/*
* 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 org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.util.SqlTemplate;
/**
* Test to see if Uniprot misspelling is present in descriptions
*
* @author dstaines
*
*/
public class DbDisplayNameUniProt extends AbstractEgCoreTestCase {
private final static String QUERY = "select db_display_name from external_db where db_display_name like binary ?";
private final static String[] TERMS = { "%SPTREMBL%", "%SWISSPROT%",
"%Uniprot%", "%UniProt/%" };
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
SqlTemplate template = getTemplate(dbre);
for (String term : TERMS) {
for (String entry : template.queryForDefaultObjectList(QUERY,
String.class, term)) {
passes = false;
ReportManager.problem(this, dbre.getConnection(),
"An external_db entry has the display name " + entry
+ " which is incorrect");
}
}
return passes;
}
/* (non-Javadoc)
* @see org.ensembl.healthcheck.testcase.AbstractTemplatedTestCase#getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to see if Uniprot (case!) misspelling is present in descriptions";
}
}