/*
* 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 org.ensembl.healthcheck.DatabaseRegistryEntry;
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;
/**
* Check compara Gene Gain/Loss tables.
*/
public class CheckGeneGainLossData extends SingleDatabaseTestCase {
public CheckGeneGainLossData() {
setDescription("Check that we have data coming from ncRNA and protein gain/loss trees");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
String sql_main = "SELECT member_type, count(*)" +
" FROM gene_tree_root gtr JOIN CAFE_gene_family cgf ON(gtr.root_id=cgf.gene_tree_root_id)" +
" WHERE gtr.tree_type = 'tree' GROUP BY gtr.member_type";
int numRows = DBUtils.getRowCount(con, sql_main);
if (numRows > 2) {
ReportManager.problem(this, con, "FAILED Gene Gain/Loss Data test. Either ncRNA or protein trees don't have gene Gain/Loss trees.");
ReportManager.problem(this, con, "FAILURE DETAILS: There are less than 2 member_types [protein/ncRNA] having gene Gain/Loss trees.");
ReportManager.problem(this, con, "USEFUL SQL: " + sql_main);
return false;
}
return true;
}
}