13444985538

Committed 20 Feb 2025 09:26PM UTC coverage: 64.835% (+0.003%) from 64.832%

Build # 13444985538

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push

github

Committed by

web-flow

Commit Message

TRUNK-6308: DatabaseUpdater.releaseDatabaseLocks doesn't release database locks after crashes (#4935)

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0 of 1 new or added line in 1 file covered. (0.0%)

5 existing lines in 4 files now uncovered.

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67.2

/api/src/main/java/org/openmrs/util/DatabaseUpdater.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.util;

import liquibase.Contexts;
import liquibase.GlobalConfiguration;
import liquibase.LabelExpression;
import liquibase.Liquibase;
import liquibase.RuntimeEnvironment;
import liquibase.Scope;
import liquibase.changelog.ChangeLogHistoryServiceFactory;
import liquibase.changelog.ChangeLogIterator;
import liquibase.changelog.ChangeSet;
import liquibase.changelog.DatabaseChangeLog;
import liquibase.changelog.filter.ChangeSetFilterResult;
import liquibase.changelog.filter.ContextChangeSetFilter;
import liquibase.changelog.filter.DbmsChangeSetFilter;
import liquibase.changelog.filter.ShouldRunChangeSetFilter;
import liquibase.changelog.visitor.UpdateVisitor;
import liquibase.command.core.StatusCommandStep;
import liquibase.database.Database;
import liquibase.database.DatabaseFactory;
import liquibase.database.jvm.JdbcConnection;
import liquibase.exception.LiquibaseException;
import liquibase.exception.LockException;
import liquibase.lockservice.LockService;
import liquibase.lockservice.LockServiceFactory;
import liquibase.resource.CompositeResourceAccessor;
import liquibase.resource.FileSystemResourceAccessor;
import liquibase.resource.ResourceAccessor;
import org.apache.commons.io.IOUtils;
import org.openmrs.api.context.Context;
import org.openmrs.liquibase.ChangeLogDetective;
import org.openmrs.liquibase.ChangeLogVersionFinder;
import org.openmrs.liquibase.ChangeSetExecutorCallback;
import org.openmrs.liquibase.LiquibaseProvider;
import org.openmrs.liquibase.OpenmrsClassLoaderResourceAccessor;
import org.openmrs.module.ModuleClassLoader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.nio.charset.StandardCharsets;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Calendar;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Properties;
import java.util.Set;

/**
 * This class uses Liquibase to update the database. <br>
 * <br>
 * See src/main/resources/liquibase-update-to-latest.xml for the changes. This class will also run
 * arbitrary liquibase xml files on the associated database as well. Details for the database are
 * taken from the openmrs runtime properties.
 *
 * @since 1.5
 */
public class DatabaseUpdater {
        
        private static final Logger log = LoggerFactory.getLogger(DatabaseUpdater.class);
        
        private static final String EMPTY_CHANGE_LOG_FILE = "liquibase-empty-changelog.xml";
        
        public static final String CONTEXT = "core";
        
        public static final String DATABASE_UPDATES_LOG_FILE = "liquibaseUpdateLogs.txt";
        
        private static Integer authenticatedUserId;
        
        private static final ChangeLogDetective changeLogDetective;
        
        private static final ChangeLogVersionFinder changeLogVersionFinder;
        
        private static LiquibaseProvider liquibaseProvider;
        
        static {
                changeLogDetective = ChangeLogDetective.getInstance();
                changeLogVersionFinder = new ChangeLogVersionFinder();
        }
        
        /**
         * Allows to inject a LiquibaseProvider instance for testing purposes.
         * 
         * @param liquibaseProvider
         */
        static void setLiquibaseProvider(LiquibaseProvider liquibaseProvider) {
                DatabaseUpdater.liquibaseProvider = liquibaseProvider;
        }

        /**
         * Removes any LiquibaseProvider instance that was set for testing purposes.
         */
        static void unsetLiquibaseProvider() {
                DatabaseUpdater.liquibaseProvider = null;
        }
        
