SONAR-6068 Improve performance of FileSystem query operation

plugins/sonar-cpd-plugin/src/test/java/org/sonar/plugins/cpd/CpdSensorTest.java

@@ -20,7 +20,9 @@
 package org.sonar.plugins.cpd;
 
 import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.config.PropertyDefinitions;
 import org.sonar.api.config.Settings;
@@ -28,24 +30,29 @@ import org.sonar.api.resources.Java;
 import org.sonar.batch.duplication.BlockCache;
 import org.sonar.plugins.cpd.index.IndexFactory;
 
+import java.io.IOException;
+
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
 
 public class CpdSensorTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   JavaCpdEngine sonarEngine;
   DefaultCpdEngine sonarBridgeEngine;
   CpdSensor sensor;
   Settings settings;
 
   @Before
-  public void setUp() {
+  public void setUp() throws IOException {
     IndexFactory indexFactory = mock(IndexFactory.class);
     sonarEngine = new JavaCpdEngine(indexFactory, null, null);
     sonarBridgeEngine = new DefaultCpdEngine(indexFactory, new CpdMappings(), null, null, mock(BlockCache.class));
     settings = new Settings(new PropertyDefinitions(CpdPlugin.class));
 
-    DefaultFileSystem fs = new DefaultFileSystem();
+    DefaultFileSystem fs = new DefaultFileSystem(temp.newFolder());
     sensor = new CpdSensor(sonarEngine, sonarBridgeEngine, settings, fs);
   }
 

plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/XooPlugin.java

@@ -31,6 +31,7 @@ import org.sonar.xoo.rule.ChecksSensor;
 import org.sonar.xoo.rule.CreateIssueByInternalKeySensor;
 import org.sonar.xoo.rule.OneIssueOnDirPerFileSensor;
 import org.sonar.xoo.rule.OneIssuePerLineSensor;
+import org.sonar.xoo.rule.RandomAccessSensor;
 import org.sonar.xoo.rule.XooFakeExporter;
 import org.sonar.xoo.rule.XooFakeImporter;
 import org.sonar.xoo.rule.XooFakeImporterWithMessages;
@@ -74,6 +75,7 @@ public class XooPlugin extends SonarPlugin {
       CoveragePerTestSensor.class,
       DependencySensor.class,
       ChecksSensor.class,
+      RandomAccessSensor.class,
 
       OneIssuePerLineSensor.class,
       OneIssueOnDirPerFileSensor.class,

plugins/sonar-xoo-plugin/src/main/java/org/sonar/xoo/rule/RandomAccessSensor.java

@@ -0,0 +1,73 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.xoo.rule;
+
+import org.apache.commons.io.FileUtils;
+import org.sonar.api.batch.fs.FilePredicates;
+import org.sonar.api.batch.fs.FileSystem;
+import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.InputFile.Type;
+import org.sonar.api.batch.sensor.Sensor;
+import org.sonar.api.batch.sensor.SensorContext;
+import org.sonar.api.batch.sensor.SensorDescriptor;
+import org.sonar.api.rule.RuleKey;
+import org.sonar.xoo.Xoo;
+
+import java.io.File;
+import java.io.IOException;
+
+public class RandomAccessSensor implements Sensor {
+
+  private static final String SONAR_XOO_RANDOM_ACCESS_ISSUE_PATHS = "sonar.xoo.randomAccessIssue.paths";
+  public static final String RULE_KEY = "RandomAccessIssue";
+
+  @Override
+  public void describe(SensorDescriptor descriptor) {
+    descriptor
+      .name("One Issue Per File with Random Access")
+      .onlyOnLanguages(Xoo.KEY)
+      .createIssuesForRuleRepositories(XooRulesDefinition.XOO_REPOSITORY)
+      .requireProperty(SONAR_XOO_RANDOM_ACCESS_ISSUE_PATHS);
+  }
+
+  @Override
+  public void execute(SensorContext context) {
+    File f = new File(context.settings().getString(SONAR_XOO_RANDOM_ACCESS_ISSUE_PATHS));
+    FileSystem fs = context.fileSystem();
+    FilePredicates p = fs.predicates();
+    try {
+      for (String path : FileUtils.readLines(f)) {
+        createIssues(fs.inputFile(p.and(p.hasPath(path), p.hasType(Type.MAIN), p.hasLanguage(Xoo.KEY))), context);
+      }
+    } catch (IOException e) {
+      throw new IllegalStateException(e);
+    }
+  }
+
+  private void createIssues(InputFile file, SensorContext context) {
+    RuleKey ruleKey = RuleKey.of(XooRulesDefinition.XOO_REPOSITORY, RULE_KEY);
+    context.newIssue()
+      .ruleKey(ruleKey)
+      .onFile(file)
+      .atLine(1)
+      .message("This issue is generated on each file")
+      .save();
+  }
+}

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/XooPluginTest.java

@@ -27,6 +27,6 @@ public class XooPluginTest {
 
   @Test
   public void provide_extensions() {
-    assertThat(new XooPlugin().getExtensions()).hasSize(19);
+    assertThat(new XooPlugin().getExtensions()).hasSize(20);
   }
 }

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/CoveragePerTestSensorTest.java

@@ -57,7 +57,7 @@ public class CoveragePerTestSensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new CoveragePerTestSensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
   }
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/DependencySensorTest.java

@@ -56,7 +56,7 @@ public class DependencySensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new DependencySensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
   }
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/MeasureSensorTest.java

@@ -65,7 +65,7 @@ public class MeasureSensorTest {
     baseDir = temp.newFolder();
     metricFinder = mock(MetricFinder.class);
     sensor = new MeasureSensor(metricFinder);
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
     storage = mock(SensorStorage.class);
     when(context.newMeasure()).then(new Answer<DefaultMeasure>() {

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/SymbolReferencesSensorTest.java

@@ -52,7 +52,7 @@ public class SymbolReferencesSensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new SymbolReferencesSensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
   }
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/SyntaxHighlightingSensorTest.java

@@ -52,7 +52,7 @@ public class SyntaxHighlightingSensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new SyntaxHighlightingSensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
   }
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/TestCaseSensorTest.java

@@ -56,7 +56,7 @@ public class TestCaseSensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new TestCaseSensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
   }
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/lang/XooTokenizerSensorTest.java

@@ -57,7 +57,7 @@ public class XooTokenizerSensorTest {
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
     sensor = new XooTokenizerSensor();
-    fileSystem = new DefaultFileSystem();
+    fileSystem = new DefaultFileSystem(baseDir);
     when(context.fileSystem()).thenReturn(fileSystem);
     settings = new Settings();
     when(context.settings()).thenReturn(settings);

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/rule/OneIssuePerLineSensorTest.java

@@ -19,7 +19,9 @@
  */
 package org.sonar.xoo.rule;
 
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.mockito.ArgumentCaptor;
 import org.mockito.invocation.InvocationOnMock;
 import org.mockito.stubbing.Answer;
@@ -34,6 +36,8 @@ import org.sonar.api.batch.sensor.issue.internal.DefaultIssue;
 import org.sonar.api.config.Settings;
 import org.sonar.xoo.Xoo;
 
+import java.io.IOException;
+
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.times;
@@ -42,6 +46,9 @@ import static org.mockito.Mockito.when;
 
 public class OneIssuePerLineSensorTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   private OneIssuePerLineSensor sensor = new OneIssuePerLineSensor();
 
   @Test
@@ -52,8 +59,8 @@ public class OneIssuePerLineSensorTest {
   }
 
   @Test
-  public void testRule() {
-    DefaultFileSystem fs = new DefaultFileSystem();
+  public void testRule() throws IOException {
+    DefaultFileSystem fs = new DefaultFileSystem(temp.newFolder());
     DefaultInputFile inputFile = new DefaultInputFile("foo", "src/Foo.xoo").setLanguage(Xoo.KEY).setLines(10);
     fs.add(inputFile);
 
