# 在 Linux 中設定 Defects4j (以v1.2.0為例)
> 引用 Defects4J github https://github.com/rjust/defects4j
> 引用 TingWei 學長寫的 "[新的虛擬機 Defects4j 設定](https://hackmd.io/@saID5sq_QhCsFgtxP02KkA/Defects4J_Set#%E6%96%B0%E7%9A%84%E8%99%9B%E6%93%AC%E6%A9%9FDefects4j%E8%A8%AD%E5%AE%9A%E3%80%82)"

## 環境要求 (Requirements)
創建新的虛擬機後先更新。

sudo apt update
sudo apt upgrade -y

> 有些linux版本沒有unzip，需要自己下載
> `sudo apt install unzip`

### 1. 下載 Java 1.7 (僅適用 Defects4j v1.5.0 以前的版本)

因為新版ubuntu可能已經不再適用Java 7，所以透過這樣的步驟實現。
( 如果要其他已經無法下載的java版本，可從Oracle上找 )

下載 [Java 1.7.10.tar.gz](https://drive.google.com/file/d/18hfujRsl0yO7DYTcl87-32CVzA1P6bJX/view?pli=1)

> 若用到 Defects4j v2.0.0 以後，請下載 Java 1.8。
> 補充1.8的檔案 [Java 1.8.tar.gz](https://drive.google.com/file/d/1q90flX7bUSYJZdHsR589ric4lgRv_nRU/view)

建立一個存放 Java 7 的資料夾，輸入下列指令。

cd ../..
cd opt
sudo mkdir JDK

回到 Downloads 資料夾，並將剛剛下載的檔案解壓縮到建立的資料夾。

cd ~
cd Downloads
sudo tar -zxvf jdk-7u80-linux-x64.tar.gz -C /opt/JDK

設定環境變數。

sudo nano ~/.bashrc

在環境變數設定檔案最後面加上，加入完成之後Ctrl+O儲存。
(注意: 這是我存 Java 7 的資料夾位置，若存的位置不一樣要自己改。)

export JAVA_HOME=/opt/JDK/jdk1.7.0_80
export PATH=$JAVA_HOME/bin:$PATH

執行環境設定。

source ~/.bashrc

確認有成功安裝。

java -version
javac -version

### 2. 安裝 Git >= 1.9

sudo apt-get install git -y
git --version

### 3. 安裝 SVN >= 1.8

sudo apt install subversion -y
svn --version

### 4. 安裝 Perl >= 5.0.10

sudo apt install perl -y
sudo apt list --installed | grep -i perl

> 若之後實驗遇到 "Can't locate DBI.pm in @INC" 的錯誤
> 再執行以下命令以安裝 DBI 模組：
> `sudo apt-get install libdbi-perl`

### 5. 安裝 cpanminus

sudo apt-get install cpanminus -y

### 6. 安裝 curl

sudo apt install curl -y

### 7. 安裝 maven

sudo apt install maven -y

### 8. 安裝 ANT

下載 ANT 的壓縮檔案。
[ant 1.9.16](https://drive.google.com/file/d/1A-sRvJlBbAfhznxUTfsQlB4KF3jl8Gzq/view)

建立一個給ANT的資料夾。

cd ../../..
cd opt
sudo mkdir ANT

回到Downloads，並解壓縮，之後設定環境變數。

cd ~
cd Downloads
sudo tar -zxvf apache-ant-1.9.16-bin.tar.gz -C /opt/ANT/

設定環境變數。

sudo nano ~/.bashrc

在環境變數設定檔案最後面加上，加入完成之後Ctrl+O儲存。

export ANT_HOME=/opt/ANT/apache-ant-1.9.16
export PATH=$ANT_HOME/bin:$PATH

執行環境設定，並確認有安裝成功。

source ~/.bashrc
ant -version

## Getting started

### 1. 下載 Defects4J，並切換到需要的版本

git clone https://github.com/rjust/defects4j.git
cd defects4j
git checkout v1.2.0

