private void typeDeletion(String name) {
BibtexEntryType type = BibtexEntryType.getType(name);
if (type instanceof CustomEntryType) {
if (BibtexEntryType.getStandardType(name) == null) {
int reply =
JOptionPane.showConfirmDialog(
frame,
Globals.lang(
"All entries of this " + "type will be declared " + "typeless. Continue?"),
Globals.lang("Delete custom format") + " '" + StringUtil.nCase(name) + '\'',
JOptionPane.YES_NO_OPTION,
JOptionPane.WARNING_MESSAGE);
if (reply != JOptionPane.YES_OPTION) {
return;
}
}
BibtexEntryType.removeType(name);
updateTypesForEntries(StringUtil.nCase(name));
changed.remove(name);
reqLists.remove(name);
optLists.remove(name);
if (biblatexMode) {
opt2Lists.remove(name);
}
}
// messageLabel.setText("'"+type.getName()+"' "+
// Globals.lang("is a standard type."));
}
@Override
public void actionPerformed(ActionEvent e) {
if (lastSelected == null) {
return;
}
defaulted.add(lastSelected);
BibtexEntryType type = BibtexEntryType.getStandardType(lastSelected);
if (type != null) {
String[] rf = type.getRequiredFieldsForCustomization(), of = type.getOptionalFields();
List<String> req, opt1, opt2;
if (rf != null) {
req = java.util.Arrays.asList(rf);
} else {
req = new ArrayList<String>();
}
opt1 = new ArrayList<String>();
opt2 = new ArrayList<String>();
if (biblatexMode) {
if (of != null) {
String[] priOptArray = type.getPrimaryOptionalFields();
String[] secOptArray = Util.getRemainder(of, priOptArray);
if (priOptArray != null) {
opt1 = java.util.Arrays.asList(priOptArray);
}
if (secOptArray != null) {
opt2 = java.util.Arrays.asList(secOptArray);
}
}
} else {
if (of != null) {
opt1 = java.util.Arrays.asList(of);
}
}
reqComp.setFields(req);
reqComp.setEnabled(true);
optComp.setFields(opt1);
if (biblatexMode) {
optComp2.setFields(opt2);
}
}
}
private static BibtexEntry getTestEntry() {
if (PreviewPrefsTab.entry != null) {
return PreviewPrefsTab.entry;
}
PreviewPrefsTab.entry = new BibtexEntry(IdGenerator.next(), BibtexEntryType.getType("article"));
PreviewPrefsTab.entry.setField(BibtexFields.KEY_FIELD, "conceicao1997");
PreviewPrefsTab.entry.setField(
"author",
"Luis E. C. Conceic{\\~a}o and Terje van der Meeren and Johan A. J. Verreth and M S. Evjen and D. F. Houlihan and H. J. Fyhn");
PreviewPrefsTab.entry.setField(
"title",
"Amino acid metabolism and protein turnover in larval turbot (Scophthalmus maximus) fed natural zooplankton or Artemia");
PreviewPrefsTab.entry.setField("year", "1997");
PreviewPrefsTab.entry.setField("journal", "Marine Biology");
PreviewPrefsTab.entry.setField("month", "January");
PreviewPrefsTab.entry.setField("number", "2");
PreviewPrefsTab.entry.setField("volume", "123");
PreviewPrefsTab.entry.setField("pdf", "conceicao1997.pdf");
PreviewPrefsTab.entry.setField("pages", "255--265");
PreviewPrefsTab.entry.setField(
"keywords", "energetics, artemia, metabolism, amino acid, turbot");
PreviewPrefsTab.entry.setField(
"url", "http://ejournals.ebsco.com/direct.asp?ArticleID=TYY4NT82XA9H7R8PFPPV");
PreviewPrefsTab.entry.setField(
"abstract",
"Abstract The present paper studied the influence of different food regimes "
+ "on the free amino acid (FAA) pool, the rate of protein turnover, the flux of amino acids, and "
+ "their relation to growth of larval turbot (Scophthalmus maximus L.) from first feeding until "
+ "metamorphosis. The amino acid profile of protein was stable during the larval period although "
+ "some small, but significant, differences were found. Turbot larvae had proteins which were rich "
+ "in leucine and aspartate, and poor in glutamate, suggesting a high leucine requirement. The "
+ "profile of the FAA pool was highly variable and quite different from the amino acid profile in "
+ "protein. The proportion of essential FAA decreased with development. High contents of free tyrosine "
+ "and phenylalanine were found on Day 3, while free taurine was present at high levels throughout "
+ "the experimental period. Larval growth rates were positively correlated with taurine levels, "
+ "suggesting a dietary dependency for taurine and/or sulphur amino acids.\n\nReduced growth rates in "
+ "Artemia-fed larvae were associated with lower levels of free methionine, indicating that this diet "
+ "is deficient in methionine for turbot larvae. Leucine might also be limiting turbot growth as the "
+ "different diet organisms had lower levels of this amino acid in the free pool than was found in the "
+ "larval protein. A previously presented model was used to describe the flux of amino acids in growing "
+ "turbot larvae. The FAA pool was found to be small and variable. It was estimated that the daily dietary "
+ "amino acid intake might be up to ten times the larval FAA pool. In addition, protein synthesis and "
+ "protein degradation might daily remove and return, respectively, the equivalent of up to 20 and 10 "
+ "times the size of the FAA pool. In an early phase (Day 11) high growth rates were associated with a "
+ "relatively low protein turnover, while at a later stage (Day 17), a much higher turnover was observed.");
return PreviewPrefsTab.entry;
}
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 BibtexEntry createNewEntry() {
// Find out what type is wanted.
