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

* upstream/master:
  Enable Merging of BibDatabases (#6689)
  Refactor file preferences (#6779)
  Interrupt all running tasks during shutdown (#6118)
  Fixes #6705 , added icon for multiple identifiers (#6809)
  Apply css files correctly to dialogs (#6828)
  Fix link
  Make template more explicit

CHANGELOG.md

@@ -1,3 +1,4 @@
+
 # Changelog
 
 All notable changes to this project will be documented in this file.
@@ -16,10 +17,15 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Changed
 
+- We restructured the 'File' tab and extracted some parts into the 'Linked files' tab [#6779](https://github.com/JabRef/jabref/pull/6779)
 - JabRef now offers journal lists from <https://abbrv.jabref.org>. JabRef the lists which use a dot inside the abbreviations. [#5749](https://github.com/JabRef/jabref/pull/5749)
 
 ### Fixed
 
+- We fixed an issue where the `.sav` file was not deleted upon exiting JabRef. [#6109](https://github.com/JabRef/jabref/issues/6109)
+- We fixed a linked identifier icon inconsistency. [#6705](https://github.com/JabRef/jabref/issues/6705)
+- We fixed the wrong behavior that font size changes are not reflected in dialogs. [#6039](https://github.com/JabRef/jabref/issues/6039)
+
 ### Removed
 
 

docs/adr/0003-use-gradle-as-build-tool.md

@@ -38,7 +38,7 @@ Chosen option: "Gradle", because it is lean and fits our development style.
 * Good, because [it offers custom dependency scopes](https://gradle.org/maven-vs-gradle/)
 * Good, because [it has good community support](https://linuxhint.com/ant-vs-maven-vs-gradle/)
 * Good, because [its performance can be 100 times more than maven's performance](https://gradle.org/gradle-vs-maven-performance/).
-* Bad, because [not that many plugins are available/maintained yet](https://blog.philipphauer.de/moving-back-from-gradle-to-maven/)
+* Bad, because [not that many plugins are available/maintained yet](https://phauer.com/2018/moving-back-from-gradle-to-maven/)
 * Bad, because [it lacks a wide variety of application server integrations](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
 * Bad, because [it has a medium popularity](http://pages.zeroturnaround.com/rs/zeroturnaround/images/java-build-tools-part-2.pdf)
 * Bad, because [it allows custom build scripts which need to be debugged](https://www.softwareyoga.com/10-reasons-why-we-chose-maven-over-gradle/)

docs/adr/0016-mutable-preferences-objects.md

@@ -0,0 +1,16 @@
+# Mutable preferences objects
+
+## Context and Problem Statement
+
+To create an immutable preferences object every time seems to be a waste of time and computer memory. 
+
+## Considered Options
+
+* Create a new object every time a preferences object should be altered by a with*-method, similar to a Builder.
+* Alter the existing object and return it.
+
+## Decision Outcome
+
+Chosen option: 1, because the preferences objects are just wrappers around the basic preferences framework of JDK. They
+should be mutable on-the-fly similar to objects with a Builder inside and to be stored immediatly again in the
+preferences.

docs/adr/template.md

@@ -1,73 +1,67 @@
-# \[short title of solved problem and solution\]
+# MADR Templae
 
-* Status: \[proposed \| rejected \| accepted \| deprecated \| … \| superseded by [ADR-0005](0005-fully-support-utf8-only-for-latex-files.md)\]
-* Deciders: \[list everyone involved in the decision\]
-* Date: \[YYYY-MM-DD when the decision was last updated\]
+The template of [MADR](https://adr.github.io/madr/) is available at <https://github.com/adr/madr#the-template>.
+You can omit the `<-- optional -->` parts, which lead to a very minimal ADR:
 
-Technical Story: \[description \| ticket/issue URL\]
+```markdown
+# [short title of solved problem and solution]
 
 ## Context and Problem Statement
 
-\[Describe the context and problem statement, e.g., in free form using two to three sentences. You may want to articulate the problem in form of a question.\]
-
-## Decision Drivers
-
-* \[driver 1, e.g., a force, facing concern, …\]
-* \[driver 2, e.g., a force, facing concern, …\]
-* …
+[Describe the context and problem statement, e.g., in free form using two to three sentences. You may want to articulate the problem in form of a question.]
 