確認切換版本成功。

git describe --tags

### 2. 初始化 Defects4J

在初始化之前，需先修改2個檔案內容(get_repos.sh 和 init.sh)。
> 因為原本的內容有些網址已被刪除，若直接按原檔案執行會出現404。

1. project_repos 資料夾中的 `get_repos.sh`
修改內容如下(可直接整個複製貼上)
:::spoiler get_repos.sh

#!/usr/bin/env bash

set -e

# The name of the archive that contains all project repos
ARCHIVE=defects4j-repos.zip

main() {
    # The BSD version of stat does not support --version or -c
    if stat --version &> /dev/null; then
        # GNU version
        cmd="stat -c %Y $ARCHIVE"
    else
        # BSD version
        cmd="stat -f %m $ARCHIVE"
    fi

    if [ -e $ARCHIVE ]; then
        old=$($cmd)
    else
        old=0
    fi
    # Only download repos if the server has a newer file
    download_url "https://defects4j.org/downloads/$ARCHIVE"

    new=$($cmd)

    # Exit if no newer file is available
    [ "$old" == "$new" ] && exit 0

    # Remove old files
    clean

    # Extract new repos
    unzip -q -u $ARCHIVE && mv defects4j/project_repos/* . && rm -r defects4j
}

clean() {
    rm -rf \
    closure-compiler.git \
    commons-lang.git \
    commons-math.git \
    jfreechart \
    joda-time.git \
    README 
}

# MacOS does not install the timeout command by default.
if [ "$(uname)" = "Darwin" ] ; then
  function timeout() { perl -e 'alarm shift; exec @ARGV' "$@"; }
fi

# Download the remote resource to a local file of the same name, if the
# remote resource is newer.  Works around connections that hang.  Takes a
# single command-line argument, a URL.
download_url() {
    BASENAME=`basename ${@: -1}`
    if [ "$(uname)" = "Darwin" ] ; then
        wget -nv -N "$@"
    else
	timeout 300 curl -s -S -R -L -O -z "$BASENAME" "$@" || (echo "retrying curl $@" && rm -f "$BASENAME" && curl -R -L -O -z "$BASENAME" "$@")
    fi
}

main

:::

2. `init.sh`
修改內容如下(可直接整個複製貼上)

:::spoiler init.sh

#!/usr/bin/env bash
#
# Exit the shell script immediately if any of the subsequent commands fails.
# immediately
set -e
#

# TODO: Major and the coverage tools should be moved to framework/lib
################################################################################
# This script initializes Defects4J. In particular, it downloads and sets up:
# - the project's version control repositories
# - the Major mutation framework
# - the supported test generation tools
# - the supported code coverage tools (TODO)
################################################################################

HOST_URL="https://defects4j.org/downloads"

# Directories for project repositories and external libraries
BASE="$(cd "$(dirname "$0")"; pwd)"
DIR_REPOS="$BASE/project_repos"
DIR_LIB_GEN="$BASE/framework/lib/test_generation/generation"
DIR_LIB_RT="$BASE/framework/lib/test_generation/runtime"
DIR_LIB_GRADLE="$BASE/framework/lib/build_systems/gradle"

################################################################################

main() {
    echo "Checking system configuration ... "
    # Check whether wget is available on OSX
    if [ "$(uname)" = "Darwin" ] ; then
        if ! wget --version > /dev/null 2>&1; then
            print_error_and_exit "Couldn't find wget to download dependencies. Please install wget and re-run this script."
        fi
    fi
    
    # Check whether curl is available
    if ! curl --version > /dev/null 2>&1; then
        print_error_and_exit "Couldn't find curl to download dependencies. Please install curl and re-run this script."
    fi
    
    # Check whether unzip is available
    if ! unzip -v > /dev/null 2>&1; then
        print_error_and_exit "Couldn't find unzip to extract dependencies. Please install unzip and re-run this script."
    fi

    # Create lib folders if necessary
    mkdir -p "$DIR_LIB_GEN" && mkdir -p "$DIR_LIB_RT" && mkdir -p "$DIR_LIB_GRADLE"

    ############################################################################
    #
    # Download project repositories if necessary
    #
    echo "Setting up project repositories ... "
    cd "$DIR_REPOS" && ./get_repos.sh

