Merge remote-tracking branch 'upstream/master' into fixCustomExportFi…

…leType

* upstream/master: (33 commits)
  Import inspection uses now same font size setttings as maintable (#4062)
  Add date checker (#4007)
  Enable tests
  macOs push to application fix
  Fix #4041 to make Push to Application work again on OSX. (#4057)
  Add NormalizeEnDashesFormatter (#4045)
  Package private for tests
  Shutdown duplicate code
  Move migrations to PreferencesMigrations
  Structure startup
  Extract migrations
  A first solution for the cli problem #4038 (#4047)
  New translations JabRef_en.properties (French) (#4052)
  Update CHANGELOG.md
  Fix checkstyle
  Make test more informative in the failing case
  New translations JabRef_en.properties (French) (#4051)
  New translations JabRef_en.properties (Vietnamese) (#4050)
  Make Formatter an abstract class (and remove AbstractFormatter)
  New Crowdin translations (#4048)
  ...

# Conflicts:
#	CHANGELOG.md

CHANGELOG.md

@@ -11,16 +11,26 @@ We refer to [GitHub issues](https://github.com/JabRef/jabref/issues) by using `#
 ## [Unreleased]
 
 ### Changed
+- We added a validity check for dates in the `date` and `urldate` fields.
 - We added a text file export for 'Find Unlinked Files'. [#3341](https://github.com/JabRef/jabref/issues/3341)
 - We added a fetcher based on RFC-IDs. [#3971](https://github.com/JabRef/jabref/issues/3971)
+- We changed the implementation of the `[shorttitle]` key pattern. It now removes small words like `a`, `an`, `on`, `the` etc. Refer to the help page for a complete overview. [Feature request in the forum](http://discourse.jabref.org/t/jabref-differences-in-shorttitle-between-versions-3-8-1-and-4-not-discounting-the-a-an-of-in-titles/1147)
+- We added a formatter for adding braces around the `title` field. E.g., `title = {ExamPle}` becomes `title = {{ExamPle}}`, which prevents BibTeX to convert it to lower case. You can use it at the [cleanup entries](http://help.jabref.org/en/CleanupEntries) functionality.
+- We added a formatter to ensure correct en dashes in the `title` field. E.g., `title = {Example - illustrative}` becomes `title = {Example -- illustrative}`.
+- We streamlined the defaults for a [cleanup of entries](http://help.jabref.org/en/CleanupEntries) in the case of BibTeX.
+- The import inspection window now uses the same font size setting as the maintable [Feature request in the forum](http://discourse.jabref.org/t/inspection-window-and-others-line-height-of-table-too-small-for-fonts/1168)
 
 ### Fixed
-We fixed an issue where the export to clipboard functionality could not be invoked [#3994](https://github.com/JabRef/jabref/issues/3994)
-We fixed an issue with the migration of invalid Look and Feels [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
-We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated [#3986](https://github.com/JabRef/jabref/issues/3986)
-We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
+- We fixed an issue where the export to clipboard functionality could not be invoked. [#3994](https://github.com/JabRef/jabref/issues/3994)
+- We fixed an issue with the migration of invalid Look and Feels. [#3995, comment](https://github.com/JabRef/jabref/issues/3995#issuecomment-385649448)
+- We fixed an issue where JabRef would no longer start, when the option "Override default font settings" was activated. [#3986](https://github.com/JabRef/jabref/issues/3986)
+- We fixed an issue where JabRef removed whitespace from the Title-fetcher which resulting in no entries being found. [#4014](https://github.com/JabRef/jabref/issues/4014)
+- We fixed an issue where fetched entries from the ACM fetcher could not be imported. [#4018](https://github.com/JabRef/jabref/issues/4018)
+- We fixed an issue to enable push to application on macOs again [#4041](https://github.com/JabRef/jabref/issues/4041)
+- We fixed an issue where custom exports could not be selected in the 'Export (selected) entries' dialog [#4013](https://github.com/JabRef/jabref/issues/4013)
+
 ### Removed
-We removed the GTK Look and Feel from the Options, as it leads to freezes in JabRef on MacOSX and Linux [#3995](https://github.com/JabRef/jabref/issues/3995)
+- We removed the GTK Look and Feel from the Options, as it leads to freezes in JabRef on MacOSX and Linux [#3995](https://github.com/JabRef/jabref/issues/3995).
 The GTK Look and Feel is now replaced with the "Nimbus" style as default.
 
