@Override
public AbstractUndoableEdit add(BibtexEntry[] entries) {
if (!supportsAdd()) {
return null;
}
if (entries != null && entries.length > 0) {
NamedCompound ce = new NamedCompound(Globals.lang("add entries to group"));
boolean modified = false;
for (BibtexEntry entry : entries) {
if (!getSearchRule().applyRule(SearchRule.NULL_QUERY, entry)) {
String oldContent = entry.getField(searchField);
String pre = Globals.prefs.get(JabRefPreferences.GROUP_KEYWORD_SEPARATOR);
String newContent = (oldContent == null ? "" : oldContent + pre) + searchExpression;
entry.setField(searchField, newContent);
// Store undo information.
ce.addEdit(new UndoableFieldChange(entry, searchField, oldContent, newContent));
modified = true;
}
}
if (modified) {
ce.end();
}
return modified ? ce : null;
}
return null;
}
/**
* Removes matches of searchString in the entry's field. This is only possible if the search
* expression is not a regExp.
*/
private void removeMatches(BibtexEntry entry) {
String content = entry.getField(searchField);
if (content == null) {
return; // nothing to modify
}
StringBuffer sbOrig = new StringBuffer(content);
StringBuffer sbLower = new StringBuffer(content.toLowerCase());
StringBuffer haystack = caseSensitive ? sbOrig : sbLower;
String needle = caseSensitive ? searchExpression : searchExpression.toLowerCase();
int i;
int j;
int k;
final String separator = Globals.prefs.get(JabRefPreferences.GROUP_KEYWORD_SEPARATOR);
while ((i = haystack.indexOf(needle)) >= 0) {
sbOrig.replace(i, i + needle.length(), "");
sbLower.replace(i, i + needle.length(), "");
// reduce spaces at i to 1
j = i;
k = i;
while (j - 1 >= 0 && separator.indexOf(haystack.charAt(j - 1)) >= 0) {
--j;
}
while (k < haystack.length() && separator.indexOf(haystack.charAt(k)) >= 0) {
++k;
}
sbOrig.replace(j, k, j >= 0 && k < sbOrig.length() ? separator : "");
sbLower.replace(j, k, j >= 0 && k < sbOrig.length() ? separator : "");
}
String result = sbOrig.toString().trim();
entry.setField(searchField, !result.isEmpty() ? result : null);
}
@Override
public AbstractUndoableEdit remove(BibtexEntry[] entries) {
if (!supportsRemove()) {
return null;
}
if (entries != null && entries.length > 0) {
NamedCompound ce = new NamedCompound(Globals.lang("remove from group"));
boolean modified = false;
for (BibtexEntry entry : entries) {
if (getSearchRule().applyRule(SearchRule.NULL_QUERY, entry)) {
String oldContent = entry.getField(searchField);
removeMatches(entry);
// Store undo information.
ce.addEdit(
new UndoableFieldChange(entry, searchField, oldContent, entry.getField(searchField)));
modified = true;
}
}
if (modified) {
ce.end();
}
return modified ? ce : null;
}
return null;
}
/**
* Returns the text stored in the given field of the given bibtex entry which belongs to the given
* database.
*
* <p>If a database is given, this function will try to resolve any string references in the
* field-value. Also, if a database is given, this function will try to find values for unset
* fields in the entry linked by the "crossref" field, if any.
*
* @param field The field to return the value of.
* @param bibtex maybenull The bibtex entry which contains the field.
* @param database maybenull The database of the bibtex entry.
* @return The resolved field value or null if not found.
*/
public static String getResolvedField(String field, BibtexEntry bibtex, BibtexDatabase database) {
if (field.equals("bibtextype")) return bibtex.getType().getName();
// TODO: Changed this to also consider alias fields, which is the expected
// behavior for the preview layout and for the check whatever all fields are present.
// But there might be unwanted side-effects?!
Object o = bibtex.getFieldOrAlias(field);
// If this field is not set, and the entry has a crossref, try to look up the
// field in the referred entry: Do not do this for the bibtex key.
if ((o == null)
&& (database != null)
&& database.followCrossrefs
&& !field.equals(BibtexFields.KEY_FIELD)) {
Object crossRef = bibtex.getField("crossref");
if (crossRef != null) {
BibtexEntry referred = database.getEntryByKey((String) crossRef);
if (referred != null) {
// Ok, we found the referred entry. Get the field value from that
// entry. If it is unset there, too, stop looking:
o = referred.getField(field);
}
}
}
return getText((String) o, database);
}
@Override
public void run() {
if (!searchAllBases.isSelected()) {
// Search only the current database:
for (BibtexEntry entry : panel.getDatabase().getEntries()) {
boolean hit = rule.applyRule(searchTerm, entry) > 0;
entry.setSearchHit(hit);
if (hit) {
hits++;
}
}
} else {
// Search all databases:
for (int i = 0; i < frame.getTabbedPane().getTabCount(); i++) {
BasePanel p = frame.baseAt(i);
for (BibtexEntry entry : p.getDatabase().getEntries()) {
boolean hit = rule.applyRule(searchTerm, entry) > 0;
entry.setSearchHit(hit);
if (hit) {
hits++;
}
}
}
}
}
public BibtexEntry makeBibtexEntry() {
BibtexEntry e = new BibtexEntry(IdGenerator.next(), BibtexEntryTypes.INCOLLECTION);
e.setField("title", "Marine finfish larviculture in Europe");
e.setField("bibtexkey", "shields01");
e.setField("year", "2001");
e.setField("author", "Kevin Shields");
return e;
}
public synchronized boolean setCiteKeyForEntry(String id, String key) {
if (!_entries.containsKey(id)) return false; // Entry doesn't exist!
