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package eu.dnetlib.goldoa.service;
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import com.fasterxml.jackson.databind.JsonNode;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.goldoa.domain.*;
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import eu.dnetlib.goldoa.service.dao.JournalDAO;
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import eu.dnetlib.goldoa.service.dao.PublicationDAO;
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import eu.dnetlib.goldoa.service.dao.PublisherDAO;
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import org.apache.commons.codec.digest.DigestUtils;
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import org.apache.log4j.Logger;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.annotation.Transactional;
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import java.io.InputStream;
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import java.net.URL;
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import java.util.*;
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/**
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* Created by antleb on 3/13/15.
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*/
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@Transactional
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public class PublicationManagerImpl implements PublicationManager {
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private static Logger logger = Logger.getLogger(PublicationManagerImpl.class);
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@Autowired
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private PublicationDAO publicationDAO;
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@Autowired
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private JournalDAO journalDAO;
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@Autowired
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private PublisherDAO publisherDAO;
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@Autowired
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private PersonManager personManager;
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@Autowired
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private OrganizationManager organizationManager;
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@Override
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public Publication getPublication(String publicationId) {
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Publication publication = publicationDAO.getPublication(publicationId);
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loadPublicationRelations(publication);
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if (publication.getJournal() != null && publication.getJournal().getId() != null)
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publication.setJournal(journalDAO.getJournal(publication.getJournal().getId()));
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else
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publication.setJournal(null);
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if (publication.getPublisher() != null && publication.getPublisher().getId() != null)
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publication.setPublisher(publisherDAO.getPublisher(publication.getPublisher().getId()));
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else
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publication.setPublisher(null);
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return publication;
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}
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private void loadPublicationRelations(Publication publication) {
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publicationDAO.loadAffiliations(publication);
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}
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@Override
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public Publication savePublication(Publication publication) {
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if (publication.getId() == null) {
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publication.setSource("portal");
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publication.setId("portal::" + DigestUtils.md5Hex(publication.getTitle()));
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}
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publicationDAO.savePublication(publication);
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deletePublicationRelations(publication);
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try {
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insertPublicationRelations(publication);
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} catch (PersonManagerException e) {
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e.printStackTrace();
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} catch (OrganizationManagerException e) {
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e.printStackTrace();
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}
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if (publication.getJournal() != null && publication.getJournal().getId() != null)
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publication.setJournal(journalDAO.getJournal(publication.getJournal().getId()));
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else
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publication.setJournal(null);
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if (publication.getPublisher() != null && publication.getPublisher().getId() != null)
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publication.setPublisher(publisherDAO.getPublisher(publication.getPublisher().getId()));
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else
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publication.setPublisher(null);
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return publication;
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}
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private void insertPublicationRelations(Publication publication) throws PersonManagerException, OrganizationManagerException {
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publicationDAO.insertIdentifiers(publication);
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if (publication.getAuthors() != null)
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for (Affiliation aff:publication.getAuthors()) {
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if (aff.getOrganization() != null && aff.getOrganization().getId() == null)
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aff.getOrganization().setId(organizationManager.saveOrganization(aff.getOrganization()));
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if (aff.getPerson() != null) {
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String personId = personManager.generateId(aff.getPerson());
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try {
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boolean affiliationExists = false;
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Person temp = personManager.getById(personId);
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for (Affiliation a:temp.getAffiliations()) {
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if (a.getOrganization() != null && aff.getOrganization() != null && a.getOrganization().getId().equals(aff.getOrganization().getId()))
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affiliationExists = true;
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}
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if (!affiliationExists) {
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temp.getAffiliations().add(aff);
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personManager.savePerson(temp);
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}
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aff.setPerson(temp);
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} catch (PersonManagerException e) {
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if (e.getErrorCause() == PersonManagerException.ErrorCause.NOT_EXISTS)
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personManager.savePerson(aff.getPerson());
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}
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}
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}
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publicationDAO.saveAffiliations(publication);
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}
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private void deletePublicationRelations(Publication publication) {
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publicationDAO.deleteIdentifiers(publication);
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publicationDAO.deleteAffiliations(publication);
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}
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@Override
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public Publication resolveDOI(String doi) throws ManagerException {
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Publication publication = new Publication();
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InputStream is = null;
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try {
