458 lines
19 KiB
Java
458 lines
19 KiB
Java
package eu.dnetlib.organizations.utils;
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import java.time.OffsetDateTime;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.LinkedHashSet;
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import java.util.List;
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import java.util.Map;
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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 java.util.function.Function;
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import java.util.stream.Collectors;
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import javax.transaction.Transactional;
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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.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.cache.annotation.Cacheable;
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import org.springframework.jdbc.core.BeanPropertyRowMapper;
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import org.springframework.jdbc.core.JdbcTemplate;
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import org.springframework.stereotype.Component;
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import org.springframework.web.bind.annotation.RequestBody;
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import eu.dnetlib.organizations.controller.UserRole;
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import eu.dnetlib.organizations.model.Acronym;
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import eu.dnetlib.organizations.model.OpenaireConflict;
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import eu.dnetlib.organizations.model.OpenaireConflictPK;
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import eu.dnetlib.organizations.model.OpenaireDuplicate;
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import eu.dnetlib.organizations.model.Organization;
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import eu.dnetlib.organizations.model.OtherIdentifier;
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import eu.dnetlib.organizations.model.OtherName;
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import eu.dnetlib.organizations.model.Relationship;
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import eu.dnetlib.organizations.model.Url;
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import eu.dnetlib.organizations.model.User;
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import eu.dnetlib.organizations.model.UserCountry;
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import eu.dnetlib.organizations.model.utils.BrowseEntry;
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import eu.dnetlib.organizations.model.utils.OrganizationConflict;
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import eu.dnetlib.organizations.model.utils.TempBrowseEntry;
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import eu.dnetlib.organizations.model.utils.VocabularyTerm;
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import eu.dnetlib.organizations.model.view.OrganizationView;
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import eu.dnetlib.organizations.model.view.UserView;
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import eu.dnetlib.organizations.repository.AcronymRepository;
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import eu.dnetlib.organizations.repository.OpenaireConflictRepository;
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import eu.dnetlib.organizations.repository.OpenaireDuplicateRepository;
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import eu.dnetlib.organizations.repository.OrganizationRepository;
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import eu.dnetlib.organizations.repository.OtherIdentifierRepository;
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import eu.dnetlib.organizations.repository.OtherNameRepository;
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import eu.dnetlib.organizations.repository.RelationshipRepository;
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import eu.dnetlib.organizations.repository.UrlRepository;
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import eu.dnetlib.organizations.repository.UserCountryRepository;
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import eu.dnetlib.organizations.repository.UserRepository;
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import eu.dnetlib.organizations.repository.readonly.OrganizationViewRepository;
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@Component
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public class DatabaseUtils {
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@Autowired
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private AcronymRepository acronymRepository;
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@Autowired
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private OrganizationRepository organizationRepository;
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@Autowired
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private OtherIdentifierRepository otherIdentifierRepository;
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@Autowired
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private OtherNameRepository otherNameRepository;
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@Autowired
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private UrlRepository urlRepository;
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@Autowired
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private RelationshipRepository relationshipRepository;
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@Autowired
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private UserRepository userRepository;
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@Autowired
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private UserCountryRepository userCountryRepository;
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@Autowired
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private OpenaireConflictRepository openaireConflictRepository;
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@Autowired
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private OpenaireDuplicateRepository openaireDuplicateRepository;
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@Autowired
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private OrganizationViewRepository organizationViewRepository;
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@Autowired
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private JdbcTemplate jdbcTemplate;
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private static final Log log = LogFactory.getLog(DatabaseUtils.class);
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public enum VocabularyTable {
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languages,
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countries,
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org_types,
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id_types,
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rel_types,
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simrel_types
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}
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@Transactional