BibtexEntry entry = getEntryById(id);
String oldKey = entry.getCiteKey();
if (key != null) entry.setField(BibtexFields.KEY_FIELD, key);
else entry.clearField(BibtexFields.KEY_FIELD);
return checkForDuplicateKeyAndAdd(oldKey, entry.getCiteKey(), false);
}
public synchronized BibtexEntry[] getEntriesByKey(String key) {
ArrayList<BibtexEntry> entries = new ArrayList<BibtexEntry>();
for (BibtexEntry entry : _entries.values()) {
if (key.equals(entry.getCiteKey())) entries.add(entry);
}
return entries.toArray(new BibtexEntry[entries.size()]);
}
/**
* Check the database to find out whether any of a set of fields are used for any of the entries.
*
* @param database The bib database.
* @param fields The set of fields to look for.
* @return true if at least one of the given fields is set in at least one entry, false otherwise.
*/
private boolean linksFound(BibtexDatabase database, String[] fields) {
for (BibtexEntry entry : database.getEntries()) {
for (String field : fields) {
if (entry.getField(field) != null) {
return true;
}
}
}
return false;
}
/**
* Take the given BibtexEntry and resolve any string references.
*
* @param entry A BibtexEntry in which all strings of the form #xxx# will be resolved against the
* hash map of string references stored in the databasee.
* @param inPlace If inPlace is true then the given BibtexEntry will be modified, if false then a
* copy is made using close made before resolving the strings.
* @return a BibtexEntry with all string references resolved. It is dependent on the value of
* inPlace whether a copy is made or the given BibtexEntries is modified.
*/
public BibtexEntry resolveForStrings(BibtexEntry entry, boolean inPlace) {
if (!inPlace) {
entry = (BibtexEntry) entry.clone();
}
for (Object field : entry.getAllFields()) {
entry.setField(field.toString(), this.resolveForStrings(entry.getField(field.toString())));
}
return entry;
}
/**
* Removes the entry with the given string.
*
* <p>Returns null if not found.
*/
public synchronized BibtexEntry removeEntry(String id) {
BibtexEntry oldValue = _entries.remove(id);
if (oldValue == null) return null;
removeKeyFromSet(oldValue.getCiteKey());
oldValue.removePropertyChangeListener(listener);
fireDatabaseChanged(
new DatabaseChangeEvent(this, DatabaseChangeEvent.ChangeType.REMOVED_ENTRY, oldValue));
return oldValue;
}
/**
* Cycle through all databases, and make sure everything is updated with the new type
* customization. This includes making sure all entries have a valid type, that no obsolete entry
* editors are around, and that the right-click menus' change type menu is up-to-date.
*/
private void updateTypesForEntries(String typeName) {
if (frame.getTabbedPane().getTabCount() == 0) {
return;
}
for (int i = 0; i < frame.getTabbedPane().getTabCount(); i++) {
BasePanel bp = (BasePanel) frame.getTabbedPane().getComponentAt(i);
// Invalidate associated cached entry editor
bp.entryEditors.remove(typeName);
for (BibtexEntry entry : bp.database().getEntries()) {
entry.updateType();
}
}
}
/**
* Inserts the entry, given that its ID is not already in use. use Util.createId(...) to make up a
* unique ID for an entry.
*/
public synchronized boolean insertEntry(BibtexEntry entry) throws KeyCollisionException {
String id = entry.getId();
if (getEntryById(id) != null) {
throw new KeyCollisionException("ID is already in use, please choose another");
}
entry.addPropertyChangeListener(listener);
_entries.put(id, entry);
fireDatabaseChanged(
new DatabaseChangeEvent(this, DatabaseChangeEvent.ChangeType.ADDED_ENTRY, entry));
return checkForDuplicateKeyAndAdd(null, entry.getCiteKey(), false);
}
private Object getField(BibtexEntry entry) {
for (int i = 0; i < field.length; i++) {
Object o = entry.getField(field[i]);
if (o != null) return o;
}
return null;
}
/** Returns the entry with the given bibtex key. */
public synchronized BibtexEntry getEntryByKey(String key) {
BibtexEntry back = null;
int keyHash = key.hashCode(); // key hash for better performance
Set<String> keySet = _entries.keySet();
for (String entrieID : keySet) {
BibtexEntry entry = getEntryById(entrieID);
if ((entry != null) && (entry.getCiteKey() != null)) {
String citeKey = entry.getCiteKey();
if (citeKey != null) {
if (keyHash == citeKey.hashCode()) {
back = entry;
}
}
}
}
return back;
}
public void setEntry(BibtexEntry entry) {
try {
updating = true;
for (FieldEditor editor : editors.values()) {
Object content = entry.getField(editor.getFieldName());
String toSet = (content == null) ? "" : content.toString();
if (!toSet.equals(editor.getText())) editor.setText(toSet);
}
this.entry = entry;
} finally {
updating = false;
}
}
@Override
public boolean contains(BibtexEntry entry) {
String content = entry.getField(searchField);
if (content == null) {
return false;
}
if (regExp) {
return pattern.matcher(content).find();
}
if (caseSensitive) {
return KeywordGroup.containsWord(searchExpression, content);
}
return KeywordGroup.containsWord(searchExpression.toLowerCase(), content.toLowerCase());
}
private void parse(ImportInspector dialog, String text, int startIndex, int firstEntryNumber) {
piv = startIndex;
int entryNumber = firstEntryNumber;
if (importBibtex) {
// TODO: Login
ArrayList<String> idSelected = new ArrayList<String>();
String id;
while ((id = parseNextEntryId(text, piv)) != null && shouldContinue) {
idSelected.add(id);
entryNumber++;
}
try {
BibtexDatabase dbase = parseBibtexDatabase(idSelected, includeAbstract);
Collection<BibtexEntry> items = dbase.getEntries();
for (BibtexEntry entry : items) {
dialog.addEntry(cleanup(entry));
dialog.setProgress(parsed + unparseable, hits);
parsed++;
}
} catch (IOException e) {
e.printStackTrace();
}
// for
} else {
BibtexEntry entry;
while ((entry = parseNextEntry(text, piv)) != null && shouldContinue) {
if (entry.getField("title") != null) {
dialog.addEntry(entry);
dialog.setProgress(parsed + unparseable, hits);
parsed++;
}
entryNumber++;
}
}
}
public void setEntry(BibtexEntry entry) {
try {
updating = true;
Iterator<FieldEditor> i = editors.values().iterator();
while (i.hasNext()) {
FieldEditor editor = i.next();
Object content = entry.getField(editor.getFieldName());
String toSet = (content == null) ? "" : content.toString();
if (!toSet.equals(editor.getText())) editor.setText(toSet);
}
this.entry = entry;
} finally {
updating = false;
}
}
private void index() {
/* Old version, from when set was a TreeSet.
