20784346756

Committed 07 Jan 2026 02:13PM UTC coverage: 63.283%. First build

Build # 20784346756

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push

github

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web-flow

Commit Message

TRUNK-6418 Run liquibase checks and data imports only when version of core or modules changes (#5603)

* TRUNK-6418: Run liquibase checks and data imports only when version of core or modules changes

(cherry picked from commit 4723e71c3)

* TRUNK-6418: Follow up adjustments

---------

Co-authored-by: IamMujuziMoses <mujuzimoses@gmail.com>

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50.27

/api/src/main/java/org/openmrs/api/context/Context.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.context;

import org.aopalliance.aop.Advice;
import org.apache.commons.lang3.StringUtils;
import org.openmrs.Allergen;
import org.openmrs.GlobalProperty;
import org.openmrs.OpenmrsObject;
import org.openmrs.PersonName;
import org.openmrs.Privilege;
import org.openmrs.Role;
import org.openmrs.User;
import org.openmrs.api.APIException;
import org.openmrs.api.AdministrationService;
import org.openmrs.api.CohortService;
import org.openmrs.api.ConceptService;
import org.openmrs.api.ConditionService;
import org.openmrs.api.DatatypeService;
import org.openmrs.api.DiagnosisService;
import org.openmrs.api.EncounterService;
import org.openmrs.api.FormService;
import org.openmrs.api.LocationService;
import org.openmrs.api.MedicationDispenseService;
import org.openmrs.api.ObsService;
import org.openmrs.api.OpenmrsService;
import org.openmrs.api.OrderService;
import org.openmrs.api.OrderSetService;
import org.openmrs.api.PatientService;
import org.openmrs.api.PersonService;
import org.openmrs.api.ProgramWorkflowService;
import org.openmrs.api.ProviderService;
import org.openmrs.api.SerializationService;
import org.openmrs.api.UserService;
import org.openmrs.api.VisitService;
import org.openmrs.api.db.ContextDAO;
import org.openmrs.hl7.HL7Service;
import org.openmrs.logic.LogicService;
import org.openmrs.messagesource.MessageSourceService;
import org.openmrs.module.ModuleMustStartException;
import org.openmrs.module.ModuleUtil;
import org.openmrs.notification.AlertService;
import org.openmrs.notification.MessageException;
import org.openmrs.notification.MessagePreparator;
import org.openmrs.notification.MessageSender;
import org.openmrs.notification.MessageService;
import org.openmrs.notification.mail.MailMessageSender;
import org.openmrs.notification.mail.velocity.VelocityMessagePreparator;
import org.openmrs.scheduler.SchedulerService;
import org.openmrs.scheduler.SchedulerUtil;
import org.openmrs.util.ConfigUtil;
import org.openmrs.util.DatabaseUpdateException;
import org.openmrs.util.DatabaseUpdater;
import org.openmrs.util.InputRequiredException;
import org.openmrs.util.LocaleUtility;
import org.openmrs.util.OpenmrsClassLoader;
import org.openmrs.util.OpenmrsConstants;
import org.openmrs.util.OpenmrsUtil;
import org.openmrs.util.PrivilegeConstants;
import org.openmrs.validator.ValidateUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.aop.Advisor;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.NoSuchBeanDefinitionException;
import org.springframework.beans.factory.NoUniqueBeanDefinitionException;

import javax.mail.Authenticator;
import javax.mail.PasswordAuthentication;
import javax.mail.Session;
import java.sql.Connection;
import java.text.SimpleDateFormat;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Properties;
import java.util.Set;
import java.util.concurrent.Future;

/**
 * Represents an OpenMRS <code>Context</code>, which may be used to authenticate to the database and
 * obtain services in order to interact with the system.<br>
 * <br>
 * The Context is split into a {@link UserContext} and {@link ServiceContext}. The UserContext is
 * lightweight and there is an instance for every user logged into the system. The ServiceContext is
 * heavier and it contains each service class. This is more static and there is only one ServiceContext
 * per OpenMRS instance. <br>
 * <br>
 * Both the {@link UserContext} and the {@link ServiceContext} should not be used directly. This
 * context class has methods to pass through to the currently defined UserContext for the thread and
 * the currently defined ServiceContext. <br>
 * <br>
 * To use the OpenMRS api there are four things that have to be done:
 * <ol>
 * <li>Call {@link Context#startup(String, String, String, Properties)} to let the Context contact
 * the database</li>
 * <li>Call {@link Context#openSession()} to start a "unit of work".</li>
 * <li>Call {@link Context#authenticate(String, String)} to authenticate the current user on the
 * current thread</li>
 * <li>Call {@link Context#closeSession()} to end your "unit of work" and commit all changes to the
 * database.</li>
 * </ol>
 * <br>
 * Example usage:
 *
 * <pre>
 *         public static void main(String[] args) {
 *                 Context.startup("jdbc:mysql://localhost:3306/db-name?autoReconnect=true", "openmrs-db-user", "3jknfjkn33ijt", new Properties());
 *                 try {
 *                         Context.openSession();
 *                         Context.authenticate("admin", "test");
 *                         List&lt;Patients&gt; patients = Context.getPatientService().getPatientsByName("Fred");
 *                         patients.get(0).setBirthdate(new Date());
 *                         Context.getPatientService().savePatient(patients.get(0));
 *                         ...
 *        }
 *                 finally {
 *                         Context.closeSession();
 *        }
 *    }
 * </pre>
 *
 * @see org.openmrs.api.context.UserContext
 * @see org.openmrs.api.context.ServiceContext
 */
public class Context {


        // Global resources
        private static ContextDAO contextDAO;

        private static Session mailSession;

        // Using "wrapper" (Object array) around UserContext to avoid ThreadLocal
        // bug in Java 1.5
        private static final ThreadLocal<Object[] /* UserContext */> userContextHolder = new ThreadLocal<>();

        private static volatile ServiceContext serviceContext;

        private static Properties runtimeProperties = new Properties();

        private static Properties configProperties = new Properties();

        private static AuthenticationScheme authenticationScheme;

        private static final Logger log = LoggerFactory.getLogger(Context.class);

