Add inference support for UCRTaint checker

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

@@ -27,6 +27,7 @@
 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.checkers.ucrtaint.UCRTaint;
 import edu.ucr.cs.riple.core.metadata.index.Error;
 import edu.ucr.cs.riple.core.module.ModuleInfo;
 import edu.ucr.cs.riple.injector.location.OnField;
@@ -75,6 +76,8 @@ public static Checker<?> getCheckerByName(String name, Context context) {
     switch (name) {
       case NullAway.NAME:
         return new NullAway(context);
+      case UCRTaint.NAME:
+        return new UCRTaint(context);
       default:
         throw new RuntimeException("Unknown checker name: " + name);
     }

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

@@ -0,0 +1,135 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2023 Nima Karimipour
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package edu.ucr.cs.riple.core.checkers.ucrtaint;
+
+import com.google.common.collect.ImmutableSet;
+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.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.injector.changes.AddTypeUseMarkerAnnotation;
+import edu.ucr.cs.riple.injector.location.Location;
+import java.io.IOException;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Set;
+import org.json.simple.JSONArray;
+import org.json.simple.JSONObject;
+import org.json.simple.parser.JSONParser;
+import org.json.simple.parser.ParseException;
+
+/**
+ * Represents <a href="https://github.com/kanaksad/UCRTaintingChecker">UCRTaint</a> checker in
+ * Annotator.
+ */
+public class UCRTaint extends CheckerBaseClass<UCRTaintError> {
+
+  /** The name of the checker. This is used to identify the checker in the configuration file. */
+  public static final String NAME = "UCRTaint";
+
+  public UCRTaint(Context context) {
+    super(context);
+  }
+
+  @Override
+  public void preprocess(AnnotationInjector injector) {}
+
+  @Override
+  public Set<UCRTaintError> deserializeErrors(ModuleInfo module) {
+    ImmutableSet<Path> paths =
+        module.getModuleConfiguration().stream()
+            .map(moduleInfo -> moduleInfo.dir.resolve("errors.json"))
+            .collect(ImmutableSet.toImmutableSet());
+    Set<UCRTaintError> errors = new HashSet<>();
+    paths.forEach(
+        path -> {
+          try {
+            String content = Files.readString(path, Charset.defaultCharset());
+            content = "{ \"errors\": [" + content.substring(0, content.length() - 1) + "]}";
+            JSONObject jsonObject = (JSONObject) new JSONParser().parse(content);
+            JSONArray errorsJson = (JSONArray) jsonObject.get("errors");
+            errorsJson.forEach(o -> errors.add(deserializeErrorFromJSON((JSONObject) o, module)));
+          } catch (IOException | ParseException e) {
+            throw new RuntimeException(e);
+          }
+        });
+    return errors;
+  }
+
+  private UCRTaintError deserializeErrorFromJSON(JSONObject errorsJson, ModuleInfo moduleInfo) {
+    String errorType = (String) errorsJson.get("messageKey");
+    int offset = ((Long) errorsJson.get("offset")).intValue();
+    Region region =
+        new Region(
+            (String) ((JSONObject) errorsJson.get("region")).get("member"),
+            (String) ((JSONObject) errorsJson.get("region")).get("class"));
+    ImmutableSet.Builder<Fix> builder = ImmutableSet.builder();
+    ((JSONArray) errorsJson.get("fixes"))
+        .forEach(
+            o -> {
+              JSONObject fixJson = (JSONObject) o;
+              Location location =
+                  Location.createLocationFromJSON((JSONObject) fixJson.get("location"));
+              location.ifField(onField -> extendVariableList(onField, moduleInfo));
+              builder.add(
+                  new Fix(
+                      new AddTypeUseMarkerAnnotation(
+                          location, "edu.ucr.cs.riple.taint.ucrtainting.qual.RUntainted"),
+                      errorType,
+                      true));
+            });
+    return new UCRTaintError(errorType, "", region, offset, builder.build());
+  }
+
+  @Override
+  public void suppressRemainingErrors(AnnotationInjector injector) {
+    throw new RuntimeException(
+        "Suppression for remaining errors is not supported for " + NAME + "yet!");
+  }
+
+  @Override
+  public void verifyCheckerCompatibility() {}
+
+  @Override
+  public void prepareConfigFilesForBuild(ImmutableSet<ModuleConfiguration> configurations) {
+    // TODO: implement this once configuration on UCRTaint is finalized.
+  }
+
+  @Override
+  public UCRTaintError createError(
+      String errorType,
+      String errorMessage,
+      Region region,
+      int offset,
+      ImmutableSet<Fix> resolvingFixes,
+      ModuleInfo moduleInfo) {
+    return new UCRTaintError(errorType, errorMessage, region, offset, resolvingFixes);
+  }
+}

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

@@ -0,0 +1,43 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2023 Nima Karimipour
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package edu.ucr.cs.riple.core.checkers.ucrtaint;
+
+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;
+
+/** Represents an error reported by {@link UCRTaint}. */
+public class UCRTaintError extends Error {
+
+  public UCRTaintError(
+      String messageType,
+      String message,
+      Region region,
+      int offset,
+      ImmutableSet<Fix> resolvingFixes) {
+    super(messageType, message, region, offset, resolvingFixes);
+  }
+}

annotator-core/src/main/java/edu/ucr/cs/riple/core/metadata/region/CompoundRegionRegistry.java

@@ -56,6 +56,7 @@ public CompoundRegionRegistry(ModuleInfo moduleInfo) {
         ImmutableSet.of(
             new FieldRegionRegistry(moduleInfo),
             methodRegionRegistry,
+            new LocalVariableRegionRegistry(),
             new ParameterRegionRegistry(moduleInfo, methodRegionRegistry));
   }
 

annotator-core/src/main/java/edu/ucr/cs/riple/core/metadata/region/LocalVariableRegionRegistry.java

