package eu.dnetlib.organizations.utils; import java.time.OffsetDateTime; import java.util.Arrays; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Map.Entry; import java.util.Set; import java.util.TreeSet; import java.util.UUID; 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.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; @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 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 alreadyApproved = StringUtils.equals(orgView.getStatus(), OrganizationStatus.approved.toString()); final String oldId = orgView.getId(); if (StringUtils.isBlank(orgView.getId())) { orgView.setId(null); } else if (!alreadyApproved) { cleanOldRelations(oldId); organizationRepository.deleteById(oldId); orgView.setId(null); } else { cleanOldRelations(orgView.getId()); } final Organization org = new Organization(orgView.getId(), orgView.getName(), orgView.getType(), orgView.getLat(), orgView.getLng(), orgView.getCity(), orgView.getCountry(), OrganizationStatus.approved.toString()); final String newId = organizationRepository.save(org).getId(); makeNewRelations(newId, orgView); updateHistoryFields(newId, user, alreadyApproved); return newId; } private void updateHistoryFields(final String id, final String user, final boolean update) { final OffsetDateTime now = OffsetDateTime.now(); if (update) { organizationRepository.updateModificationDate(id, user, now); } else { organizationRepository.updateCreationDate(id, user, now); organizationRepository.updateModificationDate(id, user, now); } } @Transactional public List saveDuplicates(final List simrels, final String email) { final OffsetDateTime now = OffsetDateTime.now(); final List list = openaireDuplicateRepository.saveAll(simrels); list.forEach(d -> openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), email, now)); return list; } private void makeNewRelations(final String orgId, final OrganizationView orgView) { 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()))); } private void cleanOldRelations(final String id) { acronymRepository.deleteByOrgId(id); otherNameRepository.deleteByOrgId(id); otherIdentifierRepository.deleteByOrgId(id); urlRepository.deleteByOrgId(id); relationshipRepository.deleteById1(id); relationshipRepository.deleteById2(id); } @Cacheable("vocs") public List listValuesOfVocabularyTable(final VocabularyTable table) { return jdbcTemplate.queryForList("select val from " + table, String.class); } @Cacheable("countries_for_user") public List listCountriesForUser(final String name) { return jdbcTemplate.queryForList("select country from user_countries where email = ?", String.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("...conflicts group 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 country as value, sum(case when status='approved' then 1 else 0 end) as approved, sum(case when status='pending' then 1 else 0 end) as pending from organizations group by country order by approved desc"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class)); } // BROWSE BY COUNTRY FOR USER public List browseCountriesForUser(final String email) { final String sql = "select o.country as value, sum(case when status='approved' then 1 else 0 end) as approved, sum(case when status='pending' then 1 else 0 end) as pending from user_countries uc left outer join organizations o on (uc.country = o.country) where uc.email=? group by o.country order by approved desc"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email); } // BROWSE BY ORG TYPE public List browseTypes() { final String sql = "select type as value, sum(case when status='approved' then 1 else 0 end) as approved, sum(case when status='pending' then 1 else 0 end) as pending from organizations group by type order by approved desc"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class)); } // BROWSE BY ORG TYPE FOR USER public List browseTypesForUser(final String email) { final String sql = "select o.type as value, " + "sum(case when status='approved' then 1 else 0 end) as approved, " + "sum(case when status='pending' then 1 else 0 end) as pending " + "from organizations o " + "left outer join user_countries uc on (uc.country = o.country) " + "where uc.email=? " + "group by o.type " + "order by approved desc;"; return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email); } 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 importSimRels() { try { log.info("Importing conflicts and duplicates..."); jdbcTemplate.update(IOUtils.toString(getClass().getResourceAsStream("/sql/importNewRels.sql"))); log.info("...done"); verifyConflictGroups(true); } catch (final Exception e) { log.error("Error importing conflicts and duplicates", e); } } @Transactional public List fixDuplicate(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); // TODO Merge the organizations ??? return makeRelation(masterId, otherId, RelationType.Merges); } }