SONAR-9574 Same file indexed in different modules

12 files changed, 68 insertions, 48 deletions

diff --git a/plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/extensions/XooProjectBuilder.java b/plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/extensions/XooProjectBuilder.java
index 28f1ec6a4eb..38e690c0671 100644
--- a/plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/extensions/XooProjectBuilder.java
+++ b/plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/extensions/XooProjectBuilder.java
@@ -19,12 +19,11 @@
  */
 package org.sonar.xoo.extensions;
 
+import java.io.File;
 import org.sonar.api.batch.bootstrap.ProjectBuilder;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.config.Settings;
 
-import java.io.File;
-
 public class XooProjectBuilder extends ProjectBuilder {
 
   private Settings settings;
@@ -39,6 +38,7 @@ public class XooProjectBuilder extends ProjectBuilder {
       return;
     }
     ProjectDefinition root = context.projectReactor().getRoot();
+    root.resetSources();
 
     ProjectDefinition module = ProjectDefinition.create()
       .setKey(root.getKey() + ":module1")
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultIndexedFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultIndexedFile.java
index 0d07003dce5..2f456b489fc 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultIndexedFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultIndexedFile.java
@@ -70,6 +70,14 @@ public class DefaultIndexedFile extends DefaultInputComponent implements Indexed
     return sensorStrategy.isGlobal() ? projectRelativePath : moduleRelativePath;
   }
 
+  public String getModuleRelativePath() {
+    return moduleRelativePath;
+  }
+
+  public String getProjectRelativePath() {
+    return projectRelativePath;
+  }
+
   @Override
   public String absolutePath() {
     return PathUtils.sanitize(path().toString());
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultInputFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultInputFile.java
index 3fe157a43e2..effb5663f31 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultInputFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultInputFile.java
@@ -125,6 +125,14 @@ public class DefaultInputFile extends DefaultInputComponent implements InputFile
     return indexedFile.relativePath();
   }
 
+  public String getModuleRelativePath() {
+    return indexedFile.getModuleRelativePath();
+  }
+
+  public String getProjectRelativePath() {
+    return indexedFile.getProjectRelativePath();
+  }
+
   @Override
   public String absolutePath() {
     return indexedFile.absolutePath();
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/scan/issue/filter/FilterableIssue.java b/sonar-plugin-api/src/main/java/org/sonar/api/scan/issue/filter/FilterableIssue.java
index 76e1a74ec29..30d039436b7 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/scan/issue/filter/FilterableIssue.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/scan/issue/filter/FilterableIssue.java
@@ -20,10 +20,8 @@
 package org.sonar.api.scan.issue.filter;
 
 import java.util.Date;
-
 import javax.annotation.CheckForNull;
 import javax.annotation.concurrent.ThreadSafe;
-
 import org.sonar.api.rule.RuleKey;
 
 /**
@@ -55,6 +53,10 @@ public interface FilterableIssue {
   @CheckForNull
   Double gap();
 
+  /**
+   * @deprecated since 6.6 useless
+   */
+  @Deprecated
   Date creationDate();
 
   String projectKey();
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultInputFileTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultInputFileTest.java
index 7d699d5bf39..5eb4b0a9d47 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultInputFileTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultInputFileTest.java
@@ -74,8 +74,6 @@ public class DefaultInputFileTest {
       .setStatus(InputFile.Status.ADDED)
       .setCharset(StandardCharsets.ISO_8859_1);
 
-    assertThat(inputFile.relativePath()).isEqualTo(MODULE_RELATIVE_PATH);
-    assertThat(new File(inputFile.relativePath())).isRelative();
     assertThat(inputFile.absolutePath()).endsWith("Foo.php");
     assertThat(inputFile.filename()).isEqualTo("Foo.php");
     assertThat(inputFile.uri()).hasPath(baseDir.resolve(PROJECT_RELATIVE_PATH).toUri().getPath());
@@ -86,8 +84,14 @@ public class DefaultInputFileTest {
     assertThat(inputFile.lines()).isEqualTo(42);
     assertThat(inputFile.charset()).isEqualTo(StandardCharsets.ISO_8859_1);
 
