merge master

.github/workflows/continuous-integration.yml

@@ -8,9 +8,9 @@ jobs:
   build-without-cache:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
@@ -19,9 +19,9 @@ jobs:
   build-with-setup-java-cache:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
@@ -31,9 +31,9 @@ jobs:
   build-with-gradle-build-action-cache:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
@@ -43,26 +43,26 @@ jobs:
   build-with-upload-artifact:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
           cache: gradle
       - name: Build with Gradle
         run: ./gradlew build --scan --no-daemon
       - name: Archive test report
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: Test report
           path: build/reports/tests/test
   parallel-processing-enabled-caching-disabled:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
@@ -73,9 +73,9 @@ jobs:
   parallel-processing-disabled-caching-disabled:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 11
           distribution: 'temurin'
@@ -87,9 +87,9 @@ jobs:
   parser-coinfiguration-17:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - name: Set up JDK 17
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           java-version: 17
           distribution: 'temurin'

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

@@ -123,9 +123,7 @@ public void analyzeDownstreamDependencies() {
             .map(
                 location ->
                     new Fix(
-                        new AddMarkerAnnotation(location, context.config.nullableAnnot),
-                        "null",
-                        false))
+                        new AddMarkerAnnotation(location, context.config.nullableAnnot), "null"))
             .collect(ImmutableSet.toImmutableSet());
     DownstreamImpactEvaluator evaluator = new DownstreamImpactEvaluator(supplier);
     ImmutableSet<Report> reports = evaluator.evaluate(fixes);

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

@@ -139,7 +139,6 @@ private NullAwayError deserializeErrorFromTSVLine(ModuleInfo moduleInfo, String
         nonnullTarget == null
             ? Set.of()
             : Set.of(new AddMarkerAnnotation(nonnullTarget, config.nullableAnnot));
-
     return createError(
         errorType,
         errorMessage,

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

@@ -52,7 +52,7 @@ public NullAwayError(
   @Override
   protected Set<Fix> computeFixesFromAnnotations(Set<AddAnnotation> annotations) {
     return annotations.stream()
-        .map(annot -> new Fix(annot, messageType, true))
+        .map(annot -> new Fix(annot, messageType))
         .collect(Collectors.toSet());
   }
 

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

@@ -192,7 +192,6 @@ public void updateStatus(
   public void mergeTriggered() {
     this.tree.addAll(Error.getResolvingFixesOfErrors(this.triggeredErrors));
     this.tree.addAll(triggeredFixesFromDownstreamErrors);
-    this.tree.forEach(fix -> fix.fixSourceIsInTarget = true);
   }
 
   @Override

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

@@ -85,8 +85,7 @@ protected Set<Fix> getTriggeredFixesFromDownstreamErrors(Node node) {
                 new Fix(
                     new AddMarkerAnnotation(
                         error.toResolvingLocation(), context.config.nullableAnnot),
-                    "PASSING_NULLABLE",
-                    false))
+                    "PASSING_NULLABLE"))
         .collect(Collectors.toSet());
   }
 }

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

@@ -50,25 +50,18 @@ public class Fix {
   public final Set<AddAnnotation> changes;
   /** Reasons this fix is suggested by NullAway in string. */
   public final ImmutableSet<String> reasons;
-  /**
-   * If true, the fix is suggested due to an error in the target module, false if the fix is
-   * suggested due to error in downstream dependencies.
-   */
-  public boolean fixSourceIsInTarget;
 
-  public Fix(AddAnnotation change, String reason, boolean fixSourceIsInTarget) {
-    this(change, ImmutableSet.of(reason), fixSourceIsInTarget);
+  public Fix(AddAnnotation change, String reason) {
+    this(change, ImmutableSet.of(reason));
   }
 
-  public Fix(AddAnnotation change, ImmutableSet<String> reasons, boolean fixSourceIsInTarget) {
-    this(ImmutableSet.of(change), reasons, fixSourceIsInTarget);
+  public Fix(AddAnnotation change, ImmutableSet<String> reasons) {
+    this(ImmutableSet.of(change), reasons);
   }
 
-  public Fix(
-      Set<AddAnnotation> changes, ImmutableSet<String> reasons, boolean fixSourceIsInTarget) {
-    this.changes = changes;
+  public Fix(ImmutableSet<AddAnnotation> change, ImmutableSet<String> reasons) {
+    this.changes = change;
     this.reasons = reasons;
-    this.fixSourceIsInTarget = fixSourceIsInTarget;
   }
 
   /**

annotator-core/src/main/java/edu/ucr/cs/riple/core/registries/region/generatedcode/LombokHandler.java

