Improve backward-compatibility when adding data to a non-indexed resource

17 files changed, 240 insertions, 216 deletions

diff --git a/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/JavaSourceImporter.java b/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/JavaSourceImporter.java
index 87e7699ba88..0e7a1c1e3f4 100644
--- a/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/JavaSourceImporter.java
+++ b/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/JavaSourceImporter.java
@@ -19,30 +19,73 @@
  */
 package org.sonar.plugins.squid;
 
+import org.apache.commons.io.FileUtils;
+import org.sonar.api.CoreProperties;
 import org.sonar.api.batch.*;
-import org.sonar.api.resources.Java;
-import org.sonar.api.resources.JavaFile;
-import org.sonar.api.resources.Resource;
+import org.sonar.api.resources.*;
+import org.sonar.api.utils.SonarException;
 import org.sonar.java.api.JavaUtils;
 
-import java.io.File;
+import java.io.IOException;
+import java.nio.charset.Charset;
 import java.util.List;
 
-@DependsUpon(classes=SquidSensor.class)
+@Phase(name = Phase.Name.PRE)
+@DependsUpon(classes = SquidSensor.class)
 @DependedUpon(JavaUtils.BARRIER_AFTER_SQUID)
-public class JavaSourceImporter extends AbstractSourceImporter {
+public final class JavaSourceImporter implements Sensor {
 
-  public JavaSourceImporter() {
-    super(Java.INSTANCE);
+  /**
+   * {@inheritDoc}
+   */
+  public boolean shouldExecuteOnProject(Project project) {
+    return isEnabled(project) && Java.KEY.equals(project.getLanguageKey());
   }
 
-  @Override
-  protected Resource createResource(File file, List<File> sourceDirs, boolean unitTest) {
-    return file != null ? JavaFile.fromIOFile(file, sourceDirs, unitTest) : null;
+  /**
+   * {@inheritDoc}
+   */
+  public void analyse(Project project, SensorContext context) {
+    analyse(project.getFileSystem(), context);
+  }
+
+  void analyse(ProjectFileSystem fileSystem, SensorContext context) {
+    parseDirs(context, fileSystem.mainFiles(Java.INSTANCE), false, fileSystem.getSourceCharset());
+    parseDirs(context, fileSystem.testFiles(Java.INSTANCE), true, fileSystem.getSourceCharset());
+  }
+
+  void parseDirs(SensorContext context, List<InputFile> inputFiles, boolean unitTest, Charset sourcesEncoding) {
+    for (InputFile inputFile : inputFiles) {
+      JavaFile javaFile = JavaFile.fromRelativePath(inputFile.getRelativePath(), unitTest);
+      importSource(context, javaFile, inputFile, sourcesEncoding);
+    }
+  }
+
+  void importSource(SensorContext context, JavaFile javaFile, InputFile inputFile, Charset sourcesEncoding) {
+    try {
+      //if (!context.isIndexed(javaFile, true)) {
+      // See http://jira.codehaus.org/browse/SONAR-791
+      // Squid is the reference plugin to index files. If a file is not indexed,
+      //  throw new SonarException("Invalid file: " + javaFile + ". Please check that Java source directories match root directories" +
+      //    " as defined by packages.");
+      //}
+      String source = FileUtils.readFileToString(inputFile.getFile(), sourcesEncoding.name());
+      context.saveSource(javaFile, source);
+
+    } catch (IOException e) {
+      throw new SonarException("Unable to read and import the source file : '" + inputFile.getFile().getAbsolutePath() + "' with the charset : '"
+          + sourcesEncoding.name() + "'.", e);
+    }
+  }
+
+  boolean isEnabled(Project project) {
+    return project.getConfiguration().getBoolean(CoreProperties.CORE_IMPORT_SOURCES_PROPERTY,
+        CoreProperties.CORE_IMPORT_SOURCES_DEFAULT_VALUE);
   }
 
   @Override
   public String toString() {
     return getClass().getSimpleName();
   }
+
 }
diff --git a/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/SquidSensor.java b/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/SquidSensor.java
index c1b242e09de..c79a60d2559 100644
--- a/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/SquidSensor.java
+++ b/plugins/sonar-squid-java-plugin/src/main/java/org/sonar/plugins/squid/SquidSensor.java
@@ -25,6 +25,7 @@ import org.sonar.api.batch.*;
 import org.sonar.api.checks.AnnotationCheckFactory;
 import org.sonar.api.checks.NoSonarFilter;
 import org.sonar.api.profiles.RulesProfile;
+import org.sonar.api.resources.InputFile;
 import org.sonar.api.resources.Java;
 import org.sonar.api.resources.JavaFile;
 import org.sonar.api.resources.Project;
@@ -82,22 +83,18 @@ public class SquidSensor implements Sensor {
   }
 
   private void browseTestSources(Project project, SensorContext context) {
-    for (File testFile : getTestSourceFiles(project)) {
-      context.index(JavaFile.fromIOFile(testFile, project.getFileSystem().getTestDirs(), true));
+    for (InputFile testFile : project.getFileSystem().testFiles(Java.INSTANCE)) {
+      context.index(JavaFile.fromRelativePath(testFile.getRelativePath(), true));
     }
   }
 
