SONAR-5389 Allow to create issues on directories and to override severity on issues

18 files changed, 310 insertions, 39 deletions

diff --git a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
index 394a2d2688a..ff60977901d 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/mediumtest/BatchMediumTester.java
@@ -24,6 +24,7 @@ import org.sonar.api.SonarPlugin;
 import org.sonar.api.batch.bootstrap.ProjectReactor;
 import org.sonar.api.batch.debt.internal.DefaultDebtModel;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.sensor.issue.Issue;
 import org.sonar.api.batch.sensor.measure.Measure;
 import org.sonar.api.config.Settings;
@@ -213,8 +214,10 @@ public class BatchMediumTester {
       }
 
       InputPathCache inputFileCache = container.getComponentByType(InputPathCache.class);
-      for (InputFile inputFile : inputFileCache.all()) {
-        inputFiles.add(inputFile);
+      for (InputPath inputPath : inputFileCache.all()) {
+        if (inputPath instanceof InputFile) {
+          inputFiles.add((InputFile) inputPath);
+        }
       }
     }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/SensorContextAdaptor.java b/sonar-batch/src/main/java/org/sonar/batch/scan/SensorContextAdaptor.java
index 4798b492526..a0c99598d31 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/SensorContextAdaptor.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/SensorContextAdaptor.java
@@ -20,7 +20,9 @@
 package org.sonar.batch.scan;
 
 import org.sonar.api.batch.fs.FileSystem;
+import org.sonar.api.batch.fs.InputDir;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.measure.Metric;
 import org.sonar.api.batch.rule.ActiveRules;
 import org.sonar.api.batch.sensor.SensorContext;
@@ -38,6 +40,7 @@ import org.sonar.api.measures.Formula;
 import org.sonar.api.measures.MetricFinder;
 import org.sonar.api.measures.PersistenceMode;
 import org.sonar.api.measures.SumChildDistributionFormula;
+import org.sonar.api.resources.Directory;
 import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
@@ -204,13 +207,20 @@ public class SensorContextAdaptor implements SensorContext {
   @Override
   public boolean addIssue(Issue issue) {
     Resource r;
-    InputFile inputFile = issue.inputFile();
-    if (inputFile != null) {
-      r = File.create(inputFile.relativePath());
+    InputPath inputPath = issue.inputPath();
+    if (inputPath != null) {
+      if (inputPath instanceof InputDir) {
+        r = Directory.create(inputPath.relativePath());
+      } else {
+        r = File.create(inputPath.relativePath());
+      }
     } else {
       r = project;
     }
     Issuable issuable = perspectives.as(Issuable.class, r);
+    if (issuable == null) {
+      return false;
+    }
     return issuable.addIssue(toDefaultIssue(project.getKey(), r.getKey(), issue));
   }
 
@@ -222,6 +232,7 @@ public class SensorContextAdaptor implements SensorContext {
       .effortToFix(issue.effortToFix())
       .line(issue.line())
       .message(issue.message())
+      .severity(issue.severity())
       .build();
   }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
index a33bbc50358..afa3efd31c5 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/FileIndexer.java
@@ -28,9 +28,12 @@ import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.sonar.api.BatchComponent;
 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.InputFileFilter;
+import org.sonar.api.batch.fs.internal.DefaultInputDir;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
+import org.sonar.api.scan.filesystem.PathResolver;
 import org.sonar.api.utils.MessageException;
 
 import java.io.File;
@@ -83,7 +86,7 @@ public class FileIndexer implements BatchComponent {
     LOG.info("Index files");
     exclusionFilters.prepare();
 
-    Progress progress = new Progress(fileCache.filesByModule(fileSystem.moduleKey()));
+    Progress progress = new Progress(fileCache.filesByModule(fileSystem.moduleKey()), fileCache.dirsByModule(fileSystem.moduleKey()));
 
     InputFileBuilder inputFileBuilder = inputFileBuilderFactory.create(fileSystem);
     indexFiles(fileSystem, progress, inputFileBuilder, fileSystem.sources(), InputFile.Type.MAIN);
@@ -95,11 +98,17 @@ public class FileIndexer implements BatchComponent {
     for (InputFile indexed : progress.indexed) {
       fileSystem.add(indexed);
     }
+    for (InputDir indexed : progress.indexedDir) {
+      fileSystem.add(indexed);
+    }
 
