MLSSTagGERPMSA.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.compara;

import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashMap;
import java.util.Iterator;
import org.apache.commons.lang.StringUtils;

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

/**
 * An EnsEMBL Healthcheck test case that looks for broken foreign-key relationships.
 */

public class MLSSTagGERPMSA extends AbstractRepairableMLSSTag {

	public String getTagToCheck() {
		return "msa_mlss_id";
	}


	/**
	 * Create an ForeignKeyMethodLinkId that applies to a specific set of databases.
	 */
	public MLSSTagGERPMSA() {
		appliesToType(DatabaseType.COMPARA);
		setDescription("Tests that proper max_alignment_length have been defined.");
		setDescription("Check method_link_species_set_tag table for the right GERP <-> MSA links and max alignment lengths");
		setTeamResponsible(Team.COMPARA);
	}


	/**
	 * Check that the each conservation score MethodLinkSpeciesSet obejct has a link to a multiple alignment MethodLinkSpeciesSet in
	 * the method_link_species_set_tag table.
	 */
	protected boolean runTest(DatabaseRegistryEntry dbre) {

		Connection con = dbre.getConnection();
		boolean result = true;

		// get all the links between conservation scores and multiple genomic alignments
		String sql = "SELECT mlss1.method_link_species_set_id," + " mlss2.method_link_species_set_id, ml1.type, ml2.type, count(*)"
				+ " FROM method_link ml1, method_link_species_set mlss1, method_link ml2," + " method_link_species_set mlss2 WHERE mlss1.method_link_id = ml1.method_link_id "
				+ " AND (ml1.class = \"ConservationScore.conservation_score\" OR ml1.class = \"ConstrainedElement.constrained_element\" )"
				+ " AND ml1.type NOT LIKE \"pGERP%\" AND ml2.type NOT LIKE \"pEPO%\" "
				+ " AND mlss1.species_set_id = mlss2.species_set_id AND mlss2.method_link_id = ml2.method_link_id"
				+ " AND (ml2.class = \"GenomicAlignBlock.multiple_alignment\" OR ml2.class LIKE \"GenomicAlignTree.%\") GROUP BY mlss1.method_link_species_set_id";

		try {
			Statement stmt = con.createStatement();
			ResultSet rs = stmt.executeQuery(sql);
			while (rs.next()) {
				if (rs.getInt(5) > 1) {
					ReportManager.problem(this, con, "MethodLinkSpeciesSet " + rs.getString(1) + " links to several multiple alignments!");
					result = false;
				} else if (rs.getString(3).equals("GERP_CONSERVATION_SCORE") || rs.getString(3).equals("GERP_CONSTRAINED_ELEMENT")) {
					EntriesToAdd.put(new Integer(rs.getInt(1)).toString(), new Integer(rs.getInt(2)).toString());
				} else {
					ReportManager.problem(this, con, "Using " + rs.getString(3) + " method_link_type is not supported by this healthcheck");
					result = false;
				}
			}
			rs.close();
			stmt.close();
		} catch (SQLException se) {
			se.printStackTrace();
			result = false;
		}

		// get all the values currently stored in the DB
		sql = "SELECT method_link_species_set_id, value, COUNT(*) FROM method_link_species_set_tag WHERE tag = \"msa_mlss_id\" GROUP BY method_link_species_set_id";

		try {
			Statement stmt = con.createStatement();
			ResultSet rs = stmt.executeQuery(sql);
			while (rs.next()) {
				if (rs.getInt(3) != 1) {
					// Delete all current entries. The right entry will be added
					EntriesToRemove.put(rs.getString(1), rs.getString(2));
					System.out.println("Too many entries for " + rs.getString(1));
				} else if (EntriesToAdd.containsKey(rs.getString(1))) {
					// Entry matches one of the required entries. Update if needed.
					if (!EntriesToAdd.get(rs.getString(1)).equals(rs.getString(2))) {
						EntriesToUpdate.put(rs.getString(1), EntriesToAdd.get(rs.getString(1)));
						System.out.println("Replace entries for " + rs.getString(1));
					}
					// Remove this entry from the set of entries to be added (as it already exits!)
					EntriesToAdd.remove(rs.getString(1));
				} else {
					// Entry is out-to-date
					EntriesToRemove.put(rs.getString(1), rs.getString(2));
					System.out.println("Remove entries for " + rs.getString(1));
				}
			}
			rs.close();
			stmt.close();
		} catch (SQLException se) {
			se.printStackTrace();
			result = false;
		}

		return result;

	} // ---------------------------------------------------------------------

}