path: root/sonar-scanner-engine/src/it/java/org/sonar/scanner/mediumtest/fs/FileSystemMediumIT.java

/*
 * SonarQube
 * Copyright (C) 2009-2025 SonarSource SA
 * mailto:info AT sonarsource DOT com
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 3 of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public License
 * along with this program; if not, write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
 */
package org.sonar.scanner.mediumtest.fs;

import com.google.common.collect.ImmutableMap;
import java.io.File;
import java.io.IOException;
import java.io.RandomAccessFile;
import java.nio.charset.StandardCharsets;
import java.nio.file.Files;
import java.nio.file.LinkOption;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.List;
import java.util.Map;
import java.util.Random;
import java.util.Set;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.SystemUtils;
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.OS;
import org.junit.jupiter.api.extension.RegisterExtension;
import org.junit.jupiter.api.io.TempDir;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.slf4j.event.Level;
import org.sonar.api.CoreProperties;
import org.sonar.api.SonarEdition;
import org.sonar.api.batch.fs.InputFile;
import org.sonar.api.batch.fs.internal.DefaultInputFile;
import org.sonar.api.internal.apachecommons.io.FilenameUtils;
import org.sonar.api.testfixtures.log.LogTesterJUnit5;
import org.sonar.api.utils.MessageException;
import org.sonar.api.utils.PathUtils;
import org.sonar.api.utils.System2;
import org.sonar.scanner.mediumtest.AnalysisResult;
import org.sonar.scanner.mediumtest.ScannerMediumTester;
import org.sonar.scanner.mediumtest.ScannerMediumTester.AnalysisBuilder;
import org.sonar.scanner.protocol.output.ScannerReport;
import org.sonar.xoo.XooPlugin;
import org.sonar.xoo.global.DeprecatedGlobalSensor;
import org.sonar.xoo.global.GlobalProjectSensor;
import org.sonar.xoo.rule.XooRulesDefinition;

import static java.nio.file.Files.createDirectory;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.assertThatThrownBy;
import static org.assertj.core.api.Assertions.tuple;
import static org.assertj.core.api.AssertionsForClassTypes.catchThrowableOfType;
import static org.junit.jupiter.api.Assumptions.assumeTrue;
import static org.slf4j.event.Level.DEBUG;

class FileSystemMediumIT {

  @TempDir
  private File temp;

  @RegisterExtension
  private final LogTesterJUnit5 logTester = new LogTesterJUnit5();

  @RegisterExtension
  private final ScannerMediumTester tester = new ScannerMediumTester()
    .setEdition(SonarEdition.COMMUNITY)
    .registerPlugin("xoo", new XooPlugin())
    .addDefaultQProfile("xoo", "Sonar Way")
    .addDefaultQProfile("xoo2", "Sonar Way");

  private File baseDir;
  private ImmutableMap.Builder<String, String> builder;

  @BeforeEach
  void prepare() throws IOException {
    logTester.setLevel(DEBUG);
    baseDir = createDirectory(temp.toPath().resolve("baseDir")).toFile();

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project");
  }

  @Test
  void scan_project_without_name() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    int ref = result.getReportReader().readMetadata().getRootComponentRef();
    assertThat(result.getReportReader().readComponent(ref).getName()).isEmpty();
    assertThat(result.inputFiles()).hasSize(1);

    DefaultInputFile file = (DefaultInputFile) result.inputFile("src/sample.xoo");
    assertThat(file).isNotNull();
    assertThat(file.type()).isEqualTo(InputFile.Type.MAIN);
    assertThat(file.relativePath()).isEqualTo("src/sample.xoo");
    assertThat(file.language()).isEqualTo("xoo");

    // file was published, since language matched xoo
    assertThat(file.isPublished()).isTrue();
    assertThat(result.getReportComponent(file.scannerId())).isNotNull();
  }

  @Test
  void log_branch_name_and_type() {
    builder.put("sonar.branch.name", "my-branch");
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    // Using sonar.branch.name when the branch plugin is not installed is an error.
    AnalysisBuilder analysisBuilder = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build());
    assertThatThrownBy(analysisBuilder::execute)
      .isInstanceOf(MessageException.class);
  }

  @Test
  void only_generate_metadata_if_needed() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDir, "sample.java", "Sample xoo\ncontent");

    logTester.setLevel(DEBUG);

    tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(logTester.logs()).anyMatch(log -> log.startsWith("2 files indexed (done) | time="));
    assertThat(logTester.logs()).contains("'src/sample.xoo' generated metadata with charset 'UTF-8'");
    assertThat(String.join("\n", logTester.logs())).doesNotContain("'src/sample.java' generated metadata");
  }

  @Test
  void preload_file_metadata() throws IOException {
    builder.put("sonar.preloadFileMetadata", "true");

    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDir, "sample.java", "Sample xoo\ncontent");

    logTester.setLevel(DEBUG);

    tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(logTester.logs()).anyMatch(log -> log.startsWith("2 files indexed (done) | time="));
    assertThat(logTester.logs()).contains("'src/sample.xoo' generated metadata with charset 'UTF-8'");
    assertThat(logTester.logs()).contains("'src/sample.java' generated metadata with charset 'UTF-8'");
  }

  @Test
  void dont_publish_files_without_detected_language() throws IOException {
    Path mainDir = baseDir.toPath().resolve("src").resolve("main");
    Files.createDirectories(mainDir);

    Path testDir = baseDir.toPath().resolve("src").resolve("test");
    Files.createDirectories(testDir);

    writeFile(testDir.toFile(), "sample.java", "Sample xoo\ncontent");
    writeFile(mainDir.toFile(), "sample.xoo", "Sample xoo\ncontent");
    writeFile(mainDir.toFile(), "sample.java", "Sample xoo\ncontent");

    logTester.setLevel(DEBUG);

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src/main")
        .put("sonar.tests", "src/test")
        .build())
      .execute();

    assertThat(logTester.logs()).containsAnyOf("'src/main/sample.java' indexed with no language", "'src\\main\\sample.java' indexed with no language");
    assertThat(logTester.logs()).anyMatch(log -> log.startsWith("3 files indexed (done) | time="));
    assertThat(logTester.logs()).contains("'src/main/sample.xoo' generated metadata with charset 'UTF-8'");
    assertThat(logTester.logs()).doesNotContain("'src/main/sample.java' generated metadata", "'src\\main\\sample.java' generated metadata");
    assertThat(logTester.logs()).doesNotContain("'src/test/sample.java' generated metadata", "'src\\test\\sample.java' generated metadata");
    DefaultInputFile javaInputFile = (DefaultInputFile) result.inputFile("src/main/sample.java");

    assertThat(javaInputFile).isNotNull();
    assertThatThrownBy(() -> result.getReportComponent(javaInputFile))
      .isInstanceOf(IllegalStateException.class)
      .hasMessageContaining("Unable to find report for component");
  }

