Addition of 11 new projects to Defects4J

.travis.yml

@@ -53,6 +53,9 @@ jobs:
 ## Chart
       script: carton exec ./test_verify_bugs.sh -p Chart
       name: "Chart"
+## Cli
+    - script: carton exec ./test_verify_bugs.sh -p Cli
+      name: "Cli"
 ## Closure
     - script: carton exec ./test_verify_bugs.sh -p Closure -b1..10
       name: "Closure 1-10"
@@ -92,11 +95,59 @@ jobs:
       name: "Closure 161-169"
     - script: carton exec ./test_verify_bugs.sh -p Closure -b170..176
       name: "Closure 170-176"
+## Codec
+    - script: carton exec ./test_verify_bugs.sh -p Codec -b1..18
+      name: "Codec"
+## Collections
+    - script: carton exec ./test_verify_bugs.sh -p Collections -b25..28
+      name: "Collections"
+## Compress
+    - script: carton exec ./test_verify_bugs.sh -p Compress
+      name: "Compress"
+## Csv
+    - script: carton exec ./test_verify_bugs.sh -p Csv -b1..16
+      name: "Csv"
+## Gson
+    - script: carton exec ./test_verify_bugs.sh -p Gson -b1..18
+      name: "Gson"
+## JacksonCore
+    - script: carton exec ./test_verify_bugs.sh -p JacksonCore
+      name: "JacksonCore"
+## JacksonDatabind
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b1..14
+      name: "JacksonDatabind 1-14"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b15..28
+      name: "JacksonDatabind 15-28"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b29..43
+      name: "JacksonDatabind 29-43"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b44..57
+      name: "JacksonDatabind 44-57"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b58..67
+      name: "JacksonDatabind 58-67"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b68..76
+      name: "JacksonDatabind 68-76"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b77..86
+      name: "JacksonDatabind 77-86"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b87..96
+      name: "JacksonDatabind 87-96"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b97..104
+      name: "JacksonDatabind 97-104"
+    - script: carton exec ./test_verify_bugs.sh -p JacksonDatabind -b105..112
+      name: "JacksonDatabind 105-112"
+## JacksonXml
+    - script: carton exec ./test_verify_bugs.sh -p JacksonXml -b1..6
+      name: "JacksonXml"
+## Jsoup
+    - script: carton exec ./test_verify_bugs.sh -p Jsoup -b1..50
+      name: "Jsoup 1-50"
+    - script: carton exec ./test_verify_bugs.sh -p Jsoup -b51..93
+      name: "Jsoup 51-93"
+## JxPath
+    - script: carton exec ./test_verify_bugs.sh -p JxPath
+      name: "JxPath"
 ## Lang
-    - script: carton exec ./test_verify_bugs.sh -p Lang -b1..32
-      name: "Lang 1-32"
-    - script: carton exec ./test_verify_bugs.sh -p Lang -b33..65
-      name: "Lang 33-65"
+    - script: carton exec ./test_verify_bugs.sh -p Lang
+      name: "Lang"
 ## Math
     - script: carton exec ./test_verify_bugs.sh -p Math -b1..18
       name: "Math 1-18"

README.md

@@ -1,4 +1,4 @@
-Defects4J -- version 1.5.0 [![Build Status](https://travis-ci.org/rjust/defects4j.svg?branch=master)](https://travis-ci.org/rjust/defects4j)
+Defects4J -- version 2.0.0 [![Build Status](https://travis-ci.org/rjust/defects4j.svg?branch=master)](https://travis-ci.org/rjust/defects4j)
 ================
 Defects4J is a collection of reproducible bugs and a supporting infrastructure
 with the goal of advancing software engineering research.
@@ -8,16 +8,27 @@ Contents of Defects4J
 
