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;
@@ -20,9 +21,8 @@
     requires org.tinylog.api;
     requires org.tinylog.api.slf4j;
     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

@@ -6,6 +6,7 @@
 import java.util.List;
 import java.util.Optional;
 
+import org.jabref.cli.converter.StringPathConverter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.quality.consistency.BibliographyConsistencyCheck;
@@ -33,7 +34,7 @@ class CheckConsistency implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = {"--input"}, description = "Input BibTeX file", required = true)
+    @Option(names = {"--input"}, converter = StringPathConverter.class, description = "Input BibTeX file", required = true)
     private String inputFile;
 
     @Option(names = {"--output-format"}, description = "Output format: txt or csv", defaultValue = "txt")

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

@@ -2,6 +2,7 @@
 
 import java.io.File;
 
+import org.jabref.cli.converter.FilePathConverter;
 import org.jabref.logic.l10n.Localization;
 
 import static picocli.CommandLine.Command;
@@ -15,10 +16,10 @@ class CheckIntegrity implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Parameters(index = "0", description = "BibTeX file to check", arity = "0..1")
+    @Parameters(index = "0", converter = FilePathConverter.class, description = "BibTeX file to check", arity = "0..1")
     private File inputFile;
 
-    @Option(names = {"--input"}, description = "Input BibTeX file")
+    @Option(names = {"--input"}, converter = FilePathConverter.class, description = "Input BibTeX file")
     private File inputOption;
 
     @Option(names = {"--output-format"}, description = "Output format: txt or csv")

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

@@ -8,6 +8,8 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.PathConverter;
+import org.jabref.cli.converter.StringPathConverter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SaveException;
@@ -36,13 +38,13 @@ public class Convert implements Runnable {
     @Mixin
     private ArgumentProcessor.SharedOptions sharedOptions = new ArgumentProcessor.SharedOptions();
 
-    @Option(names = {"--input"}, description = "Input file", required = true)
+    @Option(names = {"--input"}, converter = StringPathConverter.class, description = "Input file", required = true)
     private String inputFile;
 
     @Option(names = {"--input-format"}, description = "Input format")
     private String inputFormat;
 
-    @Option(names = {"--output"}, description = "Output file")
+    @Option(names = {"--output"}, converter = PathConverter.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.StringPathConverter;
 import org.jabref.logic.importer.ParserResult;
 import org.jabref.logic.l10n.Localization;
 import org.jabref.logic.pseudonymization.Pseudonymization;
@@ -34,10 +35,10 @@ 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)
+    @Option(names = {"--input"}, converter = StringPathConverter.class, description = "BibTeX file to be pseudonymized", required = true)
     private String inputFile;
 
-    @Option(names = {"--output"}, description = "Output pseudo-bib file")
+    @Option(names = {"--output"}, converter = StringPathConverter.class, description = "Output pseudo-bib file")
     private String outputFile;
 
     @Option(names = {"--key"}, description = "Output pseudo-keys file")

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

@@ -8,6 +8,8 @@
 import javax.xml.parsers.ParserConfigurationException;
 import javax.xml.transform.TransformerException;
 
+import org.jabref.cli.converter.PathConverter;
+import org.jabref.cli.converter.StringPathConverter;
 import org.jabref.logic.exporter.Exporter;
 import org.jabref.logic.exporter.ExporterFactory;
 import org.jabref.logic.exporter.SaveException;
@@ -46,10 +48,10 @@ class Search implements Runnable {
     @Option(names = {"--query"}, description = "Search query", required = true)
     private String query;
 
-    @Option(names = {"--input"}, description = "Input BibTeX file", required = true)
+    @Option(names = {"--input"}, converter = StringPathConverter.class, description = "Input BibTeX file", required = true)
     private String inputFile;
 
-    @Option(names = {"--output"}, description = "Output file")
+    @Option(names = {"--output"}, converter = PathConverter.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/FilePathConverter.java

@@ -0,0 +1,17 @@
+package org.jabref.cli.converter;
+
+import java.io.File;
+
+import org.jabref.logic.util.io.FileUtil;
+
+import picocli.CommandLine;
+
+/// Converts Cygwin-style paths to File objects using platform-specific formatting.
+public class FilePathConverter implements CommandLine.ITypeConverter<File> {
+
+    @Override
+    public File convert(String filePath) {
+        String normalizedPath = FileUtil.convertCygwinPathToWindows(filePath);
+        return new File(normalizedPath);
+    }
+}

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

@@ -0,0 +1,18 @@
+package org.jabref.cli.converter;
+
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+import org.jabref.logic.util.io.FileUtil;
+
+import picocli.CommandLine;
+
+/// Converts Cygwin-style paths to Path objects using platform-specific formatting.
+public class PathConverter implements CommandLine.ITypeConverter<Path> {
+
+    @Override
+    public Path convert(String value) {
+        String normalizedPath = FileUtil.convertCygwinPathToWindows(value);
+        return Paths.get(normalizedPath);
+    }
+}

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

@@ -0,0 +1,15 @@
+package org.jabref.cli.converter;
+
+import org.jabref.logic.util.io.FileUtil;
+
+import picocli.CommandLine;
+
+ /// Converts Cygwin-style paths to the standard format of the operating system.
+ /// Especially useful on Windows to handle paths like /c/Users/... -> C:\Users\...
+public class StringPathConverter implements CommandLine.ITypeConverter<String> {
+
+    @Override
+    public String convert(String filePath) {
+        return FileUtil.convertCygwinPathToWindows(filePath);
+    }
+}

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;
@@ -589,4 +590,39 @@ 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 String convertCygwinPathToWindows(String filePath) {
+        if (!OS.WINDOWS || filePath == null) {
+            return filePath;
+        }
+
+        if (filePath.startsWith("/mnt/") && filePath.length() > 5) {
+            String driveLetter = filePath.substring(5, 6).toUpperCase();
+            String path = filePath.substring(6).replace("/", "\\\\");
+            return driveLetter + ":" + path;
+        }
+
+        if (filePath.startsWith("/cygdrive/") && filePath.length() > 10) {
+            String driveLetter = filePath.substring(10, 11).toUpperCase();
+            String path = filePath.substring(11).replace("/", "\\\\");
+            return driveLetter + ":" + path;
+        }
+
+        if (filePath.matches("^/[a-zA-Z]/.*")) {
+            String driveLetter = filePath.substring(1, 2).toUpperCase();
+            String path = filePath.substring(2).replace("/", "\\\\");
+            return driveLetter + ":" + path;
+        }
+
+        return filePath;
+    }
 }

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("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(filePath, FileUtil.convertCygwinPathToWindows(filePath));
+    }
 }