/*
* 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 broken foreign-key
* relationships in the homology tables of the Compara schema.
*/
public class ForeignKeyHomologyTables extends AbstractComparaTestCase {
public ForeignKeyHomologyTables() {
setDescription("Check for broken foreign-key relationships in the homology tables.");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
Connection con = dbre.getConnection();
boolean result = true;
result &= checkForOrphans(con, "homology_member", "homology_id", "homology", "homology_id");
result &= checkForOrphans(con, "homology", "homology_id", "homology_member", "homology_id");
result &= checkForOrphans(con, "homology_member", "seq_member_id", "seq_member", "seq_member_id");
result &= checkForOrphans(con, "homology_member", "gene_member_id", "gene_member", "gene_member_id");
result &= checkOptionalRelation(con, "homology", "gene_tree_node_id", "gene_tree_node", "node_id");
result &= checkOptionalRelation(con, "homology", "gene_tree_root_id", "gene_tree_root", "root_id");
return result;
}
} // ForeignKeyHomologyTables