/*
* 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;
/**
* Test for where xrefs have been added twice to the same Ensembl object.
* This is acceptable where analysis_id is different e.g. GO terms from 2 pipelines
* @author dstaines
*
*/
public class DuplicateObjectXref extends AbstractEgCoreTestCase {
private final static String DUPLICATE_OBJ_XREF = "select count(*) from (select count(*) from xref x join object_xref ox using (xref_id) left outer join ontology_xref ontx using (object_xref_id) group by ox.ensembl_id, ox.ensembl_object_type,x.dbprimary_acc,x.external_db_id,x.info_type,x.info_text,ontx.source_xref_id,ontx.linkage_type having count(*)>1) cc";
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int nDupOX = getTemplate(dbre).queryForDefaultObject(DUPLICATE_OBJ_XREF, Integer.class);
if(nDupOX>0) {
passes = false;
ReportManager.problem(this, dbre.getConnection(), nDupOX+" duplicates found in object_xref: "+DUPLICATE_OBJ_XREF);
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test for where object_xrefs have been added twice";
}
}