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

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.")));
@@ -485,9 +485,10 @@ 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);

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;
 
@@ -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())) {

jablib/src/main/java/org/jabref/logic/util/io/FileUtil.java

@@ -32,6 +32,7 @@
 import org.jabref.model.entry.LinkedFile;
 import org.jabref.model.entry.field.StandardField;
 
+import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -146,9 +147,9 @@ public static Path addExtension(Path path, String extension) {
     }
 
     /// Looks for the shortest unique path of the parent directory in the list of paths
+    ///
     /// @param paths       List of paths as Strings
     /// @param comparePath The to be tested path
-    ///
     /// @return Optional.empty() if the paths are disjoint
     public static Optional<String> getUniquePathDirectory(List<String> paths, Path comparePath) {
         // Difference to getUniquePathFragment: We want the parent directory, so we cut off the last path fragment
@@ -161,7 +162,6 @@ public static Optional<String> getUniquePathDirectory(List<String> paths, Path c
     ///
     /// @param paths       List of paths as Strings
     /// @param comparePath The to be shortened path
-    ///
     /// @return Shortest unique path fragment (if exists) - Optional.empty() if the paths are disjoint
     public static Optional<String> getUniquePathFragment(List<String> paths, Path comparePath) {
         return uniquePathSubstrings(paths).stream()
@@ -251,23 +251,35 @@ public static boolean copyFile(Path pathToSourceFile, Path pathToDestinationFile
      * @param directories directories to check
      */
     public static Path relativize(Path file, List<Path> directories) {
+        return relativize(file, directories, null);
+    }
+
+    /**
+     *
+     * @param file The file to relativize, can be already relative or absolute
+     * @param directories File directories to resolve against
+     * @param baseDirForRelative Base directory for resolve a relative file path against first (e.g. "." )
+     * @return Relative path to the file, or the original file if it is already relative or thw
+     */
+    public static Path relativize(Path file, List<Path> directories, @Nullable Path baseDirForRelative) {
         if (!file.isAbsolute()) {
             return file;
         }
-        Optional<Path> realFileOpt = toRealPath(file);
 
         for (Path directory : directories) {
             if (file.startsWith(directory)) {
                 return directory.relativize(file);
             }
-
-            if (realFileOpt.isPresent()) {
-                Optional<Path> realDirOpt = toRealPath(directory);
-                if (realDirOpt.isPresent()) {
-                    Path realFile = realFileOpt.get();
-                    Path realDir = realDirOpt.get();
-                    if (realFile.startsWith(realDir)) {
-                        return realDir.relativize(realFile);
+            if (baseDirForRelative != null) {
+                Optional<Path> realFileOpt = toRealPath(file);
+                if (realFileOpt.isPresent()) {
+                    Optional<Path> realDirOpt = toRealPath(directory);
+                    if (realDirOpt.isPresent()) {
+                        Path realFile = realFileOpt.get();
+                        Path realDir = realDirOpt.get();
+                        if (realFile.startsWith(realDir)) {
+                            return realDir.relativize(realFile);
+                        }
                     }
                 }
             }
@@ -644,7 +656,8 @@ public static Path convertCygwinPathToWindows(String filePath) {
     }
 
     /// Builds a Windows-style path from a Cygwin-style path using a known prefix index.
-    /// @param path the input file path
+    ///
+    /// @param path        the input file path
     /// @param letterIndex the index driver letter, zero-based indexing
     /// @return a windows-style path
     private static Path buildWindowsPathWithDriveLetterIndex(String path, int letterIndex) {

jablib/src/main/java/org/jabref/model/metadata/MetaData.java

@@ -63,7 +63,7 @@ public class MetaData {
     private final EventBus eventBus = new EventBus();
     private final Map<EntryType, String> citeKeyPatterns = new HashMap<>(); // <BibType, Pattern>
     private final Map<String, String> userFileDirectory = new HashMap<>(); // <User, FilePath>
-    private final Map<String, Path> latexFileDirectory = new HashMap<>(); // <User-Host, FilePath>
+    private final Map<String, String> latexFileDirectory = new HashMap<>(); // <User-Host, FilePath>
 
     private final ObjectProperty<GroupTreeNode> groupsRoot = new SimpleObjectProperty<>(null);
     private final OptionalBinding<GroupTreeNode> groupsRootBinding = new OptionalWrapper<>(groupsRoot);
@@ -261,29 +261,10 @@ public void clearUserFileDirectory(String user) {
     }
 
     public Optional<Path> getLatexFileDirectory(String userHostString) {
-        // First try to get the LaTeX file directory for the exact user-host
-        Path path = latexFileDirectory.get(userHostString);
-        if (path != null) {
-            return Optional.of(path);
-        }
-
-        // If not found, try to find a LaTeX file directory for the same host
-        // This handles the case where a file is moved between hosts with different users
-        UserHostInfo requestedUserHost = UserHostInfo.parse(userHostString);
-        if (!requestedUserHost.host().isEmpty()) {
-            for (Map.Entry<String, Path> entry : latexFileDirectory.entrySet()) {
-                UserHostInfo entryUserHost = UserHostInfo.parse(entry.getKey());
-                if (entryUserHost.hasSameHost(requestedUserHost)) {
-                    // Found a LaTeX file directory for the same host, return it
-                    return Optional.of(entry.getValue());
-                }
-            }
-        }
-
-        return Optional.empty();
+        return Optional.ofNullable(latexFileDirectory.get(userHostString)).map(Path::of);
     }
 
