Merge branch 'main' into refine-bibentrytypes

CHANGELOG.md

@@ -42,6 +42,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We changed the duplicate handling in the Import entries dialog. Potential duplicate entries are marked with an icon and importing will now trigger the merge dialog [#10914](https://github.com/JabRef/jabref/pull/10914)
 - We made the command "Push to TexShop" more robust to allow cite commands with a character before the first slash. [forum#2699](https://discourse.jabref.org/t/push-to-texshop-mac/2699/17?u=siedlerchr)
 - We only show the notification "Saving library..." if the library contains more than 2000 entries. [#9803](https://github.com/JabRef/jabref/issues/9803)
+- JabRef now keeps previous log files upon start. [#11023](https://github.com/JabRef/jabref/pull/11023)
 - We enhanced the dialog for adding new fields in the content selector with a selection box containing a list of standard fields. [#10912](https://github.com/JabRef/jabref/pull/10912)
 - We store the citation relations in an LRU cache to avoid bloating the memory and out-of-memory exceptions. [#10958](https://github.com/JabRef/jabref/issues/10958)
 - Keywords filed are now displayed as tags. [#10910](https://github.com/JabRef/jabref/pull/10910)
@@ -53,6 +54,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where the preview panel showing the wrong entry (an entry that is not selected in the entry table). [#9172](https://github.com/JabRef/jabref/issues/9172)
 - We fixed an issue where HTML-reserved characters like '&' and '<', in addition to HTML entities like '&amp;' were not rendered correctly in entry preview. [#10677](https://github.com/JabRef/jabref/issues/10677)
 - The last page of a PDF is now indexed by the full text search. [#10193](https://github.com/JabRef/jabref/issues/10193)
+- The entry editor respects the configured custom tabs when showing "Other fields". [#11012](https://github.com/JabRef/jabref/pull/11012)
 - The default owner of an entry can be changed again. [#10924](https://github.com/JabRef/jabref/issues/10924)
 - We fixed an issue where the duplicate check did not take umlauts or other LaTeX-encoded characters into account. [#10744](https://github.com/JabRef/jabref/pull/10744)
 - We fixed the colors of the icon on hover for unset special fields. [#10431](https://github.com/JabRef/jabref/issues/10431)

config/README.md

@@ -20,7 +20,7 @@ Style-checks are done for each pull request and installing this code style confi
 # Eclipse:
 
 The Eclipse code formatter style is stored in the `eclipse.gradle` file and gets imported automatically.
-In case the formatter style needs to be adapted, configure it and export in in eclipse.
+In case the formatter style needs to be adapted, configure it and export in eclipse.
 
 1. Right click on the eclipse project "JabRef"
 2. Select "Export > General > Preferences"

src/main/java/org/jabref/Launcher.java

@@ -11,15 +11,13 @@
 import java.util.List;
 import java.util.Map;
 
-import org.jabref.architecture.AllowedToUseStandardStreams;
 import org.jabref.cli.ArgumentProcessor;
 import org.jabref.cli.JabRefCLI;
 import org.jabref.gui.Globals;
 import org.jabref.gui.JabRefGUI;
 import org.jabref.logic.UiCommand;
 import org.jabref.logic.journals.JournalAbbreviationLoader;
 import org.jabref.logic.journals.predatory.PredatoryJournalListLoader;
-import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.net.ProxyAuthenticator;
 import org.jabref.logic.net.ProxyPreferences;
 import org.jabref.logic.net.ProxyRegisterer;
@@ -48,7 +46,6 @@
  * - Handle the command line arguments
  * - Start the JavaFX application (if not in cli mode)
  */
-@AllowedToUseStandardStreams("Direct output to the user")
 public class Launcher {
     private static Logger LOGGER;
     private static boolean isDebugEnabled;
@@ -140,11 +137,14 @@ private static void addLogToDisk() {
         // The "Shared File Writer" is explained at
         // https://tinylog.org/v2/configuration/#shared-file-writer
         Map<String, String> configuration = Map.of(
-                "writerFile", "shared file",
-                "writerFile.level", isDebugEnabled ? "debug" : "info",
                 "level", isDebugEnabled ? "debug" : "info",
-                "writerFile.file", directory.resolve("log.txt").toString(),
-                "writerFile.charset", "UTF-8");
+                "writerFile", "rolling file",
+                "writerFile.level", isDebugEnabled ? "debug" : "info",
+                // We need to manually join the path, because ".resolve" does not work on Windows, because ":" is not allowed in file names on Windows
+                "writerFile.file", directory + File.separator + "log_{date:yyyy-MM-dd_HH-mm-ss}.txt",
+                "writerFile.charset", "UTF-8",
+                "writerFile.policies", "startup",
+                "writerFile.backups", "30");
 
