/*
 Copyright (C) 2004 EBI, GRL
 
 This library is free software; you can redistribute it and/or
 modify it under the terms of the GNU Lesser General Public
 License as published by the Free Software Foundation; either
 version 2.1 of the License, or (at your option) any later version.
 
 This library 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
 Lesser General Public License for more details.
 
 You should have received a copy of the GNU Lesser General Public
 License along with this library; if not, write to the Free Software
 Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 */

package org.ensembl.healthcheck.testcase.generic;

import java.sql.Connection;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;

/**
 * Healthcheck for the dna table.
 * Should be empty in an est database
 */

public class DNAEmpty extends SingleDatabaseTestCase {

    /**
     * Check the assembly_exception table.
     */
    public DNAEmpty() {
        addToGroup("post_genebuild");
        addToGroup("release");
        setDescription("Check that dna table is empty");
    }

    /**
     * Check the data in the assembly_exception table. Note referential
     * integrity checks are done in CoreForeignKeys.
     * 
     * @param dbre
     *          The database to use.
     * @return Result.
     */
    public boolean run(DatabaseRegistryEntry dbre) {

        boolean result = true;

        Connection con = dbre.getConnection();

        // check that seq_region_end > seq_region_start
        int rows = getRowCount(con, "SELECT COUNT(*) FROM dna");
        if (rows > 0) {
            result = false;
            ReportManager.problem(this, con, "dna table contains " + rows
                    + " - it should be empty");
        }


        if (result) {
            ReportManager.correct(this, con, "dna table is empty");
        }

        return result;

    }

    /**
     * This applies to all core schema databases apart from 'core'
     */
    public void types() {

        removeAppliesToType(DatabaseType.CORE);

    }


} // DNAEmpty

Test to check dna tables in non core, core schema dbs (eg. est and estgene) are empty (should be using core db as reference).
Test to check dna tables in non core, core schema dbs (eg. est and estgene)
are empty (should be using core db as reference).