-  private List<File> getTestSourceFiles(Project project) {
-    return project.getFileSystem().getTestFiles(Java.INSTANCE);
-  }
-
   private List<File> getMainSourceFiles(Project project) {
     return project.getFileSystem().getJavaSourceFiles();
   }
 
   private Collection<File> getMainBytecodeFiles(Project project) {
     Collection<File> bytecodeFiles = projectClasspath.getElements();
-    if ( !hasProjectBytecodeFiles(project)) {
+    if (!hasProjectBytecodeFiles(project)) {
       File classesDir = project.getFileSystem().getBuildOutputDir();
       if (classesDir != null && classesDir.exists()) {
         bytecodeFiles.remove(classesDir);
@@ -107,11 +104,11 @@ public class SquidSensor implements Sensor {
   }
 
   private boolean hasProjectBytecodeFiles(Project project) {
-    if ( !project.getConfiguration()
+    if (!project.getConfiguration()
         .getBoolean(CoreProperties.DESIGN_SKIP_DESIGN_PROPERTY, CoreProperties.DESIGN_SKIP_DESIGN_DEFAULT_VALUE)) {
       File classesDir = project.getFileSystem().getBuildOutputDir();
       if (classesDir != null && classesDir.exists()) {
-        return !FileUtils.listFiles(classesDir, new String[] { "class" }, true).isEmpty();
+        return !FileUtils.listFiles(classesDir, new String[]{"class"}, true).isEmpty();
       }
     }
     return false;
diff --git a/plugins/sonar-squid-java-plugin/src/test/java/org/sonar/plugins/squid/JavaSourceImporterTest.java b/plugins/sonar-squid-java-plugin/src/test/java/org/sonar/plugins/squid/JavaSourceImporterTest.java
index c6667a6920e..f90274d9964 100644
--- a/plugins/sonar-squid-java-plugin/src/test/java/org/sonar/plugins/squid/JavaSourceImporterTest.java
+++ b/plugins/sonar-squid-java-plugin/src/test/java/org/sonar/plugins/squid/JavaSourceImporterTest.java
@@ -19,42 +19,53 @@
  */
 package org.sonar.plugins.squid;
 
-import org.apache.commons.io.FileUtils;
+import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
+import org.sonar.api.batch.SensorContext;
+import org.sonar.api.resources.InputFile;
 import org.sonar.api.resources.JavaFile;
-import org.sonar.api.resources.JavaPackage;
-import org.sonar.api.resources.Resource;
-import org.sonar.api.resources.ResourceUtils;
+import org.sonar.api.utils.SonarException;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.Arrays;
+import java.nio.charset.Charset;
 
-import static org.hamcrest.CoreMatchers.is;
-import static org.junit.Assert.assertThat;
+import static org.mockito.Matchers.anyString;
+import static org.mockito.Matchers.eq;
+import static org.mockito.Mockito.*;
 
 public class JavaSourceImporterTest {
 
-  @Test
-  public void shouldDefineMainFile() throws IOException {
-    JavaSourceImporter importer = new JavaSourceImporter();
-    Resource clazz = importer.createResource(new File(newDir("source1"), "/MyClass.java"), Arrays.asList(newDir("source1")), false);
-    assertThat(clazz, is(JavaFile.class));
-    assertThat(clazz.getKey(), is(JavaPackage.DEFAULT_PACKAGE_NAME + ".MyClass"));
-    assertThat(clazz.getName(), is("MyClass"));
+  private JavaSourceImporter importer;
+  private SensorContext context;
+  private InputFile inputFile;
+
+  @Before
+  public void init() {
+    File fileToImport = new File("test-resources/rules/UndocumentedApi.java");
+    inputFile = mock(InputFile.class);
+    when(inputFile.getRelativePath()).thenReturn("UndocumentedApi.java");
+    when(inputFile.getFile()).thenReturn(fileToImport);
+    when(inputFile.getFileBaseDir()).thenReturn(fileToImport.getParentFile());
+    importer = new JavaSourceImporter();
+    context = mock(SensorContext.class);
   }
 
