14752386992

Committed 30 Apr 2025 10:25AM UTC coverage: 64.96% (-0.1%) from 65.095%

Build # 14752386992

Build Type

push

github

Committed by

web-flow

Commit Message

TRUNK-6316 Upgrade Hibernate Search to 6.2.4 (#5005)

Run Details

501 of 591 new or added lines in 24 files covered. (84.77%)

21 existing lines in 6 files now uncovered.

23344 of 35936 relevant lines covered (64.96%)

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64.29

/api/src/main/java/org/openmrs/api/db/hibernate/HibernateContextDAO.java

/**
 * This Source Code Form is subject to the terms of the Mozilla Public License,
 * v. 2.0. If a copy of the MPL was not distributed with this file, You can
 * obtain one at http://mozilla.org/MPL/2.0/. OpenMRS is also distributed under
 * the terms of the Healthcare Disclaimer located at http://openmrs.org/license.
 *
 * Copyright (C) OpenMRS Inc. OpenMRS is a registered trademark and the OpenMRS
 * graphic logo is a trademark of OpenMRS Inc.
 */
package org.openmrs.api.db.hibernate;

import java.io.File;
import java.net.URL;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.concurrent.Future;
import java.util.concurrent.TimeUnit;

import org.apache.commons.lang3.StringUtils;
import org.hibernate.CacheMode;
import org.hibernate.FlushMode;
import org.hibernate.HibernateException;
import org.hibernate.ScrollableResults;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
import org.hibernate.search.mapper.orm.Search;
import org.hibernate.search.mapper.orm.session.SearchSession;
import org.hibernate.search.mapper.orm.work.SearchIndexingPlan;
import org.hibernate.stat.QueryStatistics;
import org.hibernate.stat.Statistics;
import org.hibernate.type.StandardBasicTypes;
import org.openmrs.GlobalProperty;
import org.openmrs.OpenmrsObject;
import org.openmrs.User;
import org.openmrs.api.context.Context;
import org.openmrs.api.context.ContextAuthenticationException;
import org.openmrs.api.context.Daemon;
import org.openmrs.api.db.ContextDAO;
import org.openmrs.api.db.UserDAO;
import org.openmrs.api.db.hibernate.search.session.SearchSessionFactory;
import org.openmrs.util.OpenmrsConstants;
import org.openmrs.util.OpenmrsUtil;
import org.openmrs.util.Security;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.orm.hibernate5.SessionFactoryUtils;
import org.springframework.orm.hibernate5.SessionHolder;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionSynchronizationManager;

/**
 * Hibernate specific implementation of the {@link ContextDAO}. These methods should not be used
 * directly, instead, the methods on the static {@link Context} file should be used.
 * 
 * @see ContextDAO
 * @see Context
 */
public class HibernateContextDAO implements ContextDAO {
        
        private static final Logger log = LoggerFactory.getLogger(HibernateContextDAO.class);
        
        private static final Long DEFAULT_UNLOCK_ACCOUNT_WAITING_TIME = TimeUnit.MILLISECONDS.convert(5L, TimeUnit.MINUTES);
        
        /**
         * Hibernate session factory
         */
        private SessionFactory sessionFactory;
        
        @Autowired
        private SearchSessionFactory searchSessionFactory;
        
        private UserDAO userDao;
        
        /**
         * Session factory to use for this DAO. This is usually injected by spring and its application
         * context.
         * 
         * @param sessionFactory
         */
        public void setSessionFactory(SessionFactory sessionFactory) {
                this.sessionFactory = sessionFactory;
        }
        
        public void setUserDAO(UserDAO userDao) {
                this.userDao = userDao;
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#authenticate(java.lang.String, java.lang.String)
         */
        @Override
        @Transactional(noRollbackFor = ContextAuthenticationException.class)
        public User authenticate(String login, String password) throws ContextAuthenticationException {
                String errorMsg = "Invalid username and/or password: " + login;

