Merge branch 'master' into nimak/refactor

annotator-core/build.gradle

@@ -25,7 +25,6 @@
 import com.vanniktech.maven.publish.SonatypeHost
 
 plugins {
-    id 'com.github.sherter.google-java-format' version '0.9'
     id 'com.github.johnrengelman.shadow' version '7.1.2'
     id 'maven-publish'
     id 'application'
@@ -52,8 +51,10 @@ dependencies {
 }
 
 // Exclude formatting files under resources
-googleJavaFormat {
-    exclude 'src/test/resources/**/*.java'
+spotless {
+    java {
+        targetExclude 'src/test/resources/**/*.java'
+    }
 }
 
 // Should be the latest supporting version of NullAway.

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

@@ -51,10 +51,13 @@ public class Annotator {
 
   /** Injector instance. */
   private final AnnotationInjector injector;
+
   /** Annotator context. */
   public final Context context;
+
   /** Reports cache. */
   public final ReportCache cache;
+
   /** Annotator configuration. */
   public final Config config;
 

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

@@ -68,86 +68,111 @@ public class Config {
    * zero or less.
    */
   public final boolean bailout;
+
   /** If activated, impact of fixes will be computed in parallel. */
   public final boolean useParallelGraphProcessor;
+
   /** If activated, impact of fixes will be cached. */
   public final boolean useImpactCache;
+
   /**
    * If activated, all suggested fixes from the checker will be applied to the source code
    * regardless of their effectiveness.
    */
   public final boolean exhaustiveSearch;
+
   /**
    * If activated, all containing fixes in the fix tree will be applied to the source code,
    * otherwise only the root fix will be applied.
    */
   public final boolean chain;
+
   /**
    * If enabled, at each iteration fixes with effectiveness will be tagged to exclude them in
    * further iterations.
    */
   public final boolean useCache;
+
   /** If true, build outputs will be redirected to STD Err. */
   public final boolean redirectBuildOutputToStdErr;
+
   /** If activated, it will disable the outer loop. */
   public final boolean disableOuterLoop;
+
   /** Info of target module. */
   public final ModuleConfiguration target;
+
   /** Path to directory where all outputs of checker and scanner checker is located. */
   public final Path globalDir;
+
   /** Command to build the target module. */
   public final String buildCommand;
+
   /** Fully qualified name of the {@code nullable} annotation. */
   public final String nullableAnnot;
+
   /** Fully qualified name of the {@code initializer} annotation. */
   public final String initializerAnnot;
+
   /** If enabled, effects of public API on downstream dependencies will be considered. */
   public final boolean downStreamDependenciesAnalysisActivated;
+
   /** Sets of context path information for all downstream dependencies. */
   public final ImmutableSet<ModuleConfiguration> downstreamConfigurations;
+
   /**
    * Path to NullAway library model loader resource directory, which enables the communication
    * between annotator and NullAway when processing downstream dependencies. Annotator will write
    * annotation on files in this directory and the using Library Model Loader reads them.
    */
   public final Path nullawayLibraryModelLoaderPath;
+
   /** Command to build the all downstream dependencies at once. */
   public final String downstreamDependenciesBuildCommand;
+
   /**
    * Analysis mode. Will impact inference decisions when downstream dependency analysis is
    * activated.
    */
   public final AnalysisMode mode;
+
   /** Global counter for assigning unique id for each instance. */
   private int moduleCounterID;
+
   /**
    * If activated, Annotator will try to suppress all remaining errors. The logic is specific to the
    * checker suppression mechanism. Annotator will simply call {@link
    * edu.ucr.cs.riple.core.checkers.Checker#suppressRemainingErrors} methods.
    */
   public final boolean suppressRemainingErrors;
+
   /** Fully qualified NullUnmarked annotation. */
   public final String nullUnMarkedAnnotation;
+
   /**
    * Set of {@code @Nonnull} annotations to be acknowledged by Annotator. If an element is annotated
    * with these annotations along any other annotation ending with {@code "nonnull"}, Annotator will
    * acknowledge the annotation and will not add any {@code @Nullable} annotation to the element.
    */
   public final ImmutableSet<String> nonnullAnnotations;
+
   /** Depth of the analysis. Default to 5 if not set by the user */
   public final int depth;
+
   /**
    * Activates inference to add {@code @Nullable} qualifiers.
    *
    * <p>Note: Inference mode is mostly deactivated for experiments purposes and the default value is
    * {@code true} in production.
    */
   public final boolean inferenceActivated;
+
   /**
    * Generated code detectors. Responsible for detecting regions that are not present in the source
    * code and are generated by a processor.
    */
   public final ImmutableSet<SourceType> generatedCodeDetectors;
+
   /**
    * Checker name to retrieve the {@link edu.ucr.cs.riple.core.checkers.Checker} specific instance.
    */
@@ -685,6 +710,7 @@ public static class Builder {
     public String initializerAnnotation;
     public String nullableAnnotation;
     public String outputDir;
+
     /**
      * List of modules, did not use {@link java.util.Set} to preserve order. First project is the
      * target project.

