import java.util.*;
import java.io.*;
import java.text.*;

/**
 * Copyright (c) 2003, Regents of the University of California
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *   notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *   notice, this list of conditions and the following disclaimer in the
 *   documentation and/or other materials provided with the
 *   distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 *
**/

/**
 * The ExtractAbbrev class implements a simple algorithm for
 * extraction of abbreviations and their definitions from biomedical text.
 * Abbreviations (short forms) are extracted from the input file, and those abbreviations
 * for which a definition (long form) is found are printed out, along with that definition,
 * one per line.
 *
 * A file consisting of short-form/long-form pairs (tab separated) can be specified
 * in tandem with the -testlist option for the purposes of evaluating the algorithm.
 *
 * @see <a href="http://biotext.berkeley.edu/papers/psb03.pdf">A Simple Algorithm for Identifying Abbreviation Definitions in Biomedical Text</a> 
 * A.S. Schwartz, M.A. Hearst; Pacific Symposium on Biocomputing 8:451-462(2003) 
 * for a detailed description of the algorithm.  
 *
 * @author Ariel Schwartz
 * @version 03/12/03
 * 
 * @updated 07/20/16 by Marti Hearst to include BSD License.
 */
public class ExtractAbbrev {

    HashMap mTestDefinitions = new HashMap();
    HashMap mStats = new HashMap();
    int truePositives = 0, falsePositives = 0, falseNegatives = 0, trueNegatives = 0;
    char delimiter = '\t';
    boolean testMode = false;

    private boolean isValidShortForm(String str) {
	return (hasLetter(str) && (Character.isLetterOrDigit(str.charAt(0)) || (str.charAt(0) == '(')));
    }

    private boolean hasLetter(String str) {
	for (int i=0; i < str.length() ; i++)
	    if (Character.isLetter(str.charAt(i)))
		return true;
	return false;
    }

    private boolean hasCapital(String str) {
	for (int i=0; i < str.length() ; i++)
	    if (Character.isUpperCase(str.charAt(i)))
		return true;
	return false;
    }

    private void loadTrueDefinitions(String inFile) {
	String abbrString, defnString, str = "";
	Vector entry;
	HashMap definitions = mTestDefinitions;

	try {
	    BufferedReader fin = new BufferedReader(new FileReader (inFile));
	    while ((str = fin.readLine()) != null) {
		int j = str.indexOf(delimiter);
		abbrString = str.substring(0,j).trim();
		defnString = str.substring(j,str.length()).trim();		
		entry = (Vector)definitions.get(abbrString);
		if (entry == null)
		    entry = new Vector();
		entry.add(defnString);
		    definitions.put(abbrString, entry);
	    }
	} catch (Exception e) {
	    e.printStackTrace();
	    System.out.println(str);
	}
    }
    
    private boolean isTrueDefinition(String shortForm, String longForm) {
	Vector entry;
	Iterator itr;

	entry = (Vector)mTestDefinitions.get(shortForm);
	if (entry == null)
	    return false;
	itr = entry.iterator();
	while(itr.hasNext()){
	    if (itr.next().toString().equalsIgnoreCase(longForm))
		return true;
	}
	return false;
    }

    private Vector extractAbbrPairs(String inFile) {

	String str, tmpStr, longForm = "", shortForm = "";
	String currSentence = "";
	int openParenIndex, closeParenIndex = -1, sentenceEnd, newCloseParenIndex, tmpIndex = -1;
	boolean newParagraph = true;
	StringTokenizer shortTokenizer;
	Vector candidates = new Vector();

	try {
	    BufferedReader fin = new BufferedReader(new FileReader (inFile));
	    while ((str = fin.readLine()) != null) {
		if (str.length() == 0 || newParagraph && 
		    ! Character.isUpperCase(str.charAt(0))){
		    currSentence = "";
		    newParagraph = true;
		    continue;
		}
		newParagraph = false;
		str += " ";
		currSentence += str;
		openParenIndex =  currSentence.indexOf(" (");
		do {
		    if (openParenIndex > -1)
			openParenIndex++;
		    sentenceEnd = Math.max(currSentence.lastIndexOf(". "), currSentence.lastIndexOf(", "));
		    if ((openParenIndex == -1) && (sentenceEnd == -1)) {
			//Do nothing
		    }
		    else if (openParenIndex == -1) {
			currSentence = currSentence.substring(sentenceEnd + 2);
		    } else if ((closeParenIndex = currSentence.indexOf(')',openParenIndex)) > -1){
			sentenceEnd = Math.max(currSentence.lastIndexOf(". ", openParenIndex), 
					       currSentence.lastIndexOf(", ", openParenIndex));
			if (sentenceEnd == -1)
			    sentenceEnd = -2;
			longForm = currSentence.substring(sentenceEnd + 2, openParenIndex);
			shortForm = currSentence.substring(openParenIndex + 1, closeParenIndex);
		    }
		    if (shortForm.length() > 0 || longForm.length() > 0) {
			if (shortForm.length() > 1 && longForm.length() > 1) {
			    if ((shortForm.indexOf('(') > -1) && 
				((newCloseParenIndex = currSentence.indexOf(')', closeParenIndex + 1)) > -1)){
				shortForm = currSentence.substring(openParenIndex + 1, newCloseParenIndex);
				closeParenIndex = newCloseParenIndex;
			    }
			    if ((tmpIndex = shortForm.indexOf(", ")) > -1)
				shortForm = shortForm.substring(0, tmpIndex);			    
			    if ((tmpIndex = shortForm.indexOf("; ")) > -1)
				shortForm = shortForm.substring(0, tmpIndex);
			    shortTokenizer = new StringTokenizer(shortForm);
			    if (shortTokenizer.countTokens() > 2 || shortForm.length() > longForm.length()) {
				// Long form in ( )
				tmpIndex = currSentence.lastIndexOf(" ", openParenIndex - 2);
				tmpStr = currSentence.substring(tmpIndex + 1, openParenIndex - 1);
				longForm = shortForm;
				shortForm = tmpStr;
				if (! hasCapital(shortForm))
				    shortForm = "";
			    }
			    if (isValidShortForm(shortForm)){
				extractAbbrPair(shortForm.trim(), longForm.trim());
			    }
			}
			currSentence = currSentence.substring(closeParenIndex + 1);
		    } else if (openParenIndex > -1) {
			if ((currSentence.length() - openParenIndex) > 200)
			    // Matching close paren was not found
			    currSentence = currSentence.substring(openParenIndex + 1);
			break; // Read next line
		    }
		    shortForm = "";
		    longForm = "";
		} while ((openParenIndex =  currSentence.indexOf(" (")) > -1);
	    }
	    fin.close();
	} catch (Exception ioe) {
	    ioe.printStackTrace();
	    System.out.println(currSentence);
	    System.out.println(tmpIndex);
	}
	    return candidates;
    }

