xnat-token.sh

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

warn() {
  echo "$@" 1>&2
}

usage() {
  cat <<EOF
xnat-token: Generates a new user token for XNAT

USAGE
  xnat-token [OPTIONS]

OPTIONS
  -d    Connect to development XNAT
  -h    Displays this help message
  -u    Username for XNAT

EXAMPLES
  xnat-token -u broarr

NOTES
  XNAT tokens live for 48 hours before they're invalidated. 

EOF
}

main() {
  local url='https://xnat.bnc.brown.edu'
  local username=''
  local password=''
  local token=''
  local alias=''
  local secret=''

  while getopts ":dhu:" opt; do
    case "${opt}" in
      d)
        url="https://qa-xnat.bnc.brown.edu"
        ;;
      h)
        usage; exit 0
        ;;
      u)
        username="${OPTARG}"
        ;;
      \?)
        warn "Invalid option: -${OPTARG}"
        exit 1
        ;;
      :)
        warn "Invalid option: -${OPTARG} requires an argument"
        exit 1
        ;;
    esac
  done

  echo "Connecting to ${url}"

  if [ -z "${username}" ]; then
    echo -n "username: "
    read -r username
  fi

  echo -n "password: "
  read -sr password
  echo

  url="${url}/data/services/tokens/issue"
  token="$(curl -s -u "${username}:${password}" "${url}" )"

  # NOTE (BNR): Normally I'd be using jq for this, but jq is not available in
  #             oscar. Instead I stick to UNIX tools that should be available
  #             on every POSIX compliant machine.
  alias="$(echo "${token}" | sed -n 's/.*"alias":"\([^"]*\)".*/\1/p')"
  secret="$(echo "${token}" | sed -n 's/.*"secret":"\([^"]*\)".*/\1/p')"

  cat <<EOF


The following token will be valid for 48 hours
Use \$XNAT_TOKEN in place of username and \$XNAT_SECRET in place of password

If you are using an interact session then you will need to export this variables 


-------------------------------------------------------------------------------

export XNAT_TOKEN=${alias}
export XNAT_SECRET=${secret}

or 

export XNAT_USER=${alias}
export XNAT_PASSWORD=${secret}
-------------------------------------------------------------------------------

If you are using an sbatch script, then you can define the variables in your script. For example

-------------------------------------------------------------------------------

XNAT_TOKEN=${alias}
XNAT_SECRET=${secret}

or 

XNAT_USER=${alias}
XNAT_PASSWORD=${secret}
-------------------------------------------------------------------------------

EOF
}

main "$@"