From 18fe2cda0c72d34ae28244bf756504a9a4f9cb13 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 00:42:50 -0400
Subject: [PATCH 01/13] Added a triggering test for issue #87.

---
 framework/test/test_mutation_analysis.sh | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/framework/test/test_mutation_analysis.sh b/framework/test/test_mutation_analysis.sh
index a7eb4ae3c..0b5e119e6 100755
--- a/framework/test/test_mutation_analysis.sh
+++ b/framework/test/test_mutation_analysis.sh
@@ -78,5 +78,29 @@ num_mutants_killed=$(tail -n1 "$summary_file" | cut -f3 -d',')
 # TODO Would be nice to test the number of excluded mutants. In order to do it
 # Major has to write that number to the '$pid_bid_dir/summary.csv' file.
 
+########################################################################
+# Test mutation analysis when explicitly providing the classes to mutate
+
+# Exclude all generated mutants
+instrument_classes="$pid_bid_dir/instrument_classes.txt"
+echo "org.apache.commons.lang3.LocaleUtils" > "$instrument_classes"
+
+defects4j mutation -w "$pid_bid_dir" -i "$instrument_classes" || die "Mutation analysis (instrument LocaleUtils) failed!"
+
+# The last row of 'summary.csv' does not have an end of line character.
+# Otherwise, using wc would be more intuitive.
+num_rows=$(grep -c "^" "$summary_file")
+[ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
+
+# Columns of summary (csv) file:
+# MutantsGenerated,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
+num_mutants_generated=$(tail -n1 "$summary_file" | cut -f1 -d',')
+num_mutants_covered=$(tail -n1 "$summary_file" | cut -f2 -d',')
+num_mutants_killed=$(tail -n1 "$summary_file" | cut -f3 -d',')
+
+[ "$num_mutants_generated" -eq 184 ] || die "$num_mutants_generated mutants have been generated!"
+[ "$num_mutants_covered" -eq 184 ] || die "$num_mutants_covered mutants have been covered!"
+[ "$num_mutants_killed" -eq 158 ] || die "$num_mutants_killed mutants have been killed!"
+
 # Clean up
 rm -rf "$pid_bid_dir"

From 9e88766908679ecc365acfdb895e24b18965cbba Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 01:04:59 -0400
Subject: [PATCH 02/13] Refactored a test script.

---
 framework/test/test_mutation_analysis.sh | 110 +++++++++++------------
 1 file changed, 53 insertions(+), 57 deletions(-)

diff --git a/framework/test/test_mutation_analysis.sh b/framework/test/test_mutation_analysis.sh
index 0b5e119e6..3ace886c0 100755
--- a/framework/test/test_mutation_analysis.sh
+++ b/framework/test/test_mutation_analysis.sh
@@ -13,7 +13,8 @@ HERE=$(cd `dirname $0` && pwd)
 source "$HERE/test.include" || exit 1
 init
 
-pid="Lang" # any pid-bid should work
+# Any version should work, but the test cases below are specific to this version
+pid="Lang"
 bid="1f"
 pid_bid_dir="$TMP_DIR/$pid-$bid"
 rm -rf "$pid_bid_dir"
@@ -22,85 +23,80 @@ rm -rf "$pid_bid_dir"
 summary_file="$pid_bid_dir/summary.csv"
 mutants_file="$pid_bid_dir/mutants.log"
 
+################################################################################
+#
+# Check whether the mutation analysis results (summary.csv) match the expectations.
+#
+_check_mutation_result() {
+    [ $# -eq 3 ] || die "usage: ${FUNCNAME[0]} \
+            <expected_mutants_generated> \
+            <expected_mutants_covered> \
+            <expected_mutants_killed>"
+    local exp_mut_gen=$1
+    local exp_mut_cov=$2
+    local exp_mut_kill=$3
+
+    # Make sure Major generated the expected data files
+    [ -s "$mutants_file" ] || die "'$mutants_file' doesn't exist or is empty!"
+    [ -s "$summary_file" ] || die "'$summary_file' doesn't exist or is empty!"
+
+    # The last row of 'summary.csv' does not have an end of line character.
+    # Otherwise, using wc would be more intuitive.
+    local num_rows=$(grep -c "^" "$summary_file")
+    [ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
+
+    # Columns of summary (csv) file:
+    # MutantsGenerated,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
+    local act_mut_gen=$(tail -n1 "$summary_file" | cut -f1 -d',')
+    local act_mut_cov=$(tail -n1 "$summary_file" | cut -f2 -d',')
+    local act_mut_kill=$(tail -n1 "$summary_file" | cut -f3 -d',')
+
+    [ "$act_mut_gen"  -eq "$exp_mut_gen" ] || die "Unexpected number of mutants generated (expected: $exp_mut_gen, actual: $act_mut_gen)!"
+    [ "$act_mut_cov"  -eq "$exp_mut_cov" ] || die "Unexpected number of mutants covered (expected: $exp_mut_cov, actual: $act_mut_cov)!"
+    [ "$act_mut_kill" -eq "$exp_mut_kill" ] || die "Unexpected number of mutants killed (expected: $exp_mut_kill, actual: $act_mut_kill)!"
+
+    # TODO Would be nice to test the number of excluded mutants. In order to do it
+    # Major has to write that number to the '$pid_bid_dir/summary.csv' file.
+}
+################################################################################
+
 # Checkout project-version
 defects4j checkout -p "$pid" -v "$bid" -w "$pid_bid_dir" || die "It was not possible to checkout $pid-$bid to '$pid_bid_dir'!"
 
