AssemblyMapping.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.
 */

/**
 * AssemblyMapping
 * 
 * @author dstaines
 * @author $Author$
 * @version $Revision$
 */
package org.ensembl.healthcheck.testcase.generic;

import java.util.List;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

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.AbstractTemplatedTestCase;
import org.ensembl.healthcheck.util.SqlTemplate;
import org.ensembl.healthcheck.util.StringListMapRowMapper;

/**
 * Test to ensure assembly.mapping meta value refers to existent coordinate
 * systems
 * 
 * @author dstaines
 * 
 */
public class AssemblyMapping extends AbstractTemplatedTestCase {

	private final static String CS_SQL = "select name,version from coord_system where species_id=?";
	private final static String ASS_MAP_SQL = "select meta_value from meta where meta_key='assembly.mapping' and species_id=?";
	private final static Pattern ASS_MAP = Pattern.compile("([^:]+)(:(.+))?");

	public AssemblyMapping() {
		super();
		this.appliesToType(DatabaseType.CORE);
		this.setDescription("Test to make sure that the coord_systems and versions referred to in assembly.mapping exist");
                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);

        }

	/*
	 * (non-Javadoc)
	 * 
	 * @see
	 * org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#runTest(org
	 * .ensembl.healthcheck.DatabaseRegistryEntry)
	 */
	@Override
	protected boolean runTest(DatabaseRegistryEntry dbre) {
		SqlTemplate templ = getSqlTemplate(dbre);
		boolean result = true;
		for (int speciesId : dbre.getSpeciesIds()) {
			// 1. get coord_systems
			Map<String, List<String>> cs = templ.queryForMap(CS_SQL,
					new StringListMapRowMapper(), speciesId);
			// 2. get assembly mapping
			List<String> assMap = templ.queryForDefaultObjectList(ASS_MAP_SQL,
					String.class, speciesId);
                        for (String map : assMap) {
        			for (String mapElem : map.split("[#|]")) {
	        			Matcher m = ASS_MAP.matcher(mapElem);
		        		if (m.matches()) {
			        		if (m.groupCount() == 3) {
				        		String name = m.group(1);
					        	String version = m.group(3);
						        List<String> versions = cs.get(name);
        						if (versions == null) {
	        						ReportManager.problem(this, dbre.getConnection(),
									"No coordinate system named '" + name
											+ "' found for mapping " + assMap);
		        					result = false;
			        			} else {
				        			if (!versions.contains(version)) {
					        			ReportManager.problem(this,
										dbre.getConnection(),
										"No coordinate system named '" + name
												+ "' with version " + version
												+ " found for mapping "
												+ assMap);
						        		result = false;
        							}
	        					}
        					} else {
	        					ReportManager
								.problem(
										this,
										dbre.getConnection(),
										"Could not parse assembly mapping element "
												+ mapElem
												+ " from "
												+ assMap
												+ " does not match the expected pattern "
												+ ASS_MAP.pattern());
		        				result = false;
        					}
	        			} else {
		        			ReportManager.problem(this, dbre.getConnection(),
							"Assembly mapping element " + mapElem + " from "
									+ assMap
									+ " does not match the expected pattern "
									+ ASS_MAP.pattern());
			        		result = false;
				        }
        			}
                        }
		}
		return result;
	}

}