forked from D-Net/dnet-hadoop
Merge pull request 'subjects cleaning' (#239) from clean_subjects into beta
Reviewed-on: D-Net/dnet-hadoop#239
This commit is contained in:
commit
5066db3386
|
@ -83,4 +83,10 @@ public class Vocabulary implements Serializable {
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.orElse(null);
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}
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public Qualifier lookup(String id) {
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return Optional
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.ofNullable(getSynonymAsQualifier(id))
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.orElse(getTermAsQualifier(id));
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}
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}
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|
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@ -81,6 +81,13 @@ public class VocabularyGroup implements Serializable {
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vocs.put(id.toLowerCase(), new Vocabulary(id, name));
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}
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public Optional<Vocabulary> find(final String vocId) {
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return Optional
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.ofNullable(vocId)
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.map(String::toLowerCase)
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.map(vocs::get);
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}
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public void addTerm(final String vocId, final String id, final String name) {
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if (vocabularyExists(vocId)) {
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vocs.get(vocId.toLowerCase()).addTerm(id, name);
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|
|
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@ -1,6 +1,8 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
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import java.time.LocalDate;
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import java.time.ZoneId;
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import java.time.format.DateTimeFormatter;
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@ -16,7 +18,6 @@ import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import eu.dnetlib.dhp.common.vocabulary.Vocabulary;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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|
@ -191,8 +192,8 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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qualifier("und", "Undetermined", ModelConstants.DNET_LANGUAGES));
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}
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if (Objects.nonNull(r.getSubject())) {
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r
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.setSubject(
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List<Subject> subjects = Lists
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.newArrayList(
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r
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.getSubject()
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.stream()
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@ -201,7 +202,18 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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.filter(sp -> Objects.nonNull(sp.getQualifier()))
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.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
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.map(GraphCleaningFunctions::cleanValue)
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.collect(Collectors.toList()));
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.collect(
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Collectors
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.toMap(
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s -> Optional
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.ofNullable(s.getQualifier())
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.map(q -> q.getClassid() + s.getValue())
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.orElse(s.getValue()),
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Function.identity(),
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(s1, s2) -> Collections
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.min(Lists.newArrayList(s1, s1), new SubjectProvenanceComparator())))
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.values());
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r.setSubject(subjects);
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}
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if (Objects.nonNull(r.getTitle())) {
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r
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@ -382,14 +394,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.map(p -> {
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// hack to distinguish orcid from orcid_pending
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String pidProvenance = Optional
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.ofNullable(p.getDataInfo())
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.map(
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d -> Optional
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.ofNullable(d.getProvenanceaction())
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.map(Qualifier::getClassid)
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.orElse(""))
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.orElse("");
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String pidProvenance = getProvenance(p.getDataInfo());
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if (p
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.getQualifier()
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.getClassid()
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|
@ -520,6 +525,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
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return s;
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}
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protected static Subject cleanValue(Subject s) {
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s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
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return s;
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}
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protected static Field<String> cleanValue(Field<String> s) {
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s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
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return s;
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|
|
|
@ -14,6 +14,7 @@ import java.util.stream.Collectors;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.schema.common.AccessRightComparator;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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|
@ -141,7 +142,7 @@ public class OafMapperUtils {
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}
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public static Qualifier unknown(final String schemeid, final String schemename) {
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return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
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return qualifier(UNKNOWN, "Unknown", schemeid, schemename);
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}
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public static AccessRight accessRight(
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|
@ -189,6 +190,17 @@ public class OafMapperUtils {
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return q;
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}
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public static Subject subject(
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final String value,
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final String classid,
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final String classname,
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final String schemeid,
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final String schemename,
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final DataInfo dataInfo) {
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return subject(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
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}
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public static StructuredProperty structuredProperty(
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final String value,
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final String classid,
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|
@ -200,6 +212,20 @@ public class OafMapperUtils {
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return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
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}
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public static Subject subject(
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final String value,
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final Qualifier qualifier,
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final DataInfo dataInfo) {
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if (value == null) {
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return null;
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}
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final Subject s = new Subject();
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s.setValue(value);
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s.setQualifier(qualifier);
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s.setDataInfo(dataInfo);
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return s;
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}
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public static StructuredProperty structuredProperty(
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final String value,
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final Qualifier qualifier,
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|