                Session session = sessionFactory.getCurrentSession();

                User candidateUser = null;

                if (StringUtils.isNotBlank(login)) {
                        // loginWithoutDash is used to compare to the system id
                        String loginWithDash = login;
                        if (login.matches("\\d{2,}")) {
                                loginWithDash = login.substring(0, login.length() - 1) + "-" + login.charAt(login.length() - 1);
                        }

                        try {
                                candidateUser = session.createQuery(
                                        "from User u where (u.username = ?1 or u.systemId = ?2 or u.systemId = ?3) and u.retired = false",
                                        User.class)
                                        .setParameter(1, login).setParameter(2, login).setParameter(3, loginWithDash).uniqueResult();
                        }
                        catch (HibernateException he) {
                                log.error("Got hibernate exception while logging in: '{}'", login, he);
                        }
                        catch (Exception e) {
                                log.error("Got regular exception while logging in: '{}'", login, e);
                        }
                }

                // only continue if this is a valid username and a nonempty password
                if (candidateUser != null && password != null) {
                        log.debug("Candidate user id: {}", candidateUser.getUserId());

                        String lockoutTimeString = candidateUser.getUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP, null);
                        long lockoutTime = -1;
                        if (StringUtils.isNotBlank(lockoutTimeString) && !"0".equals(lockoutTimeString)) {
                                try {
                                        // putting this in a try/catch in case the admin decided to put junk into the property
                                        lockoutTime = Long.parseLong(lockoutTimeString);
                                }
                                catch (NumberFormatException e) {
                                        log.warn("bad value stored in {} user property: {}", OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP,
                                                lockoutTimeString);
                                }
                        }

                        // if they've been locked out, don't continue with the authentication
                        if (lockoutTime > 0) {
                                // unlock them after x mins, otherwise reset the timestamp
                                // to now and make them wait another x mins
                                final Long unlockTime = getUnlockTimeMs();
                                if (System.currentTimeMillis() - lockoutTime > unlockTime) {
                                        candidateUser.setUserProperty(OpenmrsConstants.USER_PROPERTY_LOGIN_ATTEMPTS, OpenmrsConstants.ZERO_LOGIN_ATTEMPTS_VALUE);
                                        candidateUser.removeUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP);
                                        saveUserProperties(candidateUser);
                                } else {
                                        candidateUser.setUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP, String.valueOf(System
                                                .currentTimeMillis()));
                                        throw new ContextAuthenticationException(
                                                "Invalid number of connection attempts. Please try again later.");
                                }
                        }

                        Object[] passwordAndSalt = (Object[]) session
                                .createNativeQuery("select password, salt from users where user_id = ?1")
                                .addScalar("password", StandardBasicTypes.STRING).addScalar("salt", StandardBasicTypes.STRING)
                                .setParameter(1, candidateUser.getUserId()).uniqueResult();

                        String passwordOnRecord = (String) passwordAndSalt[0];
                        String saltOnRecord = (String) passwordAndSalt[1];

                        // if the username and password match, hydrate the user and return it
                        if (passwordOnRecord != null && Security.hashMatches(passwordOnRecord, password + saltOnRecord)) {
                                // hydrate the user object
                                candidateUser.getAllRoles().size();
                                candidateUser.getUserProperties().size();
                                candidateUser.getPrivileges().size();

                                // only clean up if the were some login failures, otherwise all should be clean
                                int attempts = getUsersLoginAttempts(candidateUser);
                                if (attempts > 0) {
                                        candidateUser.setUserProperty(OpenmrsConstants.USER_PROPERTY_LOGIN_ATTEMPTS, OpenmrsConstants.ZERO_LOGIN_ATTEMPTS_VALUE);
                                        candidateUser.removeUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP);
                                }
                                setLastLoginTime(candidateUser);
                                saveUserProperties(candidateUser);

