Fix expansion of bracketed expressions in RegExpBasedFileFinder (#7338)

CHANGELOG.md

@@ -34,6 +34,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where the "Find unlinked files" dialog would freeze JabRef on importing. [#7205](https://github.com/JabRef/jabref/issues/7205)
 - We fixed an issue where the "Find unlinked files" would stop importing when importing a single file failed. [#7206](https://github.com/JabRef/jabref/issues/7206)
 - We fixed an issue where an exception would be displayed for previewing and preferences when a custom theme has been configured but is missing [#7177](https://github.com/JabRef/jabref/issues/7177)
+- We fixed an issue where the regex based file search miss-interpreted specific symbols [#4342](https://github.com/JabRef/jabref/issues/4342)
 - We fixed an issue where the Harvard RTF exporter used the wrong default file extension. [4508](https://github.com/JabRef/jabref/issues/4508)
 - We fixed an issue where the Harvard RTF exporter did not use the new authors formatter and therefore did not export "organization" authors correctly. [4508](https://github.com/JabRef/jabref/issues/4508)
 - We fixed an issue where the field `urldate` was not exported to the corresponding fields `YearAccessed`, `MonthAccessed`, `DayAccessed` in MS Office XML [#7354](https://github.com/JabRef/jabref/issues/7354)

src/main/java/org/jabref/logic/citationkeypattern/BracketedPattern.java

@@ -187,7 +187,7 @@ public static String expandBrackets(String pattern, Character keywordDelimiter,
      * @param database         The {@link BibDatabase} for field resolving. May be null.
      * @return a function accepting a bracketed expression and returning the result of expanding it
      */
-    private static Function<String, String> expandBracketContent(Character keywordDelimiter, BibEntry entry, BibDatabase database) {
+    public static Function<String, String> expandBracketContent(Character keywordDelimiter, BibEntry entry, BibDatabase database) {
         return (String bracket) -> {
             String expandedPattern;
             List<String> fieldParts = parseFieldAndModifiers(bracket);

src/main/java/org/jabref/logic/util/io/RegExpBasedFileFinder.java

@@ -8,17 +8,16 @@
 import java.nio.file.Path;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 import java.util.function.BiPredicate;
+import java.util.function.Function;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.regex.PatternSyntaxException;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.jabref.logic.citationkeypattern.BracketedPattern;
-import org.jabref.model.database.BibDatabase;
 import org.jabref.model.entry.BibEntry;
 import org.jabref.model.strings.StringUtil;
 
@@ -28,7 +27,6 @@ class RegExpBasedFileFinder implements FileFinder {
 
     private static final Pattern ESCAPE_PATTERN = Pattern.compile("([^\\\\])\\\\([^\\\\])");
 
-    private static final Pattern SQUARE_BRACKETS_PATTERN = Pattern.compile("\\[.*?\\]");
     private final String regExp;
     private final Character keywordDelimiter;
 