        /**
         * Default public constructor
         */
        public Context() {
        }

        /**
         * Gets the context's data access object
         *
         * @return ContextDAO
         */
        static ContextDAO getContextDAO() {
                if (contextDAO == null) {
                        throw new APIException("error.context.null", (Object[]) null);
                }
                return contextDAO;
        }

        /**
         * Used to set the context's DAO for the application.
         *
         * @param dao ContextDAO to set
         */
        public void setContextDAO(ContextDAO dao) {
                setDAO(dao);
        }

        public static void setDAO(ContextDAO dao) {
                contextDAO = dao;
        }

        /**
         * Spring init method that sets the authentication scheme.
         */
        private static void setAuthenticationScheme() {

                authenticationScheme = new UsernamePasswordAuthenticationScheme();

                try {
                        authenticationScheme = Context.getServiceContext().getApplicationContext().getBean(AuthenticationScheme.class); // manual autowiring (from a module)
                        log.info("An authentication scheme override was provided. Using this one in place of the OpenMRS default authentication scheme.");
                }
                catch(NoUniqueBeanDefinitionException e) {
                        log.error("Multiple authentication schemes overrides are being provided, this is currently not supported. Sticking to OpenMRS default authentication scheme.");
                }
                catch(NoSuchBeanDefinitionException e) {
                        log.debug("No authentication scheme override was provided. Sticking to OpenMRS default authentication scheme.");
                }
                catch(BeansException e){
                        log.error("Fatal error encountered when injecting the authentication scheme override. Sticking to OpenMRS default authentication scheme.");
                }
        }

        /**
         * Loads a class with an instance of the OpenmrsClassLoader. Convenience method equivalent to
         * OpenmrsClassLoader.getInstance().loadClass(className);
         *
         * @param className the class to load
         * @return the class that was loaded
         * @throws ClassNotFoundException
         * <strong>Should</strong> load class with the OpenmrsClassLoader
         */
        public static Class<?> loadClass(String className) throws ClassNotFoundException {
                return OpenmrsClassLoader.getInstance().loadClass(className);
        }

        /**
         * Sets the user context on the thread local so that the service layer can perform
         * authentication/authorization checks.<br>
         * <br>
         * This is thread safe since it stores the given user context in ThreadLocal.
         *
         * @param ctx UserContext to set
         */
        public static void setUserContext(UserContext ctx) {
                log.trace("Setting user context {}", ctx);

                Object[] arr = new Object[] { ctx };
                userContextHolder.set(arr);
        }

        /**
         * Clears the user context from the threadlocal.
         */
        public static void clearUserContext() {
                log.trace("Clearing user context {}", Arrays.toString(userContextHolder.get()));

                userContextHolder.remove();
        }

        /**
         * Gets the user context from the thread local. This might be accessed by several threads at the
         * same time.
         *
         * @return The current UserContext for this thread.
         * <strong>Should</strong> fail if session hasn't been opened
         */
        public static UserContext getUserContext() {
                Object[] arr = userContextHolder.get();
                log.trace("Getting user context {} from userContextHolder {}", Arrays.toString(arr), userContextHolder);

                if (arr == null) {
                        log.trace("userContext is null.");
                        throw new APIException(
                                        "A user context must first be passed to setUserContext()...use Context.openSession() (and closeSession() to prevent memory leaks!) before using the API");
                }
                return (UserContext) userContextHolder.get()[0];
        }

        /**
         * Gets the currently defined service context. If one is not defined, one will be created and
         * then returned.
         *
         * @return the current ServiceContext
         */
        static ServiceContext getServiceContext() {
                if (serviceContext == null) {
                        synchronized (Context.class) {
                                if (serviceContext == null) {
                                        serviceContext = ServiceContext.getInstance();
                                }
                        }
                }
                return ServiceContext.getInstance();
        }

        /**
         * Sets the service context.
         *
         * @param ctx
         */
        public void setServiceContext(ServiceContext ctx) {
                setContext(ctx);
        }

        public static void setContext(ServiceContext ctx) {
                serviceContext = ctx;
        }

        /**
         * OpenMRS provides its default authentication scheme that authenticates via DAO with OpenMRS usernames and passwords.
         * 
         * Any module can provide an authentication scheme override by Spring wiring a custom implementation of {@link AuthenticationScheme}.
         * This method would return Core's default authentication scheme unless a Spring override is provided somewhere else.
         * 
         * @return The enforced authentication scheme.
         */
        public static AuthenticationScheme getAuthenticationScheme() {
                return authenticationScheme;
        }

        /**
         * @deprecated as of 2.3.0, replaced by {@link #authenticate(Credentials)}
         * 
         * Used to authenticate user within the context
         *
         * @param username user's identifier token for login
         * @param password user's password for authenticating to context
         * @throws ContextAuthenticationException
         * <strong>Should</strong> not authenticate with null username and password
         * <strong>Should</strong> not authenticate with null password
         * <strong>Should</strong> not authenticate with null username
         * <strong>Should</strong> not authenticate with null password and proper username
         * <strong>Should</strong> not authenticate with null password and proper system id
         */
        @Deprecated
        public static void authenticate(String username, String password) throws ContextAuthenticationException {
                authenticate(new UsernamePasswordCredentials(username, password));
        }