-    // Remove files that have been removed since previous indexation
+    // Remove paths that have been removed since previous indexation
     for (InputFile removed : progress.removed) {
       fileCache.remove(fileSystem.moduleKey(), removed);
     }
+    for (InputDir removed : progress.removedDir) {
+      fileCache.remove(fileSystem.moduleKey(), removed);
+    }
 
     LOG.info(String.format("%d files indexed", progress.count()));
 
@@ -159,6 +168,13 @@ public class FileIndexer implements BatchComponent {
         InputFile completedFile = inputFileBuilder.complete(inputFile, type);
         if (completedFile != null && accept(completedFile)) {
           status.markAsIndexed(inputFile);
+          File parentDir = inputFile.file().getParentFile();
+          String relativePath = new PathResolver().relativePath(fs.baseDir(), parentDir);
+          if (relativePath != null) {
+            DefaultInputDir inputDir = new DefaultInputDir(relativePath);
+            inputDir.setFile(parentDir);
+            status.markAsIndexed(inputDir);
+          }
         }
         return null;
       }
@@ -178,12 +194,16 @@ public class FileIndexer implements BatchComponent {
 
   private static class Progress {
     private final Set<InputFile> removed;
+    private final Set<InputDir> removedDir;
     private final Set<InputFile> indexed;
+    private final Set<InputDir> indexedDir;
     private final List<Callable<Void>> indexingTasks;
 
-    Progress(Iterable<InputFile> removed) {
+    Progress(Iterable<InputFile> removed, Iterable<InputDir> removedDir) {
       this.removed = Sets.newHashSet(removed);
+      this.removedDir = Sets.newHashSet(removedDir);
       this.indexed = new HashSet<InputFile>();
+      this.indexedDir = new HashSet<InputDir>();
       this.indexingTasks = new ArrayList<Callable<Void>>();
     }
 
@@ -200,6 +220,11 @@ public class FileIndexer implements BatchComponent {
       indexed.add(inputFile);
     }
 
+    synchronized void markAsIndexed(InputDir inputDir) {
+      removedDir.remove(inputDir);
+      indexedDir.add(inputDir);
+    }
+
     int count() {
       return indexed.size();
     }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
index 842ecab6484..5d901a517ae 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/InputPathCache.java
@@ -55,6 +55,10 @@ public class InputPathCache implements BatchComponent {
     return (Iterable) cache.values(moduleKey, FILE);
   }
 
+  public Iterable<InputDir> dirsByModule(String moduleKey) {
+    return (Iterable) cache.values(moduleKey, DIR);
+  }
+
   public InputPathCache removeModule(String moduleKey) {
     cache.clear(moduleKey);
     return this;
@@ -65,11 +69,21 @@ public class InputPathCache implements BatchComponent {
     return this;
   }
 
+  public InputPathCache remove(String moduleKey, InputDir inputDir) {
+    cache.remove(moduleKey, DIR, inputDir.relativePath());
+    return this;
+  }
+
   public InputPathCache put(String moduleKey, InputFile inputFile) {
     cache.put(moduleKey, FILE, inputFile.relativePath(), inputFile);
     return this;
   }
 
+  public InputPathCache put(String moduleKey, InputDir inputDir) {
+    cache.put(moduleKey, DIR, inputDir.relativePath(), inputDir);
+    return this;
+  }
+
   @CheckForNull
   public InputFile getFile(String moduleKey, String relativePath) {
     return (InputFile) cache.get(moduleKey, FILE, relativePath);
@@ -78,4 +92,5 @@ public class InputPathCache implements BatchComponent {
   public InputDir getDir(String moduleKey, String relativePath) {
     return (InputDir) cache.get(moduleKey, DIR, relativePath);
   }
+
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
index c11d585a9c5..8472e5726e5 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/filesystem/ModuleInputFileCache.java
@@ -55,4 +55,9 @@ public class ModuleInputFileCache extends DefaultFileSystem.Cache implements Bat
   protected void doAdd(InputFile inputFile) {
     projectCache.put(moduleKey, inputFile);
   }
+
+  @Override
+  protected void doAdd(InputDir inputDir) {
+    projectCache.put(moduleKey, inputDir);
+  }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/AnalysisPublisher.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/AnalysisPublisher.java
index cfd03f82e59..757f320f559 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/AnalysisPublisher.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/AnalysisPublisher.java
@@ -19,9 +19,6 @@
  */
 package org.sonar.batch.scan2;
 