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public String insertOrUpdateOrganization(final OrganizationView orgView, final String user, final boolean isSimpleUser) {
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final String oldStatus = orgView.getId() != null ? organizationRepository.findById(orgView.getId())
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.map(Organization::getStatus)
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.orElse(null) : null;
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final boolean alreadyApproved = StringUtils.equals(oldStatus, OrganizationStatus.approved.toString());
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final String newStatus;
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if (!isSimpleUser) { // IS ADMIN
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newStatus = OrganizationStatus.approved.toString();
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} else if (isSimpleUser && oldStatus == null) {
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newStatus = OrganizationStatus.suggested.toString();
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} else if (isSimpleUser && alreadyApproved) {
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newStatus = OrganizationStatus.approved.toString();
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} else {
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throw new RuntimeException("User not authorized");
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}
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final String oldId = StringUtils.isNotBlank(orgView.getId()) ? new String(orgView.getId()) : null;
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if (oldId == null || !oldId.startsWith(OpenOrgsConstants.OPENORGS_PREFIX)) {
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orgView.setId(null);
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}
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final Organization org = new Organization(orgView.getId(),
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orgView.getName(),
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orgView.getType(),
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orgView.getLat(), orgView.getLng(),
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orgView.getCity(), orgView.getCountry(),
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newStatus);
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final String newId = organizationRepository.save(org).getId();
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final OffsetDateTime now = OffsetDateTime.now();
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organizationRepository.updateModificationDate(newId, user, now);
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if (StringUtils.equals(newId, oldId)) {
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makeRelations(newId, orgView, true);
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} else {
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organizationRepository.updateCreationDate(newId, user, now);
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makeRelations(newId, orgView, false);
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if (oldId != null) {
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final List<OpenaireDuplicate> dups = new ArrayList<>();
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dups.add(new OpenaireDuplicate(newId, oldId, SimilarityType.is_similar.toString()));
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dups.addAll(openaireDuplicateRepository.findByLocalId(oldId)
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.stream()
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.map(d -> new OpenaireDuplicate(newId, d.getOaOriginalId(), SimilarityType.suggested.toString()))
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.collect(Collectors.toList()));
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openaireDuplicateRepository.saveAll(dups);
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dups.forEach(d -> openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now));
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organizationRepository.updateStatus(oldId, OrganizationStatus.duplicate.toString());
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organizationRepository.updateModificationDate(oldId, user, now);
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}
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}
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return newId;
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}
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@Transactional
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public void saveDuplicates(final List<OpenaireDuplicate> simrels, final String user) {
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final OffsetDateTime now = OffsetDateTime.now();
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final List<OpenaireDuplicate> list = openaireDuplicateRepository.saveAll(simrels);
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list.forEach(d -> {
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openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now);
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if (d.getRelType().equals(SimilarityType.is_different.toString())) {
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updateStatus(d.getOaOriginalId(), OrganizationStatus.suggested, user, now);
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} else {
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updateStatus(d.getOaOriginalId(), OrganizationStatus.duplicate, user, now);
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}
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});
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}
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private void makeRelations(final String orgId, final OrganizationView orgView, final boolean update) {
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if (update) {
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acronymRepository.deleteByOrgId(orgId);
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otherNameRepository.deleteByOrgId(orgId);
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otherIdentifierRepository.deleteByOrgId(orgId);
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urlRepository.deleteByOrgId(orgId);
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relationshipRepository.deleteById1(orgId);
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relationshipRepository.deleteById2(orgId);
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}
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orgView.getAcronyms().forEach(s -> acronymRepository.save(new Acronym(orgId, s)));
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orgView.getOtherNames().forEach(n -> otherNameRepository.save(new OtherName(orgId, n.getName(), n.getLang())));
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orgView.getOtherIdentifiers().forEach(id -> otherIdentifierRepository.save(new OtherIdentifier(orgId, id.getId(), id.getType())));
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orgView.getUrls().forEach(u -> urlRepository.save(new Url(orgId, u)));
