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.reachables; import act.installer.bing.BingSearchRanker; import act.server.NoSQLAPI; import act.shared.Reaction; 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.apache.commons.lang3.tuple.Pair; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import java.io.IOException; import java.util.ArrayList; import java.util.HashMap; import java.util.HashSet; import java.util.List; import java.util.Map; import java.util.Set; public class ConditionalReachabilityInterpreter { private static final String GLUCOSE_INCHI = "InChI=1S/C6H12O6/c7-1-2-3(8)4(9)5(10)6(11)12-2/h2-11H,1H2/t2-,3-,4+,5-,6?/m1/s1"; private static final String ATP_INCHI = "InChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1"; private static final Set<String> BLACKLISTED_ROOT_INCHIS = new HashSet<String>() { { add(GLUCOSE_INCHI); add(ATP_INCHI); } }; public static final String OPTION_OUTPUT_FILEPATH = "o"; public static final String OPTION_INPUT_ACT_FILEPATH = "i"; public static final String OPTION_DB_NAME = "d"; private static final Logger LOGGER = LogManager.getFormatterLogger(ConditionalReachabilityInterpreter.class); public static final String HELP_MESSAGE = StringUtils.join(new String[] { "This class is used to deserialize a reachable forest and output bing search results of all chemicals within each root", "of the forest along with it's root associate." }, " "); public static final List<Option.Builder> OPTION_BUILDERS = new ArrayList<Option.Builder>() { { add(Option.builder(OPTION_OUTPUT_FILEPATH).argName("OUTPUT_FILEPATH") .desc("The full path to the output file").hasArg().required().longOpt("output_filepath") .type(String.class)); add(Option.builder(OPTION_INPUT_ACT_FILEPATH).argName("INPUT_ACT_FILEPATH") .desc("The full path to the input act file").hasArg().required().longOpt("input_act_filepath") .type(String.class)); add(Option.builder(OPTION_DB_NAME).argName("DB_NAME").desc("The name of the database").hasArg() .required().longOpt("db_name").type(String.class)); add(Option.builder("h").argName("help").desc("Prints this help message").longOpt("help")); } }; public static final HelpFormatter HELP_FORMATTER = new HelpFormatter(); static { HELP_FORMATTER.setWidth(100); } // Instance variables private ActData actData; private Set<Long> rootChemicals; private Map<Long, String> chemIdToInchi; private Map<String, Integer> depthOfMolecule; private NoSQLAPI db = new NoSQLAPI("marvin", "marvin"); public ConditionalReachabilityInterpreter(ActData actData, NoSQLAPI db) { this.actData = actData; this.rootChemicals = new HashSet<>(); this.chemIdToInchi = new HashMap<>(); this.depthOfMolecule = new HashMap<>(); this.db = db; } public static void main(String[] args) throws Exception { // Parse the command line options 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(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); System.exit(1); } if (cl.hasOption("help")) { HELP_FORMATTER.printHelp(BingSearchRanker.class.getCanonicalName(), HELP_MESSAGE, opts, null, true); return; } String inputPath = cl.getOptionValue(OPTION_INPUT_ACT_FILEPATH); String outputPath = cl.getOptionValue(OPTION_OUTPUT_FILEPATH); String dbName = cl.getOptionValue(OPTION_DB_NAME); LOGGER.info("Starting to deserialize reachables forest."); ActData.instance().deserialize(inputPath); ActData actData = ActData.instance(); LOGGER.info("Finished deserializing reachables forest."); NoSQLAPI db = new NoSQLAPI(dbName, dbName); ConditionalReachabilityInterpreter conditionalReachabilityInterpreter = new ConditionalReachabilityInterpreter( actData, db); conditionalReachabilityInterpreter.run(outputPath); } /** * This function constructs parent to children associations, while finding root chemicals from the reachables forest. * @return parent to child associations */ private Map<Long, Set<Long>> constructParentToChildAssociationsAndPopulateRootChemicals() { Map<Long, Set<Long>> parentToChildrenAssociations = new HashMap<>(); for (Map.Entry<Long, Long> childIdToParentId : this.actData.getActTree().parents.entrySet()) { Long parentId = childIdToParentId.getValue(); Long childId = childIdToParentId.getKey(); // If