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.biointerpretation.sars; import act.server.MongoDB; import com.act.biointerpretation.Utils.ReactionProjector; import com.act.biointerpretation.mechanisminspection.ErosCorpus; 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.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import java.io.File; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; import java.util.List; public class SarGenerationDriver { private static final Logger LOGGER = LogManager.getFormatterLogger(SarGenerationDriver.class); private static final String OPTION_DB = "db"; private static final String OPTION_OUTPUT_PATH = "o"; private static final String OPTION_HELP = "h"; private static final String OPTION_REACTION_LIST = "r"; private static final String OPTION_REACTIONS_FILE = "f"; public static final String HELP_MESSAGE = "This class is used to generate SARs from a set of reactions or chemicals. It has several modes of operation, " + "which are described in more detail along with the operations that run them."; public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_DB).argName("db name").desc("The name of the mongo DB to use.").hasArg() .longOpt("db-name").type(String.class).required(true)); add(Option.builder(OPTION_OUTPUT_PATH).argName("output file path") .desc("The absolute path to the file to which to write the json file of the sar corpus.") .hasArg().longOpt("output-file-path").required(true)); add(Option.builder(OPTION_REACTION_LIST).argName("specific reactions") .desc("A list of reaction IDs to build a SAR from.").hasArgs().valueSeparator(',') .longOpt("specific reactions")); add(Option.builder(OPTION_REACTIONS_FILE).argName("reactions file").desc( "Absolute path to file from which to read reaction groups. File should either be a ReactionGroupCorpus " + "in json format, or a file with one reaction group per line, where each line has comma separate values, " + "with the first value being the name of the group, and the subsequent values being reaction ids.") .hasArg().longOpt("reactions-file")); add(Option.builder(OPTION_HELP).argName("help").desc("Prints this help message.").longOpt("help")); } }; public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } private static final String LOCAL_HOST = "localhost"; private static final Integer MONGO_PORT = 27017; public static void main(String[] args) throws Exception { // Build command line parser. 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) { LOGGER.error("Argument parsing failed: %s", e.getMessage()); HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Print help. if (cl.hasOption(OPTION_HELP)) { HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } // Create DB and DbAPI MongoDB mongoDB = new MongoDB(LOCAL_HOST, MONGO_PORT, cl.getOptionValue(OPTION_DB)); DbAPI dbApi = new DbAPI(mongoDB); // Handle output file File outputFile = new File(cl.getOptionValue(OPTION_OUTPUT_PATH)); if (outputFile.isDirectory() || outputFile.exists()) { LOGGER.error("Supplied output file is a directory or already exists."); HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } outputFile.createNewFile(); // Check that there is exactly one reaction group input option if (cl.hasOption(OPTION_REACTION_LIST) && cl.hasOption(OPTION_REACTIONS_FILE)) { LOGGER.error("Cannot process both a reaction list and a reactions file as input."); HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (!cl.hasOption(OPTION_REACTION_LIST) && !cl.hasOption(OPTION_REACTIONS_FILE)) { LOGGER.error("Must supply either a reaction list or a reactions file as input."); HELP_FORMATTER.printHelp(SarGenerationDriver.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } // Build input reaction group corpus. Iterable<ReactionGroup> groups = null; if (cl.hasOption(OPTION_REACTION_LIST)) { LOGGER.info("Using specific input reactions."); ReactionGroup group = new ReactionGroup("ONLY_GROUP", "NO_DB"); for (String idString : cl.getOptionValues(OPTION_REACTION_LIST)) { group.addReactionId(Long.parseLong(idString)); } groups = Arrays.asList(group); } if (cl.hasOption(OPTION_REACTIONS_FILE)) { LOGGER.info("Using reactions file."); File inputFile = new File(cl.getOptionValue(OPTION_REACTIONS_FILE)); try { groups = ReactionGroupCorpus.loadFromJsonFile(inputFile); LOGGER.info("Successfully parsed input as json file."); } catch (IOException e) { LOGGER.info("Input file not json file. Trying txt format."); try { groups = ReactionGroupCorpus.loadFromTextFile(inputFile); LOGGER.info("Successfully parsed input as text file."); } catch (IOException f) { LOGGER.error("Reactions input file not parseable. %s", f.getMessage()); throw f; } } } // Build all pieces of SAR generator ReactionProjector projector = new ReactionProjector(); ExpandedReactionSearcher generalizer = new ExpandedReactionSearcher(projector); McsCalculator reactionMcsCalculator = new McsCalculator(McsCalculator.REACTION_BUILDING_OPTIONS); McsCalculator sarMcsCalculator = new McsCalculator(McsCalculator.SAR_OPTIONS); FullReactionBuilder reactionBuilder = new FullReactionBuilder(reactionMcsCalculator, generalizer, projector); SarFactory substructureSarFactory = new OneSubstrateSubstructureSar.Factory(sarMcsCalculator); SarFactory carbonCountSarFactory = new OneSubstrateCarbonCountSar.Factory(); List<SarFactory> sarFactories = Arrays.asList(carbonCountSarFactory, substructureSarFactory); ErosCorpus roCorpus = new ErosCorpus(); roCorpus.loadValidationCorpus(); ReactionGroupCharacterizer reactionGroupCharacterizer = new OneSubstrateOneRoCharacterizer(dbApi, sarFactories, reactionBuilder, roCorpus); SarCorpusBuilder corpusBuilder = new SarCorpusBuilder(groups, reactionGroupCharacterizer); LOGGER.info("Parsed arguments and constructed SAR corpus builder. Building corpus."); SarCorpus sarCorpus = corpusBuilder.build(); LOGGER.info("Built sar corpus. Printing to file in json format."); sarCorpus.printToJsonFile(outputFile); LOGGER.info("Complete!"); } }