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orgView.getRelations().forEach(r -> makeRelation(orgId, r.getRelatedOrgId(), RelationType.valueOf(r.getType())));
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}
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@Cacheable("vocs")
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public List<VocabularyTerm> listValuesOfVocabularyTable(final VocabularyTable table) {
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final String sql = "select val as value, name as name from " + table;
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return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(VocabularyTerm.class));
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}
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@Cacheable("countries_for_user")
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public List<VocabularyTerm> listCountriesForUser(final String name) {
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final String sql =
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"select uc.country as value, c.name as name from user_countries uc left outer join countries c on (c.val = uc.country) where uc.email = ?";
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return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(VocabularyTerm.class), name);
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}
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@Transactional
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public void saveUser(@RequestBody final UserView userView) {
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final User user = userRepository.findById(userView.getEmail()).orElseThrow(() -> new RuntimeException("User not found"));
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user.setRole(userView.getRole());
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user.setValid(userView.isValid());
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userRepository.save(user);
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userCountryRepository.deleteByEmail(userView.getEmail());
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if (userView.getCountries() != null) {
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userCountryRepository
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.saveAll(Arrays.stream(userView.getCountries()).map(c -> new UserCountry(userView.getEmail(), c)).collect(Collectors.toList()));
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}
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}
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@Transactional
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public void deleteUser(final String email) {
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userCountryRepository.deleteByEmail(email);
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userRepository.deleteById(email);
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}
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@Transactional
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public void newUser(final String email, final List<String> countries) {
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final User user = new User();
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user.setEmail(email);
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user.setRole(UserRole.PENDING.name());
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user.setValid(false);
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userRepository.save(user);
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if (countries != null) {
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userCountryRepository.saveAll(countries.stream().map(c -> new UserCountry(email, c)).collect(Collectors.toList()));
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}
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}
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/*
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* @Transactional public void verifyConflictGroups(final boolean forceUpdate) {
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*
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* if (forceUpdate || openaireConflictRepository.countByGroupNull() > 0) {
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*
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* log.info("Recreating conflicts group...");
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*
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* openaireConflictRepository.resetGroupIds();
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*
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* final Map<String, Set<String>> groups = new HashMap<>(); for (final OpenaireConflict w : openaireConflictRepository.findAll()) {
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* final List<String> list = findExistingGroupsForRel(w, groups); if (list.isEmpty()) { final String idGroup = generateGroupId();
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* groups.put(idGroup, new HashSet<>()); addToGroup(groups, idGroup, w); } else if (list.size() == 1) { addToGroup(groups, list.get(0),
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* w); } else { final String idGroup = generateGroupId(); groups.put(idGroup, new TreeSet<>()); list.forEach(id ->
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* groups.get(idGroup).addAll(groups.get(id))); list.forEach(id -> groups.remove(id)); addToGroup(groups, idGroup, w); } }
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*
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* for (final Entry<String, Set<String>> e : groups.entrySet()) { final String gid = e.getKey(); for (final String orgId : e.getValue())
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* { for (final OpenaireConflict oc : openaireConflictRepository.findById1AndGroupIsNull(orgId)) { oc.setGroup(gid);
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* openaireConflictRepository.save(oc); } for (final OpenaireConflict oc : openaireConflictRepository.findById2AndGroupIsNull(orgId)) {
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* oc.setGroup(gid); openaireConflictRepository.save(oc); } } }
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*
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* log.info("...conflict groups recreated"); } }
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*
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* private String generateGroupId() { return "group::" + UUID.randomUUID(); }
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*/
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private List<String> findExistingGroupsForRel(final OpenaireConflict w, final Map<String, Set<String>> groups) {
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return groups.entrySet()
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.stream()
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.filter(e -> {
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return e.getValue().contains(w.getId1()) || e.getValue().contains(w.getId2());
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})
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.map(e -> e.getKey())
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.distinct()
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.collect(Collectors.toList());
