/*
* 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.
*/
/*
* Copyright (C) 2004 EBI, GRL
*
* This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.
*
* This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
* FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation,
* Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package org.ensembl.healthcheck.testcase.generic;
import java.sql.Connection;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.HashSet;
import java.util.Set;
import java.util.Arrays;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import org.ensembl.healthcheck.AssemblyNameInfo;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Species;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
import org.ensembl.healthcheck.util.RowMapper;
import org.ensembl.healthcheck.util.SqlTemplate;
import org.ensembl.healthcheck.util.Utils;
/**
* Checks that changes between releases (assembly, repeatmasking or gene set) have been declared.
*/
public class CheckDeclarations extends SingleDatabaseTestCase {
public CheckDeclarations() {
setTeamResponsible(Team.GENEBUILD);
setSecondTeamResponsible(Team.RELEASE_COORDINATOR);
setDescription("Check that all changes have been correctly declared");
}
/**
* This test applies only to core dbs
*/
public void types() {
removeAppliesToType(DatabaseType.SANGER_VEGA);
removeAppliesToType(DatabaseType.VEGA);
removeAppliesToType(DatabaseType.CDNA);
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.RNASEQ);
}
/**
* Checks that changes in database have been declared.
*
* @param dbre
* The database to check.
* @return True if the test passed.
*/
public boolean run(final DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
DatabaseRegistryEntry sec = getEquivalentFromSecondaryServer(dbre);
if (sec == null) {
boolean newSpecies = checkDeclaration(dbre, "assembly");
if (!newSpecies) {
ReportManager.problem(this, con, "New database " + dbre.getName() + " has not been declared");
return false;
} else {
return true;
}
}
Connection previousCon = sec.getConnection();
result &= checkAssembly(dbre, sec);
result &= checkRepeats(dbre, sec);
result &= checkGenes(dbre, sec);
return result;
}
private boolean checkAssembly(DatabaseRegistryEntry dbre, DatabaseRegistryEntry sec) {
boolean result = true;
Connection con = dbre.getConnection();
Connection previousCon = sec.getConnection();
String sql = "CHECKSUM table assembly";
int currentAssembly = DBUtils.getRowCount(con, sql);
int previousAssembly = DBUtils.getRowCount(previousCon, sql);
if (previousAssembly != currentAssembly) {
boolean declared = checkDeclaration(dbre, "assembly");
if (!declared) {
ReportManager.problem(this, con, "Assembly has changed but has not been declared");
result = false;
}
}
return result;
}
private boolean checkRepeats(DatabaseRegistryEntry dbre, DatabaseRegistryEntry sec) {
boolean result = true;
Connection con = dbre.getConnection();
Connection previousCon = sec.getConnection();
String sql = "CHECKSUM table repeat_feature";
int currentRepeats = DBUtils.getRowCount(con, sql);
int previousRepeats = DBUtils.getRowCount(previousCon, sql);
if (currentRepeats != previousRepeats) {
boolean declared = checkDeclaration(dbre, "repeat_masking");
if (!declared) {
ReportManager.problem(this, con, "Repeats have changed but have not been declared");
result = false;
}
}
return result;
}
private boolean checkGenes(DatabaseRegistryEntry dbre, DatabaseRegistryEntry sec) {
boolean result = true;
Connection con = dbre.getConnection();
Connection previousCon = sec.getConnection();
SqlTemplate t = getSqlTemplate(dbre);
RowMapper<Set<Object>> rowMapper = new RowMapper<Set<Object>>(){
public Set<Object> mapRow(ResultSet rs, int position) throws SQLException {
Set<Object> set = new HashSet<Object>();
for (int i=1; i <= 10; i++) {
set.add(rs.getObject(i));
}
return set;
}
};
String sql = "SELECT biotype, analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_end, seq_region_strand, stable_id, is_current, version FROM gene" ;
Set<Set<Object>> currentGenes = t.queryForSet(sql, rowMapper);
Set<Set<Object>> previousGenes = getSqlTemplate(sec).queryForSet(sql, rowMapper);
if (! currentGenes.equals(previousGenes)) {
boolean declared = checkDeclaration(dbre, "gene_set");
if (!declared) {
ReportManager.problem(this, con, "Genes have changed but have not been declared");
result = false;
}
}
return result;
}
private boolean checkDeclaration(DatabaseRegistryEntry dbre, String change) {
boolean result = true;
Connection con = dbre.getConnection();
String release = DBUtils.getMetaValue(con, "schema_version");
DatabaseRegistryEntry prod = getProductionDatabase();
String sql = "SELECT count(*) FROM db_list dl, db d WHERE dl.db_id = d.db_id and db_type = 'core' and is_current = 1 AND full_db_name = '" + dbre.getName() + "' AND species_id IN (SELECT species_id FROM changelog c, changelog_species cs WHERE c.changelog_id = cs.changelog_id AND release_id = " + release + " AND status not in ('cancelled', 'postponed') AND " + change + " = 'Y')";
int rows = DBUtils.getRowCount(prod.getConnection(), sql);
if (rows == 0) {
result = false;
}
return result;
}
}