package eu.dnetlib.organizations.utils; import java.time.OffsetDateTime; import java.util.Arrays; import java.util.HashMap; import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Objects; import java.util.Optional; import java.util.Set; import java.util.function.Function; import java.util.stream.Collectors; import javax.transaction.Transactional; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.cache.annotation.Cacheable; import org.springframework.jdbc.core.BeanPropertyRowMapper; import org.springframework.jdbc.core.JdbcTemplate; import org.springframework.stereotype.Component; import org.springframework.web.bind.annotation.RequestBody; import eu.dnetlib.organizations.controller.UserRole; import eu.dnetlib.organizations.model.Acronym; import eu.dnetlib.organizations.model.OpenaireConflict; import eu.dnetlib.organizations.model.OpenaireConflictPK; import eu.dnetlib.organizations.model.OpenaireDuplicate; import eu.dnetlib.organizations.model.Organization; import eu.dnetlib.organizations.model.OtherIdentifier; import eu.dnetlib.organizations.model.OtherName; import eu.dnetlib.organizations.model.Relationship; import eu.dnetlib.organizations.model.Url; import eu.dnetlib.organizations.model.User; import eu.dnetlib.organizations.model.UserCountry; import eu.dnetlib.organizations.model.utils.BrowseEntry; import eu.dnetlib.organizations.model.utils.OrganizationConflict; import eu.dnetlib.organizations.model.utils.TempBrowseEntry; import eu.dnetlib.organizations.model.utils.VocabularyTerm; import eu.dnetlib.organizations.model.view.OrganizationView; import eu.dnetlib.organizations.model.view.UserView; import eu.dnetlib.organizations.repository.AcronymRepository; import eu.dnetlib.organizations.repository.OpenaireConflictRepository; import eu.dnetlib.organizations.repository.OpenaireDuplicateRepository; import eu.dnetlib.organizations.repository.OrganizationRepository; import eu.dnetlib.organizations.repository.OtherIdentifierRepository; import eu.dnetlib.organizations.repository.OtherNameRepository; import eu.dnetlib.organizations.repository.RelationshipRepository; import eu.dnetlib.organizations.repository.UrlRepository; import eu.dnetlib.organizations.repository.UserCountryRepository; import eu.dnetlib.organizations.repository.UserRepository; import eu.dnetlib.organizations.repository.readonly.OrganizationViewRepository; @Component public class DatabaseUtils { @Autowired private AcronymRepository acronymRepository; @Autowired private OrganizationRepository organizationRepository; @Autowired private OtherIdentifierRepository otherIdentifierRepository; @Autowired private OtherNameRepository otherNameRepository; @Autowired private UrlRepository urlRepository; @Autowired private RelationshipRepository relationshipRepository; @Autowired private UserRepository userRepository; @Autowired private UserCountryRepository userCountryRepository; @Autowired private OpenaireConflictRepository openaireConflictRepository; @Autowired private OpenaireDuplicateRepository openaireDuplicateRepository; @Autowired private OrganizationViewRepository organizationViewRepository; @Autowired private JdbcTemplate jdbcTemplate; private static final Log log = LogFactory.getLog(DatabaseUtils.class); public enum VocabularyTable { languages, countries, org_types, id_types, rel_types, simrel_types } @Transactional public String insertOrUpdateOrganization(final OrganizationView orgView, final String user, final boolean isSimpleUser) { final String oldStatus = orgView.getId() != null ? organizationRepository.findById(orgView.getId()) .map(Organization::getStatus) .orElse(null) : null; final boolean alreadyApproved = StringUtils.equals(oldStatus, OrganizationStatus.approved.toString()); final String newStatus; if (!isSimpleUser) { // IS ADMIN newStatus = OrganizationStatus.approved.toString(); } else if (isSimpleUser && oldStatus == null) { newStatus = OrganizationStatus.suggested.toString(); } else if (isSimpleUser && alreadyApproved) { newStatus = OrganizationStatus.approved.toString(); } else { throw new