 ######################################################
 # Test mutation analysis without excluding any mutants
 
-defects4j mutation -w "$pid_bid_dir" -r || die "Mutation analysis (including all mutants) failed!"
-
-# Make sure Major generated the expected data files
-[ -s "$mutants_file" ] || die "'$mutants_file' doesn't exist or is empty!"
-[ -s "$summary_file" ] || die "'$summary_file' doesn't exist or is empty!"
-
-# The last row of 'summary.csv' does not have an end of line character.
-# Otherwise, using wc would be more intuitive.
-num_rows=$(grep -c "^" "$summary_file")
-[ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
-
-# Columns of summary (csv) file:
-# MutantsGenerated,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
-num_mutants_covered=$(tail -n1 "$summary_file" | cut -f2 -d',')
-num_mutants_killed=$(tail -n1 "$summary_file" | cut -f3 -d',')
-
-[ "$num_mutants_covered" -gt 0 ] || die "0 mutants covered!"
-[ "$num_mutants_killed" -gt 0 ] || die "0 mutants killed!"
-
-# TODO Would be nice to test the number of excluded mutants. In order to do it
-# Major has to write that number to the '$pid_bid_dir/summary.csv' file.
-
-# Remove the summary file to ensure it is regenerated later
+# Remove the summary file to ensure it is regenerated
 rm "$summary_file"
 
+defects4j mutation -w "$pid_bid_dir" -r || die "Mutation analysis (including all mutants) failed!"
+_check_mutation_result 941 913 646
+
 ###################################################
 # Test mutation analysis when excluding all mutants
 
+# Remove the summary file to ensure it is regenerated
+rm "$summary_file"
+
 # Exclude all generated mutants
 exclude_file="$pid_bid_dir/exclude_all_mutants.txt"
 cut -f1 -d':' "$mutants_file" > "$exclude_file"
 
 defects4j mutation -w "$pid_bid_dir" -r -e "$exclude_file" || die "Mutation analysis (excluding all mutants) failed!"
+_check_mutation_result 941 0 0
 
-# The last row of 'summary.csv' does not have an end of line character.
-# Otherwise, using wc would be more intuitive.
-num_rows=$(grep -c "^" "$summary_file")
-[ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
-
-# Columns of summary (csv) file:
-# MutantsGenerated,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
-num_mutants_covered=$(tail -n1 "$summary_file" | cut -f2 -d',')
-num_mutants_killed=$(tail -n1 "$summary_file" | cut -f3 -d',')
-
-[ "$num_mutants_covered" -eq 0 ] || die "$num_mutants_covered mutants have been covered!"
-[ "$num_mutants_killed" -eq 0 ] || die "$num_mutants_killed mutants have been killed!"
+##########################################################################
+# Test mutation analysis when explicitly providing the class(es) to mutate
 
-# TODO Would be nice to test the number of excluded mutants. In order to do it
-# Major has to write that number to the '$pid_bid_dir/summary.csv' file.
-
-########################################################################
-# Test mutation analysis when explicitly providing the classes to mutate
+# Remove the summary file to ensure it is regenerated
+rm "$summary_file"
 