@@ -41,21 +39,41 @@ class RegExpBasedFileFinder implements FileFinder {
     }
 
     /**
-     * Takes a string that contains bracketed expression and expands each of these using getFieldAndFormat.
-     * <p>
-     * Unknown Bracket expressions are silently dropped.
+     * Creates a Pattern that matches the file name corresponding to the last element of {@code fileParts} with any bracketed patterns expanded.
+     *
+     * @throws IOException throws an IOException if a PatternSyntaxException occurs
      */
-    public static String expandBrackets(String bracketString, BibEntry entry, BibDatabase database,
-                                        Character keywordDelimiter) {
-        Matcher matcher = SQUARE_BRACKETS_PATTERN.matcher(bracketString);
-        StringBuilder expandedStringBuffer = new StringBuilder();
-        while (matcher.find()) {
-            String replacement = BracketedPattern.expandBrackets(matcher.group(), keywordDelimiter, entry, database);
-            matcher.appendReplacement(expandedStringBuffer, replacement);
+    private Pattern createFileNamePattern(String[] fileParts, String extensionRegExp, BibEntry entry) throws IOException {
+        // Protect the extension marker so that it isn't treated as a bracketed pattern
+        String filePart = fileParts[fileParts.length - 1].replace("[extension]", EXT_MARKER);
+
+        // We need to supply a custom function to deal with the content of a bracketed expression and expandBracketContent is the default function
+        Function<String, String> expandBracket = BracketedPattern.expandBracketContent(keywordDelimiter, entry, null);
+        // but, we want to post-process the expanded content so that it can be used as a regex for finding a file name
+        Function<String, String> bracketToFileNameRegex = expandBracket.andThen(RegExpBasedFileFinder::toFileNameRegex);
+
+        String expandedBracketAsFileNameRegex = BracketedPattern.expandBrackets(filePart, bracketToFileNameRegex);
+
+        String fileNamePattern = expandedBracketAsFileNameRegex
+                .replaceAll(EXT_MARKER, extensionRegExp) // Replace the extension marker
+                .replaceAll("\\\\\\\\", "\\\\");
+        try {
+            return Pattern.compile('^' + fileNamePattern + '$', Pattern.CASE_INSENSITIVE);
+        } catch (PatternSyntaxException e) {
+            throw new IOException(String.format("There is a syntax error in the regular expression %s used to search for files", fileNamePattern), e);
         }
-        matcher.appendTail(expandedStringBuffer);
+    }
 
-        return expandedStringBuffer.toString();
+    /**
+     * Helper method for both exact matching (if the file name were not created by JabRef) and cleaned file name matching.
+     *
+     * @param expandedContent the expanded content of a bracketed expression
+     * @return a String representation of a regex matching the expanded content and the expanded content cleaned for file name use
+     */
+    private static String toFileNameRegex(String expandedContent) {
+        var cleanedContent = FileNameCleaner.cleanFileName(expandedContent);
+        return expandedContent.equals(cleanedContent) ? Pattern.quote(expandedContent) :
+                "(" + Pattern.quote(expandedContent) + ")|(" + Pattern.quote(cleanedContent) + ")";
     }
 
     /**
@@ -142,9 +160,7 @@ private List<Path> findFile(final BibEntry entry, final Path directory, final St
         }
 
         for (int index = 0; index < (fileParts.length - 1); index++) {
-
             String dirToProcess = fileParts[index];
-            dirToProcess = expandBrackets(dirToProcess, entry, null, keywordDelimiter);
 
             if (dirToProcess.matches("^.:$")) { // Windows Drive Letter
                 actualDirectory = Path.of(dirToProcess + '/');
@@ -179,33 +195,21 @@ private List<Path> findFile(final BibEntry entry, final Path directory, final St
                         resultFiles.addAll(findFile(entry, path, restOfFileString, extensionRegExp));
                     }
                 } catch (UncheckedIOException ioe) {
-                    throw new IOException(ioe);
+                    throw ioe.getCause();
                 }
             } // End process directory information
         }
 
