dnet-applications/apps/dnet-orgs-database-application/src/main/java/eu/dnetlib/organizations/utils/DatabaseUtils.java

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.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 update) {

		if (update) {
			cleanOldRelations(orgView.getId());
		}

		final Organization org = new Organization(update ? orgView.getId() : null,
			orgView.getName(),
			orgView.getType(),
			orgView.getLat(), orgView.getLng(),
			orgView.getCity(), orgView.getCountry());

		final String orgId = organizationRepository.save(org).getId();

		makeNewRelations(orgView, orgId);

		updateHistoryFields(orgId, user, update);

		return orgId;
	}

	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<OpenaireDuplicate> saveDuplicates(final List<OpenaireDuplicate> simrels, final String email) {
		final OffsetDateTime now = OffsetDateTime.now();

		final List<OpenaireDuplicate> list = openaireDuplicateRepository.saveAll(simrels);
		list.forEach(d -> openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), email, now));
		return list;
	}

	private void makeNewRelations(final OrganizationView orgView, final String 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())));
	}

	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<String> listValuesOfVocabularyTable(final VocabularyTable table) {
		return jdbcTemplate.queryForList("select val from " + table, String.class);
	}

	@Cacheable("countries_for_user")
	public List<String> 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<String> 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<String, Set<String>> groups = new HashMap<>();
			for (final OpenaireConflict w : openaireConflictRepository.findAll()) {
				final List<String> 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<String, Set<String>> 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<String> findExistingGroupsForRel(final OpenaireConflict w, final Map<String, Set<String>> 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<String, Set<String>> groups, final String gid, final OpenaireConflict w) {
		groups.get(gid).add(w.getId1());
		groups.get(gid).add(w.getId2());
	}

	@Transactional
	public List<Relationship> 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);

		if (type == RelationType.Merged_In || type == RelationType.Merges) {
			openaireConflictRepository.findById(new OpenaireConflictPK(id1, id2)).ifPresent(openaireConflictRepository::delete);
			openaireConflictRepository.findById(new OpenaireConflictPK(id2, id1)).ifPresent(openaireConflictRepository::delete);
		}

		return Arrays.asList(r1, r2);
	}

	// BROWSE BY COUNTRY
	public List<BrowseEntry> browseCountries() {
		final String sql = "select country as value, count(*) as count from organizations group by country order by count desc";
		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class));
	}

	// BROWSE BY COUNTRY FOR USER
	public List<BrowseEntry> browseCountriesForUser(final String email) {
		final String sql =
			"select o.country as value, count(o.country) as count from user_countries uc left outer join organizations o on (uc.country = o.country) where uc.email=? group by o.country order by count desc";
		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email);
	}

	// BROWSE BY ORG TYPE
	public List<BrowseEntry> browseTypes() {
		final String sql = "select type as value, count(*) as count from organizations group by type order by count desc";
		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class));
	}

	// BROWSE BY ORG TYPE FOR USER
	public List<BrowseEntry> browseTypesForUser(final String email) {
		final String sql = "select o.type as value, count(o.type) as count "
			+ "from organizations o "
			+ "left outer join user_countries uc on (uc.country = o.country) "
			+ "where uc.email=? "
			+ "group by o.type "
			+ "order by count desc;";
		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(BrowseEntry.class), email);

	}

	public List<OrganizationConflict> 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);
		}
	}

}