 The projects
 ---------------
-Defects4J contains 438 bugs from the following open-source projects:
-
-| Identifier | Project name         | Number of bugs |
-|------------|----------------------|----------------|
-| Chart      | JFreeChart           |  26            |
-| Closure    | Closure compiler     | 176            |
-| Lang       | Apache commons-lang  |  65            |
-| Math       | Apache commons-math  | 106            |
-| Mockito    | Mockito              |  38            |
-| Time       | Joda-Time            |  27            |
+Defects4J contains 835 bugs from the following open-source projects:
+
+| Identifier      | Project name               | Number of bugs |
+|-----------------|----------------------------|---------------:|
+| Chart           | jfreechart                 |       26       |
+| Cli             | commons-cli                |       39       |
+| Closure         | closure-compiler           |      174       |
+| Codec           | commons-codec              |       18       |
+| Collections     | commons-collections        |        4       |
+| Compress        | commons-compress           |       47       |
+| Csv             | commons-csv                |       16       |
+| Gson            | gson                       |       18       |
+| JacksonCore     | jackson-core               |       26       |
+| JacksonDatabind | jackson-databind           |      112       |
+| JacksonXml      | jackson-dataformat-xml     |        6       |
+| Jsoup           | jsoup                      |       93       |
+| JxPath          | commons-jxpath             |       22       |
+| Lang            | commons-lang               |       64       |
+| Math            | commons-math               |      106       |
+| Mockito         | mockito                    |       38       |
+| Time            | joda-time                  |       26       |
 
 The bugs
 ---------------
@@ -36,53 +47,22 @@ Each bug has the following properties:
 The (b)uggy and (f)ixed program revisions are labelled with `<id>b` and
 `<id>f`, respectively (`<id>` is an integer).
 
-Looking for additional bugs?
------------------------------
-A number of additional bugs are available in "work-in-progress" status.
-These bugs meet the same properties as the ones above, but have only been
-minimized by one of the maintainers. Metadata and patch content can 
-potentially change before these bugs are migrated into the master repository. 
-These bugs may be used in experiments, but should not be considered as 
-"stable" as the bugs in the master repository. If you use these bugs, please 
-acknowledge their "beta status" in any publications.
-
-**Branch [commons-compress-collections](https://github.com/rjust/defects4j/tree/commons-compress-collections):**
-
-| Identifier | Project name               | Number of bugs |
-|------------|----------------------------|----------------|
-| Collections| Apache commons-collections |  28            |
-| Compress   | Apache commons-compress    |  47            |
-
-**Branch [additional-projects-4](https://github.com/rjust/defects4j/tree/additional-projects-4):**
-
-| Identifier      | Project name           | Number of bugs |
-|-----------------|------------------------|----------------|
-| Cli             | Apache commons-cli     |  40            |
-| Codec           | Apache commons-codec   |  18            |
-| Csv             | Apache commons-csv     |  16            |
-| Gson            | Google Gson            |  18            |
-| JacksonCore     | Jackson JSON parser    |  26            |
-| JacksonDatabind | Jackson data bindings  | 112            |
-| JacksonXml      | Jackson XML extension  |   6            |
-| JxPath          | Apache commons-jxpath  |  22            |
-| Jsoup           | jsoup HTML Parser      |  93            |
 
 Setting up Defects4J
 ================
 
 Requirements
 ----------------
- - Java 1.7 (see below)
+ - Java 1.8 (version 1.5.0 and older requires Java 1.7)
  - Git >= 1.9
  - SVN >= 1.8
  - Perl >= 5.0.12
 
 #### Java version
-
-* `master` branch requires Java 8.
-* `version 2.0.0`: will require Java 8.
-* `version 1.5.0` and lower: requires Java 1.7 
-
+All bugs have been reproduced and triggering tests verified, using the latest
+version of Java 1.8.
+Note that using Java 1.9+ might result in unexpected failing tests on a fixed
+program version. 
 
 #### Perl dependencies
 All required Perl modules are listed in `cpanfile`. On many Unix platforms,

framework/bug-mining/analyze-project.pl

@@ -263,7 +263,25 @@ sub _check_t2v2 {
 
         # Run t2 and get number of failing tests
         my $file = "$project->{prog_root}/v2.fail"; `>$file`;
+
         $project->run_tests($file) or die;
+
+        # Filter out invalid test names, such as testEncode[0].
+        # This problem impacts many Commons projects.
+        if(-e "$project->{prog_root}/v2.fail"){
+            rename("$project->{prog_root}/v2.fail", "$project->{prog_root}/v2.fail".'.bak');
+            open(IN, '<'."$project->{prog_root}/v2.fail".'.bak') or die $!;
+            open(OUT, '>'."$project->{prog_root}/v2.fail") or die $!;
+            while(<IN>) {
+                if($_ =~ /\-\-\-/){
+                    $_ =~ s/\[[0-9]\]//g;
+                }
+                print OUT $_;
+            }
+            close(IN);
+            close(OUT);
+        }
+
         # Get number of failing tests
         my $list = Utils::get_failing_tests($file);
         my $fail = scalar(@{$list->{"classes"}}) + scalar(@{$list->{"methods"}});