    ############################################################################
    #
    # Download Major
    #
    # Adapt Major's default wrapper scripts:
    # - set headless to true to support Chart on machines without X.
    # - do not mutate code unless an MML is specified (for historical reasons,
    #   major v1 was sometimes called without specifying an MML to simply act as
    #   javac; Major v2+'s default is to generate all mutants as opposed to none).
    #
    echo
    echo "Setting up Major ... "
    MAJOR_VERSION="3.0.1"
    MAJOR_URL="https://mutation-testing.org/downloads"
    MAJOR_ZIP="major-${MAJOR_VERSION}_jre11.zip"
    cd "$BASE" && rm -rf major \
               && download_url_and_unzip "$MAJOR_URL/$MAJOR_ZIP" \
               && rm "$MAJOR_ZIP" \
               && perl -pi -e '$_ .= qq(    -Djava.awt.headless=true \\\n) if /CodeCacheSize/' \
                    major/bin/ant \
               && perl -pi -e '$_ .= qq(\nif [ -z "\$MML" ]; then javac \$*; exit \$?; fi\n) if /^REFACTOR=/' \
                    major/bin/major \
               && perl -pi -e '$_ = qq(REFACTOR=\${REFACTOR:-"enable.decl.refactor enable.method.refactor"}\n) if /^REFACTOR=/' \
                    major/bin/major \

    ############################################################################
    #
    # Download EvoSuite
    #
    echo
    echo "Setting up EvoSuite ... "
    EVOSUITE_VERSION="0.2.0"
    EVOSUITE_URL="https://github.com/EvoSuite/evosuite/releases/download/v${EVOSUITE_VERSION}"
    EVOSUITE_JAR="evosuite-${EVOSUITE_VERSION}.jar"
    EVOSUITE_RT_JAR="evosuite-standalone-runtime-${EVOSUITE_VERSION}.jar"
    cd "$DIR_LIB_GEN" && download_url "$EVOSUITE_URL/$EVOSUITE_JAR"
    cd "$DIR_LIB_RT"  && download_url "$EVOSUITE_URL/$EVOSUITE_RT_JAR"
    # Set symlinks for the supported version of EvoSuite
    (cd "$DIR_LIB_GEN" && ln -sf "$EVOSUITE_JAR" "evosuite-current.jar")
    (cd "$DIR_LIB_RT" && ln -sf "$EVOSUITE_RT_JAR" "evosuite-rt.jar")

    ############################################################################
    #
    # Download Randoop
    #
    echo
    echo "Setting up Randoop ... "
    RANDOOP_VERSION="4.0.4"
    RANDOOP_URL="https://github.com/randoop/randoop/releases/download/v${RANDOOP_VERSION}"
    RANDOOP_ZIP="randoop-${RANDOOP_VERSION}.zip"
    RANDOOP_JAR="randoop-all-${RANDOOP_VERSION}.jar"
    REPLACECALL_JAR="replacecall-${RANDOOP_VERSION}.jar"
    COVEREDCLASS_JAR="covered-class-${RANDOOP_VERSION}.jar"
    (cd "$DIR_LIB_GEN" && download_url_and_unzip "$RANDOOP_URL/$RANDOOP_ZIP")
    # Set symlink for the supported version of Randoop
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$RANDOOP_JAR" "randoop-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$REPLACECALL_JAR" "replacecall-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$COVEREDCLASS_JAR" "covered-class-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/jacocoagent.jar" "jacocoagent.jar")

    ############################################################################
    #
    # Download build system dependencies
    #
    echo
    echo "Setting up Gradle dependencies ... "

    cd "$DIR_LIB_GRADLE"

    GRADLE_DISTS_ZIP=defects4j-gradle-dists.zip
    GRADLE_DEPS_ZIP=defects4j-gradle-deps.zip

    old_dists_ts=0
    old_deps_ts=0

    if [ -e $GRADLE_DISTS_ZIP ]; then
        old_dists_ts=$(get_modification_timestamp $GRADLE_DISTS_ZIP)
    fi
    if [ -e $GRADLE_DEPS_ZIP ]; then
        old_deps_ts=$(get_modification_timestamp $GRADLE_DEPS_ZIP)
    fi