   @Test
-  public void shouldDefineTestFile() throws IOException {
-    JavaSourceImporter importer = new JavaSourceImporter();
-    Resource resource = importer.createResource(new File(newDir("tests"), "/MyClassTest.java"), Arrays.asList(newDir("tests")), true);
-    assertThat(resource, is(JavaFile.class));
-    assertThat(ResourceUtils.isUnitTestClass(resource), is(true));
+  public void shouldSetSource() throws IOException {
+    JavaFile javaFile = JavaFile.fromRelativePath("UndocumentedApi.java", true);
+    when(context.isIndexed(javaFile, true)).thenReturn(true);
+    importer.importSource(context, javaFile, inputFile, Charset.defaultCharset());
+
+    verify(context).saveSource(eq(javaFile), anyString());
   }
 
-  private File newDir(String relativePath) throws IOException {
-    File target = new File("target", relativePath);
-    FileUtils.forceMkdir(target);
-    return target;
+  @Test(expected = SonarException.class)
+  @Ignore("see SONAR-791")
+  public void shouldFailWhenSquidDidNotIndexFile() throws IOException {
+    JavaFile javaFile = new JavaFile("Bar");
+    when(context.isIndexed(javaFile, true)).thenReturn(false);
+    importer.importSource(context, javaFile, inputFile, Charset.defaultCharset());
   }
 }
\ No newline at end of file
diff --git a/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/javaFile.java b/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/javaFile.java
deleted file mode 100644
index 5ea06251f14..00000000000
--- a/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/javaFile.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/**
- * Javadoc for this Car class
- * @author freddy
- *
- */
-public class Car {
-	
-	private int n;  //C++ inline comment
-	private String s;
-
-	public AClass(int n, String s) {
-		this.n = n;
-		this.s = s;
-	}
-
-	/*
-	 *C style comment
-	 * 
-	 */
-	public int getN() { 
-		/*
-		 * Another C style comment
-		 */
-		return n;
-	}
-
-	public String getS() {
-		return s;
-	}
-	
-}
\ No newline at end of file
diff --git a/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/plsqlFile.pak b/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/plsqlFile.pak
deleted file mode 100644
index f0e5a8535a5..00000000000
--- a/plugins/sonar-squid-java-plugin/test-resources/basic_handlers/plsqlFile.pak
+++ /dev/null
@@ -1,83 +0,0 @@
-
-CREATE OR REPLACE PACKAGE SONAR002 AS
-
--- ----------------------------------------------------------------------------
--- package version
-FUNCTION VERSION RETURN VARCHAR2;
-  PRAGMA RESTRICT_REFERENCES (VERSION, WNDS, WNPS, RNPS);
-
-
-TYPE        T_trans IS TABLE OF VARCHAR2(250) INDEX BY BINARY_INTEGER;
-A_trans     T_trans;
-w_origine   VARCHAR2(160);
-w_sqlerrm   VARCHAR2(255);
-
-header_c_langue  VARCHAR2(2);
-
-TYPE T_TAG IS RECORD ( NOM_TAG VARCHAR2(50)
-                      ,VALEUR  VARCHAR2(32000)); 
-                      
-TYPE TT_TAGS IS TABLE OF T_TAG INDEX BY BINARY_INTEGER;
-
-tb_TAGS  TT_TAGS;
-
-
-TYPE ControleData IS RECORD
-        ( pourcent           NUMBER,
-          bande              VARCHAR2(40),
-          nb_ligne           NUMBER,
-          typ_avis           VARCHAR2(25),
-          nb_brique          NUMBER,
-          no_op              operation.no_op%TYPE,
-          no_op_pere         operation.no_op%TYPE,
-          no_op_doss         operation.no_op%TYPE,
-          c_typ_contrat      operation.c_typ_contrat%TYPE,
-          ref_op             operation.ref_op%TYPE,
-          c_op_param         type_oper_param.c_op_param%TYPE,
-          c_serv             operation.c_serv%TYPE,
-          c_dev              operation.c_dev%TYPE,
-          d_op               operation.d_op%TYPE,
-          c_op_param_role    VARCHAR2(4),
-          c_phase            VARCHAR2(4),
-          c_phase_real       VARCHAR2(4),
-          id_avis            NUMBER,
-          c_form             VARCHAR2(10),
-          c_teneur_envoi     VARCHAR2(10),
-          Spool              VARCHAR2(320),
-          spool_tmp          VARCHAR2(320),
-          old_elt            VARCHAR2(10),
-          new_elt            VARCHAR2(10),
-          old_ligne          NUMBER,
-          new_ligne          NUMBER,
-          old_ordre          NUMBER,
-          new_tag            VARCHAR2(3),
-          old_tag            VARCHAR2(3),
-          new_ordre          NUMBER,
-          mode_fusion        VARCHAR2(1),
-          TRACE              VARCHAR2(80),
-          taux_cent_mille    NUMBER,
-          caractere_taux     VARCHAR2(1),
-          chemin_avis        VARCHAR2(20),
-          nbr_dec_doss       NUMBER,
-          c_dev_doss         VARCHAR2(3),
-          mt_cpta_bloc_2     NUMBER,
-          regr_aff_dest      VARCHAR2(1),
-          no_seq             NUMBER(8),
-          no_seq_pere        NUMBER(8),
-          id_envoi           NUMBER(8),
-          id_envoi_pere      NUMBER(8),
-          id_message         NUMBER(8),
-          generation         VARCHAR2(1),
-          c_uti              VARCHAR2(6),
-          c_uti_cre          VARCHAR2(6),
-          no_swift           VARCHAR2(1),
-          c_trait_202        VARCHAR2(5),
-          envoi_pere_202     VARCHAR2(5),
-          f_envoi_ga_java    VARCHAR2(1),
-          avec_templ_perso   VARCHAR2(1),
-          f_comm_prises      VARCHAR2(1),
-          liab_reduc_with_pmt VARCHAR2(1)); 
-Controle ControleData;
-
-END SONAR002;
-
diff --git a/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java b/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
index a924fba8ac1..4a4acf8bf32 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/DefaultSensorContext.java
@@ -60,8 +60,8 @@ public class DefaultSensorContext implements SensorContext {
     return index.isExcluded(reference);
   }
 