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

@@ -47,19 +47,25 @@ public class Context {
 
   /** Annotator configuration. */
   public final Config config;
+
   /** Log instance. Responsible for logging all the information about the build time and count. */
   public final Log log;
+
   /** Handler for computing the original offset of reported errors with existing changes. */
   public final OffsetHandler offsetHandler;
+
   /** The moduleInfo of target module. */
   public final ModuleInfo targetModuleInfo;
+
   /**
    * Configuration of the target module, required for building the target module and collecting
    * checkers output.
    */
   public final ModuleConfiguration targetConfiguration;
+
   /** Sets of context path information for all downstream dependencies. */
   public final ImmutableSet<ModuleConfiguration> downstreamConfigurations;
+
   /** Checker instance. Used to execute checker specific tasks. */
   public final Checker<? extends Error> checker;
 

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

@@ -43,27 +43,34 @@ public class Report {
 
   /** Effect on target module. */
   public int localEffect;
+
   /** Root of fix tree associated to this report instance. */
   public Fix root;
+
   /** Fix tree associated to this report instance. */
   public Set<Fix> tree;
+
   /**
    * Set of errors that will be triggered in target module if fix tree is applied to the source
    * code.
    */
   public ImmutableSet<Error> triggeredErrors;
+
   /**
    * Set of triggered fixes on target module that will be triggered if fix tree is applied due to
    * errors in downstream dependencies.
    */
   public ImmutableSet<Fix> triggeredFixesFromDownstreamErrors;
+
   /** If true, this report's tree has been processed for at least one iteration */
   public boolean hasBeenProcessedOnce;
+
   /**
    * Lower bound of number of errors in downstream dependencies if fix tree is applied to the target
    * module.
    */
   private int lowerBoundEffectOnDownstreamDependencies;
+
   /**
    * Upper bound of number of errors in downstream dependencies if fix tree is applied to the target
    * module.

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

@@ -38,6 +38,7 @@ public class ReportCache {
    * efficiently.
    */
   private final Map<Fix, Report> store;
+
   /** Cache activation switch. */
   private boolean enabled;
 

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

@@ -36,8 +36,10 @@ public class Impact {
 
   /** Target fix. */
   public final Fix fix;
+
   /** Set of triggered errors, if this fix is applied to source code. */
   protected ImmutableSet<Error> triggeredErrors;
+
   /**
    * Set of triggered fixes on the target module from downstream dependencies errors if containing
    * fix is applied.

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

@@ -37,6 +37,7 @@ public abstract class CheckerBaseClass<T extends Error> implements Checker<T> {
 
   /** Annotator config. */
   protected final Config config;
+
   /** Annotator context. */
   protected final Context context;
 

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

@@ -60,6 +60,7 @@ public class NullAway extends CheckerBaseClass<NullAwayError> {
    * The name of the checker. To select this checker, this name must be used in the configurations.
    */
   public static final String NAME = "NULLAWAY";
+
   /** Supported version of NullAway serialization. */
   public static final int VERSION = 3;
 

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

@@ -37,6 +37,7 @@ public class NullAwayError extends Error {
 
   /** Error type for method initialization errors from NullAway in {@code String}. */
   public static final String METHOD_INITIALIZER_ERROR = "METHOD_NO_INIT";
+
   /** Error type for field initialization errors from NullAway in {@code String}. */
   public static final String FIELD_INITIALIZER_ERROR = "FIELD_NO_INIT";
 