// The boolean "changing" is true in the situation that an entry is about to change,
// and has temporarily been removed from the entry set in this sorter. So, if we index
// now, we will cause exceptions other places because one entry has been left out of
// the indexed array. Simply waiting foth this to change can lead to deadlocks,
// so we have no other choice than to return without indexing.
if (changing)
return;
*/
synchronized (set) {
// Resort if necessary:
if (changed) {
Collections.sort(set, comp);
changed = false;
}
// Create an array of IDs for quick access, since getIdAt() is called by
// getValueAt() in EntryTableModel, which *has* to be efficient.
int count = set.size();
idArray = new String[count];
entryArray = new BibtexEntry[count];
int piv = 0;
for (BibtexEntry entry : set) {
// for (int i=0; i<idArray.length; i++) {
idArray[piv] = entry.getId();
entryArray[piv] = entry;
piv++;
}
}
}
/**
* Check whether this entry's required fields are set, taking crossreferenced entries and
* either-or fields into account:
*
* @param entry The entry to check.
* @param database The entry's database.
* @return True if required fields are set, false otherwise.
*/
@Override
public boolean hasAllRequiredFields(BibtexEntry entry, BibtexDatabase database) {
// First check if the bibtex key is set:
if (entry.getField(BibtexFields.KEY_FIELD) == null) {
return false;
}
// Then check other fields:
boolean[] isSet = new boolean[req.length];
// First check for all fields, whether they are set here or in a crossref'd entry:
for (int i = 0; i < req.length; i++) {
isSet[i] = BibtexDatabase.getResolvedField(req[i], entry, database) != null;
}
// Then go through all fields. If a field is not set, see if it is part of an either-or
// set where another field is set. If not, return false:
for (int i = 0; i < req.length; i++) {
if (!isSet[i]) {
if (!isCoupledFieldSet(req[i], entry, database)) {
return false;
}
}
}
// Passed all fields, so return true:
return true;
}
public int compare(BibtexEntry one, BibtexEntry two) {
return one.getId().compareTo(two.getId());
}
@Override
public void update() {
panel.output(Globals.lang("Searched database. Number of hits") + ": " + hits);
// Show the result in the chosen way:
if (searchAllBases.isSelected()) {
// Search all databases. This means we need to use the search results dialog.
// Turn off other search mode, if activated:
if (startedFloatSearch) {
panel.mainTable.stopShowingFloatSearch();
startedFloatSearch = false;
}
if (startedFilterSearch) {
panel.stopShowingSearchResults();
startedFilterSearch = false;
}
// Make sure the search dialog is instantiated and cleared:
instantiateSearchDialog();
searchDialog.clear();
for (int i = 0; i < frame.getTabbedPane().getTabCount(); i++) {
BasePanel p = frame.baseAt(i);
for (BibtexEntry entry : p.getDatabase().getEntries()) {
if (entry.isSearchHit()) {
searchDialog.addEntry(entry, p);
}
}
}
searchDialog.selectFirstEntry();
searchDialog.setVisible(true);
} else if (showResultsInDialog.isSelected()) {
// Turn off other search mode, if activated:
if (startedFloatSearch) {
panel.mainTable.stopShowingFloatSearch();
startedFloatSearch = false;
}
if (startedFilterSearch) {
panel.stopShowingSearchResults();
startedFilterSearch = false;
}
// Make sure the search dialog is instantiated and cleared:
instantiateSearchDialog();
searchDialog.clear();
for (BibtexEntry entry : panel.getDatabase().getEntries()) {
if (entry.isSearchHit()) {
searchDialog.addEntry(entry, panel);
}
}
searchDialog.selectFirstEntry();
searchDialog.setVisible(true);
} else if (hideSearch.isSelected()) {
// Filtering search - removes non-hits from the table:
if (startedFloatSearch) {
panel.mainTable.stopShowingFloatSearch();
startedFloatSearch = false;
}
startedFilterSearch = true;
panel.setSearchMatcher(new SearchMatcher());
} else {
// Float search - floats hits to the top of the table:
if (startedFilterSearch) {
panel.stopShowingSearchResults();
startedFilterSearch = false;
}
startedFloatSearch = true;
panel.mainTable.showFloatSearch(new SearchMatcher());
}
// Afterwards, select all text in the search field.