-# Exclude all generated mutants
+# Mutate an arbitrary, non-modified class
 instrument_classes="$pid_bid_dir/instrument_classes.txt"
 echo "org.apache.commons.lang3.LocaleUtils" > "$instrument_classes"
 
 defects4j mutation -w "$pid_bid_dir" -i "$instrument_classes" || die "Mutation analysis (instrument LocaleUtils) failed!"
-
-# The last row of 'summary.csv' does not have an end of line character.
-# Otherwise, using wc would be more intuitive.
-num_rows=$(grep -c "^" "$summary_file")
-[ "$num_rows" -eq "2" ] || die "Unexpected number of lines in '$summary_file'!"
-
-# Columns of summary (csv) file:
-# MutantsGenerated,MutantsCovered,MutantsKilled,MutantsLive,RuntimePreprocSeconds,RuntimeAnalysisSeconds
-num_mutants_generated=$(tail -n1 "$summary_file" | cut -f1 -d',')
-num_mutants_covered=$(tail -n1 "$summary_file" | cut -f2 -d',')
-num_mutants_killed=$(tail -n1 "$summary_file" | cut -f3 -d',')
-
-[ "$num_mutants_generated" -eq 184 ] || die "$num_mutants_generated mutants have been generated!"
-[ "$num_mutants_covered" -eq 184 ] || die "$num_mutants_covered mutants have been covered!"
-[ "$num_mutants_killed" -eq 158 ] || die "$num_mutants_killed mutants have been killed!"
+_check_mutation_result 184 184 158
 
 # Clean up
 rm -rf "$pid_bid_dir"

From 5c9f37fad3aff5822627f767f43d04a075edc047 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 01:25:59 -0400
Subject: [PATCH 03/13] Updated documentation of Project module.

---
 framework/core/Project.pm | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index 7384a974c..65b7371e8 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -83,6 +83,10 @@ Commons lang (L<Vcs::Git> backend)
 
 Commons math (L<Vcs::Git> backend)
 
+=item * L<Mockito|Project::Mockito>
+
+Mockito (L<Vcs::Git> backend)
+
 =item * L<Time|Project::Time>
 
 Joda-time (L<Vcs::Git> backend)

From 3e9d1172a28f4f6f009623dcb9a0f3e1c1d476d8 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:13:45 -0400
Subject: [PATCH 04/13] Added a util function for splitting a file path into
 directory + filename.

---
 framework/core/Utils.pm | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/framework/core/Utils.pm b/framework/core/Utils.pm
index bea463641..916d54cb7 100644
--- a/framework/core/Utils.pm
+++ b/framework/core/Utils.pm
@@ -37,6 +37,7 @@ use warnings;
 use strict;
 
 use File::Basename;
+use File::Spec;
 use Cwd qw(abs_path);
 use Carp qw(confess);
 
@@ -77,6 +78,20 @@ sub get_abs_path {
     return abs_path($dir);
 }
 
+=pod
+
+  Utils::get_dir(file)
+
+Returns the directory of the absolute path of F<file>.
+
+=cut
+sub get_dir {
+    @_ == 1 or die $ARG_ERROR;
+    my $path = shift;
+    my ($volume,$dir,$file) = File::Spec->splitpath($path);
+    return get_abs_path($dir);
+}
+
 =pod
 
   Utils::get_failing_tests(test_result_file)

From 50b04331fff9a7250992a67d6ba1d1895d441ca8 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:14:41 -0400
Subject: [PATCH 05/13] Avoid warning in test script.

---
 framework/test/test_mutation_analysis.sh | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/framework/test/test_mutation_analysis.sh b/framework/test/test_mutation_analysis.sh
index 3ace886c0..f88db363a 100755
--- a/framework/test/test_mutation_analysis.sh
+++ b/framework/test/test_mutation_analysis.sh
@@ -67,7 +67,7 @@ defects4j checkout -p "$pid" -v "$bid" -w "$pid_bid_dir" || die "It was not poss
 # Test mutation analysis without excluding any mutants
 
 # Remove the summary file to ensure it is regenerated
-rm "$summary_file"
+rm -f "$summary_file"
 
 defects4j mutation -w "$pid_bid_dir" -r || die "Mutation analysis (including all mutants) failed!"
 _check_mutation_result 941 913 646
@@ -76,7 +76,7 @@ _check_mutation_result 941 913 646
 # Test mutation analysis when excluding all mutants
 
 # Remove the summary file to ensure it is regenerated
-rm "$summary_file"
+rm -f "$summary_file"
 
 # Exclude all generated mutants
 exclude_file="$pid_bid_dir/exclude_all_mutants.txt"
@@ -89,7 +89,7 @@ _check_mutation_result 941 0 0
 # Test mutation analysis when explicitly providing the class(es) to mutate
 
 # Remove the summary file to ensure it is regenerated
-rm "$summary_file"
+rm -f "$summary_file"
 
 # Mutate an arbitrary, non-modified class
 instrument_classes="$pid_bid_dir/instrument_classes.txt"

From c09c767f98b0f97d8ce20878340a1bf0998cb8b4 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:15:46 -0400
Subject: [PATCH 06/13] Added create_mml to Mutation module.