@@ -76,8 +83,8 @@ public class OneIssuePerLineSensorTest {
   }
 
   @Test
-  public void testForceSeverity() {
-    DefaultFileSystem fs = new DefaultFileSystem();
+  public void testForceSeverity() throws IOException {
+    DefaultFileSystem fs = new DefaultFileSystem(temp.newFolder());
     DefaultInputFile inputFile = new DefaultInputFile("foo", "src/Foo.xoo").setLanguage(Xoo.KEY).setLines(10);
     fs.add(inputFile);
 

plugins/sonar-xoo-plugin/src/test/java/org/sonar/xoo/scm/XooBlameCommandTest.java

@@ -57,7 +57,7 @@ public class XooBlameCommandTest {
   @Before
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
-    fs = new DefaultFileSystem();
+    fs = new DefaultFileSystem(baseDir);
     input = mock(BlameInput.class);
     when(input.fileSystem()).thenReturn(fs);
   }

sonar-batch/pom.xml

@@ -9,6 +9,10 @@
 
   <artifactId>sonar-batch</artifactId>
   <name>SonarQube :: Batch</name>
+  
+  <properties>
+    <enableBenchmarkAssertions>false</enableBenchmarkAssertions>
+  </properties>
 
   <dependencies>
     <dependency>
@@ -197,4 +201,18 @@
       </plugin>
     </plugins>
   </build>
+  
+  <profiles>
+    <profile>
+      <id>runBenchmarks</id>
+      <activation>
+        <property>
+          <name>runBenchmarks</name>
+        </property>
+      </activation>
+      <properties>
+        <enableBenchmarkAssertions>true</enableBenchmarkAssertions>
+      </properties>
+    </profile>
+  </profiles>
 </project>

sonar-batch/src/main/java/org/sonar/batch/maven/MavenProjectConverter.java

@@ -36,7 +36,6 @@ import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.maven.MavenUtils;
 import org.sonar.api.task.TaskExtension;
 import org.sonar.api.utils.MessageException;
-import org.sonar.batch.scan.filesystem.DefaultModuleFileSystem;
 import org.sonar.java.api.JavaUtils;
 
 import javax.annotation.Nullable;
@@ -219,15 +218,6 @@ public class MavenProjectConverter implements TaskExtension {
     return resolvePath(pom.getBuild().getDirectory(), pom.getBasedir());
   }
 
-  public void synchronizeFileSystem(MavenProject pom, DefaultModuleFileSystem into) {
-    into.resetDirs(
-      pom.getBasedir(),
-      getBuildDir(pom),
-      mainDirs(pom),
-      testDirs(pom),
-      Arrays.asList(resolvePath(pom.getBuild().getOutputDirectory(), pom.getBasedir())));
-  }
-
   static File resolvePath(@Nullable String path, File basedir) {
     if (path != null) {
       File file = new File(StringUtils.trim(path));

sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/AdditionalFilePredicates.java

@@ -20,7 +20,7 @@
 package org.sonar.batch.scan.filesystem;
 
 import org.apache.commons.io.FilenameUtils;
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 
@@ -34,7 +34,7 @@ class AdditionalFilePredicates {
     // only static inner classes
   }
 
-  static class KeyPredicate implements FilePredicate {
+  static class KeyPredicate extends AbstractFilePredicate {
     private final String key;
 
     KeyPredicate(String key) {
@@ -47,7 +47,7 @@ class AdditionalFilePredicates {
     }
   }
 
-  static class DeprecatedKeyPredicate implements FilePredicate {
+  static class DeprecatedKeyPredicate extends AbstractFilePredicate {
     private final String key;
 
     DeprecatedKeyPredicate(String key) {
@@ -60,7 +60,7 @@ class AdditionalFilePredicates {
     }
   }
 
-  static class SourceRelativePathPredicate implements FilePredicate {
+  static class SourceRelativePathPredicate extends AbstractFilePredicate {
     private final String path;
 
     SourceRelativePathPredicate(String s) {
@@ -73,7 +73,7 @@ class AdditionalFilePredicates {
     }
   }
 
-  static class SourceDirPredicate implements FilePredicate {
+  static class SourceDirPredicate extends AbstractFilePredicate {
     private final String path;
 
     SourceDirPredicate(String s) {

sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystem.java

@@ -80,14 +80,11 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
   private DefaultModuleFileSystem(ModuleInputFileCache moduleInputFileCache, String moduleKey, Settings settings,
     FileIndexer indexer, ModuleFileSystemInitializer initializer,
     @Nullable ComponentIndexer componentIndexer) {
-    super(moduleInputFileCache);
+    super(initializer.baseDir(), moduleInputFileCache);
     this.componentIndexer = componentIndexer;
     this.moduleKey = moduleKey;
     this.settings = settings;
     this.indexer = indexer;
-    if (initializer.baseDir() != null) {
-      setBaseDir(initializer.baseDir());
-    }
     setWorkDir(initializer.workingDir());
     this.buildDir = initializer.buildDir();
     this.sourceDirsOrFiles = initializer.sources();
@@ -219,17 +216,6 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
     }
   }
 
-  public void resetDirs(File basedir, File buildDir, List<File> sourceDirs, List<File> testDirs, List<File> binaryDirs) {
-    if (initialized) {
-      throw MessageException.of("Module filesystem is already initialized. Modifications of filesystem are only allowed during Initializer phase.");
-    }
-    setBaseDir(basedir);
-    this.buildDir = buildDir;
-    this.sourceDirsOrFiles = existingDirsOrFiles(sourceDirs);
-    this.testDirsOrFiles = existingDirsOrFiles(testDirs);
-    this.binaryDirs = existingDirsOrFiles(binaryDirs);
-  }
-
   public void index() {
     if (initialized) {
       throw MessageException.of("Module filesystem can only be indexed once");
@@ -241,16 +227,6 @@ public class DefaultModuleFileSystem extends DefaultFileSystem implements Module
     }
   }
 
-  private List<File> existingDirsOrFiles(List<File> dirsOrFiles) {
-    ImmutableList.Builder<File> builder = ImmutableList.builder();
-    for (File dirOrFile : dirsOrFiles) {
-      if (dirOrFile.exists()) {
-        builder.add(dirOrFile);
-      }
-    }
-    return builder.build();
-  }
-
   private FilePredicate fromDeprecatedAttribute(String key, Collection<String> value) {
     if ("TYPE".equals(key)) {
       return predicates().or(Collections2.transform(value, new Function<String, FilePredicate>() {

sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java

@@ -24,7 +24,6 @@ import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
-import org.sonar.api.batch.fs.internal.RelativePathPredicate;
 
 public class ModuleInputFileCache extends DefaultFileSystem.Cache implements BatchComponent {
 
@@ -37,17 +36,17 @@ public class ModuleInputFileCache extends DefaultFileSystem.Cache implements Bat
   }
 
   @Override
-  protected Iterable<InputFile> inputFiles() {
+  public Iterable<InputFile> inputFiles() {
     return projectCache.filesByModule(moduleKey);
   }
 
   @Override
-  protected InputFile inputFile(RelativePathPredicate predicate) {
-    return projectCache.getFile(moduleKey, predicate.path());
+  public InputFile inputFile(String relativePath) {
+    return projectCache.getFile(moduleKey, relativePath);
   }
 
   @Override
-  protected InputDir inputDir(String relativePath) {
+  public InputDir inputDir(String relativePath) {
     return projectCache.getDir(moduleKey, relativePath);
   }
 

sonar-batch/src/test/java/org/sonar/batch/debt/SqaleRatingDecoratorTest.java

@@ -73,7 +73,7 @@ public class SqaleRatingDecoratorTest {
   public void setUp() throws Exception {
     settings = new Settings();
 
