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

* upstream/master:
  Fix error prone warnings (#4290)
  Fix freeze on import into current library (#4299)
  Upgrade gradle to 4.10 update xmlunit and postgres
  update xmlunit-matchers from 2.6.0 -> 2.6.1
  update gradle build-scan from 1.15.2 -> 1.16
  checkstyle
  execute changes only if disk db present
  fix npe in Merge entries dialog

build.gradle

@@ -15,7 +15,7 @@ buildscript {
 }
 
 plugins {
-    id 'com.gradle.build-scan' version '1.15.2'
+    id 'com.gradle.build-scan' version '1.16'
     id 'com.install4j.gradle' version '7.0.6'
     id 'com.github.johnrengelman.shadow' version '2.0.4'
     id "de.sebastianboegl.shadow.transformer.log4j" version "2.1.1"
@@ -121,7 +121,7 @@ dependencies {
 
     compile 'mysql:mysql-connector-java:8.0.12'
 
-    compile 'org.postgresql:postgresql:42.2.4'
+    compile 'org.postgresql:postgresql:42.2.5'
 
     compile 'net.java.dev.glazedlists:glazedlists_java15:1.9.1'
 
@@ -174,8 +174,8 @@ dependencies {
     testCompile 'com.github.tomakehurst:wiremock:2.18.0'
     testCompile 'org.assertj:assertj-swing-junit:3.8.0'
     testCompile 'org.reflections:reflections:0.9.11'
-    testCompile 'org.xmlunit:xmlunit-core:2.6.0'
-    testCompile 'org.xmlunit:xmlunit-matchers:2.6.0'
+    testCompile 'org.xmlunit:xmlunit-core:2.6.2'
+    testCompile 'org.xmlunit:xmlunit-matchers:2.6.2'
     testCompile 'com.tngtech.archunit:archunit-junit:0.8.3'
     testCompile "org.testfx:testfx-core:4.0.+"
     testCompile "org.testfx:testfx-junit5:4.0.+"
@@ -217,12 +217,6 @@ dependencyUpdates.resolutionStrategy = {
                 selection.reject("Cannot be upgraded to version 2")
             }
         }
-        rules.withModule("mysql:mysql-connector-java") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /[6-9].*/) {
-                selection.reject("http://dev.mysql.com/downloads/connector/j/ lists the version 5.* as last stable version.")
-            }
-        }
-
     }
 }
 

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-4.9-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-4.10-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

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

@@ -1,7 +1,5 @@
 package org.jabref.gui.collab;
 
-import java.io.File;
-import java.io.IOException;
 import java.nio.file.Path;
 import java.util.Comparator;
 import java.util.List;
@@ -39,7 +37,7 @@ public class ChangeScanner implements Runnable {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(ChangeScanner.class);
 
-    private final File file;
+    private final Optional<Path> file;
     private final Path tempFile;
     private final BibDatabaseContext databaseInMemory;
 
@@ -56,11 +54,11 @@ public class ChangeScanner implements Runnable {
 
     //  NamedCompound edit = new NamedCompound("Merged external changes")
 
-    public ChangeScanner(JabRefFrame frame, BasePanel bp, File file, Path tempFile) {
+    public ChangeScanner(JabRefFrame frame, BasePanel bp, Path file, Path tempFile) {
         this.panel = bp;
         this.frame = frame;
         this.databaseInMemory = bp.getBibDatabaseContext();
-        this.file = file;
+        this.file = Optional.ofNullable(file);
         this.tempFile = tempFile;
     }
 
@@ -74,8 +72,8 @@ public boolean changesFound() {
      */
     private static BibEntry bestFit(BibEntry targetEntry, List<BibEntry> entries) {
         return entries.stream()
-                .max(Comparator.comparingDouble(candidate -> DuplicateCheck.compareEntriesStrictly(targetEntry, candidate)))
-                .orElse(null);
+                      .max(Comparator.comparingDouble(candidate -> DuplicateCheck.compareEntriesStrictly(targetEntry, candidate)))
+                      .orElse(null);
     }
 
     public void displayResult(final DisplayResultCallback fup) {
@@ -91,7 +89,7 @@ public void displayResult(final DisplayResultCallback fup) {
             });
         } else {
             frame.getDialogService().showInformationDialogAndWait(Localization.lang("External changes"),
-                    Localization.lang("No actual changes found."));
+                                                                  Localization.lang("No actual changes found."));
 
             fup.scanResultsResolved(true);
         }
@@ -101,11 +99,11 @@ private void storeTempDatabase() {
         JabRefExecutorService.INSTANCE.execute(() -> {
             try {
                 SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences()
-                        .withMakeBackup(false)
-                        .withEncoding(panel.getBibDatabaseContext()
-                                .getMetaData()
-                                .getEncoding()
-                                .orElse(Globals.prefs.getDefaultEncoding()));
+                                                     .withMakeBackup(false)
+                                                     .withEncoding(panel.getBibDatabaseContext()
+                                                                        .getMetaData()
+                                                                        .getEncoding()
+                                                                        .orElse(Globals.prefs.getDefaultEncoding()));
 
