SONAR-4316 implement IssueFilter and support ViolationFilter

28 files changed, 449 insertions, 225 deletions

diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/CorePlugin.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/CorePlugin.java
index 741f1176f1a..8421f36b4b8 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/CorePlugin.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/CorePlugin.java
@@ -389,7 +389,6 @@ public final class CorePlugin extends SonarPlugin {
       IssueTrackingDecorator.class,
       IssueTracking.class,
       IssueHandlers.class,
-      IssueFilters.class,
       CountOpenIssuesDecorator.class,
       CountFalsePositivesDecorator.class,
       WeightedIssuesDecorator.class,
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/CountOpenIssuesDecorator.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/CountOpenIssuesDecorator.java
index 62251e4ef13..9c0b9725d32 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/CountOpenIssuesDecorator.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/CountOpenIssuesDecorator.java
@@ -274,7 +274,7 @@ public class CountOpenIssuesDecorator implements Decorator {
   }
 
   private boolean isAfter(Issue issue, @Nullable Date date) {
-    return date == null || issue.creationDate() != null && issue.creationDate().after(date);
+    return date == null || (issue.creationDate() != null && issue.creationDate().after(date));
   }
 
   private boolean shouldSaveNewMetrics(DecoratorContext context) {
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTracking.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTracking.java
index a95d9713606..ed33a132279 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTracking.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTracking.java
@@ -295,7 +295,7 @@ public class IssueTracking implements BatchExtension {
   }
 
   private boolean isSameChecksum(DefaultIssue newIssue, IssueDto pastIssue) {
-    return Objects.equal(pastIssue.getChecksum(), newIssue.getChecksum());
+    return Objects.equal(pastIssue.getChecksum(), newIssue.checksum());
   }
 
   private boolean isSameLine(DefaultIssue newIssue, IssueDto pastIssue) {
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTrackingDecorator.java b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTrackingDecorator.java
index 8e071fba49e..3e7be468505 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTrackingDecorator.java
+++ b/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueTrackingDecorator.java
@@ -31,8 +31,6 @@ import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
 import org.sonar.api.resources.ResourceUtils;
 import org.sonar.api.rules.ActiveRule;
-import org.sonar.api.rules.Rule;
-import org.sonar.api.rules.RuleFinder;
 import org.sonar.api.utils.KeyValueFormat;
 import org.sonar.batch.issue.IssueCache;
 import org.sonar.core.issue.DefaultIssue;
@@ -42,16 +40,14 @@ import org.sonar.core.issue.db.IssueDto;
 import org.sonar.core.issue.workflow.IssueWorkflow;
 
 import java.util.Collection;
-import java.util.Map;
 
 @DependsUpon({DecoratorBarriers.END_OF_VIOLATIONS_GENERATION, DecoratorBarriers.START_VIOLATION_TRACKING})
-@DependedUpon({DecoratorBarriers.END_OF_VIOLATION_TRACKING,DecoratorBarriers.END_OF_ISSUES_UPDATES})
+@DependedUpon({DecoratorBarriers.END_OF_VIOLATION_TRACKING, DecoratorBarriers.END_OF_ISSUES_UPDATES})
 public class IssueTrackingDecorator implements Decorator {
 
   private final IssueCache issueCache;
   private final InitialOpenIssuesStack initialOpenIssues;
   private final IssueTracking tracking;
-  private final IssueFilters filters;
   private final IssueHandlers handlers;
   private final IssueWorkflow workflow;
   private final IssueUpdater updater;
@@ -60,14 +56,13 @@ public class IssueTrackingDecorator implements Decorator {
   private final RulesProfile rulesProfile;
 
   public IssueTrackingDecorator(IssueCache issueCache, InitialOpenIssuesStack initialOpenIssues, IssueTracking tracking,
-                                IssueFilters filters, IssueHandlers handlers, IssueWorkflow workflow,
+                                IssueHandlers handlers, IssueWorkflow workflow,
                                 IssueUpdater updater,
                                 Project project, ResourcePerspectives perspectives,
                                 RulesProfile rulesProfile) {
     this.issueCache = issueCache;
     this.initialOpenIssues = initialOpenIssues;
     this.tracking = tracking;
-    this.filters = filters;
     this.handlers = handlers;
     this.workflow = workflow;
     this.updater = updater;
@@ -93,9 +88,7 @@ public class IssueTrackingDecorator implements Decorator {
     Collection<DefaultIssue> issues = Lists.newArrayList();
     for (Issue issue : issueCache.byComponent(resource.getEffectiveKey())) {
       issueCache.remove(issue);
-      if (filters.accept(issue)) {
-        issues.add((DefaultIssue) issue);
-      }
+      issues.add((DefaultIssue) issue);
     }
     // issues = all the issues created by rule engines during this module scan and not excluded by filters
 
@@ -143,7 +136,7 @@ public class IssueTrackingDecorator implements Decorator {
       issue.setAssignee(ref.getAssignee());
       issue.setAuthorLogin(ref.getAuthorLogin());
       if (ref.getIssueAttributes() != null) {
-          issue.setAttributes(KeyValueFormat.parse(ref.getIssueAttributes()));
+        issue.setAttributes(KeyValueFormat.parse(ref.getIssueAttributes()));
       }
 
       // fields to update with current values
@@ -168,7 +161,7 @@ public class IssueTrackingDecorator implements Decorator {
 
       ActiveRule activeRule = rulesProfile.getActiveRule(unmatchedDto.getRuleRepo(), unmatchedDto.getRule());
       boolean manualIssue = !Strings.isNullOrEmpty(unmatched.reporter());
-      boolean onDisabledRule = (activeRule==null);
+      boolean onDisabledRule = (activeRule == null);
 
       unmatched.setNew(false);
       unmatched.setEndOfLife(!manualIssue);
@@ -183,7 +176,7 @@ public class IssueTrackingDecorator implements Decorator {
       ActiveRule activeRule = rulesProfile.getActiveRule(deadDto.getRuleRepo(), deadDto.getRule());
       dead.setNew(false);
       dead.setEndOfLife(true);
-      dead.setOnDisabledRule(activeRule==null);
+      dead.setOnDisabledRule(activeRule == null);
       issues.add(dead);
     }
   }
diff --git a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueTrackingDecoratorTest.java b/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueTrackingDecoratorTest.java
index bc062f6a0ce..79178d74f49 100644
--- a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueTrackingDecoratorTest.java
+++ b/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueTrackingDecoratorTest.java
@@ -28,7 +28,6 @@ import org.sonar.api.profiles.RulesProfile;
 import org.sonar.api.resources.File;
 import org.sonar.api.resources.Project;
 import org.sonar.api.resources.Resource;
-import org.sonar.api.rules.RuleFinder;
 import org.sonar.batch.issue.IssueCache;
 import org.sonar.core.issue.DefaultIssue;
 import org.sonar.core.issue.IssueChangeContext;
@@ -49,7 +48,6 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
   IssueCache issueCache = mock(IssueCache.class);
   InitialOpenIssuesStack initialOpenIssues = mock(InitialOpenIssuesStack.class);
   IssueTracking tracking = mock(IssueTracking.class, RETURNS_MOCKS);
-  IssueFilters filters = mock(IssueFilters.class);
   IssueHandlers handlers = mock(IssueHandlers.class);
   IssueWorkflow workflow = mock(IssueWorkflow.class);
   IssueUpdater updater = mock(IssueUpdater.class);
@@ -64,7 +62,7 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
       issueCache,
       initialOpenIssues,
       tracking,
-      filters, handlers,
+      handlers,
       workflow,
       updater,
       mock(Project.class),
@@ -90,7 +88,7 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
   public void should_not_be_executed_on_classes_not_methods() throws Exception {
     DecoratorContext context = mock(DecoratorContext.class);
     decorator.decorate(JavaClass.create("org.foo.Bar"), context);
-    verifyZeroInteractions(context, issueCache, tracking, filters, handlers, workflow);
+    verifyZeroInteractions(context, issueCache, tracking, handlers, workflow);
   }
 