-    fs = new DefaultFileSystem();
+    fs = new DefaultFileSystem(temp.newFolder());
     fs.add(new DefaultInputFile("foo", file.getPath())
       .setLanguage("java")
       .setFile(temp.newFile("Foo.java")));

sonar-batch/src/test/java/org/sonar/batch/issue/ignore/scanner/IssueExclusionsLoaderTest.java

@@ -65,13 +65,14 @@ public class IssueExclusionsLoaderTest {
   @Mock
   private PatternMatcher patternMatcher;
 
-  DefaultFileSystem fs = new DefaultFileSystem().setEncoding(UTF_8);
-  IssueExclusionsLoader scanner;
-  File baseDir;
+  private DefaultFileSystem fs;
+  private IssueExclusionsLoader scanner;
+  private File baseDir;
 
   @Before
-  public void before() throws IOException {
+  public void before() throws Exception {
     baseDir = temp.newFolder();
+    fs = new DefaultFileSystem(baseDir).setEncoding(UTF_8);
     MockitoAnnotations.initMocks(this);
     scanner = new IssueExclusionsLoader(regexpScanner, exclusionPatternInitializer, inclusionPatternInitializer, fs);
   }

sonar-batch/src/test/java/org/sonar/batch/mediumtest/Benchmark.java

@@ -0,0 +1,49 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.batch.mediumtest;
+
+import org.hamcrest.Matchers;
+import org.junit.rules.ErrorCollector;
+import org.slf4j.LoggerFactory;
+
+public class Benchmark extends ErrorCollector {
+
+  private static final boolean ENABLED = "true".equals(System.getProperty("enableBenchmarkAssertions"));
+
+  static {
+    if (ENABLED) {
+      LoggerFactory.getLogger(Benchmark.class).warn("Assertions are calibrated for SonarSource dedicated box. " +
+        "They can be disabled by setting the property -DenableBenchmarkAssertions=false.");
+    }
+  }
+
+  public void expectBetween(String label, long val, long min, long max) {
+    if (ENABLED) {
+      checkThat(label, val, Matchers.allOf(Matchers.greaterThan(min), Matchers.lessThan(max)));
+    }
+  }
+
+  public void expectLessThanOrEqualTo(String label, long val, long max) {
+    if (ENABLED) {
+      checkThat(label, val, Matchers.lessThan(max));
+    }
+  }
+
+}

sonar-batch/src/test/java/org/sonar/batch/mediumtest/fs/RandomFsAccessMediumTest.java

@@ -0,0 +1,136 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.batch.mediumtest.fs;
+
+import com.google.common.base.Charsets;
+import com.google.common.collect.ImmutableMap;
+import org.apache.commons.io.FileUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.sonar.batch.mediumtest.BatchMediumTester;
+import org.sonar.batch.mediumtest.Benchmark;
+import org.sonar.batch.mediumtest.TaskResult;
+import org.sonar.batch.protocol.input.ActiveRule;
+import org.sonar.xoo.XooPlugin;
+
+import java.io.File;
+import java.io.IOException;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class RandomFsAccessMediumTest {
+
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
+  @Rule
+  public Benchmark bench = new Benchmark();
+
+  public BatchMediumTester tester = BatchMediumTester.builder()
+    .registerPlugin("xoo", new XooPlugin())
+    .addDefaultQProfile("xoo", "Sonar Way")
+    .activateRule(new ActiveRule("xoo", "RandomAccessIssue", null, "One issue per line", "MAJOR", null, "xoo"))
+    .build();
+
+  @Before
+  public void prepare() {
+    tester.start();
+  }
+
+  @After
+  public void stop() {
+    tester.stop();
+  }
+
+  @Test
+  public void testRandomFsAccessByAbsolutePath() throws IOException {
+
+    File baseDir = temp.newFolder();
+    File srcDir = prepareBigProject(baseDir);
+
+    File paths = new File(baseDir, "paths.txt");
+    int ISSUE_COUNT = 10000;
+    for (int i = 0; i < ISSUE_COUNT; i++) {
+      File xooFile = new File(srcDir, "sample" + (i / 10 + 1) + ".xoo");
+      FileUtils.write(paths, xooFile.getAbsolutePath() + "\n", Charsets.UTF_8, true);
+    }
+
+    long start = System.currentTimeMillis();
+    TaskResult result = tester.newTask()
+      .properties(ImmutableMap.<String, String>builder()
+        .put("sonar.task", "scan")
+        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
+        .put("sonar.projectKey", "com.foo.project")
+        .put("sonar.projectName", "Foo Project")
+        .put("sonar.projectVersion", "1.0-SNAPSHOT")
+        .put("sonar.projectDescription", "Description of Foo Project")
+        .put("sonar.sources", "src")
+        .put("sonar.xoo.randomAccessIssue.paths", paths.getAbsolutePath())
+        .build())
+      .start();
+
+    assertThat(result.issues()).hasSize(ISSUE_COUNT);
+    bench.expectLessThanOrEqualTo("Time to create " + ISSUE_COUNT + " issues on random files using FileSystem query", System.currentTimeMillis() - start, 2000);
+  }
+
+  @Test
+  public void testRandomFsAccessByRelativePath() throws IOException {
+
+    File baseDir = temp.newFolder();
+    File srcDir = prepareBigProject(baseDir);
+
+    File paths = new File(baseDir, "paths.txt");
+    int ISSUE_COUNT = 10000;
+    for (int i = 0; i < ISSUE_COUNT; i++) {
+      FileUtils.write(paths, "src/sample" + (i / 10 + 1) + ".xoo\n", Charsets.UTF_8, true);
+    }
+
+    TaskResult result = tester.newTask()
+      .properties(ImmutableMap.<String, String>builder()
+        .put("sonar.task", "scan")
+        .put("sonar.projectBaseDir", baseDir.getAbsolutePath())
+        .put("sonar.projectKey", "com.foo.project")
+        .put("sonar.projectName", "Foo Project")
+        .put("sonar.projectVersion", "1.0-SNAPSHOT")
+        .put("sonar.projectDescription", "Description of Foo Project")
+        .put("sonar.sources", "src")
+        .put("sonar.xoo.randomAccessIssue.paths", paths.getAbsolutePath())
+        .build())
+      .start();
+
+    assertThat(result.issues()).hasSize(ISSUE_COUNT);
+
+  }
+
+  private File prepareBigProject(File baseDir) throws IOException {
+    File srcDir = new File(baseDir, "src");
+    srcDir.mkdir();
+
+    for (int i = 1; i <= 1000; i++) {
+      File xooFile = new File(srcDir, "sample" + i + ".xoo");
+      FileUtils.write(xooFile, "foo");
+    }
+    return srcDir;
+  }
+
+}

sonar-batch/src/test/java/org/sonar/batch/rule/QProfileSensorTest.java

@@ -19,7 +19,10 @@
  */
 package org.sonar.batch.rule;
 
+import org.junit.Before;
+import org.junit.Rule;
 import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.SensorContext;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.measures.CoreMetrics;
@@ -32,10 +35,15 @@ import java.util.Date;
 
 import static org.assertj.core.api.Assertions.assertThat;
 import static org.mockito.Matchers.argThat;
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class QProfileSensorTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   static final Date DATE = UtcDateUtils.parseDateTime("2014-01-15T12:00:00+0000");
   static final QProfile JAVA_PROFILE = new QProfile().setKey("java-two").setName("Java Two").setLanguage("java")
     .setRulesUpdatedAt(DATE);
@@ -45,7 +53,12 @@ public class QProfileSensorTest {
   ModuleQProfiles moduleQProfiles = mock(ModuleQProfiles.class);
   Project project = mock(Project.class);
   SensorContext sensorContext = mock(SensorContext.class);
-  DefaultFileSystem fs = new DefaultFileSystem();
+  DefaultFileSystem fs;
+
+  @Before
+  public void prepare() throws Exception {
+    fs = new DefaultFileSystem(temp.newFolder());
+  }
 
