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.ArrayList;
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.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 List<OpenaireDuplicate> dups = new ArrayList<>();

				dups.add(new OpenaireDuplicate(newId, oldId, SimilarityType.is_similar.toString(), ""));
				dups.addAll(openaireDuplicateRepository.findByLocalId(oldId)
					.stream()
					.map(d -> new OpenaireDuplicate(newId, d.getOaOriginalId(), SimilarityType.suggested.toString(), d.getOaCollectedFrom()))
					.collect(Collectors.toList()));

				openaireDuplicateRepository.saveAll(dups);
				dups.forEach(d -> {
					openaireDuplicateRepository.updateCreatedByIfMissing(d.getLocalId(), d.getOaOriginalId(), user);
					openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now);
				});

				organizationRepository.updateStatus(oldId, OrganizationStatus.duplicate.toString());
				organizationRepository.updateModificationDate(oldId, user, now);
			}
		}

		return newId;
	}

	@Transactional
	public void saveDuplicates(final List<OpenaireDuplicate> simrels, final String user) {
		final OffsetDateTime now = OffsetDateTime.now();

		final List<OpenaireDuplicate> list = openaireDuplicateRepository.saveAll(simrels);

		list.forEach(d -> {
			openaireDuplicateRepository.updateCreatedByIfMissing(d.getLocalId(), d.getOaOriginalId(), user);
			openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now);

			if (d.getRelType().equals(SimilarityType.is_different.toString())) {
				updateStatus(d.getOaOriginalId(), OrganizationStatus.suggested, user, now);
			} else {
				updateStatus(d.getOaOriginalId(), OrganizationStatus.duplicate, 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<VocabularyTerm> listValuesOfVocabularyTable(final VocabularyTable table) {
		final String sql = "select val as value, name as name from " + table + " order by name";
		return jdbcTemplate.query(sql, new BeanPropertyRowMapper<>(VocabularyTerm.class));
	}

	@Cacheable("countries_for_user")
	public List<VocabularyTerm> 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 = ? order by c.name";
		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<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 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);
		return Arrays.asList(r1, r2);
	}

	// BROWSE BY COUNTRY
	public List<BrowseEntry> 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<BrowseEntry> 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<BrowseEntry> 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<BrowseEntry> 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<BrowseEntry> listBrowseEntries(final String sql, final Object... params) {
		final Map<String, BrowseEntry> 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<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 = ? and c.reltype = 'suggested'";
		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 void updateFulltextIndex() {
		try {
			log.info("Updating Fulltext Index...");
			jdbcTemplate.queryForList("SELECT refresh_index_search()");
			log.info("...done");
		} catch (final Exception e) {
			log.error("Error updating Fulltext Index", e);
		}
	}

	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 fixConflictSimilars(final List<String> similarIds, final String user) {

		final OffsetDateTime now = OffsetDateTime.now();

		final List<OrganizationView> views =
			similarIds.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
		similarIds.forEach(id -> hideConflictOrgs(masterId, id));

		// I reassign the duplicates to the new org
		final List<OpenaireDuplicate> newDuplicates = similarIds.stream()
			.map(openaireDuplicateRepository::findByLocalId)
			.flatMap(l -> l.stream())
			.map(d -> new OpenaireDuplicate(masterId, d.getOaOriginalId(), d.getRelType(), d.getOaCollectedFrom()))
			.collect(Collectors.toList());

		openaireDuplicateRepository.saveAll(newDuplicates);
		newDuplicates.forEach(d -> {
			openaireDuplicateRepository.updateCreatedByIfMissing(d.getLocalId(), d.getOaOriginalId(), user);
			openaireDuplicateRepository.updateModificationDate(d.getLocalId(), d.getOaOriginalId(), user, now);
		});

		for (final String similarId : similarIds) {
			openaireConflictRepository.updateMultipleStatusAndResetGroup(similarId, SimilarityType.is_different.toString(), user, now);
		}

		for (int i = 0; i < similarIds.size(); i++) {
			for (int j = i + 1; j < similarIds.size(); j++) {
				openaireConflictRepository.updateStatusAndResetGroup(similarIds.get(i), similarIds.get(j), SimilarityType.is_similar.toString(), user, now);
			}
		}

		return masterId;
	}

	@Transactional
	public void fixConflictDifferents(final List<String> differentsIds, final String user) {

		final OffsetDateTime now = OffsetDateTime.now();

		for (int i = 0; i < differentsIds.size(); i++) {
			for (int j = i + 1; j < differentsIds.size(); j++) {
				openaireConflictRepository
					.updateStatusAndResetGroup(differentsIds.get(i), differentsIds.get(j), SimilarityType.is_different.toString(), user, now);
			}
		}
	}

	@Transactional
	public Optional<User> findUser(final String email) {
		final Optional<User> user = userRepository.findById(email);
		if (user.isPresent()) {
			userRepository.updateLastAccess(email, OffsetDateTime.now());
		}
		return user;
	}

	private String findFirstString(final List<OrganizationView> views, final Function<OrganizationView, String> mapper) {
		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);
	}

}