   @Test
@@ -100,14 +98,12 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
 
     // INPUT : one issue, no open issues during previous scan, no filtering
     when(issueCache.byComponent("struts:Action.java")).thenReturn(Arrays.asList(issue));
-    when(filters.accept(issue)).thenReturn(true);
     List<IssueDto> dbIssues = Collections.emptyList();
     when(initialOpenIssues.selectAndRemove(123)).thenReturn(dbIssues);
 
     decorator.doDecorate(file);
 
     // Apply filters, track, apply transitions, notify extensions then update cache
-    verify(filters).accept(issue);
     verify(tracking).track(eq(file), eq(dbIssues), argThat(new ArgumentMatcher<Collection<DefaultIssue>>() {
       @Override
       public boolean matches(Object o) {
@@ -128,7 +124,6 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
 
     // INPUT : one issue, one open issue during previous scan, no filtering
     when(issueCache.byComponent("struts:Action.java")).thenReturn(Arrays.asList(openIssue));
-    when(filters.accept(openIssue)).thenReturn(true);
     IssueDto unmatchedIssue = new IssueDto().setKee("ABCDE").setResolution("OPEN").setStatus("OPEN").setRuleKey_unit_test_only("squid", "AvoidCycle");
 
     IssueTrackingResult trackingResult = new IssueTrackingResult();
@@ -156,7 +151,6 @@ public class IssueTrackingDecoratorTest extends AbstractDaoTestCase {
     Project project = new Project("struts");
     DefaultIssue openIssue = new DefaultIssue();
     when(issueCache.byComponent("struts")).thenReturn(Arrays.asList(openIssue));
-    when(filters.accept(openIssue)).thenReturn(true);
     IssueDto deadIssue = new IssueDto().setKee("ABCDE").setResolution("OPEN").setStatus("OPEN").setRuleKey_unit_test_only("squid", "AvoidCycle");
     when(initialOpenIssues.getAllIssues()).thenReturn(Arrays.asList(deadIssue));
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/ViolationFilters.java b/sonar-batch/src/main/java/org/sonar/batch/ViolationFilters.java
index d6edcfc5092..3df35ee05b6 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/ViolationFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/ViolationFilters.java
@@ -31,15 +31,15 @@ public class ViolationFilters {
   private ViolationFilter[] filters;
 
   public ViolationFilters(ViolationFilter[] filters) {
-    this.filters = (filters==null ? new ViolationFilter[0] : filters);
+    this.filters = filters;
   }
 
   public ViolationFilters() {
-    this(null);
+    this(new ViolationFilter[0]);
   }
 
-  public ViolationFilter[] getFilters() {
-    return filters;
+  public boolean isEmpty() {
+    return filters.length==0;
   }
 
   /**
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/Bucket.java b/sonar-batch/src/main/java/org/sonar/batch/index/Bucket.java
index 50e43abb197..6c253dd7e19 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/index/Bucket.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/Bucket.java
@@ -37,7 +37,6 @@ public final class Bucket {
 
   private Resource resource;
   private ListMultimap<String, Measure> measuresByMetric = ArrayListMultimap.create();
-  private List<Violation> violations = Lists.newLinkedList();
 
   private Bucket parent;
   private List<Bucket> children;
@@ -80,14 +79,6 @@ public final class Bucket {
     return parent;
   }
 
-  public void addViolation(Violation violation) {
-    violations.add(violation);
-  }
-
-  public List<Violation> getViolations() {
-    return violations;
-  }
-
   public void addMeasure(Measure measure) {
     List<Measure> metricMeasures = measuresByMetric.get(measure.getMetric().getKey());
 
@@ -109,7 +100,6 @@ public final class Bucket {
 
   public void clear() {
     measuresByMetric = null;
-    violations = null;
     children = null;
     if (parent != null) {
       parent.removeChild(this);
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 3a51f38ff0d..cef707b9799 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
@@ -32,19 +32,16 @@ import org.sonar.api.database.model.ResourceModel;
 import org.sonar.api.database.model.Snapshot;
 import org.sonar.api.design.Dependency;
 import org.sonar.api.measures.*;
-import org.sonar.api.profiles.RulesProfile;
 import org.sonar.api.resources.*;
-import org.sonar.api.rules.ActiveRule;
 import org.sonar.api.rules.Rule;
-import org.sonar.api.rules.RuleFinder;
 import org.sonar.api.rules.Violation;
 import org.sonar.api.utils.SonarException;
 import org.sonar.api.violations.ViolationQuery;
 import org.sonar.batch.DefaultResourceCreationLock;
 import org.sonar.batch.ProjectTree;
 import org.sonar.batch.ResourceFilters;
-import org.sonar.batch.ViolationFilters;
 import org.sonar.batch.issue.DeprecatedViolations;
+import org.sonar.batch.issue.ScanIssues;
 import org.sonar.core.component.ScanGraph;
 
 import java.util.*;
@@ -53,16 +50,14 @@ public class DefaultIndex extends SonarIndex {
 
   private static final Logger LOG = LoggerFactory.getLogger(DefaultIndex.class);
 
-  private RulesProfile profile;
   private PersistenceManager persistence;
   private DefaultResourceCreationLock lock;
   private MetricFinder metricFinder;
-  private RuleFinder ruleFinder;
-  private ScanGraph graph;
-  private SnapshotCache snapshotCache;
+  private final ScanGraph graph;
+  private final SnapshotCache snapshotCache;
+  private final ResourceCache resourceCache;
 
   // filters
-  private ViolationFilters violationFilters;
   private ResourceFilters resourceFilters;
 
   // caches
@@ -73,17 +68,18 @@ public class DefaultIndex extends SonarIndex {
   private Map<Resource, Map<Resource, Dependency>> incomingDependenciesByResource = Maps.newHashMap();
   private ProjectTree projectTree;
   private final DeprecatedViolations deprecatedViolations;
+  private ScanIssues scanIssues;
 
   public DefaultIndex(PersistenceManager persistence, DefaultResourceCreationLock lock, ProjectTree projectTree, MetricFinder metricFinder,
-                      RuleFinder ruleFinder, ScanGraph graph, DeprecatedViolations deprecatedViolations, SnapshotCache snapshotCache) {
+                      ScanGraph graph, SnapshotCache snapshotCache, ResourceCache resourceCache, DeprecatedViolations deprecatedViolations) {
     this.persistence = persistence;
     this.lock = lock;
     this.projectTree = projectTree;
     this.metricFinder = metricFinder;
-    this.ruleFinder = ruleFinder;
     this.graph = graph;
-    this.deprecatedViolations = deprecatedViolations;
     this.snapshotCache = snapshotCache;
+    this.resourceCache = resourceCache;
+    this.deprecatedViolations = deprecatedViolations;
   }
 
   public void start() {
@@ -116,13 +112,12 @@ public class DefaultIndex extends SonarIndex {
     return currentProject;
   }
 
