PhraseMarker.java

/**
 * 
 */
package fna.parsing;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.ObjectInputStream;
import java.io.ObjectOutput;
import java.io.ObjectOutputStream;
import java.io.PrintWriter;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.List;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import outputter.knowledge.TermOutputerUtilities;
import fna.parsing.ApplicationUtilities;
import fna.parsing.ParsingException;
import fna.parsing.TaxonIndexer;

/**
 * @author Hong Cui
 * convert a sentence to a format so the phrases matching terms in a knowledge source such as an ontology are marked.
 * A phrase is represented by words connected using "_"
 *
 */
public class PhraseMarker {
	private Pattern phrasepattern; //"dorsal_fin|leaf_blade"
	private String phrasestr;
	public ArrayList<String> phrases;
	public Hashtable<String, String> newphrases = new Hashtable<String, String>(); //plural => singular
	
	//private static final String BIN_FILE = "PO_phrases.bin";
	/**
	 * @param termsource: filepath to the serialized arraylist, holding the phrases 
	 */
	@SuppressWarnings("unchecked")
	public PhraseMarker(/*String termsourcepath*/) {
		try {
			File file = new File(ApplicationUtilities.getProperty("ontology.dir"),ApplicationUtilities.getProperty("ontology.uberon")+"_"+ApplicationUtilities.getProperty("uberonphrases.bin"));
			ObjectInputStream in = new ObjectInputStream(new FileInputStream(
					file));
			// Deserialize the object
		    phrases = new ArrayList();
		    phrases.addAll((HashSet<String>) in.readObject()); //phrases are words connected with " "
			in.close();			
			Collections.sort(phrases, new PhraseComparable()); //longest phrases first
			phrasestr = "";
			for(String phrase: phrases){
				//hyomandibula-opercle joint
				phrase = phrase.replaceAll("\\([^)]*\\)", "").trim();
				if(phrase.length()>0 && phrase.indexOf(" ")>0){ //can't allow single-word phrase 
					phrase = phrase.replaceAll("-", "_");//hyomandibula_opercle joint
					phrase = phraseForms(phrase);//added plural forms
					phrasestr += phrase+"|";
				}
			}
			//phrasestr="";
			phrasestr = phrasestr.replaceFirst("\\|$", ""); //space separated words in phrases
			System.out.println(phrasestr);
			this.phrasepattern =Pattern.compile("(.*?\\b)("+phrasestr+")(\\b.*)", Pattern.CASE_INSENSITIVE);
			//serialize the updated phrases
			phrases.addAll(newphrases.keySet()); //add plurals
			ObjectOutput out = new ObjectOutputStream(
					new FileOutputStream(new File(ApplicationUtilities.getProperty("ontology.dir"),ApplicationUtilities.getProperty("ontology.uberon")+"_"+ApplicationUtilities.getProperty("uberonphrases.update.bin")))); //avoid increase the size of the original
			out.writeObject(phrases);
			out.close();
			//serialize the plural-singular mapping
			file = new File(ApplicationUtilities.getProperty("ontology.dir"),ApplicationUtilities.getProperty("ontology.uberon")+"_"+ApplicationUtilities.getProperty("uberonphrases.p2s.bin"));
			out = new ObjectOutputStream(
					new FileOutputStream(file));
			out.writeObject(newphrases);
			out.close();
		} catch (Exception e) {
			//LOGGER.error("Load the updated TaxonIndexer failed.", e);
			//StringWriter sw = new StringWriter();PrintWriter pw = new PrintWriter(sw);e.printStackTrace(pw);LOGGER.error(ApplicationUtilities.getProperty("CharaParser.version")+System.getProperty("line.separator")+sw.toString());
			e.printStackTrace();
		}
	}

	/**
	 * endochondral element => endochondral element|endochondral elements
	 * @param phrase: typically in singular form
	 * @return alternative reg exp with original and plural forms
	 */
	private String phraseForms(String phrase) {
		if(phrase.indexOf(" ")>0){
			String result = phrase;
			String noun = phrase.substring(phrase.lastIndexOf(" ")).trim();
			String modifier = phrase.substring(0, phrase.lastIndexOf(" ")).trim();
			String pnoun = noun.matches("\\d+")? noun : outputter.knowledge.TermOutputerUtilities.toPlural(noun);
			if(pnoun.compareTo(noun)!=0){
				result += "|"+modifier+" "+pnoun;
				this.newphrases.put(modifier+" "+pnoun, phrase); //plural=>singluar
			}
			return result;
		}
		return phrase;
	}

	/**
	 * @param sentence : leaf blade rounded
	 * @return leaf_blade rounded
	 */
	public String markPhrases(String sentence){
		Matcher m = phrasepattern.matcher(sentence);
		//System.out.println(this.phrasestr);
		while(m.matches()){
			//System.out.println(phrasepattern);
			sentence = m.group(1)+m.group(2).replaceAll("\\s+", "_")+m.group(3);
			m = phrasepattern.matcher(sentence);
		}				
		return sentence;
	}
	/**
	 * @param args
	 */
	public static void main(String[] args) {
		
		long time1 = System.currentTimeMillis();
		String termpath = "C:/Users/updates/CharaParserTest/Ontologies/ext_terms.bin";
		PhraseMarker pm = new PhraseMarker(/*termpath*/);
		long time2 = System.currentTimeMillis();
		System.out.println("read term list took "+(time2-time1)+" ms");
		//System.out.println(pm.markPhrases("hyomandibula-opercle joint and anal fin absent . female gonad present."));
		System.out.println(pm.markPhrases("Medioventral endochondral elements of the shoulder girdle"));
		long time3 = System.currentTimeMillis();
		System.out.println("mark the sentence took "+(time3-time2)+" ms");
	}
}