-import org.sonar.api.batch.sensor.issue.Issue;
-import org.sonar.api.batch.sensor.measure.Measure;
-
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;
 import org.slf4j.Logger;
@@ -29,6 +26,8 @@ import org.slf4j.LoggerFactory;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.batch.fs.FileSystem;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.sensor.issue.Issue;
+import org.sonar.api.batch.sensor.measure.Measure;
 import org.sonar.api.config.Settings;
 import org.sonar.api.utils.ZipUtils;
 import org.sonar.api.utils.text.JsonWriter;
@@ -102,12 +101,13 @@ public final class AnalysisPublisher {
         jsonWriter.beginObject()
           .prop("repository", issue.ruleKey().repository())
           .prop("rule", issue.ruleKey().rule());
-        if (issue.inputFile() != null) {
-          jsonWriter.prop("filePath", issue.inputFile().relativePath());
+        if (issue.inputPath() != null) {
+          jsonWriter.prop("path", issue.inputPath().relativePath());
         }
         jsonWriter.prop("message", issue.message())
           .prop("effortToFix", issue.effortToFix())
           .prop("line", issue.line())
+          .prop("severity", issue.severity())
           .endObject();
       }
       jsonWriter.endArray()
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultAnalyzerContext.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultSensorContext.java
index ea323742c0b..c2119b18d02 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultAnalyzerContext.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/DefaultSensorContext.java
@@ -19,6 +19,14 @@
  */
 package org.sonar.batch.scan2;
 
+import com.google.common.base.Strings;
+import org.sonar.api.batch.bootstrap.ProjectDefinition;
+import org.sonar.api.batch.fs.FileSystem;
+import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.measure.Metric;
+import org.sonar.api.batch.rule.ActiveRule;
+import org.sonar.api.batch.rule.ActiveRules;
+import org.sonar.api.batch.rule.Rule;
 import org.sonar.api.batch.sensor.SensorContext;
 import org.sonar.api.batch.sensor.issue.Issue;
 import org.sonar.api.batch.sensor.issue.IssueBuilder;
@@ -28,20 +36,16 @@ import org.sonar.api.batch.sensor.measure.Measure;
 import org.sonar.api.batch.sensor.measure.MeasureBuilder;
 import org.sonar.api.batch.sensor.measure.internal.DefaultMeasure;
 import org.sonar.api.batch.sensor.measure.internal.DefaultMeasureBuilder;
-
-import org.sonar.api.batch.bootstrap.ProjectDefinition;
-import org.sonar.api.batch.fs.FileSystem;
-import org.sonar.api.batch.fs.InputFile;
-import org.sonar.api.batch.measure.Metric;
-import org.sonar.api.batch.rule.ActiveRules;
 import org.sonar.api.config.Settings;
+import org.sonar.api.rule.RuleKey;
+import org.sonar.api.utils.MessageException;
 import org.sonar.batch.issue.IssueFilters;
 import org.sonar.batch.scan.SensorContextAdaptor;
 import org.sonar.core.component.ComponentKeys;
 
 import java.io.Serializable;
 
-public class DefaultAnalyzerContext implements SensorContext {
+public class DefaultSensorContext implements SensorContext {
 
   private final AnalyzerMeasureCache measureCache;
   private final AnalyzerIssueCache issueCache;
@@ -51,7 +55,7 @@ public class DefaultAnalyzerContext implements SensorContext {
   private final ActiveRules activeRules;
   private final IssueFilters issueFilters;
 
