Issue #122: Support multiple instances of the same Checkstyle check

src/main/java/org/checkstyle/autofix/CheckstyleAutoFix.java

@@ -88,7 +88,7 @@ public List<Recipe> getRecipeList() {
         final ReportParser reportParser = createReportParser(getViolationReportPath());
         final List<CheckstyleViolation> violations = reportParser
                 .parse(Path.of(getViolationReportPath()));
-        final Map<CheckstyleCheck,
+        final Map<CheckstyleConfigModule,
                 CheckConfiguration> configuration = loadCheckstyleConfiguration();
 
         return CheckstyleRecipeRegistry.getRecipes(violations, configuration);
@@ -108,7 +108,7 @@ else if (path.endsWith(".sarif") || path.endsWith(".sarif.json")) {
         return result;
     }
 
-    private Map<CheckstyleCheck, CheckConfiguration> loadCheckstyleConfiguration() {
+    private Map<CheckstyleConfigModule, CheckConfiguration> loadCheckstyleConfiguration() {
         return ConfigurationLoader.loadConfiguration(getConfigurationPath(), getPropertiesPath());
     }
 }

src/main/java/org/checkstyle/autofix/CheckstyleCheck.java

@@ -37,9 +37,15 @@ public String getId() {
         return id;
     }
 
-    public static Optional<CheckstyleCheck> fromSource(String source) {
+    public static Optional<CheckstyleCheck> fromSource(String checkId) {
         return Arrays.stream(values())
-                .filter(check -> check.getId().contains(source))
+                .filter(check -> check.getId().contains(checkId))
+                .findFirst();
+    }
+
+    public static Optional<CheckstyleCheck> fromSourceExact(String checkId) {
+        return Arrays.stream(values())
+                .filter(check -> check.getId().equals(checkId))
                 .findFirst();
     }
 }

src/main/java/org/checkstyle/autofix/CheckstyleConfigModule.java

@@ -0,0 +1,38 @@
+///////////////////////////////////////////////////////////////////////////////////////////////
+// checkstyle-openrewrite-recipes: Automatically fix Checkstyle violations with OpenRewrite.
+// Copyright (C) 2025 The Checkstyle OpenRewrite Recipes Authors
+//
+// Licensed under the Apache License, Version 2.0 (the "License");
+// you may not use this file except in compliance with the License.
+// You may obtain a copy of the License at
+//
+//     http://www.apache.org/licenses/LICENSE-2.0
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+///////////////////////////////////////////////////////////////////////////////////////////////
+
+package org.checkstyle.autofix;
+
+public class CheckstyleConfigModule {
+    private final CheckstyleCheck check;
+    private final String id;
+
+    public CheckstyleConfigModule(CheckstyleCheck check, String id) {
+        this.check = check;
+        this.id = id;
+    }
+
+    public boolean matchesId(String input) {
+        return id != null && id.equals(input);
+    }
+
+    public boolean matchesCheck(String input) {
+        return CheckstyleCheck.fromSourceExact(input)
+                .map(checkFromInput -> checkFromInput == check)
+                .orElse(false);
+    }
+}

src/main/java/org/checkstyle/autofix/CheckstyleRecipeRegistry.java

@@ -43,6 +43,8 @@ public final class CheckstyleRecipeRegistry {
             CheckConfiguration, Recipe>> RECIPE_MAP_WITH_CONFIG =
             new EnumMap<>(CheckstyleCheck.class);
 
+    private static final String HASH_SEPARATOR = "#";
+
     static {
         RECIPE_MAP.put(CheckstyleCheck.UPPER_ELL, UpperEll::new);
         RECIPE_MAP.put(CheckstyleCheck.HEX_LITERAL_CASE, HexLiteralCase::new);
@@ -65,18 +67,49 @@ private CheckstyleRecipeRegistry() {
      * @return a list of generated Recipe objects
      */
     public static List<Recipe> getRecipes(List<CheckstyleViolation> violations,
-                                          Map<CheckstyleCheck, CheckConfiguration> config) {
+                                          Map<CheckstyleConfigModule, CheckConfiguration> config) {
         return violations.stream()
-                .collect(Collectors.groupingBy(CheckstyleViolation::getSource))
+                .collect(Collectors.groupingBy(CheckstyleViolation::getCheckId))
                 .entrySet()
                 .stream()
                 .map(entry -> {
-                    return createRecipe(entry.getValue(), config.get(entry.getKey()));
+                    final CheckConfiguration configuration =
+                            findMatchingConfiguration(entry.getKey(), config);
+                    return createRecipe(entry.getValue(), configuration);
                 })
                 .filter(Objects::nonNull)
                 .collect(Collectors.toList());
     }
 
