BiomailImporter.java

package net.sf.jabref.imports;

import net.sf.jabref.BibtexEntry;
import net.sf.jabref.Globals;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;

import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.regex.Pattern;
import net.sf.jabref.BibtexFields;


/**
 * Importer for the ISI Web of Science format.
 */
public class BiomailImporter extends ImportFormat {
    /**
     * Return the name of this import format.
     */
    public String getFormatName() {
        return "Biomail";
    }

    /*
     *  (non-Javadoc)
     * @see net.sf.jabref.imports.ImportFormat#getCLIId()
     */
    public String getCLIId() {
      return "biomail";
    }

    /**
     * Check whether the source is in the correct format for this importer.
     */
    public boolean isRecognizedFormat(InputStream stream)
            throws IOException {
        // Our strategy is to look for the "BioMail" line.
        BufferedReader in =
                new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
        Pattern pat1 = Pattern.compile("BioMail");

        String str;

        while ((str = in.readLine()) != null) {

            if (pat1.matcher(str).find())
                return true;
        }

        return false;
    }


    /**
     * Parse the entries in the source, and return a List of BibtexEntry
     * objects.
     */
    public List<BibtexEntry> importEntries(InputStream stream) throws IOException {
        ArrayList<BibtexEntry> bibitems = new ArrayList<BibtexEntry>();
        StringBuffer sb = new StringBuffer();

        BufferedReader in =
                new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));

        String str;

        while ((str = in.readLine()) != null) {
            if (str.length() < 3)
                continue;

            // begining of a new item
            if (str.substring(0, 6).equals("PMID- "))
                sb.append("::").append(str);
            else {
                String beg = str.substring(0, 6);

                if (beg.indexOf(" ") > 0) {
                    sb.append(" ## "); // mark the begining of each field
                    sb.append(str);
                } else {
                    sb.append("EOLEOL"); // mark the end of each line
                    sb.append(str.trim());
                }
            }
        }

        String[] entries = sb.toString().split("::");

        // skip the first entry as it is either empty or has document header
        HashMap<String, String> hm = new HashMap<String, String>();

        for (int i = 0; i < entries.length; i++) {
            String[] fields = entries[i].split(" ## ");

            if (fields.length == 0)
                fields = entries[i].split("\n");

            String Type = "";
            String pages = "";
            String shortauthor = "";
            String fullauthor = "";
            hm.clear();

            for (int j = 0; j < fields.length; j++) {
                System.out.println(">>>"+fields[j]+"<<<");

                //empty field don't do anything
                if (fields[j].length() <= 2)
                    continue;

                String beg = fields[j].substring(0, 6);
                String value = fields[j].substring(6);
                value = value.trim();

                if (beg.equals("PT  - ")) {
                    // PT = value.replaceAll("JOURNAL ARTICLE", "article").replaceAll("Journal Article", "article");
                    Type = "article"; //make all of them PT?
                } else if (beg.equals("TY  - ")) {
                    if ("CONF".equals(value))
                        Type = "inproceedings";
                } else if (beg.equals("JO  - "))
                    hm.put("booktitle", value);
                else if (beg.equals("FAU - ")) {
                    String tmpauthor = value.replaceAll("EOLEOL", " and ");

                    // if there is already someone there then append with "and"
                    if (!"".equals(fullauthor))
                        fullauthor = fullauthor + " and " + tmpauthor;
                    else
                        fullauthor = tmpauthor;
                } else if (beg.equals("AU  - ")) {
                    String tmpauthor = value.replaceAll("EOLEOL", " and ").replaceAll(" ", ", ");

                    // if there is already someone there then append with "and"
                    if (!"".equals(shortauthor))
                        shortauthor = shortauthor + " and " + tmpauthor;
                    else
                        shortauthor = tmpauthor;
                } else if (beg.equals("TI  - "))
                    hm.put("title", value.replaceAll("EOLEOL", " "));
                else if (beg.equals("TA  - "))
                    hm.put("journal", value.replaceAll("EOLEOL", " "));
                else if (beg.equals("AB  - "))
                    hm.put("abstract", value.replaceAll("EOLEOL", " "));
                else if (beg.equals("PG  - "))
                    pages = value.replaceAll("-", "--");
                else if (beg.equals("IP  - "))
                    hm.put("number", value);
                else if (beg.equals("DP  - ")) {
                    String[] parts = value.split(" "); // sometimes this is just year, sometimes full date
                    hm.put("year", parts[0]);
                } else if (beg.equals("VI  - "))
                    hm.put("volume", value);
                else if (beg.equals("AID - ")) {
                    String[] parts = value.split(" ");
                    if ("[doi]".equals(parts[1])) {
                        hm.put("doi", parts[0]);
                        hm.put("url", "http://dx.doi.org/" + parts[0]);
                    }
                }
            }

            if (!"".equals(pages))
                hm.put("pages", pages);
            if (!"".equals(fullauthor))
                hm.put("author", fullauthor);
            else if (!"".equals(shortauthor))
                hm.put("author", shortauthor);

            BibtexEntry b =
                    new BibtexEntry(BibtexFields.DEFAULT_BIBTEXENTRY_ID, Globals.getEntryType(Type)); // id assumes an existing database so don't

            // create one here
            b.setField(hm);

            // the first bibitem is always empty, presumably as a result of trying
            // to parse header informaion. So add only if we have at least author or
            // title fields.
            if (hm.get("author") != null || hm.get("title") != null)
                bibitems.add(b);
        }

        return bibitems;
    }


}