Merge branch 'main' into chronological-navigation

Author: subhramit

.github/workflows/sbom-pr.yml

@@ -58,7 +58,7 @@ jobs:
             Generated via Gradle task `cyclonedxBom` using the org.cyclonedx.bom plugin configured in the build.
           branch: chore/update-sbom
           delete-branch: true
-          labels: "dev: dependencies""
+          labels: "dev: dependencies"
           add-paths: |
             bom.json
             bom.xml

CHANGELOG.md

@@ -128,12 +128,15 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We fixed an issue where "Copy to" was enabled even if no other library was opened. [#13280](https://github.com/JabRef/jabref/pull/13280)
 - We fixed an issue where the groups were still displayed after closing all libraries. [#13382](https://github.com/JabRef/jabref/issues/13382)
 - Enhanced field selection logic in the Merge Entries dialog when fetching from DOI to prefer valid years and entry types. [#12549](https://github.com/JabRef/jabref/issues/12549)
+- We fixed an issue where the "Check Consistency" dialog is unresponsive. [#13700](https://github.com/JabRef/jabref/issues/13700)
 - We fixed an issue where opening the Three Way Merge dialog would throw an exception when year field contains an invalid year value. [#13673](https://github.com/JabRef/jabref/issues/13673)
 - We improved consistency in the Add Buttons. [#13791](https://github.com/JabRef/jabref/pull/13791)
 - We fixed an issue where theme or font size are not respected for all dialogs [#13558](https://github.com/JabRef/jabref/issues/13558)
 - We removed unnecessary spacing and margin in the AutomaticFieldEditor. [#13792](https://github.com/JabRef/jabref/pull/13792)
 - We fixed an issue where global search auto-completion only worked after switching tabs. [#11428](https://github.com/JabRef/jabref/issues/11428)
 - We fixed an issue where hierarchical keywords would only show the parent keyword in the entry editor. [#11390](https://github.com/JabRef/jabref/issues/11390)
+- We fixed an issue where some file choosers regarding LaTeX-aux files did not open in the directory of the last selected file. [#13861](https://github.com/JabRef/jabref/pull/13861)
+- We fixed an issue where the LaTeX file directory was not stored correctly in combination with the usage of groups from aux files. [#8344](https://github.com/JabRef/jabref/issues/8344)
 
 ### Removed
 

jabgui/src/main/java/org/jabref/gui/auximport/FromAuxDialogViewModel.java

@@ -82,7 +82,7 @@ public void browse() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(StandardFileType.AUX)
                 .withDefaultExtension(StandardFileType.AUX)
-                .withInitialDirectory(preferences.getFilePreferences().getWorkingDirectory()).build();
+                .withInitialDirectory(auxFileProperty.get() == null ? preferences.getFilePreferences().getWorkingDirectory().toString() : auxFileProperty.get()).build();
         dialogService.showFileOpenDialog(fileDialogConfiguration).ifPresent(file -> auxFileProperty.setValue(file.toAbsolutePath().toString()));
     }
 

jabgui/src/main/java/org/jabref/gui/consistency/ConsistencyCheckAction.java

@@ -82,7 +82,7 @@ public BibliographyConsistencyCheck.Result call() {
         });
         taskExecutor.execute(task);
 
-        dialogService.showProgressDialogAndWait(
+        dialogService.showProgressDialog(
                 Localization.lang("Check consistency"),
                 Localization.lang("Checking consistency..."),
                 task);

jabgui/src/main/java/org/jabref/gui/entryeditor/LatexCitationsTabViewModel.java

@@ -132,7 +132,7 @@ public void setLatexDirectory() {
                 .withInitialDirectory(directory.get()).build();
 
         dialogService.showDirectorySelectionDialog(directoryDialogConfiguration).ifPresent(selectedDirectory ->
-                currentDatabaseContext.getMetaData().setLatexFileDirectory(preferences.getFilePreferences().getUserAndHost(), selectedDirectory.toAbsolutePath()));
+                currentDatabaseContext.getMetaData().setLatexFileDirectory(preferences.getFilePreferences().getUserAndHost(), selectedDirectory.toAbsolutePath().toString()));
 
         checkAndUpdateDirectory();
     }

jabgui/src/main/java/org/jabref/gui/groups/GroupDialogViewModel.java

@@ -231,8 +231,8 @@ private void setupValidation() {
                             return false;
                         }
                         return FileUtil.getFileExtension(input)
-                                .map("aux"::equalsIgnoreCase)
-                                .orElse(false);
+                                       .map("aux"::equalsIgnoreCase)
+                                       .orElse(false);
                     }
                 },
                 ValidationMessage.error(Localization.lang("Please provide a valid aux file.")));
@@ -373,7 +373,9 @@ public AbstractGroup resultConverter(ButtonType button) {
                         Path.of(texGroupFilePathProperty.getValue().trim()),
                         new DefaultAuxParser(new BibDatabase()),
                         fileUpdateMonitor,
-                        currentDatabase.getMetaData());
+                        currentDatabase.getMetaData(),
+                        preferences.getFilePreferences().getUserAndHost()
+                );
             }
 