    # Only download archive if the server has a newer file
    download_url $HOST_URL/$GRADLE_DISTS_ZIP
    download_url $HOST_URL/$GRADLE_DEPS_ZIP
    new_dists_ts=$(get_modification_timestamp $GRADLE_DISTS_ZIP)
    new_deps_ts=$(get_modification_timestamp $GRADLE_DEPS_ZIP)

    # Update gradle distributions/dependencies if a newer archive was available
    [ "$old_dists_ts" != "$new_dists_ts" ] && mkdir "dists" && unzip -q -u $GRADLE_DISTS_ZIP -d "dists"
    [ "$old_deps_ts" != "$new_deps_ts" ] && unzip -q -u $GRADLE_DEPS_ZIP

    cd "$BASE"

    ############################################################################
    #
    # Download utility programs
    #
    echo
    echo "Setting up utility programs ... "

    BUILD_ANALYZER_VERSION="0.0.1"
    BUILD_ANALYZER_JAR=build-analyzer-$BUILD_ANALYZER_VERSION.jar
    BUILD_ANALYZER_URL="https://github.com/jose/build-analyzer/releases/download/v$BUILD_ANALYZER_VERSION/$BUILD_ANALYZER_JAR"
    BUILD_ANALYZER_JAR_LOCAL="analyzer.jar"
    cd "$BASE/framework/lib" && download_url "$BUILD_ANALYZER_URL"
    rm -f "$BUILD_ANALYZER_JAR_LOCAL"
    ln -s "$BUILD_ANALYZER_JAR" "$BUILD_ANALYZER_JAR_LOCAL"

    echo
    echo "Defects4J successfully initialized."
}

################################################################################
#
# Utility functions
#

# Print an error message and terminate the script.
# Takes one argument, a custom error message.
# Prints the supplied error message and a script termination notice to stderr.
# Terminates the script with exit code 1.
print_error_and_exit() {
  echo -e "${1} \nTerminating initialization... " >&2
  exit 1
}

# MacOS does not install the timeout command by default.
if [ "$(uname)" = "Darwin" ] ; then
  function timeout() { perl -e 'alarm shift; exec @ARGV' "$@"; }
fi

# Download the remote resource to a local file of the same name.
# Takes a single argument, a URL.
# Skips the download if the remote resource is newer.
# Works around connections that hang.
download_url() {
    if [ "$#" -ne 1 ]; then
        echo "Illegal number of arguments"
    fi
    URL=$1
    echo "Downloading ${URL}"
    if [ "$(uname)" = "Darwin" ] ; then
        wget -nv -N "$URL" || print_error_and_exit "Could not download $URL"
        echo "Downloaded $URL"
    else
        BASENAME="$(basename "$URL")"
        if [ -f "$BASENAME" ]; then
            ZBASENAME="-z $BASENAME"
        else
            ZBASENAME=""
        fi
        (timeout 300 curl -s -S -R -L -O "$ZBASENAME" "$URL" || (echo "retrying curl $URL" && rm -f "$BASENAME" && curl -R -L -O "$URL")) && echo "Downloaded $URL"
    fi
}

# Download the remote resource and unzip it.
# Takes a single argument, a URL.
# Skips the download if the local file of the same name is newer.
# Works around connections that hang and corrupted downloads.
download_url_and_unzip() {
    if [ "$#" -ne 1 ]; then
        echo "Illegal number of arguments"
    fi
    URL=$1
    BASENAME="$(basename "$URL")"
    download_url "$URL"
    if ! unzip -o "$BASENAME" > /dev/null ; then
        echo "retrying download and unzip"
        rm -rf "$BASENAME"
        download_url "$URL"
        unzip -o "$BASENAME"
    fi
}