  @Test
  void create_issue_on_any_file() throws IOException {
    tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssuePerUnknownFile", null, "OneIssuePerUnknownFile", "MAJOR", null, "xoo");

    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.unknown", "Sample xoo\ncontent");

    logTester.setLevel(DEBUG);

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(logTester.logs()).anyMatch(log -> log.startsWith("1 file indexed (done) | time="));
    assertThat(logTester.logs()).contains("'src/sample.unknown' indexed with no language");
    assertThat(logTester.logs()).contains("'src/sample.unknown' generated metadata with charset 'UTF-8'");
    DefaultInputFile inputFile = (DefaultInputFile) result.inputFile("src/sample.unknown");
    assertThat(inputFile).isNotNull();
    assertThat(result.getReportComponent(inputFile)).isNotNull();
  }

  @Test
  void lazyIssueExclusion() throws IOException {
    tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssuePerFile", null, "OneIssuePerFile", "MAJOR", null, "xoo");

    builder.put("sonar.issue.ignore.allfile", "1")
      .put("sonar.issue.ignore.allfile.1.fileRegexp", "pattern");
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    File unknownFile = new File(srcDir, "myfile.binary");
    byte[] b = new byte[512];
    new Random().nextBytes(b);
    FileUtils.writeByteArrayToFile(unknownFile, b);

    logTester.setLevel(DEBUG);

    tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(logTester.logs()).containsOnlyOnce("'src/myfile.binary' indexed with no language");
    assertThat(logTester.logs()).doesNotContain("Evaluate issue exclusions for 'src/myfile.binary'");
    assertThat(logTester.logs()).containsOnlyOnce("Evaluate issue exclusions for 'src/sample.xoo'");
  }

  @Test
  void preloadIssueExclusions() throws IOException {
    builder.put("sonar.issue.ignore.allfile", "1")
      .put("sonar.issue.ignore.allfile.1.fileRegexp", "pattern")
      .put("sonar.preloadFileMetadata", "true");
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\npattern");
    writeFile(srcDir, "myfile.binary", "some text");

    logTester.setLevel(DEBUG);

    tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(logTester.logs()).containsSequence("Evaluate issue exclusions for 'src/sample.xoo'",
      "  - Exclusion pattern 'pattern': all issues in this file will be ignored.");
  }

  @Test
  void publishFilesWithIssues() throws IOException {
    tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssueOnDirPerFile", null, "OneIssueOnDirPerFile", "MAJOR", null, "xoo");

    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    DefaultInputFile file = (DefaultInputFile) result.inputFile("src/sample.xoo");

    assertThat(file).isNotNull();
    assertThat(file.isPublished()).isTrue();
    assertThat(result.getReportComponent(file)).isNotNull();
  }

  @Test
  void scanProjectWithSourceDir() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
    InputFile inputFile = result.inputFile("src/sample.xoo");
    assertThat(inputFile).isNotNull();
    assertThat(inputFile.type()).isEqualTo(InputFile.Type.MAIN);
    assertThat(inputFile.relativePath()).isEqualTo("src/sample.xoo");
  }

  @Test
  void scanBigProject() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    int nbFiles = 100;
    int ruleCount = 100000;
    String fileContent = StringUtils.repeat(StringUtils.repeat("a", 100) + "\n", ruleCount / 1000);
    for (int nb = 1; nb <= nbFiles; nb++) {
      File xooFile = new File(srcDir, "sample" + nb + ".xoo");
      FileUtils.write(xooFile, fileContent, StandardCharsets.UTF_8);
    }

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(100);
  }

  @Test
  void scanProjectWithTestDir() throws IOException {
    File test = new File(baseDir, "test");
    assertThat(test.mkdir()).isTrue();

    writeFile(test, "sampleTest.xoo", "Sample test xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "")
        .put("sonar.tests", "test")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
    InputFile inputFile = result.inputFile("test/sampleTest.xoo");
    assertThat(inputFile).isNotNull();
    assertThat(inputFile.type()).isEqualTo(InputFile.Type.TEST);
  }

  /**
   * SONAR-5419
   */
  @Test
  void scanProjectWithMixedSourcesAndTests() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(baseDir, "another.xoo", "Sample xoo 2\ncontent");

    File testDir = new File(baseDir, "test");
    assertThat(testDir.mkdir()).isTrue();

    writeFile(baseDir, "sampleTest2.xoo", "Sample test xoo\ncontent");
    writeFile(testDir, "sampleTest.xoo", "Sample test xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src,another.xoo")
        .put("sonar.tests", "test,sampleTest2.xoo")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(4);
  }

  @Test
  void fileInclusionsExclusions() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(baseDir, "another.xoo", "Sample xoo 2\ncontent");

    File testDir = new File(baseDir, "test");
    assertThat(testDir.mkdir()).isTrue();

    writeFile(baseDir, "sampleTest2.xoo", "Sample test xoo\ncontent");
    writeFile(testDir, "sampleTest.xoo", "Sample test xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src,another.xoo")
        .put("sonar.tests", "test,sampleTest2.xoo")
        .put("sonar.inclusions", "src/**")
        .put("sonar.exclusions", "**/another.*")
        .put("sonar.test.inclusions", "**/sampleTest*.*")
        .put("sonar.test.exclusions", "**/sampleTest2.xoo")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(2);
  }

  @Test
  void ignoreFilesWhenGreaterThanDefinedSize() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    File fileGreaterThanLimit = writeFile(srcDir, "sample.xoo");
    writeFile(srcDir, "another.xoo", "Sample xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        // set limit to 1MB
        .put("sonar.filesize.limit", "1")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
    String expectedLog = String.format("File '%s' is bigger than 1MB and as consequence is removed from the analysis scope.",
      fileGreaterThanLimit.toPath().toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs()).contains(expectedLog);
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisDoesNotFailOnBrokenSymlink() throws IOException {
    prepareBrokenSymlinkTestScenario();

    AnalysisBuilder analysisBuilder = tester.newAnalysis().properties(builder.build());

    assertThat(catchThrowableOfType(Exception.class, analysisBuilder::execute)).isNull();
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisWarnsAndIgnoresBrokenSymlink() throws IOException {
    Path link = prepareBrokenSymlinkTestScenario();

    AnalysisResult result = tester.newAnalysis().properties(builder.build()).execute();