-  public void setCurrentProject(Project project, ResourceFilters resourceFilters, ViolationFilters violationFilters, RulesProfile profile) {
+  public void setCurrentProject(Project project, ResourceFilters resourceFilters, ScanIssues scanIssues) {
     this.currentProject = project;
 
-    // the following components depend on the current project, so they need to be reloaded.
+    // the following components depend on the current module, so they need to be reloaded.
     this.resourceFilters = resourceFilters;
-    this.violationFilters = violationFilters;
-    this.profile = profile;
+    this.scanIssues = scanIssues;
   }
 
   /**
@@ -321,10 +316,13 @@ public class DefaultIndex extends SonarIndex {
       return Collections.emptyList();
     }
 
+    List<Violation> violations = deprecatedViolations.get(bucket.getResource().getEffectiveKey());
+    if (violationQuery.getSwitchMode() == ViolationQuery.SwitchMode.BOTH) {
+      return violations;
+    }
     List<Violation> filteredViolations = Lists.newArrayList();
-    ViolationQuery.SwitchMode mode = violationQuery.getSwitchMode();
-    for (Violation violation : bucket.getViolations()) {
-      if (isFiltered(violation, mode)) {
+    for (Violation violation : violations) {
+      if (isFiltered(violation, violationQuery.getSwitchMode())) {
         filteredViolations.add(violation);
       }
     }
@@ -352,47 +350,13 @@ public class DefaultIndex extends SonarIndex {
       return;
     }
 
-    if (rule.getId() == null) {
-      Rule persistedRule = ruleFinder.findByKey(rule.getRepositoryKey(), rule.getKey());
-      if (persistedRule == null) {
-        LOG.warn("Rule does not exist. Ignoring violation {}", violation);
-        return;
-      }
-      violation.setRule(persistedRule);
-    }
-
     Bucket bucket = checkIndexed(resource);
     if (bucket == null || bucket.isExcluded()) {
       return;
     }
 
     violation.setResource(bucket.getResource());
-    if (addViolation(violation, bucket, force)) {
-      deprecatedViolations.add(violation, currentProject.getAnalysisDate());
-    }
-  }
-
-  private boolean addViolation(Violation violation, Bucket bucket, boolean force) {
-    boolean isIgnored = !force && violationFilters != null && violationFilters.isIgnored(violation);
-    if (isIgnored) {
-      return false;
-    }
-
-    // TODO this code is not the responsibility of this index. It should be moved somewhere else.
-    if (!violation.isManual()) {
-      ActiveRule activeRule = profile.getActiveRule(violation.getRule());
-      if (activeRule != null) {
-        violation.setSeverity(activeRule.getSeverity());
-      } else if (currentProject.getReuseExistingRulesConfig()) {
-        violation.setSeverity(violation.getRule().getSeverity());
-      } else {
-        LoggerFactory.getLogger(getClass()).debug("Rule is not activated, ignoring violation {}", violation);
-        return false;
-      }
-    }
-
-    bucket.addViolation(violation);
-    return true;
+    scanIssues.initAndAddViolation(violation);
   }
 
 
@@ -569,6 +533,7 @@ public class DefaultIndex extends SonarIndex {
       if (ResourceUtils.isPersistable(resource) && !Qualifiers.LIBRARY.equals(resource.getQualifier())) {
         graph.addComponent(resource, snapshot);
         snapshotCache.put(resource.getEffectiveKey(), snapshot);
+        resourceCache.add(resource);
       }
     }
 
diff --git a/sonar-batch/src/main/java/org/sonar/batch/index/ResourceCache.java b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceCache.java
new file mode 100644
index 00000000000..a6879fd751f
--- /dev/null
+++ b/sonar-batch/src/main/java/org/sonar/batch/index/ResourceCache.java
@@ -0,0 +1,48 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 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.index;
+
+import com.google.common.base.Preconditions;
+import com.google.common.base.Strings;
+import com.google.common.collect.Maps;
+import org.sonar.api.BatchComponent;
+import org.sonar.api.resources.Resource;
+
+import java.util.Map;
+
+/**
+ * @since 3.6
+ */
+public class ResourceCache implements BatchComponent {
+  // resource by component key
+  private final Map<String, Resource> resources = Maps.newHashMap();
+
+  public Resource get(String componentKey) {
+    return resources.get(componentKey);
+  }
+
+  public ResourceCache add(Resource resource) {
+    String componentKey = resource.getEffectiveKey();
+    Preconditions.checkState(!Strings.isNullOrEmpty(componentKey), "Missing resource effective key");
+    Preconditions.checkState(!resources.containsKey(componentKey), "Resource is already registered: " + componentKey);
+    resources.put(componentKey, resource);
+    return this;
+  }
+}
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/DeprecatedViolations.java b/sonar-batch/src/main/java/org/sonar/batch/issue/DeprecatedViolations.java
index adb81f8967b..936165eae69 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/DeprecatedViolations.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/DeprecatedViolations.java
@@ -19,43 +19,58 @@
  */
 package org.sonar.batch.issue;
 
+import com.google.common.collect.Lists;
 import org.sonar.api.BatchComponent;
+import org.sonar.api.issue.Issue;
 import org.sonar.api.resources.Resource;
-import org.sonar.api.rule.RuleKey;
-import org.sonar.api.rule.Severity;
+import org.sonar.api.rules.Rule;
+import org.sonar.api.rules.RuleFinder;
+import org.sonar.api.rules.RulePriority;
 import org.sonar.api.rules.Violation;
+import org.sonar.batch.index.ResourceCache;
 import org.sonar.core.issue.DefaultIssue;
-import org.sonar.core.issue.DefaultIssueBuilder;
 
 import java.util.Collection;
-import java.util.Date;
+import java.util.List;
 
+/**
+ * Bridge with violations, that have been deprecated in 3.6.
+ * @since 3.6
+ */
 public class DeprecatedViolations implements BatchComponent {
 
-  private final IssueCache cache;
-
-  public DeprecatedViolations(IssueCache cache) {
-    this.cache = cache;
-  }
+  private final IssueCache issueCache;
+  private final RuleFinder ruleFinder;
+  private final ResourceCache resourceCache;
 
-  public void add(Violation violation, Date creationDate) {
-    DefaultIssue issue = toIssue(violation, creationDate);
-    cache.put(issue);
+  public DeprecatedViolations(IssueCache issueCache, RuleFinder ruleFinder, ResourceCache resourceCache) {
+    this.issueCache = issueCache;
+    this.ruleFinder = ruleFinder;
+    this.resourceCache = resourceCache;
   }
 
-  public Collection<Violation> get(Resource resource) {
-    throw new UnsupportedOperationException("TODO");
+  public List<Violation> get(String componentKey) {
+    Collection<DefaultIssue> issues = issueCache.byComponent(componentKey);
+    List<Violation> violations = Lists.newArrayList();
+    for (DefaultIssue issue : issues) {
+      violations.add(toViolation(issue));
+    }
+    return violations;
   }
 