@@ -0,0 +1,42 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2023 Nima Karimipour
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+package edu.ucr.cs.riple.core.metadata.region;
+
+import edu.ucr.cs.riple.injector.location.Location;
+import edu.ucr.cs.riple.injector.location.OnLocalVariable;
+import java.util.Optional;
+import java.util.Set;
+
+/** Region Registry for Local variables. */
+public class LocalVariableRegionRegistry implements RegionRegistry {
+  @Override
+  public Optional<Set<Region>> getImpactedRegions(Location location) {
+    if (!location.isOnLocalVariable()) {
+      return Optional.empty();
+    }
+    OnLocalVariable localVariable = location.toLocalVariable();
+    return Optional.of(Set.of(new Region(localVariable.clazz, localVariable.encMethod.method)));
+  }
+}

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

@@ -28,10 +28,12 @@
 import com.google.common.collect.Sets;
 import edu.ucr.cs.riple.injector.Helper;
 import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.Objects;
 import java.util.function.Consumer;
 import javax.annotation.Nullable;
+import org.json.simple.JSONObject;
 
 /** Represents a location of an element in the source code. */
 public abstract class Location {
@@ -57,6 +59,19 @@ public Location(LocationKind type, Path path, String clazz) {
     this.path = path;
   }
 
+  /**
+   * Creates an instance of {@link Location} for a given type, and retrieves path and class values
+   * from the given JSON object.
+   *
+   * @param type The type of the location.
+   * @param json The JSON object containing the path and class values.
+   */
+  public Location(LocationKind type, JSONObject json) {
+    this.type = type;
+    this.clazz = (String) json.get("class");
+    this.path = Paths.get((String) json.get("path"));
+  }
+
   /**
    * Creates an instance of {@link Location} based on values written in a row of a TSV file. These
    * values should be in order of:
@@ -98,6 +113,24 @@ public static Location createLocationFromArrayInfo(String[] values) {
     throw new RuntimeException("Cannot reach this statement, values: " + Arrays.toString(values));
   }
 
+  public static Location createLocationFromJSON(JSONObject json) {
+    String kind = (String) json.get("kind");
+    switch (kind) {
+      case "METHOD":
+        return new OnMethod(json);
+      case "FIELD":
+        return new OnField(json);
+      case "PARAMETER":
+        return new OnParameter(json);
+      case "LOCAL_VARIABLE":
+        return new OnLocalVariable(json);
+      case "CLASS":
+        return new OnClass(json);
+      default:
+        throw new RuntimeException("Cannot reach this statement, kind: " + kind);
+    }
+  }
+
   /**
    * If this location is of kind {@link LocationKind#METHOD}, calls the consumer on the location.
    *

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

@@ -27,6 +27,7 @@
 import edu.ucr.cs.riple.injector.Helper;
 import java.nio.file.Path;
 import java.util.regex.Pattern;
+import org.json.simple.JSONObject;
 
 /** Represents a location for class element. This location is used to apply changes to a class. */
 public class OnClass extends Location {
@@ -45,6 +46,10 @@ public OnClass(String path, String clazz) {
     this(Helper.deserializePath(path), clazz);
   }
 
+  public OnClass(JSONObject json) {
+    super(LocationKind.CLASS, json);
+  }
+
   /**
    * Checks if flat name is for an anonymous class.
    *

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

@@ -27,9 +27,11 @@
 import edu.ucr.cs.riple.injector.Helper;
 import java.nio.file.Path;
 import java.util.Collections;
+import java.util.HashSet;
 import java.util.Objects;
 import java.util.Set;
 import java.util.function.Consumer;
+import org.json.simple.JSONObject;
 
 /**
  * Represents a location for field element. This location is used to apply changes to a class field.
@@ -59,6 +61,11 @@ public OnField(String path, String clazz, Set<String> variables) {
     this(Helper.deserializePath(path), clazz, variables);
   }
 
+  public OnField(JSONObject json) {
+    super(LocationKind.FIELD, json);
+    this.variables = new HashSet<>(Collections.singletonList((String) json.get("variables")));
+  }
+
   @Override
   public void ifField(Consumer<OnField> consumer) {
     consumer.accept(this);

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

@@ -28,6 +28,7 @@
 import java.nio.file.Path;
 import java.util.Objects;
 import java.util.function.Consumer;
+import org.json.simple.JSONObject;
 
 /**
  * Represents a location for local variable element. This location is used to apply changes to a
@@ -51,6 +52,12 @@ public OnLocalVariable(String path, String clazz, String encMethod, String varNa
     this(Helper.deserializePath(path), clazz, encMethod, varName);
   }
 
+  public OnLocalVariable(JSONObject json) {
+    super(LocationKind.LOCAL_VARIABLE, json);
+    this.encMethod = new OnMethod(json);
+    this.varName = (String) json.get("varName");
+  }
+
   @Override
   public void ifLocalVariable(Consumer<OnLocalVariable> consumer) {
     consumer.accept(this);

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

@@ -30,6 +30,7 @@
 import java.nio.file.Path;
 import java.util.Objects;
 import java.util.function.Consumer;
+import org.json.simple.JSONObject;
 
 /** Represents a location for method element. This location is used to apply changes to a method. */
 public class OnMethod extends Location {
@@ -52,6 +53,12 @@ public OnMethod(String path, String clazz, String method) {
     this(Helper.deserializePath(path), clazz, method);
   }
 
+  public OnMethod(JSONObject json) {
+    super(LocationKind.METHOD, json);
+    this.method = (String) json.get("method");
+    this.matcher = new SignatureMatcher(method);
+  }
+
   /**
    * Checks if the given method matches the method signature of this location.
    *