 ## Considered Options
 
-* \[option 1\]
-* \[option 2\]
-* \[option 3\]
-* …
+* [option 1]
+* [option 2]
+* [option 3]
+* … <!-- numbers of options can vary -->
 
 ## Decision Outcome
 
-Chosen option: "\[option 1\]", because \[justification. e.g., only option, which meets k.o. criterion decision driver \| which resolves force force \| … \| comes out best \(see below\)\].
-
-### Positive Consequences
+Chosen option: "[option 1]", because [justification. e.g., only option, which meets k.o. criterion decision driver | which resolves force force | … ].
+```
 
-* \[e.g., improvement of quality attribute satisfaction, follow-up decisions required, …\]
-* …
+In case you want to include the pros and cons of the options, the template is as follows:
 
-### Negative Consequences
+```markdown
+# [short title of solved problem and solution]
 
-* \[e.g., compromising quality attribute, follow-up decisions required, …\]
-* …
-
-## Pros and Cons of the Options
+## Context and Problem Statement
 
-### \[option 1\]
+[Describe the context and problem statement, e.g., in free form using two to three sentences. You may want to articulate the problem in form of a question.]
 
-\[example \| description \| pointer to more information \| …\]
+## Considered Options
 
-* Good, because \[argument a\]
-* Good, because \[argument b\]
-* Bad, because \[argument c\]
-* …
+* [option 1]
+* [option 2]
+* [option 3]
+* … <!-- numbers of options can vary -->
 
-### \[option 2\]
+## Decision Outcome
 
-\[example \| description \| pointer to more information \| …\]
+Chosen option: "[option 1]", because comes out best (see below).
 
-* Good, because \[argument a\]
-* Good, because \[argument b\]
-* Bad, because \[argument c\]
-* …
+## Pros and Cons of the Options
 
-### \[option 3\]
+### [option 1]
 
-\[example \| description \| pointer to more information \| …\]
+* Good, because [argument a]
+* Good, because [argument b]
+* Bad, because [argument c]
+* … <!-- numbers of pros and cons can vary -->
 
-* Good, because \[argument a\]
-* Good, because \[argument b\]
-* Bad, because \[argument c\]
-* …
+### [option 2]
 
-## Links
+* Good, because [argument a]
+* Good, because [argument b]
+* Bad, because [argument c]
+* … <!-- numbers of pros and cons can vary -->
 
-* \[Link type\] \[Link to ADR\]
-* …
+### [option 3]
 
+* Good, because [argument a]
+* Good, because [argument b]
+* Bad, because [argument c]
+* … <!-- numbers of pros and cons can vary -->
+```

src/main/java/org/jabref/JabRefExecutorService.java

@@ -22,24 +22,29 @@
 public class JabRefExecutorService {
 
     public static final JabRefExecutorService INSTANCE = new JabRefExecutorService();
+
     private static final Logger LOGGER = LoggerFactory.getLogger(JabRefExecutorService.class);
+
     private final ExecutorService executorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef CachedThreadPool");
         thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         return thread;
     });
+
     private final ExecutorService lowPriorityExecutorService = Executors.newCachedThreadPool(r -> {
         Thread thread = new Thread(r);
         thread.setName("JabRef LowPriorityCachedThreadPool");
         thread.setUncaughtExceptionHandler(new FallbackExceptionHandler());
         return thread;
     });
+
     private final Timer timer = new Timer("timer", true);
+
     private Thread remoteThread;
 
     private JabRefExecutorService() {
-    }
+   }
 
     public void execute(Runnable command) {
         Objects.requireNonNull(command);
@@ -132,13 +137,16 @@ public void submit(TimerTask timerTask, long millisecondsDelay) {
         timer.schedule(timerTask, millisecondsDelay);
     }
 
+    /**
+     * Shuts everything down. After termination, this method returns.
+     */
     public void shutdownEverything() {
-        // those threads will be allowed to finish
-        this.executorService.shutdown();
-        // those threads will be interrupted in their current task
-        this.lowPriorityExecutorService.shutdownNow();
         // kill the remote thread
         stopRemoteThread();
+
+        gracefullyShutdown(this.executorService);
+        gracefullyShutdown(this.lowPriorityExecutorService);
+
         timer.cancel();
     }
 
@@ -164,4 +172,28 @@ public void run() {
             }
         }
     }
+
+    /**
+     * Shuts down the provided executor service by first trying a normal shutdown, then waiting for the shutdown and then forcibly shutting it down.
+     * Returns if the status of the shut down is known.
+     */
+    public static void gracefullyShutdown(ExecutorService executorService) {
+        try {
+            // This is non-blocking. See https://stackoverflow.com/a/57383461/873282.
+            executorService.shutdown();
+            if (!executorService.awaitTermination(60, TimeUnit.SECONDS)) {
+                LOGGER.debug("One minute passed, {} still not completed. Trying forced shutdown.", executorService.toString());
+                // those threads will be interrupted in their current task
+                executorService.shutdownNow();
+                if (executorService.awaitTermination(60, TimeUnit.SECONDS)) {
+                    LOGGER.debug("One minute passed again - forced shutdown of {} worked.", executorService.toString());
+                } else {
+                    LOGGER.error("{} did not terminate", executorService.toString());
+                }
+            }
+        } catch (InterruptedException ie) {
+            executorService.shutdownNow();
+            Thread.currentThread().interrupt();
+        }
+    }
 }

