1007 lines
32 KiB
Java
1007 lines
32 KiB
Java
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package eu.dnetlib.dhp.schema.oaf.utils;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
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import static eu.dnetlib.dhp.schema.common.ModelConstants.OPENAIRE_META_RESOURCE_TYPE;
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import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.getProvenance;
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import java.net.MalformedURLException;
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import java.net.URL;
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import java.time.LocalDate;
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import java.time.ZoneId;
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import java.time.format.DateTimeFormatter;
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import java.time.format.DateTimeParseException;
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import java.util.*;
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import java.util.function.Function;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.lang3.StringUtils;
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import com.github.sisyphsu.dateparser.DateParserUtils;
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import com.google.common.collect.Lists;
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import com.google.common.collect.Sets;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
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import eu.dnetlib.dhp.common.vocabulary.VocabularyTerm;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import me.xuender.unidecode.Unidecode;
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public class GraphCleaningFunctions extends CleaningFunctions {
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public static final String DNET_PUBLISHERS = "dnet:publishers";
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public static final String DNET_LICENSES = "dnet:licenses";
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public static final String ORCID_CLEANING_REGEX = ".*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9]{4}).*[-–—−=].*([0-9x]{4})";
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public static final int ORCID_LEN = 19;
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public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)";
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public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*";
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public static final String TITLE_TEST = "test";
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public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
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public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
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private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
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private static final Set<String> INVALID_AUTHOR_NAMES = new HashSet<>();
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private static final Set<String> INVALID_URLS = new HashSet<>();
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private static final Set<String> INVALID_URL_HOSTS = new HashSet<>();
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private static final HashSet<String> PEER_REVIEWED_TYPES = new HashSet<>();
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static {
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PEER_REVIEWED_TYPES.add("Article");
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PEER_REVIEWED_TYPES.add("Part of book or chapter of book");
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PEER_REVIEWED_TYPES.add("Book");
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PEER_REVIEWED_TYPES.add("Doctoral thesis");
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PEER_REVIEWED_TYPES.add("Master thesis");
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PEER_REVIEWED_TYPES.add("Data Paper");
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PEER_REVIEWED_TYPES.add("Thesis");
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PEER_REVIEWED_TYPES.add("Bachelor thesis");
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PEER_REVIEWED_TYPES.add("Conference object");
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INVALID_AUTHOR_NAMES.add("(:null)");
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INVALID_AUTHOR_NAMES.add("(:unap)");
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INVALID_AUTHOR_NAMES.add("(:tba)");
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INVALID_AUTHOR_NAMES.add("(:unas)");
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INVALID_AUTHOR_NAMES.add("(:unav)");
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INVALID_AUTHOR_NAMES.add("(:unkn)");
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INVALID_AUTHOR_NAMES.add("(:unkn) unknown");
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INVALID_AUTHOR_NAMES.add(":none");
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INVALID_AUTHOR_NAMES.add(":null");
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INVALID_AUTHOR_NAMES.add(":unas");
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INVALID_AUTHOR_NAMES.add(":unav");
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INVALID_AUTHOR_NAMES.add(":unkn");
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INVALID_AUTHOR_NAMES.add("[autor desconocido]");
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INVALID_AUTHOR_NAMES.add("[s. n.]");