@ -477,4 +503,15 @@ public class OafMapperUtils {
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rel.setProperties(properties);
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return rel;
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}
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public static String getProvenance(DataInfo dataInfo) {
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return Optional
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.ofNullable(dataInfo)
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.map(
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d -> Optional
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.ofNullable(d.getProvenanceaction())
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.map(Qualifier::getClassid)
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.orElse(""))
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.orElse("");
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}
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}
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|
|
|
@ -0,0 +1,46 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
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import static org.apache.commons.lang3.StringUtils.isBlank;
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import java.util.Comparator;
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import eu.dnetlib.dhp.schema.oaf.Subject;
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public class SubjectProvenanceComparator implements Comparator<Subject> {
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@Override
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public int compare(Subject left, Subject right) {
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String lProv = getProvenance(left.getDataInfo());
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String rProv = getProvenance(right.getDataInfo());
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if (isBlank(lProv) && isBlank(rProv))
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return 0;
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if (isBlank(lProv))
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return 1;
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if (isBlank(rProv))
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return -1;
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if (lProv.equals(rProv))
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return 0;
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if (lProv.toLowerCase().contains("crosswalk"))
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return -1;
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if (rProv.toLowerCase().contains("crosswalk"))
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return 1;
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if (lProv.toLowerCase().contains("user"))
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return -1;
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if (rProv.toLowerCase().contains("user"))
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return 1;
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if (lProv.toLowerCase().contains("propagation"))
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return -1;
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if (rProv.toLowerCase().contains("propagation"))
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return 1;
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if (lProv.toLowerCase().contains("iis"))
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return -1;
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if (rProv.toLowerCase().contains("iis"))
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return 1;
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return 0;
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}
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}
|
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@ -13,6 +13,7 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.Subject;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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public class Constants {
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|
@ -58,13 +59,13 @@ public class Constants {
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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public static StructuredProperty getSubject(String sbj, String classid, String classname,
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public static Subject getSubject(String sbj, String classid, String classname,
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String diqualifierclassid) {
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if (sbj.equals(NULL))
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return null;
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StructuredProperty sp = new StructuredProperty();
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sp.setValue(sbj);
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sp
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Subject s = new Subject();
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s.setValue(sbj);
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s
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.setQualifier(
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OafMapperUtils
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.qualifier(
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|
@ -72,7 +73,7 @@ public class Constants {
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classname,
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ModelConstants.DNET_SUBJECT_TYPOLOGIES,
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ModelConstants.DNET_SUBJECT_TYPOLOGIES));
|
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sp
|
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s
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.setDataInfo(
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OafMapperUtils
|
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.dataInfo(
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|
@ -88,7 +89,7 @@ public class Constants {
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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""));
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return sp;
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return s;
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|
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}
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}
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|
|
|
@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import eu.dnetlib.dhp.schema.oaf.Subject;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.utils.DHPUtils;
|
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|
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|
@ -79,7 +80,7 @@ public class PrepareFOSSparkJob implements Serializable {
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HashSet<String> level3 = new HashSet<>();
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addLevels(level1, level2, level3, first);
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it.forEachRemaining(v -> addLevels(level1, level2, level3, v));
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List<StructuredProperty> sbjs = new ArrayList<>();
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List<Subject> sbjs = new ArrayList<>();
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level1.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level2.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level3.forEach(l -> sbjs.add(getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
|
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|
|
|
@ -24,6 +24,7 @@ import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
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import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
import eu.dnetlib.dhp.schema.oaf.Subject;
|
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
|
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import eu.dnetlib.dhp.utils.DHPUtils;
|
||||
|
||||
|
@ -73,7 +74,7 @@ public class PrepareSDGSparkJob implements Serializable {
|
|||
Result r = new Result();
|
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r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
|
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SDGDataModel first = it.next();
|
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List<StructuredProperty> sbjs = new ArrayList<>();
|
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List<Subject> sbjs = new ArrayList<>();
|
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sbjs.add(getSubject(first.getSbj(), SDG_CLASS_ID, SDG_CLASS_NAME, UPDATE_SUBJECT_SDG_CLASS_ID));
|
||||
it
|
||||
.forEachRemaining(
|
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|
|
|
@ -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,
|
||||
|
|
|
@ -281,7 +281,7 @@ object BioDBToOAF {
|
|||
d.setSubject(
|
||||
subjects
|
||||
.map(s =>
|
||||
OafMapperUtils.structuredProperty(
|
||||
OafMapperUtils.subject(
|
||||
s,
|
||||
SUBJ_CLASS,
|
||||
SUBJ_CLASS,
|
||||
|
|
|
@ -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,
|
||||
|
|
|
@ -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))
|
||||
|
|
|
@ -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<>();
|
||||
|
|
|
@ -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,
|
||||
|
|
|
@ -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
|
||||
)
|
||||
}
|
||||
|
||||
|
|
|
@ -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,
|
||||
|
|
|
@ -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)
|
||||
|
|
|
@ -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())) {
|
||||
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());
|
||||
|
|
|
@ -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']");
|
||||
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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));
|
||||
}
|
||||
|
|
|
@ -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));
|
||||
|
|
|
@ -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": {
|
||||
|
|
|
@ -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
|
|
@ -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
|
|
@ -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
|
||||
|
|
|
@ -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
2
pom.xml
|
@ -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>
|
||||
|
|
Loading…
Reference in New Issue