# Get time of last data modification of a file
get_modification_timestamp() {
    local USAGE="Usage: get_modification_timestamp <file>"
    if [ "$#" != 1 ]; then
        print_error_and_exit "$USAGE"
    fi

    local f="$1"

    # The BSD version of stat does not support --version or -c
    if stat --version &> /dev/null; then
        # GNU version
        cmd="stat -c %Y $f"
    else
        # BSD version
        cmd="stat -f %m $f"
    fi

    local ts; ts=$($cmd)
    echo "$ts"
}

main

:::

修改完成後即可執行初始化。

./init.sh

> 若初始化結果仍有錯誤，請詳讀錯誤內容，
> 重新確認 sh檔中對應的網址是否存在，以及網址的內容是否與版本相符合。
> 例如: 確認Major網址https://mutation-testing.org/downloads/ 是否為version 3.0.1

補充說明: 上面init.sh檔案中的工具可能有些版本不相容，所以請自行確認你要使用到的工具是否有版本問題，並切換。

更新: 我要用到major做mutation(人工植入bug)，但上面major v3.0.1 和 defects4j v1.2.0 不相容，所以我會用下面init_fixed.sh (將 major 改成 v1.3.2)

:::spoiler init_fixed.sh

#!/usr/bin/env bash
#
# Exit the shell script immediately if any of the subsequent commands fails.
# immediately
set -e
#

# TODO: Major and the coverage tools should be moved to framework/lib
################################################################################
# This script initializes Defects4J. In particular, it downloads and sets up:
# - the project's version control repositories
# - the Major mutation framework
# - the supported test generation tools
# - the supported code coverage tools (TODO)
################################################################################

HOST_URL="https://defects4j.org/downloads"

# Directories for project repositories and external libraries
BASE="$(cd "$(dirname "$0")"; pwd)"
DIR_REPOS="$BASE/project_repos"
DIR_LIB_GEN="$BASE/framework/lib/test_generation/generation"
DIR_LIB_RT="$BASE/framework/lib/test_generation/runtime"
DIR_LIB_GRADLE="$BASE/framework/lib/build_systems/gradle"

################################################################################

main() {
    echo "Checking system configuration ... "
    # Check whether wget is available on OSX
    if [ "$(uname)" = "Darwin" ] ; then
        if ! wget --version > /dev/null 2>&1; then
            print_error_and_exit "Couldn't find wget to download dependencies. Please install wget and re-run this script."
        fi
    fi
    
    # Check whether curl is available
    if ! curl --version > /dev/null 2>&1; then
        print_error_and_exit "Couldn't find curl to download dependencies. Please install curl and re-run this script."
    fi
    
    # Check whether unzip is available
    if ! unzip -v > /dev/null 2>&1; then
        print_error_and_exit "Couldn't find unzip to extract dependencies. Please install unzip and re-run this script."
    fi

    # Create lib folders if necessary
    mkdir -p "$DIR_LIB_GEN" && mkdir -p "$DIR_LIB_RT" && mkdir -p "$DIR_LIB_GRADLE"

    ############################################################################
    #
    # Download project repositories if necessary
    #
    echo "Setting up project repositories ... "
    cd "$DIR_REPOS" && ./get_repos.sh

    ############################################################################
    #
    # Download Major
    #
    # Adapt Major's default wrapper scripts:
    # - set headless to true to support Chart on machines without X.
    # - do not mutate code unless an MML is specified (for historical reasons,
    #   major v1 was sometimes called without specifying an MML to simply act as
    #   javac; Major v2+'s default is to generate all mutants as opposed to none).
    #
    echo
    echo "Setting up Major ... "
    MAJOR_VERSION="1.3.2"
    MAJOR_URL="https://mutation-testing.org/downloads"
    MAJOR_ZIP="major-${MAJOR_VERSION}_jre7.zip"

    # Download & unzip Major into $BASE/major
    cd "$BASE"
    rm -rf major
    download_url_and_unzip "$MAJOR_URL/$MAJOR_ZIP"
    rm -f "$MAJOR_ZIP"

