[DHP Schema refactoring]
- move the business logic from the model class to dhp-common
This commit is contained in:
Sandro La Bruzzo
parent
e517f52e30
commit
27fbc9b385
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@ -0,0 +1,74 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import java.util.HashSet;
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import java.util.Objects;
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import java.util.Optional;
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import java.util.Set;
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import org.apache.commons.lang3.StringUtils;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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public class CleaningFunctions {
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public static final String DOI_PREFIX_REGEX = "(^10\\.|\\/10\\.)";
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public static final String DOI_PREFIX = "10.";
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public static final Set<String> PID_BLACKLIST = new HashSet<>();
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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 CleaningFunctions() {}
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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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return !PidBlacklistProvider.getBlacklist(s.getQualifier().getClassid()).contains(pidValue);
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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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pid.setValue(
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normalizePidValue(
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pid.getQualifier().getClassid(),
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pid.getValue()));
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return pid;
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}
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public static String normalizePidValue(String pidType, String pidValue) {
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String value = Optional
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.ofNullable(pidValue)
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.map(String::trim)
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.orElseThrow(() -> new IllegalArgumentException("PID value cannot be empty"));
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switch (pidType) {
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// TODO add cleaning for more PID types as needed
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case "doi":
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return value.toLowerCase().replaceFirst(DOI_PREFIX_REGEX, DOI_PREFIX);
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}
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return value;
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}
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}
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@ -0,0 +1,283 @@
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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.get(PidType.doi).put(ZENODO_OD_ID, "ZENODO");
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PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "Zenodo");
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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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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, PID SUBSTRING] considered as delegated authority for that
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* PID_TYPE. Example, Zenodo is delegated to forge DOIs that contain the 'zenodo' word.
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*/
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public static final Map<PidType, Map<String, String>> DELEGATED_PID_AUTHORITY = Maps.newHashMap();
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static {
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DELEGATED_PID_AUTHORITY.put(PidType.doi, new HashMap<>());
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DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_OD_ID, "zenodo");
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DELEGATED_PID_AUTHORITY.get(PidType.doi).put(ZENODO_R3_ID, "zenodo");
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}
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/**
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* Declares the associations PID_TYPE -> [DATASOURCE ID, NAME] whose records are considered enrichment for the graph.
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* Their OpenAIRE ID is built from the declared PID type. Are merged with their corresponding record, identified by
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* the same OpenAIRE id.
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*/
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public static final Map<PidType, HashBiMap<String, String>> ENRICHMENT_PROVIDER = Maps.newHashMap();
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static {
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ENRICHMENT_PROVIDER.put(PidType.doi, HashBiMap.create());
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ENRICHMENT_PROVIDER.get(PidType.doi).put(OPEN_APC_ID, OPEN_APC_NAME);
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}
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public static Set<String> delegatedAuthorityDatasourceIds() {
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return DELEGATED_PID_AUTHORITY.values()
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.stream()
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.flatMap(m -> m.keySet().stream())
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.collect(Collectors.toCollection(HashSet::new));
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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)
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.filter(s -> s.getQualifier() != null && "doi".equalsIgnoreCase(s.getQualifier().getClassid()))
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.filter(CleaningFunctions::pidFilter)
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.findAny()
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.orElse(null);
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} else {
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if (entity.getInstance() != null) {
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pid = entity
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.getInstance()
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.stream()
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.filter(i -> i.getPid() != null)
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.flatMap(i -> i.getPid().stream())
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.filter(CleaningFunctions::pidFilter)
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.findAny()
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.orElse(null);
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}
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}
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if (pid != null)
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return idFromPid(entity, pid, true);
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return null;
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}
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/**
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* Creates an identifier from the most relevant PID (if available) provided by a known PID authority in the given
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* entity T. Returns entity.id when none of the PIDs meet the selection criteria is available.
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*
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* @param entity the entity providing PIDs and a default ID.
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* @param <T> the specific entity type. Currently Organization and Result subclasses are supported.
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* @param md5 indicates whether should hash the PID value or not.
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* @return an identifier from the most relevant PID, entity.id otherwise
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*/
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public static <T extends OafEntity> String createIdentifier(T entity, boolean md5) {
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checkArgument(StringUtils.isNoneBlank(entity.getId()), "missing entity identifier");
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final Map<String, Set<StructuredProperty>> pids = extractPids(entity);
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return pids
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.values()
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.stream()
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.flatMap(Set::stream)
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.min(new PidComparator<>(entity))
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.map(
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min -> Optional
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.ofNullable(pids.get(min.getQualifier().getClassid()))
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.map(
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p -> p
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.stream()
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.sorted(new PidValueComparator())
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.findFirst()
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.map(s -> idFromPid(entity, s, md5))
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.orElseGet(entity::getId))
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.orElseGet(entity::getId))
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.orElseGet(entity::getId);
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}
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private static <T extends OafEntity> Map<String, Set<StructuredProperty>> extractPids(T entity) {
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if (entity instanceof Result) {
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return Optional
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.ofNullable(((Result) entity).getInstance())
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.map(IdentifierFactory::mapPids)
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.orElse(new HashMap<>());
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} else {
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return entity
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.getPid()
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.stream()
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.map(CleaningFunctions::normalizePidValue)
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.filter(CleaningFunctions::pidFilter)
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.collect(
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Collectors
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.groupingBy(
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p -> p.getQualifier().getClassid(),
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Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
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}
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}
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private static Map<String, Set<StructuredProperty>> mapPids(List<Instance> instance) {
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return instance
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.stream()
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.map(i -> pidFromInstance(i.getPid(), i.getCollectedfrom(), false))
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.flatMap(Function.identity())
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.collect(
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Collectors
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.groupingBy(
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p -> p.getQualifier().getClassid(),
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Collectors.mapping(p -> p, Collectors.toCollection(HashSet::new))));
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}
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private static Stream<StructuredProperty> pidFromInstance(List<StructuredProperty> pid, KeyValue collectedFrom,
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boolean mapHandles) {
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return Optional
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.ofNullable(pid)
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.map(
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pp -> pp
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.stream()
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// filter away PIDs provided by a DS that is not considered an authority for the
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// given PID Type
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.filter(p -> shouldFilterPidByCriteria(collectedFrom, p, mapHandles))
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.map(CleaningFunctions::normalizePidValue)
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.filter(p -> isNotFromDelegatedAuthority(collectedFrom, p))
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.filter(CleaningFunctions::pidFilter))
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.orElse(Stream.empty());
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}
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private static boolean shouldFilterPidByCriteria(KeyValue collectedFrom, StructuredProperty p, boolean mapHandles) {
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final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
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if (Objects.isNull(collectedFrom)) {
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return false;
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}
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boolean isEnrich = Optional
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.ofNullable(ENRICHMENT_PROVIDER.get(pType))
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.map(enrich -> enrich.containsKey(collectedFrom.getKey())
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|| enrich.containsValue(collectedFrom.getValue()))
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.orElse(false);
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boolean isAuthority = Optional
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.ofNullable(PID_AUTHORITY.get(pType))
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.map(authorities -> authorities.containsKey(collectedFrom.getKey())
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|| authorities.containsValue(collectedFrom.getValue()))
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.orElse(false);
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return (mapHandles && pType.equals(PidType.handle)) || isEnrich || isAuthority;
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}
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private static boolean isNotFromDelegatedAuthority(KeyValue collectedFrom, StructuredProperty p) {
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final PidType pType = PidType.tryValueOf(p.getQualifier().getClassid());
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final Map<String, String> da = DELEGATED_PID_AUTHORITY.get(pType);
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if (Objects.isNull(da)) {
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return true;
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}
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if (!da.containsKey(collectedFrom.getKey())) {
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return true;
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}
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return StringUtils.contains(p.getValue(), da.get(collectedFrom.getKey()));
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}
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/**
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* @see {@link IdentifierFactory#createIdentifier(OafEntity, boolean)}
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*/
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public static <T extends OafEntity> String createIdentifier(T entity) {
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return createIdentifier(entity, true);
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}
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private static <T extends OafEntity> String idFromPid(T entity, StructuredProperty s, boolean md5) {
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return idFromPid(ModelSupport.getIdPrefix(entity.getClass()), s.getQualifier().getClassid(), s.getValue(), md5);
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}
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public static String idFromPid(String numericPrefix, String pidType, String pidValue, boolean md5) {
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return new StringBuilder()
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.append(numericPrefix)
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.append(ID_PREFIX_SEPARATOR)
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.append(createPrefix(pidType))
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.append(ID_SEPARATOR)
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.append(md5 ? md5(pidValue) : pidValue)
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.toString();
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}
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// create the prefix (length = 12)
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private static String createPrefix(String pidType) {
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StringBuilder prefix = new StringBuilder(StringUtils.left(pidType, ID_PREFIX_LEN));
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while (prefix.length() < ID_PREFIX_LEN) {
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prefix.append("_");
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}
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return prefix.substring(0, ID_PREFIX_LEN);
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}
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public static String md5(final String s) {
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try {
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final MessageDigest md = MessageDigest.getInstance("MD5");
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md.update(s.getBytes(StandardCharsets.UTF_8));
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return new String(Hex.encodeHex(md.digest()));
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} catch (final Exception e) {
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return null;
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}
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}
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}
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@ -0,0 +1,24 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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public class ModelHardLimits {
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private ModelHardLimits() {}
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public static final String LAYOUT = "index";
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public static final String INTERPRETATION = "openaire";
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public static final String SEPARATOR = "-";
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public static final int MAX_EXTERNAL_ENTITIES = 50;
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public static final int MAX_AUTHORS = 200;
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public static final int MAX_AUTHOR_FULLNAME_LENGTH = 1000;
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public static final int MAX_TITLE_LENGTH = 5000;
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public static final int MAX_TITLES = 10;
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public static final int MAX_ABSTRACT_LENGTH = 150000;
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public static final int MAX_INSTANCES = 10;
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public static String getCollectionName(String format) {
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return format + SEPARATOR + LAYOUT + SEPARATOR + INTERPRETATION;
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}
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}
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@ -251,6 +251,9 @@ public class OafMapperUtils {
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return p;
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}
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public static Journal journal(
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final String name,
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final String issnPrinted,
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|
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@ -0,0 +1,765 @@
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package eu.dnetlib.dhp.schema.oaf.utils;
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import com.google.common.base.Preconditions;
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import eu.dnetlib.dhp.common.api.zenodo.File;
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import eu.dnetlib.dhp.schema.common.AccessRightComparator;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.tuple.ImmutablePair;
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import org.apache.commons.lang3.tuple.Pair;
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import static com.google.common.base.Preconditions.checkArgument;
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import static com.ibm.icu.text.PluralRules.Operand.e;
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import java.text.ParseException;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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/**
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* The type Oaf utils class groups all
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* the utilities method used for OAF Generation
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*/
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public class OafUtils {
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/**
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* Normalize pid string.