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INVALID_AUTHOR_NAMES.add("[s.n]");
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INVALID_AUTHOR_NAMES.add("[unknown]");
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INVALID_AUTHOR_NAMES.add("anonymous");
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INVALID_AUTHOR_NAMES.add("n.n.");
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INVALID_AUTHOR_NAMES.add("nn");
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INVALID_AUTHOR_NAMES.add("no name supplied");
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INVALID_AUTHOR_NAMES.add("none");
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INVALID_AUTHOR_NAMES.add("none available");
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INVALID_AUTHOR_NAMES.add("not available not available");
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INVALID_AUTHOR_NAMES.add("null &na;");
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INVALID_AUTHOR_NAMES.add("null anonymous");
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INVALID_AUTHOR_NAMES.add("unbekannt");
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INVALID_AUTHOR_NAMES.add("unknown");
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INVALID_AUTHOR_NAMES.add("autor, Sin");
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INVALID_AUTHOR_NAMES.add("Desconocido / Inconnu,");
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INVALID_URL_HOSTS.add("creativecommons.org");
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INVALID_URL_HOSTS.add("www.academia.edu");
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INVALID_URL_HOSTS.add("academia.edu");
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INVALID_URL_HOSTS.add("researchgate.net");
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INVALID_URL_HOSTS.add("www.researchgate.net");
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INVALID_URLS.add("http://repo.scoap3.org/api");
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INVALID_URLS.add("http://ora.ox.ac.uk/objects/uuid:");
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INVALID_URLS.add("http://ntur.lib.ntu.edu.tw/news/agent_contract.pdf");
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INVALID_URLS.add("https://media.springer.com/full/springer-instructions-for-authors-assets/pdf/SN_BPF_EN.pdf");
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INVALID_URLS.add("http://www.tobaccoinduceddiseases.org/dl/61aad426c96519bea4040a374c6a6110/");
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INVALID_URLS.add("https://www.bilboard.nl/verenigingsbladen/bestuurskundige-berichten");
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}
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public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
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if (ModelSupport.isSubClass(value, Result.class)) {
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final Result res = (Result) value;
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if (shouldCleanContext(res, verifyParam)) {
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res
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.setContext(
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res
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.getContext()
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.stream()
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.filter(c -> !StringUtils.startsWith(c.getId().toLowerCase(), contextId))
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.collect(Collectors.toList()));
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}
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return (T) res;
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} else {
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return value;
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}
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}
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private static boolean shouldCleanContext(Result res, String verifyParam) {
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boolean titleMatch = res
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.getTitle()
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.stream()
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.filter(
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t -> t
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.getQualifier()
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.getClassid()
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.equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid()))
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.anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()));
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return titleMatch && Objects.nonNull(res.getContext());
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}
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public static <T extends Oaf> T cleanCountry(T value, String[] verifyParam, Set<String> hostedBy,
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String collectedfrom, String country) {
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if (ModelSupport.isSubClass(value, Result.class)) {
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final Result res = (Result) value;
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if (res.getInstance().stream().anyMatch(i -> hostedBy.contains(i.getHostedby().getKey())) ||
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!res.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equals(collectedfrom))) {