   @Test
   public void to_string() throws Exception {

sonar-batch/src/test/java/org/sonar/batch/rule/QProfileVerifierTest.java

@@ -23,24 +23,31 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 import org.slf4j.Logger;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.config.Settings;
 import org.sonar.api.utils.MessageException;
 
-import static org.mockito.Mockito.*;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.verify;
+import static org.mockito.Mockito.when;
 
 public class QProfileVerifierTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
-  DefaultFileSystem fs = new DefaultFileSystem();
-  ModuleQProfiles profiles;
-  Settings settings = new Settings();
+  private DefaultFileSystem fs;
+  private ModuleQProfiles profiles;
+  private Settings settings = new Settings();
 
   @Before
-  public void before() {
+  public void before() throws Exception {
+    fs = new DefaultFileSystem(temp.newFolder());
     profiles = mock(ModuleQProfiles.class);
     QProfile javaProfile = new QProfile().setKey("p1").setName("My Java profile").setLanguage("java");
     when(profiles.findByLanguage("java")).thenReturn(javaProfile);

sonar-batch/src/test/java/org/sonar/batch/scan/LanguageVerifierTest.java

@@ -19,9 +19,11 @@
  */
 package org.sonar.batch.scan;
 
+import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.config.Settings;
 import org.sonar.api.resources.Java;
@@ -34,13 +36,21 @@ import static org.assertj.core.api.Assertions.assertThat;
 
 public class LanguageVerifierTest {
 
-  Settings settings = new Settings();
-  LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(Java.INSTANCE));
-  DefaultFileSystem fs = new DefaultFileSystem();
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
 
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
+  private Settings settings = new Settings();
+  private LanguagesReferential languages = new DefaultLanguagesReferential(new Languages(Java.INSTANCE));
+  private DefaultFileSystem fs;
+
+  @Before
+  public void prepare() throws Exception {
+    fs = new DefaultFileSystem(temp.newFolder());
+  }
+
   @Test
   public void language_is_not_set() throws Exception {
     LanguageVerifier verifier = new LanguageVerifier(settings, languages, fs);

sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/ComponentIndexerTest.java

@@ -48,7 +48,7 @@ public class ComponentIndexerTest {
   @Rule
   public TemporaryFolder temp = new TemporaryFolder();
   private File baseDir;
-  private DefaultFileSystem fs = new DefaultFileSystem();
+  private DefaultFileSystem fs;
   private SonarIndex sonarIndex;
   private AbstractLanguage cobolLanguage;
   private Project project;
@@ -56,6 +56,7 @@ public class ComponentIndexerTest {
   @Before
   public void prepare() throws IOException {
     baseDir = temp.newFolder();
+    fs = new DefaultFileSystem(baseDir);
     sonarIndex = mock(SonarIndex.class);
     project = new Project("myProject");
     cobolLanguage = new AbstractLanguage("cobol") {

sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/DefaultModuleFileSystemTest.java

@@ -58,13 +58,13 @@ public class DefaultModuleFileSystemTest {
 
   @Test
   public void test_equals_and_hashCode() throws Exception {
-    DefaultModuleFileSystem foo1 = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem foo1 = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
-    DefaultModuleFileSystem foo2 = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem foo2 = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
-    DefaultModuleFileSystem bar = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem bar = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("bar"), settings, fileIndexer, initializer, componentIndexer);
-    DefaultModuleFileSystem branch = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem branch = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("bar", "branch", "My project"), settings, fileIndexer, initializer, componentIndexer);
 
     assertThat(foo1.moduleKey()).isEqualTo("foo");
@@ -79,7 +79,7 @@ public class DefaultModuleFileSystemTest {
 
   @Test
   public void default_source_encoding() {
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     assertThat(fs.sourceCharset()).isEqualTo(Charset.defaultCharset());
@@ -89,7 +89,7 @@ public class DefaultModuleFileSystemTest {
   @Test
   public void source_encoding_is_set() {
     settings.setProperty(CoreProperties.ENCODING_PROPERTY, "Cp1124");
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     assertThat(fs.encoding()).isEqualTo(Charset.forName("Cp1124"));
@@ -119,7 +119,7 @@ public class DefaultModuleFileSystemTest {
     javaTest.mkdirs();
     when(initializer.tests()).thenReturn(Arrays.asList(javaTest, additionalTest));
 
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     assertThat(fs.baseDir().getCanonicalPath()).isEqualTo(basedir.getCanonicalPath());
@@ -130,35 +130,9 @@ public class DefaultModuleFileSystemTest {
     assertThat(fs.binaryDirs()).hasSize(1);
   }
 
-  @Test
-  public void should_reset_dirs() throws IOException {
-    File basedir = temp.newFolder();
-    when(initializer.baseDir()).thenReturn(basedir);
-    when(initializer.workingDir()).thenReturn(basedir);
-    when(initializer.sources()).thenReturn(Arrays.asList(new File(basedir, "src/main/java")));
-
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
-      new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
-
-    File existingDir = temp.newFolder("new_folder");
-    File notExistingDir = new File(existingDir, "not_exist");
-
-    fs.resetDirs(existingDir, existingDir,
-      Lists.newArrayList(existingDir, notExistingDir), Lists.newArrayList(existingDir, notExistingDir), Lists.newArrayList(existingDir, notExistingDir));
-
-    assertThat(fs.baseDir().getCanonicalPath()).isEqualTo(existingDir.getCanonicalPath());
-    assertThat(fs.buildDir().getCanonicalPath()).isEqualTo(existingDir.getCanonicalPath());
-    assertThat(fs.sourceDirs()).hasSize(1);
-    assertThat(fs.sourceDirs().get(0).getCanonicalPath()).isEqualTo(existingDir.getCanonicalPath());
-    assertThat(fs.testDirs()).hasSize(1);
-    assertThat(fs.testDirs().get(0).getCanonicalPath()).isEqualTo(existingDir.getCanonicalPath());
-    assertThat(fs.binaryDirs()).hasSize(1);
-    assertThat(fs.binaryDirs().get(0).getCanonicalPath()).isEqualTo(existingDir.getCanonicalPath());
-  }
-
   @Test
   public void should_search_input_files() throws Exception {
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     File mainFile = temp.newFile();
@@ -176,7 +150,7 @@ public class DefaultModuleFileSystemTest {
 
   @Test
   public void should_index() throws Exception {
-    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache, 
+    DefaultModuleFileSystem fs = new DefaultModuleFileSystem(moduleInputFileCache,
       new Project("foo"), settings, fileIndexer, initializer, componentIndexer);
 
     verifyZeroInteractions(fileIndexer);

sonar-batch/src/test/java/org/sonar/batch/scan/report/JSONReportTest.java

@@ -64,11 +64,11 @@ public class JSONReportTest {
   private SimpleDateFormat SIMPLE_DATE_FORMAT = new SimpleDateFormat("yyyy-MM-dd");
 
   @org.junit.Rule
-  public TemporaryFolder temporaryFolder = new TemporaryFolder();
+  public TemporaryFolder temp = new TemporaryFolder();
 
   JSONReport jsonReport;
   Resource resource = mock(Resource.class);
-  DefaultFileSystem fs = new DefaultFileSystem();
+  DefaultFileSystem fs;
   Server server = mock(Server.class);
   ActiveRules activeRules = mock(ActiveRules.class);
   Settings settings = new Settings();
@@ -76,7 +76,8 @@ public class JSONReportTest {
   private UserRepository userRepository;
 