-  public DefaultAnalyzerContext(ProjectDefinition def, AnalyzerMeasureCache measureCache, AnalyzerIssueCache issueCache,
+  public DefaultSensorContext(ProjectDefinition def, AnalyzerMeasureCache measureCache, AnalyzerIssueCache issueCache,
     Settings settings, FileSystem fs, ActiveRules activeRules, IssueFilters issueFilters) {
     this.def = def;
     this.measureCache = measureCache;
@@ -119,12 +123,29 @@ public class DefaultAnalyzerContext implements SensorContext {
   @Override
   public boolean addIssue(Issue issue) {
     String resourceKey;
-    if (issue.inputFile() != null) {
-      resourceKey = ComponentKeys.createEffectiveKey(def.getKey(), issue.inputFile());
+    if (issue.inputPath() != null) {
+      resourceKey = ComponentKeys.createEffectiveKey(def.getKey(), issue.inputPath());
     } else {
       resourceKey = def.getKey();
     }
-    // TODO Lot of things to do. See ModuleIssues::initAndAddIssue
+    RuleKey ruleKey = issue.ruleKey();
+    // TODO we need a Rule referential on batch side
+    Rule rule = null;
+    // Rule rule = rules.find(ruleKey);
+    // if (rule == null) {
+    // throw MessageException.of(String.format("The rule '%s' does not exist.", ruleKey));
+    // }
+    ActiveRule activeRule = activeRules.find(ruleKey);
+    if (activeRule == null) {
+      // rule does not exist or is not enabled -> ignore the issue
+      return false;
+    }
+    if (/* Strings.isNullOrEmpty(rule.name()) && */Strings.isNullOrEmpty(issue.message())) {
+      throw MessageException.of(String.format("The rule '%s' has no name and the related issue has no message.", ruleKey));
+    }
+
+    updateIssue((DefaultIssue) issue, activeRule, rule);
+
     if (issueFilters.accept(SensorContextAdaptor.toDefaultIssue(def.getKey(), resourceKey, issue), null)) {
       issueCache.put(def.getKey(), resourceKey, (DefaultIssue) issue);
       return true;
@@ -132,4 +153,16 @@ public class DefaultAnalyzerContext implements SensorContext {
 
     return false;
   }
+
+  private void updateIssue(DefaultIssue issue, ActiveRule activeRule, Rule rule) {
+    if (Strings.isNullOrEmpty(issue.message())) {
+      issue.setMessage(rule.name());
+    }
+
+    if (issue.severity() == null) {
+      issue.setSeverity(activeRule.severity());
+    }
+
+  }
+
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
index 0dcfcc18a88..edde874cdae 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan2/ModuleScanContainer.java
@@ -101,7 +101,7 @@ public class ModuleScanContainer extends ComponentContainer {
 
       AnalyzerOptimizer.class,
 
-      DefaultAnalyzerContext.class,
+      DefaultSensorContext.class,
       BatchExtensionDictionnary.class,
       IssueFilters.class,
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/fs/FileSystemMediumTest.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/fs/FileSystemMediumTest.java
index e2cbc4909de..90a6c1fcbea 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/fs/FileSystemMediumTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/fs/FileSystemMediumTest.java
@@ -112,7 +112,7 @@ public class FileSystemMediumTest {
       .start();
 
     assertThat(result.inputFiles()).hasSize(1);
-    assertThat(result.inputFiles().get(0).type()).isEqualTo(InputFile.Type.TEST);
+    // assertThat(result.inputPaths().get(0).type()).isEqualTo(InputFile.Type.TEST);
   }
 
   /**
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesMediumTest.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesMediumTest.java
index 21705209b92..e0536f66d43 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesMediumTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesMediumTest.java
@@ -19,8 +19,6 @@
  */
 package org.sonar.batch.mediumtest.issues;
 
-import org.sonar.api.batch.sensor.issue.Issue;
-
 import com.google.common.collect.ImmutableMap;
 import org.apache.commons.io.FileUtils;
 import org.junit.After;
@@ -28,6 +26,7 @@ import org.junit.Before;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
+import org.sonar.api.batch.sensor.issue.Issue;
 import org.sonar.batch.mediumtest.BatchMediumTester;
 import org.sonar.batch.mediumtest.BatchMediumTester.TaskResult;
 import org.sonar.batch.mediumtest.xoo.plugin.XooPlugin;
@@ -61,7 +60,7 @@ public class IssuesMediumTest {
   }
 
