Fixes #13274: Allow cygwin-paths on Windows

CHANGELOG.md

@@ -12,6 +12,7 @@ Note that this project **does not** adhere to [Semantic Versioning](https://semv
 ### Added
 
 - We introduced a settings parameters to manage citations' relations local storage time-to-live with a default value set to 30 days. [#11189](https://github.com/JabRef/jabref/issues/11189)
+- We added support for Cygwin-file paths on a Windows Operating System. [#13274](https://github.com/JabRef/jabref/issues/13274)
 
 ### Changed
 

jabkit/src/main/java/module-info.java

@@ -3,6 +3,7 @@
 
     requires info.picocli;
     opens org.jabref.cli;
+    opens org.jabref.cli.converter;
 
     requires transitive org.jspecify;
     requires java.prefs;
@@ -22,7 +23,6 @@
     requires org.tinylog.impl;
 
     requires java.xml;
-
     // region: other libraries (alphabetically)
     requires io.github.adr;
     // endregion

jabkit/src/main/java/org/jabref/cli/CheckConsistency.java

@@ -3,9 +3,11 @@
 import java.io.IOException;
 import java.io.OutputStreamWriter;
 import java.io.Writer;
+import java.nio.file.Path;
 import java.util.List;
 import java.util.Optional;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
@@ -33,8 +35,8 @@ class CheckConsistency implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = {"--input"}, description = "Input BibTeX file", required = true)
-    private String inputFile;
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
     @Option(names = {"--output-format"}, description = "Output format: txt or csv", defaultValue = "txt")
     private String outputFormat;

jabkit/src/main/java/org/jabref/cli/CheckIntegrity.java

@@ -1,7 +1,8 @@
 package org.jabref.cli;
 
-import java.io.File;
+import java.nio.file.Path;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.l10n.Localization;
 
 import static picocli.CommandLine.Command;
@@ -15,11 +16,11 @@ class CheckIntegrity implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Parameters(index = "0", description = "BibTeX file to check", arity = "0..1")
-    private File inputFile;
+    @Parameters(index = "0", converter = CygWinPathConverter.class, description = "BibTeX file to check", arity = "0..1")
+    private Path inputFile;
 
-    @Option(names = {"--input"}, description = "Input BibTeX file")
-    private File inputOption;
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file")
+    private Path inputOption;
 
     @Option(names = {"--output-format"}, description = "Output format: txt or csv")
     private String outputFormat = "txt"; // FixMe: Default value?

jabkit/src/main/java/org/jabref/cli/Convert.java

@@ -8,6 +8,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SaveException;
@@ -36,13 +37,13 @@ public class Convert implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = {"--input"}, description = "Input file", required = true)
-    private String inputFile;
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input file", required = true)
+    private Path inputFile;
 
     @Option(names = {"--input-format"}, description = "Input format")
     private String inputFormat;
 
-    @Option(names = {"--output"}, description = "Output file")
+    @Option(names = {"--output"}, converter = CygWinPathConverter.class, description = "Output file")
     private Path outputFile;
 
     @Option(names = {"--output-format"}, description = "Output format")

jabkit/src/main/java/org/jabref/cli/Pseudonymize.java

@@ -5,6 +5,7 @@
 import java.nio.file.Path;
 import java.util.Optional;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pseudonymization.Pseudonymization;
@@ -34,11 +35,11 @@ public class Pseudonymize implements Runnable {
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
     @ADR(45)
-    @Option(names = {"--input"}, description = "BibTeX file to be pseudonymized", required = true)
-    private String inputFile;
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "BibTeX file to be pseudonymized", required = true)
+    private Path inputPath;
 
-    @Option(names = {"--output"}, description = "Output pseudo-bib file")
-    private String outputFile;
+    @Option(names = {"--output"}, converter = CygWinPathConverter.class, description = "Output pseudo-bib file")
+    private Path outputFile;
 
