imported core utilities from dhp-common
This commit is contained in:
parent
b803343669
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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 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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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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* @return false if the pid matches the filter criteria, true otherwise.
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*/
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public static boolean pidFilter(StructuredProperty s) {
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final String pidValue = s.getValue();
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if (Objects.isNull(s.getQualifier()) ||
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StringUtils.isBlank(pidValue) ||
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StringUtils.isBlank(pidValue.replaceAll("(?:\\n|\\r|\\t|\\s)", ""))) {
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return false;
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}
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if (CleaningFunctions.PID_BLACKLIST.contains(pidValue)) {
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return false;
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}
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if (PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue)) {
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return false;
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}
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return true;
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}
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/**
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* Utility method that normalises PID values on a per-type basis.
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* @param pid the PID whose value will be normalised.
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* @return the PID containing the normalised value.
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*/
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public static StructuredProperty normalizePidValue(StructuredProperty pid) {
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String value = Optional
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.ofNullable(pid.getValue())
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.map(String::trim)
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.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
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switch (pid.getQualifier().getClassid()) {
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// TODO add cleaning for more PID types as needed
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case "doi":
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pid.setValue(value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX));
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break;
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}
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return pid;
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}
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}
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@ -0,0 +1,225 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import static com.google.common.base.Preconditions.checkArgument;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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import java.io.Serializable;
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import java.nio.charset.StandardCharsets;
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import java.security.MessageDigest;
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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.codec.binary.Hex;
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import org.apache.commons.lang3.StringUtils;
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import com.google.common.collect.HashBiMap;
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import com.google.common.collect.Maps;
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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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/**
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* Factory class for OpenAIRE identifiers in the Graph
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*/
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public class IdentifierFactory implements Serializable {
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public static final String ID_SEPARATOR = "::";
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public static final String ID_PREFIX_SEPARATOR = "|";
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public static final int ID_PREFIX_LEN = 12;
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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] considered authoritative for that PID_TYPE
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*/
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public static final Map<PidType, HashBiMap<String, String>> PID_AUTHORITY = Maps.newHashMap();
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static {
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PID_AUTHORITY.put(PidType.doi, HashBiMap.create());
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PID_AUTHORITY.get(PidType.doi).put(CROSSREF_ID, "Crossref");
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PID_AUTHORITY.get(PidType.doi).put(DATACITE_ID, "Datacite");
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PID_AUTHORITY.put(PidType.pmc, HashBiMap.create());
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PID_AUTHORITY.get(PidType.pmc).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
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PID_AUTHORITY.get(PidType.pmc).put(PUBMED_CENTRAL_ID, "PubMed Central");
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PID_AUTHORITY.put(PidType.pmid, HashBiMap.create());
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PID_AUTHORITY.get(PidType.pmid).put(EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central");
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PID_AUTHORITY.get(PidType.pmid).put(PUBMED_CENTRAL_ID, "PubMed Central");
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PID_AUTHORITY.put(PidType.arXiv, HashBiMap.create());
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PID_AUTHORITY.get(PidType.arXiv).put(ARXIV_ID, "arXiv.org e-Print Archive");
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}
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public static List<StructuredProperty> getPids(List<StructuredProperty> pid, KeyValue collectedFrom) {
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return pidFromInstance(pid, collectedFrom, true).distinct().collect(Collectors.toList());
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}
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public static <T extends Result> String createDOIBoostIdentifier(T entity) {
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if (entity == null)
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return null;
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StructuredProperty pid = null;
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if (entity.getPid() != null) {
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pid = entity
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.getPid()
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.stream()
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.filter(Objects::nonNull)
|
||||
.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.findAny()
|
||||
.orElse(null);
|
||||
} else {
|
||||
if (entity.getInstance() != null) {
|
||||
pid = entity
|
||||
.getInstance()
|
||||
.stream()
|
||||
.filter(i -> i.getPid() != null)
|
||||
.flatMap(i -> i.getPid().stream())
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.findAny()
|
||||
.orElse(null);
|
||||
}
|
||||
}
|
||||
if (pid != null)
|
||||
return idFromPid(entity, pid, true);
|
||||
return null;
|
||||
}
|
||||
|
||||
/**
|
||||
* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
|
||||
* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
|
||||
*
|
||||
* @param entity the entity providing PIDs and a default ID.
|
||||
* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
|
||||
* @param md5 indicates whether should hash the PID value or not.
