uk.ac.ebi.arrayexpress.components.XmlDbConnectionPool.java Source code

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Here is the source code for uk.ac.ebi.arrayexpress.components.XmlDbConnectionPool.java

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package uk.ac.ebi.arrayexpress.components;

import java.util.Map;

import org.apache.commons.configuration.HierarchicalConfiguration;
import org.basex.server.ClientSession;
import org.basex.server.Session;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xmldb.api.DatabaseManager;
import org.xmldb.api.base.Collection;
import org.xmldb.api.base.Database;
import org.xmldb.api.base.XMLDBException;

import uk.ac.ebi.arrayexpress.app.Application;
import uk.ac.ebi.arrayexpress.app.ApplicationComponent;

/*
 * Copyright 2009-2011 European Molecular Biology Laboratory
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 *
 */

public class XmlDbConnectionPool extends ApplicationComponent {
    // logging machinery
    private final Logger logger = LoggerFactory.getLogger(getClass());

    private String driverXml;
    private String connectionString;
    private Database db;
    private Collection coll;

    public void initialize() throws Exception {
        HierarchicalConfiguration connsConf = (HierarchicalConfiguration) Application.getInstance().getPreferences()
                .getConfSubset("bs.xmldatabase");

        if (null != connsConf) {
            driverXml = connsConf.getString("driver");
            //         connectionString = connsConf.getString("connectionstring");
            connectionString = connsConf.getString("base") + "://" + connsConf.getString("host") + ":"
                    + connsConf.getString("port") + "/" + connsConf.getString("dbname");
            logger.debug("connectionString->" + connectionString);
        } else {
            logger.error("bs.xmldatabase Configuration is missing!!");
        }

        Class<?> c;
        try {

            //TODO: rpe: review this (DB open files)
            if (coll != null) {
                coll.close();
                db = null;
            }

            c = Class.forName(driverXml);

            // Class<?> c = Class.forName("org.exist.xmldb.DatabaseImpl");
            db = (Database) c.newInstance();
            DatabaseManager.registerDatabase(db);
            coll = DatabaseManager.getCollection(connectionString);

            if (coll == null) {
                logger.error("Unable to get collection from " + connectionString);
            }

        } catch (XMLDBException e) {
            // TODO Auto-generated catch block
            logger.error("Exception:->[{}]", e.getMessage());
            e.printStackTrace();
        } catch (ClassNotFoundException e) {
            // TODO Auto-generated catch block
            logger.error("Exception:->[{}]", e.getMessage());
            e.printStackTrace();
        }
        // Receive the database
        catch (InstantiationException e) {
            // TODO Auto-generated catch block
            logger.error("Exception:->[{}]", e.getMessage());
            e.printStackTrace();
        } catch (IllegalAccessException e) {
            // TODO Auto-generated catch block
            logger.error("Exception:->[{}]", e.getMessage());
            e.printStackTrace();
        }
    }

    public void terminate() throws Exception {
        coll.close();
    }

    public Collection getCollection() throws Exception {
        return coll;
    }

    public String getDBInfo(String dbHost, int dbPort, String dbPassword, String originalDbName) {
        String ret = "";
        try {

            logger.debug("* Create a client session int the Xml Database to get information about it.");

            Session session = new ClientSession(dbHost, dbPort, "admin", dbPassword);

            // ------------------------------------------------------------------------
            // Create a database
            logger.debug("* open database.");
            String logs = "";

            logs = session.execute("open " + originalDbName);
            logger.debug("open ...->" + logs);
            ret = session.execute("info db ");
            // logger.debug("info db ...->" + logs);
            logs = session.execute("close");
            logger.debug("close ...->" + logs);

            logger.debug("* Close the client session.");
            session.close();

            ret = "<table><tr><td valign='top'><u>XmlDatabase</u></td><td>" + ret + "</td></tr></table>";
        }

        catch (Exception ex) {
            // Handle exceptions
            ret = "ERROR";
            logger.error("Exception:->[{}]", ex.getMessage());
            ex.printStackTrace();
        } finally {

        }
        return ret;

    }

    public String getDBInfo() {
        String ret = "";
        try {

            logger.debug("* Create a client session int the Xml Database to get information about it.");

            String dbHost = Application.getInstance().getPreferences().getString("bs.xmldatabase.host");
            String dbPort = Application.getInstance().getPreferences().getString("bs.xmldatabase.port");
            String dbPassword = Application.getInstance().getPreferences()
                    .getString("bs.xmldatabase.adminpassword");

            String originalDbName = Application.getInstance().getPreferences().getString("bs.xmldatabase.dbname");
            ret = getDBInfo(dbHost, Integer.parseInt(dbPort), dbPassword, originalDbName);
        }

        catch (Exception ex) {
            // Handle exceptions
            ret = "ERROR - The BaseXServer is not available";
            logger.error("Exception:->[{}]", ex.getMessage());
            ex.printStackTrace();
        } finally {

        }
        return ret;

    }

    @Override
    public String getMetaDataInformation() {
        return getDBInfo();
    }

}