Merge ../defects4j-branch-master into version-3

.github/workflows/ci.yml

@@ -8,9 +8,12 @@ jobs:
       JDK_ARCH: x64
       JDK_VERSION: 8u192
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 1
+        show-progress: false
     - name: Cache JDK
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       id: cache-jdk
       with:
         path: ~/.java

Dockerfile

@@ -13,12 +13,12 @@ RUN \
   apt-get install -y openjdk-8-jdk \
                 git \
                 build-essential \
-				subversion \
-				perl \
-				curl \
-				unzip \
-				cpanminus \
-				make \
+                subversion \
+                perl \
+                curl \
+                unzip \
+                cpanminus \
+                make \
                 && \
   rm -rf /var/lib/apt/lists/*
 

README.md

@@ -109,6 +109,8 @@ Steps to set up Defects4J
 
 3. Add Defects4J's executables to your PATH:
     - `export PATH=$PATH:"path2defects4j"/framework/bin`
+    ("path2defects4j" points to the directory to which you cloned Defects4J; it
+     looks like "/user/yourComputerUserName/desktop/defects4j".)
 
 4. Check installation:
     - `defects4j info -p Lang`

framework/bug-mining/Patch-Minimization-Guide.md

@@ -261,7 +261,7 @@ Code refactoring may consist of one or more of the following:
 
 ### 2. Compiler directives and annotations
 
-1. __Changes made to import statements that are not relevant to the bug fix should be removed__  
+1. __Changes made to import statements that are not relevant to the bug fix should be removed__
     Although removing changes involving import statements might create new warnings of `unused import statements`, import statements would not communicate anything about the bug or the bug fix since they would only be necessary to support functions. It is also worth noting that these import statements could be completely removed by using the fully qualified function names.
 
 2. __Changes made to @override statements can be removed under some circumstances__  

framework/bug-mining/initialize-project-and-collect-issues.pl

@@ -189,9 +189,6 @@ =head1 OPTIONS
     system("tail -n +2 $PROJECTS_DIR/$PID/$BUGS_CSV_ACTIVE | cut -f 2- -d',' > $COMMIT_DB_FILE.orig");
     # Find all versions that have not been mined
     system("grep -vFf $COMMIT_DB_FILE.orig $COMMIT_DB_FILE > $COMMIT_DB_FILE.filter && mv $COMMIT_DB_FILE.filter $COMMIT_DB_FILE");
-    # Print header to the active bugs csv
-    my $active_header = $BUGS_CSV_BUGID.",".$BUGS_CSV_COMMIT_BUGGY.",".$BUGS_CSV_COMMIT_FIXED.",".$BUGS_CSV_ISSUE_ID.",".$BUGS_CSV_ISSUE_URL;
-    system("echo $active_header > $COMMIT_DB_FILE.new && cat $COMMIT_DB_FILE >> $COMMIT_DB_FILE.new && mv $COMMIT_DB_FILE.new $COMMIT_DB_FILE");
 }
 
 print("Project $PID has been successfully initialized!\n");

framework/core/Constants.pm

@@ -223,6 +223,21 @@ The directory name of the local gradle repository (I<.gradle_local_home>).
 
 our $GRADLE_LOCAL_HOME_DIR = ($ENV{'GRADLE_LOCAL_HOME_DIR'} // ".gradle_local_home");
 
+#
+# Check if we have the correct version of Java
+#
+# Run the 'java -version' command and capture its output
+my $java_version_output = `java -version 2>&1`;
+
+# Extract the imajor version number using regular expressions
+if ($java_version_output =~ 'version "?(?:1\.)?(\K\d+)') {
+    if ($1 != 8) {
+        die ("Java 8 is required!\n\n");
+    }
+} else {
+    die ("Failed to parse Java version! Is Java installed/on the execution path?\n\n");
+}
+
 #
 # Check whether Defects4J has been properly initialized:
 # - Project repos available?