         configuration.forEach(Configuration::set);
         initializeLogger();
@@ -169,9 +169,8 @@ private static boolean handleMultipleAppInstances(String[] args, RemotePreferenc
                 LOGGER.debug("Passing arguments passed on to running JabRef...");
                 if (remoteClient.sendCommandLineArguments(args)) {
                     // So we assume it's all taken care of, and quit.
-                    LOGGER.debug("Arguments passed on to running JabRef instance.");
-                    // Used for script-use output etc. to the user
-                    System.out.println(Localization.lang("Arguments passed on to running JabRef instance. Shutting down."));
+                    // Output to both to the log and the screen. Therefore, we do not have an additional System.out.println.
+                    LOGGER.info("Arguments passed on to running JabRef instance. Shutting down.");
                     return false;
                 } else {
                     LOGGER.warn("Could not communicate with other running JabRef instance.");

src/main/java/org/jabref/gui/entryeditor/OtherFieldsTab.java

@@ -26,7 +26,6 @@
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.entry.BibEntryType;
 import org.jabref.model.entry.BibEntryTypesManager;
-import org.jabref.model.entry.field.BibField;
 import org.jabref.model.entry.field.Field;
 import org.jabref.model.entry.field.InternalField;
 import org.jabref.model.entry.field.StandardField;
@@ -36,7 +35,7 @@
 public class OtherFieldsTab extends FieldsEditorTab {
 
     public static final String NAME = "Other fields";
-    private final List<Field> customTabFieldNames;
+    private final List<Field> customTabsFieldNames;
     private final BibEntryTypesManager entryTypesManager;
 
     public OtherFieldsTab(BibDatabaseContext databaseContext,
@@ -63,8 +62,8 @@ public OtherFieldsTab(BibDatabaseContext databaseContext,
                 indexingTaskManager);
 
         this.entryTypesManager = entryTypesManager;
-        this.customTabFieldNames = new ArrayList<>();
-        preferences.getEntryEditorPreferences().getDefaultEntryEditorTabs().values().forEach(customTabFieldNames::addAll);
+        this.customTabsFieldNames = new ArrayList<>();
+        preferences.getEntryEditorPreferences().getEntryEditorTabs().values().forEach(customTabsFieldNames::addAll);
 
         setText(Localization.lang("Other fields"));
         setTooltip(new Tooltip(Localization.lang("Show remaining fields")));
@@ -76,15 +75,21 @@ protected SequencedSet<Field> determineFieldsToShow(BibEntry entry) {
         BibDatabaseMode mode = databaseContext.getMode();
         Optional<BibEntryType> entryType = entryTypesManager.enrich(entry.getType(), mode);
         if (entryType.isPresent()) {
+            // Get all required and optional fields configured for the entry
             Set<Field> allKnownFields = entryType.get().getAllFields();
+            // Remove all fields being required or optional
             SequencedSet<Field> otherFields = entry.getFields().stream()
-                                          .filter(field -> !allKnownFields.contains(field) &&
-                                                  !(field.equals(StandardField.COMMENT) || field instanceof UserSpecificCommentField))
+                                          .filter(field -> !allKnownFields.contains(field))
                                           .collect(Collectors.toCollection(LinkedHashSet::new));
-            otherFields.removeAll(entryType.get().getDeprecatedFields(mode));
-            otherFields.removeAll(entryType.get().getOptionalFields().stream().map(BibField::field).toList());
+            // The key field is in the required tab, but has a special treatment
             otherFields.remove(InternalField.KEY_FIELD);
-            customTabFieldNames.forEach(otherFields::remove);
+            // Remove all fields contained in JabRef's tab "Deprecated"
+            otherFields.removeAll(entryType.get().getDeprecatedFields(mode));
+            // Remove all fields contained in the custom tabs
+            customTabsFieldNames.forEach(otherFields::remove);
+            // Remove all user-comment fields (tab org.jabref.gui.entryeditor.CommentsTab)
+            otherFields.removeIf(field -> field.equals(StandardField.COMMENT));
+            otherFields.removeIf(field -> field instanceof UserSpecificCommentField);
             return otherFields;
         } else {
             // Entry type unknown -> treat all fields as required (thus no other fields)

src/main/java/org/jabref/logic/importer/fetcher/DBLPFetcher.java

@@ -68,7 +68,7 @@ public void doPostCleanup(BibEntry entry) {
         FieldFormatterCleanups cleanups = new FieldFormatterCleanups(true,
                 List.of(
                         new FieldFormatterCleanup(StandardField.TIMESTAMP, new ClearFormatter()),
-                        // unescape the the contents of the URL field, e.g., some\_url\_part becomes some_url_part
+                        // unescape the contents of the URL field, e.g., some\_url\_part becomes some_url_part
                         new FieldFormatterCleanup(StandardField.URL, new LayoutFormatterBasedFormatter(new RemoveLatexCommandsFormatter()))
                 ));
         cleanups.applySaveActions(entry);

src/main/java/org/jabref/migrations/PreferencesMigrations.java

@@ -16,6 +16,8 @@
 
 import javafx.scene.control.TableColumn;
 
