/*
Copyright (C) 2002-2003 Morten O. Alver & Nizar N. Batada
All programs in this directory and
subdirectories are published under the GNU General Public License as
described below.
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or (at
your option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
USA
Further information about the GNU GPL is available at:
http://www.gnu.org/copyleft/gpl.ja.html
*/
package net.sf.jabref.imports;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.TreeSet;
import net.sf.jabref.BibtexEntry;
import net.sf.jabref.Globals;
import net.sf.jabref.Util;
import org.xml.sax.Attributes;
import org.xml.sax.helpers.DefaultHandler;
public class MedlineHandler extends DefaultHandler
{
ArrayList<BibtexEntry> bibitems= new ArrayList<BibtexEntry>();
boolean inTitle=false, inYear = false,
inJournal = false, inMonth = false,
inVolume = false, inAuthorList = false,
inAuthor =false, inLastName = false,
inInitials = false, inMedlinePgn = false,
inMedlineID = false, inURL=false,
inIssue = false, inPubDate = false,
inUrl=false, inForename=false, inAbstractText=false, inMedlineDate=false,
inPubMedID=false, inDescriptorName=false,inDoi=false,inPii=false,
inAffiliation=false, inMeshHeader=false, inQualifierName=false,
inLanguage=false, inPst=false;
String title="", journal="", keywords ="",author="",
lastName="",year="",forename="", abstractText="", affiliation="";
String month="",volume="",lastname="",initials="",number="",page="",medlineID="",url="",MedlineDate="";
String series="",editor="",booktitle="",type="article",key="",address="",
pubmedid="",doi="",pii="", majorTopic = "", minorTopics = "", language = "", pst= "";
ArrayList<String> authors=new ArrayList<String>();
TreeSet<String> descriptors = new TreeSet<String>(); // To gather keywords
int rowNum=0;
private static final String KEYWORD_SEPARATOR = "; ";
public ArrayList<BibtexEntry> getItems(){ return bibitems;}
public MedlineHandler(){
super();
}
public void startElement(String uri, String localName, String qName, Attributes atts)
{
// public void startElement(String localName, Attributes atts) {
// Get the number of attribute
if(localName.equals("PubmedArticle")){}
else if(localName.equals("ArticleTitle")){ inTitle=true; title="";}
else if(localName.equals("PubDate")){inPubDate=true;}
else if(localName.equals("Year") && inPubDate==true){inYear=true;}
else if( localName.equals("MedlineDate") && inPubDate==true){inMedlineDate=true;} // medline date does not have 4 digit dates instead it has multiyear etc
else if(localName.equals("MedlineTA")){inJournal=true;journal="";} //journal name
else if(localName.equals("Month") && inPubDate==true){inMonth=true;}
else if(localName.equals("Volume")){inVolume=true;}
else if(localName.equals("Language")){inLanguage=true;}
else if(localName.equals("PublicationStatus")){inPst=true;}
else if(localName.equals("AuthorList")){
inAuthorList=true;
authors.clear();}
else if (localName.equals("MeshHeading")) {
inMeshHeader = true;
majorTopic = "";
minorTopics = "";
}
else if(localName.equals("DescriptorName")){
inDescriptorName=true;
}
else if (localName.equals("QualifierName")) {
inQualifierName=true;
}
else if(localName.equals("Author")){inAuthor=true;author="";}
else if(localName.equals("CollectiveName")){inForename=true;forename="";} // Morten A. 20040513.
else if(localName.equals("PMID")){
// Set PMID only once, because there can be <CommentIn> tags later on that
// contain IDs of different articles.