                                // skip out of the method early (instead of throwing the exception)
                                // to indicate that this is the valid user
                                return candidateUser;
                        } else {
                                // the user failed the username/password, increment their
                                // attempts here and set the "lockout" timestamp if necessary
                                int attempts = getUsersLoginAttempts(candidateUser);

                                attempts++;

                                int allowedFailedLoginCount = 7;
                                try {
                                        allowedFailedLoginCount = Integer.parseInt(Context.getAdministrationService().getGlobalProperty(
                                                OpenmrsConstants.GP_ALLOWED_FAILED_LOGINS_BEFORE_LOCKOUT).trim());
                                }
                                catch (Exception ex) {
                                        log.error("Unable to convert the global property {} to a valid integer. Using default value of 7.",
                                                OpenmrsConstants.GP_ALLOWED_FAILED_LOGINS_BEFORE_LOCKOUT);
                                }

                                if (attempts > allowedFailedLoginCount) {
                                        // set the user as locked out at this exact time
                                        candidateUser.setUserProperty(OpenmrsConstants.USER_PROPERTY_LOCKOUT_TIMESTAMP, String.valueOf(System
                                                .currentTimeMillis()));
                                } else {
                                        candidateUser.setUserProperty(OpenmrsConstants.USER_PROPERTY_LOGIN_ATTEMPTS, String.valueOf(attempts));
                                }

                                saveUserProperties(candidateUser);
                        }
                }

                // throw this exception only once in the same place with the same
                // message regardless of username/pw combo entered
                log.info("Failed login attempt (login={}) - {}", login, errorMsg);
                throw new ContextAuthenticationException(errorMsg);
        }
        
        private void setLastLoginTime(User candidateUser) {
                candidateUser.setUserProperty(
                        OpenmrsConstants.USER_PROPERTY_LAST_LOGIN_TIMESTAMP,
                        String.valueOf(System.currentTimeMillis())
                );
        }
        
        private Long getUnlockTimeMs() {
                String unlockTimeGPValue = Context.getAdministrationService().getGlobalProperty(
                                OpenmrsConstants.GP_UNLOCK_ACCOUNT_WAITING_TIME);
                if (StringUtils.isNotBlank(unlockTimeGPValue)) {
                        return convertUnlockAccountWaitingTimeGP(unlockTimeGPValue);
                }
                else {
                        return DEFAULT_UNLOCK_ACCOUNT_WAITING_TIME;
                }
        }
        
        private Long convertUnlockAccountWaitingTimeGP(String waitingTime) {
                try {
                        return TimeUnit.MILLISECONDS.convert(Long.valueOf(waitingTime), TimeUnit.MINUTES);
                } catch (Exception ex) {
                        log.error("Unable to convert the global property "
                                        + OpenmrsConstants.GP_UNLOCK_ACCOUNT_WAITING_TIME
                                        + "to a valid Long. Using default value of 5");
                        return DEFAULT_UNLOCK_ACCOUNT_WAITING_TIME;
                }
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#getUserByUuid(java.lang.String)
         */
        @Override
        @Transactional(readOnly = true)
        public User getUserByUuid(String uuid) {
                
                // don't flush here in case we're in the AuditableInterceptor.  Will cause a StackOverflowEx otherwise
                FlushMode flushMode = sessionFactory.getCurrentSession().getHibernateFlushMode();
                sessionFactory.getCurrentSession().setHibernateFlushMode(FlushMode.MANUAL);
                
                User u = HibernateUtil.getUniqueEntityByUUID(sessionFactory, User.class, uuid);
                
                // reset the flush mode to whatever it was before
                sessionFactory.getCurrentSession().setHibernateFlushMode(flushMode);
                
                return u;
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#getUserByUsername(String)
         */
        @Override
        @Transactional(readOnly = true)
        public User getUserByUsername(String username) {
                return userDao.getUserByUsername(username);
        }
        
