/*
* 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.
*/
/**
* File: DisplayXrefIdTest.java
* Created by: dstaines
* Created on: May 27, 2009
* CVS: $$
*/
package org.ensembl.healthcheck.testcase.eg_core;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
/**
* Check to see if stable_ids have been set for each species in turn
*
* @author dstaines
*
*/
public class StableId extends AbstractEgCoreTestCase {
private final static String QUERY = "select g.gene_id from gene g "
+ "join seq_region sr using (seq_region_id) "
+ "join coord_system cs using (coord_system_id) "
+ "where g.stable_id is null and cs.species_id=?";
/*
* (non-Javadoc)
*
* @seeuk.ac.ebi.proteome.genomebuilder.genomeloader.healthcheck.egtests.
* AbstractEgTestCase#run(org.ensembl.healthcheck.DatabaseRegistryEntry)
*/
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
for (int speciesId : dbre.getSpeciesIds()) {
for (String id : getTemplate(dbre).queryForDefaultObjectList(QUERY,
String.class,speciesId)) {
passes = false;
ReportManager.problem(this, dbre.getConnection(), "Gene " + id
+ " has no stable ID");
}
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Check to see if stable_ids have been set for each species in turn";
}
}