AssemblySeqregion.java

/*
 * 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.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;

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 the assembly table and seq_region table are consistent.
 */
public class AssemblySeqregion extends SingleDatabaseTestCase {

	/**
	 * Create a new AssemlySeqregion test case.
	 */
	public AssemblySeqregion() {

		setDescription("Check that the chromosome lengths from the seq_region table agree with both the assembly table and the karyotype table.");
		setTeamResponsible(Team.GENEBUILD);
	}

	/**
	 * Data is only tested in core database, as the tables are in sync
	 */
	public void types() {

		removeAppliesToType(DatabaseType.OTHERFEATURES);
		removeAppliesToType(DatabaseType.ESTGENE);
		removeAppliesToType(DatabaseType.RNASEQ);
		removeAppliesToType(DatabaseType.CDNA);

	}

	/**
	 * @param dbre
	 *            The database to use.
	 * @return The test case result.
	 */
	public boolean run(DatabaseRegistryEntry dbre) {

		boolean result = true;

		Connection con = dbre.getConnection();

		// ---------------------------------------------------
		// Find any seq_regions that have different lengths in seq_region &
		// assembly
		// NB seq_region length should always be equal to (or possibly greater
		// than) the maximum
		// assembly length
		// The SQL returns failures
		// ----------------------------------------------------
		String sql = "SELECT sr.name AS name, sr.length, cs.name AS coord_system "
				+ "FROM seq_region sr, assembly ass, coord_system cs "
				+ "WHERE sr.coord_system_id=cs.coord_system_id "
				+ "AND ass.asm_seq_region_id = sr.seq_region_id "
				+ "GROUP BY ass.asm_seq_region_id "
				+ "HAVING sr.length < MAX(ass.asm_end)";

		try {

			Statement stmt = con.createStatement();
			ResultSet rs = stmt.executeQuery(sql);
			int i = 0;
			while (rs.next() && i++ < 50) {
				result = false;
				String cs = rs.getString("coord_system");
				String sr = rs.getString("name");
				ReportManager.problem(this, con, cs + " " + sr
						+ " is shorter in seq_region than in assembly");
			}
			if (i == 0) {
				ReportManager
						.correct(
								this,
								con,
								"Sequence region lengths are equal or greater in the seq_region table compared to the assembly table");
			}
		} catch (SQLException e) {
			System.err.println("Error executing " + sql + ":");
			e.printStackTrace();
		}

		int cs = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM coord_system");
		if (cs > 1) {
			int rows = DBUtils
					.getRowCount(con, "SELECT COUNT(*) FROM assembly");
			if (rows == 0) {
				ReportManager.problem(this, con, rows
						+ " rows found in assembly table");
			} else {
				ReportManager.correct(this, con, "Assembly table is populated");

				// -------------------------------------------------------
				// check various other things about the assembly table
				// Check for mismatched lengths of assembled and component
				// sides.
				// ie where (asm_end - asm_start + 1) != (cmp_end - cmp_start +
				// 1)
				rows = DBUtils
						.getRowCount(
								con,
								"SELECT COUNT(*) FROM assembly WHERE (asm_end - asm_start + 1) != (cmp_end - cmp_start + 1)");
				if (rows > 0) {
					ReportManager
							.problem(
									this,
									con,
									rows
											+ " rows in assembly table have mismatched lengths of assembled and component sides");
				} else {
					ReportManager
							.correct(
									this,
									con,
									"All rows in assembly table have matching lengths of assembled and component sides");
				}

				// check for start/end < 1
				rows = DBUtils
						.getRowCount(
								con,
								"SELECT COUNT(*) FROM assembly WHERE asm_start < 1 OR asm_end < 1 OR cmp_start < 1 OR cmp_end < 1");
				if (rows > 0) {
					ReportManager
							.problem(
									this,
									con,
									rows
											+ " rows in assembly table have start or end coords < 1");
				} else {
					ReportManager
							.correct(this, con,
									"All rows in assembly table have start and end coords > 0");
				}

				// check for end < start
				rows = DBUtils
						.getRowCount(
								con,
								"SELECT COUNT(*) FROM assembly WHERE asm_end < asm_start OR cmp_end < cmp_start");
				if (rows > 0) {
					ReportManager
							.problem(
									this,
									con,
									rows
											+ " rows in assembly table have start or end coords < 1");
				} else {
					ReportManager
							.correct(this, con,
									"All rows in assembly table have end coords > start coords");
				}
			}
		}

		return result;

	} // run

} // ChromosomeLengths