---
 framework/core/Mutation.pm | 43 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/framework/core/Mutation.pm b/framework/core/Mutation.pm
index 3b3d095c2..6cbf17c3c 100644
--- a/framework/core/Mutation.pm
+++ b/framework/core/Mutation.pm
@@ -54,6 +54,49 @@ my $SUMMARY_FILE = "summary.csv";
 
 =head2 Static subroutines
 
+  Mutation::create_mml(project_ref, instrument_classes, out_dir, mml_file)
+
+Generates an mml file, enabling all mutation operators for all classes listed
+in F<instrument_classes>.
+
+=cut
+sub create_mml {
+    @_ >= 3 or die $ARG_ERROR;
+    my ($project, $instrument_classes, $out_file) = @_;
+
+    my $OUT_DIR = Utils::get_dir($out_file);
+    my $TEMPLATE = `cat $MAJOR_ROOT/mml/template.mml` or die "Cannot read mml template: $!";
+
+    # The mutation operators that should be enabled in the mml file
+    my @ops =("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
+
+    system("mkdir -p $OUT_DIR");
+
+    open(IN, $instrument_classes);
+    my @classes = <IN>;
+    close(IN);
+
+    # Generate mml file by enabling operators for listed classes only
+    open(FILE, ">$out_file") or die "Cannot write mml file ($out_file): $!";
+    # Add operator definitions from template
+    print FILE $TEMPLATE;
+    # Enable operators for all classes
+    foreach my $class (@classes) {
+        chomp $class;
+        print FILE "\n// Enable operators for $class\n";
+        foreach my $op (@ops) {
+            # Skip disabled operators
+            next if $TEMPLATE =~ /-$op<"$class">/;
+            print FILE "$op<\"$class\">;\n";
+        }
+    }
+    close(FILE);
+    Utils::exec_cmd("$MAJOR_ROOT/bin/mmlc $out_file 2>&1", "Compiling mutant definition (mml)")
+            or die "Cannot compile mml file: $out_file!";
+}
+
+=pod
+
   Mutation::mutation_analysis(project_ref, log_file [, exclude_file, base_map, single_test])
 
 Runs mutation analysis for the developer-written test suites of the provided

From 26d42cfce06a56e2da32eb0dd78463454cff68ba Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:24:38 -0400
Subject: [PATCH 07/13] Improved documentation.

---
 framework/core/Mutation.pm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/framework/core/Mutation.pm b/framework/core/Mutation.pm
index 6cbf17c3c..96a032cc0 100644
--- a/framework/core/Mutation.pm
+++ b/framework/core/Mutation.pm
@@ -54,14 +54,14 @@ my $SUMMARY_FILE = "summary.csv";
 
 =head2 Static subroutines
 
-  Mutation::create_mml(project_ref, instrument_classes, out_dir, mml_file)
+  Mutation::create_mml(project_ref, instrument_classes, out_file)
 
 Generates an mml file, enabling all mutation operators for all classes listed
 in F<instrument_classes>.
 
 =cut
 sub create_mml {
-    @_ >= 3 or die $ARG_ERROR;
+    @_ == 3 or die $ARG_ERROR;
     my ($project, $instrument_classes, $out_file) = @_;
 
     my $OUT_DIR = Utils::get_dir($out_file);

From cbd6c37e735fbed6501fdbeaa1b2cdd535c0eafe Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:26:24 -0400
Subject: [PATCH 08/13] Extracted common code from mutation scripts.

---
 framework/bin/d4j/d4j-mutation | 11 +----------
 framework/bin/run_mutation.pl  | 10 +---------
 framework/core/Project.pm      | 20 +++++++++++++++++---
 3 files changed, 19 insertions(+), 22 deletions(-)

diff --git a/framework/bin/d4j/d4j-mutation b/framework/bin/d4j/d4j-mutation
index 53616aa1d..3091ebd35 100644
--- a/framework/bin/d4j/d4j-mutation
+++ b/framework/bin/d4j/d4j-mutation
@@ -140,16 +140,7 @@ $project->{prog_root} = $WORK_DIR;
 # Classes to mutate -- default is all modified classes
 my $classes = $INSTRUMENT // "$SCRIPT_DIR/projects/$pid/modified_classes/$bid.src";
 