searchField.select(0, searchField.getText().length());
}
public boolean hasAllRequiredFields(BibtexEntry entry, BibtexDatabase database) {
return entry.allFieldsPresent(getRequiredFields(), database);
}
private BibtexEntry parseNextEntry(String allText, int startIndex) {
BibtexEntry entry = null;
int index = allText.indexOf("<div class=\"detail", piv);
int endIndex = allText.indexOf("</div>", index);
if (index >= 0 && endIndex > 0) {
endIndex += 6;
piv = endIndex;
String text = allText.substring(index, endIndex);
BibtexEntryType type = null;
String sourceField = null;
String typeName = "";
Matcher typeMatcher = typePattern.matcher(text);
if (typeMatcher.find()) {
typeName = typeMatcher.group(1);
if (typeName.equalsIgnoreCase("IEEE Journals & Magazines")
|| typeName.equalsIgnoreCase("IEEE Early Access Articles")
|| typeName.equalsIgnoreCase("IET Journals & Magazines")
|| typeName.equalsIgnoreCase("AIP Journals & Magazines")
|| typeName.equalsIgnoreCase("AVS Journals & Magazines")
|| typeName.equalsIgnoreCase("IBM Journals & Magazines")
|| typeName.equalsIgnoreCase("TUP Journals & Magazines")
|| typeName.equalsIgnoreCase("BIAI Journals & Magazines")) {
type = BibtexEntryType.getType("article");
sourceField = "journal";
} else if (typeName.equalsIgnoreCase("IEEE Conference Publications")
|| typeName.equalsIgnoreCase("IET Conference Publications")
|| typeName.equalsIgnoreCase("VDE Conference Publications")) {
type = BibtexEntryType.getType("inproceedings");
sourceField = "booktitle";
} else if (typeName.equalsIgnoreCase("IEEE Standards")
|| typeName.equalsIgnoreCase("Standards")) {
type = BibtexEntryType.getType("standard");
sourceField = "number";
} else if (typeName.equalsIgnoreCase("IEEE eLearning Library Courses")) {
type = BibtexEntryType.getType("Electronic");
sourceField = "note";
} else if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")
|| typeName.equalsIgnoreCase("MIT Press eBook Chapters")
|| typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
type = BibtexEntryType.getType("inCollection");
sourceField = "booktitle";
}
}
if (type == null) {
type = BibtexEntryType.getType("misc");
sourceField = "note";
System.err.println("Type detection failed. Use MISC instead.");
unparseable++;
System.err.println(text);
}
entry = new BibtexEntry(IdGenerator.next(), type);
if (typeName.equalsIgnoreCase("IEEE Standards")) {
entry.setField("organization", "IEEE");
}
if (typeName.equalsIgnoreCase("Wiley-IEEE Press eBook Chapters")) {
entry.setField("publisher", "Wiley-IEEE Press");
} else if (typeName.equalsIgnoreCase("MIT Press eBook Chapters")) {
entry.setField("publisher", "MIT Press");
} else if (typeName.equalsIgnoreCase("IEEE USA Books & eBooks")) {
entry.setField("publisher", "IEEE USA");
}
if (typeName.equalsIgnoreCase("IEEE Early Access Articles")) {
entry.setField("note", "Early Access");
}
Set<String> fields = fieldPatterns.keySet();
for (String field : fields) {
Matcher fieldMatcher = Pattern.compile(fieldPatterns.get(field)).matcher(text);
if (fieldMatcher.find()) {
entry.setField(field, htmlConverter.format(fieldMatcher.group(1)));
if (field.equals("title") && fieldMatcher.find()) {
String sec_title = htmlConverter.format(fieldMatcher.group(1));
if (entry.getType() == BibtexEntryType.getStandardType("standard")) {
sec_title = sec_title.replaceAll("IEEE Std ", "");
}
entry.setField(sourceField, sec_title);
}
if (field.equals("pages") && fieldMatcher.groupCount() == 2) {
entry.setField(field, fieldMatcher.group(1) + "-" + fieldMatcher.group(2));
}
}
}
Matcher authorMatcher = authorPattern.matcher(text);
// System.out.println(text);
StringBuilder authorNames = new StringBuilder("");
int authorCount = 0;
while (authorMatcher.find()) {
if (authorCount >= 1) {
authorNames.append(" and ");
}
authorNames.append(htmlConverter.format(authorMatcher.group(1)));
// System.out.println(authorCount + ": " + authorMatcher.group(1));
authorCount++;
}
entry.setField("author", authorNames.toString());
if (entry.getField("author") == null
|| entry.getField("author").startsWith("a href")
|| entry
.getField("author")
.startsWith("Topic(s)")) { // Fix for some documents without authors
entry.setField("author", "");
}
if (entry.getType() == BibtexEntryType.getStandardType("inproceedings")
&& entry.getField("author").equals("")) {
entry.setType(BibtexEntryType.getStandardType("proceedings"));
}
if (includeAbstract) {
index = text.indexOf("id=\"abstract");
if (index >= 0) {
endIndex = text.indexOf("</div>", index) + 6;
text = text.substring(index, endIndex);
Matcher absMatcher = absPattern.matcher(text);
if (absMatcher.find()) {
// Clean-up abstract
String abstr = absMatcher.group(1);
