Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program 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 General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see <http://www.gnu.org/licenses/>. * * * *************************************************************************/ package com.act.lcms.db.io; import com.act.lcms.MS1; import com.act.utils.TSVParser; import com.act.lcms.db.model.CuratedStandardMetlinIon; import com.act.lcms.db.model.StandardIonResult; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.CommandLineParser; import org.apache.commons.cli.DefaultParser; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.cli.Options; import org.apache.commons.cli.ParseException; import org.apache.commons.lang3.StringUtils; import org.joda.time.LocalDateTime; import java.io.File; import java.util.ArrayList; import java.util.List; import java.util.Map; public class LoadStandardIonAnalysisTableIntoDB { public static final String OPTION_FILE_PATH = "i"; public static final String OPTION_AUTHOR = "a"; public static final String HELP_MESSAGE = StringUtils.join(new String[] { "This class is used to load a TSV file containing standard ion result data that may have been editted by a " + "scientist and correctly persist those edits to the standard ion table and the curated chemicals table. " + "One would run this class after making edits to the tsv file (usually present in the pipeline dir in github)." }, ""); public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_FILE_PATH).argName("CSV file path") .desc("The file from which data is ingested into the DB").hasArg().required()); add(Option.builder(OPTION_AUTHOR).argName("commit author").desc("The author of the commit").hasArg() .required()); // Everybody needs a little help from their friends sometime. add(Option.builder("h").argName("help").desc("Prints this help message").longOpt("help")); } }; static { // Add DB connection options. OPTION_BUILDERS.addAll(DB.DB_OPTION_BUILDERS); } public static void main(String[] args) throws Exception { Options opts = new Options(); for (Option.Builder b : OPTION_BUILDERS) { opts.addOption(b.build()); } CommandLine cl = null; try { CommandLineParser parser = new DefaultParser(); cl = parser.parse(opts, args); } catch (ParseException e) { System.err.format("Argument parsing failed: %s\n", e.getMessage()); HELP_FORMATTER.printHelp(LoadStandardIonAnalysisTableIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(LoadStandardIonAnalysisTableIntoDB.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } File inputFile = new File(cl.getOptionValue(OPTION_FILE_PATH)); if (!inputFile.exists()) { System.err.format("Unable to find input file at %s\n", cl.getOptionValue(OPTION_FILE_PATH)); new HelpFormatter().printHelp(LoadConstructAnalysisTableIntoDB.class.getCanonicalName(), opts, true); System.exit(1); } try (DB db = DB.openDBFromCLI(cl)) { db.getConn().setAutoCommit(false); TSVParser parser = new TSVParser(); parser.parse(inputFile); for (Map<String, String> row : parser.getResults()) { Integer standardIonResultId = Integer.parseInt(row.get( ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.STANDARD_ION_RESULT_ID.name())); String dbValueOfMetlinIon = ExportStandardIonResultsFromDB.NULL_VALUE; StandardIonResult ionResult = StandardIonResult.getInstance().getById(db, standardIonResultId); if (ionResult.getManualOverrideId() != null) { // There is an existing manual override ion in the DB CuratedStandardMetlinIon curatedChemical = CuratedStandardMetlinIon.getBestMetlinIon(db, ionResult.getManualOverrideId()); dbValueOfMetlinIon = curatedChemical.getBestMetlinIon(); } String manualPickOfMetlinIon = row .get(ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.MANUAL_PICK.name()); // If the manual metlin ion pick row is not NULL and it is not the same as the value stored in the DB, then // we need to add a new entry to the curated metlin ion table. if (!manualPickOfMetlinIon.equals(ExportStandardIonResultsFromDB.NULL_VALUE) && !manualPickOfMetlinIon.equals(dbValueOfMetlinIon)) { System.out.format("Manual override has been found, so updating the DB\n"); // A manual entry was created. if (!MS1.VALID_MS1_IONS.contains(manualPickOfMetlinIon)) { System.err.format("ERROR: found invalid chemical name: %s\n", manualPickOfMetlinIon); System.exit(-1); } String note = row.get(ExportStandardIonResultsFromDB.STANDARD_ION_HEADER_FIELDS.NOTE.name()); CuratedStandardMetlinIon result = CuratedStandardMetlinIon.insertCuratedStandardMetlinIonIntoDB( db, LocalDateTime.now(CuratedStandardMetlinIon.utcDateTimeZone), cl.getOptionValue(OPTION_AUTHOR), manualPickOfMetlinIon, note, standardIonResultId); if (result == null) { System.err.format( "WARNING: Could not insert curated entry to the curated metlin ion table\n", manualPickOfMetlinIon); System.exit(-1); } else { StandardIonResult getIonResult = StandardIonResult.getInstance().getById(db, standardIonResultId); getIonResult.setManualOverrideId(result.getId()); if (!StandardIonResult.getInstance().update(db, getIonResult)) { System.err.format( "WARNING: Could not insert manual override id to the standard ion table\n", manualPickOfMetlinIon); System.exit(-1); } else { System.out.format( "Successfully committed updates to the standard ion table and the curated metlin ion table\n"); } } } } db.getConn().commit(); } } }