/*
* 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.Team;
import org.ensembl.healthcheck.testcase.compara.AbstractComparaTestCase;
/**
* An EnsEMBL Healthcheck test case that looks for the consistency of the
* genomic_align_tree table
*/
public class CheckGenomicAlignTreeTable extends AbstractComparaTestCase {
public CheckGenomicAlignTreeTable() {
setDescription("Check the consistency of the genomic_align_tree table.");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
if (!tableHasRows(con, "genomic_align_tree")) {
ReportManager.correct(this, con, "NO ENTRIES in genomic_align_tree table, so nothing to test IGNORED");
return true;
}
boolean result = true;
// Check the left_node_id values are set (and assume right_node_ids have also been set)
// FIXME: this will have to be updated when left_node_id becomes NULLable
result &= checkCountIsNonZero(con, "genomic_align_tree", "left_node_id != 0");
/* Looking at distance_to_parent > 1 is true for LOW_COVERAGE but not epo */
/* Update 2015-30-04: there are nodes with distance_to_parent > 1
* in all the EPO alignments, but also for the "11 fish EPO_LOW_COVERAGE"
*/
//result &= checkCountIsZero(con, "genomic_align_tree", "distance_to_parent > 1");
return result;
}
} // CheckGenomicAlignTreeTable