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

@@ -11,6 +11,7 @@
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.FXDialog;
 import org.jabref.gui.remote.JabRefMessageHandler;
+import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyAuthenticator;
@@ -168,7 +169,11 @@ private static void applyPreferences(JabRefPreferences preferences) {
                 Globals.prefs.getXMPPreferences(), Globals.getFileUpdateMonitor());
         Globals.entryTypesManager.addCustomOrModifiedTypes(preferences.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
                 preferences.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
-        Globals.exportFactory = Globals.prefs.getExporterFactory(Globals.journalAbbreviationRepository);
+        Globals.exportFactory = ExporterFactory.create(
+                Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationRepository),
+                Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository),
+                Globals.prefs.getSavePreferencesForExport(),
+                Globals.prefs.getXMPPreferences());
 
         // Initialize protected terms loader
         Globals.protectedTermsLoader = new ProtectedTermsLoader(Globals.prefs.getProtectedTermsPreferences());

src/main/java/org/jabref/cli/ArgumentProcessor.java

@@ -273,7 +273,7 @@ private boolean exportMatches(List<ParserResult> loaded) {
 
             // export new database
             Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(formatName);
-            if (!exporter.isPresent()) {
+            if (exporter.isEmpty()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + formatName);
             } else {
                 // We have an TemplateExporter instance:
@@ -387,7 +387,7 @@ private boolean generateAux(List<ParserResult> loaded, String[] data) {
     private void saveDatabase(BibDatabase newBase, String subName) {
         try {
             System.out.println(Localization.lang("Saving") + ": " + subName);
-            SavePreferences prefs = Globals.prefs.loadForSaveFromPreferences();
+            SavePreferences prefs = Globals.prefs.getSavePreferences();
             AtomicFileWriter fileWriter = new AtomicFileWriter(Path.of(subName), prefs.getEncoding());
             BibDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, prefs, Globals.entryTypesManager);
             databaseWriter.saveDatabase(new BibDatabaseContext(newBase));
@@ -435,7 +435,7 @@ private void exportFile(List<ParserResult> loaded, String[] data) {
                     .getFileDirectories(Globals.prefs.getFilePreferences());
             System.out.println(Localization.lang("Exporting") + ": " + data[0]);
             Optional<Exporter> exporter = Globals.exportFactory.getExporterByName(data[1]);
-            if (!exporter.isPresent()) {
+            if (exporter.isEmpty()) {
                 System.err.println(Localization.lang("Unknown export format") + ": " + data[1]);
             } else {
                 // We have an exporter:
@@ -458,9 +458,9 @@ private void importPreferences() {
             Globals.entryTypesManager.addCustomOrModifiedTypes(Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBTEX),
                     Globals.prefs.loadBibEntryTypes(BibDatabaseMode.BIBLATEX));
             List<TemplateExporter> customExporters = Globals.prefs.getCustomExportFormats(Globals.journalAbbreviationRepository);
-            LayoutFormatterPreferences layoutPreferences = Globals.prefs
-                    .getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
-            SavePreferences savePreferences = Globals.prefs.loadForExportFromPreferences();
+            LayoutFormatterPreferences layoutPreferences =
+                    Globals.prefs.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
+            SavePreferences savePreferences = Globals.prefs.getSavePreferencesForExport();
             XmpPreferences xmpPreferences = Globals.prefs.getXMPPreferences();
             Globals.exportFactory = ExporterFactory.create(customExporters, layoutPreferences, savePreferences, xmpPreferences);
         } catch (JabRefException ex) {
@@ -495,7 +495,11 @@ private void automaticallySetFileLinks(List<ParserResult> loaded) {
         for (ParserResult parserResult : loaded) {
             BibDatabase database = parserResult.getDatabase();
             LOGGER.info(Localization.lang("Automatically setting file links"));
-            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(parserResult.getDatabaseContext(), Globals.prefs.getFilePreferences(), Globals.prefs.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
+            AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
+                    parserResult.getDatabaseContext(),
+                    Globals.prefs.getFilePreferences(),
+                    Globals.prefs.getAutoLinkPreferences(),
+                    ExternalFileTypes.getInstance());
             util.linkAssociatedFiles(database.getEntries(), new NamedCompound(""));
         }
     }
@@ -534,7 +538,7 @@ private Optional<ParserResult> fetch(String fetchCommand) {
         Optional<SearchBasedFetcher> selectedFetcher = fetchers.stream()
                                                                .filter(fetcher -> fetcher.getName().equalsIgnoreCase(engine))
                                                                .findFirst();
-        if (!selectedFetcher.isPresent()) {
+        if (selectedFetcher.isEmpty()) {
             System.out.println(Localization.lang("Could not find fetcher '%0'", engine));
 