RuntimeException("User not authorized"); } final String oldId = StringUtils.isNotBlank(orgView.getId()) ? new String(orgView.getId()) : null; if (oldId == null || !oldId.startsWith(OpenOrgsConstants.OPENORGS_PREFIX)) { orgView.setId(null); } final Organization org = new Organization(orgView.getId(), orgView.getName(), orgView.getType(), orgView.getLat(), orgView.getLng(), orgView.getCity(), orgView.getCountry(), newStatus); final String newId = organizationRepository.save(org).getId(); final OffsetDateTime now = OffsetDateTime.now(); organizationRepository.updateModificationDate(newId, user, now); if (StringUtils.equals(newId, oldId)) { makeRelations(newId, orgView, true); } else { organizationRepository.updateCreationDate(newId, user, now); makeRelations(newId, orgView, false); if (oldId != null) { final OpenaireDuplicate dup = new OpenaireDuplicate(); dup.setLocalId(newId); dup.setOaOriginalId(oldId); dup.setRelType(SimilarityType.is_similar.toString()); openaireDuplicateRepository.save(dup); openaireDuplicateRepository.updateModificationDate(newId, oldId, user, now); organizationRepository.updateStatus(oldId, OrganizationStatus.duplicate.toString()); organizationRepository.updateModificationDate(oldId, user, now); } } return newId; } @Transactional public void saveDuplicates(final List simrels, final String user) { final OffsetDateTime now = OffsetDateTime.now(); final List list = openaireDuplicateRepository.saveAll(simrels); list.forEach(d -> { openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now); if (d.getRelType().equals(SimilarityType.is_similar.toString())) { updateStatus(d.getOaOriginalId(), OrganizationStatus.duplicate, user, now); } else { updateStatus(d.getOaOriginalId(), OrganizationStatus.suggested, user, now); } }); } private void makeRelations(final String orgId, final OrganizationView orgView, final boolean update) { if (update) { acronymRepository.deleteByOrgId(orgId); otherNameRepository.deleteByOrgId(orgId); otherIdentifierRepository.deleteByOrgId(orgId); urlRepository.deleteByOrgId(orgId); relationshipRepository.deleteById1(orgId); relationshipRepository.deleteById2(orgId); } orgView.getAcronyms().forEach(s -> acronymRepository.save(new Acronym(orgId, s))); orgView.getOtherNames().forEach(n -> otherNameRepository.save(new OtherName(orgId, n.getName(), n.getLang()))); orgView.getOtherIdentifiers().forEach(id -> otherIdentifierRepository.save(new OtherIdentifier(orgId, id.getId(), id.getType()))); orgView.getUrls().forEach(u -> urlRepository.save(new Url(orgId, u))); orgView.getRelations().forEach(r -> makeRelation(orgId, r.getRelatedOrgId(), RelationType.valueOf(r.getType()))); } @Cacheable("vocs") public List listValuesOfVocabularyTable(final VocabularyTable table) { final String sql = "select val as value, name as name from " + table; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(VocabularyTerm.class)); } @Cacheable("countries_for_user") public List listCountriesForUser(final String name) { final String sql = "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 = ?"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(VocabularyTerm.class), name); } @Transactional public void saveUser(@RequestBody final UserView userView) { final User user = userRepository.findById(userView.getEmail()).orElseThrow(() -> new RuntimeException("User not found")); user.setRole(userView.getRole()); user.setValid(userView.isValid()); userRepository.save(user); userCountryRepository.deleteByEmail(userView.getEmail()); if (userView.getCountries() != null) { userCountryRepository .saveAll(Arrays.stream(userView.getCountries()).map(c -> new UserCountry(userView.getEmail(), c)).collect(Collectors.toList())); } } @Transactional public void deleteUser(final String email) { userCountryRepository.deleteByEmail(email); userRepository.deleteById(email); } @Transactional public void newUser(final String email, final List countries) { final User user = new User(); user.setEmail(email); user.setRole(UserRole.PENDING.name()); user.setValid(false); userRepository.save(user); if (countries != null) { userCountryRepository.saveAll(countries.stream().map(c -> new UserCountry(email, c)).collect(Collectors.toList())); } } /* * @Transactional public void verifyConflictGroups(final boolean forceUpdate) { * * if (forceUpdate || openaireConflictRepository.countByGroupNull() > 0) { * * log.info("Recreating conflicts group..."); * * openaireConflictRepository.resetGroupIds(); * * final Map> groups = new HashMap<>(); for (final OpenaireConflict w : openaireConflictRepository.findAll()) { * final List list = findExistingGroupsForRel(w, groups); if (list.isEmpty()) { final String idGroup = generateGroupId(); * groups.put(idGroup, new HashSet<>()); addToGroup(groups, idGroup, w); } else if (list.size() == 1) { addToGroup(groups, list.get(0), * w); } else { final String idGroup = generateGroupId(); groups.put(idGroup, new TreeSet<>()); list.forEach(id -> * groups.get(idGroup).addAll(groups.get(id))); list.forEach(id -> groups.remove(id)); addToGroup(groups, idGroup, w); } } * * for (final Entry> e : groups.entrySet()) { final String gid = e.getKey(); for (final String orgId : e.getValue()) * { for (final OpenaireConflict oc : openaireConflictRepository.findById1AndGroupIsNull(orgId)) { oc.setGroup(gid); * openaireConflictRepository.save(oc); } for (final OpenaireConflict oc : openaireConflictRepository.findById2AndGroupIsNull(orgId)) { * oc.setGroup(gid); openaireConflictRepository.save(oc); } } } * * log.info("...conflict groups recreated"); } } * * private String generateGroupId() { return "group::" + UUID.randomUUID(); } */ private List findExistingGroupsForRel(final OpenaireConflict w, final Map> groups) { return groups.entrySet() .stream() .filter(e -> { return e.getValue().contains(w.getId1()) || e.getValue().contains(w.getId2()); }) .map(e -> e.getKey()) .distinct() .collect(Collectors.toList()); } private void addToGroup(final Map> groups, final String gid, final OpenaireConflict w) { groups.get(gid).add(w.getId1()); groups.get(gid).add(w.getId2()); } @Transactional public List makeRelation(final String id1, final String id2, final RelationType type) { final Relationship r1 = new Relationship(id1, id2, type.toString()); final Relationship r2 = new Relationship(id2, id1, type.getInverse().toString()); relationshipRepository.save(r1); relationshipRepository.save(r2); return Arrays.asList(r1, r2); } // BROWSE BY COUNTRY public List browseCountries() { final String sql = "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"; return listBrowseEntries(sql); } // BROWSE BY COUNTRY FOR USER public List browseCountriesForUser(final String email) { final String sql = "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"; return listBrowseEntries(sql, email); } // BROWSE BY ORG TYPE public List browseTypes() { final String sql = "select type as code, type as name, status as group, count(status) as count from organizations group by type, status"; return listBrowseEntries(sql); } // BROWSE BY ORG TYPE FOR USER public List browseTypesForUser(final String email) { final String sql = "select o.type as code, o.type as name," + "o.status as group, count(o.status) as count " + "from organizations o " + "left outer join user_countries uc on (uc.country = o.country) " + "where uc.email=? " + "group by o.type, o.status"; return listBrowseEntries(sql, email); } private List listBrowseEntries(final String sql, final Object... params) { final Map map = new HashMap<>(); for (final TempBrowseEntry t : jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(TempBrowseEntry.class), params)) { if (StringUtils.isNotBlank(t.getCode())) { if (!map.containsKey(t.getCode())) { final BrowseEntry e = new BrowseEntry(); e.setCode(t.getCode()); e.setName(t.getName()); map.put(t.getCode(), e); } map.get(t.getCode()).getValues().put(t.getGroup(), t.getCount()); } } return map.values().stream().sorted((o1, o2) -> StringUtils.compare(o1.getName(), o2.getName())).collect(Collectors.toList()); } public List listConflictsForId(final String id) { final String sql = "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 = ?"