if (pubmedid.length() == 0) {
inPubMedID=true;
pubmedid="";
}
}
else if(localName.equals("LastName")){inLastName=true; lastName="";}
else if(localName.equals("ForeName") || localName.equals("FirstName")) {
inForename=true; forename="";
}
else if(localName.equals("Issue")){inIssue=true;}
else if(localName.equals("MedlinePgn")){inMedlinePgn=true;
}//pagenumber
else if(localName.equals("URL")){inUrl=true;}
else if(localName.equals("Initials")){inInitials=true;}
else if(localName.equals("AbstractText")){ inAbstractText=true;}
else if(localName.equals("ArticleId")){
for (int i = 0; i < atts.getLength(); i++) {
String value = atts.getValue(i);
if(value.equals("doi"))
inDoi=true;
else if(value.equals("pii"))
inPii=true;
}
}
else if(localName.equals("Affiliation")){ inAffiliation=true; }
return;
}
String join(Object[] sa,String delim){
StringBuffer sb=new StringBuffer();
sb.append( sa[0].toString() );
for(int i=1; i<sa.length; i++)
{
sb.append( delim );
sb.append( sa[i].toString() );
}
return sb.toString();
}
String makeBibtexString(){
String out = "";
// PENDING jeffrey.kuhn@yale.edu 2005-05-27 : added call to fixPageRange
out= "article{,\n" + " author = { " + author + " },\n title = { " + title + "},\n journal ={ " + journal + "},\n year = " + year +
"},\n volume = { " + volume + "},\n number = { "+ number + "},\n pages = { " + fixPageRange(page) + "},\n abstract = { " + abstractText + "},\n}";
return out;
}
public void endElement( String uri, String localName, String qName ) {
if(localName.equals("PubmedArticle")){
//bibitems.add( new Bibitem(null, makeBibtexString(), Globals.nextKey(),"-1" ) );
// check if year ="" then give medline date instead
if(year.equals("")){
if(!MedlineDate.equals("")) {
// multi-year date format
//System.out.println(MedlineDate);
year = MedlineDate.substring(0,4);
//Matcher m = Pattern.compile("\\b[0-9]{4}\\b").matcher(MedlineDate);
//if(m.matches())
//year = m.group();
}
}
// Build a string from the collected keywords:
StringBuffer sb = new StringBuffer();
for (Iterator<String> iterator = descriptors.iterator(); iterator.hasNext();) {
String s = iterator.next();
sb.append(s);
if (iterator.hasNext())
sb.append(KEYWORD_SEPARATOR);
}
keywords = sb.toString();
BibtexEntry b=new BibtexEntry(Util.createNeutralId(),//Globals.DEFAULT_BIBTEXENTRY_ID,
Globals.getEntryType("article")); // id assumes an existing database so don't create one here
if (!author.equals("")) {
b.setField("author",ImportFormatReader.expandAuthorInitials(author));
author = "";
}
if (!title.equals("")) b.setField("title",title);
if (!journal.equals("")) b.setField("journal",journal);
if (!year.equals("")) b.setField("year",year);
// PENDING jeffrey.kuhn@yale.edu 2005-05-27 : added call to fixPageRange
if (!page.equals("")) b.setField("pages",fixPageRange(page));
if (!volume.equals("")) b.setField("volume",volume);
if (!language.equals("")) b.setField("language",language);
if (!pst.equals("")) b.setField("medline-pst", pst);
if (!abstractText.equals("")) b.setField("abstract",abstractText.replaceAll("%","\\\\%"));
if (!keywords.equals("")) b.setField("keywords",keywords);
if (!month.equals("")) b.setField("month",month);
//if (!url.equals("")) b.setField("url",url);
if (!number.equals("")) b.setField("number",number);
if(!doi.equals("")){
b.setField("doi",doi);
b.setField("url","http://dx.doi.org/"+doi);
}
if(!pii.equals(""))
b.setField("pii",pii);
if(!affiliation.equals("")) {
b.setField("institution",affiliation.replaceAll("#", "\\\\#"));
}
// PENDING jeffrey.kuhn@yale.edu 2005-05-27 : added "pmid" bibtex field
// Older references do not have doi entries, but every
// medline entry has a unique pubmed ID (aka primary ID).
// Add a bibtex field for the pubmed ID for future use.