   @Before
-  public void before() {
+  public void before() throws Exception {
+    fs = new DefaultFileSystem(temp.newFolder());
     SIMPLE_DATE_FORMAT.setTimeZone(TimeZone.getTimeZone("GMT+02:00"));
     when(resource.getEffectiveKey()).thenReturn("Action.java");
     when(server.getVersion()).thenReturn("3.6");
@@ -161,7 +162,7 @@ public class JSONReportTest {
 
   @Test
   public void should_export_issues_to_file() throws IOException {
-    File workDir = temporaryFolder.newFolder("sonar");
+    File workDir = temp.newFolder("sonar");
     fs.setWorkDir(workDir);
 
     when(jsonReport.getIssues()).thenReturn(Collections.<DefaultIssue>emptyList());

sonar-batch/src/test/java/org/sonar/batch/sensor/AnalyzerOptimizerTest.java

@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.AnalysisMode;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
@@ -39,18 +40,20 @@ import static org.mockito.Mockito.when;
 
 public class AnalyzerOptimizerTest {
 
-  DefaultFileSystem fs = new DefaultFileSystem();
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
 
   @Rule
   public ExpectedException thrown = ExpectedException.none();
-  private AnalyzerOptimizer optimizer;
 
+  private DefaultFileSystem fs;
+  private AnalyzerOptimizer optimizer;
   private Settings settings;
-
   private AnalysisMode analysisMode;
 
   @Before
-  public void prepare() {
+  public void prepare() throws Exception {
+    fs = new DefaultFileSystem(temp.newFolder());
     settings = new Settings();
     analysisMode = mock(AnalysisMode.class);
     optimizer = new AnalyzerOptimizer(fs, new ActiveRulesBuilder().build(), settings, analysisMode);

sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorContextTest.java

@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.AnalysisMode;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
 import org.sonar.api.batch.measure.MetricFinder;
@@ -41,6 +42,9 @@ import static org.mockito.Mockito.when;
 
 public class DefaultSensorContextTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
@@ -52,9 +56,9 @@ public class DefaultSensorContextTest {
   private AnalysisMode analysisMode;
 
   @Before
-  public void prepare() {
+  public void prepare() throws Exception {
     activeRules = new ActiveRulesBuilder().build();
-    fs = new DefaultFileSystem();
+    fs = new DefaultFileSystem(temp.newFolder());
     MetricFinder metricFinder = mock(MetricFinder.class);
     when(metricFinder.findByKey(CoreMetrics.NCLOC_KEY)).thenReturn(CoreMetrics.NCLOC);
     when(metricFinder.findByKey(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION_KEY)).thenReturn(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION);

sonar-batch/src/test/java/org/sonar/batch/sensor/DefaultSensorStorageTest.java

@@ -23,6 +23,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
 import org.mockito.ArgumentCaptor;
 import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
@@ -66,6 +67,9 @@ import static org.mockito.Mockito.when;
 
 public class DefaultSensorStorageTest {
 
+  @Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
@@ -78,9 +82,9 @@ public class DefaultSensorStorageTest {
   private DefaultIndex sonarIndex;
 
   @Before
-  public void prepare() {
+  public void prepare() throws Exception {
     activeRules = new ActiveRulesBuilder().build();
-    fs = new DefaultFileSystem();
+    fs = new DefaultFileSystem(temp.newFolder());
     MetricFinder metricFinder = mock(MetricFinder.class);
     when(metricFinder.findByKey(CoreMetrics.NCLOC_KEY)).thenReturn(CoreMetrics.NCLOC);
     when(metricFinder.findByKey(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION_KEY)).thenReturn(CoreMetrics.FUNCTION_COMPLEXITY_DISTRIBUTION);

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/AbstractFilePredicate.java

@@ -0,0 +1,60 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.api.batch.fs;
+
+import com.google.common.base.Predicate;
+import com.google.common.collect.Iterables;
+import org.sonar.api.batch.fs.FileSystem.Index;
+
+/**
+ * Partial implementation of {@link FilePredicate}.
+ * @since 5.1
+ */
+public abstract class AbstractFilePredicate implements FilePredicate {
+
+  protected static final int DEFAULT_PRIORITY = 10;
+  protected static final int USE_INDEX = 20;
+
+  @Override
+  public Iterable<InputFile> filter(Iterable<InputFile> target) {
+    return Iterables.filter(target, new Predicate<InputFile>() {
+      @Override
+      public boolean apply(InputFile input) {
+        return AbstractFilePredicate.this.apply(input);
+      }
+    });
+  }
+
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    return filter(index.inputFiles());
+  }
+
+  @Override
+  public int priority() {
+    return DEFAULT_PRIORITY;
+  }
+
+  @Override
+  public int compareTo(FilePredicate o) {
+    return o.priority() - priority();
+  }
+
+}

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/FilePredicate.java

@@ -19,11 +19,35 @@
  */
 package org.sonar.api.batch.fs;
 
+import org.sonar.api.batch.fs.internal.RelativePathPredicate;
+
 /**
  * Determines if a file must be kept in search results. See {@link org.sonar.api.batch.fs.FileSystem}
  * and {@link org.sonar.api.batch.fs.FilePredicates}.
  * @since 4.2
  */
-public interface FilePredicate {
+public interface FilePredicate extends Comparable<FilePredicate> {
+  /**
+   * Test if provided file is valid for this predicate
+   */
   boolean apply(InputFile inputFile);
+
+  /**
+   * Filter provided files to keep only the ones that are valid for this predicate
+   */
+  Iterable<InputFile> filter(Iterable<InputFile> inputFiles);
+
+  /**
+   * Get all files that are valid for this predicate.
+   */
+  Iterable<InputFile> get(FileSystem.Index index);
+
+  /**
+   * For optimization. FilePredicates will be applied in priority order. For example when doing
+   * p.and(p1, p2, p3) then p1, p2 and p3 will be applied according to their priority value. Higher priority value
+   * are applied first.
+   * Assign a high priority when the predicate will likely highly reduce the set of InputFiles to filter. Also
+   * {@link RelativePathPredicate} and AbsolutePathPredicate have a high priority since they are using cache index.
+   */
+  int priority();
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/FileSystem.java

@@ -149,4 +149,17 @@ public interface FileSystem extends BatchComponent {
    * @since 5.0
    */
   File resolvePath(String path);
+
+  /**
+   * Interface of the underlying file index.
+   */
+  public static interface Index {
+    Iterable<InputFile> inputFiles();
+
+    @CheckForNull
+    InputFile inputFile(String relativePath);
+
+    @CheckForNull
+    InputDir inputDir(String relativePath);
+  }
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/AbsolutePathPredicate.java

@@ -19,18 +19,26 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.PathUtils;
 
+import java.io.File;
+import java.util.Arrays;
+import java.util.Collections;
+
 /**
  * @since 4.2
  */
-class AbsolutePathPredicate implements FilePredicate {
+class AbsolutePathPredicate extends AbstractFilePredicate {
 
   private final String path;
+  private final File baseDir;
 
-  AbsolutePathPredicate(String path) {
+  AbsolutePathPredicate(String path, File baseDir) {
+    this.baseDir = baseDir;
     this.path = PathUtils.sanitize(path);
   }
 
@@ -38,4 +46,19 @@ class AbsolutePathPredicate implements FilePredicate {
   public boolean apply(InputFile f) {
     return path.equals(f.absolutePath());
   }
+
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    String relative = PathUtils.sanitize(new PathResolver().relativePath(baseDir, new File(path)));
+    if (relative == null) {
+      return Collections.<InputFile>emptyList();
+    }
+    InputFile f = index.inputFile(relative);
+    return f != null ? Arrays.asList(f) : Collections.<InputFile>emptyList();
+  }
+
+  @Override
+  public int priority() {
+    return USE_INDEX;
+  }
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/AndPredicate.java