                 BibDatabaseWriter<SaveSession> databaseWriter = new BibtexDatabaseWriter<>(FileSaveSession::new);
                 SaveSession ss = databaseWriter.saveDatabase(databaseInTemp, prefs);
@@ -118,15 +116,14 @@ private void storeTempDatabase() {
 
     @Override
     public void run() {
-        try {
-
+        file.ifPresent(diskdb -> {
             // Parse the temporary file.
             ImportFormatPreferences importFormatPreferences = Globals.prefs.getImportFormatPreferences();
-            ParserResult result = OpenDatabase.loadDatabase(tempFile.toFile(), importFormatPreferences, Globals.getFileUpdateMonitor());
+            ParserResult result = OpenDatabase.loadDatabase(tempFile.toAbsolutePath().toString(), importFormatPreferences, Globals.getFileUpdateMonitor());
             databaseInTemp = result.getDatabaseContext();
 
             // Parse the modified file.
-            result = OpenDatabase.loadDatabase(file, importFormatPreferences, Globals.getFileUpdateMonitor());
+            result = OpenDatabase.loadDatabase(diskdb.toAbsolutePath().toString(), importFormatPreferences, Globals.getFileUpdateMonitor());
             BibDatabaseContext databaseOnDisk = result.getDatabaseContext();
 
             // Start looking at changes.
@@ -138,9 +135,7 @@ public void run() {
             differences.getPreambleDifferences().ifPresent(diff -> changes.add(new PreambleChangeViewModel(databaseInMemory.getDatabase().getPreamble().orElse(""), diff)));
             differences.getBibStringDifferences().forEach(diff -> changes.add(createBibStringDiff(diff)));
             differences.getEntryDifferences().forEach(diff -> changes.add(createBibEntryDiff(diff)));
-        } catch (IOException ex) {
-            LOGGER.warn("Problem running", ex);
-        }
+        });
     }
 
     private ChangeViewModel createBibStringDiff(BibStringDiff diff) {

src/main/java/org/jabref/gui/collab/DatabaseChangeMonitor.java

@@ -60,7 +60,7 @@ public void fileUpdated() {
 
         updatedExternally = true;
 
-        final ChangeScanner scanner = new ChangeScanner(panel.frame(), panel, database.getDatabaseFile().orElse(null), tmpFile);
+        final ChangeScanner scanner = new ChangeScanner(panel.frame(), panel, database.getDatabasePath().orElse(null), tmpFile);
 
         // Test: running scan automatically in background
         if (database.getDatabasePath().isPresent() && !FileBasedLock.waitForFileLock(database.getDatabasePath().get())) {
@@ -76,7 +76,6 @@ public void fileUpdated() {
             fileUpdated();
             return;
         }
-
         JabRefExecutorService.INSTANCE.executeInterruptableTaskAndWait(scanner);
 
         // Adding the sidepane component is Swing work, so we must do this in the Swing

src/main/java/org/jabref/gui/exporter/SaveDatabaseAction.java

@@ -409,13 +409,13 @@ private boolean checkExternalModification() {
                     JabRefExecutorService.INSTANCE.execute(() -> {
 
                         if (!FileBasedLock
-                                .waitForFileLock(panel.getBibDatabaseContext().getDatabaseFile().get().toPath())) {
+                                          .waitForFileLock(panel.getBibDatabaseContext().getDatabasePath().get())) {
                             // TODO: GUI handling of the situation when the externally modified file keeps being locked.
                             LOGGER.error("File locked, this will be trouble.");
                         }
 
                         ChangeScanner scanner = new ChangeScanner(panel.frame(), panel,
-                                panel.getBibDatabaseContext().getDatabaseFile().get(), panel.getTempFile());
+                                                                  panel.getBibDatabaseContext().getDatabasePath().orElse(null), panel.getTempFile());
                         JabRefExecutorService.INSTANCE.executeInterruptableTaskAndWait(scanner);
                         if (scanner.changesFound()) {
                             scanner.displayResult(resolved -> {