|
||||
* @return an identifier from the most relevant PID, entity.id otherwise
|
||||
*/
|
||||
public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
|
||||
|
||||
checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
|
||||
|
||||
final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
|
||||
|
||||
return pids
|
||||
.values()
|
||||
.stream()
|
||||
.flatMap(s -> s.stream())
|
||||
.min(new PidComparator<>(entity))
|
||||
.map(
|
||||
min -> Optional
|
||||
.ofNullable(pids.get(min.getQualifier().getClassid()))
|
||||
.map(
|
||||
p -> p
|
||||
.stream()
|
||||
.sorted(new PidValueComparator())
|
||||
.findFirst()
|
||||
.map(s -> idFromPid(entity, s, md5))
|
||||
.orElseGet(entity::getId))
|
||||
.orElseGet(entity::getId))
|
||||
.orElseGet(entity::getId);
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
|
||||
if (entity instanceof Result) {
|
||||
return Optional
|
||||
.ofNullable(((Result) entity).getInstance())
|
||||
.map(
|
||||
instance -> mapPids(instance))
|
||||
.orElse(new HashMap<>());
|
||||
} else {
|
||||
return entity
|
||||
.getPid()
|
||||
.stream()
|
||||
.map(CleaningFunctions::normalizePidValue)
|
||||
.filter(CleaningFunctions::pidFilter)
|
||||
.collect(
|
||||
Collectors
|
||||
.groupingBy(
|
||||
p -> p.getQualifier().getClassid(),
|
||||
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
|
||||
}
|
||||
}
|
||||
|
||||
private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
|
||||
return instance
|
||||
.stream()
|
||||
.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
|
||||
.flatMap(Function.identity())
|
||||
.collect(
|
||||
Collectors
|
||||
.groupingBy(
|
||||
p -> p.getQualifier().getClassid(),
|
||||
Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
|
||||
}
|
||||
|
||||
private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
|
||||
boolean mapHandles) {
|
||||
return Optional
|
||||
.ofNullable(pid)
|
||||
.map(
|
||||
pp -> pp
|
||||
.stream()
|
||||
// filter away PIDs provided by a DS that is not considered an authority for the
|
||||
// given PID Type
|
||||
.filter(p -> {
|
||||
return shouldFilterPid(collectedFrom, p, mapHandles);
|
||||
})
|
||||
.map(CleaningFunctions::normalizePidValue)
|
||||
.filter(CleaningFunctions::pidFilter))
|
||||
.orElse(Stream.empty());
|
||||
}
|
||||
|
||||
private static boolean shouldFilterPid(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
|
||||
final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
|
||||
return (mapHandles && pType.equals(PidType.handle)) || Optional.ofNullable(collectedFrom).isPresent() &&
|
||||
Optional
|
||||
.ofNullable(PID_AUTHORITY.get(pType))
|
||||
.map(authorities -> {
|
||||
return authorities.containsKey(collectedFrom.getKey())
|
||||
|| authorities.containsValue(collectedFrom.getValue());
|
||||
})
|
||||
.orElse(false);
|
||||
}
|
||||
|
||||
/**
|
||||
* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
|
||||
*/
|
||||
public static <T extends OafEntity> String createIdentifier(T entity) {
|
||||
|
||||
return createIdentifier(entity, true);
|
||||
}
|
||||
|
||||
private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
|
||||
return new StringBuilder()
|
||||
.append(ModelSupport.getIdPrefix(entity.getClass()))
|
||||
.append(ID_PREFIX_SEPARATOR)
|
||||
.append(createPrefix(s.getQualifier().getClassid()))
|
||||
.append(ID_SEPARATOR)
|
||||
.append(md5 ? md5(s.getValue()) : s.getValue())
|
||||
.toString();
|
||||
}
|
||||
|
||||
// create the prefix (length = 12)
|
||||
private static String createPrefix(String pidType) {
|
||||
StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
|
||||
while (prefix.length() < ID_PREFIX_LEN) {
|
||||
prefix.append("_");
|
||||
}
|
||||
return prefix.substring(0, ID_PREFIX_LEN);
|
||||
}
|
||||
|
||||
public static String md5(final String s) {
|
||||
try {
|
||||
final MessageDigest md = MessageDigest.getInstance("MD5");
|
||||
md.update(s.getBytes(StandardCharsets.UTF_8));
|
||||
return new String(Hex.encodeHex(md.digest()));
|
||||
} catch (final Exception e) {
|
||||
System.err.println("Error creating id");
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,22 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
public class ModelHardLimits {
|
||||
|
||||
public static final String LAYOUT = "index";
|
||||
public static final String INTERPRETATION = "openaire";
|
||||
public static final String SEPARATOR = "-";
|
||||
|
||||
public static final int MAX_EXTERNAL_ENTITIES = 50;
|
||||
public static final int MAX_AUTHORS = 200;
|
||||
public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
