Merge branch 'master' of https://github.com/JabRef/jabref into docboo…

…k-exporter

CHANGELOG.md

@@ -11,20 +11,25 @@ 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 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 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)
 
 ### 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
@@ -93,58 +98,37 @@ private static void ensureCorrectJavaVersion() {
     }
 
     private static void start(String[] args) {
-        // Init preferences
-        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();
-
+        // Fail on unsupported Java versions
+        ensureCorrectJavaVersion();
         FallbackExceptionHandler.installExceptionHandler();
 
-        ensureCorrectJavaVersion();
+        // Init preferences
+        final JabRefPreferences preferences = JabRefPreferences.getInstance();
+        Globals.prefs = preferences;
+        // Perform migrations
+        PreferencesMigrations.runMigrations();
 
-        ProxyPreferences proxyPreferences = preferences.getProxyPreferences();
-        ProxyRegisterer.register(proxyPreferences);
-        if (proxyPreferences.isUseProxy() && proxyPreferences.isUseAuthentication()) {
-            Authenticator.setDefault(new ProxyAuthenticator());
-        }
+        configureProxy(preferences.getProxyPreferences());
 
         Globals.startBackgroundTasks();
 
-        // Update handling of special fields based on preferences
-        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:
-        InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
-
-        // Read list(s) of journal names and abbreviations
-        Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();
-
-        /* Build list of Import and Export formats */
-        Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
-                Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
-        EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
-                preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
-        Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationLoader);
+        applyPreferences(preferences);
 
         // Process arguments
         ArgumentProcessor argumentProcessor = new ArgumentProcessor(args, ArgumentProcessor.Mode.INITIAL_START);
 
-        // Initialize protected terms loader
-        Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());
-
         // Check for running JabRef
+        if (!handleMultipleAppInstances(args) || argumentProcessor.shouldShutDown()) {
+            shutdownCurrentInstance();
+            return;
+        }
+
+        // If not, start GUI
+        SwingUtilities
+                .invokeLater(() -> new JabRefGUI(argumentProcessor.getParserResults(), argumentProcessor.isBlank()));
+    }
+
+    private static boolean handleMultipleAppInstances(String[] args) {
         RemotePreferences remotePreferences = Globals.prefs.getRemotePreferences();
         if (remotePreferences.useRemoteServer()) {
             Globals.REMOTE_LISTENER.open(new JabRefMessageHandler(), remotePreferences.getPort());
@@ -155,37 +139,51 @@ private static void start(String[] 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;
+                    return false;
                 }
             }
             // we are alone, we start the server
             Globals.REMOTE_LISTENER.start();
         }
+        return true;
+    }
+
+    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));
+        // 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:
+        InternalBibtexFields.setNumericFields(Globals.prefs.getStringList(JabRefPreferences.NUMERIC_FIELDS));
+
+        // Read list(s) of journal names and abbreviations
+        Globals.journalAbbreviationLoader = new JournalAbbreviationLoader();
+
+        /* Build list of Import and Export formats */
+        Globals.IMPORT_FORMAT_READER.resetImportFormats(Globals.prefs.getImportFormatPreferences(),
+                Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
+        EntryTypes.loadCustomEntryTypes(preferences.loadCustomEntryTypes(BibDatabaseMode.BIBTEX),
+                preferences.loadCustomEntryTypes(BibDatabaseMode.BIBLATEX));
+        Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationLoader);
+
+        // Initialize protected terms loader
+        Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());
 
         // 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/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/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/formatter/Formatters.java

@@ -6,12 +6,14 @@
 import java.util.Objects;
 import java.util.Optional;
 
+import org.jabref.logic.formatter.bibtexfields.AddBracesFormatter;
 import org.jabref.logic.formatter.bibtexfields.ClearFormatter;
 import org.jabref.logic.formatter.bibtexfields.EscapeUnderscoresFormatter;
 import org.jabref.logic.formatter.bibtexfields.HtmlToLatexFormatter;
 import org.jabref.logic.formatter.bibtexfields.HtmlToUnicodeFormatter;
 import org.jabref.logic.formatter.bibtexfields.LatexCleanupFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeDateFormatter;
+import org.jabref.logic.formatter.bibtexfields.NormalizeEnDashesFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeMonthFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizeNamesFormatter;
 import org.jabref.logic.formatter.bibtexfields.NormalizePagesFormatter;
@@ -47,10 +49,12 @@ public class Formatters {
     );
 
     private static final List<Formatter> OTHERS = Arrays.asList(
+            new AddBracesFormatter(),
             new ClearFormatter(),
             new LatexCleanupFormatter(),
             new MinifyNameListFormatter(),
             new NormalizeDateFormatter(),
+            new NormalizeEnDashesFormatter(),
             new NormalizeMonthFormatter(),
             new NormalizeNamesFormatter(),
             new NormalizePagesFormatter(),

src/main/java/org/jabref/logic/formatter/IdentityFormatter.java

@@ -8,7 +8,7 @@
 /**
  * It may seem useless, but is needed as a fallback option
  */
-public class IdentityFormatter implements Formatter {
+public class IdentityFormatter extends Formatter {
 
     @Override
     public String getName() {
@@ -35,15 +35,4 @@ public String getDescription() {
     public String getExampleInput() {
         return "JabRef";
     }
-
-    @Override
-    public int hashCode() {
-        return defaultHashCode();
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        return defaultEquals(obj);
-    }
-
 }

src/main/java/org/jabref/logic/formatter/bibtexfields/AddBracesFormatter.java

@@ -0,0 +1,41 @@
+package org.jabref.logic.formatter.bibtexfields;
+
+import java.util.Objects;
+
+import org.jabref.logic.l10n.Localization;
+import org.jabref.model.cleanup.Formatter;
+
+public class AddBracesFormatter extends Formatter {
+
+    @Override
+    public String getName() {
+        return Localization.lang("Add enclosing braces");
+    }
+
+    @Override
+    public String getKey() {
+        return "add_braces";
+    }
+
+    @Override
+    public String format(String value) {
+        Objects.requireNonNull(value);
+
+        if ((value.length() >= 2) && (value.charAt(0) != '{') && (value.charAt(value.length() - 1) != '}')) {
+            // Title does not start with { and does not end with }, then this formatter can be applied
+            return "{" + value + "}";
+        } else {
+            return value;
+        }
+    }
+
+    @Override
+    public String getDescription() {
+        return Localization.lang("Add braces encapsulating the complete field content.");
+    }
+
+    @Override
+    public String getExampleInput() {
+        return "In CDMA";
+    }
+}

src/main/java/org/jabref/logic/formatter/bibtexfields/ClearFormatter.java

@@ -5,7 +5,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.cleanup.Formatter;
 
-public class ClearFormatter implements Formatter {
+public class ClearFormatter extends Formatter {
 
     @Override
     public String getName() {

src/main/java/org/jabref/logic/formatter/bibtexfields/EscapeUnderscoresFormatter.java

@@ -6,7 +6,7 @@
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.cleanup.Formatter;
 
-public class EscapeUnderscoresFormatter implements Formatter {
+public class EscapeUnderscoresFormatter extends Formatter {
 
     private static final Pattern UNDERSCORES = Pattern.compile("_");
 

src/main/java/org/jabref/logic/formatter/bibtexfields/HtmlToLatexFormatter.java

@@ -13,7 +13,7 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class HtmlToLatexFormatter implements LayoutFormatter, Formatter {
+public class HtmlToLatexFormatter extends Formatter implements LayoutFormatter {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(HtmlToLatexFormatter.class);