Remove empty entries automatically

CHANGELOG.md

@@ -48,6 +48,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We moved the preferences option to open the last edited files on startup to the 'General' tab. [#9808](https://github.com/JabRef/jabref/pull/9808)
 - We split the 'Import and Export' tab into 'Web Search' and 'Export'. [#9839](https://github.com/JabRef/jabref/pull/9839)
 - We improved the recognition of DOIs when pasting a link containing a DOI on the maintable [#9864](https://github.com/JabRef/jabref/issues/9864s)
+- In case the library contains empty entries, they are not written to disk. [#8645](https://github.com/JabRef/jabref/issues/8645)
 - The formatter `remove_unicode_ligatures` is now called `replace_unicode_ligatures`. [#9890](https://github.com/JabRef/jabref/pull/9890)
 
 ### Fixed
@@ -368,7 +369,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Added
 
-- We added confirmation dialog when user wants to close a library where any empty entires are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
+- We added confirmation dialog when user wants to close a library where any empty entries are detected. [#8096](https://github.com/JabRef/jabref/issues/8096)
 - We added import support for CFF files. [#7945](https://github.com/JabRef/jabref/issues/7945)
 - We added the option to copy the DOI of an entry directly from the context menu copy submenu. [#7826](https://github.com/JabRef/jabref/issues/7826)
 - We added a fulltext search feature. [#2838](https://github.com/JabRef/jabref/pull/2838)

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

@@ -43,6 +43,7 @@ public class Globals {
     public static final BuildInfo BUILD_INFO = new BuildInfo();
 
     public static final RemoteListenerServerManager REMOTE_LISTENER = new RemoteListenerServerManager();
+
     /**
      * Manager for the state of the GUI.
      */

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

@@ -472,13 +472,6 @@ public boolean quit() {
         for (int i = 0; i < tabbedPane.getTabs().size(); i++) {
             LibraryTab libraryTab = getLibraryTabAt(i);
             final BibDatabaseContext context = libraryTab.getBibDatabaseContext();
-
-            if (context.hasEmptyEntries()) {
-                if (!confirmEmptyEntry(libraryTab, context)) {
-                    return false;
-                }
-            }
-
             if (libraryTab.isModified() && (context.getLocation() == DatabaseLocation.LOCAL)) {
                 tabbedPane.getSelectionModel().select(i);
                 if (!confirmClose(libraryTab)) {
@@ -1157,7 +1150,7 @@ public void addTab(LibraryTab libraryTab, boolean raisePanel) {
 
     /**
      * Opens a new tab with existing data.
-     * Asynchronous loading is done at {@link #createLibraryTab(BackgroundTask, Path, PreferencesService, StateManager, JabRefFrame, ThemeManager)}.
+     * Asynchronous loading is done at {@link org.jabref.gui.LibraryTab#createLibraryTab(BackgroundTask, Path, PreferencesService, StateManager, JabRefFrame, ThemeManager)}.
      */
     public LibraryTab addTab(BibDatabaseContext databaseContext, boolean raisePanel) {
         Objects.requireNonNull(databaseContext);
@@ -1242,60 +1235,13 @@ private boolean confirmClose(LibraryTab libraryTab) {
         return false;
     }
 