    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file that does not exist.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.WARN)).contains(logMessage);
    InputFile fileA = result.inputFile("src/target_link.xoo");
    assertThat(fileA).isNull();
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisIgnoresSymbolicLinkWithTargetOutsideBaseDir() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    File otherDir = createDirectory(temp.toPath().resolve("other_dir")).toFile();
    File targetOutside = writeFile(otherDir, "target_outside.xoo");

    Path link = Paths.get(srcDir.getPath(), "target_link.xoo");
    Files.createSymbolicLink(link, targetOutside.toPath());

    AnalysisResult result = tester.newAnalysis().properties(builder.build()).execute();

    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file not located in project basedir.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.WARN)).contains(logMessage);
    InputFile fileA = result.inputFile("src/target_link.xoo");
    assertThat(fileA).isNull();
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisIgnoresSymbolicLinkWithRelativeTargetOutsideBaseDir() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    File otherDir = createDirectory(temp.toPath().resolve("other_dir")).toFile();
    writeFile(otherDir, "target_outside.xoo");

    Path linkPath = srcDir.toPath().resolve("target_link");
    Path link = Files.createSymbolicLink(linkPath, Paths.get("../../other_dir/target_outside.xoo"));

    tester.newAnalysis().properties(builder.build()).execute();

    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file not located in project basedir.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.WARN)).contains(logMessage);
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisIgnoresSymbolicLinkWithTargetOutsideModule() throws IOException {
    File srcDirA = createModuleWithSubdirectory("module_a", "src");
    File srcDirB = createModuleWithSubdirectory("module_b", "src");

    File target = writeFile(srcDirA, "target.xoo", "Sample xoo\ncontent");
    Path link = Paths.get(srcDirB.getPath(), "target_link.xoo");
    Files.createSymbolicLink(link, target.toPath());

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project")
      .put("sonar.modules", "module_a,module_b");

    AnalysisResult result = tester.newAnalysis().properties(builder.build()).execute();

    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file not located in module basedir.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.INFO)).contains(logMessage);
    InputFile fileA = result.inputFile("module_b/src/target_link.xoo");
    assertThat(fileA).isNull();
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisIgnoresSymbolicLinkWithRelativeTargetOutsideModule() throws IOException {
    File srcA = createModuleWithSubdirectory("module_a", "src");
    File srcB = createModuleWithSubdirectory("module_b", "src");

    Path target = srcB.toPath().resolve("target.xoo");
    FileUtils.write(target.toFile(), "Sample xoo\ncontent", StandardCharsets.UTF_8);
    Path link = srcA.toPath().resolve("target_link");
    Files.createSymbolicLink(link, Paths.get("../../module_b/src/target.xoo"));

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project")
      .put("sonar.modules", "module_a,module_b");

    AnalysisResult result = tester.newAnalysis().properties(builder.build()).execute();

    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file not located in module basedir.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.INFO)).contains(logMessage);
    InputFile fileA = result.inputFile("module_b/src/target.xoo");
    assertThat(fileA).isNotNull();
  }

  @Test
  @DisabledOnOs(OS.WINDOWS)
  void analysisDoesNotIgnoreSymbolicLinkWithRelativePath() throws IOException {
    File src = createModuleWithSubdirectory("module_a", "src");
    Path target = src.toPath().resolve("target.xoo");
    FileUtils.write(target.toFile(), "Sample xoo\ncontent", StandardCharsets.UTF_8);
    Path link = src.toPath().resolve("target_link");
    Files.createSymbolicLink(link, Paths.get("target.xoo"));

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project")
      .put("sonar.modules", "module_a");

    AnalysisResult result = tester.newAnalysis().properties(builder.build()).execute();

    InputFile targetFile = result.inputFile("module_a/src/target.xoo");
    assertThat(targetFile).isNotNull();
    String logMessage = String.format("File '%s' is ignored. It is a symbolic link targeting a file that does not exist.", link.toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.WARN)).doesNotContain(logMessage);
  }

  @Test
  void test_inclusions_on_multi_modules() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "tests");
    File srcDirB = createModuleWithSubdirectory("moduleB", "tests");

    writeFile(srcDirA, "sampleTestA.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sampleTestB.xoo", "Sample xoo\ncontent");

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project")
      .put("sonar.sources", "")
      .put("sonar.tests", "tests")
      .put("sonar.modules", "moduleA,moduleB");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder.build())
      .execute();

    assertThat(result.inputFiles()).hasSize(2);

    InputFile fileA = result.inputFile("moduleA/tests/sampleTestA.xoo");
    assertThat(fileA).isNotNull();

    InputFile fileB = result.inputFile("moduleB/tests/sampleTestB.xoo");
    assertThat(fileB).isNotNull();

    result = tester.newAnalysis()
      .properties(builder
        .put("sonar.test.inclusions", "moduleA/tests/**")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);

    fileA = result.inputFile("moduleA/tests/sampleTestA.xoo");
    assertThat(fileA).isNotNull();

    fileB = result.inputFile("moduleB/tests/sampleTestB.xoo");
    assertThat(fileB).isNull();
  }

  @Test
  void test_module_level_inclusions_override_parent_on_multi_modules() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sampleA.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sampleB.xoo", "Sample xoo\ncontent");

    builder = ImmutableMap.<String, String>builder()
      .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
      .put("sonar.projectKey", "com.foo.project")
      .put("sonar.sources", "src")
      .put("sonar.modules", "moduleA,moduleB")
      .put("sonar.inclusions", "**/*.php");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder.build())
      .execute();

    assertThat(result.inputFiles()).isEmpty();

    result = tester.newAnalysis()
      .properties(builder
        .put("moduleA.sonar.inclusions", "**/*.xoo")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);

    InputFile fileA = result.inputFile("moduleA/src/sampleA.xoo");
    assertThat(fileA).isNotNull();
  }

  @Test
  void warn_user_for_outdated_scanner_side_inherited_exclusions_for_multi_module_project() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sample.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .put("sonar.exclusions", "src/sample.xoo")
        .build())
      .execute();

    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
    assertThat(fileA).isNull();

    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
    assertThat(fileB).isNull();

    assertThat(logTester.logs(Level.WARN))
      .contains("Specifying module-relative paths at project level in the property 'sonar.exclusions' is deprecated. " +
        "To continue matching files like 'moduleA/src/sample.xoo', update this property so that patterns refer to project-relative paths.");
  }

  @Test
  void support_global_server_side_exclusions_for_multi_module_project() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sample.xoo", "Sample xoo\ncontent");

    tester.addGlobalServerSettings(CoreProperties.PROJECT_EXCLUSIONS_PROPERTY, "**/*.xoo");

