/*
* 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.ReportManager;
import org.ensembl.healthcheck.Team;
import org.ensembl.healthcheck.testcase.Priority;
import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase;
import org.ensembl.healthcheck.util.DBUtils;
/**
* Check for Uniprot xrefs that have "Unreviewed" as the primary DB accession.
*/
public class UnreviewedXrefs extends SingleDatabaseTestCase {
/**
* Create a new UnreviewedXrefs testcase.
*/
public UnreviewedXrefs() {
setDescription("Check for Uniprot xrefs that have 'Unreviewed' as the primary DB accession.");
setPriority(Priority.AMBER);
setEffect("Affected xrefs will have broken hyperlinks, also problems for downstream pipelines.");
setFix("Re-run xref system or manually fix affected xrefs.");
setTeamResponsible(Team.CORE);
setSecondTeamResponsible(Team.GENEBUILD);
}
/**
* Run the test.
*
* @param dbre
* The database to use.
* @return true if the test passed.
*
*/
public boolean run(DatabaseRegistryEntry dbre) {
boolean result = true;
Connection con = dbre.getConnection();
// --------------------------------
// MGI - dbprimary_acc should have MGI: prefix
int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM xref x, external_db e WHERE e.external_db_id=x.external_db_id AND e.db_name LIKE 'UniProt%' AND x.dbprimary_acc='Unreviewed';");
if (rows > 0) {
ReportManager.problem(this, con, rows + " UniProt xrefs have \'Unreviewed\' as the primary accession.");
result = false;
} else {
ReportManager.correct(this, con, "No Uniprot xrefs have \'Unreviewed\' as the accession.");
}
return result;
} // run
} // UnreviewedXrefs