-  public boolean isIndexed(Resource reference) {
-    return index.isIndexed(reference);
+  public boolean isIndexed(Resource reference, boolean acceptExcluded) {
+    return index.isIndexed(reference, acceptExcluded);
   }
 
   public Resource getParent(Resource reference) {
@@ -155,8 +155,8 @@ public class DefaultSensorContext implements SensorContext {
     return index.getOutgoingEdges(resourceOrProject(from));
   }
 
-  public boolean saveSource(Resource reference, String source) throws DuplicatedSourceException {
-    return index.setSource(reference, source);
+  public void saveSource(Resource reference, String source) throws DuplicatedSourceException {
+    index.setSource(reference, source);
   }
 
   public void saveLink(ProjectLink link) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
index 5660bf44ade..01ba7d6b384 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/DefaultIndex.java
@@ -157,7 +157,7 @@ public final class DefaultIndex extends SonarIndex {
    * the measure is updated if it's already registered.
    */
   public Measure addMeasure(Resource resource, Measure measure) {
-    Bucket bucket = doIndex(resource);
+    Bucket bucket = checkIndexed(resource);
     if (bucket != null && !bucket.isExcluded()) {
       Metric metric = metricFinder.findByKey(measure.getMetricKey());
       if (metric == null) {
@@ -170,7 +170,6 @@ public final class DefaultIndex extends SonarIndex {
       if (measure.getPersistenceMode().useDatabase()) {
         persistence.saveMeasure(resource, measure);
       }
-
       // TODO keep database measures in cache but remove data
     }
     return measure;
@@ -295,13 +294,12 @@ public final class DefaultIndex extends SonarIndex {
   }
 
   public void addViolation(Violation violation, boolean force) {
-    Bucket bucket;
     Resource resource = violation.getResource();
     if (resource == null) {
       violation.setResource(currentProject);
     }
-    bucket = doIndex(violation.getResource());
-    if (!bucket.isExcluded()) {
+    Bucket bucket = checkIndexed(resource);
+    if (bucket != null && !bucket.isExcluded()) {
       boolean isIgnored = !force && violationFilters != null && violationFilters.isIgnored(violation);
       if (!isIgnored) {
         ActiveRule activeRule = profile.getActiveRule(violation.getRule());
@@ -366,13 +364,11 @@ public final class DefaultIndex extends SonarIndex {
     return null;
   }
 
-  public boolean setSource(Resource reference, String source) {
-    boolean result = false;
-    if (isIndexed(reference)) {
+  public void setSource(Resource reference, String source) {
+    Bucket bucket = checkIndexed(reference);
+    if (bucket != null && !bucket.isExcluded()) {
       persistence.setSource(reference, source);
-      result = true;
     }
-    return result;
   }
 