        /**
         * @throws Exception 
         * @see org.openmrs.api.db.ContextDAO#createUser(User, String)
         */
        @Override
        @Transactional
        public User createUser(User user, String password, List<String> roleNames) throws Exception {
                return Daemon.createUser(user, password, roleNames);
        }
        
        /**
         * Call the UserService to save the given user while proxying the privileges needed to do so.
         * 
         * @param user the User to save
         */
        private void saveUserProperties(User user) {
                sessionFactory.getCurrentSession().update(user);
        }
        
        /**
         * Get the integer stored for the given user that is their number of login attempts
         * 
         * @param user the user to check
         * @return the # of login attempts for this user defaulting to zero if none defined
         */
        private int getUsersLoginAttempts(User user) {
                String attemptsString = user.getUserProperty(OpenmrsConstants.USER_PROPERTY_LOGIN_ATTEMPTS, "0");
                int attempts = 0;
                try {
                        attempts = Integer.parseInt(attemptsString);
                }
                catch (NumberFormatException e) {
                        // skip over errors and leave the attempts at zero
                }
                return attempts;
        }
        
        /**
         * @see org.openmrs.api.context.Context#openSession()
         */
        private boolean participate = false;
        
        @Override
        public void openSession() {
                log.debug("HibernateContext: Opening Hibernate Session");
                if (TransactionSynchronizationManager.hasResource(sessionFactory)) {
                        log.debug("Participating in existing session ({})", sessionFactory.hashCode());
                        participate = true;
                } else {
                        log.debug("Registering session with synchronization manager ({})", sessionFactory.hashCode());
                        Session session = sessionFactory.openSession();
                        session.setHibernateFlushMode(FlushMode.MANUAL);
                        TransactionSynchronizationManager.bindResource(sessionFactory, new SessionHolder(session));
                }
        }
        
        /**
         * @see org.openmrs.api.context.Context#closeSession()
         */
        @Override
        public void closeSession() {
                log.debug("HibernateContext: closing Hibernate Session");
                if (!participate) {
                        log.debug("Unbinding session from synchronization manager (" + sessionFactory.hashCode() + ")");
                        
                        if (TransactionSynchronizationManager.hasResource(sessionFactory)) {
                                Object value = TransactionSynchronizationManager.unbindResource(sessionFactory);
                                try {
                                        if (value instanceof SessionHolder) {
                                                Session session = ((SessionHolder) value).getSession();
                                                SessionFactoryUtils.closeSession(session);
                                        }
                                }
                                catch (RuntimeException e) {
                                        log.error("Unexpected exception on closing Hibernate Session", e);
                                }
                        }
                } else {
                        log.debug("Participating in existing session, so not releasing session through synchronization manager");
                }
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#clearSession()
         */
        @Override
        @Transactional
        public void clearSession() {
                sessionFactory.getCurrentSession().clear();
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#evictFromSession(java.lang.Object)
         */
        @Override
        public void evictFromSession(Object obj) {
                sessionFactory.getCurrentSession().evict(obj);
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#evictEntity(OpenmrsObject)
         */
        @Override
        public void evictEntity(OpenmrsObject obj) {
                sessionFactory.getCache().evictEntity(obj.getClass(), obj.getId());
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#evictAllEntities(Class)
         */
        @Override
        public void evictAllEntities(Class<?> entityClass) {
                sessionFactory.getCache().evictEntityRegion(entityClass);
                sessionFactory.getCache().evictCollectionRegions();
                sessionFactory.getCache().evictQueryRegions();
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#clearEntireCache()
         */
        @Override
        public void clearEntireCache() {
                sessionFactory.getCache().evictAllRegions();
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#refreshEntity(Object)
         */
        @Override
        public void refreshEntity(Object obj) {
                sessionFactory.getCurrentSession().refresh(obj);
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#flushSession()
         */
        @Override
        @Transactional
        public void flushSession() {
                sessionFactory.getCurrentSession().flush();
        }
        