framework/bug-mining/download-issues.pl

@@ -61,8 +61,8 @@ =head1 OPTIONS
 
 =item B<-q C<query>>
 
-The query sent to the issue tracker. Suitable defaults for supported trackers
-are chosen so they identify only bugs.
+The query (i.e., filter for bug type or label) sent to the issue tracker.
+Suitable defaults for supported trackers are chosen so they identify only bugs.
 
 =item B<-u C<tracker-uri>>
 

framework/bug-mining/get-trigger.pl

@@ -213,10 +213,24 @@ =head1 DESCRIPTION
     }
 
     # Save dependent tests to $DEP_TEST_FILE
+
+    # Get contents of current dependent tests file
+    my @old_dep_tests;
+
+    if (-e $DEP_TEST_FILE){
+        open my $contents, '<', $DEP_TEST_FILE or die "Cannot open dependent tests file: $!\n";
+        my @old_dep_tests = <$contents>;
+        close $contents;    
+    }
+
     my @dependent_tests = grep { !($_ ~~  @{$list}) } @fail_in_order;
     for my $dependent_test (@dependent_tests) {
-        print " ## Warning: Dependent test ($dependent_test) is being added to list.\n";
-        system("echo '--- $dependent_test' >> $DEP_TEST_FILE");
+        # Add the test unless it is already in the list.
+        unless ($dependent_test ~~ @old_dep_tests) {
+            print " ## Warning: Dependent test ($dependent_test) is being added to list.\n";
+            system("echo '--- $dependent_test' >> $DEP_TEST_FILE");
+            push @old_dep_tests, $dependent_test;
+        }
     }
 
     # Add data

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

@@ -72,8 +72,8 @@ =head1 OPTIONS
 
 =item B<-q C<query>>
 
-The query sent to the issue tracker. Suitable defaults for supported trackers
-are chosen so they identify only bugs.
+The query (i.e., filter for bug type or label) sent to the issue tracker.
+Suitable defaults for supported trackers are chosen so they identify only bugs.
 
 =item B<-u C<tracker-uri>>
 
@@ -125,7 +125,7 @@ =head1 OPTIONS
 my $ISSUES_DIR = "$WORK_DIR/issues";
 my $ISSUES_FILE = "$WORK_DIR/issues.txt";
 my $ORGANIZATION_ID = $cmd_opts{z};
-my $QUERY = $cmd_opts{q} // "labels=Bug";
+my $QUERY = $cmd_opts{q};
 my $TRACKER_URI = $cmd_opts{u};
 my $FETCHING_LIMIT = $cmd_opts{l};
 
@@ -151,12 +151,17 @@ =head1 OPTIONS
     system("cp $PROJECTS_DIR/$PID/$PID.build.xml $WORK_DIR/framework/projects/$PID/$PID.build.xml");
 }
 
+if (defined($QUERY)) {
+    $QUERY = "-q $QUERY";
+} else {
+    $QUERY = "";
+}
 # Collect all issues from the project issue tracker
 Utils::exec_cmd("./download-issues.pl -g $ISSUE_TRACKER_NAME"
                                   . " -t $ISSUE_TRACKER_PROJECT_ID"
                                   . " -o $ISSUES_DIR"
                                   . " -f $ISSUES_FILE"
-                                  . " -q $QUERY",
+                                  . "$QUERY",
                 "Collecting all issues from the project issue tracker") or die "Cannot collect all issues from the project issue tracker!";
 
 # Collect git log

framework/bug-mining/initialize-revisions.pl

@@ -31,7 +31,7 @@ =head1 NAME
 
 =head1 SYNOPSIS
 
-initialize-revisions.pl -p project_id -w work_dir [ -b bug_id]
+initialize-revisions.pl -p project_id -w work_dir [-s subproject] [ -b bug_id] 
 
 =head1 OPTIONS
 
@@ -45,6 +45,10 @@ =head1 OPTIONS
 
 The working directory used for the bug-mining process.
 
