Java tutorial
/* * Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute * Copyright [2016-2018] 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. */ /* * Copyright (C) 2003 EBI, GRL * * This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by * the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA */ package org.ensembl.healthcheck.testcase.generic; import java.sql.Connection; import java.util.Collection; import java.util.List; import org.apache.commons.collections.CollectionUtils; 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.Priority; import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase; import org.ensembl.healthcheck.util.DBUtils; /** * Check that all the non-optional meta keys listed in the production database are present, and that all the meta keys are valid. */ public class ProductionMeta extends SingleDatabaseTestCase { /** * Constructor. */ public ProductionMeta() { setDescription( "Check that all the non-optional meta keys listed in the production database are present, and that all the meta keys are valid."); setPriority(Priority.AMBER); setEffect("Unknown/incorrect meta keys."); setTeamResponsible(Team.GENEBUILD); } /** * This test Does not apply to sangervega dbs */ public void types() { removeAppliesToType(DatabaseType.SANGER_VEGA); } /** * Run the test. * * @param dbre * The database to use. * @return true if the test passed. * */ @SuppressWarnings("unchecked") public boolean run(DatabaseRegistryEntry dbre) { boolean result = true; Connection con = dbre.getConnection(); DatabaseRegistryEntry prodDbre = getProductionDatabase(); // we'll use a different query depending on the database type; also some keys are only for certain species String databaseType = dbre.getType().getName(); // will be core, otherfeatures etc String species = dbre.getSpecies().toString(); // will be homo_sapiens etc List<String> dbMetaKeys = DBUtils.getColumnValuesList(con, "SELECT DISTINCT(meta_key) FROM meta"); // First check that keys present in database are all valid and current List<String> productionMetaKeys = DBUtils.getColumnValuesList(prodDbre.getConnection(), "SELECT mk.name " + "FROM meta_key mk LEFT JOIN (" + "meta_key_species JOIN " + "species s USING (species_id) ) USING (meta_key_id) " + "WHERE FIND_IN_SET('" + databaseType + "', mk.db_type) > 0 AND " + "(s.db_name = '" + species + "' OR s.db_name IS NULL) AND " + "mk.is_current = 1"); // remove the list of valid keys from the list of keys in the database, the remainder (if any) are invalid Collection<String> dbOnly = (Collection<String>) CollectionUtils.subtract(dbMetaKeys, productionMetaKeys); if (!dbOnly.isEmpty()) { for (String key : dbOnly) { String msg = String.format("Meta key '%s' is not in the allowed meta key list from production", key); ReportManager.problem(this, con, msg); } result = false; } else { ReportManager.correct(this, con, "Set of meta keys matches the current valid list in the production database."); } // now check that all non-optional keys in production database appear here dbMetaKeys = DBUtils.getColumnValuesList(con, "SELECT DISTINCT(meta_key) FROM meta"); productionMetaKeys = DBUtils.getColumnValuesList(prodDbre.getConnection(), "SELECT mk.name " + "FROM meta_key mk LEFT JOIN (" + "meta_key_species JOIN " + "species s USING (species_id) ) USING (meta_key_id) " + "WHERE FIND_IN_SET('" + databaseType + "', mk.db_type) > 0 AND " + "(s.db_name = '" + species + "' OR s.db_name IS NULL) AND " + "mk.is_current = 1 AND " + "mk.is_optional = 0"); // remove the keys in the database from the non-optional list, any remaining in the non-optional list are missing from the // database Collection<String> productionOnly = (Collection<String>) CollectionUtils.subtract(productionMetaKeys, dbMetaKeys); if (!productionOnly.isEmpty()) { for (String key : productionOnly) { String msg = String.format("Missing required meta key: %s", key); ReportManager.problem(this, con, msg); } result = false; } else { ReportManager.correct(this, con, "All current required meta keys are present."); } return result; } // run } // ProductionBiotypes