framework/core/Project.pm

@@ -740,17 +740,48 @@ sub monitor_test {
     my @log = `cat $log_file`;
     foreach (@log) {
         chomp;
-        s/\[Loaded ([^\$]*)(\$\S*)? from.*/$1/;
+        # Try to find the correspondent .java file of a given loaded class X.
+        #
+        # X could be
+        #  - A system class, e.g., java.io.ObjectInput, which is ignored by the following
+        #    procedure as it does not belong to the project under test.
+        #  - A "normal" class for which there is indeed a correspondent X.java file.
+        #  - A "normal" class named with one or more $ symbols, e.g., com.google.gson.internal.$Gson$Types
+        #    from Gson-{14,16,18}.
+        #
+        s/\[Loaded (.*) from.*/$1/;
+        my $found = 0;
         if (defined $src->{$_}) {
+            $found = 1;
             push(@{$classes->{src}}, $_);
             # Delete already loaded classes to avoid duplicates in the result
             delete($src->{$_});
         }
         if (defined $test->{$_}) {
+            $found = 1;
             push(@{$classes->{test}}, $_);
             # Delete already loaded classes to avoid duplicates in the result
             delete($test->{$_});
         }
+        if ($found == 0) {
+            # The correspondent .java file of a given loaded class X has not been found.
+            #
+            # It might be that X is, for example, an inner class or anonymous class for which
+            # there is no correspondent .java file, e.g., org.apache.commons.math3.util.MathArrays$OrderDirection
+            # from Math-25.  Thus, try to find the correspondent .java file of X's parent class.
+            #
+            s/([^\$]*)(\$\S*)?/$1/;
+            if (defined $src->{$_}) {
+                push(@{$classes->{src}}, $_);
+                # Delete already loaded classes to avoid duplicates in the result
+                delete($src->{$_});
+            }
+            if (defined $test->{$_}) {
+                push(@{$classes->{test}}, $_);
+                # Delete already loaded classes to avoid duplicates in the result
+                delete($test->{$_});
+            }
+        }
     }
     return $classes;
 }

framework/core/Project/JacksonDatabind.pm

@@ -63,6 +63,21 @@ sub new {
 #
 sub _post_checkout {
     my ($self, $rev_id, $work_dir) = @_;
+    my $vid = $self->{_vcs}->lookup_vid($rev_id);
+
+    # Fix compilation errors if necessary
+    my $compile_errors = "$PROJECTS_DIR/$self->{pid}/compile-errors/";
+    opendir(DIR, $compile_errors) or die "Could not find compile-errors directory.";
+    my @entries = readdir(DIR);
+    closedir(DIR);
+    foreach my $file (@entries) {
+        if ($file =~ /-(\d+)-(\d+).diff/) {
+            if ($vid >= $1 && $vid <= $2) {
+                $self->apply_patch($work_dir, "$compile_errors/$file")
+                        or confess("Couldn't apply patch ($file): $!");
+            }
+        }
+    }
 
     my $project_dir = "$PROJECTS_DIR/$self->{pid}";
     # Check whether ant build file exists

framework/core/Utils.pm

@@ -534,11 +534,11 @@ sub ensure_valid_bid {
     my $project_dir = "$PROJECTS_DIR/$pid";
 
     if ( ! -e "${project_dir}" ) {
-        confess("Error: ${pid} is a non-existent project\n");
+        confess("Error: ${pid} is not a project id; for a list, see https://github.com/rjust/defects4j#the-projects\n");
     }
 
     if ( ! -e "${project_dir}/trigger_tests/${bid}" ) {
-        confess("Error: ${pid}-${bid} is a non-existent bug\n");
+        confess("Error: ${pid}-${bid} is a not a bug id; for a list, see ${project_dir}/trigger_tests\n");
     }
 
     # Instantiate the project and get the list of all active bug ids

framework/lib/test_generation/bin/evosuite.sh

@@ -39,6 +39,13 @@ if [ $D4J_TEST_MODE != "regression" ]; then
     die "Unsupported test mode: $D4J_TEST_MODE"
 fi
 
+# Confirm D4J_FILE_TARGET_CLASSES ends in a newline character. Not ending with a
+# newline will lead to the below call to `wc -l` not counting the final line.
+# This is very likely a mistake.
+if [[ $(tail -c1 "$D4J_FILE_TARGET_CLASSES" | wc -l) -eq 0 ]]; then
+    die "File did not end in newline: $D4J_FILE_TARGET_CLASSES"
+fi
+
 # Compute the budget per target class; evenly split the time for search and assertions
 num_classes=$(cat $D4J_FILE_TARGET_CLASSES | wc -l)
 budget=$(echo "$D4J_TOTAL_BUDGET/2/$num_classes" | bc)

framework/projects/Cli/patches/3.src.patch

@@ -1,16 +1,8 @@
 diff --git a/src/java/org/apache/commons/cli/TypeHandler.java b/src/java/org/apache/commons/cli/TypeHandler.java
-index 0a0aa72..1ddde5b 100644
+index 0a0aa72..addf90b 100644
 --- a/src/java/org/apache/commons/cli/TypeHandler.java
 +++ b/src/java/org/apache/commons/cli/TypeHandler.java
-@@ -22,6 +22,7 @@ import java.net.URL;
-
- import java.util.Date;
-
-+import org.apache.commons.lang.math.NumberUtils;
- /**
-   * This is a temporary implementation. TypeHandler will handle the 
-   * pluggableness of OptionTypes and it will direct all of these types 
-@@ -158,17 +159,7 @@ public class TypeHandler {
+@@ -158,17 +158,7 @@ public class TypeHandler {
      {
          try
          {
@@ -25,7 +17,7 @@ index 0a0aa72..1ddde5b 100644
 -                    return Long.valueOf(str);
 -                }
 -            }
-+            return NumberUtils.createNumber(str);
++            return org.apache.commons.lang.math.NumberUtils.createNumber(str);
          }
          catch (NumberFormatException nfe)
          {