 
@@ -387,7 +383,7 @@ public final class DefaultIndex extends SonarIndex {
   public <R extends Resource> R getResource(R reference) {
     Bucket bucket = buckets.get(reference);
     if (bucket != null) {
-      return (R)bucket.getResource();
+      return (R) bucket.getResource();
     }
     return null;
   }
@@ -443,8 +439,7 @@ public final class DefaultIndex extends SonarIndex {
 
   private Bucket doIndex(Resource resource) {
     if (resource.getParent() != null) {
-      // SONAR-2127 backward-compatibility - create automatically parent of files
-      doIndex(resource.getParent(), currentProject);
+      doIndex(resource.getParent());
     }
     return doIndex(resource, resource.getParent());
   }
@@ -469,7 +464,7 @@ public final class DefaultIndex extends SonarIndex {
     }
 
     Bucket parentBucket = getBucket(parent, true);
-    if (parentBucket==null && parent!=null) {
+    if (parentBucket == null && parent != null) {
       LOG.warn("Resource ignored, parent is not indexed: " + resource);
       return null;
     }
@@ -480,7 +475,7 @@ public final class DefaultIndex extends SonarIndex {
 
     boolean excluded = checkExclusion(resource, parentBucket);
     if (!excluded) {
-      persistence.saveResource(currentProject, resource, (parentBucket!=null ? parentBucket.getResource() : null));
+      persistence.saveResource(currentProject, resource, (parentBucket != null ? parentBucket.getResource() : null));
     }
     return bucket;
   }
@@ -494,13 +489,30 @@ public final class DefaultIndex extends SonarIndex {
     }
   }
 
+  private Bucket checkIndexed(Resource reference) {
+    Bucket bucket = getBucket(reference, true);
+    if (bucket == null) {
+      if (lock.isLocked()) {
+        if (lock.isFailWhenLocked()) {
+          throw new ResourceNotIndexedException(reference);
+        }
+        LOG.warn("Resource will be ignored in next Sonar versions, index is locked: " + reference);
+      } else {
+        // other languages than Java - keep backward compatibility
+        bucket = doIndex(reference);
+      }
+    }
+    return bucket;
+  }
+
+
   public boolean isExcluded(Resource reference) {
     Bucket bucket = getBucket(reference, true);
     return bucket != null && bucket.isExcluded();
   }
 
-  public boolean isIndexed(Resource reference) {
-    return getBucket(reference, false) != null;
+  public boolean isIndexed(Resource reference, boolean acceptExcluded) {
+    return getBucket(reference, acceptExcluded) != null;
   }
 
   private Bucket getBucket(Resource resource, boolean acceptExcluded) {
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java
new file mode 100644
index 00000000000..203f4043ff6
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceNotIndexedException.java
@@ -0,0 +1,33 @@
+/*
+ * Sonar, open source software quality management tool.
+ * Copyright (C) 2009 SonarSource SA
+ * mailto:contact AT sonarsource DOT com
+ *
+ * Sonar 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.
+ *
+ * Sonar 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 Sonar; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02
+ */
+package org.sonar.batch.index;
+
+import org.sonar.api.resources.Resource;
+import org.sonar.api.utils.SonarException;
+
+/**
+ * @since 2.6
+ */
+public class ResourceNotIndexedException extends SonarException {
+
+  public ResourceNotIndexedException(final Resource reference) {
+    super(reference.toString());
+  }
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
index e90cd8a9b61..ef88932c7e1 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/DefaultIndexTest.java
@@ -85,7 +85,7 @@ public class DefaultIndexTest {
 
     Directory reference = new Directory("org/foo");
     assertThat(index.getResource(reference).getName(), is("org/foo"));
-    assertThat(index.isIndexed(reference), is(true));
+    assertThat(index.isIndexed(reference, true), is(true));
     assertThat(index.isExcluded(reference), is(false));
     assertThat(index.getChildren(reference).size(), is(1));
     assertThat(index.getParent(reference), is(Project.class));
@@ -103,7 +103,7 @@ public class DefaultIndexTest {
     File fileRef = new File("org/foo/Bar.java");
     assertThat(index.getResource(fileRef).getKey(), is("org/foo/Bar.java"));
     assertThat(index.getResource(fileRef).getLanguage(), is((Language) Java.INSTANCE));
-    assertThat(index.isIndexed(fileRef), is(true));
+    assertThat(index.isIndexed(fileRef, true), is(true));
     assertThat(index.isExcluded(fileRef), is(false));
     assertThat(index.getChildren(fileRef).size(), is(0));
     assertThat(index.getParent(fileRef), is(Directory.class));
@@ -116,7 +116,7 @@ public class DefaultIndexTest {
 