    AnalysisResult result = tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .build())
      .execute();

    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
    assertThat(fileA).isNull();

    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
    assertThat(fileB).isNull();
  }

  @Test
  void support_global_server_side_global_exclusions_for_multi_module_project() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sample.xoo", "Sample xoo\ncontent");

    tester.addGlobalServerSettings(CoreProperties.GLOBAL_EXCLUSIONS_PROPERTY, "**/*.xoo");

    AnalysisResult result = tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .build())
      .execute();

    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
    assertThat(fileA).isNull();

    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
    assertThat(fileB).isNull();
  }

  @Test
  void warn_user_for_outdated_server_side_inherited_exclusions_for_multi_module_project() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sample.xoo", "Sample xoo\ncontent");

    tester.addProjectServerSettings("sonar.exclusions", "src/sample.xoo");

    AnalysisResult result = tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .build())
      .execute();

    InputFile fileA = result.inputFile("moduleA/src/sample.xoo");
    assertThat(fileA).isNull();

    InputFile fileB = result.inputFile("moduleB/src/sample.xoo");
    assertThat(fileB).isNull();

    assertThat(logTester.logs(Level.WARN))
      .contains("Specifying module-relative paths at project level in the property 'sonar.exclusions' is deprecated. " +
        "To continue matching files like 'moduleA/src/sample.xoo', update this property so that patterns refer to project-relative paths.");
  }

  @Test
  void failForDuplicateInputFile() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    AnalysisBuilder analysisBuilder = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src,src/sample.xoo")
        .build());
    assertThatThrownBy(analysisBuilder::execute)
      .isInstanceOf(MessageException.class)
      .hasMessage("File src/sample.xoo can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files");
  }

  // SONAR-9574
  @Test
  void failForDuplicateInputFileInDifferentModules() throws IOException {
    File srcDir = new File(baseDir, "module1/src");
    assertThat(srcDir.mkdirs()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");

    AnalysisBuilder analysisBuilder = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "module1/src")
        .put("sonar.modules", "module1")
        .put("module1.sonar.sources", "src")
        .build());
    assertThatThrownBy(analysisBuilder::execute)
      .isInstanceOf(MessageException.class)
      .hasMessage("File module1/src/sample.xoo can't be indexed twice. Please check that inclusion/exclusion patterns produce disjoint sets for main and test files");
  }

  // SONAR-5330
  @Test
  void scanProjectWithSourceSymlink() {
    assumeTrue(!System2.INSTANCE.isOsWindows());
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-symlink").getAbsoluteFile();
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.exclusions", "**/*.xoo.measures,**/*.xoo.scm")
      .property("sonar.test.exclusions", "**/*.xoo.measures,**/*.xoo.scm")
      .property("sonar.scm.exclusions.disabled", "true")
      .execute();

    assertThat(result.inputFiles()).hasSize(3);
    // check that symlink was not resolved to target
    assertThat(result.inputFiles()).extracting(InputFile::path).allMatch(path -> path.startsWith(projectDir.toPath()));
  }

  // SONAR-6719
  @Test
  void scanProjectWithWrongCase() {
    // To please the quality gate, don't use assumeTrue, or the test will be reported as skipped
    File projectDir = new File("test-resources/mediumtest/xoo/sample");
    AnalysisBuilder analysis = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.sources", "XOURCES")
      .property("sonar.tests", "TESTX")
      .property("sonar.scm.exclusions.disabled", "true");

    if (System2.INSTANCE.isOsWindows()) { // Windows is file path case-insensitive
      AnalysisResult result = analysis.execute();

      assertThat(result.inputFiles()).hasSize(8);
      assertThat(result.inputFiles()).extractingResultOf("relativePath").containsOnly(
        "testx/ClassOneTest.xoo.measures",
        "xources/hello/helloscala.xoo.measures",
        "xources/hello/HelloJava.xoo.measures",
        "testx/ClassOneTest.xoo",
        "xources/hello/HelloJava.xoo.scm",
        "xources/hello/helloscala.xoo",
        "testx/ClassOneTest.xoo.scm",
        "xources/hello/HelloJava.xoo");
    } else if (System2.INSTANCE.isOsMac()) {
      AnalysisResult result = analysis.execute();

      assertThat(result.inputFiles()).hasSize(8);
      assertThat(result.inputFiles()).extractingResultOf("relativePath").containsOnly(
        "TESTX/ClassOneTest.xoo.measures",
        "XOURCES/hello/helloscala.xoo.measures",
        "XOURCES/hello/HelloJava.xoo.measures",
        "TESTX/ClassOneTest.xoo",
        "XOURCES/hello/HelloJava.xoo.scm",
        "XOURCES/hello/helloscala.xoo",
        "TESTX/ClassOneTest.xoo.scm",
        "XOURCES/hello/HelloJava.xoo");
    } else {
      assertThatThrownBy(analysis::execute)
        .isInstanceOf(MessageException.class)
        .hasMessageContaining("The folder 'TESTX' does not exist for 'sample'");
    }
  }

  @Test
  void indexAnyFile() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDir, "sample.other", "Sample other\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(2);
    InputFile inputFile = result.inputFile("src/sample.other");
    assertThat(inputFile).isNotNull();
    assertThat(inputFile.type()).isEqualTo(InputFile.Type.MAIN);
    assertThat(inputFile.relativePath()).isEqualTo("src/sample.other");
    assertThat(inputFile.language()).isNull();
  }

  @Test
  void scanMultiModuleProject() {
    File projectDir = new File("test-resources/mediumtest/xoo/multi-modules-sample");
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .execute();

    assertThat(result.inputFiles()).hasSize(4);
  }

  @Test
  void deprecated_global_sensor_should_see_project_relative_paths() {
    File projectDir = new File("test-resources/mediumtest/xoo/multi-modules-sample");
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property(DeprecatedGlobalSensor.ENABLE_PROP, "true")
      .execute();

    assertThat(result.inputFiles()).hasSize(4);
    assertThat(logTester.logs(Level.INFO)).contains(
      "Deprecated Global Sensor: module_a/module_a1/src/main/xoo/com/sonar/it/samples/modules/a1/HelloA1.xoo",
      "Deprecated Global Sensor: module_a/module_a2/src/main/xoo/com/sonar/it/samples/modules/a2/HelloA2.xoo",
      "Deprecated Global Sensor: module_b/module_b1/src/main/xoo/com/sonar/it/samples/modules/b1/HelloB1.xoo",
      "Deprecated Global Sensor: module_b/module_b2/src/main/xoo/com/sonar/it/samples/modules/b2/HelloB2.xoo");
  }