        /**
         * Holds the update warnings generated by the custom liquibase changesets as they are executed
         */
        private static volatile List<String> updateWarnings = null;
        
        /**
         * Convenience method to run the changesets using Liquibase to bring the database up to a version
         * compatible with the code
         */
        public static void executeChangelog() throws DatabaseUpdateException {
                final LiquibaseProvider liquibaseProvider = new DatabaseUpdaterLiquibaseProvider();
                
                final List<String> changeLogs;
                try {
                        final String version = changeLogDetective.getInitialLiquibaseSnapshotVersion(CONTEXT, liquibaseProvider);
                        log.debug(
                                "updating the database with versions of liquibase-update-to-latest files greater than '{}'",
                                version);
                        
                        changeLogs = changeLogDetective.getUnrunLiquibaseUpdateFileNames(version, CONTEXT, liquibaseProvider);
                        log.debug("found applicable Liquibase update change logs: {}", changeLogs);
                }
                catch (Exception e) {
                        log.error("Error while trying to find database changes to run", e);
                        throw new DatabaseUpdateException("Error while trying to find database changes to run", e);
                }
                
                if (changeLogs.isEmpty()) {
                        return;
                }
                
                for (String changeLog : changeLogs) {
                        log.debug("applying Liquibase changelog '{}'", changeLog);
                        executeChangelog(changeLog, (ChangeSetExecutorCallback) null);
                }
        }
        
        /**
         * Run changesets on database using Liquibase to get the database up to the most recent version
         *
         * @param changelog the liquibase changelog file to use (or null to use the default file)
         * @param userInput nullable map from question to user answer. Used if a call to update(null) threw
         *            an {@link InputRequiredException}
         * @throws DatabaseUpdateException if an error occurs
         * @deprecated as of 2.4 see {@link #executeChangelog(String, ChangeSetExecutorCallback)}
         */
        @Deprecated
        public static void executeChangelog(String changelog, Map<String, Object> userInput)
                throws DatabaseUpdateException {
                log.debug("Executing changelog: {}" , changelog);
                executeChangelog(changelog, (ChangeSetExecutorCallback) null);
        }

        /**
         * Executes the given changelog file. This file is assumed to be on the classpath.
         *
         * @param changelog The string filename of a liquibase changelog xml file to run
         * @return A list of messages or warnings generated by the executed changesets
         */
        public static List<String> executeChangelog(String changelog, ChangeSetExecutorCallback callback)
                throws DatabaseUpdateException {
                log.debug("installing the tables into the database");
                
                if (changelog == null) {
                        throw new IllegalArgumentException("changelog must not be null");
                }
                
                try {
                        log.debug("executing liquibase changelog {}", changelog);
                        return executeChangelog(changelog, new Contexts(CONTEXT), callback, null);
                }
                catch (Exception e) {
                        throw new DatabaseUpdateException("There was an error while updating the database to the latest. file: "
                                + changelog + ". Error: " + e.getMessage(), e);
                }
        }
        
        /**
         * This code was borrowed from the liquibase jar so that we can call the given callback function.
         *
         * @param changeLogFile the file to execute
         * @param contexts the liquibase changeset context
         * @param callback the function to call after every changeset
         * @return A list of messages or warnings generated by the executed changesets
         * @throws Exception
         */
        public static List<String> executeChangelog(String changeLogFile, Contexts contexts, ChangeSetExecutorCallback callback,
                ClassLoader cl) throws Exception {
                
                if (cl == null) {
                        cl = OpenmrsClassLoader.getInstance();
                }
                
                Thread.currentThread().setContextClassLoader(cl);
                
                log.debug("Setting up liquibase object to run changelog: {}", changeLogFile);
                Liquibase liquibase = getLiquibase(changeLogFile, cl);

                int numChangeSetsToRun = new StatusCommandStep()
                        .listUnrunChangeSets(contexts,
                                new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase()).size();