-  DefaultIssue toIssue(Violation violation, Date creationDate) {
-    return (DefaultIssue) new DefaultIssueBuilder()
-      .createdDate(creationDate)
-      .componentKey(violation.getResource().getEffectiveKey())
-      .ruleKey(RuleKey.of(violation.getRule().getRepositoryKey(), violation.getRule().getKey()))
-      .effortToFix(violation.getCost())
-      .line(violation.getLineId())
-      .message(violation.getMessage())
-      .severity(violation.getSeverity() != null ? violation.getSeverity().name() : Severity.MAJOR)
-      .build();
+  public Violation toViolation(DefaultIssue issue) {
+    Rule rule = ruleFinder.findByKey(issue.ruleKey());
+    Resource resource = resourceCache.get(issue.componentKey());
+    Violation violation = new Violation(rule, resource);
+    violation.setNew(issue.isNew());
+    violation.setChecksum(issue.checksum());
+    violation.setMessage(issue.message());
+    violation.setCost(issue.effortToFix());
+    violation.setLineId(issue.line());
+    violation.setCreatedAt(issue.creationDate());
+    violation.setManual(issue.reporter() != null);
+    violation.setSeverity(RulePriority.valueOf(issue.severity()));
+    violation.setSwitchedOff(Issue.RESOLUTION_FALSE_POSITIVE.equals(issue.resolution()));
+    return violation;
   }
 }
diff --git a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueFilters.java b/sonar-batch/src/main/java/org/sonar/batch/issue/IssueFilters.java
index 7b52e845618..0488c432aed 100644
--- a/plugins/sonar-core-plugin/src/main/java/org/sonar/plugins/core/issue/IssueFilters.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/IssueFilters.java
@@ -17,29 +17,43 @@
  * 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.plugins.core.issue;
+package org.sonar.batch.issue;
 
 import org.sonar.api.BatchExtension;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.issue.IssueFilter;
+import org.sonar.api.rules.Violation;
+import org.sonar.batch.ViolationFilters;
+import org.sonar.core.issue.DefaultIssue;
+
+import javax.annotation.Nullable;
 
 public class IssueFilters implements BatchExtension {
+
+  private final ViolationFilters deprecatedFilters;
+  private final DeprecatedViolations deprecatedViolations;
   private final IssueFilter[] filters;
 
-  public IssueFilters(IssueFilter[] filters) {
+  public IssueFilters(ViolationFilters deprecatedFilters, DeprecatedViolations deprecatedViolations, IssueFilter[] filters) {
+    this.deprecatedFilters = deprecatedFilters;
+    this.deprecatedViolations = deprecatedViolations;
     this.filters = filters;
   }
 
-  public IssueFilters() {
-    this(new IssueFilter[0]);
+  public IssueFilters(ViolationFilters deprecatedFilters, DeprecatedViolations deprecatedViolations) {
+    this(deprecatedFilters, deprecatedViolations, new IssueFilter[0]);
   }
 
-  public boolean accept(Issue issue) {
+  public boolean accept(DefaultIssue issue, @Nullable Violation violation) {
     for (IssueFilter filter : filters) {
       if (!filter.accept(issue)) {
         return false;
       }
     }
+    if (!deprecatedFilters.isEmpty()) {
+      Violation v = (violation != null ? violation : deprecatedViolations.toViolation(issue));
+      return !deprecatedFilters.isIgnored(v);
+    }
     return true;
   }
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/issue/ScanIssues.java b/sonar-batch/src/main/java/org/sonar/batch/issue/ScanIssues.java
index ab06a7f9cca..4d0e5863023 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/issue/ScanIssues.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/issue/ScanIssues.java
@@ -22,25 +22,54 @@ package org.sonar.batch.issue;
 import org.sonar.api.BatchComponent;
 import org.sonar.api.profiles.RulesProfile;
 import org.sonar.api.resources.Project;
+import org.sonar.api.rule.RuleKey;
 import org.sonar.api.rules.ActiveRule;
+import org.sonar.api.rules.Violation;
 import org.sonar.core.issue.DefaultIssue;
+import org.sonar.core.issue.DefaultIssueBuilder;
+
+import javax.annotation.Nullable;
 
 /**
- * Central component to manage issues
+ * Initialize the issues raised during scan.
  */
 public class ScanIssues implements BatchComponent {
 
   private final RulesProfile qProfile;
   private final IssueCache cache;
   private final Project project;
+  private final IssueFilters filters;
 
-  public ScanIssues(RulesProfile qProfile, IssueCache cache, Project project) {
+  public ScanIssues(RulesProfile qProfile, IssueCache cache, Project project, IssueFilters filters) {
     this.qProfile = qProfile;
     this.cache = cache;
     this.project = project;
+    this.filters = filters;
   }
 
   public boolean initAndAddIssue(DefaultIssue issue) {
+    return initAndAddIssue(issue, null);
+  }
+
+  public boolean initAndAddViolation(Violation violation) {
+    DefaultIssue issue = newIssue(violation);
+    return initAndAddIssue(issue, violation);
+  }
+
+  private DefaultIssue newIssue(Violation violation) {
+    return (DefaultIssue) new DefaultIssueBuilder()
+      .componentKey(violation.getResource().getEffectiveKey())
+      .ruleKey(RuleKey.of(violation.getRule().getRepositoryKey(), violation.getRule().getKey()))
+      .effortToFix(violation.getCost())
+      .line(violation.getLineId())
+      .message(violation.getMessage())
+      .severity(violation.getSeverity() != null ? violation.getSeverity().name() : null)
+      .build();
+  }
+
+  private boolean initAndAddIssue(DefaultIssue issue, @Nullable Violation violation) {
+    // TODO fail fast : if rule does not exist
+
     ActiveRule activeRule = qProfile.getActiveRule(issue.ruleKey().repository(), issue.ruleKey().rule());
     if (activeRule == null || activeRule.getRule() == null) {
       // rule does not exist or is not enabled -> ignore the issue
@@ -52,8 +81,12 @@ public class ScanIssues implements BatchComponent {
     if (issue.severity() == null) {
       issue.setSeverity(activeRule.getSeverity().name());
     }
-    cache.put(issue);
-    return true;
+
+    if (filters.accept(issue, violation)) {
+      cache.put(issue);
+      return true;
+    }
+    return false;
   }
 
 }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
index c40edc06c85..23a087ce155 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ModuleScanContainer.java
@@ -25,7 +25,6 @@ import org.sonar.api.BatchExtension;
 import org.sonar.api.batch.InstantiationStrategy;
 import org.sonar.api.batch.bootstrap.ProjectDefinition;
 import org.sonar.api.platform.ComponentContainer;
-import org.sonar.api.profiles.RulesProfile;
 import org.sonar.api.resources.Languages;
 import org.sonar.api.resources.Project;
 import org.sonar.api.scan.filesystem.FileExclusions;
@@ -40,6 +39,7 @@ import org.sonar.batch.events.EventBus;
 import org.sonar.batch.index.DefaultIndex;
 import org.sonar.batch.index.ResourcePersister;
 import org.sonar.batch.issue.IssuableFactory;
+import org.sonar.batch.issue.IssueFilters;
 import org.sonar.batch.issue.ScanIssues;
 import org.sonar.batch.phases.PhaseExecutor;
 import org.sonar.batch.phases.PhasesTimeProfiler;
@@ -103,6 +103,7 @@ public class ModuleScanContainer extends ComponentContainer {
       BatchExtensionDictionnary.class,
       DefaultTimeMachine.class,
       ViolationFilters.class,
+      IssueFilters.class,
       ResourceFilters.class,
       DeprecatedJsonReport.class,
       JsonReport.class,
@@ -136,8 +137,7 @@ public class ModuleScanContainer extends ComponentContainer {
     DefaultIndex index = getComponentByType(DefaultIndex.class);
     index.setCurrentProject(module,
       getComponentByType(ResourceFilters.class),
-      getComponentByType(ViolationFilters.class),
-      getComponentByType(RulesProfile.class));
+      getComponentByType(ScanIssues.class));
 
     getComponentByType(PhaseExecutor.class).execute(module);
   }
diff --git a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
index ae0bab858c4..857ffb174ab 100644
--- a/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
+++ b/sonar-batch/src/main/java/org/sonar/batch/scan/ProjectScanContainer.java
@@ -89,6 +89,7 @@ public class ProjectScanContainer extends ComponentContainer {
       LastSnapshots.class,
       Caches.class,
       SnapshotCache.class,
+      ResourceCache.class,
       ComponentDataCache.class,
       ComponentDataPersister.class,
 
