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package eu.dnetlib.dli;
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import java.io.InputStream;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import javax.annotation.PostConstruct;
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import com.google.common.collect.BiMap;
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import com.google.common.collect.HashBiMap;
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import com.google.gson.Gson;
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import eu.dnetlib.data.transform.Ontologies;
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import eu.dnetlib.data.transform.OntologyLoader;
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import eu.dnetlib.enabling.locators.UniqueServiceLocator;
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import eu.dnetlib.miscutils.functional.xml.DnetXsltFunctions;
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import eu.dnetlib.pid.resolver.model.PID;
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import eu.dnetlib.rmi.enabling.ISLookUpException;
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import eu.dnetlib.rmi.enabling.ISLookUpService;
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import org.apache.commons.io.IOUtils;
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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 org.springframework.beans.factory.annotation.Autowired;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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public class DLIUtils {
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public final static Map<String, Pair<String, String>> datasources = new HashMap<>();
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public static final Map<String, String> resolvedTypes = new HashMap<String, String>() {
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{
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put("pdb", "http://www.rcsb.org/pdb/explore/explore.do?structureId=%s");
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put("ncbi-n", "http://www.ncbi.nlm.nih.gov/gquery/?term=%s");
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put("pmid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");
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put("pmcid", "http://www.ncbi.nlm.nih.gov/pmc/articles/%s");
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put("pubmedid", "http://www.ncbi.nlm.nih.gov/pubmed/%s");
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put("doi", "http://dx.doi.org/%s");
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put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("nuccore", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("swiss-prot", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("arrayexpress", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("biomodels", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("bmrb", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("ena", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("genbank", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("geo", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("ensembl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("mgi", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("bind", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("pride", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("ddbj", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("bioproject", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("embl", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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put("sra", "http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank");
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}
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};
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public static Ontologies ontologies;
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private static DLIUtils instance;
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private static BiMap<String, String> relations;
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private Map<String, String> dataciteDatasource;
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@Autowired
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private UniqueServiceLocator serviceLocator;
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private static BiMap<String, String> getRelationMap() {
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if (relations == null) {
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relations = HashBiMap.create();
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relations.put("IsCitedBy", "Cites");
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relations.put("IsSupplementTo", "IsSupplementedBy");
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relations.put("IsReferencedBy", "References");
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}
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return relations;
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}
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public static String getNameFromDataSourcePrefix(final String datasourcePrefix) throws ISLookUpException {
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if (datasources.keySet().size() == 0) {
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generateDSMap();
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}
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if (!datasources.containsKey(datasourcePrefix))
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return "";
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return datasources.get(datasourcePrefix).getRight();
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}
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public static String getIdFromDataSourcePrefix(final String datasourcePrefix) throws ISLookUpException {
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if (datasources.keySet().size() == 0) {
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generateDSMap();
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}
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if (!datasources.containsKey(datasourcePrefix))
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return "";
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return datasources.get(datasourcePrefix).getLeft();
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}
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public static String getPublisherName(final String publisher) {
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if (instance.getDataciteDatasource() != null) {
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return instance.getDataciteDatasource().get(publisher.trim().toLowerCase());
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}
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return "";
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}
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public static void generateDSMap() throws ISLookUpException {
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if (datasources.keySet().size() > 0)
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return;
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final String query = "for $x in collection('/db/DRIVER/RepositoryServiceResources/RepositoryServiceResourceType') "
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+ "return concat($x//FIELD[./key='NamespacePrefix']/value/text(),'@--@',$x//FIELD[./key='DataSourceId']/value/text(),'@--@',$x//ENGLISH_NAME )";
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final ISLookUpService lookupService = instance.getServiceLocator().getService(ISLookUpService.class);
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final List<String> results = lookupService.quickSearchProfile(query);
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datasources.clear();
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if (results != null)
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results.forEach(it -> {
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final String[] splitted = it.split("@--@");
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if (splitted.length == 3) {
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datasources.put(splitted[0], new ImmutablePair<>(splitted[1], splitted[2]));
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}
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});
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}
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public static String inferPidType(final String pid, final String pidType) {
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if (pidType != null && !pidType.toLowerCase().equals("doi")) {
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if (pid != null && pid.contains("http://dx.doi.org/") || pid.contains("http://doi.org/"))
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return "doi";
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}
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return pidType;
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}
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public static String fixPID(String input) {
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if (input != null) {
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return input.replace("http://dx.doi.org/", "").replace("http://doi.org/", "");
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}
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return null;
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}
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public static String geussPidType(final String pidType, final String pid ) {
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if (isValidDoi(pid)!= null){
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return "doi";
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}
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return pidType;
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}
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public static String geussPidValue(final String pid) {
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if (isValidDoi(pid)!= null){
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return isValidDoi(pid);
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}
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return pid;
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}
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public static PID createCorrectPID(final String pid, final String pidType, final String resolvedUrl) {
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PID correctPID = createCorrectPID(pid, pidType);
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correctPID.setResolvedUrl(resolvedUrl);
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return correctPID;
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}
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public static PID createCorrectPID(final String pid, final String pidType) {
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final String validDoi = isValidDoi(pid);
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if (validDoi!= null) {
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return new PID(validDoi.toLowerCase(), "doi");
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}
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return new PID(pid, pidType);
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}
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public static String isValidDoi(final String url) {
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final String regex = "(10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?![\"&'])\\S)+)";
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final Pattern pattern = Pattern.compile(regex);
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final Matcher matcher = pattern.matcher(url);
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if (matcher.find())
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return matcher.group(0);
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return null;
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}
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public static String normalizeRelation(final String relation) {
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if (relation == null || StringUtils.isEmpty(relation)) {
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return null;
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}
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return Character.toLowerCase(relation.charAt(0)) + relation.substring(1);
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}
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public static String getInverse(final String relation) throws Exception {
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if (ontologies == null) {
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ontologies = OntologyLoader.loadOntologiesFromIS();
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}
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final String normalizedRelation = normalizeRelation(relation);
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try {
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return ontologies.getTerms(normalizedRelation).stream().findFirst().get().getInverseCode();
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} catch (Throwable e) {
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System.out.println("Relation not found = " + normalizedRelation);
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return "related";
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}
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}
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public static String generateIdentifier(final String pid, final String pidtype) {
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if (StringUtils.isBlank(pid) || StringUtils.isBlank(pidtype))
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throw new RuntimeException("Error pid or pidtype cannot be null");
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return DnetXsltFunctions.md5(String.format("%s::%s", pid.toLowerCase().trim(), pidtype.toLowerCase().trim()));
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}
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/**
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* This method is used only for test Scope
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*
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* @param mockInstance
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*/
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public static void setInstance(final DLIUtils mockInstance) {
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instance = mockInstance;
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}
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@PostConstruct
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public void registerInstance() throws Exception {
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instance = this;
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final InputStream inputStream = this.getClass().getResourceAsStream("/eu/dnetlib/transformation/data-center.json");
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dataciteDatasource = new Gson().fromJson(IOUtils.toString(inputStream), Map.class);
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}
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public UniqueServiceLocator getServiceLocator() {
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return serviceLocator;
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}
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public void setServiceLocator(final UniqueServiceLocator serviceLocator) {
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this.serviceLocator = serviceLocator;
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}
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public Map<String, String> getDataciteDatasource() {
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return dataciteDatasource;
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}
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}
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