private static void exportFieldToKeywords(
SpecialField e, String newValue, BibtexEntry be, NamedCompound ce) {
if (!SpecialFieldsUtils.keywordSyncEnabled()) {
return;
}
ArrayList<String> keywordList = Util.getSeparatedKeywords(be);
List<String> values = e.getKeyWords();
int foundPos = -1;
// cleanup keywords
for (Object value : values) {
int pos = keywordList.indexOf(value);
if (pos >= 0) {
foundPos = pos;
keywordList.remove(pos);
}
}
if (newValue != null) {
if (foundPos == -1) {
keywordList.add(newValue);
} else {
keywordList.add(foundPos, newValue);
}
}
Util.putKeywords(be, keywordList, ce);
}
/**
* @param owner the parent Window (Dialog or Frame)
* @param frame the JabRef Frame
* @param panel the currently selected BasePanel
* @param modal should this dialog be modal?
* @param metaData The metadata of the current database
* @param fieldName the field this selector is initialized for. May be null.
*/
public ContentSelectorDialog2(
Window owner,
JabRefFrame frame,
BasePanel panel,
boolean modal,
MetaData metaData,
String fieldName) {
super(owner, Localization.lang("Setup selectors"));
this.setModal(modal);
this.metaData = metaData;
this.frame = frame;
this.panel = panel;
this.currentField = fieldName;
initLayout();
setupFieldSelector();
setupWordSelector();
setupActions();
Util.bindCloseDialogKeyToCancelAction(this.rootPane, cancel.getAction());
int fieldInd = fieldListModel.indexOf(currentField);
if (fieldInd >= 0) {
fieldList.setSelectedIndex(fieldInd);
}
pack();
}
@Override
public void actionPerformed(ActionEvent e) {
try {
Util.runAbstractWorker(DbImportAction.this);
} catch (Throwable throwable) {
LOGGER.warn("Problem importing from database", throwable);
}
}
private static BibEntry downloadEntryBibTeX(String id, boolean downloadAbstract) {
try {
URL url =
new URL(
ACMPortalFetcher.START_URL
+ ACMPortalFetcher.BIBTEX_URL
+ id
+ ACMPortalFetcher.BIBTEX_URL_END);
URLConnection connection = url.openConnection();
// set user-agent to avoid being blocked as a crawler
connection.addRequestProperty(
"User-Agent", "Mozilla/5.0 (Windows NT 5.1; rv:31.0) Gecko/20100101 Firefox/31.0");
Collection<BibEntry> items = null;
try (BufferedReader in =
new BufferedReader(new InputStreamReader(connection.getInputStream()))) {
items = BibtexParser.parse(in).getDatabase().getEntries();
} catch (IOException e) {
LOGGER.info("Download of BibTeX information from ACM Portal failed.", e);
}
if ((items == null) || items.isEmpty()) {
return null;
}
BibEntry entry = items.iterator().next();
Thread.sleep(
ACMPortalFetcher.WAIT_TIME); // wait between requests or you will be blocked by ACM
// get abstract
if (downloadAbstract) {
url = new URL(ACMPortalFetcher.START_URL + ACMPortalFetcher.ABSTRACT_URL + id);
String page = Util.getResults(url);
Matcher absM = ACMPortalFetcher.ABSTRACT_PATTERN.matcher(page);
if (absM.find()) {
entry.setField("abstract", absM.group(1).trim());
}
Thread.sleep(
ACMPortalFetcher.WAIT_TIME); // wait between requests or you will be blocked by ACM
}
return entry;
} catch (NoSuchElementException e) {
LOGGER.info(
"Bad Bibtex record read at: "
+ ACMPortalFetcher.BIBTEX_URL
+ id
+ ACMPortalFetcher.BIBTEX_URL_END,
e);
return null;
} catch (MalformedURLException e) {
LOGGER.info("Malformed URL.", e);
return null;
} catch (IOException e) {
LOGGER.info("Cannot connect.", e);
return null;
} catch (InterruptedException ignored) {
return null;
}
}
/**
* @param e - Field to be handled
* @param value - may be null to state that field should be emptied
* @param be - BibTeXEntry to be handled