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is = new URL("http://api.crossref.org/works/" + doi).openStream();
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ObjectMapper mapper = new ObjectMapper();
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JsonNode root = mapper.readTree(is);
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if (root.get("status").textValue().equals("ok")) {
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publication.setTitle(root.path("message").path("title").path(0).textValue());
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publication.setDoi(doi);
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publication.setSubjects(root.path("message").path("subject").textValue());
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publication.setSource("crossref");
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publication.setId("crossref::" + DigestUtils.md5Hex(doi));
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if ("journal-article".equals(root.path("message").path("type").textValue()))
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publication.setType(Publication.Type.ARTICLE);
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else
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publication.setType(Publication.Type.MONOGRAPH);
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publication.setPublicationDate(this.parsePublicationDate(root.path("message").path("issued")));
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publication.setJournal(this.parseJournal(root.path("message").path("container-title"), root.path("message").path("ISSN")));
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publication.getJournal().setPublisher(this.parsePublisher(root.path("message").path("publisher")));
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publication.setAuthors(new ArrayList<Affiliation>());
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for (JsonNode author : root.path("message").path("author")) {
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publication.getAuthors().add(this.parseAffiliation(author));
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}
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publication.setIdentifiers(new ArrayList<PublicationIdentifier>());
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publication.getIdentifiers().add(new PublicationIdentifier("doi", doi));
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} else {
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throw new ManagerException(ManagerException.ErrorCause.NOT_EXISTS);
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}
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} catch (ManagerException e) {
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throw e;
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} catch (Exception e) {
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logger.error("Error resolving doi", e);
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throw new ManagerException(ManagerException.ErrorCause.UNKNOWN);
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} finally {
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try {
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if (is != null)
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is.close();
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} catch (Exception e) {}
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}
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return publication;
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}
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private Affiliation parseAffiliation(JsonNode author) {
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Person person = new Person();
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person.setName(author.path("given").textValue());
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person.setLastname(author.path("family").textValue());
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person.setAffiliations(new ArrayList<Affiliation>());
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Affiliation affiliation = new Affiliation();
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affiliation.setPerson(person);
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person.getAffiliations().add(affiliation);
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return affiliation;
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}
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private Publisher parsePublisher(JsonNode publisherName) {
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Publisher publisher = new Publisher();
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publisher.setName(publisherName.textValue());
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publisher.setId("crossref::" + DigestUtils.md5Hex(publisher.getName()));
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publisher.setSource("crossref");
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return publisher;
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}
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private Journal parseJournal(JsonNode name, JsonNode issn) {
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Journal journal;
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List<Vocabulary> journals = journalDAO.search(name.path(0).textValue());
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if (journals.size() > 0) {
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journal = journalDAO.getJournal(journals.get(0).getId());
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} else {
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journal = new Journal();
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journal.setTitle(name.path(0).textValue());
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journal.setAlternativeTitle(name.path(1).textValue());
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StringBuilder sb = new StringBuilder();
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Iterator<JsonNode> ssn = issn.elements();
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while (ssn.hasNext()) {
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sb.append(ssn.next().textValue()).append(",");
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}
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if (sb.length() > 0)
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sb.deleteCharAt(sb.length() - 1);
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journal.setIssn(sb.toString());
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journal.setSource("crossref");
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journal.setId("crossref::" + DigestUtils.md5Hex(journal.getTitle()));
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}
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return journal;
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}
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private Date parsePublicationDate(JsonNode node) {
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Calendar c = Calendar.getInstance();
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c.clear();
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c.setTimeZone(TimeZone.getTimeZone("UTC"));
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c.set(Calendar.YEAR, node.path("date-parts").path(0).path(0).intValue());
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c.set(Calendar.MONTH, node.path("date-parts").path(0).path(1).intValue() - 1);
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c.set(Calendar.DAY_OF_MONTH, 1 + node.path("date-parts").path(0).path(2).intValue());
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c.set(Calendar.HOUR_OF_DAY, 0);
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return c.getTime();
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}
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public PublicationDAO getPublicationDAO() {
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return publicationDAO;
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}
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public void setPublicationDAO(PublicationDAO publicationDAO) {
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this.publicationDAO = publicationDAO;
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}
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public JournalDAO getJournalDAO() {
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return journalDAO;
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}
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public void setJournalDAO(JournalDAO journalDAO) {
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this.journalDAO = journalDAO;
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}
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public PublisherDAO getPublisherDAO() {
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return publisherDAO;
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}
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public void setPublisherDAO(PublisherDAO publisherDAO) {
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this.publisherDAO = publisherDAO;
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}
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}
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