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return (T) res;
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}
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List<StructuredProperty> ids = getPidsAndAltIds(res).collect(Collectors.toList());
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if (ids
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.stream()
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.anyMatch(
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p -> p
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.getQualifier()
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.getClassid()
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.equals(PidType.doi.toString()) && pidInParam(p.getValue(), verifyParam))) {
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res
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.setCountry(
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res
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.getCountry()
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.stream()
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.filter(
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c -> toTakeCountry(c, country))
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.collect(Collectors.toList()));
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}
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return (T) res;
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} else {
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return value;
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}
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}
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private static <T extends Result> Stream<StructuredProperty> getPidsAndAltIds(T r) {
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final Stream<StructuredProperty> resultPids = Optional
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.ofNullable(r.getPid())
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.map(Collection::stream)
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.orElse(Stream.empty());
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final Stream<StructuredProperty> instancePids = Optional
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.ofNullable(r.getInstance())
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.map(
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instance -> instance
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.stream()
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.flatMap(
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i -> Optional
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.ofNullable(i.getPid())
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.map(Collection::stream)
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.orElse(Stream.empty())))
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.orElse(Stream.empty());
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final Stream<StructuredProperty> instanceAltIds = Optional
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.ofNullable(r.getInstance())
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.map(
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instance -> instance
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.stream()
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.flatMap(
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i -> Optional
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.ofNullable(i.getAlternateIdentifier())
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.map(Collection::stream)
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.orElse(Stream.empty())))
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.orElse(Stream.empty());
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return Stream
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.concat(
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Stream.concat(resultPids, instancePids),
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instanceAltIds);
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}
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private static boolean pidInParam(String value, String[] verifyParam) {
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for (String s : verifyParam)
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if (value.startsWith(s))
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return true;
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return false;
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}
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private static boolean toTakeCountry(Country c, String country) {
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// If dataInfo is not set, or dataInfo.inferenceprovenance is not set or not present then it cannot be
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// inserted via propagation
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if (!Optional.ofNullable(c.getDataInfo()).isPresent())
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return true;
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if (!Optional.ofNullable(c.getDataInfo().getInferenceprovenance()).isPresent())
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return true;
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return !(c
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.getClassid()
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.equalsIgnoreCase(country) &&
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c.getDataInfo().getInferenceprovenance().equals("propagation"));