|
||||
public static final int MAX_TITLE_LENGTH = 5000;
|
||||
public static final int MAX_TITLES = 10;
|
||||
public static final int MAX_ABSTRACT_LENGTH = 150000;
|
||||
public static final int MAX_INSTANCES = 10;
|
||||
|
||||
public static String getCollectionName(String format) {
|
||||
return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,364 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
|
||||
|
||||
import java.util.*;
|
||||
import java.util.concurrent.ConcurrentHashMap;
|
||||
import java.util.function.Function;
|
||||
import java.util.function.Predicate;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.AccessRightComparator;
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
|
||||
public class OafMapperUtils {
|
||||
|
||||
public static Oaf merge(final Oaf left, final Oaf right) {
|
||||
if (ModelSupport.isSubClass(left, OafEntity.class)) {
|
||||
return mergeEntities((OafEntity) left, (OafEntity) right);
|
||||
} else if (ModelSupport.isSubClass(left, Relation.class)) {
|
||||
((Relation) left).mergeFrom((Relation) right);
|
||||
} else {
|
||||
throw new RuntimeException("invalid Oaf type:" + left.getClass().getCanonicalName());
|
||||
}
|
||||
return left;
|
||||
}
|
||||
|
||||
public static OafEntity mergeEntities(OafEntity left, OafEntity right) {
|
||||
if (ModelSupport.isSubClass(left, Result.class)) {
|
||||
return mergeResults((Result) left, (Result) right);
|
||||
} else if (ModelSupport.isSubClass(left, Datasource.class)) {
|
||||
((Datasource) left).mergeFrom((Datasource) right);
|
||||
} else if (ModelSupport.isSubClass(left, Organization.class)) {
|
||||
((Organization) left).mergeFrom((Organization) right);
|
||||
} else if (ModelSupport.isSubClass(left, Project.class)) {
|
||||
((Project) left).mergeFrom((Project) right);
|
||||
} else {
|
||||
throw new RuntimeException("invalid OafEntity subtype:" + left.getClass().getCanonicalName());
|
||||
}
|
||||
return left;
|
||||
}
|
||||
|
||||
public static Result mergeResults(Result left, Result right) {
|
||||
if (new ResultTypeComparator().compare(left, right) < 0) {
|
||||
left.mergeFrom(right);
|
||||
return left;
|
||||
} else {
|
||||
right.mergeFrom(left);
|
||||
return right;
|
||||
}
|
||||
}
|
||||
|
||||
public static KeyValue keyValue(final String k, final String v) {
|
||||
final KeyValue kv = new KeyValue();
|
||||
kv.setKey(k);
|
||||
kv.setValue(v);
|
||||
return kv;
|
||||
}
|
||||
|
||||
public static List<KeyValue> listKeyValues(final String... s) {
|
||||
if (s.length % 2 > 0) {
|
||||
throw new RuntimeException("Invalid number of parameters (k,v,k,v,....)");
|
||||
}
|
||||
|
||||
final List<KeyValue> list = new ArrayList<>();
|
||||
for (int i = 0; i < s.length; i += 2) {
|
||||
list.add(keyValue(s[i], s[i + 1]));
|
||||
}
|
||||
return list;
|
||||
}
|
||||
|
||||
public static <T> Field<T> field(final T value, final DataInfo info) {
|
||||
if (value == null || StringUtils.isBlank(value.toString())) {
|
||||
return null;
|
||||
}
|
||||
|
||||
final Field<T> field = new Field<>();
|
||||
field.setValue(value);
|
||||
field.setDataInfo(info);
|
||||
return field;
|
||||
}
|
||||
|
||||
public static List<Field<String>> listFields(final DataInfo info, final String... values) {
|
||||
return Arrays
|
||||
.stream(values)
|
||||
.map(v -> field(v, info))
|
||||
.filter(Objects::nonNull)
|
||||
.filter(distinctByKey(f -> f.getValue()))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
|
||||
return values
|
||||
.stream()
|
||||
.map(v -> field(v, info))
|
||||
.filter(Objects::nonNull)
|
||||
.filter(distinctByKey(f -> f.getValue()))
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
public static Qualifier unknown(final String schemeid, final String schemename) {
|
||||
return qualifier("UNKNOWN", "Unknown", schemeid, schemename);
|
||||
}
|
||||
|
||||
public static AccessRight accessRight(
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename) {
|
||||
return accessRight(classid, classname, schemeid, schemename, null);
|
||||
}
|
||||
|
||||
public static AccessRight accessRight(
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename,
|
||||
final OpenAccessRoute openAccessRoute) {
|
||||
final AccessRight accessRight = new AccessRight();
|
||||
accessRight.setClassid(classid);
|
||||
accessRight.setClassname(classname);
|
||||
accessRight.setSchemeid(schemeid);
|
||||
accessRight.setSchemename(schemename);
|
||||
accessRight.setOpenAccessRoute(openAccessRoute);
|
||||
return accessRight;
|
||||
}
|
||||
|
||||
public static Qualifier qualifier(
