Change json dependency to use org.json

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

@@ -60,9 +60,8 @@
 import org.apache.commons.cli.Option;
 import org.apache.commons.cli.Options;
 import org.apache.commons.cli.ParseException;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
-import org.json.simple.parser.JSONParser;
+import org.json.JSONArray;
+import org.json.JSONObject;
 
 /**
  * Config class for Annotator. Different flags can be set with either command line arguments or an
@@ -470,13 +469,11 @@ public Config(Path configPath) {
     Preconditions.checkNotNull(configPath);
     JSONObject jsonObject;
     try {
-      Object obj =
-          new JSONParser().parse(Files.newBufferedReader(configPath, Charset.defaultCharset()));
-      jsonObject = (JSONObject) obj;
+      jsonObject = new JSONObject(Files.readString(configPath, Charset.defaultCharset()));
     } catch (Exception e) {
       throw new RuntimeException("Error in reading/parsing config at path: " + configPath, e);
     }
-    this.depth = getValueFromKey(jsonObject, "DEPTH", Long.class).orElse((long) 1).intValue();
+    this.depth = getValueFromKey(jsonObject, "DEPTH", Integer.class).orElse(1);
     this.chain = getValueFromKey(jsonObject, "CHAIN", Boolean.class).orElse(false);
     this.redirectBuildOutputToStdErr =
         getValueFromKey(jsonObject, "REDIRECT_BUILD_OUTPUT_TO_STDERR", Boolean.class).orElse(false);
@@ -501,7 +498,7 @@ public Config(Path configPath) {
         getArrayValueFromKey(
                 jsonObject,
                 "CONFIG_PATHS",
-                instance -> ModuleInfo.buildFromJson(getNextModuleUniqueID(), globalDir, instance),
+                instance -> ModuleInfo.buildFromMap(getNextModuleUniqueID(), globalDir, instance),
                 ModuleInfo.class)
             .orElse(Collections.emptyList());
     this.target = moduleInfoList.get(0);
@@ -646,24 +643,24 @@ private <T> OrElse<T> getValueFromKey(JSONObject json, String key, Class<T> klas
     try {
       ArrayList<String> keys = new ArrayList<>(Arrays.asList(key.split(":")));
       while (keys.size() != 1) {
-        if (json.containsKey(keys.get(0))) {
+        if (json.has(keys.get(0))) {
           json = (JSONObject) json.get(keys.get(0));
           keys.remove(0);
         } else {
           return new OrElse<>(null, klass);
         }
       }
-      return json.containsKey(keys.get(0))
+      return json.has(keys.get(0))
           ? new OrElse<>(json.get(keys.get(0)), klass)
           : new OrElse<>(null, klass);
     } catch (Exception e) {
       return new OrElse<>(null, klass);
     }
   }
 
-  @SuppressWarnings({"SameParameterValue", "unchecked"})
+  @SuppressWarnings("SameParameterValue")
   private <T> ListOrElse<T> getArrayValueFromKey(
-      JSONObject json, String key, Function<JSONObject, T> mapper, Class<T> klass) {
+      JSONObject json, String key, Function<Map<?, ?>, T> mapper, Class<T> klass) {
     if (json == null) {
       return new ListOrElse<>(null, klass);
     }
@@ -672,7 +669,9 @@ private <T> ListOrElse<T> getArrayValueFromKey(
       return new ListOrElse<>(null, klass);
     } else {
       if (jsonValue.value instanceof JSONArray) {
-        return new ListOrElse<>(((JSONArray) jsonValue.value).stream().map(mapper), klass);
+        return new ListOrElse<>(
+            ((JSONArray) jsonValue.value).toList().stream().map(o -> mapper.apply((Map<?, ?>) o)),
+            klass);
       }
       throw new IllegalStateException(
           "Expected type to be json array, found: " + jsonValue.value.getClass());
@@ -742,7 +741,6 @@ public static class Builder {
     public Set<SourceType> sourceTypes = new HashSet<>();
     public int depth = 1;
 