        /**
         * @param credentials
         * @throws ContextAuthenticationException
         * 
         * @since 2.3.0
         */
        public static Authenticated authenticate(Credentials credentials) throws ContextAuthenticationException {

                if (Daemon.isDaemonThread()) {
                        log.error("Authentication attempted while operating on a "
                                        + "daemon thread, authenticating is not necessary or allowed");
                        return new BasicAuthenticated(Daemon.getDaemonThreadUser(), "No auth scheme used by Context - Daemon user is always authenticated.");
                }

                if (credentials == null) {
                        throw new ContextAuthenticationException("Context cannot authenticate with null credentials.");
                }

                return getUserContext().authenticate(credentials);
        }

        /**
         * Refresh the authenticated user object in the current UserContext. This should be used when
         * updating information in the database about the current user and it needs to be reflecting in
         * the (cached) {@link #getAuthenticatedUser()} User object.
         *
         * @since 1.5
         * <strong>Should</strong> get fresh values from the database
         */
        public static void refreshAuthenticatedUser() {
                if (Daemon.isDaemonThread()) {
                        return;
                }
                log.debug("Refreshing authenticated user");

                getUserContext().refreshAuthenticatedUser();
        }

        /**
         * Become a different user. (You should only be able to do this as a superuser.)
         *
         * @param systemId
         * @throws ContextAuthenticationException
         * <strong>Should</strong> change locale when become another user
         */
        public static void becomeUser(String systemId) throws ContextAuthenticationException {
                log.info("systemId: {}", systemId);

                getUserContext().becomeUser(systemId);
        }

        /**
         * Get the runtime properties that this OpenMRS instance was started with
         *
         * @return copy of the runtime properties
         */
        public static Properties getRuntimeProperties() {
                Properties props = new Properties();
                if( runtimeProperties != null ) {
                        props.putAll(runtimeProperties);
                }
                return props;
        }

        /**
         * Set the runtime properties to be used by this OpenMRS instance
         *
         * @param props runtime properties
         */
        public static void setRuntimeProperties(Properties props) {
                runtimeProperties = props;
        }

        /**
         * @return concept dictionary-related services
         */
        public static ConceptService getConceptService() {
                return getServiceContext().getConceptService();
        }

        /**
         * @return encounter-related services
         */
        public static EncounterService getEncounterService() {
                return getServiceContext().getEncounterService();
        }

        /**
         * @return location services
         */
        public static LocationService getLocationService() {
                return getServiceContext().getLocationService();
        }

        /**
         * @return observation services
         */
        public static ObsService getObsService() {
                return getServiceContext().getObsService();
        }

        /**
         * @return patient-related services
         */
        public static PatientService getPatientService() {
                return getServiceContext().getPatientService();
        }

        public static CohortService getCohortService() {
                return getServiceContext().getCohortService();
        }

        /**
         * @return person-related services
         */
        public static PersonService getPersonService() {
                return getServiceContext().getPersonService();
        }

        /**
         * @return condition-related services
         * 
         * @since 2.2
         */
        public static ConditionService getConditionService(){
                return getServiceContext().getConditionService();
        }

        /**
         * @return diagnosis-related services
         *
         * @since 2.2
         */
        public static DiagnosisService getDiagnosisService(){
                return getServiceContext().getDiagnosisService();
        }

        /**
         * @return MedicationDispense-related service
         * @since 2.6.0
         */
        public static MedicationDispenseService getMedicationDispenseService(){
                return getServiceContext().getMedicationDispenseService();
        }

        /**
         * @return Returns the hl7Service.
         */
        public static HL7Service getHL7Service() {
                return getServiceContext().getHL7Service();
        }

        /**
         * @return user-related services
         */
        public static UserService getUserService() {
                return getServiceContext().getUserService();
        }

        /**
         * @return order service
         */
        public static OrderService getOrderService() {
                return getServiceContext().getOrderService();
        }

        /**
         * @return orderSet service
         * @since 1.12
         */
        public static OrderSetService getOrderSetService() {
                return getServiceContext().getOrderSetService();
        }

        /**
         * @return form service
         */
        public static FormService getFormService() {
                return getServiceContext().getFormService();
        }

        /**
         * @return serialization service
         * @since 1.5
         */
        public static SerializationService getSerializationService() {
                return getServiceContext().getSerializationService();
        }

        /**
         * @return logic service
         */
        public static LogicService getLogicService() {
                return getServiceContext().getLogicService();
        }

        /**
         * @return admin-related services
         */
        public static AdministrationService getAdministrationService() {
                return getServiceContext().getAdministrationService();
        }

        /**
         * @return MessageSourceService
         */
        public static MessageSourceService getMessageSourceService() {
                return getServiceContext().getMessageSourceService();
        }

        /**
         * @return scheduler service
         */
        public static SchedulerService getSchedulerService() {
                return getServiceContext().getSchedulerService();
        }

        /**
         * @return alert service
         */
        public static AlertService getAlertService() {
                return getServiceContext().getAlertService();
        }

        /**
         * @return program- and workflow-related services
         */
        public static ProgramWorkflowService getProgramWorkflowService() {
                return getServiceContext().getProgramWorkflowService();
        }
        
        /**
         * Get the message service.
         *
         * @return message service
         */
        public static MessageService getMessageService() {
                MessageService ms = getServiceContext().getMessageService();
                try {
                        // Message service dependencies
                        if (ms.getMessagePreparator() == null) {
                                ms.setMessagePreparator(getMessagePreparator());
                        }

                        if (ms.getMessageSender() == null) {
                                ms.setMessageSender(getMessageSender());
                        }

                }
                catch (Exception e) {
                        log.error("Unable to create message service due", e);
                }
                return ms;
        }

        /**
         * @return all of the configured properties that are used to configure the Mail Session in the Message Service
         * These properties are defined as all properties that are prefixed with "mail." and this will return all such
         * properties as defined in global properties, runtime properties, and/or system properties, with 
         * system properties overriding runtime properties overriding global properties.
         */
        public static Properties getMailProperties() {
                Properties p = new Properties();
                String prefix = "mail.";
                for (GlobalProperty gp : getAdministrationService().getGlobalPropertiesByPrefix(prefix)) {
                        // Historically, some mail properties defined with underscores, support these for legacy compatibility
                        if (gp.getProperty().equals("mail.transport_protocol")) {
                                p.setProperty("mail.transport.protocol", gp.getPropertyValue());
                        }
                        else if (gp.getProperty().equals("mail.smtp_host")) {
                                p.setProperty("mail.smtp.host", gp.getPropertyValue());
                        }
                        else if (gp.getProperty().equals("mail.smtp_port")) {
                                p.setProperty("mail.smtp.port", gp.getPropertyValue());
                        }
                        else if (gp.getProperty().equals("mail.smtp_auth")) {
                                p.setProperty("mail.smtp.auth", gp.getPropertyValue());
                        }
                        else {
                                p.setProperty(gp.getProperty(), gp.getPropertyValue());
                        }
                }
                for (String runtimeProperty : runtimeProperties.stringPropertyNames()) {
                        if (runtimeProperty.startsWith(prefix)) {
                                p.setProperty(runtimeProperty, runtimeProperties.getProperty(runtimeProperty));
                        }
                }
                for (String systemProperty : System.getProperties().stringPropertyNames()) {
                        if (systemProperty.startsWith(prefix)) {
                                p.setProperty(systemProperty, System.getProperty(systemProperty));
                        }
                }
                return p;
        }