                Database database = null;
                LockService lockHandler = null;
                
                try {
                        database = liquibase.getDatabase();
                        lockHandler = LockServiceFactory.getInstance().getLockService(database);
                        lockHandler.waitForLock();
                        
                        Map<String, Object> scopeValues = new HashMap<>();
                        scopeValues.put(Scope.Attr.resourceAccessor.name(), getCompositeResourceAccessor(null));
                        String scopeId = null;
                        try {
                                scopeId = Scope.enter(scopeValues);
                                DatabaseChangeLog changeLog = liquibase.getDatabaseChangeLog();
                                changeLog.setChangeLogParameters(liquibase.getChangeLogParameters());
                                changeLog.validate(database);

                                ChangeLogIterator logIterator = new ChangeLogIterator(changeLog, new ShouldRunChangeSetFilter(database),
                                        new ContextChangeSetFilter(contexts), new DbmsChangeSetFilter(database));

                                // ensure that the change log history service is initialised
                                Scope.getCurrentScope().getSingleton(ChangeLogHistoryServiceFactory.class).getChangeLogService(database).init();

                                logIterator.run(new OpenmrsUpdateVisitor(database, callback, numChangeSetsToRun),
                                        new RuntimeEnvironment(database, contexts, new LabelExpression()));
                        }
                        finally {
                                try {
                                        Scope.exit(scopeId);
                                }
                                catch (Exception e) {
                                        log.warn("An error occurred trying to exit the liquibase scope", e);
                                }
                        }
                }
                finally {
                        try {
                                if (lockHandler != null) {
                                        lockHandler.releaseLock();
                                }
                        }
                        catch (Exception e) {
                                log.error("Could not release lock", e);
                        }

                        try {
                                if (database != null && database.getConnection() != null) {
                                        database.getConnection().close();
                                }
                        }
                        catch (Exception e) {
                                //pass
                        }
                }
                
                return updateWarnings;
        }
        
        /**
         * Ask Liquibase if it needs to do any updates.
         *
         * @return true/false whether database updates are required
         * @throws Exception when an exception is raised while processing Liquibase changelog files
         */
        public static boolean updatesRequired() throws Exception {
                log.debug("checking for updates");
                List<OpenMRSChangeSet> changesets = getUnrunDatabaseChanges(new DatabaseUpdaterLiquibaseProvider());
                
                // if the db is locked, it means there was a crash
                // or someone is executing db updates right now. either way
                // returning true here stops the openmrs startup and shows
                // the user the maintenance wizard for updates
                if (isLocked() && changesets.isEmpty()) {
                        // if there is a db lock but there are no db changes we undo the
                        // lock
                        DatabaseUpdater.releaseDatabaseLock();
                        log.debug("db lock found and released automatically");
                        return false;
                }
                
                return !changesets.isEmpty();
        }
        
        /**
         * Ask Liquibase if it needs to do any updates
         *
         * @param changeLogFilenames the filenames of all files to search for unrun changesets
         * @return true/false whether database updates are required <strong>Should</strong> always have a
         *         valid update to latest file
         */
        public static boolean updatesRequired(String... changeLogFilenames) throws Exception {
                log.debug("checking for updates");
                List<OpenMRSChangeSet> changesets = getUnrunDatabaseChanges(changeLogFilenames);
                return !changesets.isEmpty();
        }
        
        /**
         * Indicates whether automatic database updates are allowed by this server. Automatic updates are
         * disabled by default. In order to enable automatic updates, the admin needs to add
         * 'auto_update_database=true' to the runtime properties file.
         *
         * @return true/false whether the 'auto_update_database' has been enabled.
         */
        public static Boolean allowAutoUpdate() {
                String allowAutoUpdate = Context.getRuntimeProperties()
                        .getProperty(OpenmrsConstants.AUTO_UPDATE_DATABASE_RUNTIME_PROPERTY, "false");
                
                return "true".equals(allowAutoUpdate);
                
        }
        
        /**
         * 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(Properties)
         */
        private static void mergeDefaultRuntimeProperties(Properties runtimeProperties) {
                