-    /**
-     * Ask if the user really wants to remove any empty entries
-     */
-    private Boolean confirmEmptyEntry(LibraryTab libraryTab, BibDatabaseContext context) {
-        String filename = libraryTab.getBibDatabaseContext()
-                                    .getDatabasePath()
-                                    .map(Path::toAbsolutePath)
-                                    .map(Path::toString)
-                                    .orElse(Localization.lang("untitled"));
-
-        ButtonType deleteEmptyEntries = new ButtonType(Localization.lang("Delete empty entries"), ButtonBar.ButtonData.YES);
-        ButtonType keepEmptyEntries = new ButtonType(Localization.lang("Keep empty entries"), ButtonBar.ButtonData.NO);
-        ButtonType cancel = new ButtonType(Localization.lang("Return to library"), ButtonBar.ButtonData.CANCEL_CLOSE);
-
-        Optional<ButtonType> response = dialogService.showCustomButtonDialogAndWait(Alert.AlertType.CONFIRMATION,
-                Localization.lang("Empty entries"),
-                Localization.lang("Library '%0' has empty entries. Do you want to delete them?", filename),
-                deleteEmptyEntries, keepEmptyEntries, cancel);
-        if (response.isPresent() && response.get().equals(deleteEmptyEntries)) {
-            // The user wants to delete.
-            try {
-                for (BibEntry currentEntry : new ArrayList<>(context.getEntries())) {
-                    if (currentEntry.getFields().isEmpty()) {
-                        context.getDatabase().removeEntries(Collections.singletonList(currentEntry));
-                    }
-                }
-                SaveDatabaseAction saveAction = new SaveDatabaseAction(libraryTab, prefs, Globals.entryTypesManager);
-                if (saveAction.save()) {
-                    return true;
-                }
-                // The action was either canceled or unsuccessful.
-                dialogService.notify(Localization.lang("Unable to save library"));
-            } catch (Throwable ex) {
-                LOGGER.error("A problem occurred when trying to delete the empty entries", ex);
-                dialogService.showErrorDialogAndWait(Localization.lang("Delete empty entries"), Localization.lang("Could not delete empty entries."), ex);
-            }
-            // Save was cancelled or an error occurred.
-            return false;
-        }
-        return !response.get().equals(cancel);
-    }
-
     private void closeTab(LibraryTab libraryTab) {
         // empty tab without database
         if (libraryTab == null) {
             return;
         }
 
         final BibDatabaseContext context = libraryTab.getBibDatabaseContext();
-        if (context.hasEmptyEntries()) {
-            if (!confirmEmptyEntry(libraryTab, context)) {
-                return;
-            }
-        }
 
         if (libraryTab.isModified() && (context.getLocation() == DatabaseLocation.LOCAL)) {
             if (confirmClose(libraryTab)) {

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

@@ -816,7 +816,7 @@ public void resetChangedProperties() {
     /**
      * Creates a new library tab. Contents are loaded by the {@code dataLoadingTask}. Most of the other parameters are required by {@code resetChangeMonitor()}.
      *
-     * @param dataLoadingTask The task to execute to load the data. It is executed using {@link Globals.TASK_EXECUTOR}.
+     * @param dataLoadingTask The task to execute to load the data. It is executed using {@link org.jabref.gui.Globals.TASK_EXECUTOR}.
      * @param file the path to the file (loaded by the dataLoadingTask)
      */
     public static LibraryTab createLibraryTab(BackgroundTask<ParserResult> dataLoadingTask, Path file, PreferencesService preferencesService, StateManager stateManager, JabRefFrame frame, ThemeManager themeManager) {

src/main/java/org/jabref/logic/bibtex/comparator/BibDatabaseDiff.java

@@ -21,7 +21,7 @@ public class BibDatabaseDiff {
     private final List<BibStringDiff> bibStringDiffs;
     private final List<BibEntryDiff> entryDiffs;
 
-    private BibDatabaseDiff(BibDatabaseContext originalDatabase, BibDatabaseContext newDatabase) {
+    private BibDatabaseDiff(BibDatabaseContext originalDatabase, BibDatabaseContext newDatabase, boolean includeEmptyEntries) {
         metaDataDiff = MetaDataDiff.compare(originalDatabase.getMetaData(), newDatabase.getMetaData()).orElse(null);
         preambleDiff = PreambleDiff.compare(originalDatabase, newDatabase).orElse(null);
         bibStringDiffs = BibStringDiff.compare(originalDatabase.getDatabase(), newDatabase.getDatabase());
@@ -31,6 +31,11 @@ private BibDatabaseDiff(BibDatabaseContext originalDatabase, BibDatabaseContext
         List<BibEntry> originalEntriesSorted = originalDatabase.getDatabase().getEntriesSorted(comparator);
         List<BibEntry> newEntriesSorted = newDatabase.getDatabase().getEntriesSorted(comparator);
 
+        if (!includeEmptyEntries) {
+            originalEntriesSorted.removeIf(BibEntry::isEmpty);
+            newEntriesSorted.removeIf(BibEntry::isEmpty);
+        }
+
         entryDiffs = compareEntries(originalEntriesSorted, newEntriesSorted, originalDatabase.getMode());
     }
 