if (!pubmedid.equals(""))
b.setField("pmid",pubmedid);
bibitems.add( b );
abstractText = "";
author = "";
title="";
journal="";
keywords ="";
doi=""; pii="";
year="";
forename="";
lastName="";
abstractText="";
affiliation="";
pubmedid="";
majorTopic = "";
minorTopics = "";
month="";volume="";language="";pst="";lastname="";initials="";number="";page="";medlineID="";url="";
MedlineDate="";
descriptors.clear();
}
else if(localName.equals("ArticleTitle")){inTitle=false;}
else if(localName.equals("PubDate")){inPubDate=false;}
else if(localName.equals("Year")){inYear=false;}
else if(localName.equals("PMID")){inPubMedID=false;}
else if(localName.equals("MedlineDate")){inMedlineDate=false;}
else if(localName.equals("MedlineTA")){inJournal=false;} //journal name
else if(localName.equals("Month")){inMonth=false;}
else if(localName.equals("Volume")){inVolume=false;}
else if(localName.equals("Language")){inLanguage=false;}
else if(localName.equals("PublicationStatus")){inPst=false;}
else if(localName.equals("AuthorList")){
author = join( authors.toArray(), " and " );
inAuthorList = false;
}
else if(localName.equals("Author")){
// forename sometimes has initials with " " in middle: is pattern [A-Z] [A-Z]
// when above is the case replace it with initials
if(forename.length()==3 && forename.charAt(1)==' '){
forename=initials;
}
author = forename + " " + lastname;
//author = initials + " " + lastname;
authors.add(author);
inAuthor=false;
forename = "";
initials = "";
lastname = "";
}
else if(localName.equals("DescriptorName")) inDescriptorName=false;
else if(localName.equals("QualifierName")) inQualifierName=false;
else if(localName.equals("MeshHeading")) {
inMeshHeader = false;
if (minorTopics.equals(""))
descriptors.add(majorTopic);
else
descriptors.add(majorTopic+", "+minorTopics);
}
else if(localName.equals("LastName")){inLastName=false;}
else if(localName.equals("ForeName")||localName.equals("FirstName")){ inForename=false;}
else if(localName.equals("Issue")){ inIssue = false;}
else if(localName.equals("MedlinePgn")){inMedlinePgn=false;}//pagenumber
else if(localName.equals("URL")){ inUrl=false;}
else if(localName.equals("Initials")){
//initials= '.' + initials + '.';
inInitials=false;
}
else if(localName.equals("AbstractText")){ inAbstractText=false;}
else if(localName.equals("Affiliation")){ inAffiliation=false; }
else if(localName.equals("ArticleId")){
if(inDoi)
inDoi=false;
else if(inPii)
inPii=false;}
}
public void characters( char[] data, int start, int length ) {
// if stack is not ready, data is not content of recognized element
if( inTitle ){ title += new String( data, start, length);}
else if(inYear){ year+=new String(data,start,length);}
else if(inJournal){journal += new String(data,start,length);}
else if(inMonth){month += new String(data,start,length);}
else if(inVolume){volume += new String(data,start,length);}
else if(inLanguage){language += new String(data,start,length).toLowerCase();}
else if(inPst){pst += new String(data,start,length);}
else if(inLastName){lastname += new String(data,start,length);}
else if(inInitials){initials += new String(data,start,length);}
else if(inIssue){number += new String(data,start,length);}
else if(inMedlinePgn){ page += new String(data,start,length);}
else if(inMedlineID){medlineID += new String(data,start,length);}
else if(inURL){url += new String(data,start,length);}
else if(inPubMedID){pubmedid = new String(data,start,length);}
else if(inQualifierName) {
if (!minorTopics.equals(""))
minorTopics = minorTopics+"/";
minorTopics = minorTopics + new String(data,start,length);
}
else if(inDescriptorName) {
majorTopic = new String(data,start,length);
}
//keywords += new String(data,start,length) + ", ";
else if(inForename){
forename += new String(data,start,length);
//System.out.println("IN FORENAME: " + forename);
}
else if(inAbstractText){ abstractText += new String(data,start,length);}
else if(inMedlineDate){ MedlineDate += new String(data,start,length);}
else if(inDoi){ doi=new String(data,start,length);}
else if(inPii){ pii=new String(data,start,length);}
else if(inAffiliation){ affiliation = new String(data,start,length);}
}
// PENDING jeffrey.kuhn@yale.edu 2005-05-27 : added fixPageRange method
// Convert medline page ranges from short form to full form.
// Medline reports page ranges in a shorthand format.
// The last page is reported using only the digits which
// differ from the first page.
// i.e. 12345-51 refers to the actual range 12345-12351
public String fixPageRange(String pageRange) {
int minusPos = pageRange.indexOf('-');
if (minusPos < 0) {
return pageRange;
}
String first = pageRange.substring(0, minusPos).trim();
String last = pageRange.substring(minusPos+1).trim();
int llast = last.length(), lfirst = first.length();
if (llast < lfirst) {
last = first.substring(0, lfirst-llast) + last;
}
return first + "--" + last;
}
}