Refactoring downstream dependency cache (#218)

Followup on #217. Minor refactoring on downstream dependencies cache implementation, preparing code for the upcoming changes.

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

@@ -37,7 +37,7 @@
 import edu.ucr.cs.riple.core.evaluators.suppliers.TargetModuleSupplier;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
 import edu.ucr.cs.riple.core.injectors.PhysicalInjector;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.core.util.Utility;
 import java.util.Set;
 import java.util.stream.Collectors;

annotator-core/src/main/java/edu/ucr/cs/riple/core/Context.java

@@ -28,9 +28,9 @@
 import edu.ucr.cs.riple.core.checkers.Checker;
 import edu.ucr.cs.riple.core.checkers.CheckerBaseClass;
 import edu.ucr.cs.riple.core.log.Log;
-import edu.ucr.cs.riple.core.metadata.index.Error;
 import edu.ucr.cs.riple.core.module.ModuleConfiguration;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
 import edu.ucr.cs.riple.injector.offsets.FileOffsetStore;
 import edu.ucr.cs.riple.injector.offsets.OffsetChange;
 import java.nio.file.Path;

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

@@ -27,9 +27,9 @@
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Sets;
 import edu.ucr.cs.riple.core.cache.downstream.DownstreamImpactCache;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.HashSet;
 import java.util.Objects;

annotator-core/src/main/java/edu/ucr/cs/riple/core/ReportCache.java

@@ -25,7 +25,7 @@
 package edu.ucr.cs.riple.core;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.HashMap;
 import java.util.Map;
 

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/BaseCache.java

@@ -25,8 +25,8 @@
 package edu.ucr.cs.riple.core.cache;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Collection;
 import java.util.Map;

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/Impact.java

@@ -25,8 +25,8 @@
 package edu.ucr.cs.riple.core.cache;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Collection;
 import java.util.Objects;

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/ImpactCache.java

@@ -25,8 +25,8 @@
 package edu.ucr.cs.riple.core.cache;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.Collection;
 import javax.annotation.Nullable;
 

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/downstream/DownstreamImpactCache.java

@@ -25,7 +25,7 @@
 package edu.ucr.cs.riple.core.cache.downstream;
 
 import edu.ucr.cs.riple.core.cache.ImpactCache;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.Set;
 
 /**

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/downstream/DownstreamImpactCacheImpl.java

@@ -29,11 +29,11 @@
 import edu.ucr.cs.riple.core.Report;
 import edu.ucr.cs.riple.core.cache.BaseCache;
 import edu.ucr.cs.riple.core.evaluators.suppliers.DownstreamDependencySupplier;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.method.MethodRecord;
-import edu.ucr.cs.riple.core.metadata.region.MethodRegionRegistry;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.method.MethodRecord;
+import edu.ucr.cs.riple.core.registries.region.MethodRegionRegistry;
 import edu.ucr.cs.riple.injector.changes.AddMarkerAnnotation;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Collection;
@@ -91,7 +91,7 @@ private ImmutableSet<Location> retrieveLocationsToCacheImpactsOnDownstreamDepend
         .filter(
             input ->
                 !methodRegionRegistry
-                    .getCallersOfMethod(input.toMethod().clazz, input.toMethod().method)
+                    .getImpactedRegionsByUse(input)
                     // skip methods that are not called anywhere. This has a significant impact
                     // on performance.
                     .isEmpty())

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/downstream/DownstreamImpactEvaluator.java

@@ -28,7 +28,7 @@
 import edu.ucr.cs.riple.core.Report;
 import edu.ucr.cs.riple.core.evaluators.BasicEvaluator;
 import edu.ucr.cs.riple.core.evaluators.suppliers.DownstreamDependencySupplier;
-import edu.ucr.cs.riple.core.metadata.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Error;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Set;
 import java.util.stream.Collectors;
@@ -51,30 +51,27 @@ protected void collectGraphResults(ImmutableSet<Report> reports) {
     this.graph
         .getNodes()
         .forEach(
-            node ->
-                node.root.ifOnMethod(
-                    method -> {
-                      // Impacted locations.
-                      Set<Location> locations =
-                          node.triggeredErrors.stream()
-                              .filter(
-                                  error ->
-                                      error.isSingleFix()
-                                          // Method is declared in the target module.
-                                          && context.targetModuleInfo.declaredInModule(
-                                              error.toResolvingLocation()))
-                              .map(Error::toResolvingLocation)
-                              .collect(Collectors.toSet());
-                      if (!locations.isEmpty()) {
-                        // Update path for each location. These triggered fixes do not have an
-                        // actual physical path since they are provided as a jar file in downstream
-                        // dependencies.
-                        locations.forEach(
-                            location ->
-                                location.path =
-                                    context.targetModuleInfo.getLocationOnClass(location.clazz)
-                                        .path);
-                      }
-                    }));
+            node -> {
+              // Impacted locations.
+              Set<Location> locations =
+                  node.triggeredErrors.stream()
+                      .filter(
+                          error ->
+                              error.isSingleFix()
+                                  // Method is declared in the target module.
+                                  && context.targetModuleInfo.declaredInModule(
+                                      error.toResolvingLocation()))
+                      .map(Error::toResolvingLocation)
+                      .collect(Collectors.toSet());
+              if (!locations.isEmpty()) {
+                // Update path for each location. These triggered fixes do not have an
+                // actual physical path since they are provided as a jar file in downstream
+                // dependencies.
+                locations.forEach(
+                    location ->
+                        location.path =
+                            context.targetModuleInfo.getLocationOnClass(location.clazz).path);
+              }
+            });
   }
 }