  @Test
  void global_sensor_should_see_project_relative_paths() {
    File projectDir = new File("test-resources/mediumtest/xoo/multi-modules-sample");
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property(GlobalProjectSensor.ENABLE_PROP, "true")
      .execute();

    assertThat(result.inputFiles()).hasSize(4);
    assertThat(logTester.logs(Level.INFO)).contains(
      "Global Sensor: module_a/module_a1/src/main/xoo/com/sonar/it/samples/modules/a1/HelloA1.xoo",
      "Global Sensor: module_a/module_a2/src/main/xoo/com/sonar/it/samples/modules/a2/HelloA2.xoo",
      "Global Sensor: module_b/module_b1/src/main/xoo/com/sonar/it/samples/modules/b1/HelloB1.xoo",
      "Global Sensor: module_b/module_b2/src/main/xoo/com/sonar/it/samples/modules/b2/HelloB2.xoo");
  }

  @Test
  void scan_project_with_comma_in_source_path() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample,1.xoo", "Sample xoo\ncontent");
    writeFile(baseDir, "another,2.xoo", "Sample xoo 2\ncontent");

    File testDir = new File(baseDir, "test");
    assertThat(testDir.mkdir()).isTrue();

    writeFile(testDir, "sampleTest,1.xoo", "Sample test xoo\ncontent");
    writeFile(baseDir, "sampleTest,2.xoo", "Sample test xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src,\"another,2.xoo\"")
        .put("sonar.tests", "\"test\",\"sampleTest,2.xoo\"")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(4);
  }

  @Test
  void language_without_publishAllFiles_should_not_auto_publish_files() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    tester.addLanguage("xoo3", "xoo3", false, ".xoo3");

    writeFile(srcDir, "sample.xoo3", "Sample xoo\ncontent");
    writeFile(srcDir, "sample2.xoo3", "Sample xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(result.inputFiles())
      .extracting(InputFile::filename, InputFile::language, f -> ((DefaultInputFile) f).isPublished())
      .containsOnly(tuple("sample.xoo3", "xoo3", false), tuple("sample2.xoo3", "xoo3", false));
    assertThat(result.getReportReader().readComponent(result.getReportReader().readMetadata().getRootComponentRef()).getChildRefCount()).isZero();
  }

  @Test
  void two_languages_with_same_extension() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDir, "sample.xoo2", "Sample xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(2);

    tester.addLanguage("xoo2", "xoo2", ".xoo");
    AnalysisBuilder analysisBuilder = tester.newAnalysis()
      .properties(builder
        .put("sonar.lang.patterns.xoo2", "**/*.xoo")
        .build());

    assertThatThrownBy(analysisBuilder::execute)
      .isInstanceOf(MessageException.class)
      .hasMessage(
        "Language of file 'src" + File.separator
          + "sample.xoo' can not be decided as the file matches patterns of both sonar.lang.patterns.xoo : **/*.xoo and sonar.lang.patterns.xoo2 : **/*.xoo");

    // SONAR-9561
    result = tester.newAnalysis()
      .properties(builder
        .put("sonar.exclusions", "**/sample.xoo")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
  }

  @Test
  void log_all_exclusions_properties_per_modules() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    writeFile(srcDirA, "sample.xoo", "Sample xoo\ncontent");
    writeFile(srcDirB, "sample.xoo", "Sample xoo\ncontent");

    tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .put("sonar.inclusions", "**/global.inclusions")
        .put("sonar.test.inclusions", "**/global.test.inclusions")
        .put("sonar.exclusions", "**/global.exclusions")
        .put("sonar.test.exclusions", "**/global.test.exclusions")
        .put("sonar.coverage.exclusions", "**/coverage.exclusions")
        .put("sonar.cpd.exclusions", "**/cpd.exclusions")
        .build())
      .execute();

    assertThat(logTester.logs(Level.INFO))
      .containsSequence("Project configuration:",
        "  Included sources: **/global.inclusions",
        "  Excluded sources: **/global.exclusions, **/global.test.inclusions",
        "  Included tests: **/global.test.inclusions",
        "  Excluded tests: **/global.test.exclusions",
        "  Excluded sources for coverage: **/coverage.exclusions",
        "  Excluded sources for duplication: **/cpd.exclusions",
        "Indexing files of module 'moduleA'",
        "  Base dir: " + srcDirA.toPath().getParent().toRealPath(LinkOption.NOFOLLOW_LINKS),
        "  Included sources: **/global.inclusions",
        "  Excluded sources: **/global.exclusions, **/global.test.inclusions",
        "  Included tests: **/global.test.inclusions",
        "  Excluded tests: **/global.test.exclusions",
        "  Excluded sources for coverage: **/coverage.exclusions",
        "  Excluded sources for duplication: **/cpd.exclusions",
        "Indexing files of module 'moduleB'",
        "  Base dir: " + srcDirB.toPath().getParent().toRealPath(LinkOption.NOFOLLOW_LINKS),
        "  Included sources: **/global.inclusions",
        "  Excluded sources: **/global.exclusions, **/global.test.inclusions",
        "  Included tests: **/global.test.inclusions",
        "  Excluded tests: **/global.test.exclusions",
        "  Excluded sources for coverage: **/coverage.exclusions",
        "  Excluded sources for duplication: **/cpd.exclusions",
        "Indexing files of module 'com.foo.project'",
        "  Base dir: " + baseDir.toPath().toRealPath(LinkOption.NOFOLLOW_LINKS),
        "  Included sources: **/global.inclusions",
        "  Excluded sources: **/global.exclusions, **/global.test.inclusions",
        "  Included tests: **/global.test.inclusions",
        "  Excluded tests: **/global.test.exclusions",
        "  Excluded sources for coverage: **/coverage.exclusions",
        "  Excluded sources for duplication: **/cpd.exclusions");
  }

  @Test
  void ignore_files_outside_project_basedir() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample1.xoo", "Sample xoo\ncontent");

    File outsideBaseDir = createDirectory(temp.toPath().resolve("outsideBaseDir")).toFile();
    File xooFile2 = writeFile(outsideBaseDir, "another.xoo", "Sample xoo 2\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src," + FilenameUtils.separatorsToUnix(xooFile2.getPath()))
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
    String expectedLog = String.format("File '%s' is ignored. It is not located in project basedir '%s'.", xooFile2.toPath().toRealPath(LinkOption.NOFOLLOW_LINKS),
      baseDir.toPath().toRealPath(LinkOption.NOFOLLOW_LINKS));
    assertThat(logTester.logs(Level.WARN)).contains(expectedLog);
  }

