Merge branch 'main' into update-gradle

Author: subhramit

CHANGELOG.md

@@ -27,6 +27,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 - We added an initial [cite as you write](https://retorque.re/zotero-better-bibtex/citing/cayw/) endpoint. [#13187](https://github.com/JabRef/jabref/issues/13187)
 - We added "copy preview as markdown" feature. [#12552](https://github.com/JabRef/jabref/issues/12552)
 - In case no citation relation information can be fetched, we show the data providers reason. [#13549](https://github.com/JabRef/jabref/pull/13549)
+- When relativizing file names, symlinks are now taken into account. [#12995](https://github.com/JabRef/jabref/issues/12995)
 - We added a new button for shortening the DOI near the DOI field in the general tab when viewing an entry. [#13639](https://github.com/JabRef/jabref/issues/13639)
 
 ### Changed

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

@@ -1,6 +1,3 @@
-/**
- *
- */
 package org.jabref.logic.importer.fileformat;
 
 import java.io.BufferedReader;

jablib/src/main/java/org/jabref/logic/openoffice/style/JStyleGetCitationMarker.java

@@ -141,11 +141,13 @@ private static String formatAuthorList(JStyle style,
         // emitAllAuthors == false means use "et al."
         boolean emitAllAuthors = (nAuthors <= maxAuthors) || (maxAuthors == -1);
 
-        int nAuthorsToEmit = emitAllAuthors
-                              ? nAuthors
-                              // If we use "et al." maxAuthorsBeforeEtAl also limits the
-                              // number of authors emitted.
-                              : Math.min(maxAuthorsBeforeEtAl, nAuthors);
+        int nAuthorsToEmit;
+        if (emitAllAuthors) {
+            nAuthorsToEmit = nAuthors;
+        } else {
+            // If we use "et al." maxAuthorsBeforeEtAl also limits the number of authors emitted.
+            nAuthorsToEmit = Math.min(maxAuthorsBeforeEtAl, nAuthors);
+        }
 
         if (nAuthorsToEmit >= 1) {
             stringBuilder.append(style.getAuthorsPartMarkupBefore());

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

@@ -144,7 +144,7 @@ public static Path addExtension(Path path, String extension) {
     /**
      * Looks for the unique directory, if any, different to the provided paths
      *
-     * @param paths List of paths as Strings
+     * @param paths       List of paths as Strings
      * @param comparePath The to be tested path
      */
     public static Optional<String> getUniquePathDirectory(List<String> paths, Path comparePath) {
@@ -153,15 +153,15 @@ public static Optional<String> getUniquePathDirectory(List<String> paths, Path c
         List<String> uniquePathParts = uniquePathSubstrings(paths);
         return uniquePathParts.stream()
                               .filter(part -> comparePath.toString().contains(part)
-                                              && !part.equals(fileName) && part.contains(File.separator))
+                                      && !part.equals(fileName) && part.contains(File.separator))
                               .findFirst()
                               .map(part -> part.substring(0, part.lastIndexOf(File.separator)));
     }
 
     /**
      * Looks for the shortest unique path of the in a list of paths
      *
-     * @param paths List of paths as Strings
+     * @param paths       List of paths as Strings
      * @param comparePath The to be shortened path
      */
     public static Optional<String> getUniquePathFragment(List<String> paths, Path comparePath) {
@@ -219,7 +219,7 @@ public static List<String> uniquePathSubstrings(List<String> paths) {
      * @param pathToSourceFile      Path Source file
      * @param pathToDestinationFile Path Destination file
      * @param replaceExisting       boolean Determines whether the copy goes on even if the file exists.
-     * @return boolean Whether the copy succeeded, or was stopped due to the file already existing.
+     * @return boolean Whether the copy succeeded or was stopped due to the file already existing.
      */
     public static boolean copyFile(Path pathToSourceFile, Path pathToDestinationFile, boolean replaceExisting) {
         // Check if the file already exists.
@@ -255,15 +255,40 @@ public static Path relativize(Path file, List<Path> directories) {
         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);
+                    }
+                }
+            }
         }
         return file;
     }
 