 

build.gradle

@@ -147,8 +147,8 @@ dependencies {
 
  compile 'com.github.tomtung:latex2unicode_2.12:0.2.2'
 
- compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.0'
- compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.0'
+ compile group: 'com.microsoft.azure', name: 'applicationinsights-core', version: '2.1.1'
+ compile group: 'com.microsoft.azure', name: 'applicationinsights-logging-log4j2', version: '2.1.1'
 
  testImplementation 'org.junit.jupiter:junit-jupiter-api:5.2.0'
  testCompile 'org.junit.jupiter:junit-jupiter-params:5.2.0'
@@ -163,7 +163,7 @@ dependencies {
  testCompile 'org.reflections:reflections:0.9.11'
  testCompile 'org.xmlunit:xmlunit-core:2.6.0'
  testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
- testCompile 'com.tngtech.archunit:archunit-junit:0.5.0'
+ testCompile 'com.tngtech.archunit:archunit-junit:0.8.0'
  testCompile "org.testfx:testfx-core:4.0.+"
  testCompile "org.testfx:testfx-junit:4.0.+"
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.7-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.6-bin.zip

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

@@ -36,16 +36,21 @@
  * JabRef MainClass
  */
 public class JabRefMain extends Application {
-
  private static final Logger LOGGER = LoggerFactory.getLogger(JabRefMain.class);
+
  private static String[] arguments;
 
  public static void main(String[] args) {
  arguments = args;
-
  launch(arguments);
  }
 
+ @Override
+ public void start(Stage mainStage) throws Exception {
+ Platform.setImplicitExit(false);
+ SwingUtilities.invokeLater(() -> start(arguments));
+ }
+
  /**
  * Tests if we are running an acceptable Java and terminates JabRef when we are sure the version is not supported.
  * This test uses the requirements for the Java version as specified in <code>gradle.build</code>. It is possible to
@@ -93,39 +98,65 @@ private static void ensureCorrectJavaVersion() {
  }
 
  private static void start(String[] args) {
+ // Fail on unsupported Java versions
+ ensureCorrectJavaVersion();
+ FallbackExceptionHandler.installExceptionHandler();
+
  // Init preferences
- JabRefPreferences preferences = JabRefPreferences.getInstance();
+ final JabRefPreferences preferences = JabRefPreferences.getInstance();
  Globals.prefs = preferences;
- // Perform Migrations
- // Perform checks and changes for users with a preference set from an older JabRef version.
- PreferencesMigrations.upgradePrefsToOrgJabRef();
- PreferencesMigrations.upgradeSortOrder();
- PreferencesMigrations.upgradeFaultyEncodingStrings();
- PreferencesMigrations.upgradeLabelPatternToBibtexKeyPattern();
- PreferencesMigrations.upgradeImportFileAndDirePatterns();
- PreferencesMigrations.upgradeStoredCustomEntryTypes();
- PreferencesMigrations.upgradeKeyBindingsToJavaFX();
- PreferencesMigrations.addCrossRefRelatedFieldsForAutoComplete();
- PreferencesMigrations.upgradeObsoleteLookAndFeels();
+ // Perform migrations
+ PreferencesMigrations.runMigrations();
+
+ configureProxy(preferences.getProxyPreferences());
+
+ Globals.startBackgroundTasks();
+
+ applyPreferences(preferences);
 
  // Process arguments
  ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START);
 
- FallbackExceptionHandler.installExceptionHandler();
+ // Check for running JabRef
+ if (!handleMultipleAppInstances(args) || argumentProcessor.shouldShutDown()) {
+ shutdownCurrentInstance();
+ return;
+ }
 
- ensureCorrectJavaVersion();
+ // If not, start GUI
+ SwingUtilities
+ .invokeLater(() -> new JabRefGUI(argumentProcessor.getParserResults(), argumentProcessor.isBlank()));
+ }
 
- ProxyPreferences proxyPreferences = preferences.getProxyPreferences();
- ProxyRegisterer.register(proxyPreferences);
- if (proxyPreferences.isUseProxy() && proxyPreferences.isUseAuthentication()) {
- Authenticator.setDefault(new ProxyAuthenticator());
+ private static boolean handleMultipleAppInstances(String[] args) {
+ RemotePreferences remotePreferences = Globals.prefs.getRemotePreferences();
+ if (remotePreferences.useRemoteServer()) {
+ Globals.REMOTE_LISTENER.open(new JabRefMessageHandler(), remotePreferences.getPort());
+
+ if (!Globals.REMOTE_LISTENER.isOpen()) {
+ // we are not alone, there is already a server out there, try to contact already running JabRef:
+ if (new RemoteClient(remotePreferences.getPort()).sendCommandLineArguments(args)) {
+ // We have successfully sent our command line options through the socket to another JabRef instance.
+ // So we assume it's all taken care of, and quit.
+ LOGGER.info(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
+ return false;
+ }
+ }
+ // we are alone, we start the server
+ Globals.REMOTE_LISTENER.start();
  }
+ return true;
+ }
 