abstr = abstr.replaceAll("<span class='snippet'>([\\w]+)</span>", "$1");
entry.setField("abstract", htmlConverter.format(abstr));
}
}
}
}
if (entry == null) {
return null;
} else {
return cleanup(entry);
}
}
private BibtexEntry cleanup(BibtexEntry entry) {
if (entry == null) {
return null;
}
// clean up title
String title = entry.getField("title");
if (title != null) {
// USe the alt-text and replace image links
title = title.replaceAll("[ ]?img src=[^ ]+ alt=\"([^\"]+)\">[ ]?", "\\$$1\\$");
// Try to sort out most of the /spl / conversions
// Deal with this specific nested type first
title = title.replaceAll("/sub /spl infin//", "\\$_\\\\infty\\$");
title = title.replaceAll("/sup /spl infin//", "\\$\\^\\\\infty\\$");
// Replace general expressions
title = title.replaceAll("/[sS]pl ([^/]+)/", "\\$\\\\$1\\$");
// Deal with subscripts and superscripts
if (Globals.prefs.getBoolean(JabRefPreferences.USE_CONVERT_TO_EQUATION)) {
title = title.replaceAll("/sup ([^/]+)/", "\\$\\^\\{$1\\}\\$");
title = title.replaceAll("/sub ([^/]+)/", "\\$_\\{$1\\}\\$");
title = title.replaceAll("\\(sup\\)([^(]+)\\(/sup\\)", "\\$\\^\\{$1\\}\\$");
title = title.replaceAll("\\(sub\\)([^(]+)\\(/sub\\)", "\\_\\{$1\\}\\$");
} else {
title = title.replaceAll("/sup ([^/]+)/", "\\\\textsuperscript\\{$1\\}");
title = title.replaceAll("/sub ([^/]+)/", "\\\\textsubscript\\{$1\\}");
title = title.replaceAll("\\(sup\\)([^(]+)\\(/sup\\)", "\\\\textsuperscript\\{$1\\}");
title = title.replaceAll("\\(sub\\)([^(]+)\\(/sub\\)", "\\\\textsubscript\\{$1\\}");
}
// Replace \infin with \infty
title = title.replaceAll("\\\\infin", "\\\\infty");
// Unit formatting
if (Globals.prefs.getBoolean(JabRefPreferences.USE_UNIT_FORMATTER_ON_SEARCH)) {
title = unitFormatter.format(title);
}
// Automatic case keeping
if (Globals.prefs.getBoolean(JabRefPreferences.USE_CASE_KEEPER_ON_SEARCH)) {
title = caseKeeper.format(title);
}
// Write back
entry.setField("title", title);
}
// clean up author
/* String author = (String)entry.getField("author");
if (author != null) {
if (author.indexOf("a href=") >= 0) { // Author parsing failed because it was empty
entry.setField("author",""); // Maybe not needed anymore due to another change
} else {
author = author.replaceAll("\\s+", " ");
author = author.replaceAll("\\.", ". ");
author = author.replaceAll("([^;]+),([^;]+),([^;]+)","$1,$3,$2"); // Change order in case of Jr. etc
author = author.replaceAll(" ", " ");
author = author.replaceAll("\\. -", ".-");
author = author.replaceAll("; ", " and ");
author = author.replaceAll(" ,", ",");
author = author.replaceAll(" ", " ");
author = author.replaceAll("[ ,;]+$", "");
entry.setField("author", author);
}
}*/
// clean up month
String month = entry.getField("month");
if (month != null && !month.isEmpty()) {
month = month.replaceAll("\\.", "");
month = month.toLowerCase();
Pattern monthPattern = Pattern.compile("(\\d*+)\\s*([a-z]*+)-*(\\d*+)\\s*([a-z]*+)");
Matcher mm = monthPattern.matcher(month);
String date = month;
if (mm.find()) {
if (mm.group(3).isEmpty()) {
if (!mm.group(2).isEmpty()) {
date = "#" + mm.group(2).substring(0, 3) + "#";
if (!mm.group(1).isEmpty()) {
date += " " + mm.group(1) + ",";
}
} else {
date = mm.group(1) + ",";
}
} else if (mm.group(2).isEmpty()) {
if (!mm.group(4).isEmpty()) {
date =
"#" + mm.group(4).substring(0, 3) + "# " + mm.group(1) + "--" + mm.group(3) + ",";
} else {
date += ",";
}
} else {
date =
"#"
+ mm.group(2).substring(0, 3)
+ "# "
+ mm.group(1)
+ "--#"
+ mm.group(4).substring(0, 3)
+ "# "
+ mm.group(3)
+ ",";
}
}
// date = date.trim();
// if (!date.isEmpty()) {
entry.setField("month", date);
// }
}
// clean up pages
String field = "pages";
String pages = entry.getField(field);
if (pages != null) {
String[] pageNumbers = pages.split("-");
if (pageNumbers.length == 2) {
if (pageNumbers[0].equals(pageNumbers[1])) { // single page
entry.setField(field, pageNumbers[0]);
} else {
entry.setField(field, pages.replaceAll("-", "--"));
}
}
}
// clean up publication field
BibtexEntryType type = entry.getType();
String sourceField = "";
if (type.getName().equals("Article")) {
sourceField = "journal";
entry.clearField("booktitle");
} else if (type.getName().equals("Inproceedings")) {
sourceField = "booktitle";
}
String fullName = entry.getField(sourceField);
if (fullName != null) {
if (type.getName().equals("Article")) {
int ind = fullName.indexOf(": Accepted for future publication");
if (ind > 0) {
fullName = fullName.substring(0, ind);
entry.setField("year", "to be published");
entry.clearField("month");
entry.clearField("pages");
entry.clearField("number");
}
String[] parts = fullName.split("[\\[\\]]"); // [see also...], [legacy...]
