Fix several aux group issues

.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

@@ -133,6 +133,8 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - 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. [#8344](https://github.com/JabRef/jabref/issues/8344)
+- We fixed an issue where the LaTeX-File directory was not stored correctly in combination with the usage of Groups from aux files. [#13820](https://github.com/JabRef/jabref/issues/13820)
 
 ### 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/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.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);

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) {
 }

jablib/src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java

@@ -273,7 +273,8 @@ private ParserResult parseFileContent() throws IOException {
         try {
             MetaData metaData = metaDataParser.parse(
                     meta,
-                    importFormatPreferences.bibEntryPreferences().getKeywordSeparator());
+                    importFormatPreferences.bibEntryPreferences().getKeywordSeparator(),
+                    importFormatPreferences.filePreferences().getUserAndHost());
             if (bibDeskGroupTreeNode != null) {
                 metaData.getGroups().ifPresentOrElse(existingGroupTree -> {
                             String existingGroups = meta.get(MetaData.GROUPSTREE);

jablib/src/main/java/org/jabref/logic/importer/util/GroupsParser.java

@@ -45,13 +45,13 @@ public class GroupsParser {
     private GroupsParser() {
     }
 
-    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
+    public static GroupTreeNode importGroups(List<String> orderedData, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData, String userAndHost)
             throws ParseException {
         try {
             GroupTreeNode cursor = null;
             GroupTreeNode root = null;
             for (String string : orderedData) {
-                // This allows to read databases that have been modified by, e.g., BibDesk
+                // This allows reading databases that have been modified by, e.g., BibDesk
                 string = string.trim();
                 if (string.isEmpty()) {
                     continue;
@@ -62,7 +62,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
                     throw new ParseException("Expected \"" + string + "\" to contain whitespace");
                 }
                 int level = Integer.parseInt(string.substring(0, spaceIndex));
-                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor, metaData);
+                AbstractGroup group = GroupsParser.fromString(string.substring(spaceIndex + 1), keywordSeparator, fileMonitor, metaData, userAndHost);
                 GroupTreeNode newNode = GroupTreeNode.fromGroup(group);
                 if (cursor == null) {
                     // create new root
@@ -92,7 +92,7 @@ public static GroupTreeNode importGroups(List<String> orderedData, Character key
      * @return New instance of the encoded group.
      * @throws ParseException If an error occurred and a group could not be created, e.g. due to a malformed regular expression.
      */
-    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData)
+    public static AbstractGroup fromString(String s, Character keywordSeparator, FileUpdateMonitor fileMonitor, MetaData metaData, String userAndHost)
             throws ParseException {
         if (s.startsWith(MetadataSerializationConfiguration.KEYWORD_GROUP_ID)) {
             return keywordGroupFromString(s, keywordSeparator);
@@ -119,13 +119,13 @@ public static AbstractGroup fromString(String s, Character keywordSeparator, Fil
             return automaticKeywordGroupFromString(s);
         }
         if (s.startsWith(MetadataSerializationConfiguration.TEX_GROUP_ID)) {
-            return texGroupFromString(s, fileMonitor, metaData);
+            return texGroupFromString(s, fileMonitor, metaData, userAndHost);
         }
 
         throw new ParseException("Unknown group: " + s);
     }
 
-    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor, MetaData metaData) throws ParseException {
+    private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor fileMonitor, MetaData metaData, String userAndHost) throws ParseException {
         QuotedStringTokenizer tok = new QuotedStringTokenizer(string.substring(MetadataSerializationConfiguration.TEX_GROUP_ID
                 .length()), MetadataSerializationConfiguration.GROUP_UNIT_SEPARATOR, MetadataSerializationConfiguration.GROUP_QUOTE_CHAR);
 
@@ -134,14 +134,14 @@ private static AbstractGroup texGroupFromString(String string, FileUpdateMonitor
         try {
             Path path = Path.of(tok.nextToken());
             try {
-                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData);
+                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), fileMonitor, metaData, userAndHost);
                 addGroupDetails(tok, newGroup);
                 return newGroup;
             } catch (IOException ex) {
                 // Problem accessing file -> create without file monitoring
                 LOGGER.warn("Could not access file {}. The group {} will not reflect changes to the aux file.", path, name, ex);
 
