resolves #71

core/src/main/java/edu/ucr/cs/riple/core/Annotator.java

@@ -53,7 +53,6 @@
 import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
-import java.util.stream.Stream;
 
 /**
  * The main class of the core module. Responsible for analyzing the target module and injecting the
@@ -185,7 +184,7 @@ private void executeNextIteration(
     Set<Fix> selectedFixes =
         latestReports.stream()
             .filter(Report::approved)
-            .flatMap(report -> config.chain ? report.tree.stream() : Stream.of(report.root))
+            .flatMap(report -> report.getSelectedFixes(config))
             .collect(Collectors.toSet());
     injector.injectFixes(selectedFixes);
 

core/src/main/java/edu/ucr/cs/riple/core/Report.java

@@ -34,6 +34,7 @@
 import java.util.Objects;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 /**
  * Container class to store information regarding effectiveness of a fix, its associated fix tree
@@ -247,4 +248,28 @@ public boolean isInProgress(Config config) {
     return (!finished && (!config.bailout || localEffect > 0))
         || triggeredFixes.stream().anyMatch(input -> !input.fixSourceIsInTarget);
   }
+
+  /**
+   * Returns the stream of fixes that needs to be applied to source code if report is tagged as
+   * {@link Tag#APPROVE}.
+   *
+   * @param config Annotator config.
+   * @return Stream of selected fixes.
+   */
+  public Stream<Fix> getSelectedFixes(Config config) {
+    return tree.stream()
+        .filter(
+            input -> {
+              // If chain is active, add all fixes
+              if (config.chain) {
+                return true;
+              }
+              // Add all fixes reported from downstream
+              if (!input.fixSourceIsInTarget) {
+                return true;
+              }
+              // Add root.
+              return input.equals(root);
+            });
+  }
 }

core/src/main/java/edu/ucr/cs/riple/core/metadata/graph/Node.java

@@ -203,7 +203,6 @@ public void updateTriggered(Collection<Fix> fixes) {
   /** Merges triggered fixes to the tree, to prepare the analysis for the next depth. */
   public void mergeTriggered() {
     this.tree.addAll(this.triggeredFixes);
-    this.tree.forEach(fix -> fix.fixSourceIsInTarget = true);
     this.triggeredFixes.clear();
   }
 

core/src/test/java/edu/ucr/cs/riple/core/tools/CoreTestHelper.java

@@ -67,6 +67,7 @@ public class CoreTestHelper {
   private boolean downstreamDependencyAnalysisActivated = false;
   private AnalysisMode mode = AnalysisMode.LOCAL;
   private Config config;
+  private boolean chain = true;
 
   public CoreTestHelper(Path projectPath, Path outDirPath, List<String> modules) {
     this.projectPath = projectPath;
@@ -150,6 +151,11 @@ public CoreTestHelper enableDownstreamDependencyAnalysis() {
     return enableDownstreamDependencyAnalysis(AnalysisMode.LOWER_BOUND);
   }
 
+  public CoreTestHelper applyRootFixOnly() {
+    this.chain = false;
+    return this;
+  }
+
   public void start() {
     Path configPath = outDirPath.resolve("config.json");
     createFiles();
@@ -264,7 +270,7 @@ private void makeAnnotatorConfigFile(Path configPath) {
     builder.outputDir = outDirPath.toString();
     builder.depth = depth;
     builder.bailout = !disableBailout;
-    builder.chain = true;
+    builder.chain = chain;
     builder.outerLoopActivation = requestCompleteLoop;
     builder.optimized = true;
     builder.downStreamDependenciesAnalysisActivated = downstreamDependencyAnalysisActivated;