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}
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public static <T extends Oaf> T fixVocabularyNames(T value) {
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if (value instanceof OafEntity) {
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OafEntity e = (OafEntity) value;
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Optional
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.ofNullable(e.getPid())
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.ifPresent(pid -> pid.forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)));
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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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Optional
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.ofNullable(i.getPid())
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.ifPresent(
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pid -> pid.forEach(p -> fixVocabName(p.getQualifier(), ModelConstants.DNET_PID_TYPES)));
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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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} else 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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}
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} else if (value instanceof Relation) {
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// nothing to clean here
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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 Relation) && (Boolean.TRUE
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.equals(
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Optional
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.ofNullable(value)
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.map(
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o -> Optional
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.ofNullable(o.getDataInfo())
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.map(
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d -> Optional
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.ofNullable(d.getInvisible())
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.orElse(true))
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.orElse(false))
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.orElse(true)))) {
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return true;
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}
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if (value instanceof Datasource) {
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final Datasource d = (Datasource) value;
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return Objects.nonNull(d.getOfficialname()) && StringUtils.isNotBlank(d.getOfficialname().getValue());
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} else if (value instanceof Project) {
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final Project p = (Project) value;
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return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue());
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} else if (value instanceof Organization) {
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// nothing to evaluate here
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} else if (value instanceof Relation) {
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// nothing to clean here
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} else if (value instanceof Result) {
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Result r = (Result) value;
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if (Objects.isNull(r.getTitle()) || r.getTitle().isEmpty()) {
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return false;
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}
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if (value instanceof Publication) {
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} else if (value instanceof Dataset) {
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} else if (value instanceof OtherResearchProduct) {
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} else if (value instanceof Software) {
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}
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}
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return true;
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}
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public static <T extends Oaf> T cleanup(T value, VocabularyGroup vocs) {
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if (Objects.isNull(value.getDataInfo())) {
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final DataInfo d = new DataInfo();
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d.setDeletedbyinference(false);
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value.setDataInfo(d);
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}
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if (value instanceof OafEntity) {
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OafEntity e = (OafEntity) value;
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if (Objects.nonNull(e.getPid())) {
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e.setPid(processPidCleaning(e.getPid()));
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}
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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 Result) {