EntryTypeDialog etd = new EntryTypeDialog(frame);
// We want to center the dialog, to make it look nicer.
Util.placeDialog(etd, frame);
etd.setVisible(true);
BibtexEntryType type = etd.getChoice();
if (type != null) { // Only if the dialog was not cancelled.
String id = Util.createNeutralId();
final BibtexEntry be = new BibtexEntry(id, type);
try {
panel.database().insertEntry(be);
// Set owner/timestamp if options are enabled:
ArrayList<BibtexEntry> list = new ArrayList<BibtexEntry>();
list.add(be);
Util.setAutomaticFields(list, true, true, false);
// Create an UndoableInsertEntry object.
panel.undoManager.addEdit(new UndoableInsertEntry(panel.database(), be, panel));
panel.output(
Globals.lang("Added new")
+ " '"
+ type.getName().toLowerCase()
+ "' "
+ Globals.lang("entry")
+ ".");
// We are going to select the new entry. Before that, make sure that we are in
// show-entry mode. If we aren't already in that mode, enter the WILL_SHOW_EDITOR
// mode which makes sure the selection will trigger display of the entry editor
// and adjustment of the splitter.
if (panel.getMode() != panel.SHOWING_EDITOR) {
panel.setMode(panel.WILL_SHOW_EDITOR);
}
/*int row = entryTable.findEntry(be);
if (row >= 0)
// Selects the entry. The selection listener will open the editor.
if (row >= 0) {
try{
entryTable.setRowSelectionInterval(row, row);
}catch(IllegalArgumentException e){
System.out.println("RowCount: " + entryTable.getRowCount());
}
//entryTable.setActiveRow(row);
entryTable.ensureVisible(row);
}
else {
// The entry is not visible in the table, perhaps due to a filtering search
// or group selection. Show the entry editor anyway:
panel.showEntry(be);
} */
panel.showEntry(be);
panel.markBaseChanged(); // The database just changed.
new FocusRequester(panel.getEntryEditor(be));
return be;
} catch (KeyCollisionException ex) {
Util.pr(ex.getMessage());
}
}
return null;
}
private void applyChanges() {
valueChanged(new ListSelectionEvent(new JList(), 0, 0, false));
// Iterate over our map of required fields, and list those types if necessary:
List<String> types = typeComp.getFields();
for (Map.Entry<String, List<String>> stringListEntry : reqLists.entrySet()) {
if (!types.contains(stringListEntry.getKey())) {
continue;
}
List<String> reqFields = stringListEntry.getValue();
List<String> optFields = optLists.get(stringListEntry.getKey());
List<String> opt2Fields = opt2Lists.get(stringListEntry.getKey());
String[] reqStr = new String[reqFields.size()];
reqStr = reqFields.toArray(reqStr);
String[] optStr = new String[optFields.size()];
optStr = optFields.toArray(optStr);
String[] opt2Str;
if (opt2Fields != null) {
opt2Str = opt2Fields.toArray(new String[opt2Fields.size()]);
} else {
opt2Str = new String[0];
}
// If this type is already existing, check if any changes have
// been made
boolean changesMade = true;
if (defaulted.contains(stringListEntry.getKey())) {
// This type should be reverted to its default setup.
