/*
* 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.variation;
import java.sql.Connection;
import java.util.List;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
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.Species;
/**
* Checks populations are entered as expected
*/
public class Population extends SingleDatabaseTestCase {
/**
* Creates a new instance of Population
*/
public Population() {
addToGroup("variation-release");
setDescription("Check the Populations are entered as expected");
setTeamResponsible(Team.VARIATION);
}
/**
*
* @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();
try {
// Check for populations without sizes
String size_stmt = "select count(*) from population pop, sample_population sp where pop.population_id = sp.population_id and pop.size is null;";
int size_rows = DBUtils.getRowCount(con,size_stmt);
if (size_rows > 0) {
result = false;
ReportManager.problem(this, con, String.valueOf(size_rows) + " populations have no stored size");
}
// Check for populations with freqs_from_gts set for mouse and human
if (dbre.getSpecies() == Species.MUS_MUSCULUS || dbre.getSpecies() == Species.HOMO_SAPIENS) {
// Check for populations without sizes
String freq_stmt = "select count(*) from population pop where pop.freqs_from_gts = 1;";
int freq_rows = DBUtils.getRowCount(con,freq_stmt);
if (freq_rows == 0) {
result = false;
ReportManager.problem(this, con, "No populations have freqs_from_gts set ");
}
}
} catch (Exception e) {
ReportManager.problem(this, con, "HealthCheck caused an exception: " + e.getMessage());
result = false;
}
return result;
}
}