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename) {
|
||||
final Qualifier q = new Qualifier();
|
||||
q.setClassid(classid);
|
||||
q.setClassname(classname);
|
||||
q.setSchemeid(schemeid);
|
||||
q.setSchemename(schemename);
|
||||
return q;
|
||||
}
|
||||
|
||||
public static Qualifier qualifier(final Qualifier qualifier) {
|
||||
final Qualifier q = new Qualifier();
|
||||
q.setClassid(qualifier.getClassid());
|
||||
q.setClassname(qualifier.getClassname());
|
||||
q.setSchemeid(qualifier.getSchemeid());
|
||||
q.setSchemename(qualifier.getSchemename());
|
||||
return q;
|
||||
}
|
||||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final String classid,
|
||||
final String classname,
|
||||
final String schemeid,
|
||||
final String schemename,
|
||||
final DataInfo dataInfo) {
|
||||
|
||||
return structuredProperty(value, qualifier(classid, classname, schemeid, schemename), dataInfo);
|
||||
}
|
||||
|
||||
public static StructuredProperty structuredProperty(
|
||||
final String value,
|
||||
final Qualifier qualifier,
|
||||
final DataInfo dataInfo) {
|
||||
if (value == null) {
|
||||
return null;
|
||||
}
|
||||
final StructuredProperty sp = new StructuredProperty();
|
||||
sp.setValue(value);
|
||||
sp.setQualifier(qualifier);
|
||||
sp.setDataInfo(dataInfo);
|
||||
return sp;
|
||||
}
|
||||
|
||||
public static ExtraInfo extraInfo(
|
||||
final String name,
|
||||
final String value,
|
||||
final String typology,
|
||||
final String provenance,
|
||||
final String trust) {
|
||||
final ExtraInfo info = new ExtraInfo();
|
||||
info.setName(name);
|
||||
info.setValue(value);
|
||||
info.setTypology(typology);
|
||||
info.setProvenance(provenance);
|
||||
info.setTrust(trust);
|
||||
return info;
|
||||
}
|
||||
|
||||
public static OAIProvenance oaiIProvenance(
|
||||
final String identifier,
|
||||
final String baseURL,
|
||||
final String metadataNamespace,
|
||||
final Boolean altered,
|
||||
final String datestamp,
|
||||
final String harvestDate) {
|
||||
|
||||
final OriginDescription desc = new OriginDescription();
|
||||
desc.setIdentifier(identifier);
|
||||
desc.setBaseURL(baseURL);
|
||||
desc.setMetadataNamespace(metadataNamespace);
|
||||
desc.setAltered(altered);
|
||||
desc.setDatestamp(datestamp);
|
||||
desc.setHarvestDate(harvestDate);
|
||||
|
||||
final OAIProvenance p = new OAIProvenance();
|
||||
p.setOriginDescription(desc);
|
||||
|
||||
return p;
|
||||
}
|
||||
|
||||
public static Journal journal(
|
||||
final String name,
|
||||
final String issnPrinted,
|
||||
final String issnOnline,
|
||||
final String issnLinking,
|
||||
final DataInfo dataInfo) {
|
||||
return journal(
|
||||
name,
|
||||
issnPrinted,
|
||||
issnOnline,
|
||||
issnLinking,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
null,
|
||||
dataInfo);
|
||||
}
|
||||
|
||||
public static Journal journal(
|
||||
final String name,
|
||||
final String issnPrinted,
|
||||
final String issnOnline,
|
||||
final String issnLinking,
|
||||
final String ep,
|
||||
final String iss,
|
||||
final String sp,
|
||||
final String vol,
|
||||
final String edition,
|
||||
final String conferenceplace,
|
||||
final String conferencedate,
|
||||
final DataInfo dataInfo) {
|
||||
|
||||
if (StringUtils.isNotBlank(name)
|
||||
|| StringUtils.isNotBlank(issnPrinted)
|
||||
|| StringUtils.isNotBlank(issnOnline)
|
||||
|| StringUtils.isNotBlank(issnLinking)) {
|
||||
final Journal j = new Journal();
|
||||
j.setName(name);
|
||||
j.setIssnPrinted(issnPrinted);
|
||||
j.setIssnOnline(issnOnline);
|
||||
j.setIssnLinking(issnLinking);
|
||||
j.setEp(ep);
|
||||
j.setIss(iss);
|
||||
j.setSp(sp);
|
||||
j.setVol(vol);
|
||||
j.setEdition(edition);
|
||||
j.setConferenceplace(conferenceplace);
|
||||
j.setConferencedate(conferencedate);
|
||||
j.setDataInfo(dataInfo);
|
||||
return j;
|
||||
} else {
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
||||
public static DataInfo dataInfo(
|
||||
final Boolean deletedbyinference,
|
||||
final String inferenceprovenance,
|
||||
final Boolean inferred,
|
||||
final Boolean invisible,
|
||||
final Qualifier provenanceaction,
|
||||
final String trust) {
|
||||
final DataInfo d = new DataInfo();
|
||||
d.setDeletedbyinference(deletedbyinference);
|
||||
d.setInferenceprovenance(inferenceprovenance);
|
||||
d.setInferred(inferred);
|
||||
d.setInvisible(invisible);
|
||||
d.setProvenanceaction(provenanceaction);
|
||||
d.setTrust(trust);
|
||||
return d;
|
||||
}
|
||||
|
||||
public static String createOpenaireId(
|
||||
final int prefix,
|
||||
final String originalId,
|
||||