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}
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private void addToGroup(final Map<String, Set<String>> groups, final String gid, final OpenaireConflict w) {
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groups.get(gid).add(w.getId1());
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groups.get(gid).add(w.getId2());
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}
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@Transactional
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public List<Relationship> makeRelation(final String id1, final String id2, final RelationType type) {
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final Relationship r1 = new Relationship(id1, id2, type.toString());
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final Relationship r2 = new Relationship(id2, id1, type.getInverse().toString());
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relationshipRepository.save(r1);
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relationshipRepository.save(r2);
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return Arrays.asList(r1, r2);
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}
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// BROWSE BY COUNTRY
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public List<BrowseEntry> browseCountries() {
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final String sql =
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"select o.country as code, c.name as name, o.status as group, count(o.status) as count from organizations o left outer join countries c on (o.country = c.val) group by o.country, c.name, o.status";
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return listBrowseEntries(sql);
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}
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// BROWSE BY COUNTRY FOR USER
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public List<BrowseEntry> browseCountriesForUser(final String email) {
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final String sql =
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"select o.country as code, c.name as name, o.status as group, count(o.status) as count from user_countries uc left outer join organizations o on (uc.country = o.country) left outer join countries c on (o.country = c.val) where uc.email=? group by o.country, c.name, o.status";
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return listBrowseEntries(sql, email);
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}
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// BROWSE BY ORG TYPE
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public List<BrowseEntry> browseTypes() {
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final String sql =
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"select type as code, type as name, status as group, count(status) as count from organizations group by type, status";
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return listBrowseEntries(sql);
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}
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// BROWSE BY ORG TYPE FOR USER
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public List<BrowseEntry> browseTypesForUser(final String email) {
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final String sql = "select o.type as code, o.type as name,"
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+ "o.status as group, count(o.status) as count "
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+ "from organizations o "
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+ "left outer join user_countries uc on (uc.country = o.country) "
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+ "where uc.email=? "
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+ "group by o.type, o.status";
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return listBrowseEntries(sql, email);
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}
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private List<BrowseEntry> listBrowseEntries(final String sql, final Object... params) {
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final Map<String, BrowseEntry> map = new HashMap<>();
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for (final TempBrowseEntry t : jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(TempBrowseEntry.class), params)) {
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if (StringUtils.isNotBlank(t.getCode())) {
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if (!map.containsKey(t.getCode())) {
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final BrowseEntry e = new BrowseEntry();
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e.setCode(t.getCode());
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e.setName(t.getName());
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map.put(t.getCode(), e);
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}
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map.get(t.getCode()).getValues().put(t.getGroup(), t.getCount());
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}
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}
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return map.values().stream().sorted((o1, o2) -> StringUtils.compare(o1.getName(), o2.getName())).collect(Collectors.toList());
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}
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public List<OrganizationConflict> listConflictsForId(final String id) {
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final String sql =
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"select o.id, o.name, o.type, o.city, o.country from oa_conflicts c left outer join organizations o on (c.id2 = o.id) where o.id is not null and c.id1 = ?";
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return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(OrganizationConflict.class), id);
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}
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@Transactional
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public void importDedupEvents() {
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try {
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log.info("Importing conflicts and duplicates...");
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jdbcTemplate.update(IOUtils.toString(getClass().getResourceAsStream("/sql/importDedupEvents.sql")));
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log.info("...done");
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// verifyConflictGroups(true);
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} catch (final Exception e) {
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log.error("Error importing conflicts and duplicates", e);
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}
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}
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@Transactional
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public OrganizationView markAsDeleted(final String id, final String user) {
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final OffsetDateTime now = OffsetDateTime.now();