-    @SuppressWarnings("unchecked")
     public void write(Path path) {
       Preconditions.checkNotNull(
           buildCommand, "Build command must be initialized to construct the config.");
@@ -773,16 +771,15 @@ public void write(Path path) {
       json.put("FORCE_RESOLVE", forceResolveActivation);
       json.put("INFERENCE_ACTIVATION", inferenceActivated);
       JSONArray configPathsJson = new JSONArray();
-      configPathsJson.addAll(
-          configPaths.stream()
-              .map(
-                  info -> {
-                    JSONObject res = new JSONObject();
-                    res.put("NULLAWAY", info.nullawayConfig.toString());
-                    res.put("SCANNER", info.scannerConfig.toString());
-                    return res;
-                  })
-              .collect(Collectors.toList()));
+      configPaths.stream()
+          .map(
+              info -> {
+                JSONObject res = new JSONObject();
+                res.put("NULLAWAY", info.nullawayConfig.toString());
+                res.put("SCANNER", info.scannerConfig.toString());
+                return res;
+              })
+          .forEach(configPathsJson::put);
       json.put("CONFIG_PATHS", configPathsJson);
       JSONObject downstreamDependency = new JSONObject();
       downstreamDependency.put("ACTIVATION", downStreamDependenciesAnalysisActivated);
@@ -809,10 +806,9 @@ public void write(Path path) {
             processors.put(sourceType.name(), st);
           });
       json.put("PROCESSORS", processors);
-
       try (BufferedWriter file =
           Files.newBufferedWriter(path.toFile().toPath(), Charset.defaultCharset())) {
-        file.write(json.toJSONString());
+        json.write(file);
       } catch (IOException e) {
         System.err.println("Error happened in writing config json: " + e);
       }

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

@@ -28,8 +28,8 @@
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.util.Map;
 import java.util.Objects;
-import org.json.simple.JSONObject;
 
 /** Container class to hold paths to nullaway and scanner config files. */
 public class ModuleInfo {
@@ -41,16 +41,19 @@ public class ModuleInfo {
   public final Path dir;
 
   /**
-   * Creates an instance of {@link ModuleInfo} from the given json object.
+   * Creates an instance of {@link ModuleInfo} from the given map object. This method is used in
+   * constructing {@link ModuleInfo} instances from a JSON object. Please note that array of
+   * dictionaries in json are parsed to {@link org.json.JSONArray} of maps. This method is called on
+   * each dictionary stored in the parsed collection to create the corresponding instance.
    *
    * @param id Global unique id for this module.
    * @param globalDir Global path for all Annotator/Scanner/NullAway outputs.
-   * @param jsonObject Json Object to retrieve values.
+   * @param mapFromJSON Map Object to retrieve require values.
    * @return An instance of {@link ModuleInfo}.
    */
-  public static ModuleInfo buildFromJson(int id, Path globalDir, JSONObject jsonObject) {
-    String nullawayConfigPath = (String) jsonObject.get("NULLAWAY");
-    String scannerConfigPath = (String) jsonObject.get("SCANNER");
+  public static ModuleInfo buildFromMap(int id, Path globalDir, Map<?, ?> mapFromJSON) {
+    String nullawayConfigPath = (String) mapFromJSON.get("NULLAWAY");
+    String scannerConfigPath = (String) mapFromJSON.get("SCANNER");
     if (nullawayConfigPath == null || scannerConfigPath == null) {
       throw new IllegalArgumentException(
           "Both paths to NullAway and Scanner config files must be set with NULLAWAY and SCANNER keys!");

annotator-core/src/main/java/edu/ucr/cs/riple/core/metadata/index/Fix.java

@@ -34,7 +34,7 @@
 import edu.ucr.cs.riple.injector.location.OnParameter;
 import java.util.Objects;
 import java.util.function.Consumer;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /**
  * Stores information suggesting adding @Nullable on an element in source code. These suggestions

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

@@ -43,6 +43,7 @@
 import java.nio.file.Path;
 import java.time.Duration;
 import java.time.temporal.ChronoUnit;
+import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
@@ -60,8 +61,8 @@
 import javax.xml.transform.stream.StreamResult;
 import me.tongfei.progressbar.ProgressBar;
 import me.tongfei.progressbar.ProgressBarStyle;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
 