             if (resultingGroup != null) {
@@ -485,9 +487,10 @@ public void texGroupBrowse() {
         FileDialogConfiguration fileDialogConfiguration = new FileDialogConfiguration.Builder()
                 .addExtensionFilter(StandardFileType.AUX)
                 .withDefaultExtension(StandardFileType.AUX)
-                .withInitialDirectory(currentDatabase.getMetaData()
-                                                     .getLatexFileDirectory(preferences.getFilePreferences().getUserAndHost())
-                                                     .orElse(FileUtil.getInitialDirectory(currentDatabase, preferences.getFilePreferences().getWorkingDirectory()))).build();
+                .withInitialDirectory(texGroupFilePathProperty.getValue().isBlank() ?
+                        currentDatabase.getMetaData()
+                                       .getLatexFileDirectory(preferences.getFilePreferences().getUserAndHost())
+                                       .orElse(FileUtil.getInitialDirectory(currentDatabase, preferences.getFilePreferences().getWorkingDirectory())).toString() : texGroupFilePathProperty.get()).build();
         dialogService.showFileOpenDialog(fileDialogConfiguration)
                      .ifPresent(file -> texGroupFilePathProperty.setValue(
                              FileUtil.relativize(file.toAbsolutePath(), getFileDirectoriesAsPaths()).toString()

jabgui/src/main/java/org/jabref/gui/libraryproperties/general/GeneralPropertiesViewModel.java

@@ -113,7 +113,7 @@ public void storeSettings() {
         if (latexFileDirectory.isEmpty()) {
             newMetaData.clearLatexFileDirectory(preferences.getFilePreferences().getUserAndHost());
         } else if (laTexFileDirectoryStatus().isValid()) {
-            newMetaData.setLatexFileDirectory(preferences.getFilePreferences().getUserAndHost(), Path.of(latexFileDirectory));
+            newMetaData.setLatexFileDirectory(preferences.getFilePreferences().getUserAndHost(), latexFileDirectory);
         }
 
         databaseContext.setMetaData(newMetaData);
@@ -271,7 +271,8 @@ public void togglePath(StringProperty fileDirectory) {
             if (!currPath.isAbsolute()) {
                 newPath = parentPath.resolve(fileDirectory.get()).toAbsolutePath().toString();
             } else if (currPath.isAbsolute()) {
-                newPath = parentPath.relativize(currPath).toString();
+                Path rel = parentPath.relativize(currPath);
+                newPath = rel.toString().isEmpty() ? "." : rel.toString();
             } else {
                 // case: convert to relative path and currPath is relative
                 return;

jabgui/src/main/java/org/jabref/gui/shared/SharedDatabaseUIManager.java

@@ -221,7 +221,8 @@ private BibDatabaseContext getBibDatabaseContextForSharedDatabase() {
                 preferences.getBibEntryPreferences().getKeywordSeparator(),
                 preferences.getFieldPreferences(),
                 preferences.getCitationKeyPatternPreferences().getKeyPatterns(),
-                fileUpdateMonitor);
+                fileUpdateMonitor,
+                preferences.getFilePreferences().getUserAndHost());
         bibDatabaseContext.convertToSharedDatabase(synchronizer);
         return bibDatabaseContext;
     }

jablib/src/main/java/org/jabref/logic/exporter/MetaDataSerializer.java

@@ -57,7 +57,7 @@ public static Map<String, String> getSerializedStringMap(MetaData metaData,
         metaData.getUserFileDirectories().forEach((user, path) -> stringyMetaData
                 .put(MetaData.FILE_DIRECTORY + '-' + user, List.of(path.trim())));
         metaData.getLatexFileDirectories().forEach((user, path) -> stringyMetaData
-                .put(MetaData.FILE_DIRECTORY_LATEX + '-' + user, List.of(path.toString().trim())));
+                .put(MetaData.FILE_DIRECTORY_LATEX + '-' + user, List.of(path.trim())));
         metaData.getVersionDBStructure().ifPresent(
                 versionDBStructure -> stringyMetaData.put(MetaData.VERSION_DB_STRUCT, List.of(versionDBStructure.trim())));
         metaData.getBlgFilePaths().forEach((user, path) -> stringyMetaData.put(MetaData.BLG_FILE_PATH + "-" + user, List.of(path.toString().trim())));

jablib/src/main/java/org/jabref/logic/importer/ImportFormatPreferences.java

@@ -1,5 +1,6 @@
 package org.jabref.logic.importer;
 
+import org.jabref.logic.FilePreferences;
 import org.jabref.logic.bibtex.FieldPreferences;
 import org.jabref.logic.citationkeypattern.CitationKeyPatternPreferences;
 import org.jabref.logic.importer.util.GrobidPreferences;
@@ -13,5 +14,6 @@ public record ImportFormatPreferences(
         FieldPreferences fieldPreferences,
         XmpPreferences xmpPreferences,
         DOIPreferences doiPreferences,
-        GrobidPreferences grobidPreferences) {
+        GrobidPreferences grobidPreferences,
+        FilePreferences filePreferences) {
 }