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BugFix for bug "#880 PubMed Import broken" #11

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Jun 28, 2014
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BugFix for bug "#880 PubMed Import broken" #11

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279 changes: 279 additions & 0 deletions src/main/java/net/sf/jabref/imports/MedlinePlainImporter.java
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/* Copyright (C) 2003-2011 JabRef contributors.
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.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

*/

package net.sf.jabref.imports;

import java.util.regex.Pattern;
import java.io.InputStream;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.List;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Iterator;

import net.sf.jabref.BibtexEntry;
import net.sf.jabref.Globals;
import net.sf.jabref.AuthorList;
import net.sf.jabref.BibtexFields;
import net.sf.jabref.OutputPrinter;

/**
* Importer for the MEDLINE Plain format.
*
* check here for details on the format
* http://www.nlm.nih.gov/bsd/mms/medlineelements.html
*
* @author vegeziel
*/
public class MedlinePlainImporter extends ImportFormat {

/**
* Return the name of this import format.
*/
public String getFormatName() {
return "MedlinePlain";
}

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

/**
* 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 "PMID - *", "PMC.*-.*", or "PMCR.*-.*" line
// (i.e., PubMed Unique Identifier, PubMed Central Identifier, PubMed Central Release)
BufferedReader in = new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
Pattern pat1 = Pattern.compile("PMID.*-.*"),
pat2 = Pattern.compile("PMC.*-.*"),
pat3 = Pattern.compile("PMCR.*-.*");

String str;
while ((str = in.readLine()) != null){
if (pat1.matcher(str).find() || pat2.matcher(str).find() || pat3.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, OutputPrinter status) 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){
sb.append(str);
sb.append("\n");
}
String[] entries = sb.toString().replaceAll("\u2013", "-").replaceAll("\u2014", "--").replaceAll("\u2015", "--").split("\\n\\n");

for (int i = 0; i < entries.length; i++){

if (entries[i].trim().length() == 0)
continue;

String type = "", author = "", editor = "", comment = "";
HashMap<String, String> hm = new HashMap<String, String>();


String[] fields = entries[i].split("\n");

for (int j = 0; j < fields.length; j++){
if(fields[j].equals(""))
continue;

StringBuffer current = new StringBuffer(fields[j]);
boolean done = false;

while (!done && (j < fields.length-1)) {
if(fields[j+1].length() <=4 )
System.out.println("aaa");
if (fields[j+1].charAt(4) != '-') {
if ((current.length() > 0)
&& !Character.isWhitespace(current.charAt(current.length()-1)))
current.append(' ');
current.append(fields[j+1].trim());
j++;
} else
done = true;
}
String entry = current.toString();

String lab = entry.substring(0, entry.indexOf('-')).trim();
String val = entry.substring(entry.indexOf('-')+1).trim();
if (lab.equals("PT")){
val = val.toLowerCase();
if (val.equals("BOOK")) type = "book";
else if (val.equals("journal article")
|| val.equals("classical article")
|| val.equals("corrected and republished article")
|| val.equals("historical article")
|| val.equals("introductory journal article")
|| val.equals("newspaper article")) type = "article";
else if (val.equals("clinical conference")
|| val.equals("consensus development conference")
|| val.equals("consensus development conference, NIH")) type = "conference";
else if (val.equals("technical report")) type = "techreport";
else if (val.equals("editorial")) type = "inproceedings";//"incollection";"inbook";
else if (val.equals("overall")) type = "proceedings";
else if(type.equals("")) type = "other";

}else if (lab.equals("TI")) {
String oldVal = hm.get("title");
if (oldVal == null)
hm.put("title", val);
else {
if (oldVal.endsWith(":") || oldVal.endsWith(".") || oldVal.endsWith("?"))
hm.put("title", oldVal+" "+val);
else
hm.put("title", oldVal+": "+val);
}
}
// =
// val;
else if (lab.equals("BTI") || lab.equals("CTI")) {
hm.put("booktitle", val);
}
else if (lab.equals("FAU")) {
if (author.equals("")) // don't add " and " for the first author
author = val;
else author += " and " + val;
}
else if (lab.equals("FED")){
if (editor.equals("")) // don't add " and " for the first editor
editor = val;
else editor += " and " + val;
}
else if (lab.equals("JT")) {
if (type.equals("inproceedings"))
hm.put("booktitle", val);
else
hm.put("journal", val);
}

else if (lab.equals("PG"))
hm.put("pages", val);

