Skip to content
Bug Report driven Program Repair
Perl Python Shell Java
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
OUTPUT/MIMIC/FixedBugs
code
data
defects4j
docs
.gitignore
INSTALL.md
LICENSE.txt
README.md
STATUS.md
brCommiter.pickle
bugIDList.pickle
cloner.sh
compileProjects.sh
config.yml
createProjects.sh
environment.yml
localizationPerformanceStatements
main.pdf
startPy.sh
testProject.sh
testProjects.sh

README.md

DOI

IFixR

I. Introduction

IFixR a patch generation system for user-reported bugs

The workflow of this technique.\label{workflow}

II. Environment

Manual installation

  • OS: macOS Mojave (10.14.3)
  • JDK7: Oracle jdk1.7 (important!)
  • JDK8: Oracle jdk1.8 (important!)
  • Defects4J: Clone and configure defects4j from its original repository
    git clone https://github.com/rjust/defects4j
    cd defects4j
    ./init.sh
    
    export PATH=$PATH:"path2defects4j"/framework/bin
    
    Please add defects4j also to path since compileProjects.sh,createProjects.sh,testProjects.sh uses defects4j
  • Download and configure Anaconda
  • Create an python environment using the environment file
    conda env create -f environment.yml

Before running

  • Update config file with corresponding user paths.
    Defects4J home path requires '/' at the end
    Example: /Users/projects/defects4j/

Docker

  • Clone the repository

  • Pull image from docker hub

    docker pull anilkoyuncu/ifixr
  • Run the docker image sharing the repository folder

    docker run -v <path_of_cloned_repository>/:/data -it anilkoyuncu/ifixr:latest /bin/bash
  • Change folder to /data

  • Follow Step III to run

III. How to run

  • Launch startPy as follows:

    bash startPy.sh [OPTIONS]

Running Options

IFixR needs three input options for running.

Usage: bash startPy.sh $1 $2 $3
where $1 is root
      $2 is job
      $3 is subject
  • root : The full path of directory where startPy.sh is located (corresponds to pwd in the examples below)

  • subject : the project name of buggy program of benchmark. (MATH,LANG are expected values but can be specific for job)

  • job : the name of the job in the pipeline , supports multiple steps which needs to executed in order:

    1.clone : Clone target project repository.

      Example: bash startPy.sh pwd clone MATH
      Example: bash startPy.sh pwd clone LANG

    2.collect : Collect all commit from repository.

      Example: bash startPy.sh pwd collect MATH
      Example: bash startPy.sh pwd collect LANG

    3.fix : Collect commits linked to a bug report.

      Example: bash startPy.sh pwd fix MATH
      Example: bash startPy.sh pwd fix LANG

    4.bugPoints : Identify the snapshot of the repository before the bug fixing commit introduced.

      Example: bash startPy.sh pwd bugPoints MATH
      Example: bash startPy.sh pwd bugPoints LANG

    5.brDownload : Download bug reports recovered from commit log

      Example: bash startPy.sh pwd brDownload MATH
      Example: bash startPy.sh pwd brDownload LANG

    6.brParser : Parse bug reports to select the bug report where type labeled as BUG and status as RESOLVED or CLOSED

      Example: bash startPy.sh pwd brParser MATH
      Example: bash startPy.sh pwd brParser LANG

    7.brFeatures : Extract bug report features

      Example: bash startPy.sh pwd brFeatures MATH
      Example: bash startPy.sh pwd brFeatures LANG

    8.verify : Extract source code features

      Example: bash startPy.sh pwd verify MATH
      Example: bash startPy.sh pwd verify LANG

    9.simi : Compute the similarity between bug reports and source code features

      Example: bash startPy.sh pwd simi MATH
      Example: bash startPy.sh pwd simi LANG

    10.features : Compute the features from similarity scores

      Example: bash startPy.sh pwd features MATH
      Example: bash startPy.sh pwd features LANG

    11.predict : Predict file level bug localization

      Example: bash startPy.sh pwd predict ALL

    12.eval : Retrieve predictions for all bug reports and suspiciousness scores of files.

      Example: bash startPy.sh pwd eval ALL

    13.stmt : Compute statement level bug localization

      Example: bash startPy.sh pwd stmt ALL (!!! Clones all defects4j bugs and compile, may take significant amount of time)

    14.gv : Execute generate-validation step to produce patch candidates.

      Execute generate-validation step on a single defects4j bug (eg Lang_15, Math_34 case sensitive)
      
        Example: bash startPy.sh pwd gv Math_34
      
      Execute generate-validation step on all dataset. (!!! Takes significant amount of time !!!)
      
        Example: bash startPy.sh pwd gv ALL

    Generated patches are placed in directory OUTPUT

Data Viewer

The data provided with replication package is listed in directory data The data is stored in different formats. (e.g. pickle, db, csv, etc..)

The see content of the .pickle file the following script could be used.

 import pickle as p
 import gzip
 def load_zipped_pickle(filename):
    with gzip.open(filename, 'rb') as f:
        loaded_object = p.load(f)
        return loaded_object

Usage

result = load_zipped_pickle('code/LANGbugReportsComplete.pickle')
# Result is pandas object which can be exported to several formats
# Details on how to export is listed in offical library documentation
# https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html

IV. Evaluation Result

APR tool Lang Math Total
jGenProg 0/0 5/18 5/18
jKali 0/0 1/14 1/14
jMutRepair 0/1 2/11 2/12
HDRepair 2/6 4/7 6/13
Nopol 3/7 1/21 4/28
ACS 3/4 12/16 15/20
ELIXIR 8/12 12/19 20/31
JAID 1/8 1/8 2/16
ssFix 5/12 10/26 15/38
CapGen 5/5 12/16 17/21
SketchFix 3/4 7/8 10/12
FixMiner 2/3 12/14 14/17
LSRepair 8/14 7/14 15/28
SimFix 9/13 14/26 23/39
kPAR 1/8 7/18 8/26
AVATAR 5/11 6/13 11/24
MIMIC_opt 11/19 10/25 21/44
MIMIC_all 6/11 7/16 13/27
MIMIC_top5 3/7 5/6 8/13

V. Generated Patches

MIMIC generates genuine/ plausible patches for 21/44 Defects4J bugs with its IR-based bug localizer.

Patches Genuineness
Lang_6 Correct
Lang_7 Correct
Lang_10 Correct
Lang_13 Plausible
Lang_18 Plausible
Lang_21 Plausible
Lang_22 Correct
Lang_24 Correct
Lang_26 Correct
Lang_33 Correct
Lang_39 Correct
Lang_43 Plausible
Lang_44 Plausible
Lang_45 Plausible
Lang_47 Correct
Lang_57 Correct
Lang_58 Plausible
Lang_59 Correct
Lang_63 Plausible
Math_2 Plausible
Math_5 Correct
Math_8 Plausible
Math_11 Correct
Math_15 Correct
Math_20 Plausible
Math_28 Plausible
Math_32 Plausible
Math_34 Correct
Math_35 Correct
Math_42 Plausible
Math_52 Plausible
Math_57 Correct
Math_58 Plausible
Math_59 Correct
Math_63 Plausible
Math_64 Plausible
Math_65 Correct
Math_70 Correct
Math_75 Correct
Math_82 Plausible
Math_95 Plausible
Math_96 Plausible
Math_97 Plausible
Math_104 Plausible

VI. Structure of the project

  |--- README.md                    :  user guidance
  |--- code                         :  code
  |--- data                         :  replication data
  |--- doc                          :  document
  |--- OUTPUT/MIMIC/FixedBugs       :  generated patches

You can’t perform that action at this time.