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*
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* @param pid the pid
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* @return the string
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*/
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public static String extractKeyFromPid(final StructuredProperty pid) {
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if (pid == null)
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return null;
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final StructuredProperty normalizedPid = CleaningFunctions.normalizePidValue(pid);
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return String.format("%s::%s", normalizedPid.getQualifier().getClassid(), normalizedPid.getValue());
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}
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/**
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* This method converts the list of instance enrichments
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* into a Map where the key is the normalized identifier
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* and the value is the instance itself
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*
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* @param ri the list of enrichment instances
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* @return the result map
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*/
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public static Map<String, Instance> toInstanceMap(final List<Instance> ri) {
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return ri
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.stream()
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.filter(i -> i.getPid() != null || i.getAlternateIdentifier() != null)
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.flatMap(i -> {
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final List<Pair<String, Instance>> result = new ArrayList<>();
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if (i.getPid() != null)
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i.getPid().stream().filter(OafUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
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if (i.getAlternateIdentifier() != null)
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i.getAlternateIdentifier().stream().filter(OafUtils::validPid).forEach(p -> result.add(new ImmutablePair<>(extractKeyFromPid(p), i)));
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return result.stream();
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}).collect(Collectors.toMap(
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Pair::getLeft,
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Pair::getRight,
|
||||
(a, b) -> a
|
||||
));
|
||||
}
|
||||
|
||||
/**
|
||||
* Valid pid boolean.
|
||||
*
|
||||
* @param p the p
|
||||
* @return the boolean
|
||||
*/
|
||||
private static boolean validPid(final StructuredProperty p) {
|
||||
return p.getValue()!= null && p.getQualifier()!= null && p.getQualifier().getClassid()!=null;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* This utility method finds the list of enrichment instances
|
||||
* that match one or more PIDs in the input list
|
||||
*
|
||||
* @param pids the list of PIDs
|
||||
* @param enrichments the List of enrichment instances having the same pid
|
||||
* @return the list
|
||||
*/
|
||||
private static List<Instance> findEnrichmentsByPID(final List<StructuredProperty> pids, final Map<String,Instance> enrichments) {
|
||||
if (pids == null || enrichments == null)
|
||||
return null;
|
||||
return pids
|
||||
.stream()
|
||||
.map(OafUtils::extractKeyFromPid)
|
||||
.map(enrichments::get)
|
||||
.filter(Objects::nonNull)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
/**
|
||||
* Is an enrichment boolean.
|
||||
*
|
||||
* @param e the e
|
||||
* @return the boolean
|
||||
*/
|
||||
public static boolean isAnEnrichment(OafEntity e) {
|
||||
return e.getDataInfo()!= null &&
|
||||
e.getDataInfo().getProvenanceaction()!= null
|
||||
&& ModelConstants.PROVENANCE_ENRICH.equalsIgnoreCase(e.getDataInfo().getProvenanceaction().getClassid());
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This method apply enrichment on a single instance
|
||||
* The enrichment consists of replacing values on
|
||||
* single attribute only if in the current instance is missing
|
||||
* The only repeatable field enriched is measures
|
||||
*
|
||||
* @param currentInstance the current instance
|
||||
* @param enrichment the enrichment instance
|
||||
*/
|
||||
private static void applyEnrichment(final Instance currentInstance, final Instance enrichment) {
|
||||
if (currentInstance == null || enrichment == null)
|
||||
return;
|
||||
|
||||
//ENRICH accessright
|
||||
if (enrichment.getAccessright()!=null && currentInstance.getAccessright() == null)
|
||||
currentInstance.setAccessright(enrichment.getAccessright());
|
||||
|
||||
//ENRICH license
|
||||
if (enrichment.getLicense()!=null && currentInstance.getLicense() == null)
|
||||
currentInstance.setLicense(enrichment.getLicense());
|
||||
|
||||
//ENRICH instanceType
|
||||
if (enrichment.getInstancetype()!=null && currentInstance.getInstancetype() == null)
|
||||
currentInstance.setInstancetype(enrichment.getInstancetype());
|
||||
|
||||
//ENRICH hostedby
|
||||
if (enrichment.getHostedby()!=null && currentInstance.getHostedby() == null)
|
||||
currentInstance.setHostedby(enrichment.getHostedby());
|
||||
|
||||
//ENRICH distributionlocation
|
||||
if (enrichment.getDistributionlocation()!=null && currentInstance.getDistributionlocation() == null)
|
||||
currentInstance.setDistributionlocation(enrichment.getDistributionlocation());
|
||||
|
||||
//ENRICH collectedfrom
|
||||
if (enrichment.getCollectedfrom()!=null && currentInstance.getCollectedfrom() == null)
|
||||
currentInstance.setCollectedfrom(enrichment.getCollectedfrom());
|
||||
|
||||
//ENRICH dateofacceptance
|
||||
if (enrichment.getDateofacceptance()!=null && currentInstance.getDateofacceptance() == null)
|
||||
currentInstance.setDateofacceptance(enrichment.getDateofacceptance());
|
||||
|
||||
//ENRICH processingchargeamount
|
||||
if (enrichment.getProcessingchargeamount()!=null && currentInstance.getProcessingchargeamount() == null)
|
||||
currentInstance.setProcessingchargeamount(enrichment.getProcessingchargeamount());
|
||||
|
||||
//ENRICH refereed
|
||||
if (enrichment.getRefereed()!=null && currentInstance.getRefereed() == null)
|
||||
currentInstance.setRefereed(enrichment.getRefereed());
|
||||
|
||||
//ENRICH measures
|
||||
if (enrichment.getMeasures()!=null)
|
||||
if (currentInstance.getMeasures() == null)
|
||||
currentInstance.setMeasures(enrichment.getMeasures());
|
||||
else
|
||||
enrichment.getMeasures().forEach(currentInstance.getMeasures()::add);
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This main method apply the enrichment of the instances
|
||||
*
|
||||
* @param toEnrichInstances the instances that could be enriched
|
||||
* @param enrichmentInstances the enrichment instances
|
||||
* @return list of instances possibly enriched
|
||||
*/
|
||||
private static List<Instance> enrichInstances(final List<Instance> toEnrichInstances,final List<Instance> enrichmentInstances) {
|
||||
final List<Instance> enrichmentResult = new ArrayList<>();
|
||||
|
||||
if (toEnrichInstances == null) {
|
||||
return enrichmentResult;
|
||||
}
|
||||
if (enrichmentInstances == null) {
|
||||
return enrichmentResult;
|
||||
}
|
||||
Map<String, Instance> ri = toInstanceMap(enrichmentInstances);
|
||||
|
||||
toEnrichInstances.forEach(i -> {
|
||||
final List<Instance> e = findEnrichmentsByPID(i.getPid(), ri);
|
||||
if (e!= null && e.size()> 0) {
|
||||
e.forEach(enr -> applyEnrichment(i, enr));
|
||||
} else {
|
||||
final List<Instance> a = findEnrichmentsByPID(i.getAlternateIdentifier(), ri);
|
||||
if (a!= null && a.size()> 0) {
|
||||
a.forEach(enr -> applyEnrichment(i, enr));
|
||||
}
|
||||
}
|
||||
enrichmentResult.add(i);
|
||||
});
|
||||
return enrichmentResult;
|
||||
}
|
||||
|
||||
/**
|
||||
* Longest lists list.
|
||||
*
|
||||
* @param a the a
|
||||
* @param b the b
|
||||
* @return the list
|
||||
*/
|
||||
public static List<Field<String>> longestLists(List<Field<String>> a, List<Field<String>> b) {
|
||||
if (a == null || b == null)
|
||||
return a == null ? b : a;
|
||||
if (a.size() == b.size()) {
|
||||
int msa = a
|
||||
.stream()
|
||||
.filter(i -> i != null && i.getValue() != null)
|
||||
.map(i -> i.getValue().length())
|
||||
.max(Comparator.naturalOrder())
|
||||
.orElse(0);
|
||||
int msb = b
|
||||
.stream()
|
||||
.filter(i -> i != null && i.getValue() != null)
|
||||
.map(i -> i.getValue().length())
|
||||
.max(Comparator.naturalOrder())
|
||||
.orElse(0);
|
||||
return msa > msb ? a : b;
|
||||
}
|
||||
return a.size() > b.size() ? a : b;
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* This method merge two oaf object of the same type
|
||||
* It should replace the mergeFrom utility inside the oaf
|
||||
* class.