                // loop over runtime properties and precede each with "hibernate" if
                // it isn't already
                // must do it this way to prevent concurrent mod errors
                Set<Object> runtimePropertyKeys = new HashSet<>(runtimeProperties.keySet());
                for (Object key : runtimePropertyKeys) {
                        String prop = (String) key;
                        String value = (String) runtimeProperties.get(key);
                        log.trace("Setting property: " + prop + ":" + value);
                        if (!prop.startsWith("hibernate") && !runtimeProperties.containsKey("hibernate." + prop)) {
                                runtimeProperties.setProperty("hibernate." + prop, value);
                        }
                }
                
                // load in the default hibernate properties from hibernate.default.properties
                InputStream propertyStream = null;
                try {
                        Properties props = new Properties();
                        // TODO: This is a dumb requirement to have hibernate in here.  Clean this up
                        propertyStream = DatabaseUpdater.class.getClassLoader().getResourceAsStream("hibernate.default.properties");
                        OpenmrsUtil.loadProperties(props, propertyStream);
                        // 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());
                                }
                        }
                }
                finally {
                        try {
                                propertyStream.close();
                        }
                        catch (Exception e) {
                                // pass
                        }
                }
        }
        
        /**
         * Exposes Liquibase instances created by this class. When calling
         * org.openmrs.util.DatabaseUpdater#getInitialLiquibaseSnapshotVersion(LiquibaseProvider) and
         * org.openmrs.util.DatabaseUpdater#getInitialLiquibaseSnapshotVersion(String,LiquibaseProvider), a
         * Liquibase instance created by this class is injected into these methods. The Liquibase instance
         * is injected into these methods instead of calling
         * org.openmrs.util.DatabaseUpdater#getLiquibase(String,ClassLoader) directly. The reason for that
         * design decision is that injecting a Liquibase instance (via a Liquibase provider) makes it
         * possible to test the two methods mentioned above in isolation. The respective integration test is
         * org.openmrs.util.DatabaseUpdateIT.
         * 
         * @see LiquibaseProvider
         * @param changeLogFile name of a Liquibase change log file
         * @return a Liquibase instance
         * @throws Exception
         */
        static Liquibase getLiquibase(String changeLogFile) throws Exception {
                if (liquibaseProvider != null) {
                        return liquibaseProvider.getLiquibase(changeLogFile);
                }
                return getLiquibase(changeLogFile, OpenmrsClassLoader.getInstance());
        }
        
        /**
         * Get a connection to the database through Liquibase. The calling method /must/ close the database
         * connection when finished with this Liquibase object.
         * liquibase.getDatabase().getConnection().close()
         *
         * @param changeLogFile the name of the file to look for the on classpath or filesystem
         * @param cl the {@link ClassLoader} to use to find the file (or null to use
         *            {@link OpenmrsClassLoader})
         * @return Liquibase object based on the current connection settings
         * @throws Exception
         */
        private static Liquibase getLiquibase(String changeLogFile, ClassLoader cl) throws Exception {
                Connection connection;
                try {
                        connection = getConnection();
                }
                catch (SQLException e) {
                        throw new Exception(
                                "Unable to get a connection to the database.  Please check your openmrs runtime properties file and make sure you have the correct connection.username and connection.password set",
                                e);
                }
                
                if (cl == null) {
                        cl = OpenmrsClassLoader.getInstance();
                }
                
                try {
                        Database database = DatabaseFactory.getInstance()
                                .findCorrectDatabaseImplementation(new JdbcConnection(connection));
                        database.setDatabaseChangeLogTableName("liquibasechangelog");
                        database.setDatabaseChangeLogLockTableName("liquibasechangeloglock");
                        
                        if (connection.getMetaData().getDatabaseProductName().contains("HSQL Database Engine")
                                || connection.getMetaData().getDatabaseProductName().contains("H2")) {
                                // a hack because hsqldb and h2 seem to be checking table names in the metadata section case sensitively
                                database.setDatabaseChangeLogTableName(database.getDatabaseChangeLogTableName().toUpperCase());
                                database.setDatabaseChangeLogLockTableName(database.getDatabaseChangeLogLockTableName().toUpperCase());
                        }

