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. */ package org.ensembl.healthcheck.testcase.funcgen; /** Can we not just modify the generic version to take a schema/dbtype type And store the variables in a hash? Set groups varaible dependant on dbtype? What is calling this? */ import java.sql.Connection; import java.sql.ResultSet; import java.sql.SQLException; import java.sql.Statement; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import org.ensembl.CoreDbNotFoundException; import org.ensembl.healthcheck.DatabaseRegistry; import org.ensembl.healthcheck.DatabaseRegistryEntry; import org.ensembl.healthcheck.MissingMetaKeyException; import org.ensembl.healthcheck.ReportManager; import org.ensembl.healthcheck.Team; import org.ensembl.healthcheck.testcase.SingleDatabaseTestCase; import org.ensembl.healthcheck.util.DBUtils; import static org.apache.commons.lang.StringUtils.join; import static org.ensembl.healthcheck.DatabaseType.CORE; /** * Check that meta_coord table contains entries for all the coordinate systems * that all the features are stored in. */ public class MetaCoord extends AbstractCoreDatabaseUsingTestCase { private String[] featureTables = getFuncgenFeatureTables(); /** * Create a new instance of MetaCoord. */ public MetaCoord() { addToGroup("funcgen"); addToGroup("funcgen-release"); setDescription( "Check that meta_coord table contains entries for all the coordinate systems that all the features are stored in"); setTeamResponsible(Team.FUNCGEN); } /** * Run the test. * * @param funcgenDbre * The database to use. * @return true if the test passed. * */ public boolean run(DatabaseRegistryEntry funcgenDbre) { boolean result = true; DatabaseRegistryEntry coreDbre; try { coreDbre = getCoreDb(funcgenDbre); } catch (MissingMetaKeyException e) { ReportManager.problem(this, funcgenDbre.getConnection(), e.getMessage()); return false; } catch (CoreDbNotFoundException e) { ReportManager.problem(this, funcgenDbre.getConnection(), e.getMessage()); return false; } Connection funcgenCon = funcgenDbre.getConnection(); Connection coreCon = coreDbre.getConnection(); // coordSystems is a hash of lists of coordinate systems that each feature // table contains Map coordSystems = new HashMap(); try { Statement funcgenStatement = funcgenCon.createStatement(); Statement coreStatement = coreCon.createStatement(); // build up a list of all the coordinate systems that are in the various // feature tables for (int tableIndex = 0; tableIndex < featureTables.length; tableIndex++) { String tableName = featureTables[tableIndex]; String funcgenSql = "SELECT DISTINCT(seq_region_id) FROM " + tableName; logger.finest("Getting seq_region_ids for " + tableName); ResultSet funcgenRs = funcgenStatement.executeQuery(funcgenSql); ArrayList<String> seqRegionIDs = new ArrayList<>(); if (!funcgenRs.isBeforeFirst()) { logger.warning("No features found for " + tableName); continue; } if (funcgenRs.next()) while (funcgenRs.next()) { seqRegionIDs.add(funcgenRs.getString(1)); } String seqRegionIDsString = seqRegionIDs.toString().replace("[", "").replace("]", ""); String coreSql = "SELECT DISTINCT(coord_system_id) FROM seq_region WHERE seq_region_id IN (" + seqRegionIDsString + ")"; logger.finest("Getting coord_system_ids for " + tableName); ResultSet coreRs = coreStatement.executeQuery(coreSql); while (coreRs.next()) { String coordSystemID = coreRs.getString(1); logger.finest("Added feature coordinate system for " + tableName + ": " + coordSystemID); // check that the meta_coord table has an entry corresponding to this int mc = DBUtils.getRowCount(funcgenCon, "SELECT COUNT(*) FROM meta_coord WHERE coord_system_id=" + coordSystemID + " AND table_name='" + tableName + "'"); if (mc == 0) { ReportManager.problem(this, funcgenCon, "No entry for coordinate system with ID " + coordSystemID + " for " + tableName + " in meta_coord"); result = false; } else if (mc > 1) { ReportManager.problem(this, funcgenCon, "Coordinate system with ID " + coordSystemID + " duplicated for " + tableName + " in meta_coord"); result = false; } else { ReportManager.correct(this, funcgenCon, "Coordinate system with ID " + coordSystemID + " for table " + tableName + " has an entry in meta_coord"); } // store in coordSystems map - create List if necessary List csList = (ArrayList) coordSystems.get(tableName); if (csList == null) { csList = new ArrayList(); } csList.add(coordSystemID); coordSystems.put(tableName, csList); } funcgenRs.close(); } // check that every meta_coord table entry refers to a coordinate system // that is used in a feature // if this isn't true it's not fatal but should be flagged String sql = "SELECT * FROM meta_coord"; ResultSet rs = funcgenStatement.executeQuery(sql); while (rs.next()) { String tableName = rs.getString("table_name"); String csID = rs.getString("coord_system_id"); logger.finest("Checking for coord_system_id " + csID + " in " + tableName); List featureCSs = (ArrayList) coordSystems.get(tableName); if (featureCSs != null && !featureCSs.contains(csID)) { ReportManager.problem(this, funcgenCon, "meta_coord has entry for coord_system ID " + csID + " in " + tableName + " but this coordinate system is not actually used in " + tableName); result = false; } } rs.close(); funcgenStatement.close(); // check that there are no null max_length entries result &= checkNoNulls(funcgenCon, "meta_coord", "max_length"); } catch (SQLException e) { e.printStackTrace(); } return result; } }