darwin

#!/bin/bash

# $1: git command to run, yell if undefined
# $2-inf: arguments to git command, except as below:
# $2: if "darwin init" is run, this declares the version control system to use

# currently supports as a backend: git

# has newline at start
RECOGNIZED_VCS="git"

RECOGNIZED_FILE_EXTENSIONS="fasta
fas
fna"

INITIAL_DIR="$(pwd)"

# directory of script
WORKING_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"

DARWIN_FOLDER=".dwn"

DARWIN_BACKEND_FILE=".dwn-backend"

# returns ms since unix epoch
timestamp() {
    date +"%s"
}

# zips files to .vcsfmt format
# $1: output directory
zip_fasta() {
    dwndiff -o "$1" -z "${@:2}"
}

# unzips files from vcsfmt format to working dir from .dwn dir
# $1: output directory
# $2-@: file(s) to unzip
unzip_fasta() {
    dwndiff -o "$1" -u "${@:2}"
}

ERROR_ROLLBACK="false"

# if command fails, set rollback to true
# $@: command to run, and arguments
upon_error_set_rollback() {
    "$@"
    if [ $? -ne 0 ]; then
        ERROR_ROLLBACK="true"
        echo "Failure at internal command: $@."
    fi
}

display_help(){
    echo "
    Usage: darwin <command> [<args>]

    Commands include:
    init:    Create a darwin repository in the current folder.
    clone:   Create a repository on the local machine mirroring a remote.
    add:     Add files [<args>] to index.
    commit:  Create an encapsulation of edits performed on files.
    push:    Upload commits to remote.
    pull:    Download commits from remote.
    status:  View currently changed files.
    rm:      Remove files from index.
    log:     View history of commits in the repository.
    diff:    View differences between files made between commits.

    Darwin is a tool built on top of git, and as a result defaults to using
    git's syntax and commands outside of the overridden functions above. Git
    documentation can be viewed at http://git-scm.com.

    This project's page is at http://github.com/igemsoftware/Vanderbilt_2014.
    Report bugs to <danieldmcclanahan@gmail.com>.
    "
}

# display help
if [ "$1" = "help" ] || [ "$1" = "--help" ] || [ "$1" = "-h" ] || \
    [ "$1" = "" ]; then

    display_help

    # the parser
elif [ "$1" = "init" ]; then

    # setup
    if [ -d "$DARWIN_FOLDER" ]; then
        echo "A darwin repository already exists!" 1>&2
    else
        upon_error_set_rollback mkdir "$DARWIN_FOLDER"
        upon_error_set_rollback cd "$DARWIN_FOLDER"

        # backend-dependent
        if [ "$2" = "git"  ]; then
            upon_error_set_rollback git init "${@:3}"
        elif [ "$2" = "" ]; then
            echo "Version control backend required in command, e.g.:
        darwin init <backend>
Recognized systems include: $RECOGNIZED_VCS" 1>&2
            ERROR_ROLLBACK="true"
        else
            echo "Version control backend $2 not recognized. Recognized systems
        include: $RECOGNIZED_VCS" 1>&2
            ERROR_ROLLBACK="true"
        fi

        # teardown
        if [ "$ERROR_ROLLBACK" = "true" ]; then
            cd "$INITIAL_DIR"
            rm -rf "$DARWIN_FOLDER"
        else
            # store type of backend used
            echo -n "$2" > "$DARWIN_BACKEND_FILE"
            git add $DARWIN_BACKEND_FILE
        fi

    fi

elif [ "$1" = "clone" ]; then

    if [ -d "$DARWIN_FOLDER" ]; then
        echo "A darwin repository already exists!" 1>&2
    else
        # setup
        upon_error_set_rollback cd "/tmp"
        TMP_FOLDER_NAME="$DARWIN_FOLDER-$(upon_error_set_rollback timestamp)"
        upon_error_set_rollback mkdir "$TMP_FOLDER_NAME"
        upon_error_set_rollback cd "$TMP_FOLDER_NAME"

        # backend-dependent
        if [ "$2" = "git" ]; then
            upon_error_set_rollback git clone "$3" "$DARWIN_FOLDER"
        else
            echo "Version control backend $2 not recognized. Recognized systems
include: $RECOGNIZED_VCS" 1>&2
            ERROR_ROLLBACK="true"
        fi

        upon_error_set_rollback mv "$DARWIN_FOLDER" "$INITIAL_DIR"
        upon_error_set_rollback cd ..
        upon_error_set_rollback rm -rf "$TMP_FOLDER_NAME"
        upon_error_set_rollback cd "$INITIAL_DIR"
        dwndiff_helper unzip . $DARWIN_FOLDER/*.vcsfmt

