/*************************************************************************
* *
* 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;
}
}
}