    # Normalize ant wrapper name: some packages ship .ant instead of ant
    if [ ! -f major/bin/ant ] && [ -f major/bin/.ant ]; then
        cp major/bin/.ant major/bin/ant
    fi

    # Set headless=true to support Chart on machines without X
    if [ -f major/bin/ant ]; then
        perl -pi -e '$_ .= qq(    -Djava.awt.headless=true \\\n) if /CodeCacheSize/' major/bin/ant
    fi

    # If MML is empty, act like javac (avoid mutating unless explicitly requested)
    if [ -f major/bin/major ]; then
        perl -pi -e '$_ .= qq(\nif [ -z "\$MML" ]; then javac \$*; exit \$?; fi\n) if /^REFACTOR=/' major/bin/major
        perl -pi -e '$_ = qq(REFACTOR=\${REFACTOR:-"enable.decl.refactor enable.method.refactor"}\n) if /^REFACTOR=/' major/bin/major
    fi


    ############################################################################
    #
    # Download EvoSuite
    #
    echo
    echo "Setting up EvoSuite ... "
    EVOSUITE_VERSION="1.0.6"
    EVOSUITE_URL="https://github.com/EvoSuite/evosuite/releases/download/v${EVOSUITE_VERSION}"
    EVOSUITE_JAR="evosuite-${EVOSUITE_VERSION}.jar"
    EVOSUITE_RT_JAR="evosuite-standalone-runtime-${EVOSUITE_VERSION}.jar"
    cd "$DIR_LIB_GEN" && download_url "$EVOSUITE_URL/$EVOSUITE_JAR"
    cd "$DIR_LIB_RT"  && download_url "$EVOSUITE_URL/$EVOSUITE_RT_JAR"
    # Set symlinks for the supported version of EvoSuite
    (cd "$DIR_LIB_GEN" && ln -sf "$EVOSUITE_JAR" "evosuite-current.jar")
    (cd "$DIR_LIB_RT" && ln -sf "$EVOSUITE_RT_JAR" "evosuite-rt.jar")

    ############################################################################
    #
    # Download Randoop
    #
    echo
    echo "Setting up Randoop ... "
    RANDOOP_VERSION="4.0.4"
    RANDOOP_URL="https://github.com/randoop/randoop/releases/download/v${RANDOOP_VERSION}"
    RANDOOP_ZIP="randoop-${RANDOOP_VERSION}.zip"
    RANDOOP_JAR="randoop-all-${RANDOOP_VERSION}.jar"
    REPLACECALL_JAR="replacecall-${RANDOOP_VERSION}.jar"
    COVEREDCLASS_JAR="covered-class-${RANDOOP_VERSION}.jar"
    (cd "$DIR_LIB_GEN" && download_url_and_unzip "$RANDOOP_URL/$RANDOOP_ZIP")
    # Set symlink for the supported version of Randoop
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$RANDOOP_JAR" "randoop-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$REPLACECALL_JAR" "replacecall-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/$COVEREDCLASS_JAR" "covered-class-current.jar")
    (cd "$DIR_LIB_GEN" && ln -sf "randoop-${RANDOOP_VERSION}/jacocoagent.jar" "jacocoagent.jar")

    ############################################################################
    #
    # Download build system dependencies
    #
    echo
    echo "Setting up Gradle dependencies ... "

    cd "$DIR_LIB_GRADLE"

    GRADLE_DISTS_ZIP=defects4j-gradle-dists.zip
    GRADLE_DEPS_ZIP=defects4j-gradle-deps.zip

    old_dists_ts=0
    old_deps_ts=0

    if [ -e $GRADLE_DISTS_ZIP ]; then
        old_dists_ts=$(get_modification_timestamp $GRADLE_DISTS_ZIP)
    fi
    if [ -e $GRADLE_DEPS_ZIP ]; then
        old_deps_ts=$(get_modification_timestamp $GRADLE_DEPS_ZIP)
    fi