fullName = parts[0];
if (parts.length == 3) {
fullName += parts[2];
}
if (entry.getField("note").equals("Early Access")) {
entry.setField("year", "to be published");
entry.clearField("month");
entry.clearField("pages");
entry.clearField("number");
}
} else {
fullName =
fullName
.replace("Conference Proceedings", "Proceedings")
.replace("Proceedings of", "Proceedings")
.replace("Proceedings.", "Proceedings");
fullName = fullName.replaceAll("International", "Int.");
fullName = fullName.replaceAll("Symposium", "Symp.");
fullName = fullName.replaceAll("Conference", "Conf.");
fullName = fullName.replaceAll(" on", " ").replace(" ", " ");
}
Matcher m1 = publicationPattern.matcher(fullName);
String abrvPattern = ".*[^,] '?\\d+\\)?";
if (m1.find()) {
String prefix = m1.group(2).trim();
String postfix = m1.group(1).trim();
String abrv = "";
String[] parts = prefix.split("\\. ", 2);
if (parts.length == 2) {
if (parts[0].matches(abrvPattern)) {
prefix = parts[1];
abrv = parts[0];
} else {
prefix = parts[0];
abrv = parts[1];
}
}
if (!prefix.matches(abrvPattern)) {
fullName = prefix + " " + postfix + " " + abrv;
fullName = fullName.trim();
} else {
fullName = postfix + " " + prefix;
}
}
if (type.getName().equals("Article")) {
fullName = fullName.replace(" - ", "-"); // IEE Proceedings-
fullName = fullName.trim();
if (Globals.prefs.getBoolean(JabRefPreferences.USE_IEEE_ABRV)) {
fullName = Globals.journalAbbrev.getMedlineAbbreviation(fullName).orElse(fullName);
}
}
if (type.getName().equals("Inproceedings")) {
Matcher m2 = proceedingPattern.matcher(fullName);
if (m2.find()) {
String prefix = m2.group(2);
String postfix = m2.group(1).replaceAll("\\.$", "");
if (!prefix.matches(abrvPattern)) {
String abrv = "";
String[] parts = postfix.split("\\. ", 2);
if (parts.length == 2) {
if (parts[0].matches(abrvPattern)) {
postfix = parts[1];
abrv = parts[0];
} else {
postfix = parts[0];
abrv = parts[1];
}
}
fullName = prefix.trim() + " " + postfix.trim() + " " + abrv;
} else {
fullName = postfix.trim() + " " + prefix.trim();
}
}
fullName = fullName.trim();
fullName =
fullName.replaceAll("^[tT]he ", "").replaceAll("^\\d{4} ", "").replaceAll("[,.]$", "");
String year = entry.getField("year");
fullName = fullName.replaceAll(", " + year + "\\.?", "");
if (!fullName.contains("Abstract")
&& !fullName.contains("Summaries")
&& !fullName.contains("Conference Record")) {
fullName = "Proc. " + fullName;
}
}
entry.setField(sourceField, fullName);
}
// clean up abstract
String abstr = entry.getField("abstract");
if (abstr != null) {
// Try to sort out most of the /spl / conversions
// Deal with this specific nested type first
abstr = abstr.replaceAll("/sub /spl infin//", "\\$_\\\\infty\\$");
abstr = abstr.replaceAll("/sup /spl infin//", "\\$\\^\\\\infty\\$");
// Replace general expressions
abstr = abstr.replaceAll("/[sS]pl ([^/]+)/", "\\$\\\\$1\\$");
// Deal with subscripts and superscripts
if (Globals.prefs.getBoolean(JabRefPreferences.USE_CONVERT_TO_EQUATION)) {
abstr = abstr.replaceAll("/sup ([^/]+)/", "\\$\\^\\{$1\\}\\$");
abstr = abstr.replaceAll("/sub ([^/]+)/", "\\$_\\{$1\\}\\$");
abstr = abstr.replaceAll("\\(sup\\)([^(]+)\\(/sup\\)", "\\$\\^\\{$1\\}\\$");
abstr = abstr.replaceAll("\\(sub\\)([^(]+)\\(/sub\\)", "\\_\\{$1\\}\\$");
} else {
abstr = abstr.replaceAll("/sup ([^/]+)/", "\\\\textsuperscript\\{$1\\}");
abstr = abstr.replaceAll("/sub ([^/]+)/", "\\\\textsubscript\\{$1\\}");
abstr = abstr.replaceAll("\\(sup\\)([^(]+)\\(/sup\\)", "\\\\textsuperscript\\{$1\\}");
abstr = abstr.replaceAll("\\(sub\\)([^(]+)\\(/sub\\)", "\\\\textsubscript\\{$1\\}");
}
// Replace \infin with \infty
abstr = abstr.replaceAll("\\\\infin", "\\\\infty");
// Write back
entry.setField("abstract", abstr);
}
// Clean up url
String url = entry.getField("url");
if (url != null) {
entry.setField("url", "http://ieeexplore.ieee.org" + url.replace("tp=&", ""));
}
return entry;
}
private boolean importPdfFiles(List<String> fileNames) {
if (panel == null) return false;
for (String fileName : fileNames) {
List<BibtexEntry> xmpEntriesInFile = readXmpEntries(fileName);
ImportDialog importDialog = new ImportDialog(dropRow, fileName);
if (!hasXmpEntries(xmpEntriesInFile)) {
importDialog.getRadioButtonXmp().setEnabled(false);
}
Tools.centerRelativeToWindow(importDialog, frame);
importDialog.showDialog();
if (importDialog.getResult() == JOptionPane.OK_OPTION) {
if (importDialog.getRadioButtonXmp().isSelected()) {
// SplDatabaseChangeListener dataListener = new SplDatabaseChangeListener(frame, panel,
// entryTable, fileName);
// panel.database().addDatabaseChangeListener(dataListener);
ImportMenuItem importer = new ImportMenuItem(frame, (entryTable == null));
importer.automatedImport(new String[] {fileName});