|
||||
*
|
||||
* @param original First object
|
||||
* @param enrich second object
|
||||
* @return the merged object
|
||||
*/
|
||||
public static Oaf mergeOAF(Oaf original, Oaf enrich) {
|
||||
if (original == null)
|
||||
return enrich;
|
||||
if (enrich == null)
|
||||
return original;
|
||||
|
||||
if (original.getClass() != enrich.getClass())
|
||||
throw new RuntimeException(String.format("Trying to merge different types of object %s, and %s",
|
||||
original.getClass().getCanonicalName(),
|
||||
enrich.getClass().getCanonicalName()));
|
||||
|
||||
Oaf result = null;
|
||||
|
||||
|
||||
|
||||
|
||||
switch (original.getClass().getSimpleName().toLowerCase()) {
|
||||
case "relation":
|
||||
result = mergeOAFRelation((Relation) original, (Relation) enrich);
|
||||
break;
|
||||
case "publication":
|
||||
result = mergeOAFPublication((Publication) original, (Publication) enrich);
|
||||
break;
|
||||
case "dataset":
|
||||
result = mergeOAFDataset((Dataset) original, (Dataset) enrich);
|
||||
break;
|
||||
case "software":
|
||||
result = mergeOAFSoftware((Software) original, (Software) enrich);
|
||||
break;
|
||||
case "otherresearchproduct":
|
||||
result = mergeOAFOtherResearchProduct((OtherResearchProduct) original, (OtherResearchProduct) enrich);
|
||||
break;
|
||||
case "project":
|
||||
result = mergeOAFProject((Project) original, (Project)enrich);
|
||||
break;
|
||||
case "organization":
|
||||
result = mergeOAFOrganization((Organization) original, (Organization)enrich);
|
||||
break;
|
||||
|
||||
|
||||
}
|
||||
checkArgument(Objects.nonNull(result), "Undefined type on merge, " +
|
||||
"allowed: relation, publication,otherresearchproduct, software and dataset");
|
||||
|
||||
result.setCollectedfrom(
|
||||
Stream
|
||||
.concat(
|
||||
Optional
|
||||
.ofNullable(original.getCollectedfrom())
|
||||
.map(Collection::stream)
|
||||
.orElse(Stream.empty()),
|
||||
Optional
|
||||
.ofNullable(enrich.getCollectedfrom())
|
||||
.map(Collection::stream)
|
||||
.orElse(Stream.empty()))
|
||||
.distinct() // relies on KeyValue.equals
|
||||
.collect(Collectors.toList()));
|
||||
|
||||
result.setLastupdatetimestamp(
|
||||
Math
|
||||
.max(
|
||||
Optional.ofNullable(original.getLastupdatetimestamp()).orElse(0L),
|
||||
Optional.ofNullable(enrich.getLastupdatetimestamp()).orElse(0L)));
|
||||
|
||||
return result;
|
||||
|
||||
}
|
||||
|
||||
|
||||
@SafeVarargs
|
||||
public static <T> List<T> mergeLists(final List<T>... lists) {
|
||||
|
||||
return Arrays
|
||||
.stream(lists)
|
||||
.filter(Objects::nonNull)
|
||||
.flatMap(List::stream)
|
||||
.filter(Objects::nonNull)
|
||||
.distinct()
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
|
||||
|
||||
private static int compareTrust(Oaf a, Oaf b) {
|
||||
return extractTrust(a).compareTo(extractTrust(b));
|
||||
}
|
||||
|
||||
private static String extractTrust(Oaf e) {
|
||||
if (e == null || e.getDataInfo() == null || e.getDataInfo().getTrust() == null)
|
||||
return "0.0";
|
||||
return e.getDataInfo().getTrust();
|
||||
}
|
||||
|
||||
|
||||
private static void mergeOAFDataInfo(Oaf from, Oaf to) {
|
||||
Optional.ofNullable(to)
|
||||
.ifPresent(other -> Optional.ofNullable(other.getDataInfo())
|
||||
.ifPresent(otherDataInfo -> Optional.ofNullable(from.getDataInfo())
|
||||
.ifPresent(thisDataInfo -> {
|
||||
if (compareTrust(from, other) < 0 || thisDataInfo.getInvisible()) {
|
||||
from.setDataInfo(otherDataInfo);
|
||||
}
|
||||
})));
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Gets main title.
|
||||
*
|
||||
* @param titles the titles
|
||||
* @return the main title
|
||||
*/
|
||||
private static StructuredProperty getMainTitle(List<StructuredProperty> titles) {
|
||||
// need to check if the list of titles contains more than 1 main title? (in that case, we should chose which
|
||||
// main title select in the list)
|
||||
for (StructuredProperty t : titles) {
|
||||
if (t.getQualifier() != null && t.getQualifier().getClassid() != null)
|
||||
if (t.getQualifier().getClassid().equals("main title"))
|
||||
return t;
|
||||
}
|
||||
return null;
|
||||
}
|
||||
|
||||
|
||||
private static OafEntity mergeEntity(OafEntity original, OafEntity enrich) {
|
||||
|
||||
final OafEntity mergedEntity = original;
|
||||
|
||||
|
||||
mergedEntity.setOriginalId(mergeLists(mergedEntity.getOriginalId(), enrich.getOriginalId()));
|
||||
|
||||
mergedEntity.setPid(mergeLists(mergedEntity.getPid(), enrich.getPid()));
|
||||
|
||||
|
||||
if (enrich.getDateofcollection() != null && compareTrust(mergedEntity, enrich) < 0)
|
||||
mergedEntity.setDateofcollection(enrich.getDateofcollection());
|
||||
|
||||
if (enrich.getDateoftransformation() != null && compareTrust(mergedEntity, enrich) < 0)
|
||||
mergedEntity.setDateoftransformation(enrich.getDateoftransformation());
|
||||
|
||||
mergedEntity.setExtraInfo(mergeLists(mergedEntity.getExtraInfo(), enrich.getExtraInfo()));
|
||||
|
||||
if (enrich.getOaiprovenance() != null && compareTrust(mergedEntity, enrich) < 0)
|
||||
mergedEntity.setOaiprovenance(enrich.getOaiprovenance());
|
||||
|
||||
return mergedEntity;
|
||||
|
||||
|
||||
}
|
||||
|
||||
private static Result mergeOAFResult(Result original, Result enrich) {
|
||||
|
||||
|
||||
final Result mergedResult = (Result) mergeEntity(original, enrich);
|
||||
|
||||
if(mergedResult.getProcessingchargeamount() == null || StringUtils.isBlank(mergedResult.getProcessingchargeamount().getValue() )){
|
||||
mergedResult.setProcessingchargeamount(enrich.getProcessingchargeamount());
|
||||
mergedResult.setProcessingchargecurrency(enrich.getProcessingchargecurrency());
|
||||
}
|
||||
|
||||
mergedResult.setMeasures(mergeLists(mergedResult.getMeasures(), enrich.getMeasures()));
|
||||
|
||||
if( !isAnEnrichment(mergedResult) && !isAnEnrichment(enrich))
|
||||
mergedResult.setInstance(mergeLists(mergedResult.getInstance(), enrich.getInstance()));
|
||||
else {
|
||||
final List<Instance> enrichmentInstances = isAnEnrichment(mergedResult) ? mergedResult.getInstance() : enrich.getInstance();
|
||||
final List<Instance> enrichedInstances= isAnEnrichment(mergedResult) ? enrich.getInstance(): mergedResult.getInstance();
|
||||
if (isAnEnrichment(mergedResult))
|
||||
mergedResult.setDataInfo(enrich.getDataInfo());
|
||||
mergedResult.setInstance(enrichInstances(enrichedInstances,enrichmentInstances));
|
||||
}
|
||||
|
||||
if (enrich.getBestaccessright() != null
|
||||
&& new AccessRightComparator().compare(enrich.getBestaccessright(), mergedResult.getBestaccessright()) < 0)
|
||||
mergedResult.setBestaccessright(enrich.getBestaccessright());
|
||||
|
||||
if (enrich.getResulttype() != null && compareTrust(mergedResult, enrich) < 0)
|
||||
mergedResult.setResulttype(enrich.getResulttype());
|
||||
|
||||
if (enrich.getLanguage() != null && compareTrust(mergedResult, enrich) < 0)
|
||||
mergedResult.setLanguage(enrich.getLanguage());
|
||||
|
||||
if (Objects.nonNull(enrich.getDateofacceptance())) {
|
||||
if (Objects.isNull(mergedResult.getDateofacceptance())) {
|
||||
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
|
||||
} else if (compareTrust(mergedResult, enrich) < 0) {
|
||||
mergedResult.setDateofacceptance(enrich.getDateofacceptance());
|
||||
}
|
||||
}
|
||||
|
||||
mergedResult.setCountry(mergeLists(mergedResult.getCountry(), enrich.getCountry()));
|
||||
|
||||
mergedResult.setSubject(mergeLists(mergedResult.getSubject(), enrich.getSubject()));
|
||||
|
||||
// merge title lists: main title with higher trust and distinct between the others
|
||||
StructuredProperty baseMainTitle = null;
|
||||
if (mergedResult.getTitle() != null) {
|
||||
baseMainTitle = getMainTitle(mergedResult.getTitle());
|
||||
if (baseMainTitle != null) {
|
||||
final StructuredProperty p = baseMainTitle;
|
||||
mergedResult.setTitle(mergedResult.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
StructuredProperty newMainTitle = null;
|
||||
if (enrich.getTitle() != null) {
|
||||
newMainTitle = getMainTitle(enrich.getTitle());
|
||||
if (newMainTitle != null) {
|
||||
final StructuredProperty p = newMainTitle;
|
||||
enrich.setTitle(enrich.getTitle().stream().filter(t -> t != p).collect(Collectors.toList()));
|
||||
}
|
||||
}
|
||||
|
||||
if (newMainTitle != null && compareTrust(mergedResult, enrich) < 0) {
|
||||
baseMainTitle = newMainTitle;
|
||||
}
|
||||
|
||||
mergedResult.setTitle(mergeLists(mergedResult.getTitle(), enrich.getTitle()));
|
||||
if (mergedResult.getTitle() != null && baseMainTitle != null) {
|
||||
mergedResult.getTitle().add(baseMainTitle);
|
||||
}
|
||||
|
||||
mergedResult.setRelevantdate (mergeLists(mergedResult.getRelevantdate(), enrich.getRelevantdate()));
|
||||
|
||||
mergedResult.setDescription( longestLists(mergedResult.getDescription(), enrich.getDescription()));
|
||||
|
||||
if (enrich.getPublisher() != null && compareTrust(mergedResult, enrich) < 0)
|
||||
mergedResult.setPublisher(enrich.getPublisher());
|
||||
|
||||
if (enrich.getEmbargoenddate() != null && compareTrust(mergedResult, enrich) < 0)
|
||||
mergedResult.setEmbargoenddate(enrich.getEmbargoenddate());
|
||||
|
||||
mergedResult.setSource(mergeLists(mergedResult.getSource(), enrich.getSource()));