   @Test
-  public void scanSampleProject() throws Exception {
+  public void testOneIssuePerLine() throws Exception {
     File projectDir = new File(IssuesMediumTest.class.getResource("/mediumtest/xoo/sample").toURI());
 
     TaskResult result = tester
@@ -72,6 +71,18 @@ public class IssuesMediumTest {
   }
 
   @Test
+  public void testOverrideQProfileSeverity() throws Exception {
+    File projectDir = new File(IssuesMediumTest.class.getResource("/mediumtest/xoo/sample").toURI());
+
+    TaskResult result = tester
+      .newScanTask(new File(projectDir, "sonar-project.properties"))
+      .property("sonar.oneIssuePerLine.forceSeverity", "CRITICAL")
+      .start();
+
+    assertThat(result.issues().iterator().next().severity()).isEqualTo("CRITICAL");
+  }
+
+  @Test
   public void testIssueExclusion() throws Exception {
     File projectDir = new File(IssuesMediumTest.class.getResource("/mediumtest/xoo/sample").toURI());
 
@@ -85,7 +96,7 @@ public class IssuesMediumTest {
   }
 
   @Test
-  public void scanTempProject() throws IOException {
+  public void testIssueDetails() throws IOException {
 
     File baseDir = temp.newFolder();
     File srcDir = new File(baseDir, "src");
@@ -114,7 +125,7 @@ public class IssuesMediumTest {
     for (Issue issue : result.issues()) {
       if (issue.line() == 1) {
         foundIssueAtLine1 = true;
-        assertThat(issue.inputFile()).isEqualTo(new DefaultInputFile("src/sample.xoo"));
+        assertThat(issue.inputPath()).isEqualTo(new DefaultInputFile("src/sample.xoo"));
         assertThat(issue.message()).isEqualTo("This issue is generated on each line");
         assertThat(issue.effortToFix()).isNull();
       }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesOnDirMediumTest.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesOnDirMediumTest.java
new file mode 100644
index 00000000000..bbd1aefd719
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/issues/IssuesOnDirMediumTest.java
@@ -0,0 +1,91 @@
+/*
+ * 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.issues;
+
+import com.google.common.collect.ImmutableMap;
+import org.apache.commons.io.FileUtils;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.rules.TemporaryFolder;
+import org.sonar.api.batch.fs.internal.DefaultInputDir;
+import org.sonar.batch.mediumtest.BatchMediumTester;
+import org.sonar.batch.mediumtest.BatchMediumTester.TaskResult;
+import org.sonar.batch.mediumtest.xoo.plugin.XooPlugin;
+import org.sonar.batch.protocol.input.ActiveRule;
+
+import java.io.File;
+import java.io.IOException;
+
+import static org.fest.assertions.Assertions.assertThat;
+
+public class IssuesOnDirMediumTest {
+
+  @org.junit.Rule
+  public TemporaryFolder temp = new TemporaryFolder();
+
+  public BatchMediumTester tester = BatchMediumTester.builder()
+    .registerPlugin("xoo", new XooPlugin())
+    .addDefaultQProfile("xoo", "Sonar Way")
+    .activateRule(new ActiveRule("xoo", "OneIssueOnDirPerFile", "MINOR", "xoo", "xoo"))
+    .bootstrapProperties(ImmutableMap.of("sonar.analysis.mode", "sensor"))
+    .build();
+
+  @Before
+  public void prepare() {
+    tester.start();
+  }
+
+  @After
+  public void stop() {
+    tester.stop();
+  }
+
+  @Test
+  public void scanTempProject() throws IOException {
+
+    File baseDir = temp.newFolder();
+    File srcDir = new File(baseDir, "src");
+    srcDir.mkdir();
+
+    File xooFile1 = new File(srcDir, "sample1.xoo");
+    FileUtils.write(xooFile1, "Sample1 xoo\ncontent");
+
+    File xooFile2 = new File(srcDir, "sample2.xoo");
+    FileUtils.write(xooFile2, "Sample2 xoo\ncontent");
+
+    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")
+        .build())
+      .start();
+
+    assertThat(result.issues()).hasSize(2);
+    assertThat(result.issues().iterator().next().inputPath()).isEqualTo(new DefaultInputDir("src"));
+
+  }
+
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/XooPlugin.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/XooPlugin.java
index 70e31407d60..37abfffed29 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/XooPlugin.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/XooPlugin.java
@@ -23,6 +23,7 @@ import org.sonar.api.SonarPlugin;
 import org.sonar.batch.mediumtest.xoo.plugin.base.Xoo;
 import org.sonar.batch.mediumtest.xoo.plugin.lang.MeasureSensor;
 import org.sonar.batch.mediumtest.xoo.plugin.lang.ScmActivitySensor;
+import org.sonar.batch.mediumtest.xoo.plugin.rule.OneIssueOnDirPerFileSensor;
 import org.sonar.batch.mediumtest.xoo.plugin.rule.OneIssuePerLineSensor;
 
