org.ensembl.healthcheck.testcase.compara.Meta.java Source code

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Here is the source code for org.ensembl.healthcheck.testcase.compara.Meta.java

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/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2018] EMBL-European Bioinformatics Institute
 * 
 * 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 org.ensembl.healthcheck.testcase.compara;

import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
import org.apache.commons.lang.StringUtils;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.Repair;
import org.ensembl.healthcheck.testcase.compara.AbstractComparaTestCase;
import org.ensembl.healthcheck.util.DBUtils;
import org.ensembl.healthcheck.util.Utils; // needed for stringInArray

/**
 * An EnsEMBL Healthcheck test case that looks for broken foreign-key relationships.
 */

public class Meta extends AbstractRepairableComparaTestCase {

    protected String getTableName() {
        return "meta";
    }

    protected String getAddQuery(String key, String value) {
        return "INSERT INTO meta VALUES (NULL, 1, \"" + key + "\", " + value + ");";
    }

    protected String getUpdateQuery(String key, String value) {
        return "UPDATE meta SET meta_value = " + value + " WHERE meta_key = \"" + key + "\";";
    }

    protected String getRemoveQuery(String key) {
        return "DELETE FROM meta WHERE meta_key = \"" + key + "\";";
    }

    /**
     * Create an ForeignKeyMethodLinkId that applies to a specific set of databases.
     */
    public Meta() {
        setDescription("Check meta table for the right schema version and species_id");
        setTeamResponsible(Team.COMPARA);
    }

    /**
     * Run the test.
     * 
     * @param dbre
     *          The database to use.
     * @return true if the test passed.
     * 
     */
    public boolean runTest(DatabaseRegistryEntry dbre) {

        boolean result = true;

        Connection con = dbre.getConnection();

        if (!DBUtils.checkTableExists(con, "meta")) {
            result = false;
            ReportManager.problem(this, con, "Meta table not present");
            return result;
        }

        // These methods return false if there is any problem with the test
        if (!isMasterDB(con)) {
            result &= checkSchemaVersionDBName(dbre);
        }

        return result;
    }

    /**
     * Check that the schema_version in the meta table is present and matches the database name.
     */
    private boolean checkSchemaVersionDBName(DatabaseRegistryEntry dbre) {

        boolean result = true;

        // get version from database name
        String dbNameVersion = dbre.getSchemaVersion();

        logger.finest("Schema version from database name: " + dbNameVersion);

        // get version from meta table
        Connection con = dbre.getConnection();

        // Get current global value from the meta table (used for backwards compatibility)
        String sql = "SELECT meta_key, meta_value" + " FROM meta WHERE meta_key = \"schema_version\"";
        try {
            Statement stmt = con.createStatement();
            ResultSet rs = stmt.executeQuery(sql);
            if (rs.first()) {
                if (rs.getInt(2) != new Integer(dbNameVersion).intValue()) {
                    EntriesToUpdate.put("schema_version", dbNameVersion);
                }
            } else {
                EntriesToAdd.put("schema_version", dbNameVersion);
            }
            rs.close();
            stmt.close();
        } catch (SQLException se) {
            se.printStackTrace();
            result = false;
        }

        return result;

    } // ---------------------------------------------------------------------

} // Meta