     @Option(names = {"--key"}, description = "Output pseudo-keys file")
     private String keyFile;
@@ -48,24 +49,23 @@ public class Pseudonymize implements Runnable {
 
     @Override
     public void run() {
-        Path inputPath = Path.of(inputFile);
-        String fileName = FileUtil.getBaseName(inputFile);
-        Path pseudoBibPath = resolveOutputPath(outputFile, inputPath, fileName + PSEUDO_SUFFIX + BIB_EXTENSION);
+        String fileName = FileUtil.getBaseName(inputPath);
+        Path pseudoBibPath = resolveOutputPath(outputFile.toString(), inputPath, fileName + PSEUDO_SUFFIX + BIB_EXTENSION);
         Path pseudoKeyPath = resolveOutputPath(keyFile, inputPath, fileName + PSEUDO_SUFFIX + CSV_EXTENSION);
 
         Optional<ParserResult> parserResult = ArgumentProcessor.importFile(
-                inputFile,
+                inputPath,
                 "bibtex",
                 argumentProcessor.cliPreferences,
                 sharedOptions.porcelain);
 
         if (parserResult.isEmpty()) {
-            System.out.println(Localization.lang("Unable to open file '%0'.", inputFile));
+            System.out.println(Localization.lang("Unable to open file '%0'.", inputPath));
             return;
         }
 
         if (parserResult.get().isInvalid()) {
-            System.out.println(Localization.lang("Input file '%0' is invalid and could not be parsed.", inputFile));
+            System.out.println(Localization.lang("Input file '%0' is invalid and could not be parsed.", inputPath));
             return;
         }
 

jabkit/src/main/java/org/jabref/cli/Search.java

@@ -8,6 +8,7 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.CygWinPathConverter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SaveException;
@@ -46,10 +47,10 @@ class Search implements Runnable {
     @Option(names = {"--query"}, description = "Search query", required = true)
     private String query;
 
-    @Option(names = {"--input"}, description = "Input BibTeX file", required = true)
-    private String inputFile;
+    @Option(names = {"--input"}, converter = CygWinPathConverter.class, description = "Input BibTeX file", required = true)
+    private Path inputFile;
 
-    @Option(names = {"--output"}, description = "Output file")
+    @Option(names = {"--output"}, converter = CygWinPathConverter.class, description = "Output file")
     private Path outputFile;
 
     @Option(names = {"--output-format"}, description = "Output format: bib, txt, etc.")

jabkit/src/main/java/org/jabref/cli/converter/CygWinPathConverter.java

@@ -0,0 +1,16 @@
+package org.jabref.cli.converter;
+
+import java.nio.file.Path;
+
+import org.jabref.logic.util.io.FileUtil;
+
+import picocli.CommandLine;
+
+/// Converts Cygwin-style paths to Path objects using platform-specific formatting.
+public class CygWinPathConverter implements CommandLine.ITypeConverter<Path> {
+
+    @Override
+    public Path convert(String path) {
+        return FileUtil.convertCygwinPathToWindows(path);
+    }
+}

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

@@ -25,6 +25,7 @@
 import org.jabref.logic.FilePreferences;
 import org.jabref.logic.citationkeypattern.BracketedPattern;
 import org.jabref.logic.layout.format.RemoveLatexCommandsFormatter;
+import org.jabref.logic.os.OS;
 import org.jabref.logic.util.StandardFileType;
 import org.jabref.model.database.BibDatabase;
 import org.jabref.model.database.BibDatabaseContext;
@@ -49,6 +50,9 @@ public class FileUtil {
     private static final String ELLIPSIS = "...";
     private static final int ELLIPSIS_LENGTH = ELLIPSIS.length();
     private static final RemoveLatexCommandsFormatter REMOVE_LATEX_COMMANDS_FORMATTER = new RemoveLatexCommandsFormatter();
+    private static final String CYGDRIVE_PREFIX = "/cygdrive/";
+    private static final String MNT_PREFIX = "/mnt/";
+    private static final Pattern ROOT_DRIVE_PATTERN = Pattern.compile("^/[a-zA-Z]/.*");
 