annotator-core/src/main/java/edu/ucr/cs/riple/core/cache/downstream/VoidDownstreamImpactCache.java

@@ -25,8 +25,8 @@
 package edu.ucr.cs.riple.core.cache.downstream;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.Collection;
 import java.util.Set;
 import javax.annotation.Nullable;

annotator-core/src/main/java/edu/ucr/cs/riple/core/checkers/Checker.java

@@ -26,11 +26,11 @@
 
 import com.google.common.collect.ImmutableSet;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.region.Region;
 import edu.ucr.cs.riple.core.module.ModuleConfiguration;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.region.Region;
 import java.util.Set;
 
 /**

annotator-core/src/main/java/edu/ucr/cs/riple/core/checkers/CheckerBaseClass.java

@@ -27,8 +27,8 @@
 import edu.ucr.cs.riple.core.Config;
 import edu.ucr.cs.riple.core.Context;
 import edu.ucr.cs.riple.core.checkers.nullaway.NullAway;
-import edu.ucr.cs.riple.core.metadata.index.Error;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
 import edu.ucr.cs.riple.injector.location.OnField;
 import java.util.Set;
 

annotator-core/src/main/java/edu/ucr/cs/riple/core/checkers/nullaway/NullAway.java

@@ -29,11 +29,11 @@
 import edu.ucr.cs.riple.core.Context;
 import edu.ucr.cs.riple.core.checkers.CheckerBaseClass;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
-import edu.ucr.cs.riple.core.metadata.field.FieldInitializationStore;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.region.Region;
 import edu.ucr.cs.riple.core.module.ModuleConfiguration;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.field.FieldInitializationStore;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.region.Region;
 import edu.ucr.cs.riple.core.util.Utility;
 import edu.ucr.cs.riple.injector.Helper;
 import edu.ucr.cs.riple.injector.changes.AddAnnotation;

annotator-core/src/main/java/edu/ucr/cs/riple/core/checkers/nullaway/NullAwayError.java

@@ -25,9 +25,9 @@
 package edu.ucr.cs.riple.core.checkers.nullaway;
 
 import com.google.common.collect.ImmutableSet;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.region.Region;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.region.Region;
 import java.util.Objects;
 
 /** Represents an error reported by {@link NullAway}. */

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/AbstractEvaluator.java

@@ -30,7 +30,7 @@
 import edu.ucr.cs.riple.core.evaluators.graph.ConflictGraph;
 import edu.ucr.cs.riple.core.evaluators.graph.processors.ConflictGraphProcessor;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 
 /**
  * Abstract class for evaluators. Subclasses of this evaluator, computes the effectiveness of fix

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/BasicEvaluator.java

@@ -29,7 +29,7 @@
 import edu.ucr.cs.riple.core.Report;
 import edu.ucr.cs.riple.core.evaluators.graph.Node;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 
 /**
  * This evaluator for each fix tree computes the effectiveness by injecting the fix tree entirely to

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/CachedEvaluator.java

@@ -33,8 +33,8 @@
 import edu.ucr.cs.riple.core.cache.Impact;
 import edu.ucr.cs.riple.core.cache.TargetModuleCache;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.Map;
 import java.util.Set;
 import java.util.stream.Collectors;

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/Evaluator.java

@@ -26,7 +26,7 @@
 
 import com.google.common.collect.ImmutableSet;
 import edu.ucr.cs.riple.core.Report;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 
 /** Interface for evaluators. Evaluators create reports from the impacts of fixes. */
 public interface Evaluator {

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/VoidEvaluator.java

@@ -26,7 +26,7 @@
 
 import com.google.common.collect.ImmutableSet;
 import edu.ucr.cs.riple.core.Report;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 
 /**
  * This evaluator does not evaluate the given fixes based on the impacts on the result of the