the parentId is null, that means the node is one of the roots of the forest. if (parentId == null) { rootChemicals.add(childId); continue; } Set<Long> childIds = parentToChildrenAssociations.get(parentId); if (childIds == null) { childIds = new HashSet<>(); parentToChildrenAssociations.put(parentId, childIds); } childIds.add(childId); } return parentToChildrenAssociations; } /** * This function constructs root to descendant mappings, creating a representation of the forest that is easy to * traverse. * @param parentToDescendantsAssociations A mapping between parent id to a set of all it's children. * @return a mapping of root id to all its descendant ids. */ private Map<Long, Set<Long>> constructRootToDescendantMappings( Map<Long, Set<Long>> parentToDescendantsAssociations) { Map<Long, Set<Long>> rootToSetOfDescendants = new HashMap<>(); for (Long rootId : rootChemicals) { // Record depth of each tree int depth = 1; String rootInchi = db .readChemicalFromInKnowledgeGraph(rootId < 0 ? Reaction.reverseNegativeId(rootId) : rootId) .getInChI(); chemIdToInchi.put(rootId, rootInchi); Set<Long> children = parentToDescendantsAssociations.get(rootId); while (children != null && children.size() > 0) { Set<Long> descendants = rootToSetOfDescendants.get(rootId); if (descendants == null) { descendants = new HashSet<>(); rootToSetOfDescendants.put(rootId, descendants); } descendants.addAll(children); /** * Record depth for each member of children and construct a Set newChildren which is the set of all children * of the variable children. */ Set<Long> newChildren = new HashSet<>(); for (Long child : children) { String childInchi = chemIdToInchi.get(child); if (childInchi == null) { childInchi = db.readChemicalFromInKnowledgeGraph( child < 0 ? Reaction.reverseNegativeId(child) : child).getInChI(); chemIdToInchi.put(child, childInchi); } // Since a child is only associated with one parent, we can simply record it's depth from that root without // worrying about possible collisions with other roots as parents as none exist. depthOfMolecule.put(childInchi, depth); Set<Long> childrenOfChil = parentToDescendantsAssociations.get(child); if (childrenOfChil != null) { newChildren.addAll(childrenOfChil); } } children = newChildren; depth++; } } return rootToSetOfDescendants; } /** * This function constructs the conditional reachability forest, from each root to its descendants, and passes that * structure to the bing search results of chemical ranking. Based on the ranking, we output a tsv file for each * molecule that is conditionally reachable, its root and bing search metadata. * @param outputFilePath The output file to write to * @throws IOException */ private void run(String outputFilePath) throws IOException { LOGGER.info("Create parent to child associations"); Map<Long, Set<Long>> parentToChildrenAssociations = constructParentToChildAssociationsAndPopulateRootChemicals(); LOGGER.info("Construct trees from the root chemicals"); Map<Long, Set<Long>> rootToSetOfDescendants = constructRootToDescendantMappings( parentToChildrenAssociations); LOGGER.info("Construct reverse mapping from descendant to root chemical"); Map<String, String> descendantInchiToRootInchi = new HashMap<>(); for (Map.Entry<Long, Set<Long>> entry : rootToSetOfDescendants.entrySet()) { String rootInchi = chemIdToInchi.get(entry.getKey()); if (BLACKLISTED_ROOT_INCHIS.contains(rootInchi)) { continue; } for (Long descendant : entry.getValue()) { // Since a chemical is only added as a child to one specific root, there is not chance for collisions to happen. descendantInchiToRootInchi.put(chemIdToInchi.get(descendant), rootInchi); } } Set<String> allInchis = new HashSet<>(); allInchis.addAll(chemIdToInchi.values()); LOGGER.info("Add chemicals to bing search results"); // Update the Bing Search results in the Installer database BingSearchRanker bingSearchRanker = new BingSearchRanker(); bingSearchRanker.addBingSearchResults(allInchis); LOGGER.info("Write chemicals to output file"); bingSearchRanker.writeBingSearchRanksAsTSVUsingConditionalReachabilityFormat(allInchis, descendantInchiToRootInchi, depthOfMolecule, outputFilePath); } }