+import org.jabref.gui.entryeditor.CommentsTab;
+import org.jabref.gui.entryeditor.EntryEditor;
 import org.jabref.gui.maintable.ColumnPreferences;
 import org.jabref.gui.maintable.MainTableColumnModel;
 import org.jabref.logic.citationkeypattern.GlobalCitationKeyPattern;
@@ -57,13 +59,14 @@ public static void runMigrations(JabRefPreferences preferences, BibEntryTypesMan
         addCrossRefRelatedFieldsForAutoComplete(preferences);
         upgradePreviewStyle(preferences);
         // changeColumnVariableNamesFor51 needs to be run before upgradeColumnPre50Preferences to ensure
-        // backwardcompatibility, as it copies the old values to new variable names and keeps th old sored with the old
+        // backward compatibility, as it copies the old values to new variable names and keeps th old sored with the old
         // variable names. However, the variables from 5.0 need to be copied to the new variable name too.
         changeColumnVariableNamesFor51(preferences);
         upgradeColumnPreferences(preferences);
         restoreVariablesForBackwardCompatibility(preferences);
         upgradeCleanups(preferences);
         moveApiKeysToKeyring(preferences);
+        removeCommentsFromCustomEditorTabs(preferences);
     }
 
     /**
@@ -545,4 +548,12 @@ static void moveApiKeysToKeyring(JabRefPreferences preferences) {
             }
         }
     }
+
+    /**
+     * The tab "Comments" is hard coded using {@link CommentsTab} since v5.10 (and thus hard-wired in {@link EntryEditor#createTabs()}.
+     * Thus, the configuration ih the preferences is obsolete
+     */
+    static void removeCommentsFromCustomEditorTabs(JabRefPreferences preferences) {
+        preferences.getEntryEditorPreferences().getEntryEditorTabs().remove("Comments");
+    }
 }

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

@@ -572,7 +572,7 @@ public Optional<String> getFieldOrAlias(Field field) {
     }
 
     /**
-     * Return the LaTeX-free contents of the given field or its alias an an Optional
+     * Return the LaTeX-free contents of the given field or its alias an Optional
      * <p>
      * For details see also {@link #getFieldOrAlias(Field)}
      *

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

@@ -16,7 +16,7 @@
  * <br>
  * The class OrFields is used to model "year/date" in this case.
  * <p>
- * Example is that a BibEntry requires either an author or an editor, but both can be be present.
+ * Example is that a BibEntry requires either an author or an editor, but both can be present.
  */
 public class OrFields implements Comparable<OrFields> {
 

src/main/java/org/jabref/preferences/JabRefPreferences.java

@@ -22,6 +22,7 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Optional;
+import java.util.SequencedMap;
 import java.util.Set;
 import java.util.TreeSet;
 import java.util.UUID;
@@ -835,10 +836,6 @@ public void setLanguageDependentDefaultValues() {
         defaults.put(CUSTOM_TAB_FIELDS + "_def1", StandardField.ABSTRACT.getName());
         defaults.put(CUSTOM_TAB_NAME + "_def1", Localization.lang("Abstract"));
 
-        // Entry editor tab 2: Comments Field - used for research comments, etc.
-        defaults.put(CUSTOM_TAB_FIELDS + "_def2", StandardField.COMMENT.getName());
-        defaults.put(CUSTOM_TAB_NAME + "_def2", Localization.lang("Comments"));
-
         defaults.put(EMAIL_SUBJECT, Localization.lang("References"));
     }
 
@@ -1508,7 +1505,7 @@ private Map<String, Set<Field>> getEntryEditorTabs() {
         List<String> tabFields = getSeries(CUSTOM_TAB_FIELDS);
 
         if (tabNames.isEmpty() || (tabNames.size() != tabFields.size())) {
-            // Nothing set, so we use the default values
+            // Nothing set (or wrong configuration), then we use default values
             tabNames = getSeries(CUSTOM_TAB_NAME + "_def");
             tabFields = getSeries(CUSTOM_TAB_FIELDS + "_def");
         }
@@ -1543,8 +1540,8 @@ private void storeEntryEditorTabs(Map<String, Set<Field>> customTabs) {
         getEntryEditorTabs();
     }
 
-    private Map<String, Set<Field>> getDefaultEntryEditorTabs() {
-        Map<String, Set<Field>> customTabsMap = new LinkedHashMap<>();
+    private SequencedMap<String, Set<Field>> getDefaultEntryEditorTabs() {
+        SequencedMap<String, Set<Field>> customTabsMap = new LinkedHashMap<>();
 
         int defNumber = 0;
         while (true) {

src/main/resources/l10n/JabRef_en.properties

@@ -77,8 +77,6 @@ Application\ to\ push\ entries\ to=Application to push entries to
 
 Apply=Apply
 
-Arguments\ passed\ on\ to\ running\ JabRef\ instance.\ Shutting\ down.=Arguments passed on to running JabRef instance. Shutting down.
-
 Assign\ the\ original\ group's\ entries\ to\ this\ group?=Assign the original group's entries to this group?
 
 Assigned\ %0\ entries\ to\ group\ "%1".=Assigned %0 entries to group "%1".