* @param ce - Filled with undo info (if necessary)
* @param nullFieldIfValueIsTheSame - true: field is nulled if value is the same than the current
* value in be
*/
public static void updateField(
SpecialField e,
String value,
BibtexEntry be,
NamedCompound ce,
boolean nullFieldIfValueIsTheSame) {
Util.updateField(be, e.getFieldName(), value, ce, nullFieldIfValueIsTheSame);
// we cannot use "value" here as updateField has side effects: "nullFieldIfValueIsTheSame" nulls
// the field if value is the same
SpecialFieldsUtils.exportFieldToKeywords(e, be.getField(e.getFieldName()), be, ce);
}
/**
* updates field values according to keywords
*
* @param ce indicates the undo named compound. May be null
*/
public static void syncSpecialFieldsFromKeywords(BibtexEntry be, NamedCompound ce) {
if (be.getField("keywords") == null) {
return;
}
ArrayList<String> keywordList = Util.getSeparatedKeywords(be.getField("keywords"));
SpecialFieldsUtils.importKeywordsForField(keywordList, Priority.getInstance(), be, ce);
SpecialFieldsUtils.importKeywordsForField(keywordList, Rank.getInstance(), be, ce);
SpecialFieldsUtils.importKeywordsForField(keywordList, Quality.getInstance(), be, ce);
SpecialFieldsUtils.importKeywordsForField(keywordList, Relevance.getInstance(), be, ce);
SpecialFieldsUtils.importKeywordsForField(keywordList, ReadStatus.getInstance(), be, ce);
SpecialFieldsUtils.importKeywordsForField(keywordList, Printed.getInstance(), be, ce);
}
private static void importKeywordsForField(
ArrayList<String> keywordList, SpecialField c, BibtexEntry be, NamedCompound nc) {
List<String> values = c.getKeyWords();
String newValue = null;
for (String val : values) {
if (keywordList.contains(val)) {
newValue = val;
break;
}
}
Util.updateField(be, c.getFieldName(), newValue, nc);
}
@Override
public void actionPerformed(ActionEvent e) {
try {
Util.openBrowser("https://github.com/JabRef/jabref");
} catch (IOException ex) {
ex.printStackTrace();
JabRef.jrf
.basePanel()
.output(
Globals.lang("Could not open browser.")
+ " "
+ Globals.lang("Please open http://github.com/JabRef/jabref manually."));
}
}
private void init() {
getContentPane().setLayout(new BorderLayout());
getContentPane().add(labelPatternPanel, BorderLayout.CENTER);
JButton ok = new JButton(Localization.lang("Ok"));
JButton cancel =
new JButton(); // label of "cancel" is set later as the label is overwritten by assigning an
// action to the button
JPanel lower = new JPanel();
lower.setBorder(BorderFactory.createEmptyBorder(2, 2, 2, 2));
ButtonBarBuilder bb = new ButtonBarBuilder(lower);
bb.addGlue();
bb.addButton(ok);
bb.addButton(cancel);
bb.addGlue();
getContentPane().add(lower, BorderLayout.SOUTH);
this.setDefaultCloseOperation(WindowConstants.DISPOSE_ON_CLOSE);
getContentPane().setPreferredSize(new Dimension(500, 600));
pack();
ok.addActionListener(
new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
metaData.setLabelPattern(labelPatternPanel.getLabelPatternAsDatabaseLabelPattern());
panel.markNonUndoableBaseChanged();
dispose();
}
});
final JDialog dialog = this;
Action cancelAction =
new AbstractAction() {
@Override
public void actionPerformed(ActionEvent e) {
dialog.dispatchEvent(new WindowEvent(dialog, WindowEvent.WINDOW_CLOSING));
}
};
cancel.setAction(cancelAction);
cancel.setText(Localization.lang("Cancel"));
Util.bindCloseDialogKeyToCancelAction(this.getRootPane(), cancelAction);
}
@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);
}
}
}
/**
* This method performs the actual changes.