@@ -98,11 +99,10 @@ public static void executeCommand(Config config, String command) {
    * @param config Annotator config.
    * @param reports Immutable set of reports.
    */
-  @SuppressWarnings("unchecked")
   public static void writeReports(Config config, ImmutableSet<Report> reports) {
     Path reportsPath = config.globalDir.resolve("reports.json");
     JSONObject result = new JSONObject();
-    JSONArray reportsJson = new JSONArray();
+    List<JSONObject> reportsList = new ArrayList<>();
     for (Report report : reports) {
       JSONObject reportJson = report.root.getJson();
       reportJson.put("LOCAL EFFECT", report.localEffect);
@@ -112,23 +112,25 @@ public static void writeReports(Config config, ImmutableSet<Report> reports) {
       reportJson.put("FINISHED", !report.requiresFurtherProcess(config));
       JSONArray followUps = new JSONArray();
       if (config.chain && report.localEffect < 1) {
-        followUps.addAll(report.tree.stream().map(Fix::getJson).collect(Collectors.toList()));
+        report.tree.remove(report.root);
+        report.tree.stream().map(Fix::getJson).forEach(followUps::put);
       }
       reportJson.put("TREE", followUps);
-      reportsJson.add(reportJson);
+      reportsList.add(reportJson);
     }
     // Sort by overall effect.
-    reportsJson.sort(
+    reportsList.sort(
         (o1, o2) -> {
-          int first = (Integer) ((JSONObject) o1).get("OVERALL EFFECT");
-          int second = (Integer) ((JSONObject) o2).get("OVERALL EFFECT");
+          int first = (Integer) o1.get("OVERALL EFFECT");
+          int second = (Integer) o2.get("OVERALL EFFECT");
           return Integer.compare(second, first);
         });
+    JSONArray reportsJson = new JSONArray();
+    reportsList.forEach(reportsJson::put);
     result.put("REPORTS", reportsJson);
     try (BufferedWriter writer =
         Files.newBufferedWriter(reportsPath.toFile().toPath(), Charset.defaultCharset())) {
-      writer.write(result.toJSONString().replace("\\/", "/").replace("\\\\\\", "\\"));
-      writer.flush();
+      result.write(writer);
     } catch (IOException e) {
       throw new RuntimeException(
           "Could not create the Annotator report json file: " + reportsPath, e);

gradle/dependencies.gradle

@@ -36,7 +36,7 @@ def versions = [
         errorProneApi          : project.hasProperty("epApiVersion") ? epApiVersion : oldestErrorProneApi,
         autoService            : "1.0-rc7",
         javaparser             : "3.24.0",
-        json                   : "1.1.1",
+        json                   : "20220924",
         guava                  : "31.0.1-jre",
         cli                    : "1.5.0",
         commonsio              : "2.11.0",
@@ -52,7 +52,7 @@ def apt = [
 
 def build = [
         guava                   : "com.google.guava:guava:${versions.guava}",
-        json                    : "com.googlecode.json-simple:json-simple:${versions.json}",
+        json                    : "org.json:json:${versions.json}",
         progressbar             : "me.tongfei:progressbar:${versions.progressbar}",
         javaparser              : "com.github.javaparser:javaparser-core:${versions.javaparser}",
         commonscli              : "commons-cli:commons-cli:${versions.cli}",

injector/build.gradle

@@ -37,6 +37,7 @@ dependencies {
     implementation deps.build.progressbar
 
     testImplementation deps.build.commonsio
+    testImplementation 'junit:junit:4.13.1'
 }
 
 compileJava.mustRunAfter verifyGoogleJavaFormat

injector/src/main/java/edu/ucr/cs/riple/injector/changes/AddAnnotation.java

@@ -24,7 +24,7 @@
 
 import edu.ucr.cs.riple.injector.location.Location;
 import java.util.Objects;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /** Used to add annotations on elements in source code. */
 public abstract class AddAnnotation extends Change {
@@ -34,7 +34,6 @@ public AddAnnotation(Location location, String annotation) {
   }
 