} else if (importDialog.getRadioButtonMrDlib().isSelected()) {
MetaDataListDialog metaDataListDialog = new MetaDataListDialog(fileName, true);
Tools.centerRelativeToWindow(metaDataListDialog, frame);
metaDataListDialog.showDialog();
XmlDocuments documents = metaDataListDialog.getXmlDocuments();
if (documents != null
&& documents.getDocuments() != null
&& documents.getDocuments().size() > 0
&& metaDataListDialog.getResult() == JOptionPane.OK_OPTION) {
int selected = metaDataListDialog.getTableMetadata().getSelectedRow();
if (selected > -1 && selected < documents.getDocuments().size()) {
XmlDocument document = documents.getDocuments().get(selected);
String id = Util.createNeutralId();
BibtexEntry entry = new BibtexEntry(id);
if (fieldExists(document.getType())) {
BibtexEntryType type = BibtexEntryType.getStandardType(document.getType());
if (type == null) {
type = BibtexEntryType.ARTICLE;
}
entry.setType(type);
} else {
entry.setType(BibtexEntryType.ARTICLE);
}
ArrayList<BibtexEntry> list = new ArrayList<BibtexEntry>();
list.add(entry);
Util.setAutomaticFields(list, true, true, false);
insertFields(entry.getRequiredFields(), entry, document);
insertFields(entry.getGeneralFields(), entry, document);
insertFields(entry.getOptionalFields(), entry, document);
panel.database().insertEntry(entry);
DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
dfh.linkPdfToEntry(fileName, entryTable, entry);
LabelPatternUtil.makeLabel(Globals.prefs.getKeyPattern(), panel.database(), entry);
} else {
createNewBlankEntry(fileName);
}
} else if (metaDataListDialog.getResult() == JOptionPane.CANCEL_OPTION) {
continue;
} else if (metaDataListDialog.getResult() == JOptionPane.NO_OPTION) {
createNewBlankEntry(fileName);
} else if (documents == null
|| documents.getDocuments() == null
|| documents.getDocuments().size() <= 0
&& metaDataListDialog.getResult() == JOptionPane.OK_OPTION) {
createNewBlankEntry(fileName);
}
} else if (importDialog.getRadioButtonNoMeta().isSelected()) {
createNewBlankEntry(fileName);
} else if (importDialog.getRadioButtonUpdateEmptyFields().isSelected()) {
MetaDataListDialog metaDataListDialog = new MetaDataListDialog(fileName, false);
Tools.centerRelativeToWindow(metaDataListDialog, frame);
metaDataListDialog.showDialog();
XmlDocuments documents = metaDataListDialog.getXmlDocuments();
if (documents != null
&& documents.getDocuments() != null
&& documents.getDocuments().size() > 0
&& metaDataListDialog.getResult() == JOptionPane.OK_OPTION) {
int selected = metaDataListDialog.getTableMetadata().getSelectedRow();
if (selected > -1 && selected < documents.getDocuments().size()) {
XmlDocument document = documents.getDocuments().get(selected);
BibtexEntry entry = entryTable.getEntryAt(dropRow);
if (fieldExists(document.getType())) {
BibtexEntryType type = BibtexEntryType.getStandardType(document.getType());
if (type != null) {
entry.setType(type);
}
}
insertFields(entry.getRequiredFields(), entry, document);
insertFields(entry.getGeneralFields(), entry, document);
insertFields(entry.getOptionalFields(), entry, document);
DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
dfh.linkPdfToEntry(fileName, entryTable, dropRow);
}
}
} else if (importDialog.getRadioButtononlyAttachPDF().isSelected()) {
DroppedFileHandler dfh = new DroppedFileHandler(frame, panel);
dfh.linkPdfToEntry(fileName, entryTable, dropRow);
}
}
}
return true;
}
private void insertFields(String[] fields, BibtexEntry entry, XmlDocument xmlDocument) {
DocumentWrapper document = new DocumentWrapper(xmlDocument);
for (String field : fields) {
if (entry.getField(field) != null) {
continue;
}
if (field.equalsIgnoreCase("author")) {
entry.setField(field, document.getAuthors("and"));
}
if (field.equalsIgnoreCase("title")) {
entry.setField(field, document.getTitle());
}
if (field.equalsIgnoreCase("abstract")) {
entry.setField(field, document.getAbstract());
}
if (field.equalsIgnoreCase("keywords")) {
entry.setField(field, document.getKeyWords());
}
if (field.equalsIgnoreCase("doi")) {
entry.setField(field, document.getDoi());
}
if (field.equalsIgnoreCase("pages")) {
entry.setField(field, document.getPages());
}
if (field.equalsIgnoreCase("volume")) {
entry.setField(field, document.getVolume());
}
if (field.equalsIgnoreCase("number")) {
entry.setField(field, document.getNumber());
}
if (field.equalsIgnoreCase("year")) {
entry.setField(field, document.getYear());
}
if (field.equalsIgnoreCase("month")) {
entry.setField(field, document.getMonth());
}
if (field.equalsIgnoreCase("day")) {
entry.setField(field, document.getDay());
}
if (field.equalsIgnoreCase("booktitle")) {
entry.setField(field, document.getVenue());
}
if (field.equalsIgnoreCase("journal")) {
entry.setField(field, document.getVenue());
}
}
}