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

@@ -9,6 +9,8 @@
 import java.util.Optional;
 import java.util.stream.Collectors;
 
+import javax.swing.SwingUtilities;
+
 import org.jabref.Globals;
 import org.jabref.gui.BasePanel;
 import org.jabref.gui.DialogService;
@@ -33,7 +35,7 @@ public class ImportAction {
     private final Optional<Importer> importer;
     private final DialogService dialogService;
     private Exception importError;
-    private TaskExecutor taskExecutor = Globals.TASK_EXECUTOR;
+    private final TaskExecutor taskExecutor = Globals.TASK_EXECUTOR;
 
     public ImportAction(JabRefFrame frame, boolean openInNew) {
         this(frame, openInNew, null);
@@ -78,26 +80,26 @@ private void reportResult(List<ImportFormatReader.UnknownFormatImport> imports)
             } else {
                 // Import in a specific format was specified. Check if we have stored error information:
                 if (importError == null) {
-                    dialogService.showErrorDialogAndWait(
-                            Localization.lang("Import failed"),
-                            Localization.lang("No entries found. Please make sure you are using the correct import filter."));
+                    dialogService.showErrorDialogAndWait(Localization.lang("Import failed"),
+                                                         Localization.lang("No entries found. Please make sure you are using the correct import filter."));
                 } else {
                     dialogService.showErrorDialogAndWait(Localization.lang("Import failed"), importError);
                 }
             }
         } else {
             if (openInNew) {
                 frame.addTab(bibtexResult.getDatabaseContext(), true);
-                frame.output(
-                        Localization.lang("Imported entries") + ": " + bibtexResult.getDatabase().getEntryCount());
+                frame.output(Localization.lang("Imported entries") + ": " + bibtexResult.getDatabase().getEntryCount());
             } else {
                 final BasePanel panel = frame.getCurrentBasePanel();
 
-                ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
-                diag.addEntries(bibtexResult.getDatabase().getEntries());
-                diag.entryListComplete();
-                diag.setVisible(true);
-                diag.toFront();
+                SwingUtilities.invokeLater(() -> {
+                    ImportInspectionDialog diag = new ImportInspectionDialog(frame, panel, Localization.lang("Import"), false);
+                    diag.addEntries(bibtexResult.getDatabase().getEntries());
+                    diag.entryListComplete();
+                    diag.setVisible(true);
+                    diag.toFront();
+                });
             }
         }
     }
@@ -147,7 +149,6 @@ private ParserResult mergeImportResults(List<ImportFormatReader.UnknownFormatImp
                 if (directParserResult == null) {
                     directParserResult = pr;
                 }
-
                 // Merge entries:
                 for (BibEntry entry : pr.getDatabase().getEntries()) {
                     database.insertEntry(entry);

src/main/java/org/jabref/gui/mergeentries/MergeEntries.java

@@ -41,6 +41,7 @@
 import org.jabref.logic.formatter.casechanger.SentenceCaseFormatter;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.util.strings.DiffHighlighting;
+import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.InternalBibtexFields;
@@ -179,7 +180,7 @@ private void initialize() {
         // Setup a PreviewPanel and a Bibtex source box for the merged entry
         mainPanel.add(boldFontLabel(Localization.lang("Merged entry")), CELL_CONSTRAINTS.xyw(1, 6, 6));
 
-        entryPreview = new PreviewPanel(null, null, Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
+        entryPreview = new PreviewPanel(null, new BibDatabaseContext(), Globals.getKeyPrefs(), Globals.prefs.getPreviewPreferences(), new FXDialogService(), ExternalFileTypes.getInstance());
         entryPreview.setEntry(mergedEntry);
         JFXPanel container = CustomJFXPanel.wrap(new Scene(entryPreview));
         mainPanel.add(container, CELL_CONSTRAINTS.xyw(1, 8, 6));

src/main/java/org/jabref/gui/mergeentries/MergeEntriesDialog.java

@@ -11,6 +11,7 @@
 import org.jabref.gui.undo.NamedCompound;
 import org.jabref.gui.undo.UndoableInsertEntry;
 import org.jabref.gui.undo.UndoableRemoveEntry;
+import org.jabref.gui.util.DefaultTaskExecutor;
 import org.jabref.gui.util.WindowLocation;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.entry.BibEntry;
@@ -51,7 +52,7 @@ private void init(List<BibEntry> selected) {
         if (selected.size() != 2) { // None selected. Inform the user to select entries first.
 