@@ -120,8 +120,7 @@ public ImmutableSet<Fix> extendForGeneratedFixes(Set<Fix> fixes) {
                                 new Fix(
                                     new AddMarkerAnnotation(
                                         getterMethod.location, change.getAnnotationName().fullName),
-                                    fix.reasons,
-                                    fix.fixSourceIsInTarget));
+                                    fix.reasons));
                           }
                         })));
     return builder.build();

annotator-core/src/test/java/edu/ucr/cs/riple/core/tools/TError.java

@@ -47,7 +47,7 @@ public TError(Location location) {
   @Override
   protected Set<Fix> computeFixesFromAnnotations(Set<AddAnnotation> annotations) {
     return annotations.stream()
-        .map(addAnnotation -> new Fix(addAnnotation, ImmutableSet.of(messageType), true))
+        .map(addAnnotation -> new Fix(addAnnotation, ImmutableSet.of(messageType)))
         .collect(Collectors.toSet());
   }
 }

annotator-core/src/test/java/edu/ucr/cs/riple/core/tools/TFix.java

@@ -36,6 +36,6 @@
 public class TFix extends Fix {
 
   public TFix(Location location) {
-    super(new DefaultAnnotation(location), ImmutableSet.of(), true);
+    super(new DefaultAnnotation(location), ImmutableSet.of());
   }
 }

annotator-core/src/test/java/edu/ucr/cs/riple/core/tools/TReport.java

@@ -50,8 +50,7 @@ public TReport(Location root, int effect) {
 
   public TReport(Location root, int effect, Tag tag) {
     super(
-        new Fix(
-            new AddMarkerAnnotation(root, "javax.annotation.Nullable"), ImmutableSet.of(), true),
+        new Fix(new AddMarkerAnnotation(root, "javax.annotation.Nullable"), ImmutableSet.of()),
         effect);
     this.expectedValue = effect;
     if (tag != null) {

gradle/dependencies.gradle

@@ -35,7 +35,7 @@ def versions = [
         errorProne             : defaultErrorProneVersion,
         errorProneApi          : project.hasProperty("epApiVersion") ? epApiVersion : oldestErrorProneApi,
         autoService            : "1.0-rc7",
-        javaparser             : "3.26.0",
+        javaparser             : "3.26.2",
         json                   : "1.1.1",
         guava                  : "31.0.1-jre",
         cli                    : "1.5.0",

injector/src/main/java/edu/ucr/cs/riple/injector/Injector.java

@@ -24,6 +24,7 @@
 
 import static java.util.stream.Collectors.groupingBy;
 
+import com.github.javaparser.ParseProblemException;
 import com.github.javaparser.ParserConfiguration;
 import com.github.javaparser.StaticJavaParser;
 import com.github.javaparser.ast.CompilationUnit;
@@ -33,6 +34,7 @@
 import edu.ucr.cs.riple.injector.changes.AnnotationChange;
 import edu.ucr.cs.riple.injector.changes.ChangeVisitor;
 import edu.ucr.cs.riple.injector.changes.RemoveAnnotation;
+import edu.ucr.cs.riple.injector.exceptions.ParseException;
 import edu.ucr.cs.riple.injector.modifications.Modification;
 import edu.ucr.cs.riple.injector.offsets.FileOffsetStore;
 import java.io.IOException;
@@ -171,6 +173,9 @@ public static CompilationUnit parse(
     StaticJavaParser.setConfiguration(parserConfiguration);
     try {
       return StaticJavaParser.parse(path);
+    } catch (ParseProblemException e) {
+      // The original exception is not useful for the user. We should provide a more informative one
+      throw new ParseException(path, e);
     } catch (NoSuchFileException e) {
       return null;
     } catch (IOException e) {

injector/src/main/java/edu/ucr/cs/riple/injector/exceptions/ParseException.java

@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2024 University of California, Riverside.
+ *
+ * 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.injector.exceptions;
+
+import com.github.javaparser.ParseProblemException;
+import java.nio.file.Path;
+
+/**
+ * Exception indicating that an error occurred while parsing a source file.
+ *
+ * <p>This serves as a wrapper for the {@link ParseProblemException} class, providing a more concise
+ * representation of the underlying issue.
+ */
+public class ParseException extends RuntimeException {
+
+  public ParseException(Path path, ParseProblemException exception) {
+    super(retrieveExceptionMessage(path, exception), exception);
+  }
+
+  private static String retrieveExceptionMessage(Path path, ParseProblemException e) {
+    String message = e.getMessage();
+    // If the message contains the stack trace, we should remove it. It does not contain any useful
+    // information.
+    int index = message.indexOf("Problem stacktrace :");
+    message = index == -1 ? message : message.substring(0, index);
+    return "javaparser was not able to parse file at: " + path + "\nParse problem:" + message;
+  }
+}