                        if (changeLogFile == null) {
                                changeLogFile = EMPTY_CHANGE_LOG_FILE;
                        }

                        configureLiquibaseDuplicateFileMode();

                        // ensure that the change log history service is initialised
                        Scope.getCurrentScope()
                                .getSingleton(ChangeLogHistoryServiceFactory.class)
                                .getChangeLogService(database)
                                .init();
                        return new Liquibase(changeLogFile, getCompositeResourceAccessor(cl), database);
                }
                catch (Exception e) {
                        // if an error occurs, close the connection
                        if (connection != null) {
                                connection.close();
                        }
                        throw e;
                }
        }
        
        /**
         * Gets a database connection for liquibase to do the updates
         *
         * @return a java.sql.connection based on the current runtime properties
         */
        public static Connection getConnection() throws Exception {
                Properties props = Context.getRuntimeProperties();
                mergeDefaultRuntimeProperties(props);
                
                String driver = props.getProperty("hibernate.connection.driver_class");
                String username = props.getProperty("hibernate.connection.username");
                String password = props.getProperty("hibernate.connection.password");
                String url = props.getProperty("hibernate.connection.url");
                
                // hack for mysql to make sure innodb tables are created
                if (url.contains("mysql") && !url.contains("InnoDB")) {
                        url = url + "&sessionVariables=default_storage_engine=InnoDB";
                }
                
                Class.forName(driver);
                return DriverManager.getConnection(url, username, password);
        }
        
        /**
         * Represents each change in the files referenced by liquibase-update-to-latest
         */
        public static class OpenMRSChangeSet {
                
                private String id;
                
                private String author;
                
                private String comments;
                
                private String description;
                
                private ChangeSet.RunStatus runStatus;
                
                private Date ranDate;
                
                /**
                 * Create an OpenmrsChangeSet from the given changeset
                 *
                 * @param changeSet
                 * @param database
                 */
                public OpenMRSChangeSet(ChangeSet changeSet, Database database) throws Exception {
                        setId(changeSet.getId());
                        setAuthor(changeSet.getAuthor());
                        setComments(changeSet.getComments());
                        setDescription(changeSet.getDescription());
                        setRunStatus(database.getRunStatus(changeSet));
                        setRanDate(database.getRanDate(changeSet));
                }
                
                /**
                 * @return the author
                 */
                public String getAuthor() {
                        return author;
                }
                
                /**
                 * @param author the author to set
                 */
                public void setAuthor(String author) {
                        this.author = author;
                }
                
                /**
                 * @return the comments
                 */
                public String getComments() {
                        return comments;
                }
                
                /**
                 * @param comments the comments to set
                 */
                public void setComments(String comments) {
                        this.comments = comments;
                }
                
                /**
                 * @return the description
                 */
                public String getDescription() {
                        return description;
                }
                
                /**
                 * @param description the description to set
                 */
                public void setDescription(String description) {
                        this.description = description;
                }
                
                /**
                 * @return the runStatus
                 */
                public ChangeSet.RunStatus getRunStatus() {
                        return runStatus;
                }
                
                /**
                 * @param runStatus the runStatus to set
                 */
                public void setRunStatus(ChangeSet.RunStatus runStatus) {
                        this.runStatus = runStatus;
                }
                
                /**
                 * @return the ranDate
                 */
                public Date getRanDate() {
                        return ranDate;
                }
                
                /**
                 * @param ranDate the ranDate to set
                 */
                public void setRanDate(Date ranDate) {
                        this.ranDate = ranDate;
                }
                
                /**
                 * @return the id
                 */
                public String getId() {
                        return id;
                }
                
                /**
                 * @param id the id to set
                 */
                public void setId(String id) {
                        this.id = id;
                }
                