|
||||
|
||||
mergedResult.setFulltext(mergeLists(mergedResult.getFulltext(), enrich.getFulltext()));
|
||||
|
||||
mergedResult.setFormat(mergeLists(mergedResult.getFormat(), enrich.getFormat()));
|
||||
|
||||
mergedResult.setContributor(mergeLists(mergedResult.getContributor(), enrich.getContributor()));
|
||||
|
||||
if (enrich.getResourcetype() != null)
|
||||
mergedResult.setResourcetype(enrich.getResourcetype());
|
||||
|
||||
mergedResult.setCoverage(mergeLists(mergedResult.getCoverage(), enrich.getCoverage()));
|
||||
|
||||
mergedResult.setContext(mergeLists(mergedResult.getContext(), enrich.getContext()));
|
||||
|
||||
mergedResult.setExternalReference(mergeLists(mergedResult.getExternalReference(), enrich.getExternalReference()));
|
||||
|
||||
return mergedResult;
|
||||
}
|
||||
|
||||
private static OtherResearchProduct mergeOAFOtherResearchProduct(OtherResearchProduct original, OtherResearchProduct enrich) {
|
||||
final OtherResearchProduct mergedORP = (OtherResearchProduct) mergeOAFResult(original, enrich);
|
||||
|
||||
|
||||
mergedORP.setContactperson(mergeLists(mergedORP.getContactperson(), enrich.getContactperson()));
|
||||
mergedORP.setContactgroup(mergeLists(mergedORP.getContactgroup(), enrich.getContactgroup()));
|
||||
mergedORP.setTool(mergeLists(mergedORP.getTool(), enrich.getTool()));
|
||||
mergeOAFDataInfo(mergedORP, enrich);
|
||||
|
||||
return mergedORP;
|
||||
}
|
||||
|
||||
private static Software mergeOAFSoftware(Software original, Software enrich) {
|
||||
final Software mergedSoftware = (Software) mergeOAFResult(original, enrich);
|
||||
|
||||
mergedSoftware.setDocumentationUrl(mergeLists(mergedSoftware.getDocumentationUrl(), enrich.getDocumentationUrl()));
|
||||
|
||||
mergedSoftware.setLicense(mergeLists(mergedSoftware.getLicense(), enrich.getLicense()));
|
||||
|
||||
mergedSoftware.setCodeRepositoryUrl(enrich.getCodeRepositoryUrl() != null && compareTrust(mergedSoftware,enrich) < 0
|
||||
? enrich.getCodeRepositoryUrl()
|
||||
: mergedSoftware.getCodeRepositoryUrl());
|
||||
|
||||
mergedSoftware.setProgrammingLanguage(enrich.getProgrammingLanguage() != null && compareTrust(mergedSoftware, enrich) < 0
|
||||
? enrich.getProgrammingLanguage()
|
||||
: mergedSoftware.getProgrammingLanguage());
|
||||
|
||||
mergeOAFDataInfo(mergedSoftware, enrich);
|
||||
return mergedSoftware;
|
||||
}
|
||||
|
||||
private static Dataset mergeOAFDataset(Dataset original, Dataset enrich) {
|
||||
|
||||
final Dataset mergedDataset = (Dataset) mergeOAFResult(original, enrich);
|
||||
|
||||
mergedDataset.setStoragedate(enrich.getStoragedate() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getStoragedate() : mergedDataset.getStoragedate());
|
||||
|
||||
mergedDataset.setDevice(enrich.getDevice() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getDevice() : mergedDataset.getDevice());
|
||||
|
||||
mergedDataset.setSize(enrich.getSize() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getSize() : mergedDataset.getSize());
|
||||
|
||||
mergedDataset.setVersion(enrich.getVersion() != null && compareTrust(mergedDataset, enrich) < 0 ? enrich.getVersion() : mergedDataset.getVersion());
|
||||
|
||||
mergedDataset.setLastmetadataupdate(
|
||||
enrich.getLastmetadataupdate() != null && compareTrust(mergedDataset,enrich) < 0
|
||||
? enrich.getLastmetadataupdate()
|
||||
: mergedDataset.getLastmetadataupdate());
|
||||
|
||||
mergedDataset.setMetadataversionnumber(
|
||||
enrich.getMetadataversionnumber() != null && compareTrust(mergedDataset, enrich) < 0
|
||||
? enrich.getMetadataversionnumber()
|
||||
: mergedDataset.getMetadataversionnumber());
|
||||
|
||||
mergedDataset.setGeolocation(mergeLists(mergedDataset.getGeolocation(), enrich.getGeolocation()));
|
||||
|
||||
mergeOAFDataInfo(mergedDataset, enrich);
|
||||
|
||||
return mergedDataset;
|
||||
}
|
||||
|
||||
private static Publication mergeOAFPublication(Publication original, Publication enrich) {
|
||||
|
||||
final Publication mergedPublication = (Publication) mergeOAFResult(original, enrich);
|
||||
|
||||
if (enrich.getJournal() != null && compareTrust(mergedPublication, enrich) < 0)
|
||||
mergedPublication.setJournal(enrich.getJournal());
|
||||
mergeOAFDataInfo(mergedPublication, enrich);
|
||||
return mergedPublication;
|
||||
}
|
||||
|
||||
|
||||
private static Relation mergeOAFRelation(Relation from, Relation to) {
|
||||
|
||||
checkArgument(Objects.equals(from.getSource(), to.getSource()), "source ids must be equal");
|
||||
checkArgument(Objects.equals(from.getTarget(), to.getTarget()), "target ids must be equal");
|
||||
checkArgument(Objects.equals(from.getRelType(), to.getRelType()), "relType(s) must be equal");
|
||||
checkArgument(
|
||||
Objects.equals(from.getSubRelType(), to.getSubRelType()), "subRelType(s) must be equal");
|
||||
checkArgument(Objects.equals(from.getRelClass(), to.getRelClass()), "relClass(es) must be equal");
|
||||
|
||||
from.setValidated(from.getValidated() || to.getValidated());
|
||||
try {
|
||||
from.setValidationDate(ModelSupport.oldest(from.getValidationDate(), to.getValidationDate()));
|
||||
} catch (ParseException e) {
|
||||
throw new IllegalArgumentException(String
|
||||
.format(
|
||||
"invalid validation date format in relation [s:%s, t:%s]: %s", from.getSource(), from.getTarget(),
|
||||
from.getValidationDate()));
|
||||
}
|
||||
|
||||
return from;
|
||||
}
|
||||
|
||||
|
||||
private static Oaf mergeOAFOrganization(Organization original, Organization enrich) {
|
||||
|
||||
final Organization mergedOrganization = (Organization) mergeEntity(original, enrich);
|
||||
|
||||
int ct = compareTrust(mergedOrganization, enrich);
|
||||
mergedOrganization.setLegalshortname(enrich.getLegalshortname() != null && ct < 0
|
||||
? enrich.getLegalshortname()
|
||||
: mergedOrganization.getLegalname());
|
||||
|
||||
|
||||
mergedOrganization.setLegalname(enrich.getLegalname() != null && ct < 0 ?
|
||||
enrich.getLegalname()
|
||||
: mergedOrganization.getLegalname());
|
||||
|
||||
mergedOrganization.setAlternativeNames(mergeLists(enrich.getAlternativeNames(), mergedOrganization.getAlternativeNames()));
|
||||
|
||||
|
||||
mergedOrganization.setWebsiteurl(enrich.getWebsiteurl() != null && ct < 0
|
||||
? enrich.getWebsiteurl()
|
||||
: mergedOrganization.getWebsiteurl());
|
||||
|
||||
mergedOrganization.setLogourl(enrich.getLogourl() != null && ct < 0
|
||||
? enrich.getLogourl()
|
||||
: mergedOrganization.getLogourl());
|
||||
|
||||
mergedOrganization.setEclegalbody(enrich.getEclegalbody() != null && ct < 0
|
||||
? enrich.getEclegalbody()
|
||||
: mergedOrganization.getEclegalbody());
|
||||
|
||||
mergedOrganization.setEclegalperson(enrich.getEclegalperson() != null && ct < 0
|
||||
? enrich.getEclegalperson()
|
||||
: mergedOrganization.getEclegalperson());
|
||||
|
||||
mergedOrganization.setEcnonprofit (enrich.getEcnonprofit() != null && ct< 0
|
||||
? enrich.getEcnonprofit()
|
||||
: mergedOrganization.getEcnonprofit());
|
||||
|
||||
mergedOrganization.setEcresearchorganization (enrich.getEcresearchorganization() != null && ct < 0
|
||||
? enrich.getEcresearchorganization()
|
||||
: mergedOrganization.getEcresearchorganization());
|
||||
|
||||
mergedOrganization.setEchighereducation (enrich.getEchighereducation() != null && ct < 0
|
||||
? enrich.getEchighereducation()
|
||||
: mergedOrganization.getEchighereducation());
|
||||
|
||||
mergedOrganization.setEcinternationalorganizationeurinterests (enrich.getEcinternationalorganizationeurinterests() != null && ct< 0
|
||||
? enrich.getEcinternationalorganizationeurinterests()
|
||||
: mergedOrganization.getEcinternationalorganizationeurinterests());
|
||||
|
||||
mergedOrganization.setEcinternationalorganization (enrich.getEcinternationalorganization() != null && ct < 0
|
||||
? enrich.getEcinternationalorganization()
|
||||
: mergedOrganization.getEcinternationalorganization());
|
||||
|
||||
mergedOrganization.setEcenterprise (enrich.getEcenterprise() != null && ct < 0
|
||||
? enrich.getEcenterprise()
|
||||
: mergedOrganization.getEcenterprise());
|
||||
|
||||
mergedOrganization.setEcsmevalidated (enrich.getEcsmevalidated() != null && ct < 0
|
||||
? enrich.getEcsmevalidated()
|
||||
: mergedOrganization.getEcsmevalidated());
|
||||
mergedOrganization.setEcnutscode( enrich.getEcnutscode() != null && ct < 0
|
||||
? enrich.getEcnutscode()
|
||||
: mergedOrganization.getEcnutscode());
|
||||
|
||||
mergedOrganization.setCountry (enrich.getCountry() != null && ct < 0 ?
|
||||
enrich.getCountry()
|
||||
:mergedOrganization.getCountry());
|
||||
|
||||
mergeOAFDataInfo(mergedOrganization, enrich);
|
||||
|
||||
return mergedOrganization;
|
||||
}
|
||||
|
||||
private static Oaf mergeOAFProject(Project original, Project enrich) {
|
||||
|
||||
final Project mergedProject = (Project) mergeEntity(original, enrich);
|
||||
|
||||
int ct = compareTrust(mergedProject, enrich);
|
||||
|
||||
|
||||
mergedProject.setWebsiteurl (enrich.getWebsiteurl() != null && ct < 0
|
||||
? enrich.getWebsiteurl()
|
||||
: mergedProject.getWebsiteurl());
|
||||
|
||||
mergedProject.setCode(enrich.getCode() != null && ct < 0 ?
