/*
* 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: IgiXrefTest.java
* Created by: dstaines
* Created on: Dec 3, 2009
* CVS: $$
*/
package org.ensembl.healthcheck.testcase.eg_core;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.ReportManager;
/**
* Test to see if IGIs have been accidentally left in
*
* @author dstaines
*
*/
public class IgiXref extends AbstractEgCoreTestCase {
/*
* (non-Javadoc)
*
* @see
* org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#runTest
* (org.ensembl.healthcheck.DatabaseRegistryEntry)
*/
@Override
protected boolean runTest(DatabaseRegistryEntry dbre) {
boolean passes = true;
int n = getTemplate(dbre).queryForDefaultObject(
"Select count(*) from xref where external_db_id=60014",
Integer.class);
if (n > 0) {
ReportManager
.problem(this, dbre.getConnection(), "IGI xrefs found");
}
return passes;
}
@Override
public boolean canRepair() {
return true;
}
@Override
public String getFix() {
return "delete ox.*,x.* from object_xref ox, xref x where x.xref_id=ox.xref_id and x.external_db_id=60014;";
}
/*
* (non-Javadoc)
*
* @see org.ensembl.healthcheck.testcase.eg_core.AbstractEgCoreTestCase#
* getEgDescription()
*/
@Override
protected String getEgDescription() {
return "Test to see if IGIs have been accidentally left in";
}
}