        }
        
        /**
         * Returns all change sets defined by (a) the Liquibase snapshot files that had been used to
         * initialise the OpenMRS database and (b) the Liquibase update files that that are applicable on
         * top of the snapshot version.
         * 
         * @return list of change sets that both have and haven't been run
         */
        public static List<OpenMRSChangeSet> getDatabaseChanges() throws Exception {
                if (Context.isSessionOpen()) { // Do not check privileges if not run in webapp context (e.g. in tests)
                        Context.requirePrivilege(PrivilegeConstants.GET_DATABASE_CHANGES);
                }
                List<OpenMRSChangeSet> result = new ArrayList<>();
                
                String initialSnapshotVersion = changeLogDetective.getInitialLiquibaseSnapshotVersion(CONTEXT,
                    new DatabaseUpdaterLiquibaseProvider());
                List<String> updateVersions = changeLogVersionFinder.getUpdateVersionsGreaterThan(initialSnapshotVersion);
                
                Map<String, List<String>> snapshotCombinations = changeLogVersionFinder.getSnapshotCombinations();

                List<String> changeLogFileNames = new ArrayList<>();
                changeLogFileNames.addAll(snapshotCombinations.get(initialSnapshotVersion));
                changeLogFileNames.addAll(changeLogVersionFinder.getUpdateFileNames(updateVersions));
                
                Liquibase liquibase = null;
                try {
                        for (String filename : changeLogFileNames) {
                                liquibase = getLiquibase(filename);
                                List<ChangeSet> changeSets = liquibase.getDatabaseChangeLog().getChangeSets();
                                
                                for (ChangeSet changeSet : changeSets) {
                                        OpenMRSChangeSet openMRSChangeSet = new OpenMRSChangeSet(changeSet, liquibase.getDatabase());
                                        result.add(openMRSChangeSet);
                                }
                                liquibase.close();
                        }
                }
                finally {
                        if (liquibase != null) {
                                try {
                                        liquibase.close();
                                }
                                catch (Exception e) {
                                        // ignore exceptions triggered by closing liquibase a second time 
                                }
                        }
                }
                
                return result;
        }
        
        /**
         * Returns a list of Liquibase change sets were not run yet.
         *
         * @param liquibaseProvider provides access to a Liquibase instance
         * @return list of change sets that were not run yet.
         */
        public static List<OpenMRSChangeSet> getUnrunDatabaseChanges(LiquibaseProvider liquibaseProvider) throws Exception {
                if (Context.isSessionOpen()) { // Do not check privileges if not run in webapp context (e.g. in tests)
                        Context.requirePrivilege(PrivilegeConstants.GET_DATABASE_CHANGES);
                }
                String initialSnapshotVersion = changeLogDetective.getInitialLiquibaseSnapshotVersion(CONTEXT, liquibaseProvider);
                log.debug("initial snapshot version is '{}'", initialSnapshotVersion);
                
                List<String> liquibaseUpdateFilenames = changeLogDetective.getUnrunLiquibaseUpdateFileNames(initialSnapshotVersion,
                    CONTEXT, liquibaseProvider);
                
                if (!liquibaseUpdateFilenames.isEmpty()) {
                        return getUnrunDatabaseChanges(liquibaseUpdateFilenames.toArray(new String[0]));
                }
                
                return new ArrayList<OpenMRSChangeSet>();
        }
        
        /**
         * Looks at the specified liquibase change log files and returns all changesets in the files that
         * have not been run on the database yet. If no argument is specified, then it looks at the current
         * liquibase-update-to-latest.xml file
         *
         * @param changeLogFilenames the filenames of all files to search for unrun changesets
         * @return list of change sets
         */
        public static List<OpenMRSChangeSet> getUnrunDatabaseChanges(String... changeLogFilenames) {
                if (Context.isSessionOpen()) { // Do not check privileges if not run in webapp context (e.g. in tests)
                        Context.requirePrivilege(PrivilegeConstants.GET_DATABASE_CHANGES);
                }
                log.debug("looking for un-run change sets in '{}'", Arrays.toString(changeLogFilenames));
                
