CleaningFunctions should only define the minimal necessary methods used in this module, the rest is moved in dnet-hadoop
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@ -1,360 +1,27 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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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 java.util.HashSet;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.Set;
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import org.apache.commons.lang3.StringUtils;
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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.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class CleaningFunctions {
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public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10.)";
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public static final String DOI_PREFIX = "10.";
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public static final String ORCID_PREFIX_REGEX = "^http(s?):\\/\\/orcid\\.org\\/";
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public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
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public static final Set<String> PID_BLACKLIST = new HashSet<>();
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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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static {
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PID_BLACKLIST.add("none");
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PID_BLACKLIST.add("na");
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}
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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.nonNull(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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// 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.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(CleaningFunctions::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 -> sp
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.getValue()
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.toLowerCase()
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.replaceAll(TITLE_FILTER_REGEX, "")
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.length() > TITLE_FILTER_RESIDUAL_LENGTH)
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.map(CleaningFunctions::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(CleaningFunctions::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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Optional
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.ofNullable(i.getPid())
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.ifPresent(pid -> {
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final Set<StructuredProperty> pids = pid
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.stream()
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.filter(Objects::nonNull)
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.collect(Collectors.toCollection(HashSet::new));
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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 = altId
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.stream()
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.filter(Objects::nonNull)
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.filter(p -> StringUtils.isNotBlank(p.getValue()))
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.collect(Collectors.toCollection(HashSet::new));
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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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}
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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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final List<Author> authors = Lists.newArrayList();
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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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p.setValue(p.getValue().trim().replaceAll(ORCID_PREFIX_REGEX, ""));
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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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StructuredProperty::getValue, Function.identity(), (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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if (StringUtils.isBlank(a.getFullname())) {
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if (StringUtils.isNotBlank(a.getName()) && StringUtils.isNotBlank(a.getSurname())) {
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a.setFullname(a.getSurname() + ", " + a.getName());
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}
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}
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if (StringUtils.isNotBlank(a.getFullname()) && isValidAuthorName(a)) {
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authors.add(a);
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}
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}
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boolean nullRank = authors
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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 : authors) {
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author.setRank(i++);
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}
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}
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r.setAuthor(authors);
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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 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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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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// HELPERS
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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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/**
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* Utility method that filter PID values on a per-type basis.
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* @param s the PID whose value will be checked.
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