+    private static CheckConfiguration findMatchingConfiguration(String source,
+                                           Map<CheckstyleConfigModule, CheckConfiguration> config) {
+        return config.entrySet().stream()
+                .filter(configEntry -> matchesSource(configEntry.getKey(), source))
+                .map(Map.Entry::getValue)
+                .findFirst()
+                .orElse(null);
+    }
+
+    private static boolean matchesSource(CheckstyleConfigModule module, String source) {
+        final boolean matches;
+        if (source.contains(HASH_SEPARATOR)) {
+            matches = matchesWithHashSeparator(module, source);
+        }
+        else {
+            matches = module.matchesId(source) || module.matchesCheck(source);
+        }
+        return matches;
+    }
+
+    private static boolean matchesWithHashSeparator(CheckstyleConfigModule module, String source) {
+        final String[] parts = source.split(HASH_SEPARATOR, 2);
+        final String checkPart = parts[0];
+        final String idPart = parts[1];
+        final boolean exactMatch = module.matchesCheck(checkPart) && module.matchesId(idPart);
+        final boolean individualMatch = module.matchesId(source) || module.matchesCheck(source);
+        return exactMatch || individualMatch;
+    }
+
     private static Recipe createRecipe(List<CheckstyleViolation> violations,
                                        CheckConfiguration checkConfig) {
         Recipe result = null;

src/main/java/org/checkstyle/autofix/parser/CheckstyleViolation.java

@@ -19,8 +19,6 @@
 
 import java.nio.file.Path;
 
-import org.checkstyle.autofix.CheckstyleCheck;
-
 public final class CheckstyleViolation {
 
     private final int line;
@@ -29,24 +27,24 @@ public final class CheckstyleViolation {
 
     private final String severity;
 
-    private final CheckstyleCheck source;
+    private final String checkId;
 
     private final String message;
 
     private final Path filePath;
 
     public CheckstyleViolation(int line, int column, String severity,
-                               CheckstyleCheck source, String message, Path filePath) {
+                               String source, String message, Path filePath) {
         this.line = line;
         this.column = column;
         this.severity = severity;
-        this.source = source;
+        this.checkId = source;
         this.message = message;
         this.filePath = filePath;
     }
 
     public CheckstyleViolation(int line, String severity,
-                               CheckstyleCheck source, String message, Path filePath) {
+                               String source, String message, Path filePath) {
         this(line, -1, severity, source, message, filePath);
     }
 
@@ -58,8 +56,8 @@ public Integer getColumn() {
         return column;
     }
 
-    public CheckstyleCheck getSource() {
-        return source;
+    public String getCheckId() {
+        return checkId;
     }
 
     public String getMessage() {

src/main/java/org/checkstyle/autofix/parser/ConfigurationLoader.java

@@ -20,11 +20,13 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.util.HashMap;
+import java.util.LinkedHashMap;
 import java.util.Map;
 import java.util.Optional;
 import java.util.Properties;
 
 import org.checkstyle.autofix.CheckstyleCheck;
+import org.checkstyle.autofix.CheckstyleConfigModule;
 
 import com.puppycrawl.tools.checkstyle.PropertiesExpander;
 import com.puppycrawl.tools.checkstyle.api.CheckstyleException;
@@ -36,14 +38,19 @@ private ConfigurationLoader() {
         // utility class
     }
 