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
index a61acdcbd09..89f0ddd43a8 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/BucketTest.java
@@ -36,9 +36,9 @@ import static org.junit.internal.matchers.IsCollectionContaining.hasItem;
 
 public class BucketTest {
 
-  private JavaPackage javaPackage = new JavaPackage("org.foo");
-  private JavaFile javaFile = new JavaFile("org.foo.Bar");
-  private Metric ncloc = new Metric("ncloc");
+  JavaPackage javaPackage = new JavaPackage("org.foo");
+  JavaFile javaFile = new JavaFile("org.foo.Bar");
+  Metric ncloc = new Metric("ncloc");
 
   @Test
   public void shouldManageRelationships() {
@@ -52,15 +52,6 @@ public class BucketTest {
   }
 
   @Test
-  public void shouldCacheViolations() {
-    Bucket fileBucket = new Bucket(javaFile);
-    Violation violation = Violation.create(Rule.create("checkstyle", "rule1", "Rule one"), javaFile);
-    fileBucket.addViolation(violation);
-    assertThat(fileBucket.getViolations().size(), is(1));
-    assertThat(fileBucket.getViolations(), hasItem(violation));
-  }
-
-  @Test
   public void shouldAddNewMeasure() {
     Bucket fileBucket = new Bucket(javaFile);
     Measure measure = new Measure(ncloc).setValue(1200.0);
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 c23a85bdd2f..598b73750ae 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
@@ -20,7 +20,6 @@
 package org.sonar.batch.index;
 
 import org.apache.commons.lang.StringUtils;
-import org.hamcrest.Matchers;
 import org.junit.Before;
 import org.junit.Test;
 import org.sonar.api.batch.ResourceFilter;
@@ -30,15 +29,7 @@ import org.sonar.api.measures.Measure;
 import org.sonar.api.measures.MeasuresFilters;
 import org.sonar.api.measures.MetricFinder;
 import org.sonar.api.profiles.RulesProfile;
-import org.sonar.api.resources.Directory;
-import org.sonar.api.resources.File;
-import org.sonar.api.resources.Java;
-import org.sonar.api.resources.JavaPackage;
-import org.sonar.api.resources.Language;
-import org.sonar.api.resources.Library;
-import org.sonar.api.resources.Project;
-import org.sonar.api.resources.Qualifiers;
-import org.sonar.api.resources.Resource;
+import org.sonar.api.resources.*;
 import org.sonar.api.rules.Rule;
 import org.sonar.api.rules.RuleFinder;
 import org.sonar.api.rules.Violation;
@@ -47,12 +38,10 @@ import org.sonar.api.violations.ViolationQuery;
 import org.sonar.batch.DefaultResourceCreationLock;
 import org.sonar.batch.ProjectTree;
 import org.sonar.batch.ResourceFilters;
-import org.sonar.batch.ViolationFilters;
 import org.sonar.batch.issue.DeprecatedViolations;
+import org.sonar.batch.issue.ScanIssues;
 import org.sonar.core.component.ScanGraph;
 
-import java.util.List;
-
 import static org.hamcrest.Matchers.nullValue;
 import static org.hamcrest.core.Is.is;
 import static org.junit.Assert.assertThat;
@@ -73,7 +62,8 @@ public class DefaultIndexTest {
     when(metricFinder.findByKey("ncloc")).thenReturn(CoreMetrics.NCLOC);
     ruleFinder = mock(RuleFinder.class);
 
-    index = new DefaultIndex(mock(PersistenceManager.class), lock, mock(ProjectTree.class), metricFinder, ruleFinder, mock(ScanGraph.class), mock(DeprecatedViolations.class), mock(SnapshotCache.class));
+    index = new DefaultIndex(mock(PersistenceManager.class), lock, mock(ProjectTree.class), metricFinder, mock(ScanGraph.class),
+      mock(SnapshotCache.class), mock(ResourceCache.class), mock(DeprecatedViolations.class));
     Project project = new Project("project");
 
     ResourceFilter filter = new ResourceFilter() {
@@ -86,7 +76,7 @@ public class DefaultIndexTest {
     rule = Rule.create("repoKey", "ruleKey", "Rule");
     rule.setId(1);
     rulesProfile.activateRule(rule, null);
-    index.setCurrentProject(project, new ResourceFilters(new ResourceFilter[]{filter}), new ViolationFilters(), rulesProfile);
+    index.setCurrentProject(project, new ResourceFilters(new ResourceFilter[]{filter}), mock(ScanIssues.class));
     index.doStart(project);
   }
 
@@ -214,25 +204,6 @@ public class DefaultIndexTest {
    * See https://jira.codehaus.org/browse/SONAR-3583
    */
   @Test
-  public void should_support_violations_with_missing_rule_id() {
-    Rule ruleWithoutId = Rule.create("repoKey", "ruleKey", "Rule");
-    Rule ruleWithId = Rule.create("repoKey", "ruleKey", "Rule");
-    ruleWithId.setId(123);
-    when(ruleFinder.findByKey("repoKey", "ruleKey")).thenReturn(ruleWithId);
-
-    File file = new File("org/foo/Bar.java");
-    Violation violation = Violation.create(ruleWithoutId, file);
-    index.addViolation(violation);
-
-    List<Violation> violations = index.getViolations(file);
-    assertThat(violations.size(), is(1));
-    assertThat(violations.get(0).getRule().getId(), Matchers.is(123));
-  }
-
-  /**
-   * See https://jira.codehaus.org/browse/SONAR-3583
-   */
-  @Test
   public void should_ignore_violation_on_unknown_rules() {
     Rule ruleWithoutID = Rule.create("repoKey", "ruleKey", "Rule");
 
@@ -243,36 +214,6 @@ public class DefaultIndexTest {
     assertThat(index.getViolations(file).size(), is(0));
   }
 