        /**
         * Gets the mail session required by the mail message service. This function forces
         * authentication via the getAdministrationService() method call
         *
         * @return a java mail session
         */
        private static Session getMailSession() {
                if (mailSession == null) {
                        synchronized (Context.class) {
                                if (mailSession == null) {
                                        Authenticator auth = new Authenticator() {

                                                @Override
                                                public PasswordAuthentication getPasswordAuthentication() {
                                                        return new PasswordAuthentication(
                                                                ConfigUtil.getProperty("mail.user"),
                                                                ConfigUtil.getProperty("mail.password")
                                                        );
                                                }
                                        };
                                        mailSession = Session.getInstance(getMailProperties(), auth);
                                }
                        }
                }
                return mailSession;
        }

        /**
         * Convenience method to allow us to change the configuration more easily. TODO Ideally, we
         * would be using Spring's method injection to set the dependencies for the message service.
         *
         * @return the ServiceContext
         */
        private static MessageSender getMessageSender() {
                return new MailMessageSender(getMailSession());
        }

        /**
         * Convenience method to allow us to change the configuration more easily. TODO See todo for
         * message sender.
         *
         * @return
         */
        private static MessagePreparator getMessagePreparator() throws MessageException {
                return new VelocityMessagePreparator();
        }

        /**
         * @return "active" user who has been authenticated, otherwise <code>null</code>
         */
        public static User getAuthenticatedUser() {
                if (Daemon.isDaemonThread()) {
                        return Daemon.getDaemonThreadUser();
                }

                return getUserContext().getAuthenticatedUser();
        }

        /**
         * @return true if user has been authenticated in this context
         */
        public static boolean isAuthenticated() {
                if (Daemon.isDaemonThread()) {
                        return true;
                } else {
                        try {
                                return getAuthenticatedUser() != null;
                        } catch (APIException e) {
                                log.info("Could not get authenticated user inside called to isAuthenticated(), assuming no user context has been defined", e);
                                return false;
                        }
                }
        }

        /**
         * logs out the "active" (authenticated) user within context
         *
         * @see #authenticate
         * <strong>Should</strong> not fail if session hasn't been opened yet
         */
        public static void logout() {
                if (!isSessionOpen()) {
                        return; // fail early if there isn't even a session open
                }
                log.debug("Logging out : {}", getAuthenticatedUser());

                getUserContext().logout();

                // reset the UserContext object (usually cleared out by closeSession()
                // soon after this)
                setUserContext(new UserContext(getAuthenticationScheme()));
        }

        /**
         * Convenience method. Passes through to userContext.getAllRoles(User)
         */
        public static Set<Role> getAllRoles(User user) throws Exception {
                return getUserContext().getAllRoles();
        }

        /**
         * Tests whether the currently authenticated user has a particular privilege
         */
        public static boolean hasPrivilege(String privilege) {
                // the daemon threads have access to all things
                if (Daemon.isDaemonThread()) {
                        return true;
                }

                return getUserContext().hasPrivilege(privilege);
        }

        /**
         * Throws an exception if the currently authenticated user does not have the specified
         * privilege.
         *
         * @param privilege
         * @throws ContextAuthenticationException
         */
        public static void requirePrivilege(String privilege) throws ContextAuthenticationException {
                if (!hasPrivilege(privilege)) {
                        String errorMessage;
                        if (StringUtils.isNotBlank(privilege)) {
                                errorMessage = Context.getMessageSourceService().getMessage("error.privilegesRequired",
                                                new Object[] { privilege }, null);
                        } else {
                                //Should we even be here if the privilege is blank?
                                errorMessage = Context.getMessageSourceService().getMessage("error.privilegesRequiredNoArgs");
                        }

                        throw new ContextAuthenticationException(errorMessage);
                }
        }
        
        /**
         * Adds one or more privileges to the list of privileges that that {@link #hasPrivilege(String)} will
         * regard as available regardless of whether the user would otherwise have the privilege.
         * <p/>
         * This is useful for situations where a system process may need access to some piece of data that the
         * user would not otherwise have access to, like a GlobalProperty. <strong>This facility should not be
         * used to return data to the user that they otherwise would be unable to see.</strong>
         * <p/>
         * The expected usage is:
         * <p/>
         * <pre>{@code
         * try {
         *   Context.addProxyPrivilege(&quot;AAA&quot;);
         *   Context.get*Service().methodRequiringAAAPrivilege();
         * }
         * finally {
         *   Context.removeProxyPrivilege(&quot;AAA&quot;);
         * }}
         * </pre>
         * <p/>
         *
         * @param privilege privileges to add in string form
         * @see #hasPrivilege(String)
         * @see #removeProxyPrivilege(String)
         */
        public static void addProxyPrivilege(String privilege) {
                getUserContext().addProxyPrivilege(privilege);
        }
        
