/*
* 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 to see if we have GO terms where there is no evidence
* @author dstaines
*
*/
public class EvidenceFreeGO extends AbstractEgCoreTestCase {
private final static String EVIDENCE_FREE_GO = "select count(*) from object_xref ox "
+ "join xref x using (xref_id) "
+ "join external_db e using (external_db_id) "
+ "left join ontology_xref oox using (object_xref_id) "
+ "where e.db_name='GO' and oox.object_xref_id is null;";
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int n = getTemplate(dbre).queryForDefaultObject(EVIDENCE_FREE_GO, Integer.class);
if(n>0) {
passes = false;
ReportManager.problem(this, dbre.getConnection(), n+" GO terms found with no evidence: "+EVIDENCE_FREE_GO);
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to see if we have GO terms where there is no evidence";
}
}