsTest {
pid.getQualifier().getClassname()));
});
assertNotNull(p_cleaned.getSubject());
List<Subject> fos_subjects = p_cleaned
.getSubject()
.stream()
.filter(s -> ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()))
.collect(Collectors.toList());
assertNotNull(fos_subjects);
assertEquals(2, fos_subjects.size());
assertTrue(
fos_subjects
.stream()
.anyMatch(
s -> "0101 mathematics".equals(s.getValue()) &
ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid()) &
"sysimport:crosswalk:datasetarchive"
.equals(s.getDataInfo().getProvenanceaction().getClassid())));
assertTrue(
fos_subjects
.stream()
.anyMatch(
s -> "0102 computer and information sciences".equals(s.getValue()) &
ModelConstants.DNET_SUBJECT_FOS_CLASSID.equals(s.getQualifier().getClassid())));
// TODO add more assertions to verity the cleaned values
System.out.println(MAPPER.writeValueAsString(p_cleaned));
}

3
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java
View File

@ -928,7 +928,8 @@ class MappersTest {
@Test
void testROHub2() throws IOException, DocumentException {
final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml")));
final String xml = IOUtils
.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub-modified.xml")));
final List<Oaf> list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml);
System.out.println("***************");
System.out.println(new ObjectMapper().writeValueAsString(list));

52
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -743,12 +743,12 @@
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
"classid": "keyword",
"classname": "keyword",
"schemeid": "dnet:subject_classification_typologies",
"schemename": "dnet:subject_classification_typologies"
},
"value": "infrared detectors"
"value": "FOS: Mathematics"
},
{
"dataInfo": {
@ -765,12 +765,12 @@
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
"classid": "keyword",
"classname": "keyword",
"schemeid": "dnet:subject_classification_typologies",
"schemename": "dnet:subject_classification_typologies"
},
"value": "lens antennas"
"value": "FOS: Computer and information sciences"
},
{
"dataInfo": {
@ -787,12 +787,34 @@
"trust": "0.9"
},
"qualifier": {
"classid": "",
"classname": "",
"schemeid": "",
"schemename": ""
"classid": "keyword",
"classname": "keyword",
"schemeid": "dnet:subject_classification_typologies",
"schemename": "dnet:subject_classification_typologies"
},
"value": "silicon"
"value": "0101 mathematics"
},
{
"dataInfo": {
"deletedbyinference": false,
"inferenceprovenance": "",
"inferred": false,
"invisible": false,
"provenanceaction": {
"classid": "subject:fos",
"classname": "subject:fos",
"schemeid": "dnet:provenanceActions",
"schemename": "dnet:provenanceActions"
},
"trust": "0.9"
},
"qualifier": {
"classid": "keyword",
"classname": "keyword",
"schemeid": "dnet:subject_classification_typologies",
"schemename": "dnet:subject_classification_typologies"
},
"value": "0101 mathematics"
},
{
"dataInfo": {

4
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt
View File

@ -1243,4 +1243,6 @@ dnet:relation_relClass @=@ IsSupplementTo @=@ isSupplementTo
dnet:relation_relClass @=@ IsSupplementedBy @=@ isSupplementedBy
dnet:relation_relClass @=@ IsRelatedTo @=@ isRelatedTo
dnet:relation_subRelType @=@ relationship @=@ publicationDataset
dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned
dnet:provenanceActions @=@ iis @=@ erroneous label to be cleaned
FOS @=@ 0101 mathematics @=@ FOS: Mathematics
FOS @=@ 0102 computer and information sciences @=@ FOS: Computer and information sciences

5
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt
View File

@ -1118,4 +1118,7 @@ dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ relationship @=@ relat
dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ review @=@ review
dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ similarity @=@ similarity
dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ supplement @=@ supplement
dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version
dnet:relation_subRelType @=@ dnet:relation_subRelType @=@ version @=@ version
FOS @=@ Fields of Science and Technology classification @=@ 0101 mathematics @=@ 0101 mathematics
FOS @=@ Fields of Science and Technology classification @=@ 0102 computer and information sciences @=@ 0102 computer and information sciences
FOS @=@ Fields of Science and Technology classification @=@ 0103 physical sciences @=@ 0103 physical sciences

4
dhp-workflows/dhp-graph-mapper/src/test/scala/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala
View File

@ -59,7 +59,7 @@ class ResolveEntitiesTest extends Serializable {
r.setId(id.toLowerCase.trim)
r.setSubject(
List(
OafMapperUtils.structuredProperty(
OafMapperUtils.subject(
FAKE_SUBJECT,
OafMapperUtils.qualifier("fos", "fosCS", "fossSchema", "fossiFIgo"),
null
@ -250,7 +250,7 @@ class ResolveEntitiesTest extends Serializable {
val r = new Result
r.setSubject(
List(
OafMapperUtils.structuredProperty(
OafMapperUtils.subject(
FAKE_SUBJECT,
OafMapperUtils.qualifier("fos", "fosCS", "fossSchema", "fossiFIgo"),
null

5
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/IndexRecordTransformerTest.java
View File

@ -85,7 +85,7 @@ public class IndexRecordTransformerTest {
public void testRiunet() throws IOException, TransformerException {
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
XmlConverterJob.schemaLocation);
XmlConverterJob.schemaLocation);
final Publication p = load("riunet.json", Publication.class);
@ -95,7 +95,6 @@ public class IndexRecordTransformerTest {
testRecordTransformation(record);
}
@Test
public void testForEOSCFutureDataTransferPilot() throws IOException, TransformerException {
final String record = IOUtils.toString(getClass().getResourceAsStream("eosc-future/data-transfer-pilot.xml"));
@ -129,8 +128,6 @@ public class IndexRecordTransformerTest {
testRecordTransformation(record);
}
@Test
void testDoiUrlNormalization() throws MalformedURLException {

2
pom.xml
View File

@ -801,7 +801,7 @@
<mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.12.2-SNAPSHOT]</dhp-schemas.version>
<dhp-schemas.version>[3.14.0]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>