     Library reference = new Library("junit", "4.8");
     assertThat(index.getResource(reference).getQualifier(), is(Qualifiers.LIBRARY));
-    assertThat(index.isIndexed(reference), is(true));
+    assertThat(index.isIndexed(reference, true), is(true));
     assertThat(index.isExcluded(reference), is(false));
   }
 
@@ -128,8 +128,8 @@ public class DefaultIndexTest {
     assertThat(index.index(file, directory), is(false));
 
     File fileRef = new File("org/foo/Bar.java");
-    assertThat(index.isIndexed(directory), is(false));
-    assertThat(index.isIndexed(fileRef), is(false));
+    assertThat(index.isIndexed(directory, true), is(false));
+    assertThat(index.isIndexed(fileRef, true), is(false));
     assertThat(index.isExcluded(fileRef), is(false));
     assertThat(index.getChildren(fileRef).size(), is(0));
     assertThat(index.getParent(fileRef), nullValue());
@@ -145,7 +145,7 @@ public class DefaultIndexTest {
 
     Directory dir = new Directory("org/foo");
     assertThat(index.index(dir), is(true));
-    assertThat(index.isIndexed(dir), is(true));
+    assertThat(index.isIndexed(dir, true), is(true));
   }
 
   @Test(expected = SonarException.class)
@@ -161,7 +161,8 @@ public class DefaultIndexTest {
   public void shouldBeExcluded() {
     File file = new File("org/foo/ExcludedBar.java");
     assertThat(index.index(file), is(false));
-    assertThat(index.isIndexed(file), is(false));
+    assertThat(index.isIndexed(file, true), is(true));
+    assertThat(index.isIndexed(file, false), is(false));
     assertThat(index.isExcluded(file), is(true));
   }
 
@@ -170,7 +171,7 @@ public class DefaultIndexTest {
     Resource dir = new Directory("org/foo");
     index.addMeasure(dir, new Measure("ncloc").setValue(50.0));
 
-    assertThat(index.isIndexed(dir), is(true));
+    assertThat(index.isIndexed(dir, true), is(true));
     assertThat(index.getMeasures(dir, MeasuresFilters.metric("ncloc")).getIntValue(), is(50));
   }
 }
diff --git a/sonar-java-api/src/main/java/org/sonar/java/api/JavaUtils.java b/sonar-java-api/src/main/java/org/sonar/java/api/JavaUtils.java
index dad567cc1e3..9fa234f5626 100644
--- a/sonar-java-api/src/main/java/org/sonar/java/api/JavaUtils.java
+++ b/sonar-java-api/src/main/java/org/sonar/java/api/JavaUtils.java
@@ -24,6 +24,7 @@ import org.apache.commons.lang.StringUtils;
 public final class JavaUtils {
 
   public static final String PACKAGE_SEPARATOR = ".";
+  public static final String DEFAULT_PACKAGE = "[default]";
 
   /**
    * All sensors executed after this barrier are sure that all Java resources are indexed.
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
index 07b58dc1a13..8ac007a1e6a 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SensorContext.java
@@ -58,15 +58,16 @@ public interface SensorContext {
   boolean index(Resource resource, Resource parentReference);
 
   /**
-   * Returns true if the referenced resource is excluded. An excluded resource is not indexed.
+   * Returns true if the referenced resource is indexed and excluded.
    * @since 2.6
    */
   boolean isExcluded(Resource reference);
 
   /**
+   * Returns true if the referenced resource is indexed.
    * @since 2.6
    */
-  boolean isIndexed(Resource reference);
+  boolean isIndexed(Resource reference, boolean acceptExcluded);
 
   /**
    * Search for an indexed resource.
@@ -88,7 +89,6 @@ public interface SensorContext {
 
   Collection<Resource> getChildren(Resource reference);
 
-
   // ----------- MEASURES ON PROJECT --------------
 
   /**
@@ -188,14 +188,13 @@ public interface SensorContext {
 
   /**
    * Save the source code of a file. The file must be have been indexed before.
-   * Note: the source stream is not closed.
    *
    * @return false if the resource is excluded or not indexed
    * @throws org.sonar.api.resources.DuplicatedSourceException
    *          if the source has already been set on this resource
    * @since 1.10. Returns a boolean since 2.6.
    */
-  boolean saveSource(Resource reference, String source) throws DuplicatedSourceException;
+  void saveSource(Resource reference, String source) throws DuplicatedSourceException;
 
