Base.java

/* Generated by Together */

package org.ensembl.mart.lib.test;

import java.net.URL;
import java.sql.Connection;
import java.sql.SQLException;
import java.util.Properties;
import java.util.logging.Level;
import java.util.logging.Logger;

import junit.framework.TestCase;

import org.ensembl.mart.lib.DetailedDataSource;
import org.ensembl.mart.lib.Engine;
import org.ensembl.mart.lib.Query;

/**
 * Base class for tests that sets up the logging system if necessary. 
 * 
 * <ol>Loads these configuration files from classpath:
 *   <li>data/test_logging.conf - loads if it exists,otherwise
 * the logging level defaults to WARNING for all classes. Can be overridden
 * by setting the JVM parameter "java.util.logging.config.file".
 *   <li>data/test_connection.properties - mart db connection settings. 
 * Defaults to latest ensmart db on kaka.sanger.ac.uk if file unavailable.
 *   <li>data/test_connection_ensj.properties - database connection settings
 * for ensembl database. Needed to compare output from martj with ensj.
 *  </ol>
 */
public abstract class Base extends TestCase {

  private Logger logger = Logger.getLogger(Base.class.getName());

  public final static String UNITTESTDIR = "data/unitTests";
  protected final static String MARTJ_DB_CONFIG_URL = Base.UNITTESTDIR + "/connection.properties";
  private URL connectionconf;
  private Properties p = new Properties();
  
  protected String databaseType;
  protected String jdbcDriver;
  protected String host;
  protected String port;
  protected String databaseName;
  protected String schema;
  protected String user;
  protected String password;
  protected String connectionName;
  
  
  protected Engine engine;
  protected Query genequery = new Query();
  protected Query snpquery = new Query();
  protected DetailedDataSource martJDataSource;

  public void init() throws Exception {

    connectionconf = ClassLoader.getSystemResource(MARTJ_DB_CONFIG_URL);

    assertTrue("Failed to find connection configuration file: " + MARTJ_DB_CONFIG_URL.toString() + "\n", connectionconf != null);

    p.load(connectionconf.openStream());

    databaseType = p.getProperty("databaseType");
    if (databaseType == null) databaseType = DetailedDataSource.DEFAULTDATABASETYPE;

    host = p.getProperty("host");

    port = p.getProperty("port");
    if (port == null) port = DetailedDataSource.DEFAULTPORT;

    databaseName = p.getProperty("databaseName");

    user = p.getProperty("user");

    jdbcDriver = p.getProperty("jdbc_driver");
    if (jdbcDriver == null) jdbcDriver = DetailedDataSource.DEFAULTDRIVER;

    password = p.getProperty("password");

    String tmp = p.getProperty("connection");
    connectionName =
      (tmp != null && tmp.length() > 1) ? tmp : DetailedDataSource.defaultName(host, port, databaseName, schema,user);
  }

  public void setUp() throws Exception {
    super.setUp();
    
    init();

    martJDataSource =
      new DetailedDataSource(
        databaseType,
        host,
        port,
        databaseName,
		schema,
        user,
        password,
        DetailedDataSource.DEFAULTPOOLSIZE,
        jdbcDriver,
        connectionName);
    
    assertTrue("Cannot connect to null DataSource\n", martJDataSource != null);
    assertTrue("Could not connect to mart Database with " + MARTJ_DB_CONFIG_URL + "\n", connected(martJDataSource));
    
    engine = new Engine();

    genequery.setMainTables(
      new String[] { "hsapiens_gene_ensembl__gene__main", "hsapiens_gene_ensembl__transcript__main" });
    genequery.setPrimaryKeys(new String[] { "gene_id_key", "transcript_id_key" });
    genequery.setDataSource(martJDataSource);
    genequery.setDataset("hsapiens_gene_ensembl");

    snpquery.setMainTables(new String[] { "hsapiens_snp__snp__main" });
    snpquery.setPrimaryKeys(new String[] { "snp_id_key" });
    snpquery.setDataSource(martJDataSource);
    snpquery.setDataset("hsapiens_snp");
  }

  public boolean connected(DetailedDataSource dsource) {
    boolean connected = false;
    Connection conf = null;
    
    try {
      conf = dsource.getConnection();
      connected = true;
    } catch (SQLException e) {
      connected = false;
    } finally {
      DetailedDataSource.close(conf);
    }
    return connected;
  }
  
  public Base(String name) {
    super(name);
    String envVar = System.getProperty("java.util.logging.config.file");
    if (envVar == null)
      Logger.getLogger("").setLevel(Level.WARNING);
  }

}