-# Create mutation definitions (mml file)
-my $mml_dir = "$WORK_DIR/mml";
-
-system("$UTIL_DIR/create_mml.pl -p $pid -c $classes -o $mml_dir -b $bid");
-my $mml_file = "$mml_dir/${bid}.mml.bin";
--e $mml_file or die "Mml file does not exist: $mml_file!";
-
-# Mutate and compile sources
-$ENV{MML} = $mml_file;
-$project->mutate() > 0 or die "Cannot mutate project!";
+$project->mutate($classes) > 0 or die "Cannot mutate project!";
 
 my $log_file = "$WORK_DIR/.mutation.log";
 # Run the test suite, according to the provided flags
diff --git a/framework/bin/run_mutation.pl b/framework/bin/run_mutation.pl
index 12eecc2fb..1adb8c8d8 100755
--- a/framework/bin/run_mutation.pl
+++ b/framework/bin/run_mutation.pl
@@ -285,15 +285,7 @@ sub _run_mutation {
       close(EXCL_FILE);
     }
 
-    # Create mutation definitions (mml file)
-    my $mml_dir = "$TMP_DIR/.mml";
-    system("$UTIL_DIR/create_mml.pl -p $PID -c $TARGET_CLASSES_DIR/$bid.src -o $mml_dir -b $bid");
-    my $mml_file = "$mml_dir/$bid.mml.bin";
-    -e $mml_file or die "Mml file does not exist: $mml_file!";
-
-    # Mutate source code
-    $ENV{MML} = $mml_file;
-    my $gen_mutants = $project->mutate();
+    my $gen_mutants = $project->mutate("$TARGET_CLASSES_DIR/$bid.src");
     $gen_mutants > 0 or die "No mutants generated for $vid!";
 
     # Compile generated tests
diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index 65b7371e8..63189efc7 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -100,6 +100,7 @@ use warnings;
 use strict;
 use Constants;
 use Utils;
+use Mutation;
 use Carp qw(confess);
 
 =pod
@@ -691,14 +692,27 @@ sub coverage_report {
 
 =pod
 
-  $project->mutate()
+  $project->mutate(instrument_classes)
 
-Mutates the checked-out program version.
+Mutates all classes listed in F<instrument_classes> in the checked-out program version.
 Returns the number of generated mutants on success, -1 otherwise.
 
 =cut
 sub mutate {
-    my $self = shift;
+    @_ == 2 or die $ARG_ERROR;
+    my ($self, $instrument_classes)  = @_;
+
+    # Create mutation definitions (mml file)
+    my $mml_src = "$self->{prog_root}/.mml/default.mml";
+    my $mml_bin = "${mml_src}.bin";
+
+    Mutation::create_mml($self, $instrument_classes, $mml_src);
+    -e "$mml_bin" or die "Mml file does not exist: $mml_bin!";
+
+    # Set environment variable MML, which is read by Major
+    $ENV{MML} = $mml_bin;
+
+    # Mutate and compile sources
     if (! $self->_ant_call("mutate")) {
         return -1;
     }

From a99d66426694e6e9da48ef4be96712ecf83d78a3 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:37:18 -0400
Subject: [PATCH 09/13] Removed unused parameter from create_mml subroutine.

---
 framework/core/Constants.pm | 6 ++++--
 framework/core/Mutation.pm  | 6 +++---
 framework/core/Project.pm   | 2 +-
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/framework/core/Constants.pm b/framework/core/Constants.pm
index e2a7b4ad2..923e3cf6a 100644
--- a/framework/core/Constants.pm
+++ b/framework/core/Constants.pm
@@ -196,8 +196,10 @@ our $CONFIG_VID = "vid";
 
 # Filename which stores build properties
 our $PROP_FILE       = "defects4j.build.properties";
-our $PROP_EXCLUDE    = "d4j.tests.exclude";
-our $PROP_INSTRUMENT = "d4j.classes.instrument";
+# Keys of stored properties
+our $PROP_EXCLUDE         = "d4j.tests.exclude";
+our $PROP_INSTRUMENT      = "d4j.classes.instrument";
+our $PROP_MUTATE          = "d4j.classes.mutate";
 our $PROP_DIR_SRC_CLASSES = "d4j.dir.src.classes";
 our $PROP_DIR_SRC_TESTS   = "d4j.dir.src.tests";
 our $PROP_CLASSES_MODIFIED= "d4j.classes.modified";
diff --git a/framework/core/Mutation.pm b/framework/core/Mutation.pm
index 96a032cc0..3eaa74ad8 100644
--- a/framework/core/Mutation.pm
+++ b/framework/core/Mutation.pm
@@ -54,15 +54,15 @@ my $SUMMARY_FILE = "summary.csv";
 
 =head2 Static subroutines
 
-  Mutation::create_mml(project_ref, instrument_classes, out_file)
+  Mutation::create_mml(instrument_classes, out_file)
 
 Generates an mml file, enabling all mutation operators for all classes listed
 in F<instrument_classes>.
 
