etm

#!/usr/bin/env bash
set -euo pipefail


function help {
    description
    usage
    commands
    options
    notes
    examples
    advanced_examples
    exit 0
}


function description {
    #     -------------------------------------------------------------------------------
    echo -e "\033[1mEpitope Matcher\033[0m"
    echo "A package that can be used to find out how well the epitopes in a patient's"
    echo "virus' will be recognized by the HLA's present in the patient."
    echo ""
}


function usage {
    #     -------------------------------------------------------------------------------
    echo "Usage:"
    echo "   etm -h | --help"
    echo "   etm info"
    echo "   etm build [--image]"
    echo "   etm run [--image] [--env] [--publish] [--entrypoint] <command>"
    echo "   etm r [--image] [--env] [--publish] <command>"
    echo "   etm rscript [--image] [--env] [--publish] <path>"
    echo "   etm serve [--image] [--env] [--publish]"
    echo "   etm get-test-set [--image] [--env]"
    echo ""
}


function commands {
    #     -------------------------------------------------------------------------------
    echo "Commands:"
    echo "   build                       Build container image"
    echo "   run                         Run containerized command against entrypoint"
    echo "   r                           Run containerized R command"
    echo "   rscript                     Run containerized R script"
    echo "   serve                       Serve web application"
    echo "   get-test-set                Download test set to ${project_dir}"
    echo "   info                        Print information about environment"
    echo ""
}


function options {
    #     -------------------------------------------------------------------------------
    echo "Options:"
    echo "   -h --help                   Show this screen"
    echo "   -i --image=<name:tag>       [Not Available] Image [default: ${default_image}]"
    echo "   -p --publish=<host:guest>   [Not Available] Port forward [default: ${default_port_forward}]"
    echo "   -e --env=<key:val>          [Not Available] Environment"
    echo "   --entrypoint=<str>          [Not Available] Entrypoint [default: ${default_entrypoint}]"
    echo ""
}


function notes {
    #     -------------------------------------------------------------------------------
    echo "Notes:"
    echo "   - To run from any location, symlink ${repo_dir}/etm to a directory on your PATH"
    echo "   - Files are only accessible from ${project_dir} down"
    echo ""
}


function examples {
    #        -------------------------------------------------------------------------------
    echo    "Examples:"
    echo    "   etm build"
    echo -e "   etm run bash  \033[33m# Drop into bash shell\033[0m"
    echo -e "   etm run echo Hello World!  \033[33m# No quotes needed for single line command\033[0m"
    echo -e "   etm run 'echo Hello World!; echo Hello World again!'  \033[33m# Single quotes needed for multi line command\033[0m"
    echo -e "   etm run bash hello-world.sh  \033[33m# Specify a program to run a script\033[0m"
    echo -e "   etm run ./hello-world.sh  \033[33m# Run an executable script containing appropriate shebang\033[0m"
    echo -e "   etm run R  \033[33m# Drop into R shell\033[0m"
    echo -e "   etm run \"Rscript -e '1 + 1'\"  \033[33m# Careful consideration of quoting required in this case, rather use convenience command for R\033[0m"
    echo -e "   etm run Rscript hello-world.r  \033[33m# Specify a program to run a script\033[0m"
    echo -e "   etm run ./hello-world.r  \033[33m# Run an executable script containing appropriate shebang\033[0m"
    echo -e "   etm r 1 + 1  \033[33m# Run R single-line command\033[0m"
    echo -e "   etm r 'print(\"Hello World!\"); print(\"Hello World again!\");'  \033[33m# Run R multi-line command\033[0m"
    echo -e "   etm rscript hello-world.r  \033[33m# Run a script with Rscript\033[0m"
    echo    "   etm serve"
    echo    "   etm get-test-set"
    echo    "   etm info"
    echo ""
}


function advanced_examples {
    #     -------------------------------------------------------------------------------
    echo "Advanced Examples:"
    echo "   [Not Available] etm build -i etm-dev:0.01a"
    echo "   [Not Available] etm run -i etm-dev:0.01a -e name=World --entrypoint 'bash -c' 'echo Hello \${name}!'"
}


function build {
    cd "${repo_dir}/container"
    "${container_engine}" build -t "${default_image}" .
}


function run {
    "${container_engine}" run --rm -it -p "${default_port_forward}" \
        --workdir "${project_dir}" -v "${project_dir}:${project_dir}" \
        "${default_image}" ${chosen_entrypoint} "$@"
}


function info {
    echo -e "\033[1mEpitope Matcher Information\033[0m"
    echo "container_engine: ${container_engine}"
    echo "repo_dir: ${repo_dir}"
    echo "project_dir: ${project_dir}"
    echo "default_image: ${default_image}"
    echo "default_port_forward: ${default_port_forward}"
    echo "default_entrypoint: ${default_entrypoint}"
}


function resolve_repo {
    ## Copied from https://stackoverflow.com/a/697552/1782641
    SELF_PATH=$(cd -P -- "$(dirname -- "$0")" && pwd -P) && SELF_PATH=$SELF_PATH/$(basename -- "$0")
    while [[ -h $SELF_PATH ]]; do
        DIR=$(dirname -- "$SELF_PATH")
        SYM=$(readlink "$SELF_PATH")
        SELF_PATH=$(cd "$DIR" && cd "$(dirname -- "$SYM")" && pwd)/$(basename -- "$SYM")
    done
    echo "$(dirname ${SELF_PATH})"
}


function set_container_engine {
    # Prefer podman, fall back to docker
    if ! command -v podman &> /dev/null
    then
        if ! command -v docker &> /dev/null
        then
            >&2 echo "Error. Requirement not satisfied. Either podman or docker must be installed." 
            exit 1
        else
            echo docker
        fi
    else
        echo podman
    fi
}

## ETM Global variables
container_engine="${container_engine:-$(set_container_engine)}"
repo_dir="$(resolve_repo)"
project_dir="$(pwd)"
default_image="etm:latest"
default_host_port=5436
default_container_port=5436
default_port_forward="${default_host_port}:${default_container_port}"
default_entrypoint="sh -c"

case "$1" in
    -h | --help)
    help
    ;;

    build)
    build
    ;;

    run)
    shift
    chosen_entrypoint="${chosen_entrypoint:-${default_entrypoint}}"
    run "$*"
    ;;

    r)
    shift
    chosen_entrypoint="Rscript -e"
    run "$*"
    ;;

    rscript)
    shift
    chosen_entrypoint="Rscript"
    run "$*"
    ;;

    serve)
    chosen_entrypoint="Rscript -e"
    run "library(EpitopeMatcher); run_EpitopeMatcher_app();"
    ;;

    get-test-set)
    chosen_entrypoint="Rscript -e"
    run "library(EpitopeMatcher); get_set_of_test_data();"
    ;;

    info)
    info
    ;;

    *)
    echo "\`$0 $@\` is an invalid command, see usage below"
    echo ""
    usage
    exit 1
    ;;

esac