@@ -19,20 +19,45 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import com.google.common.annotations.VisibleForTesting;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
 
+import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
 
 /**
  * @since 4.2
  */
-class AndPredicate implements FilePredicate {
+class AndPredicate extends AbstractFilePredicate {
 
-  private final Collection<FilePredicate> predicates;
+  private final List<FilePredicate> predicates = new ArrayList<>();
 
-  AndPredicate(Collection<FilePredicate> predicates) {
-    this.predicates = predicates;
+  private AndPredicate() {
+  }
+
+  public static FilePredicate create(Collection<FilePredicate> predicates) {
+    if (predicates.isEmpty()) {
+      return TruePredicate.TRUE;
+    }
+    AndPredicate result = new AndPredicate();
+    for (FilePredicate filePredicate : predicates) {
+      if (filePredicate == TruePredicate.TRUE) {
+        continue;
+      } else if (filePredicate == FalsePredicate.FALSE) {
+        return FalsePredicate.FALSE;
+      } else if (filePredicate instanceof AndPredicate) {
+        result.predicates.addAll(((AndPredicate) filePredicate).predicates);
+      } else {
+        result.predicates.add(filePredicate);
+      }
+    }
+    Collections.sort(result.predicates);
+    return result;
   }
 
   @Override
@@ -45,4 +70,31 @@ class AndPredicate implements FilePredicate {
     return true;
   }
 
+  @Override
+  public Iterable<InputFile> filter(Iterable<InputFile> target) {
+    Iterable<InputFile> result = target;
+    for (FilePredicate predicate : predicates) {
+      result = predicate.filter(result);
+    }
+    return result;
+  }
+
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    if (predicates.isEmpty()) {
+      return index.inputFiles();
+    }
+    // Optimization, use get on first predicate then filter with next predicates
+    Iterable<InputFile> result = predicates.get(0).get(index);
+    for (int i = 1; i < predicates.size(); i++) {
+      result = predicates.get(i).filter(result);
+    }
+    return result;
+  }
+
+  @VisibleForTesting
+  Collection<FilePredicate> predicates() {
+    return predicates;
+  }
+
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultFilePredicates.java

@@ -35,10 +35,14 @@ import java.util.List;
  * @since 4.2
  */
 public class DefaultFilePredicates implements FilePredicates {
+
+  private final File baseDir;
+
   /**
    * Client code should use {@link org.sonar.api.batch.fs.FileSystem#predicates()} to get an instance
    */
-  DefaultFilePredicates() {
+  DefaultFilePredicates(File baseDir) {
+    this.baseDir = baseDir;
   }
 
   /**
@@ -57,16 +61,13 @@ public class DefaultFilePredicates implements FilePredicates {
     return FalsePredicate.FALSE;
   }
 
-  /**
-   * Warning - not efficient because absolute path is not indexed yet.
-   */
   @Override
   public FilePredicate hasAbsolutePath(String s) {
-    return new AbsolutePathPredicate(s);
+    return new AbsolutePathPredicate(s, baseDir);
   }
 
   /**
-   * TODO document that non-normalized path and Windows-style path are supported
+   * non-normalized path and Windows-style path are supported
    */
   @Override
   public FilePredicate hasRelativePath(String s) {
@@ -160,31 +161,31 @@ public class DefaultFilePredicates implements FilePredicates {
 
   @Override
   public FilePredicate or(Collection<FilePredicate> or) {
-    return new OrPredicate(or);
+    return OrPredicate.create(or);
   }
 
   @Override
   public FilePredicate or(FilePredicate... or) {
-    return new OrPredicate(Arrays.asList(or));
+    return OrPredicate.create(Arrays.asList(or));
   }
 
   @Override
   public FilePredicate or(FilePredicate first, FilePredicate second) {
-    return new OrPredicate(Arrays.asList(first, second));
+    return OrPredicate.create(Arrays.asList(first, second));
   }
 
   @Override
   public FilePredicate and(Collection<FilePredicate> and) {
-    return new AndPredicate(and);
+    return AndPredicate.create(and);
   }
 
   @Override
   public FilePredicate and(FilePredicate... and) {
-    return new AndPredicate(Arrays.asList(and));
+    return AndPredicate.create(Arrays.asList(and));
   }
 
   @Override
   public FilePredicate and(FilePredicate first, FilePredicate second) {
-    return new AndPredicate(Arrays.asList(first, second));
+    return AndPredicate.create(Arrays.asList(first, second));
   }
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/DefaultFileSystem.java

@@ -19,7 +19,9 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import com.google.common.base.Function;
 import com.google.common.base.Preconditions;
+import com.google.common.collect.Iterables;
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.FilePredicates;
 import org.sonar.api.batch.fs.FileSystem;
@@ -35,7 +37,6 @@ import java.io.File;
 import java.io.IOException;
 import java.nio.charset.Charset;
 import java.util.ArrayList;
-import java.util.Collection;
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.Iterator;
@@ -50,25 +51,23 @@ public class DefaultFileSystem implements FileSystem {
 
   private final Cache cache;
   private final SortedSet<String> languages = new TreeSet<String>();
-  private File baseDir, workDir;
+  private final File baseDir;
+  private File workDir;
   private Charset encoding;
-  private final FilePredicates predicates = new DefaultFilePredicates();
+  private final FilePredicates predicates;
 
   /**
    * Only for testing
    */
-  public DefaultFileSystem() {
-    this.cache = new MapCache();
+  public DefaultFileSystem(File baseDir) {
+    this(baseDir, new MapCache());
   }
 
-  protected DefaultFileSystem(Cache cache) {
+  protected DefaultFileSystem(File baseDir, Cache cache) {
+    Preconditions.checkNotNull(baseDir, "Base directory can't be null");
+    this.baseDir = baseDir.getAbsoluteFile();
     this.cache = cache;
-  }
-
-  public DefaultFileSystem setBaseDir(File d) {
-    Preconditions.checkNotNull(d, "Base directory can't be null");
-    this.baseDir = d.getAbsoluteFile();
-    return this;
+    this.predicates = new DefaultFilePredicates(baseDir);
   }
 
   @Override
@@ -102,10 +101,6 @@ public class DefaultFileSystem implements FileSystem {
 
   @Override
   public InputFile inputFile(FilePredicate predicate) {
-    doPreloadFiles();
-    if (predicate instanceof RelativePathPredicate) {
-      return cache.inputFile((RelativePathPredicate) predicate);
-    }
     Iterable<InputFile> files = inputFiles(predicate);
     Iterator<InputFile> iterator = files.iterator();
     if (!iterator.hasNext()) {
@@ -133,30 +128,24 @@ public class DefaultFileSystem implements FileSystem {
   @Override
   public Iterable<InputFile> inputFiles(FilePredicate predicate) {
     doPreloadFiles();
-    return filter(cache.inputFiles(), predicate);
+    return predicate.get(cache);
   }
 
   @Override
   public boolean hasFiles(FilePredicate predicate) {
     doPreloadFiles();
-    for (InputFile element : cache.inputFiles()) {
-      if (predicate.apply(element)) {
-        return true;
-      }
-    }
-    return false;
+    return predicate.get(cache).iterator().hasNext();
   }
 
   @Override
   public Iterable<File> files(FilePredicate predicate) {
     doPreloadFiles();
-    Collection<File> result = new ArrayList<File>();
-    for (InputFile element : inputFiles(predicate)) {
-      if (predicate.apply(element)) {
-        result.add(element.file());
+    return Iterables.transform(inputFiles(predicate), new Function<InputFile, File>() {
+      @Override
+      public File apply(InputFile input) {
+        return input.file();
       }
-    }
-    return result;
+    });
   }
 