             System.out.println(Localization.lang("The following fetchers are available:"));

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

@@ -16,8 +16,8 @@
 
 import org.jabref.Globals;
 import org.jabref.gui.duplicationFinder.DuplicateResolverDialog;
-import org.jabref.logic.bibtex.DuplicateCheck;
 import org.jabref.logic.citationkeypattern.CitationKeyGenerator;
+import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.importer.FetcherException;
 import org.jabref.logic.importer.IdBasedFetcher;
 import org.jabref.logic.importer.WebFetchers;

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

@@ -25,7 +25,7 @@
 import org.jabref.gui.undo.UndoableRemoveEntries;
 import org.jabref.gui.util.BackgroundTask;
 import org.jabref.gui.util.DefaultTaskExecutor;
-import org.jabref.logic.bibtex.DuplicateCheck;
+import org.jabref.logic.database.DuplicateCheck;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;

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

@@ -70,7 +70,7 @@ public ExporterViewModel saveExporter() {
 
         // Create a new exporter to be returned to ExportCustomizationDialogViewModel, which requested it
         LayoutFormatterPreferences layoutPreferences = preferences.getLayoutFormatterPreferences(repository);
-        SavePreferences savePreferences = preferences.loadForExportFromPreferences();
+        SavePreferences savePreferences = preferences.getSavePreferencesForExport();
         TemplateExporter format = new TemplateExporter(name.get(), layoutFile.get(), extension.get(),
                 layoutPreferences, savePreferences);
         format.setCustomExport(true);

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

@@ -53,7 +53,7 @@ public ExportCommand(JabRefFrame frame, boolean selectedOnly, JabRefPreferences
     public void execute() {
         List<TemplateExporter> customExporters = preferences.getCustomExportFormats(Globals.journalAbbreviationRepository);
         LayoutFormatterPreferences layoutPreferences = preferences.getLayoutFormatterPreferences(Globals.journalAbbreviationRepository);
-        SavePreferences savePreferences = preferences.loadForExportFromPreferences();
+        SavePreferences savePreferences = preferences.getSavePreferencesForExport();
         XmpPreferences xmpPreferences = preferences.getXMPPreferences();
 
         // Get list of exporters and sort before adding to file dialog

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

@@ -187,7 +187,7 @@ private Optional<Path> askForSavePath() {
 
     private boolean save(BibDatabaseContext bibDatabaseContext, SaveDatabaseMode mode) {
         Optional<Path> databasePath = bibDatabaseContext.getDatabasePath();
-        if (!databasePath.isPresent()) {
+        if (databasePath.isEmpty()) {
             Optional<Path> savePath = askForSavePath();
             if (!savePath.isPresent()) {
                 return false;
@@ -238,10 +238,10 @@ private boolean save(Path targetPath, SaveDatabaseMode mode) {
     }
 
     private boolean saveDatabase(Path file, boolean selectedOnly, Charset encoding, SavePreferences.DatabaseSaveType saveType) throws SaveException {
-        SavePreferences preferences = this.preferences.loadForSaveFromPreferences()
+        SavePreferences preferences = this.preferences.getSavePreferences()
                                                       .withEncoding(encoding)
                                                       .withSaveType(saveType);
-        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, preferences.getEncoding(), preferences.makeBackup())) {
+        try (AtomicFileWriter fileWriter = new AtomicFileWriter(file, preferences.getEncoding(), preferences.shouldMakeBackup())) {
             BibtexDatabaseWriter databaseWriter = new BibtexDatabaseWriter(fileWriter, preferences, entryTypesManager);
 
             if (selectedOnly) {

src/main/java/org/jabref/gui/externalfiles/AutoLinkFilesAction.java

@@ -52,8 +52,12 @@ public void execute() {
         List<BibEntry> entries = stateManager.getSelectedEntries();
 
         final NamedCompound nc = new NamedCompound(Localization.lang("Automatically set file links"));
-        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(database, preferences.getFilePreferences(), preferences.getAutoLinkPreferences(), ExternalFileTypes.getInstance());
-        Task<List<BibEntry>> linkFilesTask = new Task<List<BibEntry>>() {
+        AutoSetFileLinksUtil util = new AutoSetFileLinksUtil(
+                database,
+                preferences.getFilePreferences(),
+                preferences.getAutoLinkPreferences(),
+                ExternalFileTypes.getInstance());
+        Task<List<BibEntry>> linkFilesTask = new Task<>() {
 
             @Override
             protected List<BibEntry> call() {