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.twentyn.patentScorer; import com.fasterxml.jackson.annotation.JsonProperty; import com.fasterxml.jackson.databind.ObjectMapper; import com.twentyn.patentExtractor.PatentCorpusReader; import com.twentyn.patentExtractor.PatentDocument; import com.twentyn.patentExtractor.PatentProcessor; 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.io.input.ReaderInputStream; import org.apache.logging.log4j.Level; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; import org.apache.logging.log4j.core.LoggerContext; import org.apache.logging.log4j.core.config.Configuration; import org.apache.logging.log4j.core.config.LoggerConfig; import org.xml.sax.SAXException; import javax.xml.parsers.ParserConfigurationException; import javax.xml.transform.TransformerConfigurationException; import javax.xml.transform.TransformerException; import javax.xml.xpath.XPathExpressionException; import java.io.File; import java.io.FileWriter; import java.io.IOException; import java.io.Reader; import java.nio.CharBuffer; import java.nio.charset.Charset; public class PatentScorer implements PatentProcessor { public static final Logger LOGGER = LogManager.getLogger(PatentScorer.class); public static void main(String[] args) throws Exception { System.out.println("Starting up..."); System.out.flush(); Options opts = new Options(); opts.addOption(Option.builder("i").longOpt("input").hasArg().required() .desc("Input file or directory to score").build()); opts.addOption(Option.builder("o").longOpt("output").hasArg().required() .desc("Output file to which to write score JSON").build()); opts.addOption(Option.builder("h").longOpt("help").desc("Print this help message and exit").build()); opts.addOption(Option.builder("v").longOpt("verbose").desc("Print verbose log output").build()); HelpFormatter helpFormatter = new HelpFormatter(); CommandLineParser cmdLineParser = new DefaultParser(); CommandLine cmdLine = null; try { cmdLine = cmdLineParser.parse(opts, args); } catch (ParseException e) { System.out.println("Caught exception when parsing command line: " + e.getMessage()); helpFormatter.printHelp("DocumentIndexer", opts); System.exit(1); } if (cmdLine.hasOption("help")) { helpFormatter.printHelp("DocumentIndexer", opts); System.exit(0); } if (cmdLine.hasOption("verbose")) { // With help from http://stackoverflow.com/questions/23434252/programmatically-change-log-level-in-log4j2 LoggerContext ctx = (LoggerContext) LogManager.getContext(false); Configuration ctxConfig = ctx.getConfiguration(); LoggerConfig logConfig = ctxConfig.getLoggerConfig(LogManager.ROOT_LOGGER_NAME); logConfig.setLevel(Level.DEBUG); ctx.updateLoggers(); LOGGER.debug("Verbose logging enabled"); } String inputFileOrDir = cmdLine.getOptionValue("input"); File splitFileOrDir = new File(inputFileOrDir); if (!(splitFileOrDir.exists())) { LOGGER.error("Unable to find directory at " + inputFileOrDir); System.exit(1); } try (FileWriter writer = new FileWriter(cmdLine.getOptionValue("output"))) { PatentScorer scorer = new PatentScorer(PatentModel.getModel(), writer); PatentCorpusReader corpusReader = new PatentCorpusReader(scorer, splitFileOrDir); corpusReader.readPatentCorpus(); } } public static final String LINE_SEPARATOR = System.lineSeparator(); private PatentModel patentModel; private FileWriter outputWriter; private ObjectMapper objectMapper; public PatentScorer(PatentModel patentModel, FileWriter outputWriter) { this.patentModel = patentModel; this.outputWriter = outputWriter; this.objectMapper = new ObjectMapper(); } @Override public void processPatentText(File patentFile, Reader patentTextReader, int patentTextLength) throws IOException, ParserConfigurationException, SAXException, TransformerConfigurationException, TransformerException, XPathExpressionException { System.out.println("Patent text length: " + patentTextLength); CharBuffer buff = CharBuffer.allocate(patentTextLength); int read = patentTextReader.read(buff); System.out.println("Read bytes: " + read); patentTextReader.reset(); String fullContent = new String(buff.array()); PatentDocument patentDocument = PatentDocument .patentDocumentFromXMLStream(new ReaderInputStream(patentTextReader, Charset.forName("utf-8"))); if (patentDocument == null) { LOGGER.info("Found non-patent type document, skipping."); return; } double pr = this.patentModel.ProbabilityOf(fullContent); this.outputWriter .write(objectMapper.writeValueAsString(new ClassificationResult(patentDocument.getFileId(), pr))); this.outputWriter.write(LINE_SEPARATOR); System.out.println("Doc " + patentDocument.getFileId() + " has score " + pr); } public static class ClassificationResult { @JsonProperty("doc_id") protected String docId; @JsonProperty("score") protected Double score; protected ClassificationResult() { } public ClassificationResult(String docId, Double score) { this.docId = docId; this.score = score; } public String getDocId() { return docId; } public Double getScore() { return score; } } }