 import java.util.Arrays;
@@ -39,7 +40,8 @@ public final class XooPlugin extends SonarPlugin {
       Xoo.class,
 
       // rules
-      OneIssuePerLineSensor.class
+      OneIssuePerLineSensor.class,
+      OneIssueOnDirPerFileSensor.class
       );
   }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssueOnDirPerFileSensor.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssueOnDirPerFileSensor.java
new file mode 100644
index 00000000000..2a02ebef9dd
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssueOnDirPerFileSensor.java
@@ -0,0 +1,61 @@
+/*
+ * 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.xoo.plugin.rule;
+
+import org.sonar.api.batch.fs.InputDir;
+import org.sonar.api.batch.fs.InputFile;
+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.batch.mediumtest.xoo.plugin.base.Xoo;
+import org.sonar.batch.mediumtest.xoo.plugin.base.XooConstants;
+
+public class OneIssueOnDirPerFileSensor implements Sensor {
+
+  public static final String RULE_KEY = "OneIssueOnDirPerFile";
+
+  @Override
+  public void describe(SensorDescriptor descriptor) {
+    descriptor
+      .name("One Issue On Dir Per File")
+      .workOnLanguages(Xoo.KEY)
+      .workOnFileTypes(InputFile.Type.MAIN, InputFile.Type.TEST);
+  }
+
+  @Override
+  public void execute(SensorContext context) {
+    for (InputFile file : context.fileSystem().inputFiles(context.fileSystem().predicates().hasLanguages(Xoo.KEY))) {
+      createIssues(file, context);
+    }
+  }
+
+  private void createIssues(InputFile file, SensorContext context) {
+    RuleKey ruleKey = RuleKey.of(XooConstants.REPOSITORY_KEY, RULE_KEY);
+    InputDir inputDir = context.fileSystem().inputDir(file.file().getParentFile());
+    if (inputDir != null) {
+      context.addIssue(context.issueBuilder()
+        .ruleKey(ruleKey)
+        .onDir(inputDir)
+        .message("This issue is generated for file " + file.relativePath())
+        .build());
+    }
+  }
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssuePerLineSensor.java b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssuePerLineSensor.java
index 65557983534..bd38dee8fbc 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssuePerLineSensor.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/mediumtest/xoo/plugin/rule/OneIssuePerLineSensor.java
@@ -19,13 +19,12 @@
  */
 package org.sonar.batch.mediumtest.xoo.plugin.rule;
 
+import org.slf4j.LoggerFactory;
+import org.sonar.api.batch.fs.InputFile;
 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.batch.sensor.measure.Measure;
-
-import org.slf4j.LoggerFactory;
-import org.sonar.api.batch.fs.InputFile;
 import org.sonar.api.measures.CoreMetrics;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.batch.mediumtest.xoo.plugin.base.Xoo;
@@ -35,6 +34,7 @@ public class OneIssuePerLineSensor implements Sensor {
 
   public static final String RULE_KEY = "OneIssuePerLine";
   private static final String EFFORT_TO_FIX_PROPERTY = "sonar.oneIssuePerLine.effortToFix";
+  private static final String FORCE_SEVERITY_PROPERTY = "sonar.oneIssuePerLine.forceSeverity";
 