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Result r = (Result) value;
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if (Objects.isNull(r.getContext())) {
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r.setContext(new ArrayList<>());
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}
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if (Objects.nonNull(r.getFulltext())
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&& (ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
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ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
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r.setFulltext(null);
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}
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if (Objects.nonNull(r.getDateofacceptance())) {
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Optional<String> date = cleanDateField(r.getDateofacceptance());
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if (date.isPresent()) {
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r.getDateofacceptance().setValue(date.get());
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} else {
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r.setDateofacceptance(null);
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}
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}
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if (Objects.nonNull(r.getRelevantdate())) {
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r
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.setRelevantdate(
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r
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.getRelevantdate()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> Objects.nonNull(sp.getQualifier()))
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.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
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.map(sp -> {
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sp.setValue(GraphCleaningFunctions.cleanDate(sp.getValue()));
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return sp;
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})
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.collect(Collectors.toList()));
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}
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if (Objects.nonNull(r.getPublisher())) {
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if (StringUtils.isBlank(r.getPublisher().getValue())) {
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r.setPublisher(null);
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} else {
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r
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.getPublisher()
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.setValue(
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r
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.getPublisher()
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.getValue()
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.replaceAll(NAME_CLEANING_REGEX, " "));
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if (vocs.vocabularyExists(DNET_PUBLISHERS)) {
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vocs
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.find(DNET_PUBLISHERS)
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.map(voc -> voc.getTermBySynonym(r.getPublisher().getValue()))
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.map(VocabularyTerm::getName)
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.ifPresent(publisher -> r.getPublisher().setValue(publisher));
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}
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}
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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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List<Subject> subjects = Lists
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.newArrayList(
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r
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.getSubject()
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.stream()
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.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(s -> {
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if ("dnet:result_subject".equals(s.getQualifier().getClassid())) {
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s.getQualifier().setClassid(ModelConstants.DNET_SUBJECT_TYPOLOGIES);
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s.getQualifier().setClassname(ModelConstants.DNET_SUBJECT_TYPOLOGIES);
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}
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return s;
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})
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.map(GraphCleaningFunctions::cleanValue)
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.collect(
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Collectors
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.toMap(
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s -> Optional
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.ofNullable(s.getQualifier())
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.map(q -> q.getClassid() + s.getValue())
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.orElse(s.getValue()),
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Function.identity(),
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(s1, s2) -> Collections