 =cut
 sub create_mml {
-    @_ == 3 or die $ARG_ERROR;
-    my ($project, $instrument_classes, $out_file) = @_;
+    @_ == 2 or die $ARG_ERROR;
+    my ($instrument_classes, $out_file) = @_;
 
     my $OUT_DIR = Utils::get_dir($out_file);
     my $TEMPLATE = `cat $MAJOR_ROOT/mml/template.mml` or die "Cannot read mml template: $!";
diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index 63189efc7..8b0a8fbc0 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -706,7 +706,7 @@ sub mutate {
     my $mml_src = "$self->{prog_root}/.mml/default.mml";
     my $mml_bin = "${mml_src}.bin";
 
-    Mutation::create_mml($self, $instrument_classes, $mml_src);
+    Mutation::create_mml($instrument_classes, $mml_src);
     -e "$mml_bin" or die "Mml file does not exist: $mml_bin!";
 
     # Set environment variable MML, which is read by Major

From bf5a6b943be355d24eb50b42badca0e7dcdde660 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 02:37:47 -0400
Subject: [PATCH 10/13] Simplified create_mml script: use functionality
 provided in Mutation module.

---
 framework/util/create_mml.pl | 37 +++++++-----------------------------
 1 file changed, 7 insertions(+), 30 deletions(-)

diff --git a/framework/util/create_mml.pl b/framework/util/create_mml.pl
index b8bdedc50..afff475d0 100755
--- a/framework/util/create_mml.pl
+++ b/framework/util/create_mml.pl
@@ -73,6 +73,7 @@ =head1 OPTIONS
 
 use lib abs_path("$FindBin::Bin/../core");
 use Constants;
+use Mutation;
 use Utils;
 
 #
@@ -83,6 +84,7 @@ =head1 OPTIONS
 
 pod2usage(1) unless defined $cmd_opts{p} and defined $cmd_opts{c} and defined $cmd_opts{o} and defined $cmd_opts{b};
 
+# TODO: Unused parameter: PID
 my $PID = $cmd_opts{p};
 my $CLASSES = Utils::get_abs_path($cmd_opts{c});
 my $OUT_DIR = Utils::get_abs_path($cmd_opts{o});
@@ -91,33 +93,8 @@ =head1 OPTIONS
 $BID =~ /^(\d+)$/ or die "Wrong bug id format (\\d+): $BID!";
 -e $CLASSES or die "File with classes to mutate does not exist: $CLASSES";
 
-my $TEMPLATE = `cat $MAJOR_ROOT/mml/template.mml` or die "Cannot read mml template: $!";
-
-# The mutation operators that should be enabled in the mml file
-my @ops =("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
-
-system("mkdir -p $OUT_DIR");
-
-open(IN, $CLASSES);
-my @classes = <IN>;
-close(IN);
-
-my $file = "$OUT_DIR/$BID.mml";
-
-# Generate mml file by enabling operators for listed classes only
-open(FILE, ">$file") or die "Cannot write mml file ($file): $!";
-# Add operator definitions from template
-print FILE $TEMPLATE;
-# Enable operators for all classes
-foreach my $class (@classes) {
-    chomp $class;
-    print FILE "\n// Enable operators for $class\n";
-    foreach my $op (@ops) {
-        # Skip disabled operators
-        next if $TEMPLATE =~ /-$op<"$class">/;
-        print FILE "$op<\"$class\">;\n";
-    }
-}
-close(FILE);
-my $log = `$MAJOR_ROOT/bin/mmlc $file 2>&1`;
-$? == 0 or die "Cannot compile mml file: $file\n$log";
+my $mml_src = "$OUT_DIR/$BID.mml";
+my $mml_bin = "${mml_src}.bin";
+
+Mutation::create_mml($CLASSES, $mml_src);
+-e "$mml_bin" or die "Mml file does not exist: $mml_bin!";

From e4124fe015ff4ae7267adb6e01311ad656680d33 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Wed, 9 Aug 2017 03:12:03 -0400
Subject: [PATCH 11/13] Write the mutated classes to the properties file; fixes
 issue #87.