-    public static Map<CheckstyleCheck, CheckConfiguration> mapConfiguration(Configuration config) {
-        final Map<CheckstyleCheck, CheckConfiguration> result = new HashMap<>();
+    public static Map<CheckstyleConfigModule,
+            CheckConfiguration> mapConfiguration(Configuration config) {
+
+        final Map<CheckstyleConfigModule, CheckConfiguration> result = new LinkedHashMap<>();
         final Map<String, String> inherited = getProperties(config);
 
         final Optional<CheckstyleCheck> module = CheckstyleCheck.fromSource(config.getName());
         module.ifPresent(checkstyleCheck -> {
-            result.put(checkstyleCheck, new CheckConfiguration(checkstyleCheck, new HashMap<>(),
-                    getProperties(config)));
+            final Map<String, String> properties = getProperties(config);
+            final CheckstyleConfigModule configModule = new CheckstyleConfigModule(
+                    checkstyleCheck, properties.get("id"));
+            result.put(configModule,
+                    new CheckConfiguration(checkstyleCheck, new HashMap<>(), properties));
         });
 
         for (Configuration child : config.getChildren()) {
@@ -69,7 +76,7 @@ private static Map<String, String> getProperties(Configuration config) {
         return props;
     }
 
-    public static Map<CheckstyleCheck, CheckConfiguration> loadConfiguration(
+    public static Map<CheckstyleConfigModule, CheckConfiguration> loadConfiguration(
             String checkstyleConfigurationPath, String propFile) {
         Properties props = new Properties();
         if (propFile == null) {

src/main/java/org/checkstyle/autofix/parser/SarifReportParser.java

@@ -25,8 +25,6 @@
 import java.util.List;
 import java.util.Optional;
 
-import org.checkstyle.autofix.CheckstyleCheck;
-
 import de.jcup.sarif_2_1_0.SarifSchema210ImportExportSupport;
 import de.jcup.sarif_2_1_0.model.PhysicalLocation;
 import de.jcup.sarif_2_1_0.model.Region;
@@ -57,17 +55,14 @@ public List<CheckstyleViolation> parse(Path reportPath) {
         for (final Run run: report.getRuns()) {
             if (run.getResults() != null) {
                 run.getResults().forEach(resultEntry -> {
-                    CheckstyleCheck.fromSource(resultEntry.getRuleId()).ifPresent(check -> {
-                        final CheckstyleViolation violation = createViolation(check, resultEntry);
-                        result.add(violation);
-                    });
+                    result.add(createViolation(resultEntry.getRuleId(), resultEntry));
                 });
             }
         }
         return result;
     }
 
-    private CheckstyleViolation createViolation(CheckstyleCheck check, Result result) {
+    private CheckstyleViolation createViolation(String checkId, Result result) {
         final String severity = result.getLevel().name();
         final String message = result.getMessage().getText();
         final PhysicalLocation location = result.getLocations().get(0).getPhysicalLocation();
@@ -76,8 +71,8 @@ private CheckstyleViolation createViolation(CheckstyleCheck check, Result result
         final int line = region.getStartLine();
         final Optional<Integer> columnMaybe = Optional.ofNullable(region.getStartColumn());
         return columnMaybe.map(column -> {
-            return new CheckstyleViolation(line, column, severity, check, message, filePath);
-        }).orElse(new CheckstyleViolation(line, severity, check, message, filePath));
+            return new CheckstyleViolation(line, column, severity, checkId, message, filePath);
+        }).orElse(new CheckstyleViolation(line, severity, checkId, message, filePath));
     }
 
     private Path getFilePath(PhysicalLocation location) {

src/main/java/org/checkstyle/autofix/parser/XmlReportParser.java

@@ -25,7 +25,6 @@
 import java.util.Iterator;
 import java.util.List;
 import java.util.Objects;
-import java.util.Optional;
 
 import javax.xml.stream.XMLEventReader;
 import javax.xml.stream.XMLInputFactory;
@@ -34,8 +33,6 @@
 import javax.xml.stream.events.StartElement;
 import javax.xml.stream.events.XMLEvent;
 