final boolean to_md5) {
|
||||
if (StringUtils.isBlank(originalId)) {
|
||||
return null;
|
||||
} else if (to_md5) {
|
||||
final String nsPrefix = StringUtils.substringBefore(originalId, "::");
|
||||
final String rest = StringUtils.substringAfter(originalId, "::");
|
||||
return String.format("%s|%s::%s", prefix, nsPrefix, IdentifierFactory.md5(rest));
|
||||
} else {
|
||||
return String.format("%s|%s", prefix, originalId);
|
||||
}
|
||||
}
|
||||
|
||||
public static String createOpenaireId(
|
||||
final String type,
|
||||
final String originalId,
|
||||
final boolean to_md5) {
|
||||
switch (type) {
|
||||
case "datasource":
|
||||
return createOpenaireId(10, originalId, to_md5);
|
||||
case "organization":
|
||||
return createOpenaireId(20, originalId, to_md5);
|
||||
case "person":
|
||||
return createOpenaireId(30, originalId, to_md5);
|
||||
case "project":
|
||||
return createOpenaireId(40, originalId, to_md5);
|
||||
default:
|
||||
return createOpenaireId(50, originalId, to_md5);
|
||||
}
|
||||
}
|
||||
|
||||
public static String asString(final Object o) {
|
||||
return o == null ? "" : o.toString();
|
||||
}
|
||||
|
||||
public static <T> Predicate<T> distinctByKey(
|
||||
final Function<? super T, ?> keyExtractor) {
|
||||
final Map<Object, Boolean> seen = new ConcurrentHashMap<>();
|
||||
return t -> seen.putIfAbsent(keyExtractor.apply(t), Boolean.TRUE) == null;
|
||||
}
|
||||
|
||||
public static Qualifier createBestAccessRights(final List<Instance> instanceList) {
|
||||
return getBestAccessRights(instanceList);
|
||||
}
|
||||
|
||||
protected static Qualifier getBestAccessRights(final List<Instance> instanceList) {
|
||||
if (instanceList != null) {
|
||||
final Optional<AccessRight> min = instanceList
|
||||
.stream()
|
||||
.map(i -> i.getAccessright())
|
||||
.min(new AccessRightComparator<>());
|
||||
|
||||
final Qualifier rights = min.isPresent() ? qualifier(min.get()) : new Qualifier();
|
||||
|
||||
if (StringUtils.isBlank(rights.getClassid())) {
|
||||
rights.setClassid(UNKNOWN);
|
||||
}
|
||||
if (StringUtils.isBlank(rights.getClassname())
|
||||
|| UNKNOWN.equalsIgnoreCase(rights.getClassname())) {
|
||||
rights.setClassname(NOT_AVAILABLE);
|
||||
}
|
||||
if (StringUtils.isBlank(rights.getSchemeid())) {
|
||||
rights.setSchemeid(DNET_ACCESS_MODES);
|
||||
}
|
||||
if (StringUtils.isBlank(rights.getSchemename())) {
|
||||
rights.setSchemename(DNET_ACCESS_MODES);
|
||||
}
|
||||
|
||||
return rights;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,38 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class OrganizationPidComparator implements Comparator<StructuredProperty> {
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
|
||||
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
|
||||
|
||||
if (lClass.equals(PidType.openorgs))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.openorgs))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.GRID))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.GRID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.mag_id))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.mag_id))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.urn))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.urn))
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,8 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.HashMap;
|
||||
import java.util.HashSet;
|
||||
|
||||
public class PidBlacklist extends HashMap<String, HashSet<String>> {
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.HashSet;
|
||||
import java.util.Optional;
|
||||
import java.util.Set;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
public class PidBlacklistProvider {
|
||||
|
||||
private static final PidBlacklist blacklist;
|
||||
|
||||
static {
|
||||
try {
|
||||
String json = IOUtils.toString(IdentifierFactory.class.getResourceAsStream("pid_blacklist.json"));
|
||||
blacklist = new ObjectMapper().readValue(json, PidBlacklist.class);
|
||||
|
||||
} catch (IOException e) {
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
public static PidBlacklist getBlacklist() {
|
||||
return blacklist;
|
||||
}
|
||||
|
||||
public static Set<String> getBlacklist(String pidType) {
|
||||
return Optional
|
||||
.ofNullable(getBlacklist().get(pidType))
|
||||
.orElse(new HashSet<>());
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,48 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
import eu.dnetlib.dhp.schema.oaf.Organization;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class PidComparator<T extends OafEntity> implements Comparator<StructuredProperty> {
