Merge pull request #11 from vegeziel/master

BugFix for bug "#880 PubMed Import broken"

src/main/java/net/sf/jabref/imports/MedlinePlainImporter.java

@@ -0,0 +1,279 @@
+/*  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;
+
+    }
+}

src/main/java/net/sf/jabref/imports/RisImporter.java

@@ -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;
         }
 

src/main/resources/plugins/net.sf.jabref.core/plugin.xml

@@ -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">