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(OrganizationConflict.class), id); } @Transactional public void importDedupEvents() { try { log.info("Importing conflicts and duplicates..."); jdbcTemplate.update(IOUtils.toString(getClass().getResourceAsStream("/sql/importDedupEvents.sql"))); log.info("...done"); // verifyConflictGroups(true); } catch (final Exception e) { log.error("Error importing conflicts and duplicates", e); } } @Transactional public OrganizationView markAsDeleted(final String id, final String user) { final OffsetDateTime now = OffsetDateTime.now(); updateStatus(id, OrganizationStatus.deleted, user, now); return organizationViewRepository.findById(id).get(); } @Transactional public OrganizationView markAsDiscarded(final String id, final String user) { final OffsetDateTime now = OffsetDateTime.now(); updateStatus(id, OrganizationStatus.discarded, user, now); return organizationViewRepository.findById(id).get(); } private void updateStatus(final String id, final OrganizationStatus status, final String user, final OffsetDateTime now) { organizationRepository.updateStatus(id, status.toString()); organizationRepository.updateModificationDate(id, user, now); } @Transactional public String fixConflict(final List ids, final String user) { final List views = ids.stream().map(organizationViewRepository::findById).filter(Optional::isPresent).map(Optional::get).collect(Collectors.toList()); // I create a new org final OrganizationView newOrg = new OrganizationView(); newOrg.setId(null); newOrg.setStatus(null); newOrg.setName(findFirstString(views, OrganizationView::getName)); newOrg.setType(findFirstString(views, OrganizationView::getType)); newOrg.setLat(findFirstNumber(views, OrganizationView::getLat)); newOrg.setLng(findFirstNumber(views, OrganizationView::getLng)); newOrg.setCity(findFirstString(views, OrganizationView::getCity)); newOrg.setCountry(findFirstString(views, OrganizationView::getCountry)); newOrg.setOtherIdentifiers(findAll(views, OrganizationView::getOtherIdentifiers)); newOrg.setOtherNames(findAll(views, OrganizationView::getOtherNames)); newOrg.setAcronyms(findAll(views, OrganizationView::getAcronyms)); newOrg.setUrls(findAll(views, OrganizationView::getUrls)); newOrg.setRelations(findAll(views, OrganizationView::getRelations)); newOrg.getOtherNames() .addAll(views.stream() .map(OrganizationView::getName) .filter(StringUtils::isNotBlank) .filter(s -> StringUtils.equalsIgnoreCase(s, newOrg.getName())) .map(s -> new eu.dnetlib.organizations.model.view.OtherName(s, "UNKNOWN")) .collect(Collectors.toList())); final String masterId = insertOrUpdateOrganization(newOrg, user, false); // I hide the merged organizations ids.forEach(id -> hideConflictOrgs(masterId, id)); // I reassign the duplicated to the new org final List newDuplicates = ids.stream() .map(openaireDuplicateRepository::findByLocalId) .flatMap(l -> l.stream()) .filter(d -> d.getRelType().equals(SimilarityType.is_similar.toString())) .map(d -> new OpenaireDuplicate(masterId, d.getOaOriginalId(), d.getRelType())) .collect(Collectors.toList()); newDuplicates.forEach(d -> d.setLocalId(masterId)); final OffsetDateTime now = OffsetDateTime.now(); for (int i = 0; i < ids.size(); i++) { for (int j = i + 1; j < ids.size(); j++) { openaireConflictRepository.updateStatus(ids.get(i), ids.get(j), SimilarityType.is_similar.toString(), user, now); } } return masterId; } private String findFirstString(final List views, final Function mapper) { return views.stream().map(mapper).filter(StringUtils::isNotBlank).findFirst().orElse(null); } private Double findFirstNumber(final List views, final Function mapper) { return views.stream().map(mapper).filter(Objects::nonNull).filter(n -> n != 0).findFirst().orElse(0.0); } private Set findAll(final List views, final Function> mapper) { return views.stream().map(mapper).flatMap(s -> s.stream()).collect(Collectors.toCollection(LinkedHashSet::new)); } private List 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); } }