|
||||
|
||||
private T entity;
|
||||
|
||||
public PidComparator(T entity) {
|
||||
this.entity = entity;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
if (ModelSupport.isSubClass(entity, Result.class)) {
|
||||
return compareResultPids(left, right);
|
||||
}
|
||||
if (ModelSupport.isSubClass(entity, Organization.class)) {
|
||||
return compareOrganizationtPids(left, right);
|
||||
}
|
||||
|
||||
// Else (but unlikely), lexicographical ordering will do.
|
||||
return left.getQualifier().getClassid().compareTo(right.getQualifier().getClassid());
|
||||
}
|
||||
|
||||
private int compareResultPids(StructuredProperty left, StructuredProperty right) {
|
||||
return new ResultPidComparator().compare(left, right);
|
||||
}
|
||||
|
||||
private int compareOrganizationtPids(StructuredProperty left, StructuredProperty right) {
|
||||
return new OrganizationPidComparator().compare(left, right);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,29 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import org.apache.commons.lang3.EnumUtils;
|
||||
|
||||
public enum PidType {
|
||||
|
||||
// Result
|
||||
doi, pmid, pmc, handle, arXiv, nct, pdb,
|
||||
|
||||
// Organization
|
||||
openorgs, corda, corda_h2020, GRID, mag_id, urn,
|
||||
|
||||
// Used by dedup
|
||||
undefined, original;
|
||||
|
||||
public static boolean isValid(String type) {
|
||||
return EnumUtils.isValidEnum(PidType.class, type);
|
||||
}
|
||||
|
||||
public static PidType tryValueOf(String s) {
|
||||
try {
|
||||
return PidType.valueOf(s);
|
||||
} catch (Exception e) {
|
||||
return PidType.original;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
import java.util.Optional;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class PidValueComparator implements Comparator<StructuredProperty> {
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
StructuredProperty l = CleaningFunctions.normalizePidValue(left);
|
||||
StructuredProperty r = CleaningFunctions.normalizePidValue(right);
|
||||
|
||||
return Optional
|
||||
.ofNullable(l.getValue())
|
||||
.map(
|
||||
lv -> Optional
|
||||
.ofNullable(r.getValue())
|
||||
.map(rv -> lv.compareTo(rv))
|
||||
.orElse(-1))
|
||||
.orElse(1);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,53 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Comparator;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
|
||||
|
||||
public class ResultPidComparator implements Comparator<StructuredProperty> {
|
||||
|
||||
@Override
|
||||
public int compare(StructuredProperty left, StructuredProperty right) {
|
||||
|
||||
PidType lClass = PidType.tryValueOf(left.getQualifier().getClassid());
|
||||
PidType rClass = PidType.tryValueOf(right.getQualifier().getClassid());
|
||||
|
||||
if (lClass.equals(PidType.doi))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.doi))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pmid))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pmid))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pmc))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pmc))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.handle))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.handle))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.arXiv))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.arXiv))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.nct))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.nct))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(PidType.pdb))
|
||||
return -1;
|
||||
if (rClass.equals(PidType.pdb))
|
||||
return 1;
|
||||
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static eu.dnetlib.dhp.schema.common.ModelConstants.CROSSREF_ID;
|
||||
|
||||
import java.util.Comparator;
|
||||
import java.util.HashSet;
|
||||
import java.util.Optional;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class ResultTypeComparator implements Comparator<Result> {
|
||||
|
||||
@Override
|
||||
public int compare(Result left, Result right) {
|
||||
|
||||
if (left == null && right == null)
|
||||
return 0;
|
||||
if (left == null)
|
||||
return 1;
|
||||
if (right == null)
|
||||
return -1;
|
||||
|
||||
HashSet<String> lCf = getCollectedFromIds(left);
|
||||
HashSet<String> rCf = getCollectedFromIds(right);
|
||||
|
||||
if (lCf.contains(CROSSREF_ID) && !rCf.contains(CROSSREF_ID)) {
|
||||
return -1;
|
||||
}
|
||||
if (!lCf.contains(CROSSREF_ID) && rCf.contains(CROSSREF_ID)) {
|
||||
return 1;
|
||||
}
|
||||
|
||||
String lClass = left.getResulttype().getClassid();
|
||||