   // ----------- LINKS --------------
 
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SonarIndex.java b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SonarIndex.java
index 06ae5ae80fd..cf441562c1b 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/batch/SonarIndex.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/batch/SonarIndex.java
@@ -39,6 +39,7 @@ public abstract class SonarIndex implements DirectedGraphAccessor<Resource, Depe
 
   /**
    * Indexes a resource as a direct child of project. This method does nothing and returns true if the resource already indexed.
+   * If the method resource.getParent() does not return null, then this parent will be indexed too.
    *
    * @return false if the resource is excluded
    * @since 2.6
@@ -65,7 +66,7 @@ public abstract class SonarIndex implements DirectedGraphAccessor<Resource, Depe
   /**
    * @since 2.6
    */
-  public abstract boolean isIndexed(Resource reference);
+  public abstract boolean isIndexed(Resource reference, boolean acceptExcluded);
 
   /**
    * Search for an indexed resource.
@@ -95,7 +96,7 @@ public abstract class SonarIndex implements DirectedGraphAccessor<Resource, Depe
    * @throws org.sonar.api.resources.DuplicatedSourceException
    *          if the source has already been set on this resource
    */
-  public abstract boolean setSource(Resource reference, String source) throws DuplicatedSourceException;
+  public abstract void setSource(Resource reference, String source) throws DuplicatedSourceException;
 
   public abstract Project getProject();
 
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
index 4b7837779e3..85a47eb8945 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/DefaultProjectFileSystem.java
@@ -353,11 +353,11 @@ public class DefaultProjectFileSystem implements ProjectFileSystem {
     return getFiles(getTestDirs(), false /* FIXME should be true? */, langs);
   }
 
-  private class DefaultInputFile implements InputFile {
+  private static final class DefaultInputFile implements InputFile {
     private File basedir;
     private File file;
 
-    public DefaultInputFile(File basedir, File file) {
+    DefaultInputFile(File basedir, File file) {
       this.basedir = basedir;
       this.file = file;
     }
@@ -369,6 +369,10 @@ public class DefaultProjectFileSystem implements ProjectFileSystem {
     public File getFile() {
       return file;
     }
+
+    public String getRelativePath() {
+      return DefaultProjectFileSystem.getRelativePath(file, basedir);
+    }
   }
 
   /**
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/File.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/File.java
index 24b7d32b6b8..40872867c7e 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/File.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/File.java
@@ -38,7 +38,7 @@ public class File extends Resource<Directory> {
   private String filename;
   private Language language;
   private Directory parent;
-  private String qualifier = Resource.QUALIFIER_FILE;
+  private String qualifier = Qualifiers.FILE;
 
   /**
    * File in project. Key is the path relative to project source directories. It is not the absolute path and it does not include the path
@@ -187,8 +187,8 @@ public class File extends Resource<Directory> {
   /**
    * @return SCOPE_ENTITY
    */
-  public String getScope() {
-    return Resource.SCOPE_ENTITY;
+  public final String getScope() {
+    return SCOPE;
   }
 
   /**
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/InputFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/InputFile.java
index 6e87e3445ad..4c926f897e1 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/InputFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/InputFile.java
@@ -30,4 +30,14 @@ public interface InputFile {
 
   File getFile();
 
+  /**
+   * Path relative to basedir. Directory separator is slash '/', whatever the platform.
+   * 
+   * Example on windows: if basedir is c:\project\src\ and file is c:\project\src\org\foo\Bar.java, then relative path
+   * is org/foo/Bar.java
+   *
+   * Example on unix: if basedir is /project/src and file is /project/src/org/foo/Bar.java, then relative path
+   * is org/foo/Bar.java as well.
+   */
+  String getRelativePath();
 }
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaFile.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaFile.java
index ef940898ced..009a04e670a 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaFile.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaFile.java
@@ -37,7 +37,7 @@ public class JavaFile extends Resource<JavaPackage> {
   private String longName;
   private String packageKey;
   private boolean unitTest;
-  private JavaPackage parent = null;
+  private JavaPackage parent;
 