+    private static Optional<Path> toRealPath(Path path) {
+        if (Files.exists(path)) {
+            try {
+                return Optional.of(path.toRealPath());
+            } catch (IOException e) {
+                LOGGER.warn("Could not resolve real path for {}", path, e);
+                return Optional.empty();
+            }
+        } else {
+            return Optional.of(path.toAbsolutePath());
+        }
+    }
+
     /**
      * Converts an absolute file to a relative one, if possible. Returns the parameter file itself if no shortening is
      * possible.
@@ -342,8 +367,8 @@ public static String createFileNameFromPattern(BibDatabase database, BibEntry en
     /**
      * Determines directory name provided by an entry in a database
      *
-     * @param database        the database, where the entry is located
-     * @param entry           the entry to which the directory should be linked to
+     * @param database             the database, where the entry is located
+     * @param entry                the entry to which the directory should be linked to
      * @param directoryNamePattern the dirname pattern
      * @return a suggested dirName
      */
@@ -370,9 +395,9 @@ public static String createDirNameFromPattern(BibDatabase database, BibEntry ent
     public static Optional<Path> findSingleFileRecursively(String filename, Path rootDirectory) {
         try (Stream<Path> pathStream = Files.walk(rootDirectory)) {
             return pathStream
-                             .filter(Files::isRegularFile)
-                             .filter(f -> f.getFileName().toString().equals(filename))
-                             .findFirst();
+                    .filter(Files::isRegularFile)
+                    .filter(f -> f.getFileName().toString().equals(filename))
+                    .findFirst();
         } catch (UncheckedIOException | IOException ex) {
             LOGGER.error("Error trying to locate the file {} inside the directory {}", filename, rootDirectory, ex);
         }
@@ -410,9 +435,8 @@ public static Optional<Path> find(String fileName, List<Path> directories) {
     /**
      * Converts a relative filename to an absolute one, if necessary.
      *
-     * @param fileName the filename (e.g., a .pdf file), may contain path separators
+     * @param fileName  the filename (e.g., a .pdf file), may contain path separators
      * @param directory the directory which should be search starting point
-     *
      * @return an empty optional if the file does not exist, otherwise, the absolute path
      */
     public static Optional<Path> find(String fileName, Path directory) {
@@ -504,10 +528,9 @@ public static Path getInitialDirectory(BibDatabaseContext databaseContext, Path
     /**
      * Detect illegal characters in given filename.
      *
-     * @see org.jabref.logic.util.io.FileNameCleaner#cleanFileName
-     *
      * @param fileName the fileName to detect
      * @return Boolean whether there is an illegal name.
+     * @see org.jabref.logic.util.io.FileNameCleaner#cleanFileName
      */
     public static boolean detectBadFileName(String fileName) {
         // fileName could be a path, we want to check the fileName only (and don't care about the path)
@@ -579,9 +602,9 @@ public static String shortenFileName(String fileName, Integer maxLength) {
         numCharsAfterEllipsis = Math.min(numCharsAfterEllipsis, name.length() - numCharsBeforeEllipsis);
 
         return name.substring(0, numCharsBeforeEllipsis) +
-               ELLIPSIS +
-               name.substring(name.length() - numCharsAfterEllipsis) +
-               extension;
+                ELLIPSIS +
+                name.substring(name.length() - numCharsAfterEllipsis) +
+                extension;
     }
 
     public static boolean isCharLegal(char c) {

jablib/src/main/resources/l10n/JabRef_ar.properties

@@ -823,3 +823,4 @@ File\ not\ found=لم يتم العثور على الملف
 
 # Entry Table Customization Dialog
 
+# Git

jablib/src/main/resources/l10n/JabRef_da.properties

@@ -1103,3 +1103,4 @@ Path\ to\ %0=Sti til %0
 
 # Entry Table Customization Dialog
 
+# Git

jablib/src/main/resources/l10n/JabRef_de.properties

@@ -3037,3 +3037,4 @@ Saved\ %0.=%0 gespeichert.
 Open\ all\ linked\ files=Alle verknüpften Dateien öffnen
 Cancel\ file\ opening=Öffnen der Datei abbrechen
 
+# Git

jablib/src/main/resources/l10n/JabRef_el.properties

@@ -1843,3 +1843,4 @@ Related\ articles=Σχετικά άρθρα
 
 # Entry Table Customization Dialog
 
+# Git

jablib/src/main/resources/l10n/JabRef_es.properties

@@ -2507,3 +2507,4 @@ Warning\:\ The\ selected\ directory\ is\ not\ a\ valid\ directory.=Atención\: e
 
 # Entry Table Customization Dialog
 
+# Git

jablib/src/main/resources/l10n/JabRef_fa.properties

@@ -769,3 +769,4 @@ Auto\ complete\ enabled.=تکمیل خودکار غیرفعال شد.
 
 # Entry Table Customization Dialog
 
+# Git