// System.out.println("Defaulting: "+typeName);
String nm = StringUtil.nCase(stringListEntry.getKey());
BibtexEntryType.removeType(nm);
updateTypesForEntries(nm);
continue;
}
BibtexEntryType oldType = BibtexEntryType.getType(stringListEntry.getKey());
if (oldType != null) {
String[] oldReq = oldType.getRequiredFields(), oldOpt = oldType.getOptionalFields();
if (biblatexMode) {
String[] priOpt = oldType.getPrimaryOptionalFields();
String[] secOpt = Util.getRemainder(oldOpt, priOpt);
if (equalArrays(oldReq, reqStr)
&& equalArrays(oldOpt, optStr)
&& equalArrays(secOpt, opt2Str)) {
changesMade = false;
}
} else if (equalArrays(oldReq, reqStr) && equalArrays(oldOpt, optStr)) {
changesMade = false;
}
}
if (changesMade) {
// System.out.println("Updating: "+typeName);
CustomEntryType typ =
biblatexMode
? new CustomEntryType(
StringUtil.nCase(stringListEntry.getKey()), reqStr, optStr, opt2Str)
: new CustomEntryType(StringUtil.nCase(stringListEntry.getKey()), reqStr, optStr);
BibtexEntryType.ALL_TYPES.put(stringListEntry.getKey().toLowerCase(), typ);
updateTypesForEntries(typ.getName());
}
}
Set<Object> toRemove = new HashSet<Object>();
for (String o : BibtexEntryType.ALL_TYPES.keySet()) {
if (!types.contains(o)) {
toRemove.add(o);
}
}
// Remove those that should be removed:
if (!toRemove.isEmpty()) {
for (Object aToRemove : toRemove) {
typeDeletion((String) aToRemove);
}
}
updateTables();
}
@Override
public void valueChanged(ListSelectionEvent e) {
if (e.getValueIsAdjusting()) {
return;
}
if (lastSelected != null) {
// The entry type lastSelected is now unselected, so we store the current settings
// for that type in our two maps.
reqLists.put(lastSelected, reqComp.getFields());
optLists.put(lastSelected, optComp.getFields());
if (biblatexMode) {
opt2Lists.put(lastSelected, optComp2.getFields());
}
}
String s = typeComp.getFirstSelected();
if (s == null) {
return;
}
List<String> rl = reqLists.get(s);
if (rl == null) {
BibtexEntryType type = BibtexEntryType.getType(s);
if (type != null) {
String[] rf = type.getRequiredFieldsForCustomization(), of = type.getOptionalFields();
List<String> req, opt;
if (rf != null) {
req = java.util.Arrays.asList(rf);
} else {
req = new ArrayList<String>();
}
if (!biblatexMode) {
if (of != null) {
opt = java.util.Arrays.asList(of);
} else {
opt = new ArrayList<String>();
}
} else {
String[] priOf = type.getPrimaryOptionalFields();
if (priOf != null) {
opt = java.util.Arrays.asList(priOf);
} else {
opt = new ArrayList<String>();
}
List<String> opt2 = new ArrayList<String>();
if (of != null) {
for (String anOf : of) {
if (!opt.contains(anOf)) {
opt2.add(anOf);
}
}
}
optComp2.setFields(opt2);
optComp2.setEnabled(true);
}
reqComp.setFields(req);
reqComp.setEnabled(true);
optComp.setFields(opt);
optComp.setEnabled(true);
} else {
// New entry, veintle
reqComp.setFields(new ArrayList<String>());
reqComp.setEnabled(true);
optComp.setFields(new ArrayList<String>());
optComp.setEnabled(true);
if (biblatexMode) {
optComp2.setFields(new ArrayList<String>());
optComp2.setEnabled(true);
}
new FocusRequester(reqComp);
}
} else {
reqComp.setFields(rl);
optComp.setFields(optLists.get(s));
if (biblatexMode) {
optComp2.setFields(opt2Lists.get(s));
}
}
lastSelected = s;
typeComp.enable(s, changed.contains(lastSelected) && !defaulted.contains(lastSelected));
}
/**
* Will parse the BibTex-Data found when reading from reader.
*
* <p>The reader will be consumed.
*
* <p>Multiple calls to parse() return the same results
*
* @return ParserResult
* @throws IOException
*/
public ParserResult parse() throws IOException {
// If we already parsed this, just return it.
if (_pr != null) return _pr;
_db = new BibtexDatabase(); // Bibtex related contents.
_meta = new HashMap<String, String>(); // Metadata in comments for Bibkeeper.
entryTypes = new HashMap<String, BibtexEntryType>(); // To store custem entry types parsed.