+    assertThat(inputFile.getModuleRelativePath()).isEqualTo(MODULE_RELATIVE_PATH);
+    assertThat(inputFile.getProjectRelativePath()).isEqualTo(PROJECT_RELATIVE_PATH);
+
+    assertThat(inputFile.relativePath()).isEqualTo(MODULE_RELATIVE_PATH);
+    assertThat(new File(inputFile.relativePath())).isRelative();
     sensorStrategy.setGlobal(true);
     assertThat(inputFile.relativePath()).isEqualTo(PROJECT_RELATIVE_PATH);
+    assertThat(new File(inputFile.relativePath())).isRelative();
   }
 
   @Test
diff --git a/sonar-plugin-api/src/test/java/org/sonar/api/batch/sensor/cpd/internal/DefaultCpdTokensTest.java b/sonar-plugin-api/src/test/java/org/sonar/api/batch/sensor/cpd/internal/DefaultCpdTokensTest.java
index 62a268f00f7..30126f0271d 100644
--- a/sonar-plugin-api/src/test/java/org/sonar/api/batch/sensor/cpd/internal/DefaultCpdTokensTest.java
+++ b/sonar-plugin-api/src/test/java/org/sonar/api/batch/sensor/cpd/internal/DefaultCpdTokensTest.java
@@ -23,7 +23,6 @@ import org.junit.Test;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.TestInputFileBuilder;
 import org.sonar.api.batch.sensor.internal.SensorStorage;
-import org.sonar.api.config.Settings;
 import org.sonar.api.config.internal.MapSettings;
 
 import static org.assertj.core.api.Assertions.assertThat;
@@ -146,7 +145,7 @@ public class DefaultCpdTokensTest {
       tokens.addToken(INPUT_FILE.newRange(1, 2, 1, 5), "foo");
       fail("Expected exception");
     } catch (Exception e) {
-      assertThat(e).hasMessage("Tokens of file [moduleKey=foo, relative=src/Foo.java, basedir=foo] should be provided in order.\n" +
+      assertThat(e).hasMessage("Tokens of file src/Foo.java should be provided in order.\n" +
         "Previous token: Range[from [line=1, lineOffset=6] to [line=1, lineOffset=10]]\n" +
         "Last token: Range[from [line=1, lineOffset=2] to [line=1, lineOffset=5]]");
     }
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
index 4b78ce2f6c6..33cd3749c1b 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/FileIndexer.java
@@ -31,9 +31,7 @@ import java.nio.file.Path;
 import java.nio.file.attribute.BasicFileAttributes;
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Set;
 import java.util.concurrent.ExecutionException;
 import java.util.concurrent.ExecutorService;
 import java.util.concurrent.Executors;
@@ -43,7 +41,6 @@ import java.util.concurrent.atomic.AtomicInteger;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.batch.ScannerSide;
-import org.sonar.api.batch.fs.IndexedFile;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.InputFile.Type;
 import org.sonar.api.batch.fs.InputFileFilter;
@@ -184,8 +181,8 @@ public class FileIndexer {
     }
     String parentRelativePath = getParentRelativePath(inputFile);
     synchronized (this) {
-      indexFileAndParentDir(inputFile, parentRelativePath);
       progress.markAsIndexed(inputFile);
+      indexFileAndParentDir(inputFile, parentRelativePath);
     }
     LOG.debug("'{}' indexed {}with language '{}'", relativePath, type == Type.TEST ? "as test " : "", inputFile.language());
     inputFileBuilder.checkMetadata(inputFile);
@@ -271,16 +268,16 @@ public class FileIndexer {
   }
 
   private class Progress {
-    private final Set<Path> indexed = new HashSet<>();
+    private AtomicInteger indexedCount = new AtomicInteger(0);
     private AtomicInteger excludedByPatternsCount = new AtomicInteger(0);
 
