Merge remote-tracking branch 'upstream/master' into exportPDF

* upstream/master:
  fix ID consideration in DuplicateCheck
  Add ArXiv identifier batch lookup (#2710)
  Update mockito from 2.7.19 to 2.7.21
  More defensive identifier list #2708
  Revert "Add more identifier field names #2708"
  Add more identifier field names #2708
  Consider entries as equal if their DOI matches #2708
  Imports
  Imports
  Move duplicate detection to logic
  Reuse edit distance class
  Refactoring
  EntryTypeDialog Fetching Autogenerates BibTeX Key (#2709)
  Add changelog entry
  Increase permitted size of StringUtil
  Make sure that JavaFx shuts down in case another JabRef instance is already open

CHANGELOG.md

@@ -56,7 +56,7 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The `Move linked files to default file directory`-Cleanup operation respects the `File directory pattern` setting 
 - We separated the `Move file` and `Rename Pdfs` logic and context menu entries in the `General`-Tab for the Field `file` to improve the semantics
 - A scrollbar was added to the cleanup panel, as a result of issue [#2501](https://github.com/JabRef/jabref/issues/2501)
-- Using "Look up document identifier" in the quality menu, it is possible to look up DOIs and other identifiers for multiple entries.
+- Using "Look up document identifier" in the quality menu, it is possible to look up DOIs, ArXiv ids and other identifiers for multiple entries.
 - F4 opens selected file in current JTable context not just from selected entry inside the main table [#2355](https://github.com/JabRef/jabref/issues/2355)
 - We added an option to copy the title of BibTeX entries to the clipboard through `Edit -> Copy title` (implements [#210](https://github.com/koppor/jabref/issues/210))
 - Several scrollbars were added to the preference dialog which show up when content is too large [#2559](https://github.com/JabRef/jabref/issues/2559)
@@ -66,6 +66,8 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 - The `day` part of the biblatex `date` field is now exported to the corresponding `day` field in MS-Office XML. [#2691](https://github.com/JabRef/jabref/issues/2691)
 
 ### Fixed
+ - We fixed an issue of duplicate keys after using a fetcher, e.g., DOI or ISBN [#2867](https://github.com/JabRef/jabref/issues/2687)
+ - We fixed an issue that prevented multiple parallel JabRef instances from terminating gracefully. [#2698](https://github.com/JabRef/jabref/issues/2698)
  - We fixed an issue where authors with multiple surnames were not presented correctly in the main table. [#2534](https://github.com/JabRef/jabref/issues/2534)
  - Repairs the handling of apostrophes in the LaTeX to unicode conversion. [#2500](https://github.com/JabRef/jabref/issues/2500)
  - Fix import of journal title in ris format. [#2506](https://github.com/JabRef/jabref/issues/2506)

build.gradle

@@ -140,7 +140,7 @@ dependencies {
  compile 'com.github.tomtung:latex2unicode_2.12:0.2'
 
  testCompile 'junit:junit:4.12'
- testCompile 'org.mockito:mockito-core:2.7.19'
+ testCompile 'org.mockito:mockito-core:2.7.21'
  testCompile 'com.github.tomakehurst:wiremock:2.5.1'
  testCompile 'org.assertj:assertj-swing-junit:3.5.0'
  testCompile 'org.reflections:reflections:0.9.11'

src/main/java/org/jabref/JabRefMain.java

@@ -116,6 +116,8 @@ private static void start(String[] args) {
  // So we assume it's all taken care of, and quit.
  LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
  Globals.shutdownThreadPools();
+ // needed to tell JavaFx to stop
+ Platform.exit();
  return;
  }
  }

src/main/java/org/jabref/collab/ChangeScanner.java

@@ -17,6 +17,7 @@
 import org.jabref.JabRefExecutorService;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.JabRefFrame;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.bibtex.comparator.EntryComparator;
 import org.jabref.logic.exporter.BibDatabaseWriter;
 import org.jabref.logic.exporter.BibtexDatabaseWriter;
@@ -29,7 +30,6 @@
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.Defaults;
-import org.jabref.model.DuplicateCheck;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.EntrySorter;

src/main/java/org/jabref/collab/EntryChange.java

@@ -13,8 +13,8 @@
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableFieldChange;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.DuplicateCheck;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 