_pr = new ParserResult(_db, _meta, entryTypes);
// First see if we can find the version number of the JabRef version that
// wrote the file:
String versionNum = readJabRefVersionNumber();
if (versionNum != null) {
_pr.setJabrefVersion(versionNum);
setMajorMinorVersions();
} else {
// No version number found. However, we have only
}
skipWhitespace();
try {
while (!_eof) {
boolean found = consumeUncritically('@');
if (!found) break;
skipWhitespace();
String entryType = parseTextToken();
BibtexEntryType tp = BibtexEntryType.getType(entryType);
boolean isEntry = (tp != null);
// Util.pr(tp.getName());
if (!isEntry) {
// The entry type name was not recognized. This can mean
// that it is a string, preamble, or comment. If so,
// parse and set accordingly. If not, assume it is an entry
// with an unknown type.
if (entryType.toLowerCase().equals("preamble")) {
_db.setPreamble(parsePreamble());
} else if (entryType.toLowerCase().equals("string")) {
BibtexString bs = parseString();
try {
_db.addString(bs);
} catch (KeyCollisionException ex) {
_pr.addWarning(Globals.lang("Duplicate string name") + ": " + bs.getName());
// ex.printStackTrace();
}
} else if (entryType.toLowerCase().equals("comment")) {
StringBuffer commentBuf = parseBracketedTextExactly();
/**
* Metadata are used to store Bibkeeper-specific information in .bib files.
*
* <p>Metadata are stored in bibtex files in the format
*
* @comment{jabref-meta: type:data0;data1;data2;...}
* <p>Each comment that starts with the META_FLAG is stored in the meta HashMap,
* with type as key. Unluckily, the old META_FLAG bibkeeper-meta: was used in JabRef
* 1.0 and 1.1, so we need to support it as well. At least for a while. We'll always
* save with the new one.
*/
String comment = commentBuf.toString().replaceAll("[\\x0d\\x0a]", "");
if (comment
.substring(0, Math.min(comment.length(), GUIGlobals.META_FLAG.length()))
.equals(GUIGlobals.META_FLAG)
|| comment
.substring(0, Math.min(comment.length(), GUIGlobals.META_FLAG_OLD.length()))
.equals(GUIGlobals.META_FLAG_OLD)) {
String rest;
if (comment.substring(0, GUIGlobals.META_FLAG.length()).equals(GUIGlobals.META_FLAG))
rest = comment.substring(GUIGlobals.META_FLAG.length());
else rest = comment.substring(GUIGlobals.META_FLAG_OLD.length());
int pos = rest.indexOf(':');
if (pos > 0) _meta.put(rest.substring(0, pos), rest.substring(pos + 1));
// We remove all line breaks in the metadata - these
// will have been inserted
// to prevent too long lines when the file was
// saved, and are not part of the data.
}
/**
* A custom entry type can also be stored in a
*
* @comment:
*/
if (comment
.substring(0, Math.min(comment.length(), GUIGlobals.ENTRYTYPE_FLAG.length()))
.equals(GUIGlobals.ENTRYTYPE_FLAG)) {
CustomEntryType typ = CustomEntryType.parseEntryType(comment);
entryTypes.put(typ.getName().toLowerCase(), typ);
}
} else {
// The entry type was not recognized. This may mean that
// it is a custom entry type whose definition will
// appear
// at the bottom of the file. So we use an
// UnknownEntryType
// to remember the type name by.
tp = new UnknownEntryType(entryType.toLowerCase());
// System.out.println("unknown type: "+entryType);
isEntry = true;
}
}
if (isEntry) // True if not comment, preamble or string.
{
/**
* Morten Alver 13 Aug 2006: Trying to make the parser more robust. If an exception is
* thrown when parsing an entry, drop the entry and try to resume parsing. Add a warning
* for the user.
*
* <p>An alternative solution is to try rescuing the entry for which parsing failed, by
* returning the entry with the exception and adding it before parsing is continued.
*/
try {
BibtexEntry be = parseEntry(tp);
boolean duplicateKey = _db.insertEntry(be);
if (duplicateKey) // JZTODO lyrics
_pr.addWarning(
Globals.lang("duplicate BibTeX key")
+ ": "
+ be.getCiteKey()
+ " ("
+ Globals.lang("grouping may not work for this entry")
+ ")");
else if (be.getCiteKey() == null || be.getCiteKey().equals("")) {
_pr.addWarning(
Globals.lang("empty BibTeX key")
+ ": "
+ be.getAuthorTitleYear(40)
+ " ("
+ Globals.lang("grouping may not work for this entry")
+ ")");
}
} catch (IOException ex) {
ex.printStackTrace();
_pr.addWarning(
Globals.lang("Error occured when parsing entry")
+ ": '"
+ ex.getMessage()
+ "'. "
+ Globals.lang("Skipped entry."));
}
}
skipWhitespace();
}
// Before returning the database, update entries with unknown type
// based on parsed type definitions, if possible.
checkEntryTypes(_pr);
return _pr;
} catch (KeyCollisionException kce) {
// kce.printStackTrace();
throw new IOException("Duplicate ID in bibtex file: " + kce.toString());
}
}