                Database database = null;
                try {
                        if (changeLogFilenames == null || changeLogFilenames.length == 0) {
                                throw new IllegalArgumentException("changeLogFilenames can neither null nor an empty array");
                        }
                        
                        List<OpenMRSChangeSet> results = new ArrayList<>();
                        
                        for (String changelogFile : changeLogFilenames) {
                                Liquibase liquibase = getLiquibase(changelogFile, null);
                                database = liquibase.getDatabase();
                                
                                List<ChangeSet> changeSets = new StatusCommandStep()
                                        .listUnrunChangeSets(new Contexts(CONTEXT),
                                                new LabelExpression(), liquibase.getDatabaseChangeLog(), liquibase.getDatabase());

                                for (ChangeSet changeSet : changeSets) {
                                        OpenMRSChangeSet omrschangeset = new OpenMRSChangeSet(changeSet, database);
                                        results.add(omrschangeset);
                                }
                        }
                        
                        return results;
                        
                }
                catch (Exception e) {
                        throw new RuntimeException(
                                "Error occurred while trying to get the updates needed for the database. " + e.getMessage(), e);
                }
                finally {
                        try {
                                database.getConnection().close();
                        }
                        catch (Exception e) {
                                //pass
                        }
                }
        }
        
        /**
         * @return the authenticatedUserId
         */
        public static Integer getAuthenticatedUserId() {
                return authenticatedUserId;
        }
        
        /**
         * @param userId the authenticatedUserId to set
         */
        public static void setAuthenticatedUserId(Integer userId) {
                authenticatedUserId = userId;
        }
        
        /**
         * This method is called by an executing custom changeset to register warning messages.
         *
         * @param warnings list of warnings to append to the end of the current list
         */
        public static void reportUpdateWarnings(List<String> warnings) {
                if (updateWarnings == null) {
                        updateWarnings = new LinkedList<>();
                }
                updateWarnings.addAll(warnings);
        }
        
        /**
         * This method writes the given text to the database updates log file located in the application
         * data directory.
         *
         * @param text text to be written to the file
         */
        public static void writeUpdateMessagesToFile(String text) {
                OutputStreamWriter streamWriter = null;
                PrintWriter writer = null;
                File destFile = new File(OpenmrsUtil.getApplicationDataDirectory(), DatabaseUpdater.DATABASE_UPDATES_LOG_FILE);
                try {
                        String lineSeparator = System.getProperty("line.separator");
                        Date date = Calendar.getInstance().getTime();
                        
                        streamWriter = new OutputStreamWriter(new FileOutputStream(destFile, true), StandardCharsets.UTF_8);
                        writer = new PrintWriter(new BufferedWriter(streamWriter));
                        writer.write("********** START OF DATABASE UPDATE LOGS AS AT " + date + " **********");
                        writer.write(lineSeparator);
                        writer.write(lineSeparator);
                        writer.write(text);
                        writer.write(lineSeparator);
                        writer.write(lineSeparator);
                        writer.write("*********** END OF DATABASE UPDATE LOGS AS AT " + date + " ***********");
                        writer.write(lineSeparator);
                        writer.write(lineSeparator);
                        
                        //check if there was an error while writing to the file
                        if (writer.checkError()) {
                                log.warn("An Error occured while writing warnings to the database update log file'");
                        }
                        
                        writer.close();
                }
                catch (FileNotFoundException e) {
                        log.warn("Failed to find the database update log file", e);
                }
                finally {
                        IOUtils.closeQuietly(streamWriter);
                        IOUtils.closeQuietly(writer);
                }
        }
        
