Merge branch 'main' into reduce-log-noise

Author: koppor

.github/PULL_REQUEST_TEMPLATE.md

@@ -11,9 +11,12 @@ The title of the PR must not reference an issue, because GitHub does not support
 - [x] done; [ ] not done / not applicable
 -->
 
+```[tasklist]
+### Compulsory checks
 - [ ] Change in `CHANGELOG.md` described in a way that is understandable for the average user (if applicable)
 - [ ] Tests created for changes (if applicable)
 - [ ] Manually tested changed features in running JabRef (always required)
 - [ ] Screenshots added in PR description (for UI changes)
 - [ ] [Checked developer's documentation](https://devdocs.jabref.org/): Is the information available and up to date? If not, I outlined it in this pull request.
 - [ ] [Checked documentation](https://docs.jabref.org/): Is the information available and up to date? If not, I created an issue at <https://github.com/JabRef/user-documentation/issues> or, even better, I submitted a pull request to the documentation repository.
+```

CHANGELOG.md

@@ -23,10 +23,14 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 ### Changed
 
 - 'Get full text' now also checks the file url. [#568](https://github.com/koppor/jabref/issues/568)
+- We modified the `Add Group` dialog to use the most recently selected group hierarchical context. [#9141](https://github.com/JabRef/jabref/issues/9141)
 - We refined the 'main directory not found' error message. [#9625](https://github.com/JabRef/jabref/pull/9625)
+- JabRef writes a new backup file only if there is a change. Before, JabRef created a backup upon start. [#9679](https://github.com/JabRef/jabref/pull/9679)
+- Backups of libraries are not stored per JabRef version, but collected together.
+- We streamlined the paths for logs and backups: The parent path fragement is always `logs` or `backups`.
 - `log.txt` now contains debug messages. Debugging needs to be enabled explicitly. [#9678](https://github.com/JabRef/jabref/pull/9678)
 - `log.txt` does not contain entries for non-found files during PDF indexing. [#9678](https://github.com/JabRef/jabref/pull/9678)
-- We modified the `Add Group` dialog to use the most recently selected group hierarchical context [#9141](https://github.com/JabRef/jabref/issues/9141)
+- We improved the Medline importer to correctly import ISO dates for `revised`. [#9536](https://github.com/JabRef/jabref/issues/9536)
 
 
 

build.gradle

@@ -259,7 +259,6 @@ processResources {
 
 task generateSource(dependsOn: ["generateBstGrammarSource",
                                 "generateSearchGrammarSource",
-                                "generateMedlineSource",
                                 "generateBibtexmlSource",
                                 "generateEndnoteSource",
                                 "generateModsSource",
@@ -290,15 +289,6 @@ tasks.register("generateSearchGrammarSource", JavaExec) {
     args  = ["-o","src-gen/main/java/org/jabref/search" , "-visitor", "-no-listener", "-package", "org.jabref.search", "$projectDir/src/main/antlr4/org/jabref/search/Search.g4"]
 }
 
-task generateMedlineSource(type: XjcTask) {
-    group = 'JabRef'
-    description = "Generates java files for the medline importer."
-
-    schemaFile = "src/main/resources/xjc/medline/medline.xsd"
-    outputDirectory = "src-gen/main/java"
-    javaPackage = "org.jabref.logic.importer.fileformat.medline"
-}
-
 task generateBibtexmlSource(type: XjcTask) {
     group = 'JabRef'
     description = "Generates java files for the bibtexml importer."

docs/Gemfile

@@ -5,7 +5,7 @@ gem "jekyll", "~> 4.3" # installed by `gem jekyll`
 # Homepage: https://github.com/paulrobertlloyd/jekyll-figure#jekyll-figure
 gem 'jekyll-figure'
 
-gem "just-the-docs", "0.4.0.rc3"
+gem "just-the-docs", "0.4.2"
 
 gem "jekyll-remote-theme"
 

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

@@ -22,6 +22,7 @@
 import org.jabref.logic.remote.RemotePreferences;
 import org.jabref.logic.remote.client.RemoteClient;
 import org.jabref.logic.util.BuildInfo;
+import org.jabref.logic.util.OS;
 import org.jabref.migrations.PreferencesMigrations;
 import org.jabref.model.database.BibDatabaseContext;
 import org.jabref.model.database.BibDatabaseMode;
@@ -90,10 +91,12 @@ public static void main(String[] args) {
      * the log configuration programmatically anymore.
      */
     private static void addLogToDisk() {
-        Path directory = Path.of(AppDirsFactory.getInstance().getUserLogDir(
-                "jabref",
-                new BuildInfo().version.toString(),
-                "org.jabref"));
+        Path directory = Path.of(AppDirsFactory.getInstance()
+                                               .getUserDataDir(
+                OS.APP_DIR_APP_NAME,
+                "logs",
+                OS.APP_DIR_APP_AUTHOR))
+                .resolve(new BuildInfo().version.toString());
         try {
             Files.createDirectories(directory);
         } catch (IOException e) {

src/main/java/org/jabref/gui/backup/BackupResolverDialog.java

@@ -32,7 +32,7 @@ public BackupResolverDialog(Path originalPath) {
         getDialogPane().setMinHeight(180);
         getDialogPane().getButtonTypes().setAll(RESTORE_FROM_BACKUP, REVIEW_BACKUP, IGNORE_BACKUP);
 
-        Optional<Path> backupPathOpt = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP);
+        Optional<Path> backupPathOpt = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP);
         String backupFilename = backupPathOpt.map(Path::getFileName).map(Path::toString).orElse(Localization.lang("File not found"));
         String content = new StringBuilder()
                 .append(Localization.lang("A backup file for '%0' was found at [%1]",

src/main/java/org/jabref/gui/dialogs/BackupUIManager.java

@@ -63,7 +63,7 @@ private static Optional<ParserResult> showReviewBackupDialog(DialogService dialo
             // This will be modified by using the `DatabaseChangesResolverDialog`.
             BibDatabaseContext originalDatabase = originalParserResult.getDatabaseContext();
 
-            Path backupPath = BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow();
+            Path backupPath = BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP).orElseThrow();
             BibDatabaseContext backupDatabase = OpenDatabase.loadDatabase(backupPath, importFormatPreferences, new DummyFileUpdateMonitor()).getDatabaseContext();
 
             DatabaseChangeResolverFactory changeResolverFactory = new DatabaseChangeResolverFactory(dialogService, originalDatabase, preferencesService.getBibEntryPreferences());

src/main/java/org/jabref/logic/autosaveandbackup/BackupManager.java

@@ -64,7 +64,7 @@ public class BackupManager {
     // During a write, the less recent backup file is deleted
     private final Queue<Path> backupFilesQueue = new LinkedBlockingQueue<>();
 
-    private boolean needsBackup = true;
+    private boolean needsBackup = false;
 
     BackupManager(BibDatabaseContext bibDatabaseContext, BibEntryTypesManager entryTypesManager, PreferencesService preferences) {
         this.bibDatabaseContext = bibDatabaseContext;
@@ -87,7 +87,7 @@ static Path getBackupPathForNewBackup(Path originalPath) {
      * Determines the most recent existing backup file name
      */
     static Optional<Path> getLatestBackupPath(Path originalPath) {
-        return BackupFileUtil.getPathOfLatestExisingBackupFile(originalPath, BackupFileType.BACKUP);
+        return BackupFileUtil.getPathOfLatestExistingBackupFile(originalPath, BackupFileType.BACKUP);
     }
 
     /**