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

@@ -48,12 +48,16 @@ public abstract class AbstractEvaluator implements Evaluator {
 
   /** Annotator context. */
   protected final Context context;
+
   /** Conflict graph to storing unprocessed fixes. */
   protected final ConflictGraph graph;
+
   /** Depth of analysis. */
   protected final int depth;
+
   /** Graph processor to process the graph. */
   protected ConflictGraphProcessor processor;
+
   /** Supplier used for initialization. */
   protected final Supplier supplier;
 

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

@@ -45,6 +45,7 @@ public class ConflictGraph {
 
   /** Nodes in this graph */
   public final Multimap<Integer, Node> nodes;
+
   /**
    * Groups in this graph, nodes which does not have any conflict in regions will in the same group.
    * Please note that this is a graph coloring problem, set of groups is calculated using a greedy

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

@@ -49,23 +49,31 @@ public class Node {
 
   /** Root fix of the tree. */
   public final Fix root;
+
   /** Set of all fixes in tree. */
   public final Set<Fix> tree;
+
   /** Set of potentially impacted by any node in tree. */
   public final Set<Region> regions;
+
   /** Set of triggered errors if tree is applied on target module. */
   public ImmutableSet<Error> triggeredErrors;
+
   /**
    * Set of triggered fixes on target module that will be triggered if fix tree is applied due to
    * errors in downstream dependencies.
    */
   public ImmutableSet<Fix> triggeredFixesFromDownstreamErrors;
+
   /** Unique id of Node across all nodes. */
   public int id;
+
   /** Effect of applying containing change */
   public int effect;
+
   /** Corresponding report of processing root. */
   public Report report;
+
   /** Regions where original errors reported and NullAway suggested root for that. */
   private ImmutableSet<Region> origins;
 

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

@@ -40,14 +40,19 @@ public abstract class AbstractConflictGraphProcessor implements ConflictGraphPro
 
   /** Injector used in the processor to inject / remove fixes. */
   protected final AnnotationInjector injector;
+
   /** Error store instance to store state of fixes before and after of injections. */
   protected final ErrorStore errorStore;
+
   /** Downstream impact cache to retrieve impacts of fixes globally. */
   protected final DownstreamImpactCache downstreamImpactCache;
+
   /** Annotator context. */
   protected final Context context;
+
   /** Handler to re-run compiler. */
   protected final CompilerRunner compilerRunner;
+
   /** ModuleInfo of the input module which the impact of fixes are computed on. */
   protected final ModuleInfo moduleInfo;
 

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

@@ -35,12 +35,16 @@ public abstract class AbstractSupplier implements Supplier {
 
   /** Error Store instance. */
   protected final ErrorStore errorStore;
+
   /** Injector instance. */
   protected final AnnotationInjector injector;
+
   /** ModuleInfo of the module which the impact of fixes are computed on. */
   protected final ModuleInfo moduleInfo;
+
   /** Depth of analysis. */
   protected final int depth;
+
   /** Annotator context. */
   protected final Context context;
 

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

@@ -48,13 +48,16 @@ public class VirtualInjector extends AnnotationInjector {
 
   /** Path to library model loader resources directory */
   private final Path libraryModelResourcesDirectoryPath;
+
   /**
    * Annotator configuration, required to check if downstream dependencies analysis is activated or
    * retrieve the path to library model loader.
    */
   private final Config config;
+
   /** Name of the resource file in library model loader which contains list of nullable methods. */
   public static final String NULLABLE_METHOD_LIST_FILE_NAME = "nullable-methods.tsv";
+
   /** Name of the resource file in library model loader which contains list of nullable fields. */
   public static final String NULLABLE_FIELD_LIST_FILE_NAME = "nullable-fields.tsv";
 

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

@@ -35,12 +35,16 @@ public class Log {
 
   /** Sum of number of nodes constructed in each {@link ConflictGraph}. */
   private long nodes;
+
   /** Number of build requests. */
   private long requested;
+
   /** Total time spent for annotator from start to finish. */
   private long totalTime;
+
   /** Total time spent in building targets. */
   private long buildTime = 0;
+
   /**
    * Set of approved and injected annotations. These annotations are evaluated and approved and will
    * not get removed from the source code.