   @Override
-  @SuppressWarnings("unchecked")
   public JSONObject getJson() {
     JSONObject res = super.getJson();
     res.put("INJECT", true);

injector/src/main/java/edu/ucr/cs/riple/injector/changes/Change.java

@@ -30,7 +30,7 @@
 import edu.ucr.cs.riple.injector.modifications.Modification;
 import java.util.Objects;
 import javax.annotation.Nullable;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /** Represents a change in the AST of the source code. */
 public abstract class Change {
@@ -86,7 +86,6 @@ public int hashCode() {
     return Objects.hash(location, annotation);
   }
 
-  @SuppressWarnings("unchecked")
   public JSONObject getJson() {
     JSONObject res = new JSONObject();
     res.put("LOCATION", location.getJson());

injector/src/main/java/edu/ucr/cs/riple/injector/changes/RemoveAnnotation.java

@@ -33,7 +33,7 @@
 import java.util.Objects;
 import java.util.Optional;
 import javax.annotation.Nullable;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /**
  * Used to remove <a
@@ -65,7 +65,6 @@ public <T extends NodeWithAnnotations<?> & NodeWithRange<?>> Modification visit(
   }
 
   @Override
-  @SuppressWarnings("unchecked")
   public JSONObject getJson() {
     JSONObject res = super.getJson();
     res.put("INJECT", false);

injector/src/main/java/edu/ucr/cs/riple/injector/location/Location.java

@@ -38,7 +38,7 @@
 import java.util.Objects;
 import java.util.function.Consumer;
 import javax.annotation.Nullable;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /** Represents a location of an element in the source code. */
 public abstract class Location {
@@ -154,12 +154,11 @@ public Modification apply(CompilationUnit tree, Change change) {
     return applyToMember(clazz, change);
   }
 
-  @SuppressWarnings("unchecked")
   public JSONObject getJson() {
     JSONObject res = new JSONObject();
-    res.put(KEYS.CLASS, clazz);
-    res.put(KEYS.KIND, type.toString());
-    res.put(KEYS.PATH, path);
+    res.put(KEYS.CLASS.toString(), clazz);
+    res.put(KEYS.KIND.toString(), type.toString());
+    res.put(KEYS.PATH.toString(), path);
     fillJsonInformation(res);
     return res;
   }

injector/src/main/java/edu/ucr/cs/riple/injector/location/OnClass.java

@@ -34,7 +34,7 @@
 import java.util.Optional;
 import java.util.regex.Pattern;
 import javax.annotation.Nullable;
-import org.json.simple.JSONObject;
+import org.json.JSONObject;
 
 /** Represents a location for class element. This location is used to apply changes to a class. */
 public class OnClass extends Location {
@@ -67,6 +67,9 @@ protected Modification applyToMember(NodeList<BodyDeclaration<?>> members, Chang
     return change.visit(((BodyDeclaration<?>) optionalClass.get()));
   }
 
+  @Override
+  protected void fillJsonInformation(JSONObject res) {}
+
   /**
    * Checks if flat name is for an anonymous class.
    *
@@ -76,11 +79,6 @@ public static boolean isAnonymousClassFlatName(String flatName) {
     return anonymousClassPattern.matcher(flatName).matches();
   }
 
-  @Override
-  protected void fillJsonInformation(JSONObject res) {
-    // no op
-  }
-
   @Override
   public String toString() {
     return "OnClass{" + "type=" + type + ", clazz='" + clazz + '\'' + ", path=" + path + '}';

injector/src/main/java/edu/ucr/cs/riple/injector/location/OnField.java

@@ -37,8 +37,8 @@
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.function.Consumer;
 import javax.annotation.Nullable;
-import org.json.simple.JSONArray;
-import org.json.simple.JSONObject;
+import org.json.JSONArray;
+import org.json.JSONObject;
 
 /**
  * Represents a location for field element. This location is used to apply changes to a class field.
@@ -68,12 +68,11 @@ public OnField(String path, String clazz, Set<String> variables) {
     this(Helper.deserializePath(path), clazz, variables);
   }
 
-  @SuppressWarnings("unchecked")
   @Override
   protected void fillJsonInformation(JSONObject res) {
     JSONArray fields = new JSONArray();
-    fields.addAll(variables);
-    res.put(KEYS.VARIABLES, fields);
+    variables.forEach(fields::put);
+    res.put(KEYS.VARIABLES.toString(), fields);
   }
 
   @Override