// else if (lab.equals("STAT")) {
// if (val.equals("MEDLINE"))
// hm.put("publisher", "PubMed");
// else
// hm.put("publisher", val);
// }
else if (lab.equals("PL"))
hm.put("address", val);
else if (lab.equals("IS"))
hm.put("issn", val);
else if (lab.equals("VI"))
hm.put("volume", val);
// else if (lab.equals(""))
// hm.put("number", val);
else if (lab.equals("AB")) {
String oldAb = hm.get("abstract");
if (oldAb == null)
hm.put("abstract", val);
else
hm.put("abstract", oldAb+"\n"+val);
}
else if ((lab.equals("DP"))) {
String[] parts = val.split(" ");
hm.put("year", parts[0]);
if ((parts.length > 1) && (parts[1].length() > 0)) {
hm.put("month", parts[1]);
}
}

else if (lab.equals("MH") || lab.equals("OT")){
if (!hm.containsKey("keywords")) hm.put("keywords", val);
else{
String kw = hm.get("keywords");
hm.put("keywords", kw + ", " + val);
}
}
else if (lab.equals("CON") || lab.equals("CIN") || lab.equals("EIN")
|| lab.equals("EFR") || lab.equals("CRI") || lab.equals("CRF")
|| lab.equals("PRIN") || lab.equals("PROF") || lab.equals("RPI")
|| lab.equals("RPF") || lab.equals("RIN") || lab.equals("ROF")
|| lab.equals("UIN") || lab.equals("UOF") || lab.equals("SPIN")
|| lab.equals("ORI")) {
if (comment.length() > 0)
comment = comment+"\n";
comment = comment+val;
}
// // Added ID import 2005.12.01, Morten Alver:
// else if (lab.equals("ID"))
// hm.put("refid", val);
// // Added doi import (sciencedirect.com) 2011.01.10, Alexander Hug <alexander@alexanderhug.info>
else if (lab.equals("AID")){
String doi = val;
if (doi.startsWith("doi:")){
doi = doi.replaceAll("(?i)doi:", "").trim();
hm.put("doi", doi);
}
}
}
// fix authors
if (author.length() > 0) {
author = AuthorList.fixAuthor_lastNameFirst(author);
hm.put("author", author);
}
if (editor.length() > 0) {
editor = AuthorList.fixAuthor_lastNameFirst(editor);
hm.put("editor", editor);
}
if (comment.length() > 0) {
hm.put("comment", comment);
}

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

// Remove empty fields:
ArrayList<Object> toRemove = new ArrayList<Object>();
for (Iterator<String> it = hm.keySet().iterator(); it.hasNext();) {
Object key = it.next();
String content = hm.get(key);
if ((content == null) || (content.trim().length() == 0))
toRemove.add(key);
}
for (Iterator<Object> iterator = toRemove.iterator(); iterator.hasNext();) {
hm.remove(iterator.next());

}

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

}

return bibitems;

}
}
6 changes: 2 additions & 4 deletions src/main/java/net/sf/jabref/imports/RisImporter.java
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Expand Up @@ -60,14 +60,12 @@ public boolean isRecognizedFormat(InputStream stream) throws IOException {

// Our strategy is to look for the "AU - *" line.
BufferedReader in = new BufferedReader(ImportFormatReader.getReaderDefaultEncoding(stream));
Pattern pat1 = Pattern.compile("AU - .*"),
pat2 = Pattern.compile("A1 - .*"),
pat3 = Pattern.compile("A2 - .*");
Pattern pat1 = Pattern.compile("TY - .*");


String str;
while ((str = in.readLine()) != null){
if (pat1.matcher(str).find() || pat2.matcher(str).find() || pat3.matcher(str).find())
if (pat1.matcher(str).find())
return true;
}

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9 changes: 9 additions & 0 deletions src/main/resources/plugins/net.sf.jabref.core/plugin.xml
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Expand Up @@ -32,6 +32,15 @@
<parameter id="description"
value="Import format for Medline references." />
</extension>

<extension id="MedlinePlainImporter" plugin-id="net.sf.jabref.core"
point-id="ImportFormat">
<parameter id="importFormat"
value="net.sf.jabref.imports.MedlinePlainImporter" />
<parameter id="name" value="Medline Plain Importer" />
<parameter id="description"
value="Import format for Medline references (not XML)." />
</extension>

<!-- To extend JabRef with an Entry Fetcher use the following extension point -->
<extension-point id="EntryFetcher">
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