        /**
         * @see org.openmrs.api.context.Context#startup(Properties)
         */
        @Override
        @Transactional
        public void startup(Properties properties) {
        }
        
        /**
         * @see org.openmrs.api.context.Context#shutdown()
         */
        @Override
        public void shutdown() {
                if (log.isInfoEnabled()) {
                        showUsageStatistics();
                }
                
                if (sessionFactory != null) {
                        
                        log.debug("Closing any open sessions");
                        closeSession();
                        
                        log.debug("Shutting down threadLocalSession factory");
                        if (!sessionFactory.isClosed()) {
                                sessionFactory.close();
                        }
                        
                        log.debug("The threadLocalSession has been closed");
                        
                } else {
                        log.error("SessionFactory is null");
                }
                
        }
        
        /**
         * Convenience method to print out the hibernate cache usage stats to the log
         */
        private void showUsageStatistics() {
                if (sessionFactory.getStatistics().isStatisticsEnabled()) {
                        log.debug("Getting query statistics: ");
                        Statistics stats = sessionFactory.getStatistics();
                        for (String query : stats.getQueries()) {
                                log.info("QUERY: " + query);
                                QueryStatistics qstats = stats.getQueryStatistics(query);
                                log.info("Cache Hit Count : " + qstats.getCacheHitCount());
                                log.info("Cache Miss Count: " + qstats.getCacheMissCount());
                                log.info("Cache Put Count : " + qstats.getCachePutCount());
                                log.info("Execution Count : " + qstats.getExecutionCount());
                                log.info("Average time    : " + qstats.getExecutionAvgTime());
                                log.info("Row Count       : " + qstats.getExecutionRowCount());
                        }
                }
        }
        
        /**
         * Takes the default properties defined in /metadata/api/hibernate/hibernate.default.properties
         * and merges it into the user-defined runtime properties
         * 
         * @see org.openmrs.api.db.ContextDAO#mergeDefaultRuntimeProperties(java.util.Properties)
         * <strong>Should</strong> merge default runtime properties
         */
        @Override
        public void mergeDefaultRuntimeProperties(Properties runtimeProperties) {
                
                Map<String, String> cache = new HashMap<>();
                // loop over runtime properties and precede each with "hibernate" if
                // it isn't already
                for (Map.Entry<Object, Object> entry : runtimeProperties.entrySet()) {
                        Object key = entry.getKey();
                        String prop = (String) key;
                        String value = (String) entry.getValue();
                        log.trace("Setting property: " + prop + ":" + value);
                        if (!prop.startsWith("hibernate") && !runtimeProperties.containsKey("hibernate." + prop)) {
                                cache.put("hibernate." + prop, value);
                        }
                }
                runtimeProperties.putAll(cache);
                
                // load in the default hibernate properties from hibernate.default.properties
                Properties props = new Properties();
                URL url = getClass().getResource("/hibernate.default.properties");
                File file = new File(url.getPath());
                OpenmrsUtil.loadProperties(props, file);
                
                // add in all default properties that don't exist in the runtime
                // properties yet
                for (Map.Entry<Object, Object> entry : props.entrySet()) {
                        if (!runtimeProperties.containsKey(entry.getKey())) {
                                runtimeProperties.put(entry.getKey(), entry.getValue());
                        }
                }
        }
        
        @Override
        @Transactional
        public void updateSearchIndexForType(Class<?> type) {
                Session session = sessionFactory.getCurrentSession();
                SearchSession searchSession = searchSessionFactory.getSearchSession();
                SearchIndexingPlan indexingPlan = searchSession.indexingPlan();
                
                //Prepare session for batch work
                session.flush();
                indexingPlan.execute();
                session.clear();

                //Purge all search indexes of the given type
                Search.mapping(sessionFactory).scope(type).workspace().purge();
                