        /**
         * This method releases the liquibase db lock, and is intended to be usd after a crashed database update.
         * <br>
         * This should only be called if the user is sure that no one else is currently running database
         * updates. This method should be used if there was a db crash while updates were being written and
         * the lock table was never cleaned up.
         *
         * @throws LockException
         */
        public static synchronized void releaseDatabaseLock() throws LockException {
                Database database = null;
                try {
                        Liquibase liquibase = getLiquibase(null, null);
                        database = liquibase.getDatabase();
                        LockService lockService = LockServiceFactory.getInstance().getLockService(database);
                        if (isLocked()) {
                                lockService.forceReleaseLock();
                        }
                }
                catch (Exception e) {
                        throw new LockException(e);
                }
                finally {
                        try {
                                database.getConnection().close();
                        }
                        catch (Exception e) {
                                // pass
                        }
                }
        }
        
        /**
         * This method currently checks the liquibasechangeloglock table to see if there is a row with a
         * lock in it. This uses the liquibase API to do this
         *
         * @return true if database is currently locked
         */
        public static boolean isLocked() {
                Database database = null;
                try {
                        Liquibase liquibase = getLiquibase(null, null);
                        database = liquibase.getDatabase();
                        return LockServiceFactory.getInstance().getLockService(database).listLocks().length > 0;
                }
                catch (Exception e) {
                        return false;
                }
                finally {
                        try {
                                database.getConnection().close();
                        }
                        catch (Exception e) {
                                // pass
                        }
                }
        }

        private final static class OpenmrsUpdateVisitor extends UpdateVisitor {

                private final ChangeSetExecutorCallback callback;

                private final int numChangeSetsToRun;

                public OpenmrsUpdateVisitor(Database database, ChangeSetExecutorCallback callback, int numChangeSetsToRun) {
                        super(database, null);
                        this.callback = callback;
                        this.numChangeSetsToRun = numChangeSetsToRun;
                }

                @Override
                public void visit(ChangeSet changeSet, DatabaseChangeLog databaseChangeLog, Database database,
                        Set<ChangeSetFilterResult> filterResults) throws LiquibaseException {
                        if (callback != null) {
                                callback.executing(changeSet, numChangeSetsToRun);
                        }
                        Map<String, Object> scopeValues = new HashMap<>();
                        scopeValues.put(Scope.Attr.resourceAccessor.name(), getCompositeResourceAccessor(null));
                        String scopeId = null;
                        try {
                                scopeId = Scope.enter(scopeValues);
                                super.visit(changeSet, databaseChangeLog, database, filterResults);
                        }
                        catch (Exception e) {
                                throw new LiquibaseException("Unable to execute change set: " + changeSet, e);
                        }
                        finally {
                                try {
                                        Scope.exit(scopeId);
                                }
                                catch (Exception e) {
                                        log.warn("An error occurred trying to exit the liquibase scope", e);
                                }
                        }
                }
        }

        /**
         * @return a resourceAccessor that includes both classpath and filesystem at the application data directory
         */
        private static CompositeResourceAccessor getCompositeResourceAccessor(ClassLoader classLoader) {
                if (classLoader == null) {
                        classLoader = Thread.currentThread().getContextClassLoader();
                        if (!(classLoader instanceof OpenmrsClassLoader) && !(classLoader instanceof ModuleClassLoader)) {
                                classLoader = OpenmrsClassLoader.getInstance();
                        }
                }
                
                ResourceAccessor openmrsFO = new OpenmrsClassLoaderResourceAccessor(classLoader);
                ResourceAccessor fsFO = new FileSystemResourceAccessor(OpenmrsUtil.getApplicationDataDirectoryAsFile());
                return new CompositeResourceAccessor(openmrsFO, fsFO);
        }
        
        private static void configureLiquibaseDuplicateFileMode() {
                final String dupFlagModeKey = GlobalConfiguration.DUPLICATE_FILE_MODE.getKey();
                final String dupFlagMode = Context.getRuntimeProperties().getProperty(dupFlagModeKey);

                if (dupFlagMode != null) {
                        System.setProperty(dupFlagModeKey, dupFlagMode);
                } else if (System.getProperty(dupFlagModeKey) == null) {
                        System.setProperty(dupFlagModeKey, OpenmrsConstants.LIQUIBASE_DUPLICATE_FILE_MODE_DEFAULT);
                }
        }
}

openmrs / openmrs-core / 13444985538

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