   /**
    * Creates a JavaFile that is not a class of test based on package and file names
@@ -52,7 +52,7 @@ public class JavaFile extends Resource<JavaPackage> {
    * @param unitTest whether it is a unit test file or a source file
    */
   public JavaFile(String packageKey, String className, boolean unitTest) {
-    if (className==null) {
+    if (className == null) {
       throw new IllegalArgumentException("Java filename can not be null");
     }
     if (className.indexOf('$') >= 0) {
@@ -86,10 +86,10 @@ public class JavaFile extends Resource<JavaPackage> {
    * @param unitTest whether it is a unit test file or a source file
    */
   public JavaFile(String key, boolean unitTest) {
-    if (key==null) {
+    if (key == null) {
       throw new IllegalArgumentException("Java filename can not be null");
     }
-    if (key != null && key.indexOf('$') >= 0) {
+    if (key.indexOf('$') >= 0) {
       throw new IllegalArgumentException("Java inner classes are not supported : " + key);
     }
     String realKey = StringUtils.trim(key);
@@ -117,6 +117,7 @@ public class JavaFile extends Resource<JavaPackage> {
       parent = new JavaPackage(packageKey);
     }
     return parent;
+
   }
 
   /**
@@ -151,14 +152,14 @@ public class JavaFile extends Resource<JavaPackage> {
    * @return SCOPE_ENTITY
    */
   public String getScope() {
-    return Resource.SCOPE_ENTITY;
+    return Scopes.FILE;
   }
 
   /**
    * @return QUALIFIER_UNIT_TEST_CLASS or QUALIFIER_CLASS depending whether it is a unit test class
    */
   public String getQualifier() {
-    return unitTest ? Qualifiers.UNIT_TEST_FILE : Resource.QUALIFIER_CLASS;
+    return unitTest ? Qualifiers.UNIT_TEST_FILE : Qualifiers.CLASS;
   }
 
   /**
@@ -179,23 +180,14 @@ public class JavaFile extends Resource<JavaPackage> {
     if (!fileKey.endsWith(".java")) {
       fileKey += ".java";
     }
-    if (StringUtils.substringAfterLast(antPattern, "/").indexOf(".")<0) {
+    if (StringUtils.substringAfterLast(antPattern, "/").indexOf(".") < 0) {
       antPattern += ".*";
     }
     WildcardPattern matcher = WildcardPattern.create(antPattern, ".");
     return matcher.match(fileKey);
   }
 
-  /**
-   * Creates a JavaFile from a file in the source directories
-   *
-   * @return the JavaFile created if exists, null otherwise
-   */
-  public static JavaFile fromIOFile(File file, List<File> sourceDirs, boolean unitTest) {
-    if (file == null || !StringUtils.endsWithIgnoreCase(file.getName(), ".java")) {
-      return null;
-    }
-    String relativePath = DefaultProjectFileSystem.getRelativePath(file, sourceDirs);
+  public static JavaFile fromRelativePath(String relativePath, boolean unitTest) {
     if (relativePath != null) {
       String pacname = null;
       String classname = relativePath;
@@ -212,6 +204,19 @@ public class JavaFile extends Resource<JavaPackage> {
   }
 
   /**
+   * Creates a JavaFile from a file in the source directories
+   *
+   * @return the JavaFile created if exists, null otherwise
+   */
+  public static JavaFile fromIOFile(File file, List<File> sourceDirs, boolean unitTest) {
+    if (file == null || !StringUtils.endsWithIgnoreCase(file.getName(), ".java")) {
+      return null;
+    }
+    String relativePath = DefaultProjectFileSystem.getRelativePath(file, sourceDirs);
+    return fromRelativePath(relativePath, unitTest);
+  }
+
+  /**
    * Shortcut to fromIOFile with an abolute path
    */
   public static JavaFile fromAbsolutePath(String path, List<File> sourceDirs, boolean unitTest) {
@@ -230,4 +235,25 @@ public class JavaFile extends Resource<JavaPackage> {
         .append("unitTest", unitTest)
         .toString();
   }
+
+//  @Override
+//  public boolean equals(Object o) {
+//    if (this == o) return true;
+//    if (o == null || getClass() != o.getClass()) return false;
+//    if (!super.equals(o)) return false;
+//
+//    JavaFile javaFile = (JavaFile) o;
+//    if (unitTest != javaFile.unitTest) return false;
+//    if (!getKey().equals(javaFile.getKey())) return false;
+//
+//    return true;
+//  }
+//
+//  @Override
+//  public int hashCode() {
+//    int result = super.hashCode();
+//    result = 31 * result + getKey().hashCode();
+//    result = 31 * result + (unitTest ? 1 : 0);
+//    return result;
+//  }
 }
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaPackage.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaPackage.java
index d61088c1b45..0ec5528ca9f 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaPackage.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/JavaPackage.java
@@ -80,7 +80,7 @@ public class JavaPackage extends Resource {
    * @return QUALIFIER_PACKAGE
    */
   public String getQualifier() {
-    return Resource.QUALIFIER_PACKAGE;
+    return Qualifiers.PACKAGE;
   }
 
   /**