-import org.checkstyle.autofix.CheckstyleCheck;
-
 public class XmlReportParser implements ReportParser {
 
     private static final String FILE_TAG = "file";
@@ -78,7 +75,7 @@ public List<CheckstyleViolation> parse(Path xmlPath) {
                         }
                         else if (ERROR_TAG.equals(startElementName)) {
                             Objects.requireNonNull(filename, "File name can not be null");
-                            parseErrorTag(startElement, filename).ifPresent(result::add);
+                            result.add(parseErrorTag(startElement, filename));
                         }
                     }
                 }
@@ -111,14 +108,13 @@ private String parseFileTag(StartElement startElement) {
         return fileName;
     }
 
-    private Optional<CheckstyleViolation> parseErrorTag(StartElement startElement,
+    private CheckstyleViolation parseErrorTag(StartElement startElement,
                                                                String filename) {
         int line = -1;
         int column = -1;
         String message = null;
         String severity = null;
-        CheckstyleViolation violation = null;
-        Optional<CheckstyleCheck> source = Optional.empty();
+        String source = null;
 
         final Iterator<Attribute> attributes = startElement.getAttributes();
         while (attributes.hasNext()) {
@@ -138,17 +134,14 @@ private Optional<CheckstyleViolation> parseErrorTag(StartElement startElement,
                     message = attribute.getValue();
                     break;
                 case SOURCE_ATTR:
-                    source = CheckstyleCheck.fromSource(attribute.getValue());
+                    source = attribute.getValue();
                     break;
                 default:
                     break;
             }
         }
-        if (source.isPresent()) {
-            violation = new CheckstyleViolation(line, column, severity,
-                    source.get(), message, Path.of(filename));
-        }
-        return Optional.ofNullable(violation);
+        return new CheckstyleViolation(line, column, severity,
+                source, message, Path.of(filename));
 
     }
 }

src/test/java/org/checkstyle/autofix/parser/CheckstyleReportsParserTest.java

@@ -25,7 +25,6 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import org.checkstyle.autofix.CheckstyleCheck;
 import org.junit.jupiter.api.Test;
 
 public class CheckstyleReportsParserTest {
@@ -49,7 +48,7 @@ public void testParseFromResource() throws Exception {
         assertEquals(13, record.getColumn());
         assertEquals("error", record.getSeverity());
         assertEquals("Example message", record.getMessage());
-        assertEquals(CheckstyleCheck.UPPER_ELL, record.getSource());
+        assertEquals("com.puppycrawl.tools.checkstyle.checks.UpperEllCheck", record.getCheckId());
         assertEquals(Path.of("Example.java"), record.getFilePath());
     }
 

src/test/resources/org/checkstyle/autofix/recipe/finallocalvariable/singlelocaltest/DiffSingleLocalTest.diff

@@ -1,6 +1,6 @@
 --- src/test/resources/org/checkstyle/autofix/recipe/finallocalvariable/singlelocaltest/InputSingleLocalTest.java
 +++ src/test/resources/org/checkstyle/autofix/recipe/finallocalvariable/singlelocaltest/OutputSingleLocalTest.java
-@@ -15,37 +15,37 @@
+@@ -17,37 +17,37 @@
  import java.util.HashMap;
  import java.util.List;
 

src/test/resources/org/checkstyle/autofix/recipe/finallocalvariable/singlelocaltest/InputSingleLocalTest.java

@@ -1,7 +1,9 @@
 /*xml
 <module name="Checker">
   <module name="TreeWalker">
-    <module name="com.puppycrawl.tools.checkstyle.checks.coding.FinalLocalVariableCheck"/>
+    <module name="com.puppycrawl.tools.checkstyle.checks.coding.FinalLocalVariableCheck">
+      <property name="id" value="UpperEll"/>
+    </module>
   </module>
 </module>
 

src/test/resources/org/checkstyle/autofix/recipe/finallocalvariable/singlelocaltest/OutputSingleLocalTest.java

@@ -1,7 +1,9 @@
 /*xml
 <module name="Checker">
   <module name="TreeWalker">
-    <module name="com.puppycrawl.tools.checkstyle.checks.coding.FinalLocalVariableCheck"/>
+    <module name="com.puppycrawl.tools.checkstyle.checks.coding.FinalLocalVariableCheck">
+      <property name="id" value="UpperEll"/>
+    </module>
   </module>
 </module>