-  @Test
-  public void testGetViolations() {
-    File file = new File("org/foo/Bar.java");
-    Violation violation1 = Violation.create(rule, file);
-    index.addViolation(violation1);
-    Violation violation2 = Violation.create(rule, file);
-    violation2.setSwitchedOff(true);
-    index.addViolation(violation2);
-    Violation violation3 = Violation.create(rule, file);
-    violation3.setSwitchedOff(true);
-    index.addViolation(violation3);
-
-    assertThat(index.getViolations(file).size(), is(1));
-  }
-
-  @Test
-  public void testGetViolationsWithQuery() {
-    File file = new File("org/foo/Bar.java");
-    Violation violation1 = Violation.create(rule, file);
-    index.addViolation(violation1);
-    Violation violation2 = Violation.create(rule, file);
-    violation2.setSwitchedOff(true);
-    index.addViolation(violation2);
-    Violation violation3 = Violation.create(rule, file);
-    violation3.setSwitchedOff(true);
-    index.addViolation(violation3);
-
-    assertThat(index.getViolations(ViolationQuery.create().forResource(file).setSwitchedOff(true)).size(), is(2));
-  }
-
   @Test(expected = IllegalArgumentException.class)
   public void testGetViolationsWithQueryWithNoResource() {
     index.getViolations(ViolationQuery.create());
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java
new file mode 100644
index 00000000000..ad16edcb02f
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/ResourceCacheTest.java
@@ -0,0 +1,68 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 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.index;
+
+import org.junit.Test;
+import org.sonar.api.resources.JavaFile;
+import org.sonar.api.resources.Resource;
+
+import static org.fest.assertions.Assertions.assertThat;
+import static org.fest.assertions.Fail.fail;
+
+public class ResourceCacheTest {
+  @Test
+  public void should_cache_resource() throws Exception {
+    ResourceCache cache = new ResourceCache();
+    String componentKey = "struts:org.struts.Action";
+    Resource resource = new JavaFile("org.struts.Action").setEffectiveKey(componentKey);
+    cache.add(resource);
+
+    assertThat(cache.get(componentKey)).isSameAs(resource);
+    assertThat(cache.get("other")).isNull();
+  }
+
+  @Test
+  public void should_fail_if_add_twice() throws Exception {
+    ResourceCache cache = new ResourceCache();
+    String componentKey = "struts:org.struts.Action";
+    Resource resource = new JavaFile("org.struts.Action").setEffectiveKey(componentKey);
+    cache.add(resource);
+    try {
+      cache.add(resource);
+      fail();
+    } catch (IllegalStateException e) {
+      // success
+      assertThat(e).hasMessage("Resource is already registered: struts:org.struts.Action");
+    }
+  }
+
+  @Test
+  public void should_fail_if_missing_component_key() throws Exception {
+    ResourceCache cache = new ResourceCache();
+    Resource resource = new JavaFile("org.struts.Action").setEffectiveKey(null);
+    try {
+      cache.add(resource);
+      fail();
+    } catch (IllegalStateException e) {
+      // success
+      assertThat(e).hasMessage("Missing resource effective key");
+    }
+  }
+}
diff --git a/sonar-batch/src/test/java/org/sonar/batch/index/SnapshotCacheTest.java b/sonar-batch/src/test/java/org/sonar/batch/index/SnapshotCacheTest.java
index 81776a93518..29df021f0c8 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/index/SnapshotCacheTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/index/SnapshotCacheTest.java
@@ -28,7 +28,7 @@ import static org.mockito.Mockito.mock;
 
 public class SnapshotCacheTest {
 
-  private Snapshot snapshot = mock(Snapshot.class);
+  Snapshot snapshot = mock(Snapshot.class);
 
   @Test
   public void should_cache_snapshots() throws Exception {
@@ -49,6 +49,7 @@ public class SnapshotCacheTest {
       fail();
     } catch (IllegalStateException e) {
       // success
+      assertThat(e).hasMessage("Component is already registered: org.apache.struts:struts-core");
     }
   }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/DeprecatedViolationsTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/DeprecatedViolationsTest.java
new file mode 100644
index 00000000000..bff9ae4e2d0
--- /dev/null
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/DeprecatedViolationsTest.java
@@ -0,0 +1,88 @@
+/*
+ * SonarQube, open source software quality management tool.
+ * Copyright (C) 2008-2013 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.issue;
+
+import org.junit.Test;
+import org.sonar.api.resources.JavaFile;
+import org.sonar.api.resources.Project;
+import org.sonar.api.rule.RuleKey;
+import org.sonar.api.rule.Severity;
+import org.sonar.api.rules.Rule;
+import org.sonar.api.rules.RuleFinder;
+import org.sonar.api.rules.RulePriority;
+import org.sonar.api.rules.Violation;
+import org.sonar.batch.index.ResourceCache;
+import org.sonar.core.issue.DefaultIssue;
+
+import java.util.Arrays;
+import java.util.List;
+
+import static org.fest.assertions.Assertions.assertThat;
+import static org.mockito.Mockito.mock;
+import static org.mockito.Mockito.when;
+
+public class DeprecatedViolationsTest {
+
+  IssueCache issueCache = mock(IssueCache.class);
+  RuleFinder ruleFinder = mock(RuleFinder.class);
+  ResourceCache resourceCache = mock(ResourceCache.class);
+  DeprecatedViolations deprecatedViolations = new DeprecatedViolations(issueCache, ruleFinder, resourceCache);
+
+  @Test
+  public void test_toViolation() throws Exception {
+    RuleKey ruleKey = RuleKey.of("squid", "AvoidCycles");
+    when(ruleFinder.findByKey(ruleKey)).thenReturn(new Rule("squid", "AvoidCycles"));
+    when(resourceCache.get("org.apache:struts")).thenReturn(new Project("org.apache:struts"));
+
+    DefaultIssue issue = newIssue(ruleKey);
+
+    Violation violation = deprecatedViolations.toViolation(issue);
+    assertThat(violation.getLineId()).isEqualTo(42);
+    assertThat(violation.getSeverity()).isEqualTo(RulePriority.BLOCKER);
+    assertThat(violation.isManual()).isTrue();
+    assertThat(violation.getRule().getRepositoryKey()).isEqualTo("squid");
+    assertThat(violation.getRule().getKey()).isEqualTo("AvoidCycles");
+    assertThat(violation.getResource()).isNotNull();
+  }
+
+  private DefaultIssue newIssue(RuleKey ruleKey) {
+    DefaultIssue issue = new DefaultIssue();
+    issue.setKey("ABCDE");
+    issue.setRuleKey(ruleKey);
+    issue.setComponentKey("org.apache:struts");
+    issue.setLine(42);
+    issue.setEffortToFix(3.14);
+    issue.setReporter("leon");
+    issue.setSeverity(Severity.BLOCKER);
+    return issue;
+  }
+
+  @Test
+  public void test_get() throws Exception {
+    RuleKey ruleKey = RuleKey.of("squid", "AvoidCycles");
+    when(ruleFinder.findByKey(ruleKey)).thenReturn(new Rule("squid", "AvoidCycles"));
+    when(resourceCache.get("org.apache:struts")).thenReturn(new Project("org.apache:struts"));
+    when(issueCache.byComponent("org.apache:struts")).thenReturn(Arrays.asList(newIssue(ruleKey)));
+
+    List<Violation> violations = deprecatedViolations.get("org.apache:struts");
+
+    assertThat(violations).hasSize(1);
+  }
+}
diff --git a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueFiltersTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/IssueFiltersTest.java
index d6dbe9cec3d..731c78d536f 100644
--- a/plugins/sonar-core-plugin/src/test/java/org/sonar/plugins/core/issue/IssueFiltersTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/IssueFiltersTest.java
@@ -17,11 +17,13 @@
  * 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.plugins.core.issue;
+package org.sonar.batch.issue;
 
 import org.junit.Test;
 import org.sonar.api.issue.Issue;
 import org.sonar.api.issue.IssueFilter;
+import org.sonar.api.rules.Violation;
+import org.sonar.batch.ViolationFilters;
 import org.sonar.core.issue.DefaultIssue;
 
 import static org.fest.assertions.Assertions.assertThat;
@@ -30,27 +32,42 @@ import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
 public class IssueFiltersTest {
+
+  DeprecatedViolations deprecatedViolations = mock(DeprecatedViolations.class);
+  ViolationFilters deprecatedFilters = mock(ViolationFilters.class);
+
   @Test
-  public void test_accept() throws Exception {
+  public void accept() throws Exception {
     IssueFilter ok = mock(IssueFilter.class);
     when(ok.accept(any(Issue.class))).thenReturn(true);
 