src/main/java/org/jabref/collab/EntryDeleteChange.java

@@ -7,8 +7,8 @@
 import org.jabref.gui.PreviewPanel;
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableRemoveEntry;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.DuplicateCheck;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 

src/main/java/org/jabref/gui/DuplicateSearch.java

@@ -14,8 +14,8 @@
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableRemoveEntry;
 import org.jabref.gui.worker.CallBack;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
-import org.jabref.model.DuplicateCheck;
 import org.jabref.model.entry.BibEntry;
 
 import spin.Spin;

src/main/java/org/jabref/gui/EntryTypeDialog.java

@@ -28,6 +28,7 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.keyboard.KeyBinding;
+import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternUtil;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
 import org.jabref.logic.importer.WebFetchers;
@@ -96,7 +97,6 @@ private JPanel createEntryGroupsPanel() {
  if (!customTypes.isEmpty()) {
  panel.add(createEntryGroupPanel(Localization.lang("Custom"), customTypes));
  }
-
  } else {
  panel.add(createEntryGroupPanel("BibTeX", BibtexEntryTypes.ALL));
  panel.add(createEntryGroupPanel("IEEETran", IEEETranEntryTypes.ALL));
@@ -182,7 +182,7 @@ private JPanel createIdFetcherPanel() {
  JPanel jPanel = new JPanel();
 
  GridBagConstraints constraints = new GridBagConstraints();
- constraints.insets = new Insets(4,4,4,4);
+ constraints.insets = new Insets(4, 4, 4, 4);
 
  GridBagLayout layout = new GridBagLayout();
  jPanel.setLayout(layout);
@@ -305,15 +305,19 @@ protected void done() {
  try {
  Optional<BibEntry> result = get();
  if (result.isPresent()) {
- frame.getCurrentBasePanel().insertEntry(result.get());
+ final BibEntry bibEntry = result.get();
+ // Regenerate CiteKey of imported BibEntry
+ BibtexKeyPatternUtil.makeAndSetLabel(Globals.prefs.getBibtexKeyPatternPreferences().getKeyPattern(), frame.getCurrentBasePanel().getDatabase(), bibEntry, Globals.prefs.getBibtexKeyPatternPreferences());
+
+ frame.getCurrentBasePanel().insertEntry(bibEntry);
  dispose();
  } else if (searchID.trim().isEmpty()) {
  JOptionPane.showMessageDialog(frame, Localization.lang("The given search ID was empty."), Localization.lang("Empty search ID"), JOptionPane.WARNING_MESSAGE);
  } else if (!fetcherException) {
- JOptionPane.showMessageDialog(frame, Localization.lang("Fetcher_'%0'_did_not_find_an_entry_for_id_'%1'.", fetcher.getName(), searchID)+ "\n" + fetcherExceptionMessage, Localization.lang("No files found."), JOptionPane.WARNING_MESSAGE);
+ JOptionPane.showMessageDialog(frame, Localization.lang("Fetcher_'%0'_did_not_find_an_entry_for_id_'%1'.", fetcher.getName(), searchID) + "\n" + fetcherExceptionMessage, Localization.lang("No files found."), JOptionPane.WARNING_MESSAGE);
  } else {
  JOptionPane.showMessageDialog(frame,
- Localization.lang("Error while fetching from %0", fetcher.getName()) +"." + "\n" + fetcherExceptionMessage,
+ Localization.lang("Error while fetching from %0", fetcher.getName()) + "." + "\n" + fetcherExceptionMessage,
  Localization.lang("Error"), JOptionPane.ERROR_MESSAGE);
  }
  fetcherWorker = new FetcherWorker();
@@ -328,5 +332,4 @@ protected void done() {
  }
  }
  }
-
 }

src/main/java/org/jabref/gui/FindUnlinkedFilesDialog.java

@@ -87,10 +87,6 @@
 
 /**
  * GUI Dialog for the feature "Find unlinked files".
- *
- * @author Nosh&Dan
- * @version 25.11.2008 | 23:13:29
- *
  */
 public class FindUnlinkedFilesDialog extends JDialog {
  private static final Log LOGGER = LogFactory.getLog(FindUnlinkedFilesDialog.class);
@@ -130,7 +126,7 @@ public class FindUnlinkedFilesDialog extends JDialog {
  private JButton buttonClose;
  /* Options for the TreeView */
  private JButton buttonOptionSelectAll;
- private JButton buttonOptionUnselectAll;
+ private JButton buttonOptionDeselectAll;
  private JButton buttonOptionExpandAll;
  private JButton buttonOptionCollapseAll;
 