             dialogService.showInformationDialogAndWait(Localization.lang("Merge entries"),
-                    Localization.lang("You have to choose exactly two entries to merge."));
+                                                       Localization.lang("You have to choose exactly two entries to merge."));
 
             this.dispose();
             return;
@@ -88,15 +89,18 @@ private void init(List<BibEntry> selected) {
             // Create a new entry and add it to the undo stack
             // Remove the other two entries and add them to the undo stack (which is not working...)
             BibEntry mergedEntry = mergeEntries.getMergeEntry();
-            panel.insertEntry(mergedEntry);
-            ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), mergedEntry));
-            ce.addEdit(new UndoableRemoveEntry(panel.getDatabase(), one, panel));
-            panel.getDatabase().removeEntry(one);
-            ce.addEdit(new UndoableRemoveEntry(panel.getDatabase(), two, panel));
-            panel.getDatabase().removeEntry(two);
-            ce.end();
-            panel.getUndoManager().addEdit(ce);
-            panel.output(Localization.lang("Merged entries"));
+            DefaultTaskExecutor.runInJavaFXThread(() -> {
+                panel.insertEntry(mergedEntry);
+                ce.addEdit(new UndoableInsertEntry(panel.getDatabase(), mergedEntry));
+                ce.addEdit(new UndoableRemoveEntry(panel.getDatabase(), one, panel));
+                panel.getDatabase().removeEntry(one);
+                ce.addEdit(new UndoableRemoveEntry(panel.getDatabase(), two, panel));
+                panel.getDatabase().removeEntry(two);
+                ce.end();
+                panel.getUndoManager().addEdit(ce);
+                panel.output(Localization.lang("Merged entries"));
+            });
+
             dispose();
         });
 
@@ -110,8 +114,8 @@ private void init(List<BibEntry> selected) {
         layout.insertColumn(1, ColumnSpec.decode(MARGIN));
 
         WindowLocation pw = new WindowLocation(this, JabRefPreferences.MERGEENTRIES_POS_X,
-                JabRefPreferences.MERGEENTRIES_POS_Y, JabRefPreferences.MERGEENTRIES_SIZE_X,
-                JabRefPreferences.MERGEENTRIES_SIZE_Y);
+                                               JabRefPreferences.MERGEENTRIES_POS_Y, JabRefPreferences.MERGEENTRIES_SIZE_X,
+                                               JabRefPreferences.MERGEENTRIES_SIZE_Y);
         pw.displayWindowAtStoredLocation();
 
         // Show what we've got

src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java

@@ -47,8 +47,8 @@
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.junit.jupiter.api.Assertions.assertThrows;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -1172,7 +1172,7 @@ void parsePreambleAndEntryWithoutNewLine() throws IOException {
     @Test
     void parseFileHeaderAndPreambleWithoutNewLine() throws IOException {
         ParserResult result = parser
-                .parse(new StringReader("% Encoding: US-ASCII@preamble{some text and \\latex}"));
+                .parse(new StringReader("\\% Encoding: US-ASCII@preamble{some text and \\latex}"));
 
         assertFalse(result.hasWarnings());
         assertEquals(Optional.of("some text and \\latex"), result.getDatabase().getPreamble());

src/test/java/org/jabref/logic/l10n/LocalizationConsistencyTest.java

@@ -12,16 +12,21 @@
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 import java.util.Properties;
+import java.util.ResourceBundle;
 import java.util.Set;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.MethodSource;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotNull;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class LocalizationConsistencyTest {
@@ -140,6 +145,31 @@ void localizationParameterMustIncludeAString() throws IOException {
         }
     }
 
+    private static Language[] installedLanguages() {
+        return Language.values();
+    }
+
+    @ParameterizedTest
+    @MethodSource("installedLanguages")
+    void resourceBundleExists(Language language) {
+        Path messagesPropertyFile = Paths.get("src/main/resources").resolve(Localization.RESOURCE_PREFIX + "_" + language.getId() + ".properties");
+        assertTrue(Files.exists(messagesPropertyFile));
+    }
+
+    @ParameterizedTest
+    @MethodSource("installedLanguages")
+    void languageCanBeLoaded(Language language) {
+        Locale oldLocale = Locale.getDefault();
+        try {
+            Locale locale = Language.convertToSupportedLocale(language).get();
+            Locale.setDefault(locale);
+            ResourceBundle messages = ResourceBundle.getBundle(Localization.RESOURCE_PREFIX, locale, new EncodingControl(StandardCharsets.UTF_8));
+            assertNotNull(messages);
+        } finally {
+            Locale.setDefault(oldLocale);
+        }
+    }
+
     private static class DuplicationDetectionProperties extends Properties {
 
         private static final long serialVersionUID = 1L;