     IssueFilter ko = mock(IssueFilter.class);
     when(ko.accept(any(Issue.class))).thenReturn(false);
 
-    IssueFilters filters = new IssueFilters(new IssueFilter[]{ok, ko});
-    assertThat(filters.accept(new DefaultIssue())).isFalse();
+    when(deprecatedFilters.isEmpty()).thenReturn(true);
+    IssueFilters filters = new IssueFilters(deprecatedFilters, deprecatedViolations, new IssueFilter[]{ok, ko});
+    assertThat(filters.accept(new DefaultIssue(), null)).isFalse();
 
-    filters = new IssueFilters(new IssueFilter[]{ok});
-    assertThat(filters.accept(new DefaultIssue())).isTrue();
+    filters = new IssueFilters(deprecatedFilters, deprecatedViolations, new IssueFilter[]{ok});
+    assertThat(filters.accept(new DefaultIssue(), null)).isTrue();
 
-    filters = new IssueFilters(new IssueFilter[]{ko});
-    assertThat(filters.accept(new DefaultIssue())).isFalse();
+    filters = new IssueFilters(deprecatedFilters, deprecatedViolations, new IssueFilter[]{ko});
+    assertThat(filters.accept(new DefaultIssue(), null)).isFalse();
   }
 
   @Test
   public void should_always_accept_if_no_filters() {
-    IssueFilters filters = new IssueFilters();
-    assertThat(filters.accept(new DefaultIssue())).isTrue();
+    when(deprecatedFilters.isEmpty()).thenReturn(true);
+    IssueFilters filters = new IssueFilters(deprecatedFilters, deprecatedViolations);
+    assertThat(filters.accept(new DefaultIssue(), null)).isTrue();
+  }
+
+  @Test
+  public void should_check_deprecated_violation_filters() throws Exception {
+    when(deprecatedFilters.isEmpty()).thenReturn(false);
+    when(deprecatedFilters.isIgnored(any(Violation.class))).thenReturn(true);
+    IssueFilters filters = new IssueFilters(deprecatedFilters, deprecatedViolations, new IssueFilter[0]);
+    assertThat(filters.accept(new DefaultIssue(), null)).isFalse();
+
   }
 }
diff --git a/sonar-batch/src/test/java/org/sonar/batch/issue/ScanIssuesTest.java b/sonar-batch/src/test/java/org/sonar/batch/issue/ScanIssuesTest.java
index 730a0508faf..a41a12657a8 100644
--- a/sonar-batch/src/test/java/org/sonar/batch/issue/ScanIssuesTest.java
+++ b/sonar-batch/src/test/java/org/sonar/batch/issue/ScanIssuesTest.java
@@ -22,12 +22,15 @@ package org.sonar.batch.issue;
 import org.junit.Test;
 import org.mockito.ArgumentCaptor;
 import org.sonar.api.profiles.RulesProfile;
+import org.sonar.api.resources.JavaFile;
 import org.sonar.api.resources.Project;
+import org.sonar.api.resources.Resource;
 import org.sonar.api.rule.RuleKey;
 import org.sonar.api.rule.Severity;
 import org.sonar.api.rules.ActiveRule;
 import org.sonar.api.rules.Rule;
 import org.sonar.api.rules.RulePriority;
+import org.sonar.api.rules.Violation;
 import org.sonar.core.issue.DefaultIssue;
 
 import java.util.Date;
@@ -40,7 +43,8 @@ public class ScanIssuesTest {
   IssueCache cache = mock(IssueCache.class);
   RulesProfile qProfile = mock(RulesProfile.class);
   Project project = mock(Project.class);
-  ScanIssues scanIssues = new ScanIssues(qProfile, cache, project);
+  IssueFilters filters = mock(IssueFilters.class);
+  ScanIssues scanIssues = new ScanIssues(qProfile, cache, project, filters);
 
   @Test
   public void should_ignore_null_active_rule() throws Exception {
@@ -68,11 +72,11 @@ public class ScanIssuesTest {
 
   @Test
   public void should_add_issue_to_cache() throws Exception {
-    Rule rule = Rule.create("repoKey", "ruleKey");
+    Rule rule = Rule.create("squid", "AvoidCycle");
     ActiveRule activeRule = mock(ActiveRule.class);
     when(activeRule.getRule()).thenReturn(rule);
     when(activeRule.getSeverity()).thenReturn(RulePriority.INFO);
-    when(qProfile.getActiveRule(anyString(), anyString())).thenReturn(activeRule);
+    when(qProfile.getActiveRule("squid", "AvoidCycle")).thenReturn(activeRule);
 
     Date analysisDate = new Date();
     when(project.getAnalysisDate()).thenReturn(analysisDate);
@@ -81,6 +85,8 @@ public class ScanIssuesTest {
       .setKey("ABCDE")
       .setRuleKey(RuleKey.of("squid", "AvoidCycle"))
       .setSeverity(Severity.CRITICAL);
+    when(filters.accept(issue, null)).thenReturn(true);
+
     boolean added = scanIssues.initAndAddIssue(issue);
 
     assertThat(added).isTrue();
@@ -92,16 +98,17 @@ public class ScanIssuesTest {
 
   @Test
   public void should_use_severity_from_active_rule_if_no_severity() throws Exception {
-    Rule rule = Rule.create("repoKey", "ruleKey");
+    Rule rule = Rule.create("squid", "AvoidCycle");
     ActiveRule activeRule = mock(ActiveRule.class);
     when(activeRule.getRule()).thenReturn(rule);
     when(activeRule.getSeverity()).thenReturn(RulePriority.INFO);
-    when(qProfile.getActiveRule(anyString(), anyString())).thenReturn(activeRule);
+    when(qProfile.getActiveRule("squid", "AvoidCycle")).thenReturn(activeRule);
 
     Date analysisDate = new Date();
     when(project.getAnalysisDate()).thenReturn(analysisDate);
 
     DefaultIssue issue = new DefaultIssue().setRuleKey(RuleKey.of("squid", "AvoidCycle")).setSeverity(null);
+    when(filters.accept(issue, null)).thenReturn(true);
     scanIssues.initAndAddIssue(issue);
 