framework/projects/Cli/patches/36.src.patch

@@ -22,23 +22,15 @@ index dc6d5db..322053f 100644
      /** the name of the selected option */
      private String selected;
 diff --git a/src/main/java/org/apache/commons/cli/Options.java b/src/main/java/org/apache/commons/cli/Options.java
-index 796fe5c..0ee4eea 100644
+index 796fe5c..721baaf 100644
 --- a/src/main/java/org/apache/commons/cli/Options.java
 +++ b/src/main/java/org/apache/commons/cli/Options.java
-@@ -21,6 +21,7 @@ import java.io.Serializable;
- import java.util.ArrayList;
- import java.util.Collection;
- import java.util.Collections;
-+import java.util.HashMap;
- import java.util.HashSet;
- import java.util.LinkedHashMap;
- import java.util.List;
-@@ -57,7 +58,7 @@ public class Options implements Serializable
+@@ -57,7 +57,7 @@ public class Options implements Serializable
      private final List<Object> requiredOpts = new ArrayList<Object>();
 
      /** a map of the option groups */
 -    private final Map<String, OptionGroup> optionGroups = new LinkedHashMap<String, OptionGroup>();
-+    private final Map<String, OptionGroup> optionGroups = new HashMap<String, OptionGroup>();
++    private final Map<String, OptionGroup> optionGroups = new java.util.HashMap<String, OptionGroup>();
 
      /**
       * Add the specified option group.

framework/projects/Closure/patches/153.src.patch

@@ -1,5 +1,5 @@
 diff --git a/src/com/google/javascript/jscomp/Normalize.java b/src/com/google/javascript/jscomp/Normalize.java
-index c14ac8f1..4c99858e 100644
+index c14ac8f..4c99858 100644
 --- a/src/com/google/javascript/jscomp/Normalize.java
 +++ b/src/com/google/javascript/jscomp/Normalize.java
 @@ -628,7 +628,6 @@ class Normalize implements CompilerPass {
@@ -54,18 +54,10 @@ index c14ac8f1..4c99858e 100644
      }
 
 diff --git a/src/com/google/javascript/jscomp/SyntacticScopeCreator.java b/src/com/google/javascript/jscomp/SyntacticScopeCreator.java
-index eb6e1eab..04bafcf0 100644
+index eb6e1ea..9494792 100644
 --- a/src/com/google/javascript/jscomp/SyntacticScopeCreator.java
 +++ b/src/com/google/javascript/jscomp/SyntacticScopeCreator.java
-@@ -20,6 +20,7 @@ import com.google.common.base.Preconditions;
- import com.google.javascript.rhino.JSDocInfo;
- import com.google.javascript.rhino.Node;
- import com.google.javascript.rhino.Token;
-+import com.google.javascript.rhino.jstype.JSType;
-
-
- /**
-@@ -91,7 +92,7 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -91,7 +91,7 @@ class SyntacticScopeCreator implements ScopeCreator {
        // been declared in the outer scope.
        String fnName = fnNameNode.getString();
        if (!fnName.isEmpty() && NodeUtil.isFunctionExpression(n)) {
@@ -74,7 +66,7 @@ index eb6e1eab..04bafcf0 100644
        }
 
        // Args: Declare function variables
-@@ -99,7 +100,7 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -99,7 +99,7 @@ class SyntacticScopeCreator implements ScopeCreator {
        for (Node a = args.getFirstChild(); a != null;
             a = a.getNext()) {
          Preconditions.checkState(a.getType() == Token.NAME);
@@ -83,7 +75,7 @@ index eb6e1eab..04bafcf0 100644
        }
 
        // Body
-@@ -121,7 +122,9 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -121,7 +121,9 @@ class SyntacticScopeCreator implements ScopeCreator {
          for (Node child = n.getFirstChild();
               child != null;) {
            Node next = child.getNext();
@@ -94,7 +86,7 @@ index eb6e1eab..04bafcf0 100644
            child = next;
          }
          return;
-@@ -136,7 +139,7 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -136,7 +138,7 @@ class SyntacticScopeCreator implements ScopeCreator {
            // This is invalid, but allow it so the checks can catch it.
            return;
          }
@@ -103,7 +95,7 @@ index eb6e1eab..04bafcf0 100644
          return;   // should not examine function's children
 
        case Token.CATCH:
-@@ -148,7 +151,7 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -148,7 +150,7 @@ class SyntacticScopeCreator implements ScopeCreator {
          final Node var = n.getFirstChild();
          final Node block = var.getNext();
 