+=item B<-s F<subproject>>
+
+The subproject to be mined (if not the root directory)
+
 =item B<-b C<bug_id>>
 
 Only analyze this bug id. The bug_id has to follow the format B<(\d+)(:(\d+))?>.
@@ -67,13 +71,14 @@ =head1 OPTIONS
 use Utils;
 
 my %cmd_opts;
-getopts('p:b:w:', \%cmd_opts) or pod2usage(1);
+getopts('p:b:w:s:', \%cmd_opts) or pod2usage(1);
 
 pod2usage(1) unless defined $cmd_opts{p} and defined $cmd_opts{w};
 
 my $PID = $cmd_opts{p};
 my $BID = $cmd_opts{b};
 my $WORK_DIR = abs_path($cmd_opts{w});
+my $SUBPROJ = $cmd_opts{s};
 
 # Check format of target bug id
 if (defined $BID) {
@@ -120,6 +125,11 @@ sub _init_version {
     # minimized patch to obtain the buggy version.
     $project->{_vcs}->checkout_vid("${vid}", $work_dir) or die "Cannot checkout $vid version";
 
+    if (defined $SUBPROJ) {
+        $work_dir .= "/$SUBPROJ/";
+        $project->{prog_root} = $work_dir;
+    }
+
     system("mkdir -p $ANALYZER_OUTPUT/$bid");
     if (-e "$work_dir/build.xml") {
         my $cmd = " cd $work_dir" .
@@ -128,7 +138,7 @@ sub _init_version {
     } elsif (-e "$work_dir/pom.xml") {
         # Run maven-ant plugin and overwrite the original build.xml whenever a maven build file exists
         my $cmd = " cd $work_dir" .
-                  " && mvn ant:ant -Doverwrite=true 2>&1" .
+                  " && mvn ant:ant -Doverwrite=true 2>&1 -Dhttps.protocols=TLSv1.2" .
                   " && patch build.xml $PROJECT_DIR/build.xml.patch 2>&1" .
                   " && rm -rf $GEN_BUILDFILE_DIR/$rev_id && mkdir -p $GEN_BUILDFILE_DIR/$rev_id 2>&1" .
                   " && cp maven-build.* $GEN_BUILDFILE_DIR/$rev_id 2>&1" .
@@ -138,10 +148,14 @@ sub _init_version {
         $cmd = " cd $work_dir" .
                " && java -jar $LIB_DIR/analyzer.jar $work_dir $ANALYZER_OUTPUT/$bid maven-build.xml 2>&1";
         Utils::exec_cmd($cmd, "Run build-file analyzer on maven-ant.xml.") or die;
+
+        # Fix broken dependency links
+        my $fix_dep = "cd $work_dir && sed \'s\/https:\\/\\/oss\\.sonatype\\.org\\/content\\/repositories\\/snapshots\\//http:\\/\\/central\\.maven\\.org\\/maven2\\/\/g\' maven-build.xml >> temp && mv temp maven-build.xml";
+        Utils::exec_cmd($fix_dep, "Fixing broken dependency links.");
 
         # Get dependencies if it is maven-ant project
         my $download_dep = "cd $work_dir && ant -Dmaven.repo.local=\"$PROJECT_DIR/lib\" get-deps";
-        Utils::exec_cmd($download_dep, "Download dependencies for maven-ant.xml");
+        Utils::exec_cmd($download_dep, "Download dependencies for maven-ant.xml.");
     } else {
         # TODO add support for other build systems
         die "Unsupported build system";

framework/bug-mining/minimize-patch.pl

@@ -171,7 +171,7 @@ =head1 EDITOR
     # Is the list of triggering test still the same?
     my $local_trigger_tests = "$TMP_DIR/trigger_tests";
     system(">$local_trigger_tests");
-    $project->run_tests($local_trigger_tests);
+    $project->run_relevant_tests($local_trigger_tests);
 
     system("grep \"^--- \" $trigger_tests | sort > $local_trigger_tests.sorted.original");
     system("grep \"^--- \" $local_trigger_tests | sort > $local_trigger_tests.sorted.minimal");