    # Only download archive if the server has a newer file
    download_url $HOST_URL/$GRADLE_DISTS_ZIP
    download_url $HOST_URL/$GRADLE_DEPS_ZIP
    new_dists_ts=$(get_modification_timestamp $GRADLE_DISTS_ZIP)
    new_deps_ts=$(get_modification_timestamp $GRADLE_DEPS_ZIP)

    # Update gradle distributions/dependencies if a newer archive was available
    [ "$old_dists_ts" != "$new_dists_ts" ] && mkdir "dists" && unzip -q -u $GRADLE_DISTS_ZIP -d "dists"
    [ "$old_deps_ts" != "$new_deps_ts" ] && unzip -q -u $GRADLE_DEPS_ZIP

    cd "$BASE"

    ############################################################################
    #
    # Download utility programs
    #
    echo
    echo "Setting up utility programs ... "

    BUILD_ANALYZER_VERSION="0.0.1"
    BUILD_ANALYZER_JAR=build-analyzer-$BUILD_ANALYZER_VERSION.jar
    BUILD_ANALYZER_URL="https://github.com/jose/build-analyzer/releases/download/v$BUILD_ANALYZER_VERSION/$BUILD_ANALYZER_JAR"
    BUILD_ANALYZER_JAR_LOCAL="analyzer.jar"
    cd "$BASE/framework/lib" && download_url "$BUILD_ANALYZER_URL"
    rm -f "$BUILD_ANALYZER_JAR_LOCAL"
    ln -s "$BUILD_ANALYZER_JAR" "$BUILD_ANALYZER_JAR_LOCAL"

    echo
    echo "Defects4J successfully initialized."
}

################################################################################
#
# Utility functions
#

# Print an error message and terminate the script.
# Takes one argument, a custom error message.
# Prints the supplied error message and a script termination notice to stderr.
# Terminates the script with exit code 1.
print_error_and_exit() {
  echo -e "${1} \nTerminating initialization... " >&2
  exit 1
}

# MacOS does not install the timeout command by default.
if [ "$(uname)" = "Darwin" ] ; then
  function timeout() { perl -e 'alarm shift; exec @ARGV' "$@"; }
fi

# Download the remote resource to a local file of the same name.
# Takes a single argument, a URL.
# Skips the download if the remote resource is newer.
# Works around connections that hang.
download_url() {
    if [ "$#" -ne 1 ]; then
        echo "Illegal number of arguments"
    fi
    URL=$1
    echo "Downloading ${URL}"
    if [ "$(uname)" = "Darwin" ] ; then
        wget -nv -N "$URL" || print_error_and_exit "Could not download $URL"
        echo "Downloaded $URL"
    else
        BASENAME="$(basename "$URL")"
        if [ -f "$BASENAME" ]; then
            ZBASENAME="-z $BASENAME"
        else
            ZBASENAME=""
        fi
        (timeout 300 curl -f -sS -R -L $ZBASENAME -O "$URL" || (echo "retrying curl $URL" && rm -f "$BASENAME" && curl -f -sS -R -L -O "$URL")) && echo "Downloaded $URL"
    fi
}

# Download the remote resource and unzip it.
# Takes a single argument, a URL.
# Skips the download if the local file of the same name is newer.
# Works around connections that hang and corrupted downloads.
download_url_and_unzip() {
    if [ "$#" -ne 1 ]; then
        echo "Illegal number of arguments"
    fi
    URL=$1
    BASENAME="$(basename "$URL")"
    download_url "$URL"
    if ! unzip -o "$BASENAME" > /dev/null ; then
        echo "retrying download and unzip"
        rm -rf "$BASENAME"
        download_url "$URL"
        unzip -o "$BASENAME"
    fi
}

# Get time of last data modification of a file
get_modification_timestamp() {
    local USAGE="Usage: get_modification_timestamp <file>"
    if [ "$#" != 1 ]; then
        print_error_and_exit "$USAGE"
    fi

    local f="$1"

    # The BSD version of stat does not support --version or -c
    if stat --version &> /dev/null; then
        # GNU version
        cmd="stat -c %Y $f"
    else
        # BSD version
        cmd="stat -f %m $f"
    fi

    local ts; ts=$($cmd)
    echo "$ts"
}

main

:::