String rClass = right.getResulttype().getClassid();
|
||||
|
||||
if (lClass.equals(rClass))
|
||||
return 0;
|
||||
|
||||
if (lClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
if (lClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||
return -1;
|
||||
if (rClass.equals(ModelConstants.ORP_RESULTTYPE_CLASSID))
|
||||
return 1;
|
||||
|
||||
// Else (but unlikely), lexicographical ordering will do.
|
||||
return lClass.compareTo(rClass);
|
||||
}
|
||||
|
||||
protected HashSet<String> getCollectedFromIds(Result left) {
|
||||
return Optional
|
||||
.ofNullable(left.getCollectedfrom())
|
||||
.map(
|
||||
cf -> cf
|
||||
.stream()
|
||||
.map(c -> c.getKey())
|
||||
.collect(Collectors.toCollection(HashSet::new)))
|
||||
.orElse(new HashSet<>());
|
||||
}
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -0,0 +1,21 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import java.util.Set;
|
||||
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
public class BlackListProviderTest {
|
||||
|
||||
@Test
|
||||
public void blackListTest() {
|
||||
|
||||
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist());
|
||||
Assertions.assertNotNull(PidBlacklistProvider.getBlacklist().get("doi"));
|
||||
Assertions.assertTrue(PidBlacklistProvider.getBlacklist().get("doi").size() > 0);
|
||||
final Set<String> xxx = PidBlacklistProvider.getBlacklist("xxx");
|
||||
Assertions.assertNotNull(xxx);
|
||||
Assertions.assertEquals(0, xxx.size());
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,75 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
|
||||
import java.io.IOException;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
|
||||
public class IdentifierFactoryTest {
|
||||
|
||||
private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@Test
|
||||
public void testCreateIdentifierForPublication() throws IOException {
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_doi1.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_doi2.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_doi3.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_doi4.json", "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
|
||||
|
||||
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
|
||||
verifyIdentifier("publication_3.json", defaultID, true);
|
||||
verifyIdentifier("publication_4.json", defaultID, true);
|
||||
verifyIdentifier("publication_5.json", defaultID, true);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testCreateIdentifierForPublicationNoHash() throws IOException {
|
||||
|
||||
verifyIdentifier("publication_doi1.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
|
||||
verifyIdentifier("publication_doi2.json", "50|doi_________::10.1016/j.cmet.2010.03.013", false);
|
||||
verifyIdentifier("publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
|
||||
verifyIdentifier(
|
||||
"publication_urn1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", false);
|
||||
|
||||
final String defaultID = "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f";
|
||||
verifyIdentifier("publication_3.json", defaultID, false);
|
||||
verifyIdentifier("publication_4.json", defaultID, false);
|
||||
verifyIdentifier("publication_5.json", defaultID, false);
|
||||
}
|
||||
|
||||
protected void verifyIdentifier(String filename, String expectedID, boolean md5) throws IOException {
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
|
||||
final Publication pub = OBJECT_MAPPER.readValue(json, Publication.class);
|
||||
|
||||
String id = IdentifierFactory.createIdentifier(pub, md5);
|
||||
|
||||
assertNotNull(id);
|
||||
assertEquals(expectedID, id);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,69 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
import eu.dnetlib.dhp.schema.oaf.KeyValue;
|
||||
import eu.dnetlib.dhp.schema.oaf.Publication;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class OafMapperUtilsTest {
|
||||
|
||||
private static ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@Test
|
||||
public void testMergePubs() throws IOException {
|
||||
Publication p1 = read("publication_1.json", Publication.class);
|
||||
Publication p2 = read("publication_2.json", Publication.class);
|
||||
Dataset d1 = read("dataset_1.json", Dataset.class);
|
||||
Dataset d2 = read("dataset_2.json", Dataset.class);
|
||||
|
||||
assertEquals(p1.getCollectedfrom().size(), 1);
|
||||
assertEquals(p1.getCollectedfrom().get(0).getKey(), ModelConstants.CROSSREF_ID);
|
||||
assertEquals(d2.getCollectedfrom().size(), 1);
|
||||
assertFalse(cfId(d2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