- Globals.startBackgroundTasks();
+ private static void shutdownCurrentInstance() {
+ Globals.shutdownThreadPools();
+ // needed to tell JavaFx to stop
+ Platform.exit();
+ }
 
+ private static void applyPreferences(JabRefPreferences preferences) {
  // Update handling of special fields based on preferences
- InternalBibtexFields
- .updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
+ InternalBibtexFields.updateSpecialFields(Globals.prefs.getBoolean(JabRefPreferences.SERIALIZESPECIALFIELDS));
  // Update name of the time stamp field based on preferences
  InternalBibtexFields.updateTimeStampField(Globals.prefs.getTimestampPreferences().getTimestampField());
  // Update which fields should be treated as numeric, based on preferences:
@@ -144,48 +175,15 @@ private static void start(String[] args) {
  // Initialize protected terms loader
  Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());
 
- // Check for running JabRef
- RemotePreferences remotePreferences = Globals.prefs.getRemotePreferences();
- if (remotePreferences.useRemoteServer()) {
- Globals.REMOTE_LISTENER.open(new JabRefMessageHandler(), remotePreferences.getPort());
-
- if (!Globals.REMOTE_LISTENER.isOpen()) {
- // we are not alone, there is already a server out there, try to contact already running JabRef:
- if (new RemoteClient(remotePreferences.getPort()).sendCommandLineArguments(args)) {
- // We have successfully sent our command line options through the socket to another JabRef instance.
- // 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;
- }
- }
- // we are alone, we start the server
- Globals.REMOTE_LISTENER.start();
- }
-
  // override used newline character with the one stored in the preferences
  // The preferences return the system newline character sequence as default
  OS.NEWLINE = Globals.prefs.get(JabRefPreferences.NEWLINE);
-
- // See if we should shut down now
- if (argumentProcessor.shouldShutDown()) {
- Globals.shutdownThreadPools();
- Platform.exit();
- return;
- }
-
- // If not, start GUI
- SwingUtilities
- .invokeLater(() -> new JabRefGUI(argumentProcessor.getParserResults(),
- argumentProcessor.isBlank()));
  }
 
- @Override
- public void start(Stage mainStage) throws Exception {
- Platform.setImplicitExit(false);
- SwingUtilities.invokeLater(() -> start(arguments)
- );
+ private static void configureProxy(ProxyPreferences proxyPreferences) {
+  ProxyRegisterer.register(proxyPreferences);
+ if (proxyPreferences.isUseProxy() && proxyPreferences.isUseAuthentication()) {
+  Authenticator.setDefault(new ProxyAuthenticator());
+ }
  }
 }

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

@@ -73,6 +73,7 @@ public EntryTypeDialog(JabRefFrame frame) {
  setTitle(Localization.lang("Select entry type"));
 
  addWindowListener(new WindowAdapter() {
+
  @Override
  public void windowClosing(WindowEvent e) {
  cancelAction.actionPerformed(null);
@@ -246,7 +247,6 @@ static class TypeButton extends JButton implements Comparable<TypeButton> {
 
  private final EntryType type;
 
-
  TypeButton(String label, EntryType type) {
  super(label);
  this.type = type;
@@ -263,6 +263,7 @@ public EntryType getType() {
  }
 
  class CancelAction extends AbstractAction {
+
  public CancelAction() {
  super("Cancel");
  }
@@ -275,6 +276,7 @@ public void actionPerformed(ActionEvent e) {
  }
 
  private class FetcherWorker extends SwingWorker<Optional<BibEntry>, Void> {
+
  private boolean fetcherException = false;
  private String fetcherExceptionMessage = "";
  private IdBasedFetcher fetcher = null;
@@ -288,10 +290,9 @@ protected Optional<BibEntry> doInBackground() throws Exception {
  generateButton.setText(Localization.lang("Searching..."));
  });
 