        # teardown
        if [ "$ERROR_ROLLBACK" = "true" ]; then
            cd "$INITIAL_DIR"
            rm -rf "$DARWIN_FOLDER"
            rm -rf "/tmp/$TMP_FOLDER_NAME"
        else
            # store type of backend used
            cd $DARWIN_FOLDER
            echo -n "$2" > "$DARWIN_BACKEND_FILE"
            git add $DARWIN_BACKEND_FILE
        fi

    fi

else

    # error handling
    # if no folder found
    if [ ! -d "$DARWIN_FOLDER" ]; then
        echo "Error: no darwin repository was found." 1>&2
        exit -1
    fi

    BACKEND_VCS_TYPE="$(cat $DARWIN_FOLDER/$DARWIN_BACKEND_FILE)"
    # if no backend file found
    if [ "$(echo $RECOGNIZED_VCS | grep $BACKEND_VCS_TYPE)" = "" ]; then
        if [ -d ".git" ]; then
            BACKEND_VCS_TYPE="git"
        else
            echo "Error: incorrectly initialized repository." 1>&2
            echo "Try checking out again." 1>&2
            exit -1
        fi
        echo -n "$BACKEND_VCS_TYPE" > "$DARWIN_FOLDER/$DARWIN_BACKEND_FILE"
    fi

    # actual commands
    if [ "$1" = "add" ]; then

        # setup
        while read -r file_extension; do
            dwndiff_helper zip "$DARWIN_FOLDER" *.$file_extension
        done <<< "$RECOGNIZED_FILE_EXTENSIONS"

        # backend-dependent
        if [ "$BACKEND_VCS_TYPE" = "git" ]; then
            cd "$DARWIN_FOLDER"
            upon_error_set_rollback git add "$2.vcsfmt"
        fi

    elif [ "$1" = "commit" ]; then

        if [ "$2" = "" ]; then
            echo "Enter a message describing your changes, e.g.:"
            echo "    darwin commit \"slightly modified GFP sector\""
            exit -1
        else
            # backend-dependent
            # "BACKEND_VCS_TYPE" = "git"
            cd "$DARWIN_FOLDER"
            upon_error_set_rollback git commit -m "$2" \
                | grep -v "$DARWIN_BACKEND_FILE"
        fi

    elif [ "$1" = "push" ]; then

        # backend-dependent
        # "$BACKEND_VCS_TYPE" = "git"
        cd "$DARWIN_FOLDER"
        upon_error_set_rollback git push "${@:2}"

    elif [ "$1" = "pull" ]; then

        # backend-dependent
        # "$BACKEND_VCS_TYPE" = "git"
        cd "$DARWIN_FOLDER"
        upon_error_set_rollback git pull "${@:2}"
        exist_changes="no"
        git diff --name-only HEAD | while read changed_file; do
            exist_changes="yes"
            dwndiff_helper unzip-changes .. $changed_file
        done

        if [ "$exist-changes" != "" ]; then
            echo "Changes were made upstream. You'll have to manually merge the
files with the extension .new-file."
        fi

    elif [ "$1" = "status" ]; then

        # backend-dependent
        # "$BACKEND_VCS_TYPE" = "git"
        cd "$DARWIN_FOLDER"
        upon_error_set_rollback git status "${@:2}" | sed -e "s/\.vcsfmt//g" \
            | grep -v "$DARWIN_BACKEND_FILE"

    elif [ "$1" = "rm" ]; then

        # backend-dependent
        # "$BACKEND_VCS_TYPE" = "git"
        cd "$DARWIN_FOLDER"
        upon_error_set_rollback git rm "$2.vcsfmt"
        cd "$INITIAL_DIR"
        upon_error_set_rollback rm "$2"

    elif [ "cat $WORKING_DIR/all_possible_git_commands | grep $1" != "" ]; then
        # if command is git command

        # backend-dependent
        # "$BACKEND_VCS_TYPE" = "git"
        cd "$DARWIN_FOLDER"
        upon_error_set_rollback git "$@"

    else

        echo "Command $1 not found." 1>&2
        display_help
        exit -1

    fi

fi