     ArgumentCaptor<DefaultIssue> argument = ArgumentCaptor.forClass(DefaultIssue.class);
@@ -109,4 +116,54 @@ public class ScanIssuesTest {
     assertThat(argument.getValue().severity()).isEqualTo(Severity.INFO);
     assertThat(argument.getValue().creationDate()).isEqualTo(analysisDate);
   }
+
+  @Test
+  public void should_add_deprecated_violation() throws Exception {
+    Rule rule = Rule.create("squid", "AvoidCycle");
+    Resource resource = new JavaFile("org.struts.Action").setEffectiveKey("struts:org.struts.Action");
+    Violation violation = new Violation(rule, resource);
+    violation.setLineId(42);
+    violation.setSeverity(RulePriority.CRITICAL);
+    violation.setMessage("the message");
+
+    ActiveRule activeRule = mock(ActiveRule.class);
+    when(activeRule.getRule()).thenReturn(rule);
+    when(activeRule.getSeverity()).thenReturn(RulePriority.INFO);
+    when(qProfile.getActiveRule("squid", "AvoidCycle")).thenReturn(activeRule);
+    when(filters.accept(any(DefaultIssue.class), eq(violation))).thenReturn(true);
+
+    boolean added = scanIssues.initAndAddViolation(violation);
+    assertThat(added).isTrue();
+
+    ArgumentCaptor<DefaultIssue> argument = ArgumentCaptor.forClass(DefaultIssue.class);
+    verify(cache).put(argument.capture());
+    DefaultIssue issue = argument.getValue();
+    assertThat(issue.severity()).isEqualTo(Severity.CRITICAL);
+    assertThat(issue.line()).isEqualTo(42);
+    assertThat(issue.message()).isEqualTo("the message");
+    assertThat(issue.key()).isNotEmpty();
+    assertThat(issue.ruleKey().toString()).isEqualTo("squid:AvoidCycle");
+    assertThat(issue.componentKey().toString()).isEqualTo("struts:org.struts.Action");
+  }
+
+  @Test
+  public void should_filter_issue() throws Exception {
+    Rule rule = Rule.create("squid", "AvoidCycle");
+    ActiveRule activeRule = mock(ActiveRule.class);
+    when(activeRule.getRule()).thenReturn(rule);
+    when(activeRule.getSeverity()).thenReturn(RulePriority.INFO);
+    when(qProfile.getActiveRule("squid", "AvoidCycle")).thenReturn(activeRule);
+
+    DefaultIssue issue = new DefaultIssue()
+      .setKey("ABCDE")
+      .setRuleKey(RuleKey.of("squid", "AvoidCycle"))
+      .setSeverity(Severity.CRITICAL);
+
+    when(filters.accept(issue, null)).thenReturn(false);
+
+    boolean added = scanIssues.initAndAddIssue(issue);
+
+    assertThat(added).isFalse();
+    verifyZeroInteractions(cache);
+  }
 }
diff --git a/sonar-core/src/main/java/org/sonar/core/issue/DefaultIssue.java b/sonar-core/src/main/java/org/sonar/core/issue/DefaultIssue.java
index 56fb83bebe4..d573da495d6 100644
--- a/sonar-core/src/main/java/org/sonar/core/issue/DefaultIssue.java
+++ b/sonar-core/src/main/java/org/sonar/core/issue/DefaultIssue.java
@@ -241,7 +241,7 @@ public class DefaultIssue implements Issue {
 
 
   @CheckForNull
-  public String getChecksum() {
+  public String checksum() {
     return checksum;
   }
 
diff --git a/sonar-core/src/main/java/org/sonar/core/issue/db/IssueDto.java b/sonar-core/src/main/java/org/sonar/core/issue/db/IssueDto.java
index 0d1390fd5cd..84d6677376e 100644
--- a/sonar-core/src/main/java/org/sonar/core/issue/db/IssueDto.java
+++ b/sonar-core/src/main/java/org/sonar/core/issue/db/IssueDto.java
@@ -343,7 +343,7 @@ public final class IssueDto {
       .setResolution(issue.resolution())
       .setStatus(issue.status())
       .setSeverity(issue.severity())
-      .setChecksum(issue.getChecksum())
+      .setChecksum(issue.checksum())
       .setManualSeverity(issue.manualSeverity())
       .setReporter(issue.reporter())
       .setAssignee(issue.assignee())
@@ -371,7 +371,7 @@ public final class IssueDto {
       .setResolution(issue.resolution())
       .setStatus(issue.status())
       .setSeverity(issue.severity())
-      .setChecksum(issue.getChecksum())
+      .setChecksum(issue.checksum())
       .setManualSeverity(issue.manualSeverity())
       .setReporter(issue.reporter())
       .setAssignee(issue.assignee())
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/database/model/Snapshot.java b/sonar-plugin-api/src/main/java/org/sonar/api/database/model/Snapshot.java
index 8f5cbd8aaf8..de5390d3a2a 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/database/model/Snapshot.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/database/model/Snapshot.java
@@ -32,6 +32,7 @@ import javax.persistence.Table;
 import javax.persistence.Temporal;
 import javax.persistence.TemporalType;
 
+import java.io.Serializable;
 import java.util.Date;
 
 /**
@@ -39,7 +40,7 @@ import java.util.Date;
  */
 @Entity
 @Table(name = "snapshots")
-public class Snapshot extends BaseIdentifiable {
+public class Snapshot extends BaseIdentifiable implements Serializable {
 
   /**
    * This status is set on the snapshot at the beginning of the batch
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/resources/Resource.java b/sonar-plugin-api/src/main/java/org/sonar/api/resources/Resource.java
index 95dcdd084d2..c6e22cdd408 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/resources/Resource.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/resources/Resource.java
@@ -19,12 +19,14 @@
  */
 package org.sonar.api.resources;
 
+import java.io.Serializable;
+
 /**
  * The interface to implement to create a resource in Sonar
  * 
  * @since 1.10
  */
-public abstract class Resource<P extends Resource> {
+public abstract class Resource<P extends Resource> implements Serializable {
 
   /**
    * @deprecated since 2.6. Use Scopes.PROJECT.
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/rules/Violation.java b/sonar-plugin-api/src/main/java/org/sonar/api/rules/Violation.java
index 906aea24aad..d1091b62cf9 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/rules/Violation.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/rules/Violation.java
@@ -27,7 +27,9 @@ import java.util.Date;
 
 /**
  * A class that represents a violation. A violation happens when a resource does not respect a defined rule.
+ * @deprecated in 3.6. Replaced by {@link org.sonar.api.issue.Issue}.
  */
+@Deprecated
 public class Violation {
 
   private Resource resource;
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/rules/ViolationFilter.java b/sonar-plugin-api/src/main/java/org/sonar/api/rules/ViolationFilter.java
index 71e8cecf495..612e8eb054d 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/rules/ViolationFilter.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/rules/ViolationFilter.java
@@ -27,8 +27,10 @@ import org.sonar.api.batch.DependedUpon;
  * Filter violations to save. For example, ignore a violation if it occurs on a line of code commented with //NOSONAR
  *
  * @since 1.12
+ * @deprecated in 3.6. Replaced by {@link org.sonar.api.issue.IssueFilter}.
  */
 @DependedUpon(value = DecoratorBarriers.START_VIOLATIONS_GENERATION)
+@Deprecated
 public interface ViolationFilter extends BatchExtension {
 
   /**
diff --git a/sonar-plugin-api/src/main/java/org/sonar/api/violations/ViolationQuery.java b/sonar-plugin-api/src/main/java/org/sonar/api/violations/ViolationQuery.java
index 70ca8ee5f13..470e3929648 100644
--- a/sonar-plugin-api/src/main/java/org/sonar/api/violations/ViolationQuery.java
+++ b/sonar-plugin-api/src/main/java/org/sonar/api/violations/ViolationQuery.java
@@ -25,7 +25,9 @@ import org.sonar.api.resources.Resource;
  * Class that allows to query the Sonar index about violations.
  * 
  * @since 2.8
+ * @deprecated in 3.6 for the merge of violations and reviews into issues.
  */
+@Deprecated
 public final class ViolationQuery {
 
   public static enum SwitchMode {