    private String findBestLongForm(String shortForm, String longForm) {
	int sIndex;
	int lIndex;
	char currChar;

	sIndex = shortForm.length() - 1;
	lIndex = longForm.length() - 1;
	for ( ; sIndex >= 0; sIndex--) {
	    currChar = Character.toLowerCase(shortForm.charAt(sIndex));
	    if (!Character.isLetterOrDigit(currChar))
		continue;
	    while (((lIndex >= 0) && (Character.toLowerCase(longForm.charAt(lIndex)) != currChar)) ||
		   ((sIndex == 0) && (lIndex > 0) && (Character.isLetterOrDigit(longForm.charAt(lIndex - 1)))))
		lIndex--;
	    if (lIndex < 0)
		return null;
	    lIndex--;
	}
	lIndex = longForm.lastIndexOf(" ", lIndex) + 1;
	return longForm.substring(lIndex);
    }

    private void extractAbbrPair(String shortForm, String longForm) {
	String bestLongForm;
	StringTokenizer tokenizer;
	int longFormSize, shortFormSize;

	if (shortForm.length() == 1)
	    return;
	bestLongForm = findBestLongForm(shortForm, longForm);
	if (bestLongForm == null)
	    return;
	tokenizer = new StringTokenizer(bestLongForm, " \t\n\r\f-");
	longFormSize = tokenizer.countTokens();
	shortFormSize = shortForm.length();
	for (int i=shortFormSize - 1; i >= 0; i--)
	    if (!Character.isLetterOrDigit(shortForm.charAt(i)))
		shortFormSize--;
	if (bestLongForm.length() < shortForm.length() || 
	    bestLongForm.indexOf(shortForm + " ") > -1 ||
	    bestLongForm.endsWith(shortForm) ||
	    longFormSize > shortFormSize * 2 ||
	    longFormSize > shortFormSize + 5 ||
	    shortFormSize > 10)
	    return;

	if (testMode) {
	    if (isTrueDefinition(shortForm, bestLongForm)) {
		System.out.println(shortForm + delimiter + bestLongForm + delimiter + "TP");
		truePositives++;
	    }
	    else {
		falsePositives++;
		System.out.println(shortForm + delimiter + bestLongForm + delimiter + "FP");
	    }	
	}
	else {
	    System.out.println(shortForm + delimiter + bestLongForm);
	}
    }
    

    private static void usage() {
        System.err.println("Usage: ExtractAbbrev [-options] <filename>");
        System.err.println("       <filename> contains text from which abbreviations are extracted" );
        System.err.println("       -testlist <file> = list of true abbreviation definition pairs");
	System.err.println("       -usage or -help = this message");
        System.exit(1);
    }

    public static void main(String[] args) {
	String shortForm, longForm, defnString, str;
	ExtractAbbrev extractAbbrev = new ExtractAbbrev();
	Vector candidates;	
	String[] candidate;
	String filename =  null;
	String testList = null;
	
	//parse arguments
        for (int i = 0; i < args.length; i++) {
            if (args[i].equals("-testlist")) {
                if (i == args.length - 1) {
                    usage();
                }
                testList = args[++i];
		extractAbbrev.testMode = true;
            } else if (args[i].equals("-usage")) {
                usage();
            } else if (args[i].equals("-help")) {
                usage();
            } else {
                filename = args[i];
                // Must be last arg
                if (i != args.length - 1) {
                    usage();
                }
            }
        }
        if (filename == null) {
            usage();
        }

	if (extractAbbrev.testMode)
	    extractAbbrev.loadTrueDefinitions(testList);
	extractAbbrev.extractAbbrPairs(filename);
	if (extractAbbrev.testMode)
	    System.out.println("TP: " + extractAbbrev.truePositives + " FP: " + extractAbbrev.falsePositives + 
			       " FN: " + extractAbbrev.falseNegatives + " TN: " + extractAbbrev.trueNegatives);
    }
}