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.db.io.parser.PlateCompositionParser; import com.act.lcms.db.model.DeliveredStrainWell; import com.act.lcms.db.model.FeedingLCMSWell; import com.act.lcms.db.model.InductionWell; import com.act.lcms.db.model.LCMSWell; import com.act.lcms.db.model.Plate; import com.act.lcms.db.model.PregrowthWell; import com.act.lcms.db.model.StandardWell; 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 java.io.File; import java.util.Arrays; import java.util.List; public class LoadPlateCompositionIntoDB { // TODO: add argument parser and/or usage message. public static void main(String[] args) throws Exception { Options opts = new Options(); opts.addOption(Option.builder("t").argName("type") .desc("The type of plate composition in this file, valid options are: " + StringUtils.join(Arrays.asList(Plate.CONTENT_TYPE.values()), ", ")) .hasArg().longOpt("plate-type").required().build()); opts.addOption(Option.builder("i").argName("path").desc("The plate composition file to read").hasArg() .longOpt("input-file").required().build()); // DB connection options. opts.addOption(Option.builder().argName("database url") .desc("The url to use when connecting to the LCMS db").hasArg().longOpt("db-url").build()); opts.addOption(Option.builder("u").argName("database user").desc("The LCMS DB user").hasArg() .longOpt("db-user").build()); opts.addOption(Option.builder("p").argName("database password").desc("The LCMS DB password").hasArg() .longOpt("db-pass").build()); opts.addOption(Option.builder("H").argName("database host") .desc(String.format("The LCMS DB host (default = %s)", DB.DEFAULT_HOST)).hasArg().longOpt("db-host") .build()); opts.addOption(Option.builder("P").argName("database port") .desc(String.format("The LCMS DB port (default = %d)", DB.DEFAULT_PORT)).hasArg().longOpt("db-port") .build()); opts.addOption(Option.builder("N").argName("database name") .desc(String.format("The LCMS DB name (default = %s)", DB.DEFAULT_DB_NAME)).hasArg() .longOpt("db-name").build()); // Everybody needs a little help from their friends. opts.addOption( Option.builder("h").argName("help").desc("Prints this help message").longOpt("help").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()); HelpFormatter fmt = new HelpFormatter(); fmt.printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true); System.exit(1); } if (cl.hasOption("help")) { new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true); return; } File inputFile = new File(cl.getOptionValue("input-file")); if (!inputFile.exists()) { System.err.format("Unable to find input file at %s\n", cl.getOptionValue("input-file")); new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true); System.exit(1); } PlateCompositionParser parser = new PlateCompositionParser(); parser.processFile(inputFile); Plate.CONTENT_TYPE contentType = null; try { contentType = Plate.CONTENT_TYPE.valueOf(cl.getOptionValue("plate-type")); } catch (IllegalArgumentException e) { System.err.format("Unrecognized plate type '%s'\n", cl.getOptionValue("plate-type")); new HelpFormatter().printHelp(LoadPlateCompositionIntoDB.class.getCanonicalName(), opts, true); System.exit(1); } DB db; if (cl.hasOption("db-url")) { db = new DB().connectToDB(cl.getOptionValue("db-url")); } else { Integer port = null; if (cl.getOptionValue("P") != null) { port = Integer.parseInt(cl.getOptionValue("P")); } db = new DB().connectToDB(cl.getOptionValue("H"), port, cl.getOptionValue("N"), cl.getOptionValue("u"), cl.getOptionValue("p")); } try { db.getConn().setAutoCommit(false); Plate p = Plate.getOrInsertFromPlateComposition(db, parser, contentType); switch (contentType) { case LCMS: List<LCMSWell> LCMSWells = LCMSWell.getInstance().insertFromPlateComposition(db, parser, p); for (LCMSWell LCMSWell : LCMSWells) { System.out.format("%d: %d x %d %s %s\n", LCMSWell.getId(), LCMSWell.getPlateColumn(), LCMSWell.getPlateRow(), LCMSWell.getMsid(), LCMSWell.getComposition()); } break; case STANDARD: List<StandardWell> standardWells = StandardWell.getInstance().insertFromPlateComposition(db, parser, p); for (StandardWell standardWell : standardWells) { System.out.format("%d: %d x %d %s\n", standardWell.getId(), standardWell.getPlateColumn(), standardWell.getPlateRow(), standardWell.getChemical()); } break; case DELIVERED_STRAIN: List<DeliveredStrainWell> deliveredStrainWells = DeliveredStrainWell.getInstance() .insertFromPlateComposition(db, parser, p); for (DeliveredStrainWell deliveredStrainWell : deliveredStrainWells) { System.out.format("%d: %d x %d (%s) %s %s \n", deliveredStrainWell.getId(), deliveredStrainWell.getPlateColumn(), deliveredStrainWell.getPlateRow(), deliveredStrainWell.getWell(), deliveredStrainWell.getMsid(), deliveredStrainWell.getComposition()); } break; case INDUCTION: List<InductionWell> inductionWells = InductionWell.getInstance().insertFromPlateComposition(db, parser, p); for (InductionWell inductionWell : inductionWells) { System.out.format("%d: %d x %d %s %s %s %d\n", inductionWell.getId(), inductionWell.getPlateColumn(), inductionWell.getPlateRow(), inductionWell.getMsid(), inductionWell.getComposition(), inductionWell.getChemical(), inductionWell.getGrowth()); } break; case PREGROWTH: List<PregrowthWell> pregrowthWells = PregrowthWell.getInstance().insertFromPlateComposition(db, parser, p); for (PregrowthWell pregrowthWell : pregrowthWells) { System.out.format("%d: %d x %d (%s @ %s) %s %s %d\n", pregrowthWell.getId(), pregrowthWell.getPlateColumn(), pregrowthWell.getPlateRow(), pregrowthWell.getSourcePlate(), pregrowthWell.getSourceWell(), pregrowthWell.getMsid(), pregrowthWell.getComposition(), pregrowthWell.getGrowth()); } break; case FEEDING_LCMS: List<FeedingLCMSWell> feedingLCMSWells = FeedingLCMSWell.getInstance() .insertFromPlateComposition(db, parser, p); for (FeedingLCMSWell feedingLCMSWell : feedingLCMSWells) { System.out.format("%d: %d x %d (%s @ %s) %s %s %f\n", feedingLCMSWell.getId(), feedingLCMSWell.getPlateColumn(), feedingLCMSWell.getPlateRow(), feedingLCMSWell.getMsid(), feedingLCMSWell.getComposition(), feedingLCMSWell.getExtract(), feedingLCMSWell.getChemical(), feedingLCMSWell.getConcentration()); } break; default: System.err.format("Unrecognized/unimplemented data type '%s'\n", contentType); break; } // If we didn't encounter an exception, commit the transaction. db.getConn().commit(); } catch (Exception e) { System.err.format("Caught exception when trying to load plate composition, rolling back. %s\n", e.getMessage()); db.getConn().rollback(); throw (e); } finally { db.getConn().close(); } } }