|
||||
enrich.getCode() :
|
||||
mergedProject.getCode());
|
||||
|
||||
mergedProject.setAcronym(enrich.getAcronym() != null && ct < 0
|
||||
? enrich.getAcronym()
|
||||
: mergedProject.getAcronym());
|
||||
|
||||
mergedProject.setTitle (enrich.getTitle() != null && ct < 0
|
||||
? enrich.getTitle()
|
||||
: mergedProject.getTitle());
|
||||
mergedProject.setStartdate (enrich.getStartdate() != null && ct < 0
|
||||
? enrich.getStartdate()
|
||||
: mergedProject.getStartdate());
|
||||
mergedProject.setEnddate (enrich.getEnddate() != null && ct < 0
|
||||
? enrich.getEnddate()
|
||||
: mergedProject.getEnddate());
|
||||
mergedProject.setCallidentifier ( enrich.getCallidentifier() != null && ct < 0
|
||||
? enrich.getCallidentifier()
|
||||
: mergedProject.getCallidentifier());
|
||||
mergedProject.setKeywords ( enrich.getKeywords() != null && ct < 0
|
||||
? enrich.getKeywords()
|
||||
: mergedProject.getKeywords());
|
||||
|
||||
mergedProject.setDuration ( enrich.getDuration() != null && ct < 0
|
||||
? enrich.getDuration()
|
||||
: mergedProject.getDuration());
|
||||
mergedProject.setEcsc39 ( enrich.getEcsc39() != null && ct < 0
|
||||
? enrich.getEcsc39() :
|
||||
mergedProject.getEcsc39());
|
||||
mergedProject.setOamandatepublications ( enrich.getOamandatepublications() != null && ct < 0
|
||||
? enrich.getOamandatepublications()
|
||||
: mergedProject.getOamandatepublications());
|
||||
mergedProject.setEcarticle29_3 (enrich.getEcarticle29_3() != null && ct < 0
|
||||
? enrich.getEcarticle29_3()
|
||||
: mergedProject.getEcarticle29_3());
|
||||
|
||||
mergedProject.setSubjects (mergeLists(mergedProject.getSubjects(), enrich.getSubjects()));
|
||||
mergedProject.setFundingtree (mergeLists(mergedProject.getFundingtree(), enrich.getFundingtree()));
|
||||
mergedProject.setContracttype (enrich.getContracttype() != null && ct < 0
|
||||
? enrich.getContracttype()
|
||||
: mergedProject.getContracttype());
|
||||
mergedProject.setOptional1 ( enrich.getOptional1() != null && ct < 0
|
||||
? enrich.getOptional1()
|
||||
: mergedProject.getOptional1());
|
||||
mergedProject.setOptional2 (enrich.getOptional2() != null && ct < 0
|
||||
? enrich.getOptional2()
|
||||
: mergedProject.getOptional2());
|
||||
|
||||
mergedProject.setJsonextrainfo ( enrich.getJsonextrainfo() != null && ct < 0
|
||||
? enrich.getJsonextrainfo()
|
||||
: mergedProject.getJsonextrainfo());
|
||||
|
||||
mergedProject.setContactfullname ( enrich.getContactfullname() != null && ct < 0
|
||||
? enrich.getContactfullname()
|
||||
: mergedProject.getContactfullname());
|
||||
|
||||
mergedProject.setContactfax ( enrich.getContactfax() != null && ct < 0
|
||||
? enrich.getContactfax()
|
||||
: mergedProject.getContactfax());
|
||||
|
||||
mergedProject.setContactphone (enrich.getContactphone() != null && ct < 0
|
||||
? enrich.getContactphone()
|
||||
: mergedProject.getContactphone());
|
||||
|
||||
mergedProject.setContactemail ( enrich.getContactemail() != null && ct < 0
|
||||
? enrich.getContactemail()
|
||||
: mergedProject.getContactemail());
|
||||
|
||||
mergedProject.setSummary ( enrich.getSummary() != null && ct < 0
|
||||
? enrich.getSummary()
|
||||
: mergedProject.getSummary());
|
||||
|
||||
mergedProject.setCurrency( enrich.getCurrency() != null && ct < 0
|
||||
? enrich.getCurrency()
|
||||
: mergedProject.getCurrency());
|
||||
|
||||
if (enrich.getH2020topiccode() != null && StringUtils.isEmpty(mergedProject.getH2020topiccode())){
|
||||
mergedProject.setH2020topiccode(enrich.getH2020topiccode());
|
||||
mergedProject.setH2020topicdescription(enrich.getH2020topicdescription());
|
||||
}
|
||||
|
||||
mergedProject.setH2020classification (mergeLists(mergedProject.getH2020classification(), enrich.getH2020classification()));
|
||||
|
||||
mergeOAFDataInfo(mergedProject, enrich);
|
||||
|
||||
return mergedProject;
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
|
@ -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 +1,39 @@
|
|||
|
||||
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<>());
|
||||
}
|
||||
|
||||
private PidBlacklistProvider() {}
|
||||
|
||||
}
|
||||
|
|
@ -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 final 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 +1,79 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import org.apache.commons.lang3.EnumUtils;
|
||||
|
||||
public enum PidType {
|
||||
|
||||
/**
|
||||
* The DOI syntax shall be made up of a DOI prefix and a DOI suffix separated by a forward slash.
|
||||
*
|
||||
* There is no defined limit on the length of the DOI name, or of the DOI prefix or DOI suffix.
|
||||
*
|
||||
* The DOI name is case-insensitive and can incorporate any printable characters from the legal graphic characters
|
||||
* of Unicode. Further constraints on character use (e.g. use of language-specific alphanumeric characters) can be
|
||||
* defined for an application by the ISO 26324 Registration Authority.
|
||||
*
|
||||
*
|
||||
* DOI prefix: The DOI prefix shall be composed of a directory indicator followed by a registrant code.
|
||||
* These two components shall be separated by a full stop (period). The directory indicator shall be "10" and
|
||||
* distinguishes the entire set of character strings (prefix and suffix) as digital object identifiers within the
|
||||
* resolution system.
|
||||
*
|
||||
* Registrant code: The second element of the DOI prefix shall be the registrant code. The registrant code is a
|
||||
* unique string assigned to a registrant.
|
||||
*
|
||||
* DOI suffix: The DOI suffix shall consist of a character string of any length chosen by the registrant.
|
||||
* Each suffix shall be unique to the prefix element that precedes it. The unique suffix can be a sequential number,
|
||||
* or it might incorporate an identifier generated from or based on another system used by the registrant
|
||||
* (e.g. ISAN, ISBN, ISRC, ISSN, ISTC, ISNI; in such cases, a preferred construction for such a suffix can be
|
||||
* specified, as in Example 1).
|
||||
*
|
||||
* Source: https://www.doi.org/doi_handbook/2_Numbering.html#2.2
|
||||
*/
|
||||
doi,
|
||||
|
||||
/**
|
||||
* PubMed Unique Identifier (PMID)
|
||||
*
|
||||
* This field is a 1-to-8 digit accession number with no leading zeros. It is present on all records and is the
|
||||
* accession number for managing and disseminating records. PMIDs are not reused after records are deleted.
|
||||
*
|
||||
* Beginning in February 2012 PMIDs include extensions following a decimal point to account for article versions
|
||||
* (e.g., 21804956.2). All citations are considered version 1 until replaced. The extended PMID is not displayed
|
||||
* on the MEDLINE format.
|
||||
*
|
||||
* View the citation in abstract format in PubMed to access additional versions when available (see the article in
|
||||
* the Jan-Feb 2012 NLM Technical Bulletin).
|
||||
*
|
||||
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmid
|
||||
*/
|
||||
pmid,
|
||||
|
||||
/**
|
||||
* This field contains the unique identifier for the cited article in PubMed Central. The identifier begins with the
|
||||
* prefix PMC.
|
||||
*
|
||||
* Source: https://www.nlm.nih.gov/bsd/mms/medlineelements.html#pmc
|
||||
*/
|
||||
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 +1,77 @@
|
|||
|
||||
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.KeyValue;
|
||||
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(KeyValue::getKey)
|
||||
.collect(Collectors.toCollection(HashSet::new)))
|
||||
.orElse(new HashSet<>());
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,21 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import java.util.Set;
|
||||
|
||||
class BlackListProviderTest {
|
||||
|
||||
@Test
|
||||
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 +1,80 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
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;
|
||||
|
||||
class IdentifierFactoryTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
|
||||
.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
||||
|
||||
@Test
|
||||
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_doi5.json", "50|doi_________::3bef95c0ca26dd55451fc8839ea69d27", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_pmc1.json", "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_pmc2.json", "50|pmc_________::94e4cb08c93f8733b48e2445d04002ac", true);
|
||||
|
||||
verifyIdentifier(
|
||||
"publication_openapc.json", "50|doi_________::79dbc7a2a56dc1532659f9038843256e", 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
|
||||
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 +1,617 @@
|
|||
|
||||
package eu.dnetlib.dhp.schema.oaf.utils;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.io.InputStream;
|
||||
import java.time.format.DateTimeParseException;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
/**
|
||||
* The type Merge test.
|
||||
*/
|
||||
class MergeTest {
|
||||
|
||||
/**
|
||||
* The Oaf.
|
||||
*/
|
||||
OafEntity oaf;
|
||||
|
||||
/**
|
||||
* Sets up.
|
||||
*/
|
||||
@BeforeEach
|
||||
public void setUp() {
|
||||
oaf = new Publication();
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge lists test.
|
||||
*/
|
||||
@Test
|
||||
@SuppressWarnings("unchecked")
|
||||
void mergeListsTest() {
|
||||
|
||||
// string list merge test
|
||||
List<String> a = Arrays.asList("a", "b", "c", "e");
|
||||
List<String> b = Arrays.asList("a", "b", "c", "d");
|
||||
List<String> c = null;
|
||||
|
||||
System.out.println("merge result 1 = " + OafUtils.mergeLists(a, b));
|
||||
|
||||
System.out.println("merge result 2 = " + OafUtils.mergeLists(a, c));
|
||||
|
||||
System.out.println("merge result 3 = " + OafUtils.mergeLists(c, c));
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication collected from test.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationCollectedFromTest() {
|
||||
|
||||
Publication a = publication();
|
||||
Publication b = publication();
|
||||
|
||||
a.setCollectedfrom(Arrays.asList(setKV("a", "open"), setKV("b", "closed")));
|
||||
b.setCollectedfrom(Arrays.asList(setKV("A", "open"), setKV("b", "Open")));
|
||||
|
||||
a = (Publication) OafUtils.mergeOAF(a, b);
|
||||
|
||||
|
||||
assertNotNull(a.getCollectedfrom());
|
||||
assertEquals(3, a.getCollectedfrom().size());
|
||||
}
|
||||
|
||||
/**
|
||||
* Load resource result list.