@@ -110,7 +115,7 @@ private static boolean hasEqualCitationKey(BibEntry oneEntry, BibEntry twoEntry)
     }
 
     public static BibDatabaseDiff compare(BibDatabaseContext base, BibDatabaseContext changed) {
-        return new BibDatabaseDiff(base, changed);
+        return new BibDatabaseDiff(base, changed, false);
     }
 
     public Optional<MetaDataDiff> getMetaDataDifferences() {

src/main/java/org/jabref/logic/exporter/BibDatabaseWriter.java

@@ -171,7 +171,11 @@ public List<FieldChange> getSaveActionsFieldChanges() {
      * Saves the complete database.
      */
     public void saveDatabase(BibDatabaseContext bibDatabaseContext) throws IOException {
-        savePartOfDatabase(bibDatabaseContext, bibDatabaseContext.getDatabase().getEntries());
+        List<BibEntry> entries = bibDatabaseContext.getDatabase().getEntries()
+                                                .stream()
+                                                .filter(entry -> !entry.isEmpty())
+                                                .toList();
+        savePartOfDatabase(bibDatabaseContext, entries);
     }
 
     /**

src/main/java/org/jabref/model/database/BibDatabase.java

@@ -112,7 +112,7 @@ public boolean hasEntries() {
     /**
      * Returns the list of entries sorted by the given comparator.
      */
-    public synchronized List<BibEntry> getEntriesSorted(Comparator<BibEntry> comparator) {
+    public List<BibEntry> getEntriesSorted(Comparator<BibEntry> comparator) {
         List<BibEntry> entriesSorted = new ArrayList<>(entries);
         entriesSorted.sort(comparator);
 

src/main/java/org/jabref/model/database/BibDatabaseContext.java

@@ -237,15 +237,6 @@ public List<BibEntry> getEntries() {
         return database.getEntries();
     }
 
-    /**
-     * check if the database has any empty entries
-     *
-     * @return true if the database has any empty entries; otherwise false
-     */
-    public boolean hasEmptyEntries() {
-        return this.getEntries().stream().anyMatch(entry -> entry.getFields().isEmpty());
-    }
-
     public Path getFulltextIndexPath() {
         Path appData = OS.getNativeDesktop().getFulltextIndexBaseDirectory();
         Path indexPath;

src/main/java/org/jabref/model/entry/BibEntry.java

@@ -1157,4 +1157,11 @@ public void mergeWith(BibEntry other, Set<Field> otherPrioritizedFields) {
             }
         }
     }
+
+    public boolean isEmpty() {
+        if (this.fields.isEmpty()) {
+            return true;
+        }
+        return StandardField.AUTOMATIC_FIELDS.containsAll(this.getFields());
+    }
 }

src/main/java/org/jabref/model/entry/field/StandardField.java

@@ -137,6 +137,8 @@ public enum StandardField implements Field {
     CREATIONDATE("creationdate", FieldProperty.DATE),
     MODIFICATIONDATE("modificationdate", FieldProperty.DATE);
 
+    public static Set<Field> AUTOMATIC_FIELDS = Set.of(OWNER, TIMESTAMP, CREATIONDATE, MODIFICATIONDATE);
+
     private final String name;
     private final String displayName;
     private final Set<FieldProperty> properties;

src/main/resources/l10n/JabRef_en.properties

@@ -1,15 +1,5 @@
 Proxy\ requires\ password=Proxy requires password
 
-Could\ not\ delete\ empty\ entries.=Could not delete empty entries.
-
-Delete\ empty\ entries=Delete empty entries
-
-Empty\ entries=Empty entries
-
-Keep\ empty\ entries=Keep empty entries
-
-Library\ '%0'\ has\ empty\ entries.\ Do\ you\ want\ to\ delete\ them?=Library '%0' has empty entries. Do you want to delete them?
-
 Unable\ to\ monitor\ file\ changes.\ Please\ close\ files\ and\ processes\ and\ restart.\ You\ may\ encounter\ errors\ if\ you\ continue\ with\ this\ session.=Unable to monitor file changes. Please close files and processes and restart. You may encounter errors if you continue with this session.
 %0\ contains\ the\ regular\ expression\ <b>%1</b>=%0 contains the regular expression <b>%1</b>
 

src/test/java/org/jabref/logic/exporter/BibtexDatabaseWriterTest.java

@@ -362,13 +362,15 @@ void writeEntryWithCustomizedTypeAlsoWritesTypeDeclaration() throws Exception {
                         new OrFields(StandardField.AUTHOR),
                         new OrFields(StandardField.DATE)));
         entryTypesManager.addCustomOrModifiedType(customizedBibType, BibDatabaseMode.BIBTEX);
-        BibEntry entry = new BibEntry(customizedType);
+        BibEntry entry = new BibEntry(customizedType).withCitationKey("key");
+        // needed to get a proper serialization
+        entry.setChanged(true);
         database.insertEntry(entry);
         bibtexContext.setMode(BibDatabaseMode.BIBTEX);
 
         databaseWriter.saveDatabase(bibtexContext);
 