public void run() {
if (!goOn) return;
for (int i = 0; i < entries.length; i++) {
BibtexEntry entry = entries[i];
// Make a list of all PDFs linked from this entry:
List<File> files = new ArrayList<File>();
// First check the (legacy) "pdf" field:
String pdf = entry.getField("pdf");
String dir = panel.metaData().getFileDirectory("pdf");
File f = Util.expandFilename(pdf, new String[] {dir, "."});
if (f != null) files.add(f);
// Then check the "file" field:
dir = panel.metaData().getFileDirectory(GUIGlobals.FILE_FIELD);
String field = entry.getField(GUIGlobals.FILE_FIELD);
if (field != null) {
FileListTableModel tm = new FileListTableModel();
tm.setContent(field);
for (int j = 0; j < tm.getRowCount(); j++) {
FileListEntry flEntry = tm.getEntry(j);
if ((flEntry.getType() != null)
&& (flEntry.getType().getName().toLowerCase().equals("pdf"))) {
f = Util.expandFilename(flEntry.getLink(), new String[] {dir, "."});
if (f != null) files.add(f);
}
}
}
optDiag.progressArea.append(entry.getCiteKey() + "\n");
if (files.size() == 0) {
skipped++;
optDiag.progressArea.append(" " + Globals.lang("Skipped - No PDF linked") + ".\n");
} else
for (File file : files) {
if (!file.exists()) {
skipped++;
optDiag.progressArea.append(
" " + Globals.lang("Skipped - PDF does not exist") + ":\n");
optDiag.progressArea.append(" " + file.getPath() + "\n");
} else {
try {
XMPUtil.writeXMP(file, entry, database);
optDiag.progressArea.append(" " + Globals.lang("Ok") + ".\n");
entriesChanged++;
} catch (Exception e) {
optDiag.progressArea.append(
" " + Globals.lang("Error while writing") + " '" + file.getPath() + "':\n");
optDiag.progressArea.append(" " + e.getLocalizedMessage() + "\n");
errors++;
}
}
}
if (optDiag.canceled) {
optDiag.progressArea.append("\n" + Globals.lang("Operation canceled.\n"));
break;
}
}
optDiag.progressArea.append(
"\n"
+ Globals.lang(
"Finished writing XMP for %0 file (%1 skipped, %2 errors).",
String.valueOf(entriesChanged), String.valueOf(skipped), String.valueOf(errors)));
optDiag.done();
}
public int compare(BibtexEntry e1, BibtexEntry e2) {
Object f1, f2;
if (isTypeHeader) {
// Sort by type.
f1 = e1.getType().getName();
f2 = e2.getType().getName();
} else {
// If the field is author or editor, we rearrange names so they are
// sorted according to last name.
f1 = getField(e1);
f2 = getField(e2);
}
/*
* [ 1598777 ] Month sorting
*
* http://sourceforge.net/tracker/index.php?func=detail&aid=1598777&group_id=92314&atid=600306
*/
int localMultiplier = multiplier;
if (isMonthField) localMultiplier = -localMultiplier;
// Catch all cases involving null:
if (f1 == null) return f2 == null ? 0 : localMultiplier;
if (f2 == null) return -localMultiplier;
// Now we now that both f1 and f2 are != null
if (isNameField) {
f1 = AuthorList.fixAuthorForAlphabetization((String) f1);
f2 = AuthorList.fixAuthorForAlphabetization((String) f2);
} else if (isYearField) {
/*
* [ 1285977 ] Impossible to properly sort a numeric field
*
* http://sourceforge.net/tracker/index.php?func=detail&aid=1285977&group_id=92314&atid=600307
*/
f1 = Util.toFourDigitYear((String) f1);
f2 = Util.toFourDigitYear((String) f2);
} else if (isMonthField) {
/*
* [ 1535044 ] Month sorting
*
* http://sourceforge.net/tracker/index.php?func=detail&aid=1535044&group_id=92314&atid=600306
*/
f1 = new Integer(Util.getMonthNumber((String) f1));
f2 = new Integer(Util.getMonthNumber((String) f2));
}
if (isNumeric) {
Integer i1 = null, i2 = null;
try {
i1 = Integer.parseInt((String) f1);
} catch (NumberFormatException ex) {
// Parsing failed.
}
try {
i2 = Integer.parseInt((String) f2);
} catch (NumberFormatException ex) {
// Parsing failed.
}
if (i2 != null && i1 != null) {
// Ok, parsing was successful. Update f1 and f2:
f1 = i1;
f2 = i2;
} else if (i1 != null) {
// The first one was parseable, but not the second one.
// This means we consider one < two
f1 = i1;
f2 = new Integer(i1.intValue() + 1);
} else if (i2 != null) {
// The second one was parseable, but not the first one.
// This means we consider one > two
f2 = i2;
f1 = new Integer(i2.intValue() + 1);
}
// Else none of them were parseable, and we can fall back on comparing strings.
}
int result = 0;
if ((f1 instanceof Integer) && (f2 instanceof Integer)) {
result = (((Integer) f1).compareTo((Integer) f2));
} else if (f2 instanceof Integer) {
Integer f1AsInteger = new Integer(f1.toString());
result = -((f1AsInteger).compareTo((Integer) f2));
} else if (f1 instanceof Integer) {
Integer f2AsInteger = new Integer(f2.toString());
result = -(((Integer) f1).compareTo(f2AsInteger));
} else {
String ours = ((String) f1).toLowerCase(), theirs = ((String) f2).toLowerCase();
result = collator.compare(ours, theirs); // ours.compareTo(theirs);
}
return result * localMultiplier;
}