|
||||
*
|
||||
* @param <T> the type parameter
|
||||
* @param path the path
|
||||
* @param clazz the clazz
|
||||
* @return the list
|
||||
* @throws Exception the exception
|
||||
*/
|
||||
private <T extends Result> List<Result> loadResourceResult(final String path, final Class<T> clazz ) throws Exception {
|
||||
final ObjectMapper mapper = new ObjectMapper();
|
||||
final InputStream str = Objects.requireNonNull(getClass().getResourceAsStream(path));
|
||||
// LOAD test publications
|
||||
return IOUtils.readLines(str).stream().map(s -> {
|
||||
try {
|
||||
return mapper.readValue(s, clazz);
|
||||
} catch (IOException e) {
|
||||
return null;
|
||||
}
|
||||
}).filter(Objects::nonNull).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Apply to any test list result the same pid of the enrichment instance
|
||||
*
|
||||
* @param source the source
|
||||
* @param enrichment the enrichment
|
||||
* @param overrideAlternateIdentifier the override alternate identifier
|
||||
*/
|
||||
private void updatePidIntoPublicationInstance(final List<Result> source, final List<Result>enrichment, final boolean overrideAlternateIdentifier) {
|
||||
for(int i = 0 ; i< source.size(); i++) {
|
||||
final Result currentPub = source.get(i);
|
||||
final Result currentEnrichment = enrichment.get(i);
|
||||
final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
|
||||
if (overrideAlternateIdentifier)
|
||||
currentInstance.setAlternateIdentifier(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
|
||||
else
|
||||
currentInstance.setPid(Objects.requireNonNull(currentEnrichment.getInstance()).get(0).getPid());
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private void applyAndVerifyEnrichment(final List<Result> l1, final List<Result> l2) {
|
||||
// Apply Merge and verify that enrichments works
|
||||
for(int i = 0 ; i< l1.size(); i++) {
|
||||
final Result currentPub = l2.get(i);
|
||||
final Result currentEnrichment = l1.get(i);
|
||||
currentPub.mergeFrom(currentEnrichment);
|
||||
assertEquals(1, currentPub.getInstance().size());
|
||||
final Instance currentInstance = Objects.requireNonNull(currentPub.getInstance()).get(0);
|
||||
assertNotNull(currentInstance.getMeasures());
|
||||
assertNotNull(currentPub.getTitle());
|
||||
assertFalse(Result.isAnEnrichment(currentPub));
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Test the merge of the APC at the level of the result and the instance.
|
||||
*
|
||||
* @throws Exception the exception
|
||||
*/
|
||||
|
||||
@Test
|
||||
void testAPCMerge() throws Exception {
|
||||
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc.json", Publication.class);
|
||||
System.out.println(publications.size());
|
||||
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
|
||||
publications.forEach(p -> assertTrue(p.getProcessingchargeamount() != null ));
|
||||
publications.forEach(p -> assertTrue(p.getProcessingchargecurrency() != null ));
|
||||
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargeamount().getValue() )));
|
||||
publications.forEach(p -> assertTrue(StringUtils.isNotBlank(p.getProcessingchargecurrency().getValue() )));
|
||||
|
||||
publications.forEach(p -> p.getInstance().stream()
|
||||
.forEach(i -> assertTrue(i.getProcessingchargeamount() != null)));
|
||||
publications.forEach(p -> p.getInstance().stream()
|
||||
.forEach(i -> assertTrue(i.getProcessingchargecurrency() != null)));
|
||||
|
||||
publications.forEach(p -> p.getInstance().stream()
|
||||
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargeamount().getValue()))));
|
||||
publications.forEach(p -> p.getInstance().stream()
|
||||
.forEach(i -> assertTrue(StringUtils.isNotBlank(i.getProcessingchargecurrency().getValue()))));
|
||||
|
||||
Result p1 = publications.get(0);
|
||||
Result p2 = publications.get(1);
|
||||
|
||||
p1.mergeFrom(p2);
|
||||
|
||||
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
|
||||
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
|
||||
|
||||
assertEquals(2 , p1.getInstance().size());
|
||||
|
||||
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargeamount() != null));
|
||||
p1.getInstance().stream().forEach(i -> assertTrue(i.getProcessingchargecurrency() != null));
|
||||
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("2000.47"));
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount().getValue().equals("1721.47"));
|
||||
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("EUR"));
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency().getValue().equals("USD"));
|
||||
System.out.println(new ObjectMapper().writeValueAsString(p1));
|
||||
}
|
||||
@Test
|
||||
void testAPCMerge2() throws Exception {
|
||||
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publication_apc2.json", Publication.class);
|
||||
System.out.println(publications.size());
|
||||
publications.forEach(p -> assertEquals(1, p.getInstance().size()));
|
||||
assertTrue(publications.get(0).getProcessingchargeamount() != null );
|
||||
assertTrue(publications.get(0).getProcessingchargecurrency() != null );
|
||||
assertTrue(publications.get(1).getProcessingchargeamount() == null );
|
||||
|
||||
Result p1 = publications.get(1);
|
||||
Result p2 = publications.get(0);
|
||||
|
||||
//merge visible record with OpenAPC
|
||||
p1 = (Result) OafUtils.mergeOAF(p1, p2);
|
||||
|
||||
assertFalse(p1.getDataInfo().getInvisible());
|
||||
assertEquals("1721.47", p1.getProcessingchargeamount().getValue());
|
||||
assertEquals("EUR", p1.getProcessingchargecurrency().getValue());
|
||||
|
||||
assertEquals(2 , p1.getInstance().size());
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
|
||||
|
||||
p1.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
|
||||
|
||||
assertEquals("1721.47", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
|
||||
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
|
||||
|
||||
assertEquals("EUR", p1.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
|
||||
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
|
||||
assertFalse(p1.getDataInfo().getInvisible());
|
||||
System.out.println(new ObjectMapper().writeValueAsString(p1));
|
||||
|
||||
//merge OpenAPC with visible record
|
||||
|
||||
p2 = (Result) OafUtils.mergeOAF(p2, p1);
|
||||
|
||||
assertFalse(p2.getDataInfo().getInvisible());
|
||||
assertEquals("1721.47", p2.getProcessingchargeamount().getValue());
|
||||
assertEquals("EUR", p2.getProcessingchargecurrency().getValue());
|
||||
|
||||
assertEquals(2 , p2.getInstance().size());
|
||||
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargeamount() != null);
|
||||
|
||||
p2.getInstance().stream().anyMatch(i -> i.getProcessingchargecurrency() != null);
|
||||
|
||||
assertEquals("1721.47", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
|
||||
.collect(Collectors.toList()).get(0).getProcessingchargeamount().getValue());
|
||||
|
||||
assertEquals("EUR", p2.getInstance().stream().filter(i -> i.getProcessingchargeamount() != null)
|
||||
.collect(Collectors.toList()).get(0).getProcessingchargecurrency().getValue());
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Test enrichment function.
|
||||
*
|
||||
* @throws Exception the exception
|
||||
*/
|
||||
@Test
|
||||
void testEnrichment() throws Exception {
|
||||
|
||||
|
||||
// 1 TEST UPDATING PID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
|
||||
// LOAD test publications
|
||||
List<Result> publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
|
||||
// Assert that each publication has only one instance and inside that all the measure field is empty
|
||||
publications.forEach(p -> {
|
||||
assertEquals(1, p.getInstance().size());
|
||||
final Instance currentInstance = Objects.requireNonNull(p.getInstance()).get(0);
|
||||
assertNull(currentInstance.getMeasures());
|
||||
});
|
||||
|
||||
// LOAD test enrichments
|
||||
List<Result> enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
|
||||
|
||||
updatePidIntoPublicationInstance(publications, enrichment, false);
|
||||
applyAndVerifyEnrichment(publications, enrichment);
|
||||
|
||||
|
||||
// 2 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE CURRENT PUBLICATION WITH ENRICHMENT
|
||||
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
|
||||
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
|
||||
updatePidIntoPublicationInstance(publications, enrichment, true);
|
||||
applyAndVerifyEnrichment(publications, enrichment);
|
||||
|
||||
|
||||
// 3 TEST UPDATING PID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
|
||||
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
|
||||
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
|
||||
updatePidIntoPublicationInstance(publications, enrichment, false);
|
||||
applyAndVerifyEnrichment( enrichment, publications);
|
||||
|
||||
// 4 TEST UPDATING ALTERNATE ID INSTANCE AND MERGE ENRICHMENT WITH CURRENT PUBLICATION
|
||||
publications = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/publications.json", Publication.class);
|
||||
enrichment = loadResourceResult("/eu/dnetlib/dhp/schema/oaf/utils/enrichment.json", Result.class);
|
||||
updatePidIntoPublicationInstance(publications, enrichment, true);
|
||||
applyAndVerifyEnrichment( enrichment, publications);
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test both present.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_bothPresent() {
|
||||
|
||||
Publication a = publication();
|
||||
Publication b = publication();
|
||||
|
||||
a.setDateofacceptance(field("2021-06-18"));
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test both present 1.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_bothPresent_1() {
|
||||
|
||||
Publication a = publication("0.8");
|
||||
Publication b = publication("0.9");
|
||||
|
||||
a.setDateofacceptance(field("2021-06-18"));
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test both present 2.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_bothPresent_2() {
|
||||
|
||||
Publication a = publication("0.9");
|
||||
Publication b = publication("0.8");
|
||||
|
||||
a.setDateofacceptance(field("2021-06-18"));
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-18", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test left missing.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_leftMissing() {
|
||||
|
||||
Publication a = publication();
|
||||
Publication b = publication();
|
||||
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test left missing 1.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_leftMissing_1() {
|
||||
|
||||
Publication a = publication("0.9");
|
||||
Publication b = publication("0.8");
|
||||
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test left missing 2.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_leftMissing_2() {
|
||||
|
||||
Publication a = publication("0.8");
|
||||
Publication b = publication("0.9");
|
||||
|
||||
b.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test right missing.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_rightMissing() {
|
||||
|
||||
Publication a = publication();
|
||||
Publication b = publication();
|
||||
|
||||
a.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test right missing 1.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_rightMissing_1() {
|
||||
|
||||
Publication a = publication("0.8");
|
||||
Publication b = publication("0.9");
|
||||
|
||||
a.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication date of acceptance test right missing 2.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationDateOfAcceptanceTest_rightMissing_2() {
|
||||
|
||||
Publication a = publication("0.9");
|
||||
Publication b = publication("0.8");
|
||||
|
||||
a.setDateofacceptance(field("2021-06-19"));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getDateofacceptance());
|
||||
assertEquals("2021-06-19", a.getDateofacceptance().getValue());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge publication subject test.