  @Test
  void dont_log_warn_about_files_out_of_basedir_if_they_arent_included() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    writeFile(srcDir, "sample1.xoo", "Sample xoo\ncontent");

    File outsideBaseDir = createDirectory(temp.toPath().resolve("outsideBaseDir")).toFile();
    File xooFile2 = new File(outsideBaseDir, "another.xoo");
    FileUtils.write(xooFile2, "Sample xoo 2\ncontent", StandardCharsets.UTF_8);

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src," + PathUtils.canonicalPath(xooFile2))
        .put("sonar.inclusions", "**/sample1.xoo")
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);
    assertThat(logTester.logs(Level.WARN)).doesNotContain("File '" + xooFile2.getAbsolutePath() + "' is ignored. It is not located in project basedir '" + baseDir + "'.");
  }

  @Test
  void ignore_files_outside_module_basedir() throws IOException {
    File moduleA = new File(baseDir, "moduleA");
    assertThat(moduleA.mkdir()).isTrue();

    writeFile(moduleA, "src/sampleA.xoo", "Sample xoo\ncontent");
    File xooFile2 = writeFile(baseDir, "another.xoo", "Sample xoo 2\ncontent");
    Path xooFile2Path = xooFile2.toPath().toRealPath(LinkOption.NOFOLLOW_LINKS);

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.modules", "moduleA")
        .put("moduleA.sonar.sources", "src," + FilenameUtils.separatorsToUnix(xooFile2.getPath()))
        .build())
      .execute();

    assertThat(result.inputFiles()).hasSize(1);

    Path moduleAPath = new File(baseDir, "moduleA").toPath().toRealPath(LinkOption.NOFOLLOW_LINKS);
    assertThat(logTester.logs(Level.WARN))
      .contains(String.format("File '%s' is ignored. It is not located in module basedir '%s'.", xooFile2Path, moduleAPath));
  }

  @Test
  void exclusion_based_on_scm_info() {
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-ignored-file");
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.exclusions", "**/*.xoo.ignore")
      .property("sonar.test.exclusions", "**/*.xoo.ignore")
      .execute();

    assertThat(result.inputFile("xources/hello/ClassTwo.xoo")).isNull();
    assertThat(result.inputFile("testx/ClassTwoTest.xoo")).isNull();

    assertThat(result.inputFile("xources/hello/ClassOne.xoo")).isNotNull();
    assertThat(result.inputFile("testx/ClassOneTest.xoo")).isNotNull();
  }

  @Test
  void no_exclusion_when_scm_exclusions_is_disabled() {
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-ignored-file");
    AnalysisResult result = tester
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.scm.exclusions.disabled", "true")
      .property("sonar.exclusions", "**/*.xoo.ignore")
      .property("sonar.test.exclusions", "**/*.xoo.ignore")
      .execute();

    assertThat(result.inputFiles()).hasSize(4);

    assertThat(result.inputFile("xources/hello/ClassTwo.xoo")).isNotNull();
    assertThat(result.inputFile("testx/ClassTwoTest.xoo")).isNotNull();
    assertThat(result.inputFile("xources/hello/ClassOne.xoo")).isNotNull();
    assertThat(result.inputFile("testx/ClassOneTest.xoo")).isNotNull();
  }

  @Test
  void index_basedir_by_default() throws IOException {
    writeFile(baseDir, "sample.xoo", "Sample xoo\ncontent");
    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .build())
      .execute();

    assertThat(logTester.logs()).anyMatch(log -> log.startsWith("1 file indexed (done) | time="));
    assertThat(result.inputFile("sample.xoo")).isNotNull();
  }

  @Test
  void givenExclusionEndingWithOneWildcardWhenAnalysedThenOnlyDirectChildrenFilesShouldBeExcluded() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", true);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    // src/srcSubDir/srcSubSubDir/subSubSrc.xoo
    File srcSubSubDir = createDir(srcSubDir, "srcSubSubDir", true);
    writeFile(srcSubSubDir, "subSubSrc.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.exclusions", "src/srcSubDir/*")
        .build())
      .execute();

    assertAnalysedFiles(result, "src/src.xoo", "src/srcSubDir/srcSubSubDir/subSubSrc.xoo");
  }

  @Test
  void givenPathsWithoutReadPermissionWhenAllChildrenAreExcludedThenScannerShouldSkipIt() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", false);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    // src/srcSubDir2/srcSub2.xoo
    File srcSubDir2 = createDir(srcDir, "srcSubDir2", true);
    boolean fileNotReadable = writeFile(srcSubDir2, "srcSub2.xoo", "Sample 2 xoo\ncontent").setReadable(false);
    assumeTrue(fileNotReadable);

    // src/srcSubDir2/srcSubSubDir2/srcSubSub2.xoo
    File srcSubSubDir2 = createDir(srcSubDir2, "srcSubSubDir2", false);
    writeFile(srcSubSubDir2, "srcSubSub2.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.exclusions", "src/srcSubDir/**/*,src/srcSubDir2/**")
        .build())
      .execute();

    assertAnalysedFiles(result, "src/src.xoo");
    assertThat(logTester.logs()).contains("1 file ignored because of inclusion/exclusion patterns");
  }

  @Test
  void givenFileWithoutAccessWhenChildrenAreExcludedThenThenScanShouldFail() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    boolean fileNotReadable = writeFile(srcDir, "src.xoo", "Sample xoo\ncontent").setReadable(false);
    assumeTrue(fileNotReadable);

    AnalysisBuilder result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.exclusions", "src/src.xoo/**/*") // incorrect pattern, but still the scan should fail if src.xoo is not accessible
        .build());

    assertThatThrownBy(result::execute)
      .isExactlyInstanceOf(IllegalStateException.class)
      .hasMessageStartingWith("java.lang.IllegalStateException: Unable to read file");
  }

  @Test
  void givenDirectoryWithoutReadPermissionWhenIncludedThenScanShouldFail() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", false);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    AnalysisBuilder result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.exclusions", "src/srcSubDir/*") // srcSubDir should not be excluded unless all children are excluded (src/srcSubDir/**/*)
        .build());

    assertThatThrownBy(result::execute)
      .isExactlyInstanceOf(IllegalStateException.class)
      .hasMessageEndingWith("Failed to preprocess files");
  }

  @Test
  void givenDirectoryWhenAllChildrenAreExcludedThenSkippedFilesShouldBeReported() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", true);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    // src/srcSubDir2/srcSub2.xoo
    File srcSubDir2 = createDir(srcDir, "srcSubDir2", true);
    boolean fileNotReadable = writeFile(srcSubDir2, "srcSub2.xoo", "Sample 2 xoo\ncontent").setReadable(false);
    assumeTrue(fileNotReadable);