-                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), metaData);
+                TexGroup newGroup = TexGroup.create(name, context, path, new DefaultAuxParser(new BibDatabase()), metaData, userAndHost);
                 addGroupDetails(tok, newGroup);
                 return newGroup;
             }
@@ -187,7 +187,7 @@ private static AbstractGroup automaticKeywordGroupFromString(String string) {
      *
      * @param s The String representation obtained from KeywordGroup.toString()
      */
-    private static KeywordGroup keywordGroupFromString(String s, Character keywordSeparator) throws ParseException {
+    private static KeywordGroup keywordGroupFromString(String s, Character keywordSeparator) {
         if (!s.startsWith(MetadataSerializationConfiguration.KEYWORD_GROUP_ID)) {
             throw new IllegalArgumentException("KeywordGroup cannot be created from \"" + s + "\".");
         }
@@ -267,7 +267,7 @@ private static ExplicitGroup legacyExplicitGroupFromString(String input, Charact
     /**
      * Called only when created fromString.
      * JabRef used to store the entries of an explicit group in the serialization, e.g.
-     *  ExplicitGroup:GroupName\;0\;Key1\;Key2\;;
+     * ExplicitGroup:GroupName\;0\;Key1\;Key2\;;
      * This method exists for backwards compatibility.
      */
     private static void addLegacyEntryKeys(QuotedStringTokenizer tok, ExplicitGroup group) {

jablib/src/main/java/org/jabref/logic/importer/util/MetaDataParser.java

@@ -32,7 +32,6 @@
 import org.jabref.model.metadata.ContentSelectors;
 import org.jabref.model.metadata.MetaData;
 import org.jabref.model.metadata.SaveOrder;
-import org.jabref.model.metadata.UserHostInfo;
 import org.jabref.model.strings.StringUtil;
 import org.jabref.model.util.FileUpdateMonitor;
 
@@ -94,16 +93,16 @@ public static Optional<BibEntryType> parseCustomEntryType(String comment) {
     /**
      * Parses the given data map and returns a new resulting {@link MetaData} instance.
      */
-    public MetaData parse(Map<String, String> data, Character keywordSeparator) throws ParseException {
-        return parse(new MetaData(), data, keywordSeparator);
+    public MetaData parse(Map<String, String> data, Character keywordSeparator, String userAndHost) throws ParseException {
+        return parse(new MetaData(), data, keywordSeparator, userAndHost);
     }
 
     /**
      * Parses the data map and changes the given {@link MetaData} instance respectively.
      *
      * @return the given metaData instance (which is modified, too)
      */
-    public MetaData parse(MetaData metaData, Map<String, String> data, Character keywordSeparator) throws ParseException {
+    public MetaData parse(MetaData metaData, Map<String, String> data, Character keywordSeparator, String userAndHost) throws ParseException {
         CitationKeyPattern defaultCiteKeyPattern = CitationKeyPattern.NULL_CITATION_KEY_PATTERN;
         Map<EntryType, CitationKeyPattern> nonDefaultCiteKeyPatterns = new HashMap<>();
 
