/*
 * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
 * Copyright [2016-2017] 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.generic;

import java.sql.Connection;
import java.util.ArrayList;
import java.util.List;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;

/**
 * Check that transcript frameshift attributes have been calculated.
 */

public class FrameshiftAttributes extends SingleDatabaseTestCase {

	/**
	 * Create a new FrameshiftAttributes testcase.
	 */
	public FrameshiftAttributes() {

		setDescription("Check that transcript frameshift attributes have been calculated.");
		setTeamResponsible(Team.GENEBUILD);
	}

	/**
	 * Only applies to core dbs.
	 */
	public void types() {

		List types = new ArrayList();

		types.add(DatabaseType.CORE);
                types.add(DatabaseType.PRE_SITE);

		setAppliesToTypes(types);

	}

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

		boolean result = true;

		Connection con = dbre.getConnection();

		int rows = DBUtils
				.getRowCount(
						con,
						"SELECT COUNT(*) FROM attrib_type at, transcript_attrib ta WHERE at.attrib_type_id=ta.attrib_type_id AND at.code='Frameshift'");

		if (rows == 0) {

			ReportManager
					.problem(
							this,
							con,
							"No transcript frameshift attributes found\n --> make sure you ran script ensembl/misc_scripts/frameshift_transcript_attribs.pl");
			result = false;

		} else {

			ReportManager.correct(this, con, rows
					+ " transcript frameshift attributes found");

		}

		return result;

	} // run

	// ----------------------------------------------------------------------

} // ESTStableID