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 act.installer.reachablesexplorer; import com.act.utils.CLIUtil; import com.act.utils.TSVWriter; import org.apache.commons.cli.CommandLine; import org.apache.commons.cli.HelpFormatter; import org.apache.commons.cli.Option; import org.apache.commons.lang3.StringUtils; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.mongojack.DBCursor; import org.mongojack.DBQuery; import org.mongojack.JacksonDBCollection; import java.io.File; import java.util.ArrayList; import java.util.Arrays; import java.util.Collections; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.stream.Collectors; /** * This class outputs a TSV file that can be consumed by various web services that support the reachables wiki. */ public class WikiWebServicesExporter { private static final Logger LOGGER = LogManager.getFormatterLogger(WikiWebServicesExporter.class); private static final List<String> HEADER = Arrays.asList("inchi", "inchi_key", "display_name", "image_name"); private static final String OPTION_INPUT_DB = "d"; private static final String OPTION_INPUT_DB_HOST = "H"; private static final String OPTION_INPUT_DB_PORT = "p"; private static final String OPTION_INPUT_DB_COLLECTION = "c"; private static final String OPTION_OUTPUT_FILE = "o"; private static final String OPTION_EXPORT_SOME = "m"; private static final String OPTION_INPUT_SEQUENCE_COLLECTION = "s"; private static final String DEFAULT_HOST = "localhost"; private static final String DEFAULT_PORT = "27017"; // TODO change the defaults to something more plain/easy to know why they are like they are (No version numbers etc.) private static final String DEFAULT_DB = "wiki_reachables"; private static final String DEFAULT_COLLECTION = "reachablesv7"; private static final String DEFAULT_SEQUENCES_COLLECTION = "sequencesv7"; private static final String DEFAULT_RENDERING_CACHE = "/tmp"; // We wont touch this db, but need it for the Loader's constructor private static final String UNUSED_SOURCE_DB = "dummy_source_db"; private static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_INPUT_DB).argName("db name") .desc(String.format("The name of the reachables database to read (default: %s)", DEFAULT_DB)) .hasArg().longOpt("db")); add(Option .builder(OPTION_INPUT_DB_HOST).argName("db host").desc(String .format("The host to which connect when reading from a DB (default: %s)", DEFAULT_HOST)) .hasArg().longOpt("host")); add(Option .builder(OPTION_INPUT_DB_PORT).argName("db port").desc(String .format("The port to which connect when reading from a DB (default: %s)", DEFAULT_PORT)) .hasArg().longOpt("port")); add(Option.builder(OPTION_INPUT_DB_COLLECTION).argName("collection") .desc(String.format("The collection from which to read reachables documents (default: %s)", DEFAULT_COLLECTION)) .hasArg().longOpt("collection")); add(Option.builder(OPTION_OUTPUT_FILE).argName("file name").desc("The name of the output tsv to write") .hasArg().required().longOpt("out")); add(Option.builder(OPTION_INPUT_SEQUENCE_COLLECTION).argName("sequence-collection") .desc("The sequence collection that should be used for export.").hasArg() .longOpt("sequence-collection")); add(Option.builder(OPTION_EXPORT_SOME).argName("ids") .desc("Only export molecules with the specified ids").hasArgs().valueSeparator(',') .longOpt("only-export")); } }; private static final String HELP_MESSAGE = StringUtils.join(new String[] { "This class write the contents of a Reachables collection as a TSV that can be consumed by the substructure ", "search service" }, ""); private static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } public static void main(String[] args) throws Exception { CLIUtil cliUtil = new CLIUtil(WikiWebServicesExporter.class, HELP_MESSAGE, OPTION_BUILDERS); CommandLine cl = cliUtil.parseCommandLine(args); String host = cl.getOptionValue(OPTION_INPUT_DB_HOST, DEFAULT_HOST); Integer port = Integer.parseInt(cl.getOptionValue(OPTION_INPUT_DB_PORT, DEFAULT_PORT)); String dbName = cl.getOptionValue(OPTION_INPUT_DB, DEFAULT_DB); String collection = cl.getOptionValue(OPTION_INPUT_DB_COLLECTION, DEFAULT_COLLECTION); String sequenceCollection = cl.getOptionValue(OPTION_INPUT_SEQUENCE_COLLECTION, DEFAULT_SEQUENCES_COLLECTION); LOGGER.info("Attempting to connect to DB %s:%d/%s, collection %s", host, port, dbName, collection); Loader loader = new Loader(host, port, UNUSED_SOURCE_DB, dbName, collection, sequenceCollection, DEFAULT_RENDERING_CACHE); JacksonDBCollection<Reachable, String> reachables = loader.getJacksonReachablesCollection(); LOGGER.info("Connected to DB, reading reachables"); List<Long> exportIds = !cl.hasOption(OPTION_EXPORT_SOME) ? Collections.emptyList() : Arrays.stream(cl.getOptionValues(OPTION_EXPORT_SOME)).map(Long::valueOf) .collect(Collectors.toList()); TSVWriter<String, String> tsvWriter = new TSVWriter<>(HEADER); tsvWriter.open(new File(cl.getOptionValue(OPTION_OUTPUT_FILE))); try { DBCursor<Reachable> cursor = exportIds.isEmpty() ? reachables.find() : reachables.find(DBQuery.in("_id", exportIds)); int written = 0; while (cursor.hasNext()) { final Reachable r = cursor.next(); Map<String, String> row = new HashMap<String, String>() { { put("inchi", r.getInchi()); put("inchi_key", r.getInchiKey()); put("display_name", r.getPageName()); put("image_name", r.getStructureFilename()); } }; tsvWriter.append(row); tsvWriter.flush(); written++; } LOGGER.info("Wrote %d reachables to output TSV", written); } finally { tsvWriter.close(); } } }