/*
* 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.
*/
/**
* UniprotGeneNameObjectXref
*
* @author dstaines
* @author $Author$
* @version $Revision$
*/
package org.ensembl.healthcheck.testcase.eg_core;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.AbstractRowCountTestCase;
/**
* Test to find uniprot gene names as object_xrefs (they should only ever be
* used for display xrefs)
*
* @author dstaines
*
*/
public class UniprotGeneNameObjectXref extends AbstractRowCountTestCase {
public UniprotGeneNameObjectXref() {
this.addToGroup(AbstractEgCoreTestCase.EG_GROUP);
this.appliesToType(DatabaseType.CORE);
this.setTeamResponsible(Team.ENSEMBL_GENOMES);
}
/*
* (non-Javadoc)
*
* @see
* org.ensembl.healthcheck.testcase.AbstractRowCountTestCase#getExpectedCount
* ()
*/
@Override
protected int getExpectedCount() {
return 0;
}
/*
* (non-Javadoc)
*
* @see org.ensembl.healthcheck.testcase.AbstractIntegerTestCase#getSql()
*/
@Override
protected String getSql() {
return "select count(*) from object_xref o, xref x, external_db e where o.xref_id=x.xref_id and x.external_db_id=e.external_db_id and e.db_name IN ('Uniprot_gn', 'Uniprot_gn_gene_name', 'Uniprot_gn_trans_name')";
}
/*
* (non-Javadoc)
*
* @see
* org.ensembl.healthcheck.testcase.AbstractIntegerTestCase#getErrorMessage
* ()
*/
@Override
protected String getErrorMessage(int count) {
return "Found " + count
+ " Uniprot_gn* entries in object_xref - these should be removed from object_xref";
}
}