- Globals.prefs.put(JabRefPreferences.ID_ENTRY_GENERATOR,String.valueOf(comboBox.getSelectedItem()));
- searchID = idTextField.getText().trim();
- searchID = searchID.replaceAll(" ", "");
+ Globals.prefs.put(JabRefPreferences.ID_ENTRY_GENERATOR, String.valueOf(comboBox.getSelectedItem()));
  fetcher = WebFetchers.getIdBasedFetchers(Globals.prefs.getImportFormatPreferences()).get(comboBox.getSelectedIndex());
+ searchID = idTextField.getText();
  if (!searchID.isEmpty()) {
  try {
  bibEntry = fetcher.performSearchById(searchID);
@@ -311,7 +312,7 @@ protected void done() {
  if (result.isPresent()) {
  final BibEntry bibEntry = result.get();
  if ((DuplicateCheck.containsDuplicate(frame.getCurrentBasePanel().getDatabase(), bibEntry, frame.getCurrentBasePanel().getBibDatabaseContext().getMode()).isPresent())) {
-  //If there are duplicates starts ImportInspectionDialog
+  //If there are duplicates starts ImportInspectionDialog
  final BasePanel panel = (BasePanel) frame.getTabbedPane().getSelectedComponent();
 
  ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
@@ -321,7 +322,7 @@ protected void done() {
  diag.setVisible(true);
  diag.toFront();
  } else {
-  // Regenerate CiteKey of imported BibEntry
+  // Regenerate CiteKey of imported BibEntry
  new BibtexKeyGenerator(frame.getCurrentBasePanel().getBibDatabaseContext(), Globals.prefs.getBibtexKeyPatternPreferences()).generateAndSetKey(bibEntry);
  // Update Timestamps
  if (Globals.prefs.getTimestampPreferences().includeCreatedTimestamp()) {

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

@@ -1358,6 +1358,12 @@ class EntryTable extends JTable {
  public EntryTable(TableModel model) {
  super(model);
  getTableHeader().setReorderingAllowed(false);
+
+ setFont(GUIGlobals.currentFont);
+ int maxOfIconsAndFontSize = Math.max(GUIGlobals.currentFont.getSize(), Globals.prefs.getInt(JabRefPreferences.ICON_SIZE_SMALL));
+ setRowHeight(Globals.prefs.getInt(JabRefPreferences.TABLE_ROW_PADDING) + maxOfIconsAndFontSize);
+ // Update Table header with new settings
+ this.getTableHeader().resizeAndRepaint();
  }
 
  @Override

src/main/java/org/jabref/gui/importer/fetcher/ACMPortalFetcher.java

@@ -78,7 +78,7 @@ public class ACMPortalFetcher implements PreviewEntryFetcher {
 
  private static final Pattern FULL_CITATION_PATTERN = Pattern.compile("<a href=\"(citation.cfm.*)\" target.*");
 
- private static final Pattern ID_PATTERN = Pattern.compile("citation.cfm\\?id=(\\d+)&.*");
+ private static final Pattern ID_PATTERN = Pattern.compile("citation.cfm\\?id=(\\d+).*");
 
  // Patterns used to extract information for the preview:
  private static final Pattern TITLE_PATTERN = Pattern.compile("<a href=.*?\">([^<]*)</a>");

src/main/java/org/jabref/gui/push/AbstractPushToApplication.java

@@ -71,7 +71,19 @@ public void pushEntries(BibDatabase database, List<BibEntry> entries, String key
  try {
  if (OS.OS_X) {
  String[] commands = getCommandLine(keyString);
- ProcessBuilder processBuilder = new ProcessBuilder("open -a " + commands[0] + " -n --args " + commands[1] + " " + commands[2]);
+ if (commands.length < 3) {
+ LOGGER.error("Commandline does not contain enough parameters to \"push to application\"");
+ return;
+ }
+ ProcessBuilder processBuilder = new ProcessBuilder(
+ "open",
+ "-a",
+ commands[0],
+ "-n",
+ "--args",
+ commands[1],
+ commands[2]
+ );
  processBuilder.start();
  } else {
  ProcessBuilder processBuilder = new ProcessBuilder(getCommandLine(keyString));

src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java

@@ -294,7 +294,8 @@ else if (val.matches("edtr\\d+")) {
  } else if ("fulltitle".equals(val)) {
  return entry.getResolvedFieldOrAlias(FieldName.TITLE, database).orElse("");
  } else if ("shorttitle".equals(val)) {
- return getTitleWords(3, entry.getResolvedFieldOrAlias(FieldName.TITLE, database).orElse(""));
+ return getTitleWords(3,
+ removeSmallWords(entry.getResolvedFieldOrAlias(FieldName.TITLE, database).orElse("")));
  } else if ("shorttitleINI".equals(val)) {
  return keepLettersAndDigitsOnly(
  applyModifiers(getTitleWordsWithSpaces(3, entry.getResolvedFieldOrAlias(FieldName.TITLE, database).orElse("")),