*
* @param panel
* @param pr
* @param fileDir The path to the file directory to set, or null if it should not be set.
*/
private void makeChanges(
BasePanel panel,
ParserResult pr,
boolean upgradePrefs,
boolean upgradeDatabase,
String fileDir) {
if (upgradeDatabase) {
// Update file links links in the database:
NamedCompound ce =
Util.upgradePdfPsToFile(pr.getDatabase(), FileLinksUpgradeWarning.FIELDS_TO_LOOK_FOR);
panel.undoManager.addEdit(ce);
panel.markBaseChanged();
}
if (fileDir != null) {
Globals.prefs.put(GUIGlobals.FILE_FIELD + "Directory", fileDir);
}
if (upgradePrefs) {
// Exchange table columns:
Globals.prefs.putBoolean(JabRefPreferences.PDF_COLUMN, Boolean.FALSE);
Globals.prefs.putBoolean(JabRefPreferences.FILE_COLUMN, Boolean.TRUE);
// Modify General fields if necessary:
// If we don't find the file field, insert it at the bottom of the first tab:
if (!showsFileInGenFields()) {
String gfs = Globals.prefs.get(JabRefPreferences.CUSTOM_TAB_FIELDS + "0");
// System.out.println(gfs);
StringBuilder sb = new StringBuilder(gfs);
if (gfs.length() > 0) {
sb.append(";");
}
sb.append(GUIGlobals.FILE_FIELD);
Globals.prefs.put(JabRefPreferences.CUSTOM_TAB_FIELDS + "0", sb.toString());
Globals.prefs.updateEntryEditorTabList();
panel.frame().removeCachedEntryEditors();
}
panel.frame().setupAllTables();
}
}
@Override
public String[] getSecondaryOptionalFields() {
return Util.getRemainder(opt, priOpt);
}
private void doRenamePDFs(BibtexEntry entry, NamedCompound ce) {
// Extract the path
String oldValue = entry.getField(Globals.FILE_FIELD);
if (oldValue == null) {
return;
}
FileListTableModel flModel = new FileListTableModel();
flModel.setContent(oldValue);
if (flModel.getRowCount() == 0) {
return;
}
boolean changed = false;
for (int i = 0; i < flModel.getRowCount(); i++) {
String realOldFilename = flModel.getEntry(i).getLink();
if (cleanUpRenamePDFonlyRelativePaths.isSelected()
&& (new File(realOldFilename).isAbsolute())) {
continue;
}
String newFilename = Util.getLinkedFileName(panel.database(), entry);
// String oldFilename = bes.getField(GUIGlobals.FILE_FIELD); // would have to be stored for
// undoing purposes
// Add extension to newFilename
newFilename = newFilename + "." + flModel.getEntry(i).getType().getExtension();
// get new Filename with path
// Create new Path based on old Path and new filename
File expandedOldFile =
FileUtil.expandFilename(
realOldFilename, panel.metaData().getFileDirectory(Globals.FILE_FIELD));
if (expandedOldFile.getParent() == null) {
// something went wrong. Just skip this entry
continue;
}
String newPath =
expandedOldFile
.getParent()
.concat(System.getProperty("file.separator"))
.concat(newFilename);
if (new File(newPath).exists()) {
// we do not overwrite files
// TODO: we could check here if the newPath file is linked with the current entry. And if
// not, we could add a link
continue;
}
// do rename
boolean renameSuccessful = FileUtil.renameFile(expandedOldFile.toString(), newPath);
if (renameSuccessful) {
changed = true;
// Change the path for this entry
String description = flModel.getEntry(i).getDescription();
ExternalFileType type = flModel.getEntry(i).getType();
flModel.removeEntry(i);
// we cannot use "newPath" to generate a FileListEntry as newPath is absolute, but we want
// to keep relative paths whenever possible
File parent = (new File(realOldFilename)).getParentFile();
String newFileEntryFileName;
if (parent == null) {
newFileEntryFileName = newFilename;
} else {
newFileEntryFileName =
parent.toString().concat(System.getProperty("file.separator")).concat(newFilename);
}
flModel.addEntry(i, new FileListEntry(description, newFileEntryFileName, type));
} else {
unsuccessfulRenames++;
}
}
if (changed) {
String newValue = flModel.getStringRepresentation();
assert (!oldValue.equals(newValue));
entry.setField(Globals.FILE_FIELD, newValue);
// we put an undo of the field content here
// the file is not being renamed back, which leads to inconsistencies
// if we put a null undo object here, the change by "doMakePathsRelative" would overwrite the
// field value nevertheless.
