source_params () {
    if [ ! -f "${MDS_PARAMS}" ]; then 
        exit_error "Cannot find sumbission parameters file '${MDS_PARAMS}'. Use -genparams to create a new one."
    fi
    dos2unix ${MDS_PARAMS} >/dev/null 2>&1
    source ${MDS_PARAMS}
}

list_units () {
    local upath=$1
    for uf in $( ls -1 $upath/*.sh ); do
        eval $( cat $uf | sed -n '/^# DESCRIPTION/s/^# DESCRIPTION \([^ ]\+\) \(.*\)$/echo_y -ne \1; echo \\\t\2/p' )
    done
}

list_modules () {
    local module=$1
    case $module in 
        software)
            list_units ${MDS_LIBEXEC_PATH}/software
            ;;
        infrastructure|infrastructures)
            list_units ${MDS_LIBEXEC_PATH}/grid/infrastructures
            ;;
        portal|portals)
            list_units ${MDS_LIBEXEC_PATH}/portals
            ;;
        *)
            exit_error "Wrong module type '$module' specified."
            ;;
    esac
}

source_module () {
    local moduletype=$1
    local modulename=$2
    case $moduletype in
        software)
            modulepath="${MDS_LIBEXEC_PATH}/software/${modulename}.sh"
            ;;
        infrastructure)
            modulepath="${MDS_LIBEXEC_PATH}/grid/infrastructures/${modulename}.sh"
            ;;
        portal)
            modulepath="${MDS_LIBEXEC_PATH}/portals/${modulename}.sh"
            ;;
        *)
            exit_error "Wrong module type '$moduletype' specified."
            ;;
    esac
    [ -f "$modulepath" ] && source $modulepath || exit_error "There is no $moduletype module '$modulename'" 
}

infrasrtucture_gen_params_default () {
    [ -n "$(type -t jobdescription_gen_params)" ] && jobdescription_gen_params
    [ -n "$(type -t submission_gen_params)" ] && submission_gen_params
    [ -n "$(type -t proxy_gen_params)" ] && proxy_gen_params
}

generate_params () {
    [ -n "$(type -t software_gen_params)" ] && software_gen_params
    [ -n "$(type -t infrastructure_gen_params)" ] && infrasrtucture_gen_params || infrasrtucture_gen_params_default
    [ -n "$(type -t portal_gen_params)" ] && portal_gen_params
}

usage () {
    echo_g "MolDynSub CLI version $VERSION usage:"
    echo_r -e "\t${0##*/} [ OPTIONS ]"
    echo_g "MODULES OPTIONS:"
    echo_y -e "\t--list {software|infrastructures|portals}"
    echo   -e "\t\tlist avaialable modules for specified type"
    echo_y -e "\t--software <name>"
    echo   -e "\t\tdefine software module to use (default is 'gromacs-md-mdrun')"
    echo_y -e "\t--infrastructure <name>"
    echo   -e "\t\tdefine infrastructure to use (default is 'arc')"
    echo_y -e "\t--portal {<name>|none}"
    echo   -e "\t\tdefine portal implementation to use (default is 'moldyngrid')"
    echo_g "GENERAL OPTIONS:"
    echo_y -e "\t--params <path>"
    echo   -e "\t\tredefine configured params file location ($MDS_PARAMS)"
    echo_y -e "\t--genparams"
    echo   -e "\t\tfill params file with the default template for choosen software module"
    echo_y -e "\t--dryrun"
    echo   -e "\t\tonly generate necessary files, but disable actual job submission"
    echo_y -e "\t--help"
    echo   -e "\t\tprint this help message"
    [ -n "$(type -t software_usage)" ] && software_usage
    [ -n "$(type -t infrastructure_usage)" ] && infrastructure_usage
    [ -n "$(type -t portal_usage)" ] && portal_usage
    exit 0
}

source_default_modules () {
    if [ -z "${MDS_SOFTWARE}" ]; then
        MDS_SOFTWARE=$MDS_DEFAULT_SOFTWARE
        source_module 'software' $MDS_SOFTWARE
    fi
    if [ -z "$MDS_INFRASTRUCTURE" ]; then
        MDS_INFRASTRUCTURE=$MDS_DEFAULT_INFRASTRUCTURE
        source_module 'infrastructure' $MDS_INFRASTRUCTURE
    fi
    if [ -z "$MDS_PORTAL" ]; then 
        MDS_PORTAL=$MDS_DEFAULT_PORTAL
        source_module 'portal' $MDS_PORTAL
    fi
}

parse_cmd_options () {
    while [ $# -ne 0 ]; do
      case $1 in
        --list|-l)
            list_modules $2
            exit 0
            ;;
        --software|-s)
            MDS_SOFTWARE=$2
            source_module 'software' $MDS_SOFTWARE
            shift 2
            ;;
        --infrastructure|-i)
            MDS_INFRASTRUCTURE=$2
            source_module 'infrastructure' $MDS_INFRASTRUCTURE
            shift 2
            ;;
        --portal|-p)
            MDS_PORTAL=$2
            [ "$MDS_PORTAL" = "none" ] && DISABLEPORTAL=1 || \
            source_module 'portal' $MDS_PORTAL
            shift 2
            ;;
        --params)
            MDS_PARAMS=$2
            shift 2
            ;;
        --genparams)
            GEN_PARAMS=1
            shift
            ;;
        --dryrun)
            DRYRUN=1
            shift
            ;;
        --help|-h)
            source_default_modules
            usage
            ;;
        *)
            source_default_modules
            [ -n "$(type -t software_parse_cmd_options)" ] && software_parse_cmd_options $@
            [ -n "$(type -t infrastructure_parse_cmd_options)" ] && infrastructure_parse_cmd_options $@
            [ -n "$(type -t portal_parse_cmd_options)" ] && portal_parse_cmd_options $@
            [ -n "$PARSED_BY_MODULE" ] && shift $PARSED_BY_MODULE || usage
            ;;
      esac
    done

    source_default_modules
    if [ -n "$GEN_PARAMS" ]; then
        generate_params > "$MDS_PARAMS"
        exit 0
    fi
}

next_idx_var () {
    local name_base=$1
    local value_base=$2
    local name_value=$3
    local value_value=$4
    
    local n_idx=0
    name_var="${name_base}${n_idx}"
    while [ -n "${!name_var}" ]; do
        n_idx=$((n_idx+1))
        name_var="${name_base}${n_idx}"
    done
    value_var="${value_base}${n_idx}"
    eval ${name_var}="${name_value}"
    eval ${value_var}="${value_value}"
}