/*
 * Created on Apr 29, 2005
 */
/*
 * Copyright (c) 2002-5 Gregor Heinrich. 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 AUTHOR ``AS IS'' AND ANY EXPRESSED 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 AUTHOR 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.
 */

package org.knowceans.freshmind.cluster;

import java.io.BufferedReader;
import java.io.BufferedWriter;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.HashSet;
import java.util.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

/**
 * BibFileMod takes a LaTeX document and a list of BibTeX database files and
 * creates a new BibTeX database that contains the subset of the union of
 * bibliographic entries referenced in the LaTeX document.
 * <p>
 * The file uses a simple regex pattern to find the references in the LaTeX
 * file, as taken by the "\cite*{}" commands (plain and natbib packages and
 * BibTeX styles).
 * <p>
 * On the BibTeX entries, a regex identifies the entries with the keys.
 * <p>
 * TODO: bibtex file can be loaded automatically already. Make consistent with
 * multiple bibtex files case. (e.g., -o option for file output)
 *
 * @author heinrich
 */
public class BibFileMod {

    private static String bibtexfile = null;
    private static String path;

    /**
     * @param args
     */
    public static void main(String[] args) {

        // String[] test = {"D:/_mlpraktikum/themen2/themen.tex",
        // "D:/_disswnew/_bibliography/all20041029.bib",
        // "D:/_mlpraktikum/themen2/themenurs.tex.bib"};
        // args = test;

        System.out.println("BibFileMod BibTeX file modifier");

        if (args.length < 1) {
            System.out
                .println("Use with arguments: <file.tex> ( <file.bib> )+");
            System.out.println("Writes to <file.tex>.bib");
            System.out
                .println("If no bib file given, the one referenced in the \n"
                    + "tex file is used as source.");
            System.exit(1);
        }

        HashSet<String> citations = getCitations(args[0]);

        if (bibtexfile != null) {
            System.out
                .println("Referenced BibTeX file: " + bibtexfile + ".bib");

        }

        System.out.println("Found citation keys:");
        for (String cit : citations) {
            System.out.println(cit);
        }

        TreeMap<String, String> bibentries = new TreeMap<String, String>();
        for (int i = 1; i < args.length; i++) {
            getBibEntries(args[i], citations, bibentries);
        }
        if (args.length < 2 && bibtexfile != null) {
            getBibEntries(bibtexfile + ".bib", citations, bibentries);
        }

        String outfile = args[0] + ".bib";
        System.out.println("Write to " + outfile);
        write(outfile, bibentries);

    }

    /**
     * @param filename
     * @param bibentries
     */
    private static void write(String filename,
        TreeMap<String, String> bibentries) {
        try {
            BufferedWriter bw = new BufferedWriter(new FileWriter(filename));
            bw
                .write("%% Created with BibFileMod by GH (http://www.arbylon.net/projects)");
            bw.write("\n");
            System.out.println("Write entries found in database:");
            for (String key : bibentries.keySet()) {
                System.out.println(key);
                bw.write(bibentries.get(key));
                bw.write("\n");
            }
            bw.close();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }

    /**
     * Open the BibTeX file and add to the bibentries vector all BibTeX entries
     * whose key is in citations and not in the bibentries map.
     *
     * @param string BibTeX file path
     * @param citations list of citation keys
     * @param bibentries map of citation->BibTeX entry string entries
     */
    private static void getBibEntries(String texfile,
        HashSet<String> citations, TreeMap<String, String> bibentries) {

        StringBuffer content = new StringBuffer();

        try {
            BufferedReader br = new BufferedReader(new FileReader(texfile));
            String line;
            while ((line = br.readLine()) != null) {
                content.append(line).append("\n");
            }
            br.close();
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }

        String entryPattern = "(?si)(@[\\w]+\\{" + // opening entry
            "([\\w_\\-,]+)," + // bibtex key
            ".*?" + // non-greedy content
            "\\}\\s*,*\\s*\\})";

        Pattern p = Pattern.compile(entryPattern);
        Matcher m = p.matcher(content);
        while (m.find()) {
            String ref = m.group(2);
            String entry = m.group(1);
            if (citations.contains(ref)) {
                // System.out.println("Found entry: " + ref);
                // System.out.println(entry);
                bibentries.put(ref, entry);
            }
        }

    }

    /**
     * Parse the LaTeX file for citations with the usual "\cite*{}" format.
     *
     * @param texfile
     * @return
     */
    private static HashSet<String> getCitations(String texfile) {
        HashSet<String> citations = new HashSet<String>();

        path = new File(texfile).getParent().toString();

        StringBuffer content = new StringBuffer();

        try {
            BufferedReader br = new BufferedReader(new FileReader(texfile));
            String line;
            while ((line = br.readLine()) != null) {
                content.append(line).append(" ");
            }
            br.close();
        } catch (FileNotFoundException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }

        String citationPattern = "\\\\cite[^\\{]*\\{([\\w_\\-,]+)\\}";
        // TODO: does not work with line comments...
        String bibfilePattern = "\\\\bibliography\\{([^\\}]+)\\}";
        // String replaced;
        //
        // replaced = content.toString().replaceAll(citation, "\nCITATION[$1]");
        // System.out.println(replaced);

        Pattern p = Pattern.compile(citationPattern);
        Matcher m = p.matcher(content);
        while (m.find()) {
            String ref = m.group(1);
            String[] refs = ref.split(",");
            for (String oneref : refs) {
                citations.add(oneref);
            }
        }

        p = Pattern.compile(bibfilePattern);
        m = p.matcher(content);
        while (m.find()) {
            bibtexfile = m.group(1);
        }
        if (bibtexfile != null) {
            File f = new File(bibtexfile);
            if (!f.isAbsolute()) {
                try {
                    bibtexfile = new File(path + "/" + bibtexfile)
                        .getCanonicalPath();
                } catch (IOException e) {
                    e.printStackTrace();
                }
            }
        }
        return citations;
    }

}