/*
* 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 transcripts with no rank 1 exon
* @author dstaines
*
*/
public class IncorrectExonRank extends AbstractEgCoreTestCase {
private final static String NO_RANK_ONE = "select count(*) from transcript where transcript_id not in "
+ "(select transcript_id from exon_transcript where rank=1)";
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int n = getTemplate(dbre).queryForDefaultObject(NO_RANK_ONE, Integer.class);
if(n>0) {
passes = false;
ReportManager.problem(this, dbre.getConnection(), n+" transcripts found with no rank 1: "+NO_RANK_ONE);
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to see if we have transcripts with no rank 1 exon";
}
}