---
 framework/core/Constants.pm |  1 +
 framework/core/Project.pm   | 16 ++++++++++++++++
 2 files changed, 17 insertions(+)

diff --git a/framework/core/Constants.pm b/framework/core/Constants.pm
index 923e3cf6a..2935ba6d3 100644
--- a/framework/core/Constants.pm
+++ b/framework/core/Constants.pm
@@ -236,6 +236,7 @@ $CONFIG_VID
 $PROP_FILE
 $PROP_EXCLUDE
 $PROP_INSTRUMENT
+$PROP_MUTATE
 $PROP_DIR_SRC_CLASSES
 $PROP_DIR_SRC_TESTS
 $PROP_CLASSES_MODIFIED
diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index 8b0a8fbc0..ac76c1d2d 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -701,6 +701,22 @@ Returns the number of generated mutants on success, -1 otherwise.
 sub mutate {
     @_ == 2 or die $ARG_ERROR;
     my ($self, $instrument_classes)  = @_;
+    my $work_dir = $self->{prog_root};
+
+    # Read all classes that should be mutated
+    -e $instrument_classes or die "Classes file ($instrument_classes) does not exist!";
+    open(IN, "<$instrument_classes") or die "Cannot read $instrument_classes";
+    my @classes = ();
+    while(<IN>) {
+        s/\r?\n//;
+        push(@classes, $_);
+    }
+    close(IN);
+    # Update properties
+    my $list = join(",", @classes);
+    my $config = {$PROP_MUTATE => $list};
+    Utils::write_config_file("$work_dir/$PROP_FILE", $config);
+
 
     # Create mutation definitions (mml file)
     my $mml_src = "$self->{prog_root}/.mml/default.mml";

From dcb7e46af53d63b5ac3139ac14704e11281d0c7c Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Fri, 11 Aug 2017 09:44:31 -0400
Subject: [PATCH 12/13] Removed unnecessary empty line.

---
 framework/core/Project.pm | 1 -
 1 file changed, 1 deletion(-)

diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index ac76c1d2d..679d8554b 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -717,7 +717,6 @@ sub mutate {
     my $config = {$PROP_MUTATE => $list};
     Utils::write_config_file("$work_dir/$PROP_FILE", $config);
 
-
     # Create mutation definitions (mml file)
     my $mml_src = "$self->{prog_root}/.mml/default.mml";
     my $mml_bin = "${mml_src}.bin";

From aa6955bd6bab25f14a259c15b206ed8bdc36e418 Mon Sep 17 00:00:00 2001
From: rjust <rjust.dev@gmail.com>
Date: Sat, 12 Aug 2017 13:03:27 -0400
Subject: [PATCH 13/13] Made the set of mutation operators a parameter in the
 core modules; they are currently hard-coded in the mutation scripts, though.

---
 framework/bin/d4j/d4j-mutation |  5 ++++-
 framework/bin/run_mutation.pl  |  5 ++++-
 framework/core/Mutation.pm     | 17 ++++++++---------
 framework/core/Project.pm      | 11 ++++++-----
 framework/util/create_mml.pl   |  5 ++++-
 5 files changed, 26 insertions(+), 17 deletions(-)

diff --git a/framework/bin/d4j/d4j-mutation b/framework/bin/d4j/d4j-mutation
index 3091ebd35..149b8b343 100644
--- a/framework/bin/d4j/d4j-mutation
+++ b/framework/bin/d4j/d4j-mutation
@@ -133,6 +133,9 @@ if ($type eq "b") {
     exit 1;
 }
 
+# The mutation operators that should be enabled
+my @MUT_OPS = ("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
+
 # Instantiate project and set working directory
 my $project = Project::create_project($pid);
 $project->{prog_root} = $WORK_DIR;
@@ -140,7 +143,7 @@ $project->{prog_root} = $WORK_DIR;
 # Classes to mutate -- default is all modified classes
 my $classes = $INSTRUMENT // "$SCRIPT_DIR/projects/$pid/modified_classes/$bid.src";
 
-$project->mutate($classes) > 0 or die "Cannot mutate project!";
+$project->mutate($classes, \@MUT_OPS) > 0 or die "Cannot mutate project!";
 
 my $log_file = "$WORK_DIR/.mutation.log";
 # Run the test suite, according to the provided flags
diff --git a/framework/bin/run_mutation.pl b/framework/bin/run_mutation.pl
index 1adb8c8d8..548ca6db6 100755
--- a/framework/bin/run_mutation.pl
+++ b/framework/bin/run_mutation.pl
@@ -131,6 +131,9 @@ =head1 DESCRIPTION
 # Enable debugging if flag is set
 $DEBUG = 1 if defined $cmd_opts{D};
 
+# The mutation operators that should be enabled
+my @MUT_OPS = ("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
+
 # Set up project
 my $project = Project::create_project($PID);
 
@@ -285,7 +288,7 @@ sub _run_mutation {
       close(EXCL_FILE);
     }
 
-    my $gen_mutants = $project->mutate("$TARGET_CLASSES_DIR/$bid.src");
+    my $gen_mutants = $project->mutate("$TARGET_CLASSES_DIR/$bid.src", \@MUT_OPS);
     $gen_mutants > 0 or die "No mutants generated for $vid!";
 