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.exclusions", "src/srcSubDir/**/*,src/srcSubDir2/*")
        .build())
      .execute();

    assertAnalysedFiles(result, "src/src.xoo");
    assertThat(logTester.logs()).contains("2 files ignored because of inclusion/exclusion patterns");
  }

  @Test
  void givenDirectoryWithoutReadPermissionWhenNotIncludedThenScanShouldSkipIt() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", true);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    // src/srcSubDir2/srcSub2.xoo
    File srcSubDir2 = createDir(srcDir, "srcSubDir2", false);
    writeFile(srcSubDir2, "srcSub2.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .put("sonar.inclusions", "src/srcSubDir/**/*")
        .build())
      .execute();

    assertAnalysedFiles(result, "src/srcSubDir/srcSub.xoo");
  }

  @Test
  void givenDirectoryWithoutReadPermissionUnderSourcesWhenAnalysedThenShouldFail() throws IOException {
    // src/src.xoo
    File srcDir = createDir(baseDir, "src", true);
    writeFile(srcDir, "src.xoo", "Sample xoo 2\ncontent");

    // src/srcSubDir/srcSub.xoo
    File srcSubDir = createDir(srcDir, "srcSubDir", false);
    writeFile(srcSubDir, "srcSub.xoo", "Sample xoo\ncontent");

    AnalysisBuilder result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build());

    assertThatThrownBy(result::execute)
      .isExactlyInstanceOf(IllegalStateException.class)
      .hasMessageEndingWith("Failed to preprocess files");
  }

  @ParameterizedTest
  @ValueSource(booleans = {
    true,
    false
  })
  void shouldScanAndAnalyzeAllHiddenFiles(boolean setHiddenFileScanningExplicitly) throws IOException {
    prepareHiddenFileProject();
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-hidden-files");
    AnalysisBuilder analysisBuilder = tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssuePerFile", null, "Issue Per File", "MAJOR", null, "xoo")
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.oneIssuePerFile.enableHiddenFileProcessing", "true");

    if (setHiddenFileScanningExplicitly) {
      // default is assumed to be false, here we set it explicitly
      analysisBuilder.property("sonar.scanner.excludeHiddenFiles", "false");
    }

    AnalysisResult result = analysisBuilder.execute();

    for (Map.Entry<String, Boolean> pathToHiddenStatus : hiddenFileProjectExpectedHiddenStatus().entrySet()) {
      String filePath = pathToHiddenStatus.getKey();
      boolean expectedIsHidden = pathToHiddenStatus.getValue();
      assertHiddenFileScan(result, filePath, expectedIsHidden, true);
      // we expect the sensor to process all files, regardless of visibility
      assertFileIssue(result, filePath, true);
    }
    assertThat(result.inputFiles()).hasSize(10);
  }

  @Test
  void shouldScanAllFilesAndOnlyAnalyzeNonHiddenFiles() throws IOException {
    prepareHiddenFileProject();
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-hidden-files");
    AnalysisResult result = tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssuePerFile", null, "Issue Per File", "MAJOR", null, "xoo")
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.oneIssuePerFile.enableHiddenFileProcessing", "false")
      .execute();

    for (Map.Entry<String, Boolean> pathToHiddenStatus : hiddenFileProjectExpectedHiddenStatus().entrySet()) {
      String filePath = pathToHiddenStatus.getKey();
      boolean expectedHiddenStatus = pathToHiddenStatus.getValue();
      assertHiddenFileScan(result, filePath, expectedHiddenStatus, true);
      // sensor should not process hidden files, we only expect issues on non-hidden files
      assertFileIssue(result, filePath, !expectedHiddenStatus);
    }
    assertThat(result.inputFiles()).hasSize(10);
  }

  @ParameterizedTest
  @ValueSource(booleans = {
    true,
    false
  })
  void shouldNotScanAndAnalyzeHiddenFilesWhenHiddenFileScanningIsDisabled(boolean sensorHiddenFileProcessingEnabled) throws IOException {
    prepareHiddenFileProject();
    File projectDir = new File("test-resources/mediumtest/xoo/sample-with-hidden-files");
    AnalysisResult result = tester
      .addRules(new XooRulesDefinition())
      .addActiveRule("xoo", "OneIssuePerFile", null, "Issue Per File", "MAJOR", null, "xoo")
      .newAnalysis(new File(projectDir, "sonar-project.properties"))
      .property("sonar.scanner.excludeHiddenFiles", "true")
      // hidden files are not scanned, so issues can't be raised on them regardless if the sensor wants to process them
      .property("sonar.oneIssuePerFile.enableHiddenFileProcessing", String.valueOf(sensorHiddenFileProcessingEnabled))
      .execute();

    for (Map.Entry<String, Boolean> pathToHiddenStatus : hiddenFileProjectExpectedHiddenStatus().entrySet()) {
      String filePath = pathToHiddenStatus.getKey();
      boolean expectedHiddenStatus = pathToHiddenStatus.getValue();
      assertHiddenFileScan(result, filePath, expectedHiddenStatus, false);
      if (!expectedHiddenStatus) {
        assertFileIssue(result, filePath, true);
      }
    }
    assertThat(result.inputFiles()).hasSize(1);
  }

  @Test
  void hiddenFilesAssignedToALanguageShouldNotBePublishedByDefault() throws IOException {
    tester
      .addRules(new XooRulesDefinition());

    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    File hiddenFile = writeFile(srcDir, ".xoo", "Sample xoo\ncontent");
    setFileAsHiddenOnWindows(hiddenFile.toPath());
    File hiddenFileWithoutLanguage = writeFile(srcDir, ".bar", "Sample bar\ncontent");
    setFileAsHiddenOnWindows(hiddenFileWithoutLanguage.toPath());
    writeFile(srcDir, "file.xoo", "Sample xoo\ncontent");

    AnalysisResult result = tester.newAnalysis()
      .properties(builder
        .put("sonar.sources", "src")
        .build())
      .execute();

    DefaultInputFile hiddenInputFile = (DefaultInputFile) result.inputFile("src/.xoo");

    assertThat(hiddenInputFile).isNotNull();
    assertThat(hiddenInputFile.isPublished()).isFalse();
    assertThatThrownBy(() -> result.getReportComponent(hiddenInputFile))
      .isInstanceOf(IllegalStateException.class)
      .hasMessageContaining("Unable to find report for component");

