/* * 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 for any coord_system.versions that are blank ('') - they should be NULL for various other things to work. */ public class BlankCoordSystemVersions extends SingleDatabaseTestCase { /** * Create a new BlankCoordSystem testcase. */ public BlankCoordSystemVersions() { setDescription("Check for any coord_system.version that are blank ('') - they should be NULL."); setTeamResponsible(Team.GENEBUILD);// this is now inaccurate for funcgen usecase } /** * Data is only tested in core database, as the tables are in sync */ public void types() { removeAppliesToType(DatabaseType.OTHERFEATURES); removeAppliesToType(DatabaseType.ESTGENE); removeAppliesToType(DatabaseType.RNASEQ); removeAppliesToType(DatabaseType.CDNA); } /** * 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(); int rows = DBUtils.getRowCount(con, "SELECT COUNT(*) FROM coord_system WHERE version = ''"); if (rows > 0) { ReportManager.problem(this, con, rows + " rows in coord_system have a blank versions - should be set to null"); result = false; } else { ReportManager.correct(this, con, "No blank versions in coord_system"); } return result; } // run } // BlankCoordSystemVersions