        /**
         * Adds one or more privileges to the list of privileges that that {@link #hasPrivilege(String)} will
         * regard as available regardless of whether the user would otherwise have the privilege.
         * <p/>
         * This is useful for situations where a system process may need access to some piece of data that the
         * user would not otherwise have access to, like a GlobalProperty. <strong>This facility should not be
         * used to return data to the user that they otherwise would be unable to see.</strong>
         * <p/>
         * The expected usage is:
         * <p/>
         * <pre>{@code
         * try {
         *   Context.addProxyPrivilege(&quot;AAA&quot;);
         *   Context.get*Service().methodRequiringAAAPrivilege();
         * }
         * finally {
         *   Context.removeProxyPrivilege(&quot;AAA&quot;);
         * }}
         * </pre>
         * <p/>
         *
         * @param privileges privileges to add in string form
         * @see #hasPrivilege(String)
         * @see #removeProxyPrivilege(String...)
         * @since 3.0.0, 2.8.2, 2.7.8
         */
        public static void addProxyPrivilege(String... privileges) {
                getUserContext().addProxyPrivilege(privileges);
        }

        /**
         * Removes one or more privileges from the list of privileges that that {@link #hasPrivilege(String)} will
         * regard as available regardless of whether the user would otherwise have the privilege.
         * <p/>
         * This is the compliment for {@link #addProxyPrivilege(String...)} to clean-up the context.
         * <p/>
         *
         * @param privilege privileges to remove in string form
         * @see #hasPrivilege(String)
         * @see #addProxyPrivilege(String)
         */
        public static void removeProxyPrivilege(String privilege) {
                getUserContext().removeProxyPrivilege(privilege);
        }

        /**
         * Removes a privilege from the list of privileges that that {@link #hasPrivilege(String)} will
         * regard as available regardless of whether the user would otherwise have the privilege.
         * <p/>
         * This is the compliment for {@link #addProxyPrivilege(String...)} to clean-up the context.
         * <p/>
         *
         * @param privileges privileges to remove in string form
         * @see #hasPrivilege(String)
         * @see #addProxyPrivilege(String...)
         * * @since 3.0.0, 2.8.2, 2.7.8
         */
        public static void removeProxyPrivilege(String... privileges) {
                getUserContext().removeProxyPrivilege(privileges);
        }

        /**
         * Convenience method. Passes through to {@link UserContext#setLocale(Locale)}
         */
        public static void setLocale(Locale locale) {
                getUserContext().setLocale(locale);
        }

        /**
         * Convenience method. Passes through to {@link UserContext#getLocale()}
         *
         * <strong>Should</strong> not fail if session hasn't been opened
         */
        public static Locale getLocale() {
                // if a session hasn't been opened, just fetch the default
                if (!isSessionOpen()) {
                        return LocaleUtility.getDefaultLocale();
                }

                return getUserContext().getLocale();
        }

        /**
         * Used to define a unit of work. All "units of work" should be surrounded by openSession and
         * closeSession calls.
         */
        public static void openSession() {
                log.trace("opening session");
                setUserContext(new UserContext(getAuthenticationScheme())); // must be cleared out in
                // closeSession()
                getContextDAO().openSession();
        }

        /**
         * Used to define a unit of work. All "units of work" should be surrounded by openSession and
         * closeSession calls.
         */
        public static void closeSession() {
                log.trace("closing session");
                clearUserContext(); // because we set a UserContext on the current
                // thread in openSession()
                getContextDAO().closeSession();
        }

        /**
         * Used to define a unit of work which does not require clearing out the currently authenticated
         * user. Remember to call closeSessionWithCurrentUser in a, preferably, finally block after this
         * work.
         *
         * @since 1.10
         */
        public static void openSessionWithCurrentUser() {
                getContextDAO().openSession();
        }

        /**
         * Used when the a unit of work which started with a call for openSessionWithCurrentUser has
         * finished. This should be in a, preferably, finally block.
         *
         * @since 1.10
         */
        public static void closeSessionWithCurrentUser() {
                getContextDAO().closeSession();
        }

        /**
         * Clears cached changes made so far during this unit of work without writing them to the
         * database. If you call this method, and later call closeSession() or flushSession() your
         * changes are still lost.
         */
        public static void clearSession() {
                log.trace("clearing session");
                getContextDAO().clearSession();
        }

        /**
         * Forces any changes made so far in this unit of work to be written to the database
         *
         * @since 1.6
         */
        public static void flushSession() {
                log.trace("flushing session");
                getContextDAO().flushSession();
        }

        /**
         * This method tells whether {@link #openSession()} has been called or not already. If it hasn't
         * been called, some methods won't work correctly because a {@link UserContext} isn't available.
         *
         * @return true if {@link #openSession()} has been called already.
         * @since 1.5
         * <strong>Should</strong> return true if session is closed
         */
        public static boolean isSessionOpen() {
                return userContextHolder.get() != null;
        }

        /**
         * Used to re-read the state of the given instance from the underlying database.
         * @since 2.0
         * @param obj The object to refresh from the database in the session
         */
        public static void refreshEntity(Object obj) {
                log.trace("refreshing object: {}", obj);
                getContextDAO().refreshEntity(obj);
        }

        /**
         * Used to clear a cached object out of a session in the middle of a unit of work. Future
         * updates to this object will not be saved. Future gets of this object will not fetch this
         * cached copy
         *
         * @param obj The object to evict/remove from the session
         */
        public static void evictFromSession(Object obj) {
                log.trace("clearing session");
                getContextDAO().evictFromSession(obj);
        }

        /**
         * Evicts the entity data for a particular entity instance.
         *
         * @param object entity instance to evict from the DB cache
         */
        public static void evictEntity(OpenmrsObject object) {
                log.debug("Clearing DB cache for entity: {} with id: {}", object.getClass(), object.getId());
                getContextDAO().evictEntity(object);
        }
        
        /**
         * Evicts all entity data of a particular class from the given region.
         * 
         * @param entityClass entity class to evict from the DB cache
         */
        public static void evictAllEntities(Class<?> entityClass) {
                log.debug("Clearing DB cache for entities of type: {}", entityClass);
                getContextDAO().evictAllEntities(entityClass);
        }
        