ce.addEdit(new UndoableFieldChange(entry, Globals.FILE_FIELD, oldValue, newValue));
}
}
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();
}
public CustomEntryType(String name_, String[] req_, String[] priOpt_, String[] secOpt_) {
name = StringUtil.capitalizeFirst(name_);
parseRequiredFields(req_);
priOpt = priOpt_;
opt = Util.arrayConcat(priOpt_, secOpt_);
}
@Override
public void run() {
if (cancelled) {
return;
}
int choice = showCleanUpDialog();
if (choice != JOptionPane.OK_OPTION) {
cancelled = true;
return;
}
storeSettings();
boolean choiceCleanUpSuperscripts = cleanUpSuperscripts.isSelected();
boolean choiceCleanUpDOI = cleanUpDOI.isSelected();
boolean choiceCleanUpMonth = cleanUpMonth.isSelected();
boolean choiceCleanUpPageNumbers = cleanUpPageNumbers.isSelected();
boolean choiceCleanUpDate = cleanUpDate.isSelected();
boolean choiceCleanUpUpgradeExternalLinks = cleanUpUpgradeExternalLinks.isSelected();
boolean choiceMakePathsRelative = cleanUpMakePathsRelative.isSelected();
boolean choiceRenamePDF = cleanUpRenamePDF.isSelected();
boolean choiceConvertHTML = cleanUpHTML.isSelected();
boolean choiceConvertCase = cleanUpCase.isSelected();
boolean choiceConvertLaTeX = cleanUpLaTeX.isSelected();
boolean choiceConvertUnits = cleanUpUnits.isSelected();
boolean choiceConvertUnicode = cleanUpUnicode.isSelected();
boolean choiceConvertToBiblatex = cleanUpBibLatex.isSelected();
if (choiceRenamePDF && Globals.prefs.getBoolean(CleanUpAction.AKS_AUTO_NAMING_PDFS_AGAIN)) {
CheckBoxMessage cbm =
new CheckBoxMessage(
Localization.lang("Auto-generating PDF-Names does not support undo. Continue?"),
Localization.lang("Disable this confirmation dialog"),
false);
int answer =
JOptionPane.showConfirmDialog(
frame, cbm, Localization.lang("Autogenerate PDF Names"), JOptionPane.YES_NO_OPTION);
if (cbm.isSelected()) {
Globals.prefs.putBoolean(CleanUpAction.AKS_AUTO_NAMING_PDFS_AGAIN, false);
}
if (answer == JOptionPane.NO_OPTION) {
cancelled = true;
return;
}
}
// first upgrade the external links
// we have to use it separately as the Utils function generates a separate Named Compound
if (choiceCleanUpUpgradeExternalLinks) {
NamedCompound ce =
Util.upgradePdfPsToFile(
Arrays.asList(panel.getSelectedEntries()), new String[] {"pdf", "ps"});
if (ce.hasEdits()) {
panel.undoManager.addEdit(ce);
panel.markBaseChanged();
panel.updateEntryEditorIfShowing();
panel.output(Localization.lang("Upgraded links."));
}
}
for (BibtexEntry entry : panel.getSelectedEntries()) {
// undo granularity is on entry level
NamedCompound ce = new NamedCompound(Localization.lang("Cleanup entry"));
if (choiceCleanUpSuperscripts) {