-        assertEquals("@Customizedtype{," + OS.NEWLINE + "}" + OS.NEWLINE + OS.NEWLINE
+        assertEquals("@Customizedtype{key," + OS.NEWLINE + "}" + OS.NEWLINE + OS.NEWLINE
                         + "@Comment{jabref-meta: databaseType:bibtex;}"
                         + OS.NEWLINE + OS.NEWLINE
                         + "@Comment{jabref-entrytype: customizedtype: req[title;author;date] opt[year;month;publisher]}" + OS.NEWLINE,

src/test/java/org/jabref/model/database/BibDatabaseTest.java

@@ -16,7 +16,6 @@
 import org.jabref.model.entry.field.UnknownField;
 import org.jabref.model.entry.types.StandardEntryType;
 import org.jabref.model.event.EventListenerTest;
-import org.jabref.model.metadata.MetaData;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -37,25 +36,6 @@ void setUp() {
         database = new BibDatabase();
     }
 
-    @Test
-    void noEmptyEntry() {
-        BibEntry entry = new BibEntry();
-        entry.setField(StandardField.AUTHOR, "#AAA#");
-        database.insertEntry(entry);
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(database, new MetaData());
-        assertEquals(false, bibDatabaseContext.hasEmptyEntries());
-    }
-
-    @Test
-    void withEmptyEntry() {
-        BibEntry entry = new BibEntry();
-        database.insertEntry(entry);
-        BibDatabaseContext bibDatabaseContext = new BibDatabaseContext(database, new MetaData());
-        assertEquals(true, bibDatabaseContext.hasEmptyEntries());
-        bibDatabaseContext.getDatabase().removeEntries(Collections.singletonList(entry));
-        assertEquals(Collections.emptyList(), bibDatabaseContext.getEntries());
-    }
-
     @Test
     void insertEntryAddsEntryToEntriesList() {
         BibEntry entry = new BibEntry();

src/test/java/org/jabref/model/entry/BibEntryTest.java

@@ -9,6 +9,7 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
+import java.util.stream.Stream;
 
 import org.jabref.model.FieldChange;
 import org.jabref.model.database.BibDatabase;
@@ -25,6 +26,8 @@
 import com.google.common.collect.Sets;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.parallel.Execution;
+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.assertFalse;
@@ -809,4 +812,38 @@ void mergeEntriesWithOverlapAndPriorityGivenToOverlappingField() {
         copyEntry.mergeWith(otherEntry, otherPrioritizedFields);
         assertEquals(expected.getFields(), copyEntry.getFields());
     }
+
+    public static Stream<BibEntry> isEmpty() {
+        return Stream.of(
+                new BibEntry(),
+                new BibEntry(StandardEntryType.Book),
+                new BibEntry().withField(StandardField.OWNER, "test"),
+                new BibEntry().withField(StandardField.CREATIONDATE, "test"),
+                new BibEntry()
+                        .withField(StandardField.OWNER, "test")
+                        .withField(StandardField.CREATIONDATE, "test"),
+                // source: https://github.com/JabRef/jabref/issues/8645
+                new BibEntry()
+                        .withField(StandardField.OWNER, "mlep")
+                        .withField(StandardField.CREATIONDATE, "2022-04-05T10:41:54"));
+    }
+
+    @ParameterizedTest
+    @MethodSource
+    void isEmpty(BibEntry entry) {
+        assertTrue(entry.isEmpty());
+    }
+
+    public static Stream<BibEntry> isNotEmpty() {
+        return Stream.of(
+                new BibEntry().withCitationKey("test"),
+                new BibEntry().withField(StandardField.AUTHOR, "test")
+        );
+    }
+
+    @ParameterizedTest
+    @MethodSource
+    void isNotEmpty(BibEntry entry) {
+        assertFalse(entry.isEmpty());
+    }
 }