@@ -131,20 +130,7 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY_LATEX)) {
                 // The user-host string starts directly after FILE_DIRECTORY_LATEX + '-'
                 String userHostString = entry.getKey().substring(MetaData.FILE_DIRECTORY_LATEX.length() + 1);
-                Path path = Path.of(parseDirectory(entry.getValue())).normalize();
-
-                UserHostInfo userHostInfo = UserHostInfo.parse(userHostString);
-                String currentHost = org.jabref.logic.os.OS.getHostName();
-
-                if (!userHostInfo.host().isEmpty() && !userHostInfo.host().equals(currentHost)) {
-                    // If the host doesn't match the current host, we need to use the current user-host
-                    // This w that the LaTeX file directory is set for the current user on the current host
-                    LOGGER.warn("Host mismatch for LaTeX file directory: {} vs current host {}", userHostInfo.host(), currentHost);
-                    // We don't have access to the current user-host here, so we'll just store the path
-                    // The correct user-host will be used when the path is retrieved via the GUI
-                }
-
-                metaData.setLatexFileDirectory(userHostString, path);
+                metaData.setLatexFileDirectory(userHostString, parseDirectory(entry.getValue()));
             } else if (MetaData.SAVE_ACTIONS.equals(entry.getKey())) {
                 metaData.setSaveActions(fieldFormatterCleanupsParse(values));
             } else if (MetaData.DATABASE_TYPE.equals(entry.getKey())) {
@@ -160,7 +146,7 @@ public MetaData parse(MetaData metaData, Map<String, String> data, Character key
             } else if (MetaData.SAVE_ORDER_CONFIG.equals(entry.getKey())) {
                 metaData.setSaveOrder(SaveOrder.parse(values));
             } else if (MetaData.GROUPSTREE.equals(entry.getKey()) || MetaData.GROUPSTREE_LEGACY.equals(entry.getKey())) {
-                metaData.setGroups(GroupsParser.importGroups(values, keywordSeparator, fileMonitor, metaData));
+                metaData.setGroups(GroupsParser.importGroups(values, keywordSeparator, fileMonitor, metaData, userAndHost));
             } else if (MetaData.GROUPS_SEARCH_SYNTAX_VERSION.equals(entry.getKey())) {
                 Version version = Version.parse(getSingleItem(values));
                 metaData.setGroupSearchSyntaxVersion(version);

jablib/src/main/java/org/jabref/logic/preferences/JabRefCliPreferences.java

@@ -2411,7 +2411,8 @@ public ImportFormatPreferences getImportFormatPreferences() {
                 getFieldPreferences(),
                 getXmpPreferences(),
                 getDOIPreferences(),
-                getGrobidPreferences());
+                getGrobidPreferences(),
+                getFilePreferences());
     }
 
     // endregion

jablib/src/main/java/org/jabref/logic/shared/DBMSSynchronizer.java

@@ -57,10 +57,11 @@ public class DBMSSynchronizer implements DatabaseSynchronizer {
     private final FieldPreferences fieldPreferences;
     private final FileUpdateMonitor fileMonitor;
     private Optional<BibEntry> lastEntryChanged;
+    private final String userAndHost;
 
     public DBMSSynchronizer(BibDatabaseContext bibDatabaseContext, Character keywordSeparator,
                             FieldPreferences fieldPreferences,
-                            GlobalCitationKeyPatterns globalCiteKeyPattern, FileUpdateMonitor fileMonitor) {
+                            GlobalCitationKeyPatterns globalCiteKeyPattern, FileUpdateMonitor fileMonitor, String userAndHost) {
         this.bibDatabaseContext = Objects.requireNonNull(bibDatabaseContext);
         this.bibDatabase = bibDatabaseContext.getDatabase();
         this.metaData = bibDatabaseContext.getMetaData();
@@ -70,6 +71,7 @@ public DBMSSynchronizer(BibDatabaseContext bibDatabaseContext, Character keyword
         this.keywordSeparator = keywordSeparator;
         this.globalCiteKeyPattern = Objects.requireNonNull(globalCiteKeyPattern);
         this.lastEntryChanged = Optional.empty();
+        this.userAndHost = userAndHost;
     }
 
     /**
@@ -267,7 +269,7 @@ public void synchronizeLocalMetaData() {
         try {
             metaData.setEventPropagation(false);
             MetaDataParser parser = new MetaDataParser(fileMonitor);
-            parser.parse(metaData, dbmsProcessor.getSharedMetaData(), keywordSeparator);
+            parser.parse(metaData, dbmsProcessor.getSharedMetaData(), keywordSeparator, userAndHost);
             metaData.setEventPropagation(true);
         } catch (ParseException e) {
             LOGGER.error("Parse error", e);