|
||||
|
||||
assertTrue(
|
||||
OafMapperUtils
|
||||
.mergeResults(p1, d2)
|
||||
.getResulttype()
|
||||
.getClassid()
|
||||
.equals(ModelConstants.PUBLICATION_RESULTTYPE_CLASSID));
|
||||
|
||||
assertEquals(p2.getCollectedfrom().size(), 1);
|
||||
assertFalse(cfId(p2.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
|
||||
assertEquals(d1.getCollectedfrom().size(), 1);
|
||||
assertTrue(cfId(d1.getCollectedfrom()).contains(ModelConstants.CROSSREF_ID));
|
||||
|
||||
assertTrue(
|
||||
OafMapperUtils
|
||||
.mergeResults(p2, d1)
|
||||
.getResulttype()
|
||||
.getClassid()
|
||||
.equals(ModelConstants.DATASET_RESULTTYPE_CLASSID));
|
||||
}
|
||||
|
||||
protected HashSet<String> cfId(List<KeyValue> collectedfrom) {
|
||||
return collectedfrom.stream().map(c -> c.getKey()).collect(Collectors.toCollection(HashSet::new));
|
||||
}
|
||||
|
||||
protected <T extends Result> T read(String filename, Class<T> clazz) throws IOException {
|
||||
final String json = IOUtils.toString(getClass().getResourceAsStream(filename));
|
||||
return OBJECT_MAPPER.readValue(json, clazz);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1g", "resuttype" : { "classid" : "dataset" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository B"} ]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resuttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value" : "Crossref"} ]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", "resuttype" : { "classid" : "publication" }, "pid":[{"qualifier":{"classid":"doi"},"value":"10.1016/j.cmet.2011.03.013"},{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}], "collectedfrom" : [ { "key" : "10|openaire____::081b82f96300b6a6e3d282bad31cb6e3", "value" : "Repository A"} ]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"scp-number"},"value":"79953761260"}]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[]}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f"}
|
||||
|
|
@ -0,0 +1,33 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
|
||||
"value": "Crossref"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "urn"},
|
||||
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "scp-number"},
|
||||
"value": "79953761260"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2",
|
||||
"value": "Crossref"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
|
||||
"value": "Europe PubMed Central"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "urn"},
|
||||
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "scp-number"},
|
||||
"value": "79953761260"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|openaire____::1234",
|
||||
"value": "Zenodo"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
|
||||
"value": "Europe PubMed Central"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "urn"},
|
||||
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "scp-number"},
|
||||
"value": "79953761260"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,37 @@
|
|||
{
|
||||
"id": "50|od______2852::38861c44e6052a8d49f59a4c39ba5e66",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|openaire____::1234",
|
||||
"value": "Zenodo"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "handle"},
|
||||
"value": "11012/83840"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::2852",
|
||||
"value": "Digital library of Brno University of Technology"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "handle"},
|
||||
"value": "11012/83840"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1 @@
|
|||
{"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f","pid":[{"qualifier":{"classid":"urn"},"value":"urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"},{"qualifier":{"classid":"scp-number"},"value":"79953761260"},{"qualifier":{"classid":"pmc"},"value":"21459329"}]}
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
{
|
||||
"id":"50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c",
|
||||
"value": "Europe PubMed Central"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
},
|
||||
{
|
||||
"qualifier":{"classid":"pmc"},
|
||||
"value":"21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
@ -0,0 +1,23 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {
|
||||
"classid": "urn"
|
||||
},
|
||||
"value": "urn:nbn:nl:ui:29-f3ed5f9e-edf6-457e-8848-61b58a4075e2"
|
||||
},
|
||||
{
|
||||
"qualifier": {
|
||||
"classid": "scp-number"
|
||||
},
|
||||
"value": "79953761260"
|
||||
},
|
||||
{
|
||||
"qualifier": {
|
||||
"classid": "pmcid"
|
||||
},
|
||||
"value": "21459329"
|
||||
}
|
||||
]
|
||||
}
|
||||
Loading…
Reference in New Issue