|
||||
*/
|
||||
@Test
|
||||
void mergePublicationSubjectTest() {
|
||||
|
||||
Publication a = publication();
|
||||
Publication b = publication();
|
||||
|
||||
a.setSubject(Arrays.asList(setSP("a", "open", "classe"), setSP("b", "open", "classe")));
|
||||
b.setSubject(Arrays.asList(setSP("A", "open", "classe"), setSP("c", "open", "classe")));
|
||||
|
||||
a.mergeFrom(b);
|
||||
|
||||
assertNotNull(a.getSubject());
|
||||
assertEquals(3, a.getSubject().size());
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge relation test.
|
||||
*/
|
||||
@Test
|
||||
void mergeRelationTest() {
|
||||
|
||||
Relation a = createRel(null, null);
|
||||
Relation b = createRel(null, null);
|
||||
a.mergeFrom(b);
|
||||
assertEquals(a, b);
|
||||
|
||||
a = createRel(true, null);
|
||||
b = createRel(null, null);
|
||||
a.mergeFrom(b);
|
||||
assertEquals(true, a.getValidated());
|
||||
|
||||
a = createRel(true, null);
|
||||
b = createRel(false, null);
|
||||
a.mergeFrom(b);
|
||||
assertEquals(true, a.getValidated());
|
||||
|
||||
a = createRel(true, null);
|
||||
b = createRel(true, "2016-04-05T12:41:19.202Z");
|
||||
a.mergeFrom(b);
|
||||
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
|
||||
|
||||
a = createRel(true, "2016-05-07T12:41:19.202Z");
|
||||
b = createRel(true, "2016-04-05T12:41:19.202Z");
|
||||
a.mergeFrom(b);
|
||||
assertEquals("2016-04-05T12:41:19.202Z", a.getValidationDate());
|
||||
|
||||
a = createRel(true, "2020-09-10 11:08:52");
|
||||
b = createRel(true, "2021-09-10 11:08:52");
|
||||
a.mergeFrom(b);
|
||||
assertEquals("2020-09-10 11:08:52", a.getValidationDate());
|
||||
|
||||
a = createRel(true, "2021-03-16T10:32:42Z");
|
||||
b = createRel(true, "2020-03-16T10:32:42Z");
|
||||
a.mergeFrom(b);
|
||||
assertEquals("2020-03-16T10:32:42Z", a.getValidationDate());
|
||||
|
||||
|
||||
}
|
||||
|
||||
/**
|
||||
* Merge relation test parse exception.
|
||||
*/
|
||||
@Test
|
||||
void mergeRelationTestParseException() {
|
||||
assertThrows(DateTimeParseException.class, () -> {
|
||||
Relation a = createRel(true, "Once upon a time ...");
|
||||
Relation b = createRel(true, "... in a far away land");
|
||||
a.mergeFrom(b);
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Create rel relation.
|
||||
*
|
||||
* @param validated the validated
|
||||
* @param validationDate the validation date
|
||||
* @return the relation
|
||||
*/
|
||||
private Relation createRel(Boolean validated, String validationDate) {
|
||||
Relation rel = new Relation();
|
||||
rel.setSource("1");
|
||||
rel.setTarget("2");
|
||||
rel.setRelType("reltype");
|
||||
rel.setSubRelType("subreltype");
|
||||
rel.setRelClass("relclass");
|
||||
rel.setValidated(validated);
|
||||
rel.setValidationDate(validationDate);
|
||||
return rel;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets kv.
|
||||
*
|
||||
* @param key the key
|
||||
* @param value the value
|
||||
* @return the kv
|
||||
*/
|
||||
private KeyValue setKV(final String key, final String value) {
|
||||
|
||||
KeyValue k = new KeyValue();
|
||||
|
||||
k.setKey(key);
|
||||
k.setValue(value);
|
||||
|
||||
return k;
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets sp.
|
||||
*
|
||||
* @param value the value
|
||||
* @param schema the schema
|
||||
* @param classname the classname
|
||||
* @return the sp
|
||||
*/
|
||||
private StructuredProperty setSP(
|
||||
final String value, final String schema, final String classname) {
|
||||
StructuredProperty s = new StructuredProperty();
|
||||
s.setValue(value);
|
||||
Qualifier q = new Qualifier();
|
||||
q.setClassname(classname);
|
||||
q.setClassid(classname);
|
||||
q.setSchemename(schema);
|
||||
q.setSchemeid(schema);
|
||||
s.setQualifier(q);
|
||||
return s;
|
||||
}
|
||||
|
||||
/**
|
||||
* Field field.
|
||||
*
|
||||
* @param <T> the type parameter
|
||||
* @param value the value
|
||||
* @return the field
|
||||
*/
|
||||
private <T> Field<T> field(T value) {
|
||||
Field<T> f = new Field();
|
||||
f.setValue(value);
|
||||
return f;
|
||||
}
|
||||
|
||||
/**
|
||||
* Publication publication.
|
||||
*
|
||||
* @return the publication
|
||||
*/
|
||||
private Publication publication() {
|
||||
Publication p = new Publication();
|
||||
p.setDataInfo(df("0.9"));
|
||||
return p;
|
||||
}
|
||||
|
||||
/**
|
||||
* Publication publication.
|
||||
*
|
||||
* @param trust the trust
|
||||
* @return the publication
|
||||
*/
|
||||
private Publication publication(String trust) {
|
||||
Publication p = new Publication();
|
||||
p.setDataInfo(df(trust));
|
||||
return p;
|
||||
}
|
||||
|
||||
/**
|
||||
* Df data info.
|
||||
*
|
||||
* @param trust the trust
|
||||
* @return the data info
|
||||
*/
|
||||
private DataInfo df(String trust) {
|
||||
DataInfo d = new DataInfo();
|
||||
d.setTrust(trust);
|
||||
return d;
|
||||
}
|
||||
}
|
||||
|
|
@ -1,140 +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"
|
||||
}
|
||||
],
|
||||
"instance": [
|
||||
{
|
||||
"refereed": {
|
||||
"classid": "0000",
|
||||
"classname": "UNKNOWN",
|
||||
"schemeid": "dnet:review_levels",
|
||||
"schemename": "dnet:review_levels"
|
||||
},
|
||||
"hostedby": {
|
||||
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
"value": "Zenodo"
|
||||
},
|
||||
"accessright": {
|
||||
"classid": "OPEN",
|
||||
"classname": "Open Access",
|
||||
"schemeid": "dnet:access_modes",
|
||||
"schemename": "dnet:access_modes"
|
||||
},
|
||||
"processingchargecurrency": {
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"value": "EUR"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "doi",
|
||||
"classname": "Digital Object Identifier",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
||||
"value": "10.1371/journal.pone.0085605"
|
||||
}
|
||||
],
|
||||
"distributionlocation": "",
|
||||
"url": ["https://doi.org/10.1371/journal.pone.0085605"],
|
||||
"alternateIdentifier": [
|
||||
{
|
||||
"dataInfo": {
|
||||
"provenanceaction": {
|
||||
"classid": "sysimport:crosswalk:datasetarchive",
|
||||
"classname": "Harvested",
|
||||
"schemeid": "dnet:provenanceActions",
|
||||
"schemename": "dnet:provenanceActions"
|
||||
},
|
||||
"deletedbyinference": false,
|
||||
"inferred": false,
|
||||
"inferenceprovenance": "",
|
||||
"invisible": true,
|
||||
"trust": "0.9"
|
||||
},
|
||||
"qualifier": {
|
||||
"classid": "pmid",
|
||||
"classname": "PubMed ID",
|
||||
"schemeid": "dnet:pid_types",
|
||||
"schemename": "dnet:pid_types"
|
||||
},
|
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{
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||||
"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|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
"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 +1,37 @@
|
|||
{
|
||||
"id": "50|DansKnawCris::0829b5191605bdbea36d6502b8c1ce1f",
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|opendoar____::358aee4cc897452c00244351e4d91f69",
|
||||
"value": "Zenodo"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.5281/zenodo.5121485"
|
||||
}
|
||||
]
|
||||
},
|
||||
{
|
||||
"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 +1,31 @@
|
|||
{
|
||||
"id": "50|openapc_____::000023f9cb6e3a247c764daec4273cbc",
|
||||
"resuttype": {
|
||||
"classid": "publication"
|
||||
},
|
||||
"instance": [
|
||||
{
|
||||
"collectedfrom": {
|
||||
"key": "10|apc_________::e2b1600b229fc30663c8a1f662debddf",
|
||||
"value": "OpenAPC Global Initiative"
|
||||
},
|
||||
"pid": [
|
||||
{
|
||||
"qualifier": {"classid": "doi"},
|
||||
"value": "10.1016/j.cmet.2010.03.013"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmc"},
|
||||
"value": "21459329"
|
||||
},
|
||||
{
|
||||
"qualifier": {"classid": "pmid"},
|
||||
"value": "25811027"
|
||||
}
|
||||
],
|
||||
"url":["https://doi.org/10.1155/2015/439379"]
|
||||
}
|
||||
]
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
{
|
||||
"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"
|
||||
}
|
||||
]
|
||||
}
|
||||
File diff suppressed because one or more lines are too long
|
|
@ -511,7 +511,7 @@ object DoiBoostMappingUtil {
|
|||
if (!ret.startsWith(DOI_PREFIX))
|
||||
return null
|
||||
|
||||
return ret
|
||||
ret
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,50 @@
|
|||
