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461 lines
14 KiB
Java
461 lines
14 KiB
Java
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package eu.dnetlib.dhp.schema.oaf.utils;
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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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import java.time.format.DateTimeParseException;
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import java.util.*;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.lang3.StringUtils;
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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.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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import me.xuender.unidecode.Unidecode;
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public class GraphCleaningFunctions extends CleaningFunctions {
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public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
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public static final int ORCID_LEN = 19;
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public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
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public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
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public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]";
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public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10;
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public static <T extends Oaf> T fixVocabularyNames(T value) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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// nothing to clean here
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} else if (value instanceof Organization) {
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Organization o = (Organization) value;
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if (Objects.nonNull(o.getCountry())) {
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fixVocabName(o.getCountry(), ModelConstants.DNET_COUNTRY_TYPE);
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}
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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fixVocabName(r.getLanguage(), ModelConstants.DNET_LANGUAGES);
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fixVocabName(r.getResourcetype(), ModelConstants.DNET_DATA_CITE_RESOURCE);
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fixVocabName(r.getBestaccessright(), ModelConstants.DNET_ACCESS_MODES);
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if (Objects.nonNull(r.getSubject())) {
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r.getSubject().forEach(s -> fixVocabName(s.getQualifier(), ModelConstants.DNET_SUBJECT_TYPOLOGIES));
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}
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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fixVocabName(i.getAccessright(), ModelConstants.DNET_ACCESS_MODES);
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fixVocabName(i.getRefereed(), ModelConstants.DNET_REVIEW_LEVELS);
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
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r.getAuthor().stream().filter(Objects::nonNull).forEach(a -> {
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if (Objects.nonNull(a.getPid())) {
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a.getPid().stream().filter(Objects::nonNull).forEach(p -> {
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fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES);
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});
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}
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});
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}
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if (value instanceof Publication) {
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} else if (value instanceof Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return value;
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}
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public static <T extends Oaf> boolean filter(T value) {
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if (value instanceof Datasource) {
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// nothing to evaluate here
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} else if (value instanceof Project) {
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// nothing to evaluate here
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} else if (value instanceof Organization) {
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// nothing to evaluate here
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) {
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return false;
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}
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if (value instanceof Publication) {
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} else if (value instanceof Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return true;
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}
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public static <T extends Oaf> T cleanup(T value) {
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if (value instanceof Datasource) {
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// nothing to clean here
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} else if (value instanceof Project) {
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// nothing to clean here
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} else if (value instanceof Organization) {
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Organization o = (Organization) value;
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if (Objects.isNull(o.getCountry()) || StringUtils.isBlank(o.getCountry().getClassid())) {
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o.setCountry(ModelConstants.UNKNOWN_COUNTRY);
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}
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} else if (value instanceof Relation) {
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Relation r = (Relation) value;
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Optional<String> validationDate = doCleanDate(r.getValidationDate());
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if (validationDate.isPresent()) {
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r.setValidationDate(validationDate.get());
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r.setValidated(true);
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} else {
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r.setValidationDate(null);
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r.setValidated(false);
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}
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} else if (value instanceof Result) {
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Result r = (Result) value;
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if (Objects.nonNull(r.getDateofacceptance())) {
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Optional<String> date = cleanDateField(r.getDateofacceptance());
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if (date.isPresent()) {
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r.getDateofacceptance().setValue(date.get());
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} else {
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r.setDateofacceptance(null);
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}
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}
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if (Objects.nonNull(r.getRelevantdate())) {
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r
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.setRelevantdate(
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r
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.getRelevantdate()
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.stream()
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.filter(Objects::nonNull)
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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(sp -> {
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sp.setValue(GraphCleaningFunctions.cleanDate(sp.getValue()));
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return sp;
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})
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
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r.setPublisher(null);
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}
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if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
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r
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.setLanguage(
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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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r
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.getSubject()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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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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}
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if (Objects.nonNull(r.getTitle())) {
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r
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.setTitle(
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r
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.getTitle()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.filter(
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sp -> {
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final String title = sp
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.getValue()
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.toLowerCase();
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final String residual = Unidecode
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.decode(title)
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.replaceAll(TITLE_FILTER_REGEX, "");
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return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH;
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})
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.map(GraphCleaningFunctions::cleanValue)
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getDescription())) {
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r
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.setDescription(
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r
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.getDescription()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.map(GraphCleaningFunctions::cleanValue)
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getPid())) {
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r.setPid(processPidCleaning(r.getPid()));
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}
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if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
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r
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.setResourcetype(
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qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
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}
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if (Objects.nonNull(r.getInstance())) {
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for (Instance i : r.getInstance()) {
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if (Objects.nonNull(i.getPid())) {
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i.setPid(processPidCleaning(i.getPid()));
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}
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if (Objects.nonNull(i.getAlternateIdentifier())) {
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i.setAlternateIdentifier(processPidCleaning(i.getAlternateIdentifier()));
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}
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Optional
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.ofNullable(i.getPid())
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.ifPresent(pid -> {
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final Set<StructuredProperty> pids = Sets.newHashSet(pid);
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Optional
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.ofNullable(i.getAlternateIdentifier())
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.ifPresent(altId -> {
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final Set<StructuredProperty> altIds = Sets.newHashSet(altId);
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i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids)));
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});