    DefaultInputFile hiddenInputFileWithoutLanguage = (DefaultInputFile) result.inputFile("src/.bar");
    assertThat(hiddenInputFileWithoutLanguage).isNotNull();
    assertThat(hiddenInputFileWithoutLanguage.isPublished()).isFalse();
    assertThatThrownBy(() -> result.getReportComponent(hiddenInputFileWithoutLanguage))
      .isInstanceOf(IllegalStateException.class)
      .hasMessageContaining("Unable to find report for component");

    DefaultInputFile visibleInputFile = (DefaultInputFile) result.inputFile("src/file.xoo");
    assertThat(visibleInputFile).isNotNull();
    assertThat(visibleInputFile.isPublished()).isTrue();
    assertThat(result.getReportComponent(visibleInputFile)).isNotNull();
  }

  @Test
  void shouldDetectHiddenFilesFromMultipleModules() throws IOException {
    File srcDirA = createModuleWithSubdirectory("moduleA", "src");
    File srcDirB = createModuleWithSubdirectory("moduleB", "src");

    File fileModuleA = writeFile(srcDirA, ".xoo", "Sample xoo\ncontent");
    setFileAsHiddenOnWindows(fileModuleA.toPath());
    File fileModuleB = writeFile(srcDirB, ".xoo", "Sample xoo\ncontent");
    setFileAsHiddenOnWindows(fileModuleB.toPath());

    AnalysisResult result = tester.newAnalysis()
      .properties(ImmutableMap.<String, String>builder()
        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
        .put("sonar.projectKey", "com.foo.project")
        .put("sonar.sources", "src")
        .put("sonar.modules", "moduleA,moduleB")
        .build())
      .execute();

    assertHiddenFileScan(result, "moduleA/src/.xoo", true, true);
    assertHiddenFileScan(result, "moduleB/src/.xoo", true, true);
  }

  private File createModuleWithSubdirectory(String moduleName, String subDirName) {
    File moduleBaseDir = new File(baseDir, moduleName);
    File srcDir = moduleBaseDir.toPath().resolve(subDirName).toFile();
    assertThat(srcDir.mkdirs()).isTrue();
    return srcDir;
  }

  private static void assertAnalysedFiles(AnalysisResult result, String... files) {
    assertThat(result.inputFiles().stream().map(InputFile::toString).toList()).contains(files);
  }

  private static File createDir(File parentDir, String name, boolean isReadable) {
    File dir = new File(parentDir, name);
    assertThat(dir.mkdir()).isTrue();
    boolean fileSystemOperationSucceded = dir.setReadable(isReadable);
    assumeTrue(fileSystemOperationSucceded); // On windows + java there is no reliable way to play with readable/not readable flag
    return dir;
  }

  private static File writeFile(File parent, String name, String content) throws IOException {
    File file = new File(parent, name);
    FileUtils.write(file, content, StandardCharsets.UTF_8);
    return file;
  }

  private static File writeFile(File parent, String name) throws IOException {
    File file = new File(parent, name);
    RandomAccessFile raf = new RandomAccessFile(file, "rw");
    raf.setLength(1024 * 1024 + 1);
    raf.close();
    return file;
  }

  private Path prepareBrokenSymlinkTestScenario() throws IOException {
    File srcDir = new File(baseDir, "src");
    assertThat(srcDir.mkdir()).isTrue();

    File target = writeFile(srcDir, "target.xoo");
    Path link = Paths.get(srcDir.getPath(), "target_link.xoo");
    Files.createSymbolicLink(link, target.toPath());
    Files.delete(target.toPath());

    return link;
  }

  private Map<String, Boolean> hiddenFileProjectExpectedHiddenStatus() {
    return Map.of(
      "xources/.hidden/.xoo", true,
      "xources/.hidden/Class.xoo", true,
      "xources/.hidden/.nestedHidden/.xoo", true,
      "xources/.hidden/.nestedHidden/Class.xoo", true,
      "xources/.hidden/.nestedHidden/visibleInHiddenFolder/.xoo", true,
      "xources/.hidden/.nestedHidden/visibleInHiddenFolder/Class.xoo", true,
      "xources/nonHidden/.xoo", true,
      "xources/nonHidden/Class.xoo", false,
      "xources/nonHidden/.hiddenInVisibleFolder/.xoo", true,
      "xources/nonHidden/.hiddenInVisibleFolder/Class.xoo", true);
  }

  private static void prepareHiddenFileProject() throws IOException {
    if (!SystemUtils.IS_OS_WINDOWS) {
      return;
    }

    // On Windows, we need to set the hidden attribute on the file system
    Set<String> dirAndFilesToHideOnWindows = Set.of(
      "xources/.hidden",
      "xources/.hidden/.xoo",
      "xources/.hidden/.nestedHidden",
      "xources/.hidden/.nestedHidden/.xoo",
      "xources/.hidden/.nestedHidden/visibleInHiddenFolder/.xoo",
      "xources/nonHidden/.xoo",
      "xources/nonHidden/.hiddenInVisibleFolder",
      "xources/nonHidden/.hiddenInVisibleFolder/.xoo");

    for (String path : dirAndFilesToHideOnWindows) {
      Path pathFromResources = Path.of("test-resources/mediumtest/xoo/sample-with-hidden-files", path);
      setFileAsHiddenOnWindows(pathFromResources);
    }
  }

  private static void setFileAsHiddenOnWindows(Path path) throws IOException {
    if (SystemUtils.IS_OS_WINDOWS) {
      Files.setAttribute(path, "dos:hidden", true, LinkOption.NOFOLLOW_LINKS);
    }
  }

  private static void assertHiddenFileScan(AnalysisResult result, String filePath, boolean expectedHiddenStatus, boolean hiddenFilesShouldBeScanned) {
    InputFile file = result.inputFile(filePath);

    if (!hiddenFilesShouldBeScanned && expectedHiddenStatus) {
      assertThat(file).isNull();
    } else {
      assertThat(file).withFailMessage(String.format("File \"%s\" was not analyzed", filePath)).isNotNull();
      assertThat(file.isHidden())
        .withFailMessage(String.format("Expected file \"%s\" hidden status to be \"%s\", however was \"%s\"", filePath, expectedHiddenStatus, file.isHidden()))
        .isEqualTo(expectedHiddenStatus);
    }
  }

  private static void assertFileIssue(AnalysisResult result, String filePath, boolean expectToHaveIssue) {
    InputFile file = result.inputFile(filePath);
    assertThat(file).isNotNull();
    List<ScannerReport.Issue> issues = result.issuesFor(file);
    if (expectToHaveIssue) {
      assertThat(issues).hasSize(1);
    } else {
      assertThat(issues).isEmpty();
    }
  }
}