package eu.dnetlib.doiboost
|
||||
|
||||
import eu.dnetlib.dhp.schema.common.ModelConstants
|
||||
import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo}
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils._
|
||||
import scala.collection.JavaConverters._
|
||||
|
||||
object DoiBoostTransformationUtils {
|
||||
|
||||
|
||||
val TRUST = "0.9"
|
||||
|
||||
def generateDataInfo(): DataInfo = {
|
||||
val di = new DataInfo
|
||||
di.setDeletedbyinference(false)
|
||||
di.setInferred(false)
|
||||
di.setInvisible(false)
|
||||
di.setTrust(TRUST)
|
||||
di.setProvenanceaction(
|
||||
OafMapperUtils.qualifier(
|
||||
ModelConstants.SYSIMPORT_ACTIONSET,
|
||||
ModelConstants.SYSIMPORT_ACTIONSET,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
||||
ModelConstants.DNET_PROVENANCE_ACTIONS
|
||||
)
|
||||
)
|
||||
di
|
||||
}
|
||||
|
||||
|
||||
|
||||
def generateOAFAuthor(given: String, family: String, orcid: String, index: Int): Author = {
|
||||
val a = new Author
|
||||
a.setName(given)
|
||||
a.setSurname(family)
|
||||
a.setFullname(s"$given $family")
|
||||
a.setRank(index + 1)
|
||||
if (StringUtils.isNotBlank(orcid))
|
||||
a.setPid(
|
||||
List(
|
||||
structuredProperty(orcid, qualifier(ModelConstants.ORCID_PENDING,ModelConstants.ORCID_PENDING,ModelConstants.DNET_PID_TYPES,ModelConstants.DNET_PID_TYPES), generateDataInfo)
|
||||
).asJava
|
||||
)
|
||||
|
||||
a
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -5,8 +5,7 @@ import eu.dnetlib.dhp.schema.common.ModelConstants
|
|||
import eu.dnetlib.dhp.schema.oaf._
|
||||
import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils}
|
||||
import eu.dnetlib.dhp.utils.DHPUtils
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil
|
||||
import eu.dnetlib.doiboost.DoiBoostMappingUtil._
|
||||
|
||||
import org.apache.commons.lang.StringUtils
|
||||
import org.apache.commons.lang3.tuple
|
||||
import org.json4s
|
||||
|
|
@ -15,6 +14,8 @@ import org.json4s.JsonAST._
|
|||
import org.json4s.jackson.JsonMethods._
|
||||
import org.slf4j.{Logger, LoggerFactory}
|
||||
|
||||
import eu.dnetlib.doiboost.DoiBoostTransformationUtils._
|
||||
|
||||
import java.util
|
||||
import scala.collection.JavaConverters._
|
||||
import scala.collection.mutable
|
||||
|
|
@ -34,62 +35,9 @@ case class mappingAuthor(
|
|||
|
||||
case class mappingFunder(name: String, DOI: Option[String], award: Option[List[String]]) {}
|
||||
|
||||
case object Crossref2Oaf {
|
||||
object Crossref2Oaf {
|
||||
val logger: Logger = LoggerFactory.getLogger(Crossref2Oaf.getClass)
|
||||
|
||||
// val mappingCrossrefType = Map(
|
||||
// "book-section" -> "publication",
|
||||
// "book" -> "publication",
|
||||
// "book-chapter" -> "publication",
|
||||
// "book-part" -> "publication",
|
||||
// "book-series" -> "publication",
|
||||
// "book-set" -> "publication",
|
||||
// "book-track" -> "publication",
|
||||
// "edited-book" -> "publication",
|
||||
// "reference-book" -> "publication",
|
||||
// "monograph" -> "publication",
|
||||
// "journal-article" -> "publication",
|
||||
// "dissertation" -> "publication",
|
||||
// "other" -> "publication",
|
||||
// "peer-review" -> "publication",
|
||||
// "proceedings" -> "publication",
|
||||
// "proceedings-article" -> "publication",
|
||||
// "reference-entry" -> "publication",
|
||||
// "report" -> "publication",
|
||||
// "report-series" -> "publication",
|
||||
// "standard" -> "publication",
|
||||
// "standard-series" -> "publication",
|
||||
// "posted-content" -> "publication",
|
||||
// "dataset" -> "dataset"
|
||||
// )
|
||||
//
|
||||
// val mappingCrossrefSubType = Map(
|
||||
// "book-section" -> "0013 Part of book or chapter of book",
|
||||
// "book" -> "0002 Book",
|
||||
// "book-chapter" -> "0013 Part of book or chapter of book",
|
||||
// "book-part" -> "0013 Part of book or chapter of book",
|
||||
// "book-series" -> "0002 Book",
|
||||
// "book-set" -> "0002 Book",
|
||||
// "book-track" -> "0002 Book",
|
||||
// "edited-book" -> "0002 Book",
|
||||
// "reference-book" -> "0002 Book",
|
||||
// "monograph" -> "0002 Book",
|
||||
// "journal-article" -> "0001 Article",
|
||||
// "dissertation" -> "0044 Thesis",
|
||||
// "other" -> "0038 Other literature type",
|
||||
// "peer-review" -> "0015 Review",
|
||||
// "proceedings" -> "0004 Conference object",
|
||||
// "proceedings-article" -> "0004 Conference object",
|
||||
// "reference-entry" -> "0013 Part of book or chapter of book",
|
||||
// "report" -> "0017 Report",
|
||||
// "report-series" -> "0017 Report",
|
||||
// "standard" -> "0038 Other literature type",
|
||||
// "standard-series" -> "0038 Other literature type",
|
||||
// "dataset" -> "0021 Dataset",
|
||||
// "preprint" -> "0016 Preprint",
|
||||
// "report" -> "0017 Report"
|
||||
// )
|
||||
|
||||
def mappingResult(result: Result, json: JValue, resourceType:Qualifier, instanceType: Qualifier): Result = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
|
||||
|
|
@ -216,7 +164,7 @@ case object Crossref2Oaf {
|
|||
)
|
||||
|
||||
result.setAuthor(sorted_list.zipWithIndex.map { case (a, index) =>
|
||||
generateAuhtor(a.given.orNull, a.family, a.ORCID.orNull, index)
|
||||
generateOAFAuthor(a.given.orNull, a.family, a.ORCID.orNull, index)
|
||||
}.asJava)
|
||||
|
||||
// Mapping instance
|
||||
|
|
@ -268,10 +216,7 @@ case object Crossref2Oaf {
|
|||
instance.setDateofacceptance(asField(createdDate.getValue))
|
||||
}
|
||||
val s: List[String] = List("https://doi.org/" + doi)
|
||||
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
|
||||
// if (links.nonEmpty) {
|
||||
// instance.setUrl(links.asJava)
|
||||
// }
|
||||
|
||||
if (s.nonEmpty) {
|
||||
instance.setUrl(s.asJava)
|
||||
}
|
||||
|
|
@ -297,26 +242,7 @@ case object Crossref2Oaf {
|
|||
result
|
||||
}
|
||||
|
||||
def generateAuhtor(given: String, family: String, orcid: String, index: Int): Author = {
|
||||
val a = new Author
|
||||
a.setName(given)
|
||||
a.setSurname(family)
|
||||
a.setFullname(s"$given $family")
|
||||
a.setRank(index + 1)
|
||||
if (StringUtils.isNotBlank(orcid))
|
||||
a.setPid(
|
||||
List(
|
||||
createSP(
|
||||
orcid,
|
||||
ModelConstants.ORCID_PENDING,
|
||||
ModelConstants.DNET_PID_TYPES,
|
||||
generateDataInfo()
|
||||
)
|
||||
).asJava
|
||||
)
|
||||
|
||||
a
|
||||
}
|
||||
|
||||
def convert(input: String, vocabularies: VocabularyGroup): List[Oaf] = {
|
||||
implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats
|
||||
|
|
|
|||
|
|
@ -5,6 +5,8 @@ import org.json4s.DefaultFormats
|
|||
import org.json4s.JsonAST.JString
|
||||
import org.json4s.jackson.JsonMethods.parse
|
||||
import org.junit.jupiter.api.Test
|
||||
|
||||
import java.io.PrintWriter
|
||||
class CrossrefFunderTest {
|
||||
|
||||
|
||||
|
|
@ -29,18 +31,16 @@ class CrossrefFunderTest {
|
|||
|
||||
var i = 0
|
||||
|
||||
// val w =new PrintWriter("/tmp/funder_names")
|
||||
val w =new PrintWriter("/tmp/funder_names")
|
||||
|
||||
|
||||
|
||||
val data = cf.toIterator.next()
|
||||
|
||||
println(data)
|
||||
|
||||
// cf.map(s=>parse_funder(s)).foreach(s=> w.write(s"${s._1} \t${s._2} \t${s._3.mkString("--")}\t\n"))
|
||||
//
|
||||
//
|
||||
// w.close()
|
||||
cf.map(s=>parse_funder(s)).foreach(s=> w.write(s"${s._1} \t${s._2} \t${s._3.mkString("--")}\t\n"))
|
||||
|
||||
|
||||
w.close()
|
||||
|
||||
// cf.foreach{_ =>
|
||||
//
|
||||
|
|
@ -50,11 +50,11 @@ class CrossrefFunderTest {
|
|||
// println(s"get $i documents")
|
||||
//
|
||||
// }
|
||||
|
||||
|
||||
|
||||
|
||||
println(s"Total item $i")
|
||||
//
|
||||
//
|
||||
//
|
||||
//
|
||||
// println(s"Total item $i")
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
2
pom.xml
2
pom.xml
|
|
@ -801,7 +801,7 @@
|
|||
<mockito-core.version>3.3.3</mockito-core.version>
|
||||
<mongodb.driver.version>3.4.2</mongodb.driver.version>
|
||||
<vtd.version>[2.12,3.0)</vtd.version>
|
||||
<dhp-schemas.version>[2.12.0]</dhp-schemas.version>
|
||||
<dhp-schemas.version>2.12.1-DOIBOOST_REFACTOR-SNAPSHOT</dhp-schemas.version>
|
||||
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
|
||||
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
|
||||
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>
|
||||
|
|
|
|||
Loading…
Reference in New Issue