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;
}
}