        /**
         * Evicts data from both DB and API cache.
         */
        public static void clearEntireCache() {
                log.debug("Clearing DB cache");
                getContextDAO().clearEntireCache();
                log.debug("Clearing API cache");
                getServiceContext().clearEntireApiCache();
        }
        
        /**
         * Starts the OpenMRS System Should be called prior to any kind of activity
         *
         * @param props Runtime properties to use for startup
         * @throws InputRequiredException if the {@link DatabaseUpdater} has determined that updates
         *             cannot continue without input from the user
         * @throws DatabaseUpdateException if database updates are required, see
         *             {@link DatabaseUpdater#executeChangelog()}
         * @throws ModuleMustStartException if a module that should be started is not able to
         * @see InputRequiredException#getRequiredInput() InputRequiredException#getRequiredInput() for
         *      the required question/datatypes
         */
        public static synchronized void startup(Properties props) throws DatabaseUpdateException, InputRequiredException,
        ModuleMustStartException {
                // do any context database specific startup
                getContextDAO().startup(props);

                if (getAdministrationService().isCoreSetupOnVersionChangeNeeded()) {
                        log.info("Detected core version change. Running core setup hooks and Liquibase.");
                        getAdministrationService().runCoreSetupOnVersionChange();
                }

                // this should be first in the startup routines so that the application
                // data directory can be set from the runtime properties
                OpenmrsUtil.startup(props);
                
                openSession();
                clearSession();

                // add any privileges/roles that /must/ exist for openmrs to work
                // correctly.
                checkCoreDataset();
                
                getContextDAO().setupSearchIndex();

                // Loop over each module and startup each with these custom properties
                ModuleUtil.startup(props);
        }

        /**
         * Starts the OpenMRS System in a _non-webapp_ environment<br>
         * <br>
         * <b>Note:</b> This method calls {@link Context#openSession()}, so you must call
         * {@link Context#closeSession()} somewhere on the same thread of this application so as to not
         * leak memory.
         *
         * @param url database url like "jdbc:mysql://localhost:3306/openmrs?autoReconnect=true"
         * @param username Connection username
         * @param password Connection password
         * @param properties Other startup properties
         * @throws InputRequiredException if the {@link DatabaseUpdater} has determined that updates
         *             cannot continue without input from the user
         * @throws DatabaseUpdateException if the database must be updated. See {@link DatabaseUpdater}
         * @throws ModuleMustStartException if a module that should start is not able to
         * @see #startup(Properties)
         * @see InputRequiredException#getRequiredInput() InputRequiredException#getRequiredInput() for
         *      the required question/datatypes
         */
        public static synchronized void startup(String url, String username, String password, Properties properties)
                        throws DatabaseUpdateException, InputRequiredException, ModuleMustStartException {
                if (properties == null) {
                        properties = new Properties();
                }

                properties.put("connection.url", url);
                properties.put("connection.username", username);
                properties.put("connection.password", password);
                setRuntimeProperties(properties);

                openSession(); // so that the startup method can use proxyPrivileges

                startup(properties);

                // start the scheduled tasks
                SchedulerUtil.startup(properties);

                closeSession();
        }

        /**
         * Stops the OpenMRS System Should be called after all activity has ended and application is
         * closing
         */
        public static void shutdown() {
                log.debug("Shutting down the scheduler");
                try {
                        // Needs to be shutdown before Hibernate
                        SchedulerUtil.shutdown();
                }
                catch (Exception e) {
                        log.warn("Error while shutting down scheduler service", e);
                }

                log.debug("Shutting down the modules");
                try {
                        ModuleUtil.shutdown();
                }
                catch (Exception e) {
                        log.warn("Error while shutting down module system", e);
                }

                log.debug("Shutting down the context");
                try {
                        ContextDAO dao = null;
                        try {
                                dao = getContextDAO();
                        }
                        catch (APIException e) {
                                // pass
                        }
                        if (dao != null) {
                                dao.shutdown();
                        }
                }
                catch (Exception e) {
                        log.warn("Error while shutting down context dao", e);
                }
        }

        /**
         * Used for getting services not in the previous get*Service() calls
         *
         * @param cls The Class of the service to get
         * @return The requested Service
         * <strong>Should</strong> return the same object when called multiple times for the same class
         */
        public static <T> T getService(Class<? extends T> cls) {
                return getServiceContext().getService(cls);
        }

        /**
         * Adds an AOP advisor around the given Class <code>cls</code>
         * <p>
         * Advisors can wrap around a method and effect the method before or after
         *
         * @param cls
         * @param advisor
         */
        public static void addAdvisor(Class cls, Advisor advisor) {
                getServiceContext().addAdvisor(cls, advisor);
        }

        /**
         * Adds an AOP advice object around the given Class <code>cls</code>
         * <p>
         * Advice comes in the form of before or afterReturning methods
         *
         * @param cls
         * @param advice
         */
        public static void addAdvice(Class cls, Advice advice) {
                getServiceContext().addAdvice(cls, advice);
        }

        /**
         * Removes the given AOP advisor from Class <code>cls</code>
         *
         * @param cls
         * @param advisor
         */
        public static void removeAdvisor(Class cls, Advisor advisor) {
                getServiceContext().removeAdvisor(cls, advisor);
        }

        /**
         * Removes the given AOP advice object from Class <code>cls</code>
         *
         * @param cls
         * @param advice
         */
        public static void removeAdvice(Class cls, Advice advice) {
                getServiceContext().removeAdvice(cls, advice);
        }

        /**
         * Runs through the core data (e.g. privileges, roles, and global properties) and adds them if
         * necessary.
         */
        public static void checkCoreDataset() {
                // setting core roles
                try {
                        Context.addProxyPrivilege(PrivilegeConstants.MANAGE_ROLES);
                        Set<String> currentRoleNames = new HashSet<>();
                        for (Role role : Context.getUserService().getAllRoles()) {
                                currentRoleNames.add(role.getRole().toUpperCase());
                        }
                        Map<String, String> map = OpenmrsUtil.getCoreRoles();
                        for (Map.Entry<String, String> entry : map.entrySet()) {
                                String roleName = entry.getKey();
                                if (!currentRoleNames.contains(roleName.toUpperCase())) {
                                        Role role = new Role();
                                        role.setRole(roleName);
                                        role.setDescription(entry.getValue());
                                        Context.getUserService().saveRole(role);
                                }
                        }
                }
                catch (Exception e) {
                        log.error("Error while setting core roles for openmrs system", e);
                }
                finally {
                        Context.removeProxyPrivilege(PrivilegeConstants.MANAGE_ROLES);
                }