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.min(Lists.newArrayList(s1, s2), new SubjectProvenanceComparator())))
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.values());
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r.setSubject(subjects);
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}
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if (Objects.nonNull(r.getTitle())) {
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r
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.setTitle(
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r
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.getTitle()
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.stream()
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.filter(Objects::nonNull)
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.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
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.filter(
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sp -> {
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final String title = sp
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.getValue()
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.toLowerCase();
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final String decoded = Unidecode.decode(title);
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if (StringUtils.contains(decoded, TITLE_TEST)) {
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return decoded
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.replaceAll(TITLE_FILTER_REGEX, "")
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.length() > TITLE_FILTER_RESIDUAL_LENGTH;
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}
|
|
return !decoded
|
|
.replaceAll("\\W|\\d", "")
|
|
.isEmpty();
|
|
})
|
|
.map(GraphCleaningFunctions::cleanValue)
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (Objects.nonNull(r.getFormat())) {
|
|
r
|
|
.setFormat(
|
|
r
|
|
.getFormat()
|
|
.stream()
|
|
.map(GraphCleaningFunctions::cleanValue)
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (Objects.nonNull(r.getDescription())) {
|
|
r
|
|
.setDescription(
|
|
r
|
|
.getDescription()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
|
|
.map(GraphCleaningFunctions::cleanValue)
|
|
.sorted((s1, s2) -> s2.getValue().length() - s1.getValue().length())
|
|
.limit(ModelHardLimits.MAX_ABSTRACTS)
|
|
.collect(Collectors.toList()));
|
|
}
|
|
if (Objects.isNull(r.getResourcetype()) || StringUtils.isBlank(r.getResourcetype().getClassid())) {
|
|
r
|
|
.setResourcetype(
|
|
qualifier(ModelConstants.UNKNOWN, "Unknown", ModelConstants.DNET_DATA_CITE_RESOURCE));
|
|
}
|
|
if (Objects.nonNull(r.getInstance())) {
|
|
|
|
for (Instance i : r.getInstance()) {
|
|
if (!vocs
|
|
.termExists(ModelConstants.DNET_PUBLICATION_RESOURCE, i.getInstancetype().getClassid())) {
|
|
if (r instanceof Publication) {
|
|
i
|
|
.setInstancetype(
|
|
OafMapperUtils
|
|
.qualifier(
|
|
"0038", "Other literature type",
|
|
ModelConstants.DNET_PUBLICATION_RESOURCE,
|
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
|
} else if (r instanceof Dataset) {
|
|
i
|
|
.setInstancetype(
|
|
OafMapperUtils
|
|
.qualifier(
|
|
"0039", "Other dataset type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
|
} else if (r instanceof Software) {
|
|
i
|
|
.setInstancetype(
|
|
OafMapperUtils
|
|
.qualifier(
|
|
"0040", "Other software type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
|
} else if (r instanceof OtherResearchProduct) {
|
|
i
|
|
.setInstancetype(
|
|
OafMapperUtils
|
|
.qualifier(
|
|
"0020", "Other ORP type", ModelConstants.DNET_PUBLICATION_RESOURCE,
|
|
ModelConstants.DNET_PUBLICATION_RESOURCE));
|
|
}
|
|
}
|
|
|
|
if (Objects.nonNull(i.getPid())) {
|
|
i.setPid(processPidCleaning(i.getPid()));
|
|
}
|
|
if (Objects.nonNull(i.getAlternateIdentifier())) {
|
|
i.setAlternateIdentifier(processPidCleaning(i.getAlternateIdentifier()));
|
|
}
|
|
Optional
|
|
.ofNullable(i.getPid())
|
|
.ifPresent(pid -> {
|
|
final Set<StructuredProperty> pids = Sets.newHashSet(pid);
|
|
Optional
|
|
.ofNullable(i.getAlternateIdentifier())
|
|
.ifPresent(altId -> {
|
|
final Set<StructuredProperty> altIds = Sets.newHashSet(altId);
|
|
i.setAlternateIdentifier(Lists.newArrayList(Sets.difference(altIds, pids)));
|
|
});
|
|
});
|
|
|
|
if (Objects.isNull(i.getAccessright())
|
|
|| StringUtils.isBlank(i.getAccessright().getClassid())) {
|
|
i
|
|
.setAccessright(
|
|
accessRight(
|
|
ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,
|
|
ModelConstants.DNET_ACCESS_MODES));
|
|
}
|
|
if (Objects.isNull(i.getHostedby()) || StringUtils.isBlank(i.getHostedby().getKey())) {
|
|
i.setHostedby(ModelConstants.UNKNOWN_REPOSITORY);
|
|
}
|
|
if (Objects.isNull(i.getRefereed()) || StringUtils.isBlank(i.getRefereed().getClassid())) {
|
|
i.setRefereed(qualifier("0000", "Unknown", ModelConstants.DNET_REVIEW_LEVELS));
|
|
}
|
|
|
|
if (Objects.nonNull(i.getLicense()) && Objects.nonNull(i.getLicense().getValue())) {
|
|
vocs
|
|
.find(DNET_LICENSES)
|
|
.map(voc -> voc.getTermBySynonym(i.getLicense().getValue()))
|
|
.map(VocabularyTerm::getId)
|
|
.ifPresent(license -> i.getLicense().setValue(license));
|
|
}
|
|
|
|
// from the script from Dimitris
|
|
if ("0000".equals(i.getRefereed().getClassid())) {
|
|
final boolean isFromCrossref = Optional
|
|
.ofNullable(i.getCollectedfrom())
|
|
.map(KeyValue::getKey)
|
|
.map(id -> id.equals(ModelConstants.CROSSREF_ID))
|
|
.orElse(false);
|
|
final boolean hasDoi = Optional
|
|
.ofNullable(i.getPid())
|
|
.map(
|
|
pid -> pid
|
|
.stream()
|
|
.anyMatch(
|
|
p -> PidType.doi.toString().equals(p.getQualifier().getClassid())))
|
|
.orElse(false);
|
|