-    public void setLatexFileDirectory(@NonNull String userHostString, @NonNull Path path) {
+    public void setLatexFileDirectory(@NonNull String userHostString, @NonNull String path) {
         latexFileDirectory.put(userHostString, path);
         postChange();
     }
@@ -380,7 +361,7 @@ public Map<String, String> getUserFileDirectories() {
         return Collections.unmodifiableMap(userFileDirectory);
     }
 
-    public Map<String, Path> getLatexFileDirectories() {
+    public Map<String, String> getLatexFileDirectories() {
         return Collections.unmodifiableMap(latexFileDirectory);
     }
 

jablib/src/test/java/org/jabref/logic/exporter/BibDatabaseWriterTest.java

@@ -810,7 +810,7 @@ void writeProtectedFlag() throws IOException {
     void writeFileDirectories() throws IOException {
         metaData.setLibrarySpecificFileDirectory("\\Literature\\");
         metaData.setUserFileDirectory("defaultOwner-user", "D:\\Documents");
-        metaData.setLatexFileDirectory("defaultOwner-user", Path.of("D:\\Latex"));
+        metaData.setLatexFileDirectory("defaultOwner-user", "D:\\Latex");
 
         databaseWriter.savePartOfDatabase(bibtexContext, List.of());
 

jablib/src/test/java/org/jabref/model/groups/TexGroupTest.java

@@ -52,7 +52,7 @@ void containsReturnsTrueForEntryNotInAux() throws IOException, URISyntaxExceptio
     void getFilePathReturnsRelativePath() throws URISyntaxException {
         Path auxFile = Path.of(TexGroupTest.class.getResource("paper.aux").toURI());
         String user = "Darwin";
-        metaData.setLatexFileDirectory(user, auxFile.getParent());
+        metaData.setLatexFileDirectory(user, auxFile.getParent().toString());
         TexGroup group = new TexGroup("paper", GroupHierarchyType.INDEPENDENT, auxFile, new DefaultAuxParser(new BibDatabase()), new DummyFileUpdateMonitor(), metaData, user);
 
         assertEquals("paper.aux", group.getFilePath().toString());

jablib/src/test/java/org/jabref/model/metadata/MetaDataTest.java

@@ -1,13 +1,11 @@
 package org.jabref.model.metadata;
 
-import java.nio.file.Path;
 import java.util.Optional;
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
-import static org.junit.jupiter.api.Assertions.assertTrue;
 
 class MetaDataTest {
 
@@ -22,70 +20,9 @@ void setUp() {
     void emptyGroupsIfNotSet() {
         assertEquals(Optional.empty(), metaData.getGroups());
     }
-    
+
     @Test
     void getLatexFileDirectoryReturnsEmptyWhenNotSet() {
         assertEquals(Optional.empty(), metaData.getLatexFileDirectory("user-host"));
     }
-
-    @Test
-    void getLatexFileDirectoryReturnsPathForExactUserHostMatch() {
-        String userHost = "user-host";
-        Path expectedPath = Path.of("/path/to/latex");
-        metaData.setLatexFileDirectory(userHost, expectedPath);
-
-        Optional<Path> result = metaData.getLatexFileDirectory(userHost);
-
-        assertTrue(result.isPresent());
-        assertEquals(expectedPath, result.get());
-    }
-
-    @Test
-    void getLatexFileDirectoryReturnsPathForSameHostButDifferentUser() {
-        String originalUserHost = "user1-host";
-        String newUserHost = "user2-host";
-        Path expectedPath = Path.of("/path/to/latex");
-        metaData.setLatexFileDirectory(originalUserHost, expectedPath);
-
-        Optional<Path> result = metaData.getLatexFileDirectory(newUserHost);
-
-        assertTrue(result.isPresent());
-        assertEquals(expectedPath, result.get());
-    }
-
-    @Test
-    void getLatexFileDirectoryReturnsEmptyForDifferentHost() {
-        String userHost1 = "user-host1";
-        Path path1 = Path.of("/path/for/host1");
-        metaData.setLatexFileDirectory(userHost1, path1);
-
-        Optional<Path> result = metaData.getLatexFileDirectory("user-host2");
-
-        assertEquals(Optional.empty(), result);
-    }
-
-    @Test
-    void getLatexFileDirectoryHandlesMultipleEntriesCorrectly() {
-        String userHost1 = "user1-host1";
-        String userHost2 = "user2-host2";
-        String userHost3 = "user3-host1";
-
-        Path path1 = Path.of("/path/for/host1/user1");
-        Path path2 = Path.of("/path/for/host2");
-        Path path3 = Path.of("/path/for/host1/user3");
-
-        metaData.setLatexFileDirectory(userHost1, path1);
-        metaData.setLatexFileDirectory(userHost2, path2);
-        metaData.setLatexFileDirectory(userHost3, path3);
-
-        assertEquals(path1, metaData.getLatexFileDirectory(userHost1).get());
-        assertEquals(path2, metaData.getLatexFileDirectory(userHost2).get());
-        assertEquals(path3, metaData.getLatexFileDirectory(userHost3).get());
-
-        String newUserOnHost1 = "newuser-host1";
-        Optional<Path> resultForNewUser = metaData.getLatexFileDirectory(newUserOnHost1);
-        assertTrue(resultForNewUser.isPresent());
-
-        assertEquals(Optional.empty(), metaData.getLatexFileDirectory("user-differenthost"));
-    }
 }