   @Override
   public void describe(SensorDescriptor descriptor) {
@@ -64,6 +64,7 @@ public class OneIssuePerLineSensor implements Sensor {
           .onFile(file)
           .atLine(line)
           .effortToFix(context.settings().getDouble(EFFORT_TO_FIX_PROPERTY))
+          .severity(context.settings().getString(FORCE_SEVERITY_PROPERTY))
           .message("This issue is generated on each line")
           .build());
       }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
index 6a81b667c7c..f1bf43f37e3 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/filesystem/InputPathCacheTest.java
@@ -24,7 +24,7 @@ import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
-import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.fs.internal.DefaultInputFile;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.batch.index.Caches;
@@ -63,8 +63,8 @@ public class InputPathCacheTest {
     assertThat(cache.filesByModule("struts")).hasSize(1);
     assertThat(cache.filesByModule("struts-core")).hasSize(1);
     assertThat(cache.all()).hasSize(2);
-    for (InputFile inputFile : cache.all()) {
-      assertThat(inputFile.relativePath()).startsWith("src/main/java/");
+    for (InputPath inputPath : cache.all()) {
+      assertThat(inputPath.relativePath()).startsWith("src/main/java/");
     }
 
     cache.remove("struts", fooFile);
diff --git a/sonar-batch/src/test/java/org/sonar/batch/scan/report/JsonReportTest.java b/sonar-batch/src/test/java/org/sonar/batch/scan/report/JsonReportTest.java
index 59092657927..6cd93d93da0 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/scan/report/JsonReportTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/scan/report/JsonReportTest.java
@@ -28,7 +28,9 @@ import org.junit.Test;
 import org.junit.rules.TemporaryFolder;
 import org.skyscreamer.jsonassert.JSONAssert;
 import org.sonar.api.batch.fs.InputFile;
+import org.sonar.api.batch.fs.InputPath;
 import org.sonar.api.batch.fs.internal.DefaultFileSystem;
+import org.sonar.api.batch.fs.internal.DefaultInputDir;
 import org.sonar.api.batch.fs.internal.DeprecatedDefaultInputFile;
 import org.sonar.api.config.Settings;
 import org.sonar.api.issue.Issue;
@@ -85,11 +87,13 @@ public class JsonReportTest {
     mode = mock(AnalysisMode.class);
     when(mode.isPreview()).thenReturn(true);
     userFinder = mock(UserFinder.class);
+    DefaultInputDir inputDir = new DefaultInputDir("src/main/java/org/apache/struts");
+    inputDir.setKey("struts:src/main/java/org/apache/struts");
     DeprecatedDefaultInputFile inputFile = new DeprecatedDefaultInputFile("src/main/java/org/apache/struts/Action.java");
     inputFile.setKey("struts:src/main/java/org/apache/struts/Action.java");
     inputFile.setStatus(InputFile.Status.CHANGED);
     InputPathCache fileCache = mock(InputPathCache.class);
-    when(fileCache.all()).thenReturn(Arrays.<InputFile>asList(inputFile));
+    when(fileCache.all()).thenReturn(Arrays.<InputPath>asList(inputDir, inputFile));
     Project rootModule = new Project("struts");
     Project moduleA = new Project("struts-core");
     moduleA.setParent(rootModule).setPath("core");
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report-without-resolved-issues.json b/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report-without-resolved-issues.json
index 59c9c3272bb..d699073ee83 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report-without-resolved-issues.json
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report-without-resolved-issues.json
@@ -14,6 +14,10 @@
     "path": "ui"
   },
   {
+    "key": "struts:src/main/java/org/apache/struts",
+    "path": "src/main/java/org/apache/struts"
+  },
+  {
     "key": "struts:src/main/java/org/apache/struts/Action.java",
     "path": "src/main/java/org/apache/struts/Action.java"
   }
diff --git a/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report.json b/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report.json
index 7ff8f67abc0..f5c32f1aabb 100644
--- a/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report.json
+++ b/sonar-batch/src/test/resources/org/sonar/batch/scan/report/JsonReportTest/report.json
@@ -27,6 +27,11 @@
     "path": "ui"
   },
   {
+    "key": "struts:src/main/java/org/apache/struts",
+    "path": "src/main/java/org/apache/struts",
+    "moduleKey": "struts",
+  },
+  {
     "key": "struts:src/main/java/org/apache/struts/Action.java",
     "path": "src/main/java/org/apache/struts/Action.java",
     "moduleKey": "struts",