final boolean isPeerReviewedType = PEER_REVIEWED_TYPES
|
|
.contains(i.getInstancetype().getClassname());
|
|
final boolean noOtherLitType = r
|
|
.getInstance()
|
|
.stream()
|
|
.noneMatch(ii -> "Other literature type".equals(ii.getInstancetype().getClassname()));
|
|
if (isFromCrossref && hasDoi && isPeerReviewedType && noOtherLitType) {
|
|
i.setRefereed(qualifier("0001", "peerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
|
|
} else {
|
|
i.setRefereed(qualifier("0002", "nonPeerReviewed", ModelConstants.DNET_REVIEW_LEVELS));
|
|
}
|
|
}
|
|
|
|
if (Objects.nonNull(i.getDateofacceptance())) {
|
|
Optional<String> date = cleanDateField(i.getDateofacceptance());
|
|
if (date.isPresent()) {
|
|
i.getDateofacceptance().setValue(date.get());
|
|
} else {
|
|
i.setDateofacceptance(null);
|
|
}
|
|
}
|
|
if (StringUtils.isNotBlank(i.getFulltext()) &&
|
|
(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
|
|
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
|
|
i.setFulltext(null);
|
|
}
|
|
if (Objects.nonNull(i.getUrl())) {
|
|
i
|
|
.setUrl(
|
|
i
|
|
.getUrl()
|
|
.stream()
|
|
.filter(GraphCleaningFunctions::urlFilter)
|
|
.collect(Collectors.toList()));
|
|
}
|
|
}
|
|
}
|
|
if (Objects.isNull(r.getBestaccessright())
|
|
|| StringUtils.isBlank(r.getBestaccessright().getClassid())) {
|
|
Qualifier bestaccessrights = OafMapperUtils.createBestAccessRights(r.getInstance());
|
|
if (Objects.isNull(bestaccessrights)) {
|
|
r
|
|
.setBestaccessright(
|
|
qualifier(
|
|
ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE,
|
|
ModelConstants.DNET_ACCESS_MODES));
|
|
} else {
|
|
r.setBestaccessright(bestaccessrights);
|
|
}
|
|
}
|
|
if (Objects.nonNull(r.getAuthor())) {
|
|
r
|
|
.setAuthor(
|
|
r
|
|
.getAuthor()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.filter(GraphCleaningFunctions::isValidAuthorName)
|
|
.map(GraphCleaningFunctions::cleanupAuthor)
|
|
.collect(Collectors.toList()));
|
|
|
|
boolean nullRank = r
|
|
.getAuthor()
|
|
.stream()
|
|
.anyMatch(a -> Objects.isNull(a.getRank()));
|
|
if (nullRank) {
|
|
int i = 1;
|
|
for (Author author : r.getAuthor()) {
|
|
author.setRank(i++);
|
|
}
|
|
}
|
|
|
|
for (Author a : r.getAuthor()) {
|
|
if (Objects.isNull(a.getPid())) {
|
|
a.setPid(Lists.newArrayList());
|
|
} else {
|
|
a
|
|
.setPid(
|
|
a
|
|
.getPid()
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.filter(p -> Objects.nonNull(p.getQualifier()))
|
|
.filter(p -> StringUtils.isNotBlank(p.getValue()))
|
|
.filter(
|
|
p -> StringUtils
|
|
.contains(StringUtils.lowerCase(p.getQualifier().getClassid()), ORCID))
|
|
.map(p -> {
|
|
// hack to distinguish orcid from orcid_pending
|
|
String pidProvenance = getProvenance(p.getDataInfo());
|
|
if (p
|
|
.getQualifier()
|
|
.getClassid()
|
|
.toLowerCase()
|
|
.contains(ModelConstants.ORCID)) {
|
|
if (pidProvenance
|
|
.equals(ModelConstants.SYSIMPORT_CROSSWALK_ENTITYREGISTRY) ||
|
|
pidProvenance.equals("ORCID_ENRICHMENT")) {
|
|
p.getQualifier().setClassid(ModelConstants.ORCID);
|
|
} else {
|
|
p.getQualifier().setClassid(ModelConstants.ORCID_PENDING);
|
|
}
|
|
final String orcid = p
|
|
.getValue()
|
|
.trim()
|
|
.toLowerCase()
|
|
.replaceAll(ORCID_CLEANING_REGEX, "$1-$2-$3-$4");
|
|
if (orcid.length() == ORCID_LEN) {
|
|
p.setValue(orcid);
|
|
} else {
|
|
p.setValue("");
|
|
}
|
|
}
|
|
return p;
|
|
})
|
|
.filter(p -> StringUtils.isNotBlank(p.getValue()))
|
|
.collect(
|
|
Collectors
|
|
.toMap(
|
|
p -> p.getQualifier().getClassid() + p.getValue(),
|
|
Function.identity(),
|
|
(p1, p2) -> p1,
|
|
LinkedHashMap::new))
|
|
.values()
|
|
.stream()
|
|
.collect(Collectors.toList()));
|
|
}
|
|
}
|
|
}
|
|
if (value instanceof Publication) {
|
|
|
|
} else if (value instanceof Dataset) {
|
|
|
|
} else if (value instanceof OtherResearchProduct) {
|
|
|
|
} else if (value instanceof Software) {
|
|
|
|
}
|
|
|
|
}
|
|
|
|
} else if (value instanceof Relation) {
|
|
Relation r = (Relation) value;
|
|
|
|
Optional<String> validationDate = doCleanDate(r.getValidationDate());
|
|
if (validationDate.isPresent()) {
|
|
r.setValidationDate(validationDate.get());
|
|
r.setValidated(true);
|
|
} else {
|
|
r.setValidationDate(null);
|
|
r.setValidated(false);
|
|
}
|
|
}
|
|
|
|
return value;
|
|
}
|
|
|
|
private static Author cleanupAuthor(Author author) {
|
|
if (StringUtils.isNotBlank(author.getFullname())) {
|
|
author
|
|
.setFullname(
|
|
author
|
|
.getFullname()
|
|
.replaceAll(NAME_CLEANING_REGEX, " ")
|
|
.replace("\"", "\\\""));
|
|
}
|
|
if (StringUtils.isNotBlank(author.getName())) {
|
|
author
|
|
.setName(
|
|
author
|
|
.getName()
|
|
.replaceAll(NAME_CLEANING_REGEX, " ")
|
|
.replace("\"", "\\\""));
|
|
}
|
|
if (StringUtils.isNotBlank(author.getSurname())) {
|
|
author
|
|
.setSurname(
|
|
author
|
|
.getSurname()
|
|
.replaceAll(NAME_CLEANING_REGEX, " ")
|
|
.replace("\"", "\\\""));
|
|
}
|
|
|
|
return author;
|
|
}
|
|
|
|
private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
|
|
return Optional
|
|
.ofNullable(dateofacceptance)
|
|
.map(Field::getValue)
|
|
.map(GraphCleaningFunctions::cleanDate)
|
|
.filter(Objects::nonNull);
|
|
}
|
|
|
|
protected static Optional<String> doCleanDate(String date) {
|
|
return Optional.ofNullable(cleanDate(date));
|
|
}
|
|
|
|
public static String cleanDate(final String inputDate) {
|
|
|
|
if (StringUtils.isBlank(inputDate)) {
|
|
return null;
|
|
}
|
|
|
|
try {
|
|
final LocalDate date = DateParserUtils
|
|
.parseDate(inputDate.trim())
|
|
.toInstant()
|
|
.atZone(ZoneId.systemDefault())
|
|
.toLocalDate();
|
|
return DateTimeFormatter.ofPattern(ModelSupport.DATE_FORMAT).format(date);
|
|
} catch (DateTimeParseException e) {
|
|
return null;
|
|
}
|
|
}
|
|
|
|