         // Last step: check if the given file can be found in this directory
-        String filePart = fileParts[fileParts.length - 1].replace("[extension]", EXT_MARKER);
-        String filenameToLookFor = expandBrackets(filePart, entry, null, keywordDelimiter).replaceAll(EXT_MARKER, extensionRegExp);
-
-        try {
-            final Pattern toMatch = Pattern.compile('^' + filenameToLookFor.replaceAll("\\\\\\\\", "\\\\") + '$',
-                    Pattern.CASE_INSENSITIVE);
-            BiPredicate<Path, BasicFileAttributes> matcher = (path, attributes) -> toMatch.matcher(path.getFileName().toString()).matches();
-            resultFiles.addAll(collectFilesWithMatcher(actualDirectory, matcher));
-        } catch (UncheckedIOException | PatternSyntaxException e) {
-            throw new IOException("Could not look for " + filenameToLookFor, e);
-        }
-
-        return resultFiles;
-    }
-
-    private List<Path> collectFilesWithMatcher(Path actualDirectory, BiPredicate<Path, BasicFileAttributes> matcher) {
+        Pattern toMatch = createFileNamePattern(fileParts, extensionRegExp, entry);
+        BiPredicate<Path, BasicFileAttributes> matcher = (path, attributes) -> toMatch.matcher(path.getFileName().toString()).matches();
         try (Stream<Path> pathStream = Files.find(actualDirectory, 1, matcher, FileVisitOption.FOLLOW_LINKS)) {
-            return pathStream.collect(Collectors.toList());
-        } catch (UncheckedIOException | IOException ioe) {
-            return Collections.emptyList();
+            resultFiles.addAll(pathStream.collect(Collectors.toList()));
+        } catch (UncheckedIOException uncheckedIOException) {
+            // Previously, an empty list were returned here on both IOException and UncheckedIOException
+            throw uncheckedIOException.getCause();
         }
+        return resultFiles;
     }
 
     private boolean isSubDirectory(Path rootDirectory, Path path) {

src/test/java/org/jabref/logic/citationkeypattern/BracketedPatternTest.java

@@ -324,4 +324,44 @@ void expandBracketsLastNameWithChineseCharacters() {
 
         assertEquals("杨秀群", BracketedPattern.expandBrackets("[auth]", null, bibEntry, null));
     }
+
+    @Test
+    void expandBracketsWithTestCasesFromRegExpBasedFileFinder() {
+        BibEntry entry = new BibEntry(StandardEntryType.Article).withCitationKey("HipKro03");
+        entry.setField(StandardField.AUTHOR, "Eric von Hippel and Georg von Krogh");
+        entry.setField(StandardField.TITLE, "Open Source Software and the \"Private-Collective\" Innovation Model: Issues for Organization Science");
+        entry.setField(StandardField.JOURNAL, "Organization Science");
+        entry.setField(StandardField.YEAR, "2003");
+        entry.setField(StandardField.VOLUME, "14");
+        entry.setField(StandardField.PAGES, "209--223");
+        entry.setField(StandardField.NUMBER, "2");
+        entry.setField(StandardField.ADDRESS, "Institute for Operations Research and the Management Sciences (INFORMS), Linthicum, Maryland, USA");
+        entry.setField(StandardField.DOI, "http://dx.doi.org/10.1287/orsc.14.2.209.14992");
+        entry.setField(StandardField.ISSN, "1526-5455");
+        entry.setField(StandardField.PUBLISHER, "INFORMS");
+
+        BibDatabase database = new BibDatabase();
+        database.insertEntry(entry);
+
+        assertEquals("", BracketedPattern.expandBrackets("", ',', entry, database));
+
+        assertEquals("dropped", BracketedPattern.expandBrackets("drop[unknownkey]ped", ',', entry, database));
+
+        assertEquals("Eric von Hippel and Georg von Krogh",
+                BracketedPattern.expandBrackets("[author]", ',', entry, database));
+
+        assertEquals("Eric von Hippel and Georg von Krogh are two famous authors.",
+                BracketedPattern.expandBrackets("[author] are two famous authors.", ',', entry, database));
+
+        assertEquals("Eric von Hippel and Georg von Krogh are two famous authors.",
+                BracketedPattern.expandBrackets("[author] are two famous authors.", ',', entry, database));
+
+        assertEquals(
+                "Eric von Hippel and Georg von Krogh have published Open Source Software and the \"Private-Collective\" Innovation Model: Issues for Organization Science in Organization Science.",
+                BracketedPattern.expandBrackets("[author] have published [fulltitle] in [journal].", ',', entry, database));
+
+        assertEquals(
+                "Eric von Hippel and Georg von Krogh have published Open Source Software and the \"Private Collective\" Innovation Model: Issues for Organization Science in Organization Science.",
+                BracketedPattern.expandBrackets("[author] have published [title] in [journal].", ',', entry, database));
+    }
 }