-    void markAsIndexed(IndexedFile inputFile) {
-      if (indexed.contains(inputFile.path())) {
+    void markAsIndexed(DefaultInputFile inputFile) {
+      if (componentStore.getFile(inputFile.getProjectRelativePath()) != null) {
         throw MessageException.of("File " + inputFile + " can't be indexed twice. Please check that inclusion/exclusion patterns produce "
           + "disjoint sets for main and test files");
       }
-      indexed.add(inputFile.path());
-      progressReport.message(indexed.size() + " " + pluralizeFiles(indexed.size()) + " indexed...  (last one was " + inputFile.relativePath() + ")");
+      int count = indexedCount.incrementAndGet();
+      progressReport.message(count + " " + pluralizeFiles(count) + " indexed...  (last one was " + inputFile.relativePath() + ")");
     }
 
     void increaseExcludedByPatternsCount() {
@@ -292,7 +289,7 @@ public class FileIndexer {
     }
 
     int count() {
-      return indexed.size();
+      return indexedCount.get();
     }
   }
 
diff --git a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputComponentStore.java b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputComponentStore.java
index bec0e176f10..ee1b34a8d95 100644
--- a/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputComponentStore.java
+++ b/sonar-scanner-engine/src/main/java/org/sonar/scanner/scan/filesystem/InputComponentStore.java
@@ -110,7 +110,7 @@ public class InputComponentStore {
 
   public InputComponentStore remove(InputFile inputFile) {
     DefaultInputFile file = (DefaultInputFile) inputFile;
-    inputFileCache.remove(file.moduleKey(), inputFile.relativePath());
+    inputFileCache.remove(file.moduleKey(), file.getModuleRelativePath());
     return this;
   }
 
@@ -123,8 +123,8 @@ public class InputComponentStore {
   public InputComponentStore put(InputFile inputFile) {
     DefaultInputFile file = (DefaultInputFile) inputFile;
     addToLanguageCache(file);
-    inputFileCache.put(file.moduleKey(), inputFile.relativePath(), inputFile);
-    globalInputFileCache.put(getProjectRelativePath(file), inputFile);
+    inputFileCache.put(file.moduleKey(), file.getModuleRelativePath(), inputFile);
+    globalInputFileCache.put(file.getProjectRelativePath(), inputFile);
     inputComponents.put(inputFile.key(), inputFile);
     filesByNameCache.put(inputFile.filename(), inputFile);
     filesByExtensionCache.put(FileExtensionPredicate.getExtension(inputFile), inputFile);
@@ -142,15 +142,12 @@ public class InputComponentStore {
   public InputComponentStore put(InputDir inputDir) {
     DefaultInputDir dir = (DefaultInputDir) inputDir;
     inputDirCache.put(dir.moduleKey(), inputDir.relativePath(), inputDir);
+    // FIXME an InputDir can be already indexed by another module
     globalInputDirCache.put(getProjectRelativePath(dir), inputDir);
     inputComponents.put(inputDir.key(), inputDir);
     return this;
   }
 
-  private String getProjectRelativePath(DefaultInputFile file) {
-    return PathResolver.relativePath(getProjectBaseDir(), file.path());
-  }
-
   private String getProjectRelativePath(DefaultInputDir dir) {
     return PathResolver.relativePath(getProjectBaseDir(), dir.path());
   }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/DefaultFileLinesContextTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/DefaultFileLinesContextTest.java
index 76e59e815f4..f3a47b46ec8 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/DefaultFileLinesContextTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/DefaultFileLinesContextTest.java
@@ -95,13 +95,13 @@ public class DefaultFileLinesContextTest {
 
   @Test
   public void validateLineGreaterThanZero() {
-    thrown.expectMessage("Line number should be positive for file [moduleKey=foo, relative=src/foo.php, basedir=foo].");
+    thrown.expectMessage("Line number should be positive for file src/foo.php.");
     fileLineMeasures.setIntValue(HITS_METRIC_KEY, 0, 2);
   }
 