@@ -711,9 +707,9 @@ public void windowClosing(WindowEvent e) {
  buttonOptionSelectAll = new JButton();
  buttonOptionSelectAll.setMnemonic('A');
  buttonOptionSelectAll.setAction(actionSelectAll);
- buttonOptionUnselectAll = new JButton();
- buttonOptionUnselectAll.setMnemonic('U');
- buttonOptionUnselectAll.setAction(actionUnselectAll);
+ buttonOptionDeselectAll = new JButton();
+ buttonOptionDeselectAll.setMnemonic('U');
+ buttonOptionDeselectAll.setAction(actionUnselectAll);
  buttonOptionExpandAll = new JButton();
  buttonOptionExpandAll.setMnemonic('E');
  buttonOptionExpandAll.setAction(actionExpandTree);
@@ -809,7 +805,7 @@ GridBagConstraints.HORIZONTAL, GridBagConstraints.WEST, new Insets(18, 3, 18, 6)
  GridBagConstraints.NORTHEAST, basicInsets, 1, 1, 1, 1, 0, 0, 0, 0);
  FindUnlinkedFilesDialog.addComponent(gbl, panelOptions, buttonOptionSelectAll, GridBagConstraints.HORIZONTAL,
  GridBagConstraints.NORTH, noInsets, 0, 0, 1, 1, 1, 0, 0, 0);
- FindUnlinkedFilesDialog.addComponent(gbl, panelOptions, buttonOptionUnselectAll, GridBagConstraints.HORIZONTAL,
+ FindUnlinkedFilesDialog.addComponent(gbl, panelOptions, buttonOptionDeselectAll, GridBagConstraints.HORIZONTAL,
  GridBagConstraints.NORTH, noInsets, 0, 1, 1, 1, 0, 0, 0, 0);
  FindUnlinkedFilesDialog.addComponent(gbl, panelOptions, buttonOptionExpandAll, GridBagConstraints.HORIZONTAL,
  GridBagConstraints.NORTH, new Insets(6, 0, 0, 0), 0, 2, 1, 1, 0, 0, 0, 0);

src/main/java/org/jabref/gui/JabRefFrame.java

@@ -1177,7 +1177,7 @@ private void fillMenu() {
  quality.add(findUnlinkedFiles);
  quality.add(autoLinkFile);
 
- for (IdFetcher fetcher : WebFetchers.getIdFetchers()) {
+ for (IdFetcher fetcher : WebFetchers.getIdFetchers(Globals.prefs.getImportFormatPreferences())) {
  lookupIdentifiers.add(new LookupIdentifierAction(this, fetcher));
  }
  quality.add(lookupIdentifiers);

src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java

@@ -75,6 +75,7 @@
 import org.jabref.gui.undo.UndoableRemoveEntry;
 import org.jabref.gui.util.comparator.IconComparator;
 import org.jabref.gui.util.component.CheckBoxMessage;
+import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.bibtex.comparator.FieldComparator;
 import org.jabref.logic.bibtexkeypattern.BibtexKeyPatternUtil;
 import org.jabref.logic.help.HelpFile;
@@ -83,7 +84,6 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.UpdateField;
 import org.jabref.model.Defaults;
-import org.jabref.model.DuplicateCheck;
 import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;

src/main/java/org/jabref/gui/importer/UnlinkedFilesCrawler.java

@@ -54,7 +54,7 @@ public CheckableTreeNode searchDirectory(File directory, FileFilter filter) {
  * resolve its recursion and return what it has saved so far.
  */
  public CheckableTreeNode searchDirectory(File directory, UnlinkedPDFFileFilter ff, AtomicBoolean state, ChangeListener changeListener) {
- /* Cancelation of the search from outside! */
+ /* Cancellation of the search from outside! */
  if ((state == null) || !state.get()) {
  return null;
  }