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
JabRef · May 27, 2018 · d0df7ca · d0df7ca
2 parents 1a0cde3 + d2ddf93
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diff --git a/CHANGELOG.md b/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.
 
 

diff --git a/build.gradle b/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.+"
 

diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
diff --git a/gradle/wrapper/gradle-wrapper.properties b/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
diff --git a/src/main/java/org/jabref/JabRefMain.java b/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());
+        }
     }
 }
diff --git a/src/main/java/org/jabref/gui/EntryTypeDialog.java b/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()) {

diff --git a/src/main/java/org/jabref/gui/importer/ImportInspectionDialog.java b/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

diff --git a/src/main/java/org/jabref/gui/importer/fetcher/ACMPortalFetcher.java b/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>");

diff --git a/src/main/java/org/jabref/gui/push/AbstractPushToApplication.java b/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));

diff --git a/src/main/java/org/jabref/logic/bibtexkeypattern/BracketedPattern.java b/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("")),