/*
* 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.apache.commons.lang.StringUtils;
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;
/**
* An EnsEMBL Healthcheck test case that looks for broken foreign-key
* relationships.
*/
public class MultipleGenomicAlignBlockIds extends SingleDatabaseTestCase {
public MultipleGenomicAlignBlockIds() {
setDescription("Check that every genomic_align_block_id is linked to more than one single genomic_align_id.");
setTeamResponsible(Team.COMPARA);
}
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
if (tableHasRows(con, "genomic_align")) {
// The test does not apply to EPO alignments because they store
// ancestral sequences in a different genomic_align_block_id
String sqlNonEPOmlss_ids = "SELECT method_link_species_set_id FROM method_link_species_set JOIN method_link USING (method_link_id) WHERE class LIKE 'GenomicAlign%' AND class != 'GenomicAlignTree.ancestral_alignment'";
String[] nonEPOmlss_ids = DBUtils.getColumnValues(con, sqlNonEPOmlss_ids);
for (String mlss_id : nonEPOmlss_ids) {
result &= checkForSinglesWithConstraint(con, "genomic_align", "genomic_align_block_id", "WHERE method_link_species_set_id = " + mlss_id);
}
} else {
ReportManager.correct(this, con, "NO ENTRIES in genomic_align table, so nothing to test IGNORED");
}
return result;
}
} // MultipleGenomicAlignBlockIds