   @Override
@@ -169,16 +158,6 @@ public class DefaultFileSystem implements FileSystem {
     return cache.inputDir(relativePath);
   }
 
-  public static Collection<InputFile> filter(Iterable<InputFile> target, FilePredicate predicate) {
-    Collection<InputFile> result = new ArrayList<InputFile>();
-    for (InputFile element : target) {
-      if (predicate.apply(element)) {
-        result.add(element);
-      }
-    }
-    return result;
-  }
-
   /**
    * Adds InputFile to the list and registers its language, if present.
    * Synchronized because PersistIt Exchange is not concurrent
@@ -228,14 +207,17 @@ public class DefaultFileSystem implements FileSystem {
     // nothing to do by default
   }
 
-  public abstract static class Cache {
-    protected abstract Iterable<InputFile> inputFiles();
+  public abstract static class Cache implements Index {
+    @Override
+    public abstract Iterable<InputFile> inputFiles();
 
+    @Override
     @CheckForNull
-    protected abstract InputFile inputFile(RelativePathPredicate predicate);
+    public abstract InputFile inputFile(String relativePath);
 
+    @Override
     @CheckForNull
-    protected abstract InputDir inputDir(String relativePath);
+    public abstract InputDir inputDir(String relativePath);
 
     protected abstract void doAdd(InputFile inputFile);
 
@@ -264,12 +246,12 @@ public class DefaultFileSystem implements FileSystem {
     }
 
     @Override
-    public InputFile inputFile(RelativePathPredicate predicate) {
-      return fileMap.get(predicate.path());
+    public InputFile inputFile(String relativePath) {
+      return fileMap.get(relativePath);
     }
 
     @Override
-    protected InputDir inputDir(String relativePath) {
+    public InputDir inputDir(String relativePath) {
       return dirMap.get(relativePath);
     }
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/FalsePredicate.java

@@ -19,10 +19,14 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
 
-class FalsePredicate implements FilePredicate {
+import java.util.Collections;
+
+class FalsePredicate extends AbstractFilePredicate {
 
   static final FilePredicate FALSE = new FalsePredicate();
 
@@ -30,4 +34,14 @@ class FalsePredicate implements FilePredicate {
   public boolean apply(InputFile inputFile) {
     return false;
   }
+
+  @Override
+  public Iterable<InputFile> filter(Iterable<InputFile> target) {
+    return Collections.emptyList();
+  }
+
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    return Collections.emptyList();
+  }
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/LanguagePredicate.java

@@ -19,13 +19,14 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+
 import org.sonar.api.batch.fs.InputFile;
 
 /**
  * @since 4.2
  */
-class LanguagePredicate implements FilePredicate {
+class LanguagePredicate extends AbstractFilePredicate {
   private final String language;
 
   LanguagePredicate(String language) {

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/NotPredicate.java

@@ -19,13 +19,15 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.InputFile;
 
 /**
  * @since 4.2
  */
-class NotPredicate implements FilePredicate {
+class NotPredicate extends AbstractFilePredicate {
 
   private final FilePredicate predicate;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/OrPredicate.java

@@ -19,25 +19,41 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import com.google.common.annotations.VisibleForTesting;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.FilePredicate;
 import org.sonar.api.batch.fs.InputFile;
 
-import java.util.Arrays;
+import java.util.ArrayList;
 import java.util.Collection;
 
 /**
  * @since 4.2
  */
-class OrPredicate implements FilePredicate {
+class OrPredicate extends AbstractFilePredicate {
 
-  private final Collection<FilePredicate> predicates;
+  private final Collection<FilePredicate> predicates = new ArrayList<>();
 
-  OrPredicate(Collection<FilePredicate> predicates) {
+  private OrPredicate() {
+  }
+
+  public static FilePredicate create(Collection<FilePredicate> predicates) {
     if (predicates.isEmpty()) {
-      this.predicates = Arrays.asList(TruePredicate.TRUE);
-    } else {
-      this.predicates = predicates;
+      return TruePredicate.TRUE;
+    }
+    OrPredicate result = new OrPredicate();
+    for (FilePredicate filePredicate : predicates) {
+      if (filePredicate == TruePredicate.TRUE) {
+        return TruePredicate.TRUE;
+      } else if (filePredicate == FalsePredicate.FALSE) {
+        continue;
+      } else if (filePredicate instanceof OrPredicate) {
+        result.predicates.addAll(((OrPredicate) filePredicate).predicates);
+      } else {
+        result.predicates.add(filePredicate);
+      }
     }
+    return result;
   }
 
   @Override
@@ -50,4 +66,9 @@ class OrPredicate implements FilePredicate {
     return false;
   }
 
+  @VisibleForTesting
+  Collection<FilePredicate> predicates() {
+    return predicates;
+  }
+
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/PathPatternPredicate.java

@@ -19,13 +19,14 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+
 import org.sonar.api.batch.fs.InputFile;
 
 /**
  * @since 4.2
  */
-class PathPatternPredicate implements FilePredicate {
+class PathPatternPredicate extends AbstractFilePredicate {
 
   private final PathPattern pattern;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/RelativePathPredicate.java

@@ -19,14 +19,18 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.utils.PathUtils;
 
+import java.util.Arrays;
+import java.util.Collections;
+
 /**
  * @since 4.2
  */
-public class RelativePathPredicate implements FilePredicate {
+public class RelativePathPredicate extends AbstractFilePredicate {
 
   private final String path;
 
@@ -43,4 +47,15 @@ public class RelativePathPredicate implements FilePredicate {
     return path.equals(f.relativePath());
   }
 
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    InputFile f = index.inputFile(this.path);
+    return f != null ? Arrays.asList(f) : Collections.<InputFile>emptyList();
+  }
+
+  @Override
+  public int priority() {
+    return USE_INDEX;
+  }
+
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/StatusPredicate.java

@@ -19,13 +19,14 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+
 import org.sonar.api.batch.fs.InputFile;
 
 /**
  * @since 4.2
  */
-class StatusPredicate implements FilePredicate {
+class StatusPredicate extends AbstractFilePredicate {
 
   private final InputFile.Status status;
 

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/TruePredicate.java

@@ -19,10 +19,12 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import org.sonar.api.batch.fs.AbstractFilePredicate;
 import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.FileSystem.Index;
 import org.sonar.api.batch.fs.InputFile;
 
-class TruePredicate implements FilePredicate {
+class TruePredicate extends AbstractFilePredicate {
 
   static final FilePredicate TRUE = new TruePredicate();
 
@@ -30,4 +32,14 @@ class TruePredicate implements FilePredicate {
   public boolean apply(InputFile inputFile) {
     return true;
   }
+
+  @Override
+  public Iterable<InputFile> get(Index index) {
+    return index.inputFiles();
+  }
+
+  @Override
+  public Iterable<InputFile> filter(Iterable<InputFile> target) {
+    return target;
+  }
 }

sonar-plugin-api/src/main/java/org/sonar/api/batch/fs/internal/TypePredicate.java

@@ -19,13 +19,14 @@
  */
 package org.sonar.api.batch.fs.internal;
 
-import org.sonar.api.batch.fs.FilePredicate;
+import org.sonar.api.batch.fs.AbstractFilePredicate;
+
 import org.sonar.api.batch.fs.InputFile;
 
 /**
  * @since 4.2
  */
-class TypePredicate implements FilePredicate {
+class TypePredicate extends AbstractFilePredicate {
 
   private final InputFile.Type type;
 