     /**
      * MUST ALWAYS BE A SORTED ARRAY because it is used in a binary search
@@ -589,4 +593,47 @@ public static String shortenFileName(String fileName, Integer maxLength) {
     public static boolean isCharLegal(char c) {
         return Arrays.binarySearch(ILLEGAL_CHARS, c) < 0;
     }
+
+    /// Converts a Cygwin-style file path to a Windows-style path if the operating system is Windows.
+    ///
+    /// Supported formats:
+    /// - /cygdrive/c/Users/... → C:\Users\...
+    /// - /mnt/c/Users/...      → C:\Users\...
+    /// - /c/Users/...          → C:\Users\...
+    ///
+    /// @param filePath the input file path
+    /// @return the converted path if running on Windows and path is in Cygwin format; otherwise, returns the original path
+    public static Path convertCygwinPathToWindows(String filePath) {
+        if (filePath == null) {
+            return null;
+        }
+
+        if (!OS.WINDOWS) {
+            return Path.of(filePath);
+        }
+
+        if (filePath.startsWith(MNT_PREFIX) && filePath.length() > 5) {
+            return buildWindowsPathWithDriveLetterIndex(filePath, 5);
+        }
+
+        if (filePath.startsWith(CYGDRIVE_PREFIX) && filePath.length() > 10) {
+            return buildWindowsPathWithDriveLetterIndex(filePath, 10);
+        }
+
+        if (ROOT_DRIVE_PATTERN.matcher(filePath).matches()) {
+            return buildWindowsPathWithDriveLetterIndex(filePath, 1);
+        }
+
+        return Path.of(filePath);
+    }
+
+    /// Builds a Windows-style path from a Cygwin-style path using a known prefix index.
+    /// @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) {
+        String driveLetter = path.substring(letterIndex, letterIndex + 1).toUpperCase();
+        String windowsPath = path.substring(letterIndex + 1).replace("/", "\\\\");
+        return Path.of(driveLetter + ":" + windowsPath);
+    }
 }

jablib/src/test/java/org/jabref/logic/util/io/FileUtilTest.java

@@ -21,6 +21,7 @@
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
 import org.junit.jupiter.api.condition.DisabledOnOs;
+import org.junit.jupiter.api.condition.EnabledOnOs;
 import org.junit.jupiter.api.io.TempDir;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.Arguments;
@@ -518,4 +519,20 @@ void illegalPaths(String fileName) {
     void shortenFileName(String expected, String fileName, Integer maxLength) {
         assertEquals(expected, FileUtil.shortenFileName(fileName, maxLength));
     }
+
+    @EnabledOnOs(value = org.junit.jupiter.api.condition.OS.WINDOWS)
+    @ParameterizedTest
+    @ValueSource(strings = {"/c/Users/username/Downloads/test.bib",
+            "/cygdrive/c/Users/username/Downloads/test.bib",
+            "/mnt/c/Users/username/Downloads/test.bib"})
+    void convertCygwinPathToWindowsShouldConvertToWindowsFormatWhenRunningOnWindows(String filePath) {
+        assertEquals(Path.of("C:\\\\Users\\\\username\\\\Downloads\\\\test.bib"), FileUtil.convertCygwinPathToWindows(filePath));
+    }
+
+    @DisabledOnOs(value = org.junit.jupiter.api.condition.OS.WINDOWS, disabledReason = "Test in others operational systems")
+    @ParameterizedTest
+    @ValueSource(strings = {"/home/username/Downloads/test.bib"})
+    void convertCygwinPathToWindowsShouldReturnOriginalFilePathWhenRunningOnWindows(String filePath) {
+        assertEquals(Path.of(filePath), FileUtil.convertCygwinPathToWindows(filePath));
+    }
 }