     # Compile generated tests
diff --git a/framework/core/Mutation.pm b/framework/core/Mutation.pm
index 3eaa74ad8..c77c88026 100644
--- a/framework/core/Mutation.pm
+++ b/framework/core/Mutation.pm
@@ -54,22 +54,21 @@ my $SUMMARY_FILE = "summary.csv";
 
 =head2 Static subroutines
 
-  Mutation::create_mml(instrument_classes, out_file)
+  Mutation::create_mml(instrument_classes, out_file, mut_ops)
 
-Generates an mml file, enabling all mutation operators for all classes listed
-in F<instrument_classes>.
+Generates an mml file, enabling all mutation operators defined by the array
+reference C<mut_ops> for all classes listed in F<instrument_classes>. The mml
+(source) file is written to C<out_file>. This subroutine also compiles the mml
+file to F<'out_file'.bin>.
 
 =cut
 sub create_mml {
-    @_ == 2 or die $ARG_ERROR;
-    my ($instrument_classes, $out_file) = @_;
+    @_ == 3 or die $ARG_ERROR;
+    my ($instrument_classes, $out_file, $mut_ops) = @_;
 
     my $OUT_DIR = Utils::get_dir($out_file);
     my $TEMPLATE = `cat $MAJOR_ROOT/mml/template.mml` or die "Cannot read mml template: $!";
 
-    # The mutation operators that should be enabled in the mml file
-    my @ops =("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
-
     system("mkdir -p $OUT_DIR");
 
     open(IN, $instrument_classes);
@@ -84,7 +83,7 @@ sub create_mml {
     foreach my $class (@classes) {
         chomp $class;
         print FILE "\n// Enable operators for $class\n";
-        foreach my $op (@ops) {
+        foreach my $op (@{$mut_ops}) {
             # Skip disabled operators
             next if $TEMPLATE =~ /-$op<"$class">/;
             print FILE "$op<\"$class\">;\n";
diff --git a/framework/core/Project.pm b/framework/core/Project.pm
index 679d8554b..cc3e6bb22 100644
--- a/framework/core/Project.pm
+++ b/framework/core/Project.pm
@@ -692,15 +692,16 @@ sub coverage_report {
 
 =pod
 
-  $project->mutate(instrument_classes)
+  $project->mutate(instrument_classes, mut_ops)
 
-Mutates all classes listed in F<instrument_classes> in the checked-out program version.
+Mutates all classes listed in F<instrument_classes>, using all mutation operators
+defined by the array reference C<mut_ops>, in the checked-out program version.
 Returns the number of generated mutants on success, -1 otherwise.
 
 =cut
 sub mutate {
-    @_ == 2 or die $ARG_ERROR;
-    my ($self, $instrument_classes)  = @_;
+    @_ == 3 or die $ARG_ERROR;
+    my ($self, $instrument_classes, $mut_ops)  = @_;
     my $work_dir = $self->{prog_root};
 
     # Read all classes that should be mutated
@@ -721,7 +722,7 @@ sub mutate {
     my $mml_src = "$self->{prog_root}/.mml/default.mml";
     my $mml_bin = "${mml_src}.bin";
 
-    Mutation::create_mml($instrument_classes, $mml_src);
+    Mutation::create_mml($instrument_classes, $mml_src, $mut_ops);
     -e "$mml_bin" or die "Mml file does not exist: $mml_bin!";
 
     # Set environment variable MML, which is read by Major
diff --git a/framework/util/create_mml.pl b/framework/util/create_mml.pl
index afff475d0..5b02b7256 100755
--- a/framework/util/create_mml.pl
+++ b/framework/util/create_mml.pl
@@ -93,8 +93,11 @@ =head1 OPTIONS
 $BID =~ /^(\d+)$/ or die "Wrong bug id format (\\d+): $BID!";
 -e $CLASSES or die "File with classes to mutate does not exist: $CLASSES";
 
+# The mutation operators that should be enabled
+my @MU_OPS = ("AOR", "LOR","SOR", "COR", "ROR", "ORU", "LVR", "STD");
+
 my $mml_src = "$OUT_DIR/$BID.mml";
 my $mml_bin = "${mml_src}.bin";
 
-Mutation::create_mml($CLASSES, $mml_src);
+Mutation::create_mml($CLASSES, $mml_src, \@MUT_OPS);
 -e "$mml_bin" or die "Mml file does not exist: $mml_bin!";