                // setting core privileges
                try {
                        Context.addProxyPrivilege(PrivilegeConstants.MANAGE_PRIVILEGES);
                        Set<String> currentPrivilegeNames = new HashSet<>();
                        for (Privilege privilege : Context.getUserService().getAllPrivileges()) {
                                currentPrivilegeNames.add(privilege.getPrivilege().toUpperCase());
                        }
                        Map<String, String> map = OpenmrsUtil.getCorePrivileges();
                        for (Map.Entry<String, String> entry : map.entrySet()) {
                                String privilegeName = entry.getKey();
                                if (!currentPrivilegeNames.contains(privilegeName.toUpperCase())) {
                                        Privilege p = new Privilege();
                                        p.setPrivilege(privilegeName);
                                        p.setDescription(entry.getValue());
                                        Context.getUserService().savePrivilege(p);
                                }
                        }
                }
                catch (Exception e) {
                        log.error("Error while setting core privileges", e);
                }
                finally {
                        Context.removeProxyPrivilege(PrivilegeConstants.MANAGE_PRIVILEGES);
                }

                // setting core global properties
                try {
                        Context.addProxyPrivilege(PrivilegeConstants.MANAGE_GLOBAL_PROPERTIES);
                        Context.addProxyPrivilege(PrivilegeConstants.GET_GLOBAL_PROPERTIES);
                        Set<String> currentPropNames = new HashSet<>();
                        Map<String, GlobalProperty> propsMissingDescription = new HashMap<>();
                        Map<String, GlobalProperty> propsMissingDatatype = new HashMap<>();
                        for (GlobalProperty prop : Context.getAdministrationService().getAllGlobalProperties()) {
                                currentPropNames.add(prop.getProperty().toUpperCase());
                                if (prop.getDescription() == null) {
                                        propsMissingDescription.put(prop.getProperty().toUpperCase(), prop);
                                }
                                if (prop.getDatatypeClassname() == null) {
                                        propsMissingDatatype.put(prop.getProperty().toUpperCase(), prop);
                                }
                        }

                        for (GlobalProperty coreProp : OpenmrsConstants.CORE_GLOBAL_PROPERTIES()) {
                                String corePropName = coreProp.getProperty().toUpperCase();
                                // if the prop doesn't exist, save it
                                if (!currentPropNames.contains(corePropName)) {
                                        Context.getAdministrationService().saveGlobalProperty(coreProp);
                                        currentPropNames.add(corePropName); // add to list in case
                                        // of duplicates
                                } else {
                                        // if the prop is missing its description, update it
                                        GlobalProperty propToUpdate = propsMissingDescription.get(corePropName);
                                        if (propToUpdate != null) {
                                                propToUpdate.setDescription(coreProp.getDescription());
                                                Context.getAdministrationService().saveGlobalProperty(propToUpdate);
                                        }
                                        // set missing datatypes
                                        propToUpdate = propsMissingDatatype.get(corePropName);
                                        if (propToUpdate != null && coreProp.getDatatypeClassname() != null) {
                                                propToUpdate.setDatatypeClassname(coreProp.getDatatypeClassname());
                                                propToUpdate.setDatatypeConfig(coreProp.getDatatypeConfig());
                                                propToUpdate.setPreferredHandlerClassname(coreProp.getPreferredHandlerClassname());
                                                propToUpdate.setHandlerConfig(coreProp.getHandlerConfig());
                                                Context.getAdministrationService().saveGlobalProperty(propToUpdate);
                                        }
                                }
                        }
                }
                catch (Exception e) {
                        log.error("Error while setting core global properties", e);
                }
                finally {
                        Context.removeProxyPrivilege(PrivilegeConstants.MANAGE_GLOBAL_PROPERTIES);
                        Context.removeProxyPrivilege(PrivilegeConstants.GET_GLOBAL_PROPERTIES);
                }

                // setting default validation rule
                AdministrationService as = Context.getAdministrationService();
                Boolean disableValidation = Boolean.valueOf(as.getGlobalProperty(OpenmrsConstants.GP_DISABLE_VALIDATION, "false"));
                ValidateUtil.setDisableValidation(disableValidation);

                PersonName.setFormat(Context.getAdministrationService().getGlobalProperty(
                                OpenmrsConstants.GLOBAL_PROPERTY_LAYOUT_NAME_FORMAT));

                Allergen.setOtherNonCodedConceptUuid(Context.getAdministrationService().getGlobalProperty(
                                OpenmrsConstants.GP_ALLERGEN_OTHER_NON_CODED_UUID));
        }

        /**
         * Updates the openmrs database to the latest. This is only needed if using the API alone. <br>
         * <br>
         * The typical use-case would be: Try to {@link #startup(String, String, String, Properties)},
         * if that fails, call this method to get the database up to speed.
         *
         * @param userInput (can be null) responses from the user about needed input
         * @throws DatabaseUpdateException if an error occurred while updating
         * @since 1.5
         * @deprecated as of 2.4
         * 
         */
        @Deprecated
        public static void updateDatabase(Map<String, Object> userInput) throws DatabaseUpdateException {
                throw new UnsupportedOperationException("As of 2.4, this method is not longer implemented");
        }

        /**
         * Gets the simple date format for the current user's locale. The format will be similar in size
         * to mm/dd/yyyy
         *
         * @return SimpleDateFormat for the user's current locale
         * @see org.openmrs.util.OpenmrsUtil#getDateFormat(Locale)
         * <strong>Should</strong> return a pattern with four y characters in it
         */
        public static SimpleDateFormat getDateFormat() {
                return OpenmrsUtil.getDateFormat(getLocale());
        }