doCleanUpSuperscripts(entry, ce);
}
if (choiceCleanUpDOI) {
doCleanUpDOI(entry, ce);
}
if (choiceCleanUpMonth) {
doCleanUpMonth(entry, ce);
}
if (choiceCleanUpPageNumbers) {
doCleanUpPageNumbers(entry, ce);
}
if (choiceCleanUpDate) {
doCleanUpDate(entry, ce);
}
fixWrongFileEntries(entry, ce);
if (choiceMakePathsRelative) {
doMakePathsRelative(entry, ce);
}
if (choiceRenamePDF) {
doRenamePDFs(entry, ce);
}
if (choiceConvertHTML) {
doConvertHTML(entry, ce);
}
if (choiceConvertUnits) {
doConvertUnits(entry, ce);
}
if (choiceConvertCase) {
doConvertCase(entry, ce);
}
if (choiceConvertLaTeX) {
doConvertLaTeX(entry, ce);
}
if (choiceConvertUnicode) {
doConvertUnicode(entry, ce);
}
if (choiceConvertToBiblatex) {
convertToBiblatex(entry, ce);
}
ce.end();
if (ce.hasEdits()) {
modifiedEntriesCount++;
panel.undoManager.addEdit(ce);
}
}
}
@Override
public boolean processQueryGetPreview(
String query, FetcherPreviewDialog preview, OutputPrinter status) {
this.terms = query;
piv = 0;
shouldContinue = true;
acmOrGuide = acmButton.isSelected();
fetchAbstract = absCheckBox.isSelected();
String address = makeUrl();
LinkedHashMap<String, JLabel> previews = new LinkedHashMap<>();
try {
URL url = new URL(address);
String page = Util.getResults(url);
String resultsFound = "<div id=\"resfound\">";
int hits = getNumberOfHits(page, resultsFound, ACMPortalFetcher.HITS_PATTERN);
int index = page.indexOf(resultsFound);
if (index >= 0) {
page = page.substring(index + resultsFound.length());
}
if (hits == 0) {
status.showMessage(
Localization.lang("No entries found for the search string '%0'", terms),
Localization.lang("Search ACM Portal"),
JOptionPane.INFORMATION_MESSAGE);
return false;
} else if (hits > 20) {
status.showMessage(
Localization.lang(
"%0 entries found. To reduce server load, only %1 will be downloaded.",
String.valueOf(hits), String.valueOf(PER_PAGE)),
Localization.lang("Search ACM Portal"),
JOptionPane.INFORMATION_MESSAGE);
}
hits = getNumberOfHits(page, "<div class=\"pagerange\">", ACMPortalFetcher.MAX_HITS_PATTERN);
parse(page, Math.min(hits, PER_PAGE), previews);
for (Map.Entry<String, JLabel> entry : previews.entrySet()) {
preview.addEntry(entry.getKey(), entry.getValue());
}
return true;
} catch (MalformedURLException e) {
LOGGER.warn("Problem with ACM fetcher URL", e);
} catch (ConnectException e) {
status.showMessage(
Localization.lang("Connection to ACM Portal failed"),
Localization.lang("Search ACM Portal"),
JOptionPane.ERROR_MESSAGE);
} catch (IOException e) {
status.showMessage(
e.getMessage(), Localization.lang("Search ACM Portal"), JOptionPane.ERROR_MESSAGE);
LOGGER.warn("Problem with ACM Portal", e);
}
return false;
}