                FlushMode flushMode = session.getHibernateFlushMode();
                CacheMode cacheMode = session.getCacheMode();
                try {
                        session.setHibernateFlushMode(FlushMode.MANUAL);
                        session.setCacheMode(CacheMode.IGNORE);

                        //Scrollable results will avoid loading too many objects in memory
                        try (ScrollableResults results = HibernateUtil.getScrollableResult(sessionFactory, type, 1000)) {
                                int index = 0;
                                while (results.next()) {
                                        index++;
                                        //index each element
                                        indexingPlan.addOrUpdate(results.get(0));
                                        if (index % 1000 == 0) {
                                                //apply changes to search indexes
                                                indexingPlan.execute();
                                                //free memory since the queue is processed
                                                session.clear();
                                                // reset index to avoid overflows
                                                index = 0;
                                        }
                                }
                        } finally {
                                indexingPlan.execute();
                                session.clear();
                        }
                }
                finally {
                        session.setHibernateFlushMode(flushMode);
                        session.setCacheMode(cacheMode);
                }
        }

        @Override
        @Transactional
        public void updateSearchIndex(Class<?>... types) {
                try {
                        searchSessionFactory.getSearchSession().massIndexer(types).startAndWait();
                } catch (InterruptedException e) {
                        throw new RuntimeException(e);
                }
        }

        /**
         * @see org.openmrs.api.db.ContextDAO#updateSearchIndexForObject(java.lang.Object)
         */
        @Override
        @Transactional
        public void updateSearchIndexForObject(Object object) {
                SearchIndexingPlan indexingPlan = searchSessionFactory.getSearchSession().indexingPlan();
                indexingPlan.addOrUpdate(object);
                indexingPlan.execute();
        }
        
        /**
         * @see org.openmrs.api.db.ContextDAO#setupSearchIndex()
         */
        @Override
        public void setupSearchIndex() {
                String gp = Context.getAdministrationService().getGlobalProperty(OpenmrsConstants.GP_SEARCH_INDEX_VERSION, "");
                
                if (!OpenmrsConstants.SEARCH_INDEX_VERSION.toString().equals(gp)) {
                        updateSearchIndex();
                }
        }
        
        /**
         * @see ContextDAO#updateSearchIndex()
         */
        @Override
        public void updateSearchIndex() {
                try {
                        log.info("Updating the search index... It may take a few minutes.");
                        searchSessionFactory.getSearchSession().massIndexer().startAndWait();
                        GlobalProperty gp = Context.getAdministrationService().getGlobalPropertyObject(
                            OpenmrsConstants.GP_SEARCH_INDEX_VERSION);
                        if (gp == null) {
                                gp = new GlobalProperty(OpenmrsConstants.GP_SEARCH_INDEX_VERSION);
                        }
                        gp.setPropertyValue(OpenmrsConstants.SEARCH_INDEX_VERSION.toString());
                        Context.getAdministrationService().saveGlobalProperty(gp);
                        log.info("Finished updating the search index");
                }
                catch (Exception e) {
                        throw new RuntimeException("Failed to update the search index", e);
                }
        }

        /**
         * @see ContextDAO#updateSearchIndexAsync()
         */
        @Override
        public Future<?> updateSearchIndexAsync() {
                try {
                        log.info("Started asynchronously updating the search index...");
                        return searchSessionFactory.getSearchSession().massIndexer().start().toCompletableFuture();
                }
                catch (Exception e) {
                        throw new RuntimeException("Failed to start asynchronous search index update", e);
                }
        }

        /**
         * @see ContextDAO#getDatabaseConnection() 
         */
        public Connection getDatabaseConnection() {
                try {
                        return SessionFactoryUtils.getDataSource(sessionFactory).getConnection();
                }
                catch (SQLException e) {
                        throw new RuntimeException("Unable to retrieve a database connection", e);
                }
        }
}

openmrs / openmrs-core / 14752386992

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