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updateStatus(id, OrganizationStatus.deleted, user, now);
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return organizationViewRepository.findById(id).get();
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}
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@Transactional
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public OrganizationView markAsDiscarded(final String id, final String user) {
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final OffsetDateTime now = OffsetDateTime.now();
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updateStatus(id, OrganizationStatus.discarded, user, now);
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openaireDuplicateRepository.findByLocalId(id).forEach(d -> updateStatus(d.getOaOriginalId(), OrganizationStatus.suggested, user, now));
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return organizationViewRepository.findById(id).get();
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}
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private void updateStatus(final String id, final OrganizationStatus status, final String user, final OffsetDateTime now) {
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organizationRepository.updateStatus(id, status.toString());
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organizationRepository.updateModificationDate(id, user, now);
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}
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@Transactional
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public String fixConflict(final List<String> ids, final String user) {
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final List<OrganizationView> views =
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ids.stream().map(organizationViewRepository::findById).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toList());
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// I create a new org
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final OrganizationView newOrg = new OrganizationView();
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newOrg.setId(null);
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newOrg.setStatus(null);
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newOrg.setName(findFirstString(views, OrganizationView::getName));
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newOrg.setType(findFirstString(views, OrganizationView::getType));
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newOrg.setLat(findFirstNumber(views, OrganizationView::getLat));
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newOrg.setLng(findFirstNumber(views, OrganizationView::getLng));
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newOrg.setCity(findFirstString(views, OrganizationView::getCity));
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newOrg.setCountry(findFirstString(views, OrganizationView::getCountry));
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newOrg.setOtherIdentifiers(findAll(views, OrganizationView::getOtherIdentifiers));
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newOrg.setOtherNames(findAll(views, OrganizationView::getOtherNames));
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newOrg.setAcronyms(findAll(views, OrganizationView::getAcronyms));
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newOrg.setUrls(findAll(views, OrganizationView::getUrls));
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newOrg.setRelations(findAll(views, OrganizationView::getRelations));
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newOrg.getOtherNames()
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.addAll(views.stream()
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.map(OrganizationView::getName)
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.filter(StringUtils::isNotBlank)
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.filter(s -> StringUtils.equalsIgnoreCase(s, newOrg.getName()))
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.map(s -> new eu.dnetlib.organizations.model.view.OtherName(s, "UNKNOWN"))
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.collect(Collectors.toList()));
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final String masterId = insertOrUpdateOrganization(newOrg, user, false);
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// I hide the merged organizations
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ids.forEach(id -> hideConflictOrgs(masterId, id));
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// I reassign the duplicated to the new org
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final List<OpenaireDuplicate> newDuplicates = ids.stream()
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.map(openaireDuplicateRepository::findByLocalId)
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.flatMap(l -> l.stream())
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.filter(d -> d.getRelType().equals(SimilarityType.is_similar.toString()))
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.map(d -> new OpenaireDuplicate(masterId, d.getOaOriginalId(), d.getRelType()))
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.collect(Collectors.toList());
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newDuplicates.forEach(d -> d.setLocalId(masterId));
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final OffsetDateTime now = OffsetDateTime.now();
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for (int i = 0; i < ids.size(); i++) {
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for (int j = i + 1; j < ids.size(); j++) {
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openaireConflictRepository.updateStatus(ids.get(i), ids.get(j), SimilarityType.is_similar.toString(), user, now);
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}
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}
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return masterId;
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}
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private String findFirstString(final List<OrganizationView> views, final Function<OrganizationView, String> mapper) {
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return views.stream().map(mapper).filter(StringUtils::isNotBlank).findFirst().orElse(null);
|
|
}
|
|
|
|
private Double findFirstNumber(final List<OrganizationView> views, final Function<OrganizationView, Double> mapper) {
|
|
return views.stream().map(mapper).filter(Objects::nonNull).filter(n -> n != 0).findFirst().orElse(0.0);
|
|
}
|
|
|
|
private <T> Set<T> findAll(final List<OrganizationView> views, final Function<OrganizationView, Set<T>> mapper) {
|
|
return views.stream().map(mapper).flatMap(s -> s.stream()).collect(Collectors.toCollection(LinkedHashSet::new));
|
|
}
|
|
|
|
private List<Relationship> hideConflictOrgs(final String masterId, final String otherId) {
|
|
organizationRepository.updateStatus(otherId, OrganizationStatus.hidden.toString());
|
|
openaireConflictRepository.findById(new OpenaireConflictPK(masterId, otherId)).ifPresent(openaireConflictRepository::delete);
|
|
openaireConflictRepository.findById(new OpenaireConflictPK(otherId, masterId)).ifPresent(openaireConflictRepository::delete);
|
|
return makeRelation(masterId, otherId, RelationType.Merges);
|
|
}
|
|
|
|
}
|