ubic.gemma.core.externalDb.GoldenPath.java Source code

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Here is the source code for ubic.gemma.core.externalDb.GoldenPath.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2006 University of British Columbia
 *
 * 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.
 *
 */
package ubic.gemma.core.externalDb;

import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.datasource.DriverManagerDataSource;
import ubic.gemma.model.common.description.DatabaseType;
import ubic.gemma.model.common.description.ExternalDatabase;
import ubic.gemma.model.genome.Taxon;
import ubic.gemma.persistence.util.Settings;

import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.SQLException;

/**
 * Perform useful queries against GoldenPath (UCSC) databases.
 *
 * @author pavlidis
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Possible external use
public class GoldenPath {

    static final Log log = LogFactory.getLog(GoldenPath.class);
    JdbcTemplate jdbcTemplate;
    private ExternalDatabase searchedDatabase;
    private String databaseName = null;
    private Taxon taxon;
    private int port;
    private String host;
    private String user;
    private String password;
    private String url;

    /**
     * Get golden path for the default database (human);
     */
    public GoldenPath() {
        this.taxon = Taxon.Factory.newInstance();
        taxon.setCommonName("human");
        this.readConfig();
    }

    public GoldenPath(int port, String databaseName, String host, String user, String password) {
        this.databaseName = databaseName;

        this.getTaxonForDbName(databaseName);

        this.port = port;
        this.host = host;
        this.user = user;
        this.password = password;

        this.init();
    }

    public GoldenPath(String databaseName) {
        this.getTaxonForDbName(databaseName);
        this.readConfig();
    }

    public GoldenPath(Taxon taxon) {
        this.taxon = taxon;
        this.readConfig();
    }

    public String getDatabaseName() {
        return databaseName;
    }

    public JdbcTemplate getJdbcTemplate() {
        return jdbcTemplate;
    }

    public ExternalDatabase getSearchedDatabase() {
        return searchedDatabase;
    }

    public Taxon getTaxon() {
        return taxon;
    }

    protected Connection getConnection() {
        try {
            return DriverManager.getConnection(url, user, password);
        } catch (SQLException e) {
            throw new RuntimeException(e);
        }
    }

    void init() {
        assert databaseName != null;
        DriverManagerDataSource dataSource = new DriverManagerDataSource();

        this.url = "jdbc:mysql://" + host + ":" + port + "/" + databaseName + "?relaxAutoCommit=true";
        GoldenPath.log.info("Connecting to " + databaseName);
        GoldenPath.log.debug("Connecting to Golden Path : " + url + " as " + user);

        dataSource.setDriverClassName(this.getDriver());
        dataSource.setUrl(url);
        dataSource.setUsername(user);
        dataSource.setPassword(password);

        jdbcTemplate = new JdbcTemplate(dataSource);
        jdbcTemplate.setFetchSize(50);

    }

    private String getDriver() {
        String driver = Settings.getString("gemma.goldenpath.db.driver");
        if (StringUtils.isBlank(driver)) {
            driver = Settings.getString("gemma.db.driver");
            GoldenPath.log
                    .warn("No DB driver configured for GoldenPath, falling back on gemma.db.driver=" + driver);
        }
        return driver;
    }

    private void getTaxonForDbName(String dbname) {
        // This is a little dumb
        this.taxon = Taxon.Factory.newInstance();
        if (dbname.startsWith("hg")) {
            taxon.setCommonName("human");
        } else if (dbname.startsWith("mm")) {
            taxon.setCommonName("mouse");
        } else if (dbname.startsWith("rn")) {
            taxon.setCommonName("rat");
        } else {
            throw new IllegalArgumentException("Cannot infer taxon for " + dbname);
        }
    }

    private void readConfig() {
        if (taxon == null)
            throw new IllegalStateException("Taxon cannot be null");
        String commonName = taxon.getCommonName();
        switch (commonName) {
        case "mouse":
            databaseName = Settings.getString("gemma.goldenpath.db.mouse");
            break;
        case "human":
            databaseName = Settings.getString("gemma.goldenpath.db.human");
            break;
        case "rat":
            databaseName = Settings.getString("gemma.goldenpath.db.rat");
            break;
        default:
            throw new IllegalArgumentException("No GoldenPath database for  " + taxon);
        }

        this.host = Settings.getString("gemma.goldenpath.db.host");
        try {
            this.port = Integer.valueOf(Settings.getString("gemma.goldenpath.db.port"));
        } catch (NumberFormatException e) {
            throw new RuntimeException("Could not get configuration of port for goldenpath database");
        }

        this.user = Settings.getString("gemma.goldenpath.db.user");
        this.password = Settings.getString("gemma.goldenpath.db.password");

        searchedDatabase = ExternalDatabase.Factory.newInstance();
        searchedDatabase.setName(databaseName);
        searchedDatabase.setType(DatabaseType.SEQUENCE);

        this.init();

    }

}