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/graph/ConflictGraph.java

@@ -26,7 +26,7 @@
 
 import com.google.common.collect.Multimap;
 import com.google.common.collect.MultimapBuilder;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/graph/Node.java

@@ -27,12 +27,12 @@
 import com.google.common.collect.ImmutableSet;
 import com.google.common.collect.Sets;
 import edu.ucr.cs.riple.core.Report;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.ErrorStore;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.region.Region;
-import edu.ucr.cs.riple.core.metadata.region.RegionRegistry;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.ErrorStore;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.region.Region;
+import edu.ucr.cs.riple.core.registries.region.RegionRegistry;
 import edu.ucr.cs.riple.injector.location.OnMethod;
 import java.util.Collection;
 import java.util.Collections;
@@ -109,7 +109,7 @@ public void reCollectPotentiallyImpactedRegions(RegionRegistry regionRegistry) {
     // Add origins.
     this.regions.addAll(this.origins);
     this.tree.forEach(
-        fix -> regionRegistry.getImpactedRegions(fix.toLocation()).ifPresent(regions::addAll));
+        fix -> this.regions.addAll(regionRegistry.getImpactedRegions(fix.toLocation())));
     // Add class initialization region, if a fix is modifying a parameter on constructor.
     this.tree.stream()
         .filter(fix -> fix.isOnParameter() && fix.isModifyingConstructor())

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/graph/processors/AbstractConflictGraphProcessor.java

@@ -29,9 +29,9 @@
 import edu.ucr.cs.riple.core.evaluators.graph.Node;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
-import edu.ucr.cs.riple.core.metadata.index.ErrorStore;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.ErrorStore;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.injector.changes.AddMarkerAnnotation;
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Set;

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/graph/processors/ParallelConflictGraphProcessor.java

@@ -28,11 +28,11 @@
 import edu.ucr.cs.riple.core.evaluators.graph.ConflictGraph;
 import edu.ucr.cs.riple.core.evaluators.graph.Node;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.index.Result;
-import edu.ucr.cs.riple.core.metadata.region.Region;
-import edu.ucr.cs.riple.core.metadata.region.RegionRegistry;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Result;
+import edu.ucr.cs.riple.core.registries.region.Region;
+import edu.ucr.cs.riple.core.registries.region.RegionRegistry;
 import edu.ucr.cs.riple.core.util.Utility;
 import java.util.Collection;
 import java.util.HashSet;

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/graph/processors/SequentialConflictGraphProcessor.java

@@ -27,8 +27,8 @@
 import edu.ucr.cs.riple.core.Context;
 import edu.ucr.cs.riple.core.evaluators.graph.ConflictGraph;
 import edu.ucr.cs.riple.core.evaluators.suppliers.Supplier;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
-import edu.ucr.cs.riple.core.metadata.index.Result;
+import edu.ucr.cs.riple.core.registries.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Result;
 import edu.ucr.cs.riple.core.util.Utility;
 import java.util.Set;
 import me.tongfei.progressbar.ProgressBar;

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/suppliers/AbstractSupplier.java

@@ -26,9 +26,9 @@
 
 import edu.ucr.cs.riple.core.Context;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.ErrorStore;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.ErrorStore;
 
 /** Base class for all instances of {@link Supplier}. */
 public abstract class AbstractSupplier implements Supplier {

annotator-core/src/main/java/edu/ucr/cs/riple/core/evaluators/suppliers/Supplier.java

@@ -30,9 +30,9 @@
 import edu.ucr.cs.riple.core.evaluators.AbstractEvaluator;
 import edu.ucr.cs.riple.core.evaluators.graph.processors.ConflictGraphProcessor;
 import edu.ucr.cs.riple.core.injectors.AnnotationInjector;
-import edu.ucr.cs.riple.core.metadata.index.Error;
-import edu.ucr.cs.riple.core.metadata.index.ErrorStore;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
+import edu.ucr.cs.riple.core.registries.index.Error;
+import edu.ucr.cs.riple.core.registries.index.ErrorStore;
 
 /** Supplier for initializing an {@link AbstractEvaluator} instance. */
 public interface Supplier {

annotator-core/src/main/java/edu/ucr/cs/riple/core/injectors/AnnotationInjector.java

@@ -25,7 +25,7 @@
 package edu.ucr.cs.riple.core.injectors;
 
 import edu.ucr.cs.riple.core.Context;
-import edu.ucr.cs.riple.core.metadata.index.Fix;
+import edu.ucr.cs.riple.core.registries.index.Fix;
 import edu.ucr.cs.riple.injector.changes.AddAnnotation;
 import edu.ucr.cs.riple.injector.changes.RemoveAnnotation;
 import java.util.Set;