/*
 * 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_compara;

import java.util.List;

import org.apache.commons.lang.StringUtils;
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;

public class EGMethodLinkSpeciesSetIdStats extends
		AbstractTemplatedTestCase {

	private final static String QUERY = "SELECT method_link_species_set_id FROM "
			+ "(SELECT mlss.method_link_species_set_id, tc.stats_related_tags "
			+ "FROM method_link_species_set mlss "
			+ "INNER JOIN method_link ml ON mlss.method_link_id = ml.method_link_id "
			+ "LEFT JOIN (SELECT count(*) stats_related_tags, method_link_species_set_id "
			+ "FROM method_link_species_set_tag WHERE tag IN "
			+ "('non_ref_coding_exon_length', 'non_ref_genome_coverage','non_ref_genome_length', "
			+ "'non_ref_insertions', 'non_ref_matches', 'non_ref_mis_matches', 'non_ref_uncovered', "
			+ "'ref_coding_exon_length', 'ref_genome_coverage', 'ref_genome_length', 'ref_insertions', "
			+ "'ref_matches', 'ref_mis_matches', 'ref_uncovered') "
			+ "GROUP BY method_link_species_set_id) as tc "
			+ "ON mlss.method_link_species_set_id = tc.method_link_species_set_id "
			+ "WHERE ml.type IN ('BLASTZ_NET', 'LASTZ_NET', 'TRANSLATED_BLAT_NET', 'ATAC') "
			+ "HAVING (stats_related_tags != 14) OR (stats_related_tags IS NULL)) as find_missing_stats";

	public EGMethodLinkSpeciesSetIdStats() {
		setTeamResponsible(Team.ENSEMBL_GENOMES);
		appliesToType(DatabaseType.COMPARA);
		setDescription("Checks whether stats have been generated for all MLSSs");
	}

	@Override
	protected boolean runTest(DatabaseRegistryEntry dbre) {
		boolean result = true;
		final List<String> mlsss = getTemplate(dbre).queryForDefaultObjectList(
				QUERY, String.class);
		if (mlsss.size() > 0) {
			ReportManager.problem(
					this,
					dbre.getConnection(),
					"MLSSs found with no statistics: "
							+ StringUtils.join(mlsss, ","));
			result = false;
		}
		return result;
	}

}