        /**
         * Gets the simple time format for the current user's locale. The format will be similar to
         * hh:mm a
         *
         * @return SimpleDateFormat for the user's current locale
         * @see org.openmrs.util.OpenmrsUtil#getTimeFormat(Locale)
         * <strong>Should</strong> return a pattern with two h characters in it
         */
        public static SimpleDateFormat getTimeFormat() {
                return OpenmrsUtil.getTimeFormat(getLocale());
        }

        /**
         * Gets the simple datetime format for the current user's locale. The format will be similar to
         * mm/dd/yyyy hh:mm a
         *
         * @return SimpleDateFormat for the user's current locale
         * @see org.openmrs.util.OpenmrsUtil#getDateTimeFormat(Locale)
         * <strong>Should</strong> return a pattern with four y characters and two h characters in it
         */
        public static SimpleDateFormat getDateTimeFormat() {
                return OpenmrsUtil.getDateTimeFormat(getLocale());
        }

        /**
         * @return true/false whether the service context is currently being refreshed
         * @see org.openmrs.api.context.ServiceContext#isRefreshingContext()
         */
        public static boolean isRefreshingContext() {
                return getServiceContext().isRefreshingContext();
        }

        /**
         * @since 1.5
         * @see ServiceContext#getRegisteredComponents(Class)
         */
        public static <T> List<T> getRegisteredComponents(Class<T> type) {
                return getServiceContext().getRegisteredComponents(type);
        }

        /**
         * @see ServiceContext#getRegisteredComponent(String, Class)
         * @since 1.9.4
         */
        public static <T> T getRegisteredComponent(String beanName, Class<T> type) throws APIException {
                return getServiceContext().getRegisteredComponent(beanName, type);
        }

        /**
         * @see ServiceContext#getModuleOpenmrsServices(String)
         * @since 1.9
         */
        public static List<OpenmrsService> getModuleOpenmrsServices(String modulePackage) {
                return getServiceContext().getModuleOpenmrsServices(modulePackage);
        }

        /**
         * @since 1.9
         * @see ServiceContext#getVisitService()
         */
        public static VisitService getVisitService() {
                return getServiceContext().getVisitService();
        }

        /**
         * @since 1.9
         * @see ServiceContext#getProviderService()
         */
        public static ProviderService getProviderService() {
                return getServiceContext().getProviderService();
        }

        /**
         * @since 1.9
         * @see ServiceContext#getDatatypeService()
         */
        public static DatatypeService getDatatypeService() {
                return getServiceContext().getDatatypeService();
        }

        /**
         * Add or replace a property in the config properties list
         *
         * @param key name of the property
         * @param value value of the property
         * @since 1.9
         */
        public static void addConfigProperty(Object key, Object value) {
                configProperties.put(key, value);
        }

        /**
         * Remove a property from the list of config properties
         *
         * @param key name of the property
         * @since 1.9
         */
        public static void removeConfigProperty(Object key) {
                configProperties.remove(key);
        }

        /**
         * Get the config properties that have been added to this OpenMRS instance
         *
         * @return copy of the module properties
         * @since 1.9
         */
        public static Properties getConfigProperties() {
                Properties props = new Properties();
                props.putAll(configProperties);
                return props;
        }

        /**
         * Updates the search index. It is a blocking operation, which may take even a few minutes
         * depending on the index size.
         * <p>
         * There is no need to call this method in normal usage since the index is automatically updated
         * whenever DB transactions are committed.
         * <p>
         * The method is designated to be used in tests, which rollback transactions. Note that if the
         * transaction is rolled back, changes to the index will not be reverted.
         *
         * @since 1.11
         */
        public static void updateSearchIndex() {
                getContextDAO().updateSearchIndex();
        }

        /**
         * Updates the search index. It is an asynchronous operation.
         * <p>
         * There is no need to call this method in normal usage since the index is automatically updated
         * whenever DB transactions are committed.
         * <p>
         *
         * @return object representing the result of the started asynchronous operation
         */
        public static Future<?> updateSearchIndexAsync() {
                return getContextDAO().updateSearchIndexAsync();
        }

        /**
         * It should be used <b>IN TESTS ONLY</b>. See {@link #updateSearchIndex(Class[])} for normal use.
         * <p>
         * Updates the search index for objects of the given type.
         *
         * @see #updateSearchIndex()
         * @see #updateSearchIndex(Class[]) 
         * @param type
         * @since 1.11
         */
        public static void updateSearchIndexForType(Class<?> type) {
                getContextDAO().updateSearchIndexForType(type);
        }

        /**
         * Updates the search index for objects of the given types using mass indexer.
         * 
         * @see #updateSearchIndex() 
         * @param types
         * @since 2.8.0
         */
        public static void updateSearchIndex(Class<?>... types) {
                getContextDAO().updateSearchIndex(types);
        }

        /**
         * Updates the search index for the given object.
         *
         * @see #updateSearchIndex()
         * @param object
         * @since 1.11
         */
        public static void updateSearchIndexForObject(Object object) {
                getContextDAO().updateSearchIndexForObject(object);
        }

        /**
         * @see org.openmrs.api.context.ServiceContext#setUseSystemClassLoader(boolean)
         * @since 1.10
         */
        public static void setUseSystemClassLoader(boolean useSystemClassLoader) {
                getServiceContext().setUseSystemClassLoader(useSystemClassLoader);
        }

        /**
         * @see org.openmrs.api.context.ServiceContext#isUseSystemClassLoader()
         * @since 1.10
         */
        public static boolean isUseSystemClassLoader() {
                return getServiceContext().isUseSystemClassLoader();
        }

        /**
         * @return a Connection from the OpenMRS database connection pool
         * @since 2.5.7
         */
        public static Connection getDatabaseConnection() {
                return getContextDAO().getDatabaseConnection();
        }
}

openmrs / openmrs-core / 20784346756

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