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});
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if (Objects.isNull(i.getAccessright()) || StringUtils.isBlank(i.getAccessright().getClassid())) {
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i
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.setAccessright(
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accessRight(
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ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,
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ModelConstants.DNET_ACCESS_MODES));
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}
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if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
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i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
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}
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if (Objects.isNull(i.getRefereed())) {
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i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
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}
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if (Objects.nonNull(i.getDateofacceptance())) {
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Optional<String> date = cleanDateField(i.getDateofacceptance());
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if (date.isPresent()) {
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i.getDateofacceptance().setValue(date.get());
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} else {
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i.setDateofacceptance(null);
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}
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}
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}
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}
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if (Objects.isNull(r.getBestaccessright()) || StringUtils.isBlank(r.getBestaccessright().getClassid())) {
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Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance());
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if (Objects.isNull(bestaccessrights)) {
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r
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.setBestaccessright(
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qualifier(
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ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,
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ModelConstants.DNET_ACCESS_MODES));
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} else {
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r.setBestaccessright(bestaccessrights);
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}
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}
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if (Objects.nonNull(r.getAuthor())) {
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r
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.setAuthor(
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r
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.getAuthor()
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.stream()
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.filter(Objects::nonNull)
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.filter(a -> StringUtils.isNotBlank(a.getFullname()))
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.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
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.collect(Collectors.toList()));
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boolean nullRank = r
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.getAuthor()
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.stream()
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.anyMatch(a -> Objects.isNull(a.getRank()));
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if (nullRank) {
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int i = 1;
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for (Author author : r.getAuthor()) {
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author.setRank(i++);
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}
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}
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for (Author a : r.getAuthor()) {
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if (Objects.isNull(a.getPid())) {
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a.setPid(Lists.newArrayList());
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} else {
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a
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.setPid(
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a
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.getPid()
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.stream()
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.filter(Objects::nonNull)
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.filter(p -> Objects.nonNull(p.getQualifier()))
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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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if (p
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.getQualifier()
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.getClassid()
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.toLowerCase()
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.contains(ModelConstants.ORCID)) {
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if (pidProvenance
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.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY)) {
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p.getQualifier().setClassid(ModelConstants.ORCID);
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} else {
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p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
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}
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final String orcid = p
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.getValue()
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.trim()
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.toLowerCase()
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.replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4");
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if (orcid.length() == ORCID_LEN) {
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p.setValue(orcid);
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} else {
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p.setValue("");
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}
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}
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return p;
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})
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.collect(
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Collectors
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.toMap(
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p -> p.getQualifier().getClassid() + p.getValue(),
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Function.identity(),
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(p1, p2) -> p1,
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LinkedHashMap::new))
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.values()
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.stream()
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.collect(Collectors.toList()));
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}
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}
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}
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if (value instanceof Publication) {
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} else if (value instanceof Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return value;
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}
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private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
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return Optional
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.ofNullable(dateofacceptance)
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.map(Field::getValue)
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.map(GraphCleaningFunctions::cleanDate)
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.filter(Objects::nonNull);
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}
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protected static Optional<String> doCleanDate(String date) {
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return Optional.ofNullable(cleanDate(date));
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}
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public static String cleanDate(final String inputDate) {
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if (StringUtils.isBlank(inputDate)) {
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return null;
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}
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try {
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final LocalDate date = DateParserUtils
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.parseDate(inputDate.trim())
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.toInstant()
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.atZone(ZoneId.systemDefault())
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.toLocalDate();
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return DateTimeFormatter.ofPattern(ModelSupport.DATE_FORMAT).format(date);
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} catch (DateTimeParseException e) {
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return null;
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}
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}
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// HELPERS
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private static boolean isValidAuthorName(Author a) {
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return !Stream
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.of(a.getFullname(), a.getName(), a.getSurname())
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.filter(s -> s != null && !s.isEmpty())
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.collect(Collectors.joining(""))
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.toLowerCase()
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.matches(INVALID_AUTHOR_REGEX);
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}
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private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {
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return pids
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
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.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
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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(CleaningFunctions::normalizePidValue)
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.filter(CleaningFunctions::pidFilter)
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.collect(Collectors.toList());
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}
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private static void fixVocabName(Qualifier q, String vocabularyName) {
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if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
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q.setSchemeid(vocabularyName);
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q.setSchemename(vocabularyName);
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}
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}
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private static AccessRight accessRight(String classid, String classname, String scheme) {
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return OafMapperUtils
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.accessRight(
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classid, classname, scheme, scheme);
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}
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private static Qualifier qualifier(String classid, String classname, String scheme) {
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return OafMapperUtils
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.qualifier(
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classid, classname, scheme, scheme);
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}
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protected static StructuredProperty cleanValue(StructuredProperty 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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}
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}
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