@@ -112,7 +104,7 @@ index eb6e1eab..04bafcf0 100644
          scanVars(block, n);
          return;  // only one child to scan
 
-@@ -174,7 +177,8 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -174,7 +176,8 @@ class SyntacticScopeCreator implements ScopeCreator {
     */
    interface RedeclarationHandler {
      void onRedeclaration(
@@ -122,7 +114,7 @@ index eb6e1eab..04bafcf0 100644
    }
 
    /**
-@@ -182,8 +186,8 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -182,8 +185,8 @@ class SyntacticScopeCreator implements ScopeCreator {
     */
    private class DefaultRedeclarationHandler implements RedeclarationHandler {
      public void onRedeclaration(
@@ -133,14 +125,14 @@ index eb6e1eab..04bafcf0 100644
 
        // Don't allow multiple variables to be declared at the top level scope
        if (scope.isGlobal()) {
-@@ -228,17 +232,16 @@ class SyntacticScopeCreator implements ScopeCreator {
+@@ -228,17 +231,16 @@ class SyntacticScopeCreator implements ScopeCreator {
     * @param n The node corresponding to the variable name.
     * @param declaredType The variable's type, according to JSDoc
     */
 -  private void declareVar(Node n) {
 -    Preconditions.checkState(n.getType() == Token.NAME);
 +  private void declareVar(String name, Node n, Node parent,
-+                          Node gramps, JSType declaredType,
++                          Node gramps, com.google.javascript.rhino.jstype.JSType declaredType,
 +                          Node nodeWithLineNumber) {
 
 -    CompilerInput input = compiler.getInput(sourceName);

framework/projects/Closure/patches/158.src.patch

@@ -1,5 +1,5 @@
 diff --git a/src/com/google/javascript/jscomp/AbstractCommandLineRunner.java b/src/com/google/javascript/jscomp/AbstractCommandLineRunner.java
-index e2e102c6..3a7f427f 100644
+index e2e102c..3a7f427 100644
 --- a/src/com/google/javascript/jscomp/AbstractCommandLineRunner.java
 +++ b/src/com/google/javascript/jscomp/AbstractCommandLineRunner.java
 @@ -194,11 +194,12 @@ abstract class AbstractCommandLineRunner<A extends Compiler,
@@ -79,7 +79,7 @@ index e2e102c6..3a7f427f 100644
 -  }
  }
 diff --git a/src/com/google/javascript/jscomp/CommandLineRunner.java b/src/com/google/javascript/jscomp/CommandLineRunner.java
-index b1a7472a..d9a381b5 100644
+index b1a7472..d9a381b 100644
 --- a/src/com/google/javascript/jscomp/CommandLineRunner.java
 +++ b/src/com/google/javascript/jscomp/CommandLineRunner.java
 @@ -23,7 +23,6 @@ import com.google.common.collect.Maps;
@@ -200,25 +200,17 @@ index b1a7472a..d9a381b5 100644
            .setCharset(flags.charset)
            .setManageClosureDependencies(flags.manage_closure_dependencies)
 diff --git a/src/com/google/javascript/jscomp/DiagnosticGroups.java b/src/com/google/javascript/jscomp/DiagnosticGroups.java
-index cf0beda1..271492f2 100644
+index cf0beda..d2d38c5 100644
 --- a/src/com/google/javascript/jscomp/DiagnosticGroups.java
 +++ b/src/com/google/javascript/jscomp/DiagnosticGroups.java
-@@ -20,6 +20,7 @@ import com.google.common.base.Preconditions;
- import com.google.common.collect.ImmutableMap;
- import com.google.common.collect.Maps;
-
-+import java.util.List;
- import java.util.Map;
-
- /**
-@@ -182,10 +183,12 @@ public class DiagnosticGroups {
+@@ -182,10 +182,12 @@ public class DiagnosticGroups {
    /**
     * Adds warning levels by name.
     */
 -  void setWarningLevel(CompilerOptions options,
 -      String name, CheckLevel level) {
 +  void setWarningLevels(CompilerOptions options,
-+      List<String> diagnosticGroups, CheckLevel level) {
++      java.util.List<String> diagnosticGroups, CheckLevel level) {
 +    for (String name : diagnosticGroups) {
      DiagnosticGroup group = forName(name);
      Preconditions.checkNotNull(group, "No warning class for name: " + name);

framework/projects/Gson/loaded_classes/10.src

@@ -3,6 +3,8 @@ com.google.gson.annotations.SerializedName
 com.google.gson.FieldNamingPolicy
 com.google.gson.FieldNamingStrategy
 com.google.gson.Gson
+com.google.gson.internal.$Gson$Preconditions
+com.google.gson.internal.$Gson$Types
 com.google.gson.internal.bind.ArrayTypeAdapter
 com.google.gson.internal.bind.CollectionTypeAdapterFactory
 com.google.gson.internal.bind.DateTypeAdapter