/*
* 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: GeneDescriptionSourceTest.java
* Created by: dstaines
* Created on: May 26, 2009
* CVS: $$
*/
package org.ensembl.healthcheck.testcase.eg_core;
import java.util.regex.Pattern;
import org.apache.commons.lang.StringUtils;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
/**
* Test to see if [Source:] tag is set in the description
*
* @author dstaines
*
*/
public class GeneDescriptionSource extends AbstractEgCoreTestCase {
private final static String QUERY = "select description from gene where description is not null";
private final static Pattern DES_P = Pattern
.compile("[Source:[^;]+];Acc:[^]]+\\]");
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int n = 0;
for (String des : getTemplate(dbre).queryForDefaultObjectList(QUERY,
String.class)) {
n++;
if (StringUtils.isEmpty(des) || DES_P.matcher(des).matches()) {
passes = false;
ReportManager
.problem(
this,
dbre.getConnection(),
"Description "
+ des
+ " does not contain the expected source string");
}
}
if (n == 0) {
ReportManager.problem(this, dbre.getConnection(),
"Warning: No descriptions found with source lines");
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to see if [Source:] tag is set in the description";
}
}