// HELPERS
|
|
|
|
private static boolean isValidAuthorName(Author a) {
|
|
return StringUtils.isNotBlank(a.getFullname()) &&
|
|
StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")) &&
|
|
!INVALID_AUTHOR_NAMES.contains(StringUtils.lowerCase(a.getFullname()).trim()) &&
|
|
!Stream
|
|
.of(a.getFullname(), a.getName(), a.getSurname())
|
|
.filter(StringUtils::isNotBlank)
|
|
.collect(Collectors.joining(""))
|
|
.toLowerCase()
|
|
.matches(INVALID_AUTHOR_REGEX);
|
|
}
|
|
|
|
private static boolean urlFilter(String u) {
|
|
try {
|
|
final URL url = new URL(u);
|
|
if (StringUtils.isBlank(url.getPath()) || "/".equals(url.getPath())) {
|
|
return false;
|
|
}
|
|
if (INVALID_URL_HOSTS.contains(url.getHost())) {
|
|
return false;
|
|
}
|
|
return !INVALID_URLS.contains(url.toString());
|
|
} catch (MalformedURLException ex) {
|
|
return false;
|
|
}
|
|
}
|
|
|
|
private static List<StructuredProperty> processPidCleaning(List<StructuredProperty> pids) {
|
|
return pids
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.filter(sp -> StringUtils.isNotBlank(StringUtils.trim(sp.getValue())))
|
|
.filter(sp -> !PID_BLACKLIST.contains(sp.getValue().trim().toLowerCase()))
|
|
.filter(sp -> Objects.nonNull(sp.getQualifier()))
|
|
.filter(sp -> StringUtils.isNotBlank(sp.getQualifier().getClassid()))
|
|
.map(PidCleaner::normalizePidValue)
|
|
.filter(CleaningFunctions::pidFilter)
|
|
.collect(Collectors.toList());
|
|
}
|
|
|
|
private static void fixVocabName(Qualifier q, String vocabularyName) {
|
|
if (Objects.nonNull(q) && StringUtils.isBlank(q.getSchemeid())) {
|
|
q.setSchemeid(vocabularyName);
|
|
q.setSchemename(vocabularyName);
|
|
}
|
|
}
|
|
|
|
private static AccessRight accessRight(String classid, String classname, String scheme) {
|
|
return OafMapperUtils
|
|
.accessRight(
|
|
classid, classname, scheme, scheme);
|
|
}
|
|
|
|
private static Qualifier qualifier(String classid, String classname, String scheme) {
|
|
return OafMapperUtils
|
|
.qualifier(
|
|
classid, classname, scheme, scheme);
|
|
}
|
|
|
|
protected static StructuredProperty cleanValue(StructuredProperty s) {
|
|
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
|
|
return s;
|
|
}
|
|
|
|
protected static Subject cleanValue(Subject s) {
|
|
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
|
|
return s;
|
|
}
|
|
|
|
protected static Field<String> cleanValue(Field<String> s) {
|
|
s.setValue(s.getValue().replaceAll(CLEANING_REGEX, " "));
|
|
return s;
|
|
}
|
|
|
|
public static OafEntity applyCoarVocabularies(OafEntity entity, VocabularyGroup vocs) {
|
|
|
|
if (entity instanceof Result) {
|
|
final Result result = (Result) entity;
|
|
|
|
Optional
|
|
.ofNullable(result.getInstance())
|
|
.ifPresent(
|
|
instances -> instances
|
|
.forEach(
|
|
instance -> {
|
|
if (Objects.isNull(instance.getInstanceTypeMapping())) {
|
|
List<InstanceTypeMapping> mapping = Lists.newArrayList();
|
|
mapping
|
|
.add(
|
|
OafMapperUtils
|
|
.instanceTypeMapping(
|
|
instance.getInstancetype().getClassname(),
|
|
OPENAIRE_COAR_RESOURCE_TYPES_3_1));
|
|
instance.setInstanceTypeMapping(mapping);
|
|
}
|
|
Optional<InstanceTypeMapping> optionalItm = instance
|
|
.getInstanceTypeMapping()
|
|
.stream()
|
|
.filter(GraphCleaningFunctions::originalResourceType)
|
|
.findFirst();
|
|
if (optionalItm.isPresent()) {
|
|
InstanceTypeMapping coarItm = optionalItm.get();
|
|
Optional
|
|
.ofNullable(
|
|
vocs
|
|
.lookupTermBySynonym(
|
|
OPENAIRE_COAR_RESOURCE_TYPES_3_1, coarItm.getOriginalType()))
|
|
.ifPresent(type -> {
|
|
coarItm.setTypeCode(type.getClassid());
|
|
coarItm.setTypeLabel(type.getClassname());
|
|
});
|
|
final List<InstanceTypeMapping> mappings = Lists.newArrayList();
|
|
if (vocs.vocabularyExists(OPENAIRE_USER_RESOURCE_TYPES)) {
|
|
Optional
|
|
.ofNullable(
|
|
vocs
|
|
.lookupTermBySynonym(
|
|
OPENAIRE_USER_RESOURCE_TYPES, coarItm.getTypeCode()))
|
|
.ifPresent(
|
|
type -> mappings
|
|
.add(
|
|
OafMapperUtils
|
|
.instanceTypeMapping(coarItm.getTypeCode(), type)));
|
|
}
|
|
if (!mappings.isEmpty()) {
|
|
instance.getInstanceTypeMapping().addAll(mappings);
|
|
}
|
|
}
|
|
}));
|
|
result.setMetaResourceType(getMetaResourceType(result.getInstance(), vocs));
|
|
}
|
|
|
|
return entity;
|
|
}
|
|
|
|
private static boolean originalResourceType(InstanceTypeMapping itm) {
|
|
return StringUtils.isNotBlank(itm.getOriginalType()) &&
|
|
OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(itm.getVocabularyName()) &&
|
|
StringUtils.isBlank(itm.getTypeCode()) &&
|
|
StringUtils.isBlank(itm.getTypeLabel());
|
|
}
|
|
|
|
private static Qualifier getMetaResourceType(final List<Instance> instances, final VocabularyGroup vocs) {
|
|
return Optional
|
|
.ofNullable(instances)
|
|
.map(ii -> {
|
|
if (vocs.vocabularyExists(OPENAIRE_META_RESOURCE_TYPE)) {
|
|
Optional<InstanceTypeMapping> itm = ii
|
|
.stream()
|
|
.filter(Objects::nonNull)
|
|
.flatMap(
|
|
i -> Optional
|
|
.ofNullable(i.getInstanceTypeMapping())
|
|
.map(Collection::stream)
|
|
.orElse(Stream.empty()))
|
|
.filter(t -> OPENAIRE_COAR_RESOURCE_TYPES_3_1.equals(t.getVocabularyName()))
|
|
.findFirst();
|
|
|
|
if (!itm.isPresent() || Objects.isNull(itm.get().getTypeCode())) {
|
|
return null;
|
|
} else {
|
|
final String typeCode = itm.get().getTypeCode();
|
|
return Optional
|
|
.ofNullable(vocs.lookupTermBySynonym(OPENAIRE_META_RESOURCE_TYPE, typeCode))
|
|
.orElseThrow(
|
|
() -> new IllegalStateException("unable to find a synonym for '" + typeCode + "' in " +
|
|
OPENAIRE_META_RESOURCE_TYPE));
|
|
}
|
|
} else {
|
|
throw new IllegalStateException("vocabulary '" + OPENAIRE_META_RESOURCE_TYPE + "' not available");
|
|
}
|
|
})
|
|
.orElse(null);
|
|
}
|
|
|
|
}
|