es.uvigo.ei.sing.rubioseq.gui.util.DBInitializer.java Source code

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Here is the source code for es.uvigo.ei.sing.rubioseq.gui.util.DBInitializer.java

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/*
   This file is part of RUbioSeq-GUI.
    
   RUbioSeq-GUI is free software: you can redistribute it and/or modify
   it under the terms of the GNU General Public License as published by
   the Free Software Foundation, either version 3 of the License, or
   (at your option) any later version.
    
   RUbioSeq-GUI is distributed in the hope that it will be useful,
   but WITHOUT ANY WARRANTY; without even the implied warranty of
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
   GNU General Public License for more details.
    
   You should have received a copy of the GNU General Public License
   along with RUbioSeq-GUI.  If not, see <http://www.gnu.org/licenses/>.
*/
package es.uvigo.ei.sing.rubioseq.gui.util;

import java.util.LinkedList;
import java.util.List;

import javax.persistence.EntityManager;
import javax.persistence.EntityManagerFactory;
import javax.persistence.EntityTransaction;
import javax.persistence.Persistence;
import javax.servlet.ServletContextEvent;
import javax.servlet.ServletContextListener;

import org.apache.commons.codec.digest.DigestUtils;

import es.uvigo.ei.sing.rubioseq.DataStore;
import es.uvigo.ei.sing.rubioseq.DataStoreMode;
import es.uvigo.ei.sing.rubioseq.DataStoreType;
import es.uvigo.ei.sing.rubioseq.RUbioSeqConfiguration;
import es.uvigo.ei.sing.rubioseq.User;

/**
 * This class is responsible for the initializacion of the BD. See method 
 * initDatabase() for more information.
 * 
 * @author hlfernandez
 */
public class DBInitializer implements ServletContextListener {

    @Override
    public void contextDestroyed(ServletContextEvent arg0) {
    }

    /**
     * This method is responsible for the initializacion of the BD, that is:
     * - Creating the default RUbioSeqConfiguration.
     * - Creating the default users.
     * - Creating a datastore pointing to "/" for the admin user.
     * 
     * This method also plays a key role in the deployment of the application 
     * since it prints the message "[DBInitializer] DB initialized." which is
     * triggered by the launch-rubioseq-gui.sh in order to know that the app. is
     * deployed and launch a browser.
     * 
     * @author hlfernandez
     */
    static void initDatabase() {
        System.out.println("[DBInitializer] Initializing DB ...");

        EntityManagerFactory emf = Persistence.createEntityManagerFactory("rubioseq-database");
        EntityManager em = emf.createEntityManager();
        EntityTransaction tx = null;
        try {
            /*
             * Store Global Configuration
             */
            if (em.createQuery("SELECT u FROM RUbioSeqConfiguration u").getResultList().size() == 0) {
                RUbioSeqConfiguration config = new RUbioSeqConfiguration();
                config.setRubioseqCommand("/opt/RUbioSeq3.7/RUbioSeq.pl");
                config.setPrivateDatastoresRootDirectory("/path/to/private/datastores/root");
                config.setCreatePrivateDatastoresOnUserRegistration(false);

                tx = em.getTransaction();
                try {
                    tx.begin();
                    em.persist(config);
                    tx.commit();
                } finally {
                    if (tx != null && tx.isActive()) {
                        tx.rollback();
                    }
                }
            }
            /*
             * Create Default Users
             */
            if (em.createQuery("SELECT u FROM User u").getResultList().size() == 0) {
                User user = new User();
                user.setUsername("rubiosequser");
                user.setPassword(DigestUtils.md5Hex("rubioseqpass"));
                user.setAdmin(false);
                user.setEmail("rubiosequser@rubioseg.org");

                tx = em.getTransaction();
                try {
                    tx.begin();
                    em.persist(user);
                    tx.commit();
                } finally {
                    if (tx != null && tx.isActive()) {
                        tx.rollback();
                    }
                }

                user = new User();
                user.setUsername("admin");
                user.setPassword(DigestUtils.md5Hex("admin"));
                user.setAdmin(true);
                user.setEmail("rubiosequser@rubioseg.org");

                tx = em.getTransaction();
                try {
                    tx.begin();
                    em.persist(user);
                    tx.commit();
                } finally {
                    if (tx != null && tx.isActive()) {
                        tx.rollback();
                    }
                }
            }
            /*
             * Create Default Datastores
             */
            boolean createDefaultAdminDatastore = true;
            List<User> adminUsers = getAdminUsers(em);
            @SuppressWarnings("unchecked")
            List<DataStore> datastores = (List<DataStore>) em.createQuery("SELECT d FROM DataStore d")
                    .getResultList();
            for (User adminUser : adminUsers) {
                if (datastores.size() == 0) {
                    createDefaultAdminDatastore = true;
                } else {
                    for (DataStore d : datastores) {
                        if (d.getUser() != null && d.getUser().equals(adminUser) && d.getPath().equals("/")) {
                            createDefaultAdminDatastore = false;
                        }
                    }
                }
                if (createDefaultAdminDatastore) {
                    DataStore adminDS = new DataStore();
                    adminDS.setUser(adminUser);
                    adminDS.setPath("/");
                    adminDS.setMode(DataStoreMode.Private);
                    adminDS.setType(DataStoreType.Input_Output);
                    adminDS.setName(adminUser.getUsername() + "_default");

                    tx = em.getTransaction();
                    try {
                        tx.begin();
                        em.persist(adminDS);
                        tx.commit();
                    } finally {
                        if (tx != null && tx.isActive()) {
                            tx.rollback();
                        }
                    }
                }
            }
        } finally {
            em.close();
        }

        System.out.println("[DBInitializer] DB initialized.");
    }

    @SuppressWarnings("unchecked")
    private static List<User> getAdminUsers(EntityManager em) {
        List<User> toret = new LinkedList<User>();
        for (User u : (List<User>) em.createQuery("SELECT u FROM User u").getResultList()) {
            if (u.isAdmin()) {
                toret.add(u);
            }
        }
        return toret;
    }

    public void contextInitialized(ServletContextEvent servletContextEvent) {
        initDatabase();
    }

    public static EntityManager getRUbioSeqEntityMananger() {
        EntityManagerFactory emf = Persistence.createEntityManagerFactory("rubioseq-database");
        EntityManager em = emf.createEntityManager();
        return em;
    }

}