@@ -39,4 +40,3 @@ class TypePredicate implements FilePredicate {
   }
 
 }
-

sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/AndPredicateTest.java

@@ -0,0 +1,75 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.api.batch.fs.internal;
+
+import org.junit.Test;
+import org.sonar.api.batch.fs.FilePredicate;
+
+import java.util.Arrays;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class AndPredicateTest {
+
+  @Test
+  public void flattenNestedAnd() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    PathPatternPredicate pathPatternPredicate3 = new PathPatternPredicate(PathPattern.create("foo3/**"));
+    FilePredicate andPredicate = AndPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      AndPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate2, pathPatternPredicate3))));
+    assertThat(((AndPredicate) andPredicate).predicates()).containsExactly(pathPatternPredicate1, pathPatternPredicate2, pathPatternPredicate3);
+  }
+
+  @Test
+  public void sortPredicatesByPriority() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    RelativePathPredicate relativePathPredicate = new RelativePathPredicate("foo");
+    FilePredicate andPredicate = AndPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      relativePathPredicate, pathPatternPredicate2));
+    assertThat(((AndPredicate) andPredicate).predicates()).containsExactly(relativePathPredicate, pathPatternPredicate1, pathPatternPredicate2);
+  }
+
+  @Test
+  public void simplifyAndExpressionsWhenEmpty() {
+    FilePredicate andPredicate = AndPredicate.create(Arrays.<FilePredicate>asList());
+    assertThat(andPredicate).isEqualTo(TruePredicate.TRUE);
+  }
+
+  @Test
+  public void simplifyAndExpressionsWhenTrue() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    FilePredicate andPredicate = AndPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      TruePredicate.TRUE, pathPatternPredicate2));
+    assertThat(((AndPredicate) andPredicate).predicates()).containsExactly(pathPatternPredicate1, pathPatternPredicate2);
+  }
+
+  @Test
+  public void simplifyAndExpressionsWhenFalse() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    FilePredicate andPredicate = AndPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      FalsePredicate.FALSE, pathPatternPredicate2));
+    assertThat(andPredicate).isEqualTo(FalsePredicate.FALSE);
+  }
+
+}

sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultFilePredicatesTest.java

@@ -41,10 +41,11 @@ public class DefaultFilePredicatesTest {
   public TemporaryFolder temp = new TemporaryFolder();
 
   DefaultInputFile javaFile;
-  FilePredicates predicates = new DefaultFilePredicates();
+  FilePredicates predicates;
 
   @Before
   public void before() throws IOException {
+    predicates = new DefaultFilePredicates(temp.newFolder());
     javaFile = new DefaultInputFile("foo", "src/main/java/struts/Action.java")
       .setFile(temp.newFile("Action.java"))
       .setLanguage("java")

sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/DefaultFileSystemTest.java

@@ -19,6 +19,7 @@
  */
 package org.sonar.api.batch.fs.internal;
 
+import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
@@ -37,12 +38,18 @@ public class DefaultFileSystemTest {
   @Rule
   public ExpectedException thrown = ExpectedException.none();
 
+  private DefaultFileSystem fs;
+
+  private File basedir;
+
+  @Before
+  public void prepare() throws Exception {
+    basedir = temp.newFolder();
+    fs = new DefaultFileSystem(basedir);
+  }
+
   @Test
   public void test_directories() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
-
-    File basedir = temp.newFolder();
-    fs.setBaseDir(basedir);
     assertThat(fs.baseDir()).isAbsolute().isDirectory().exists();
     assertThat(fs.baseDir().getCanonicalPath()).isEqualTo(basedir.getCanonicalPath());
 
@@ -54,8 +61,6 @@ public class DefaultFileSystemTest {
 
   @Test
   public void test_encoding() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
-
     assertThat(fs.isDefaultJvmEncoding()).isTrue();
     assertThat(fs.encoding()).isEqualTo(Charset.defaultCharset());
 
@@ -66,8 +71,6 @@ public class DefaultFileSystemTest {
 
   @Test
   public void add_languages() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
-
     assertThat(fs.languages()).isEmpty();
 
     fs.addLanguages("java", "php", "cobol");
@@ -76,8 +79,6 @@ public class DefaultFileSystemTest {
 
   @Test
   public void files() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
-
     assertThat(fs.inputFiles(fs.predicates().all())).isEmpty();
 
     fs.add(new DefaultInputFile("foo", "src/Foo.php").setLanguage("php").setFile(temp.newFile()));
@@ -108,7 +109,6 @@ public class DefaultFileSystemTest {
 
   @Test
   public void input_file_returns_null_if_file_not_found() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
     assertThat(fs.inputFile(fs.predicates().hasRelativePath("src/Bar.java"))).isNull();
     assertThat(fs.inputFile(fs.predicates().hasLanguage("cobol"))).isNull();
   }
@@ -118,7 +118,6 @@ public class DefaultFileSystemTest {
     thrown.expect(IllegalArgumentException.class);
     thrown.expectMessage("expected one element");
 
-    DefaultFileSystem fs = new DefaultFileSystem();
     fs.add(new DefaultInputFile("foo", "src/Bar.java").setLanguage("java").setFile(temp.newFile()));
     fs.add(new DefaultInputFile("foo", "src/Baz.java").setLanguage("java").setFile(temp.newFile()));
 
@@ -127,7 +126,6 @@ public class DefaultFileSystemTest {
 
   @Test
   public void input_file_supports_non_indexed_predicates() throws Exception {
-    DefaultFileSystem fs = new DefaultFileSystem();
     fs.add(new DefaultInputFile("foo", "src/Bar.java").setLanguage("java").setFile(temp.newFile()));
 
     // it would fail if more than one java file

sonar-plugin-api/src/test/java/org/sonar/api/batch/fs/internal/OrPredicateTest.java

@@ -0,0 +1,65 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2014 SonarSource
+ * mailto:contact AT sonarsource DOT com
+ *
+ * SonarQube 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.
+ *
+ * SonarQube 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.api.batch.fs.internal;
+
+import org.junit.Test;
+import org.sonar.api.batch.fs.FilePredicate;
+
+import java.util.Arrays;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+public class OrPredicateTest {
+
+  @Test
+  public void flattenNestedOr() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    PathPatternPredicate pathPatternPredicate3 = new PathPatternPredicate(PathPattern.create("foo3/**"));
+    FilePredicate orPredicate = OrPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      OrPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate2, pathPatternPredicate3))));
+    assertThat(((OrPredicate) orPredicate).predicates()).containsExactly(pathPatternPredicate1, pathPatternPredicate2, pathPatternPredicate3);
+  }
+
+  @Test
+  public void simplifyOrExpressionsWhenEmpty() {
+    FilePredicate orPredicate = OrPredicate.create(Arrays.<FilePredicate>asList());
+    assertThat(orPredicate).isEqualTo(TruePredicate.TRUE);
+  }
+
+  @Test
+  public void simplifyOrExpressionsWhenFalse() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    FilePredicate andPredicate = OrPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      FalsePredicate.FALSE, pathPatternPredicate2));
+    assertThat(((OrPredicate) andPredicate).predicates()).containsExactly(pathPatternPredicate1, pathPatternPredicate2);
+  }
+
+  @Test
+  public void simplifyAndExpressionsWhenTrue() {
+    PathPatternPredicate pathPatternPredicate1 = new PathPatternPredicate(PathPattern.create("foo1/**"));
+    PathPatternPredicate pathPatternPredicate2 = new PathPatternPredicate(PathPattern.create("foo2/**"));
+    FilePredicate andPredicate = OrPredicate.create(Arrays.<FilePredicate>asList(pathPatternPredicate1,
+      TruePredicate.TRUE, pathPatternPredicate2));
+    assertThat(andPredicate).isEqualTo(TruePredicate.TRUE);
+  }
+
+}