PositiveCoordinates.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.eg_core;

import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.Statement;
import java.util.HashSet;
import java.util.Set;

import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;

/**
 * @author mnuhn
 * 
 *         <p>
 *         Checks that that start and end coordinates of genes, transcripts,
 *         translations and the other tables specified in the attribute "table"
 *         are positive integers.
 *         </p>
 * 
 */
public class PositiveCoordinates extends AbstractEgCoreTestCase {

	protected String[] table = { "gene", "transcript", "translation",
			"protein_feature", "simple_feature", "exon", "dna_align_feature",
			"density_feature", "marker_feature", "misc_feature", "operon",
			"operon_transcript", "prediction_exon", "prediction_transcript",
			"protein_align_feature", "repeat_feature" };

	Set<String> just_seq_tables = new HashSet<String>() {
		{
			add("translation");
			add("protein_feature");
		}
	};

	protected String create_sql_for_table(String table) {

		String tableNamePrefix = "seq_region";

		if (just_seq_tables.contains(table)) {
			tableNamePrefix = "seq";
		}

		String sql = "select count(*) as c " + "from " + table + " where "
				+ tableNamePrefix + "_start<1 or " + tableNamePrefix
				+ "_end<1;";
		return sql;
	}

	@Override
	protected boolean runTest(DatabaseRegistryEntry dbre) {

		Connection con = dbre.getConnection();

		boolean passed = true;

		for (String currentTable : table) {

			String currentSql = create_sql_for_table(currentTable);

			try {
				Statement stmt = con.createStatement();
				ResultSet rs = stmt.executeQuery(currentSql);
				if (rs != null) {

					while (rs.next()) {

						int numProblemRows = rs.getInt("c");

						if (numProblemRows > 0) {

							ReportManager
									.problem(
											this,
											con,
											"The table "
													+ currentTable
													+ " has "
													+ numProblemRows
													+ " rows in which the start or "
													+ "end coordinates are not positive integers.");
							ReportManager.problem(this, con, "USEFUL SQL: "
									+ currentSql);
							passed = false;
						}
					}
				}
				rs.close();
				stmt.close();
			} catch (Exception e) {
				e.printStackTrace();
			}
		}
		return passed;
	}

	/*
	 * (non-Javadoc)
	 * 
	 * @see org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#
	 * getEgDescription()
	 */
	@Override
	protected String getEgDescription() {
		return "Checks that that start and end coordinates of genes, transcripts, translations " +
				"and the other tables specified in the attribute 'table' are positive integers.";
	}
}