   @Test
   public void validateLineLowerThanLineCount() {
-    thrown.expectMessage("Line 4 is out of range for file [moduleKey=foo, relative=src/foo.php, basedir=foo]. File has 3 lines");
+    thrown.expectMessage("Line 4 is out of range for file src/foo.php. File has 3 lines");
     fileLineMeasures.setIntValue(HITS_METRIC_KEY, 4, 2);
   }
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
index 5f2add6955a..a48b94bf2a1 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumTest.java
@@ -562,12 +562,32 @@ public class FileSystemMediumTest {
     FileUtils.write(xooFile, "Sample xoo\ncontent");
 
     thrown.expect(MessageException.class);
-    thrown.expectMessage("can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files");
+    thrown.expectMessage("File src/sample.xoo can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files");
     tester.newTask()
       .properties(builder
         .put("sonar.sources", "src,src/sample.xoo")
         .build())
       .execute();
+  }
+
+  // SONAR-9574
+  @Test
+  public void failForDuplicateInputFileInDifferentModules() throws IOException {
+    File srcDir = new File(baseDir, "module1/src");
+    srcDir.mkdir();
+
+    File xooFile = new File(srcDir, "sample.xoo");
+    FileUtils.write(xooFile, "Sample xoo\ncontent");
+
+    thrown.expect(MessageException.class);
+    thrown.expectMessage("File module1/src/sample.xoo can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files");
+    tester.newTask()
+      .properties(builder
+        .put("sonar.sources", "module1/src")
+        .put("sonar.modules", "module1")
+        .put("module1.sonar.sources", "src")
+        .build())
+      .execute();
 
   }
 
@@ -713,22 +733,4 @@ public class FileSystemMediumTest {
     assertThat(result.inputFiles()).hasSize(1);
   }
 
-  @Test
-  public void detectDuplicatedFilesInDifferentModules() throws IOException {
-    File srcDir = new File(baseDir, "module1/src");
-    srcDir.mkdir();
-
-    File xooFile = new File(srcDir, "sample.xoo");
-    FileUtils.write(xooFile, "Sample xoo\ncontent");
-
-    TaskResult result = tester.newTask()
-      .properties(builder
-        .put("sonar.sources", "module1/src")
-        .put("sonar.modules", "module1")
-        .put("module1.sonar.sources", "src")
-        .build())
-      .execute();
-
-    assertThat(result.inputFiles()).hasSize(1);
-  }
 }
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
index 35eab16b110..bf86ea126c1 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/mediumtest/fs/ProjectBuilderMediumTest.java
@@ -190,7 +190,7 @@ public class ProjectBuilderMediumTest {
   }
 
   private File prepareProject() throws IOException {
-    File baseDir = temp.getRoot();
+    File baseDir = temp.newFolder();
     File module1Dir = new File(baseDir, "module1");
     module1Dir.mkdir();
 
diff --git a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
index 6611f15302b..482b215cee0 100644
--- a/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
+++ b/sonar-scanner-engine/src/test/java/org/sonar/scanner/scan/filesystem/InputFileBuilderTest.java
@@ -21,6 +21,7 @@ package org.sonar.scanner.scan.filesystem;
 
 import java.io.IOException;
 import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
 import java.nio.file.Path;
 import org.junit.Before;
 import org.junit.Rule;
@@ -56,8 +57,10 @@ public class InputFileBuilderTest {
       .setBaseDir(baseDir.toFile())
       .setWorkDir(workDir.toFile())
       .setKey("root"), 0);
+    Path moduleBaseDir = baseDir.resolve("module1");
+    Files.createDirectories(moduleBaseDir);
     DefaultInputModule module = new DefaultInputModule(ProjectDefinition.create()
-      .setBaseDir(baseDir.resolve("module1").toFile())
+      .setBaseDir(moduleBaseDir.toFile())
       .setWorkDir(workDir.toFile())
       .setKey("module1"), 0);