/*
* 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.
*/
package org.ensembl.healthcheck.testcase.generic;
import java.sql.Connection;
import org.ensembl.healthcheck.DatabaseRegistryEntry;
import org.ensembl.healthcheck.DatabaseType;
import org.ensembl.healthcheck.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check that HGNC_curated_genes xrefs are on genes, _transcript are on
* transcript etc.
*/
public class HGNCTypes extends SingleDatabaseTestCase {
/**
* Creates a new instance of HGNCTypes.
*/
public HGNCTypes() {
setDescription("Check that HGNC_curated_genes xrefs are on genes, _transcript are on transcript etc");
setTeamResponsible(Team.CORE);
}
/**
* This test only applies to core databases.
*/
public void types() {
removeAppliesToType(DatabaseType.OTHERFEATURES);
removeAppliesToType(DatabaseType.ESTGENE);
removeAppliesToType(DatabaseType.VEGA);
removeAppliesToType(DatabaseType.CDNA);
removeAppliesToType(DatabaseType.RNASEQ);
}
/**
* Run the test.
*
* @param dbre
* The database to use.
* @return Result.
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// note these are looking for the *wrong* assignments
result &= checkType(con, "HGNC_curated_gene", "Transcript");
result &= checkType(con, "HGNC_automatic_gene", "Transcript");
result &= checkType(con, "HGNC_curated_transcript", "Gene");
result &= checkType(con, "HGNC_curated_transcript", "Gene");
return result;
}
// ----------------------------------------------------------------------
private boolean checkType(Connection con, String source, String wrongObject) {
boolean result = true;
int rows = DBUtils
.getRowCount(
con,
"SELECT COUNT(*) FROM xref x, external_db e, object_xref ox WHERE e.external_db_id=x.external_db_id AND x.xref_id=ox.xref_id AND e.db_name='"
+ source
+ "' AND ox.ensembl_object_type='"
+ wrongObject + "'");
if (rows > 0) {
ReportManager.problem(this, con, rows + " " + source
+ " xrefs are assigned to " + wrongObject.toLowerCase()
+ "s");
result = false;
} else {
ReportManager.correct(this, con, "All " + source
+ " xrefs assigned to correct object type");
}
return result;
}
// ----------------------------------------------------------------------
}