### 3. 設定 Defects4J 環境變數

sudo nano ~/.bashrc

輸入以下環境變數。

export PATH=$PATH:~/defects4j/framework/bin
export DEFECTS4J_HOME=~/defects4j

執行環境設定，並確認能夠使用defects4j指令。

source ~/.bashrc
defects4j

(若想要知道"defects4j"這個指令在哪裡就輸入"`whereis defects4j`"，就能取得位置。)

### 4. 使用 Defects4J (以 Chart 為例)

輸入指令能夠查看 Chart 整體的資訊。

defects4j info -p Chart

輸入指令則是查看 Chart-1 的詳細資訊。

defects4j info -p Chart -b 1

下載 Chart-1 (存放位置自訂)。

defects4j checkout -p [Project名稱] -v [project的版本][b表示buggy version] -w [要存放的位置，最後的"chart_1_buggy"表示資料夾要存甚麼名稱，可以自訂]
defects4j checkout -p Chart -v 1b -w ~/d4j_project/Chart/chart_1_buggy

進到 Chart-1 的資料夾中，輸入指令可編譯或測試。

defects4j compile
defects4j test

## 自動 compile 所有的 bug-id

可以建立一個 sh檔，自動把所有的資料下載下來。

### 1. 建立一個想要存放 defects4j project 的資料夾
( p.s. : 要建立各個專案資料夾，不然容易出錯。)
( p.s. : 變數看清楚，常常因為變數問題出錯。)
> 我是在Home下建立一個 "d4j_project" 資料夾，
> 在裡面再建立 "chart"、"closure"、"math"、"time"、"lang" 資料夾，
> 可以直接打開 Document 手動添加。

### 2. 建立一個 sh檔
> 名稱設定為"all_D4J"。

touch all_D4J.sh

### 3. 寫入 sh檔內容

:::spoiler all_D4J.sh

dir=~/d4j_project/ # Store the buggy projects.

proj=Chart
proj2=chart
for bug_id in $(seq 1 26)
do
	cd ~/defects4j/
	defects4j checkout -p $proj -v ${bug_id}b -w ${dir}${proj2}/${proj2}_${bug_id}_buggy
	#cd to checkout folder
	cd ${dir}${proj2}/${proj2}_${bug_id}_buggy 
	defects4j compile
    	defects4j test
done

proj=Closure
proj2=closure
for bug_id in $(seq 1 133)
do
	cd ~/defects4j/
	defects4j checkout -p $proj -v ${bug_id}b -w ${dir}${proj2}/${proj2}_${bug_id}_buggy
	#cd to checkout folder
	cd ${dir}${proj2}/${proj2}_${bug_id}_buggy 
	defects4j compile
    	defects4j test
done

proj=Math
proj2=math
for bug_id in $(seq 1 106)
do
	cd ~/defects4j/
	defects4j checkout -p $proj -v ${bug_id}b -w ${dir}${proj2}/${proj2}_${bug_id}_buggy
	#cd to checkout folder
	cd ${dir}${proj2}/${proj2}_${bug_id}_buggy 
	defects4j compile
    	defects4j test
done

proj=Time
proj2=time
for bug_id in $(seq 1 27)
do
	cd ~/defects4j/
	defects4j checkout -p $proj -v ${bug_id}b -w ${dir}${proj2}/${proj2}_${bug_id}_buggy
	#cd to checkout folder
	cd ${dir}${proj2}/${proj2}_${bug_id}_buggy 
	defects4j compile
    	defects4j test
done

proj=Lang
proj2=lang
for bug_id in $(seq 1 65)
do
	cd ~/defects4j/
	defects4j checkout -p $proj -v ${bug_id}b -w ${dir}${proj2}/${proj2}_${bug_id}_buggy
	#cd to checkout folder
	cd ${dir}${proj2}/${proj2}_${bug_id}_buggy 
	defects4j compile
    	defects4j test
done

:::

### 4. 將 sh檔加入執行權限，並執行

chmod +x all_D4J.sh
./all_D4J.sh