enter

#!/bin/bash

SCRIPT_NAME=$(basename "${0}")
DEFAULT_STUDY_DIR="${HOME}/data/mystudy"
DEFAULT_GRADIENT_COEFFS_DIR="${HOME}/projects/HCPpipelinesPrereqs/gradient_coefficients_files"
DEFAULT_FREESURFER_LICENSE_DIR="${HOME}/projects/HCPpipelinesPrereqs/FreeSurferLicense"

usage()
{
	cat <<EOF

${SCRIPT_NAME}:

  This script demonstrates how to "enter" the HCPprocessPipelines.simg CONTAINER or
  HCPprocessPipelinesSandbox SANDBOX for verifying configuration and testing.

Usage: ${SCRIPT_NAME} PARAMETER ...

PARAMETERs are: [ ] = optional; < > = user supplied value

  [--help] : show this usage information and exit

  Path to study directory
  -----------------------

  [--study-dir=<path-to-study-directory>]

    The specified path will be bound (i.e. mounted) from your system
    to a known location (/study) in the container or sandbox. This is 
    where the study data must be found within the container or sandbox.

    It is assumed that your study directory contains subdirectories that 
    correspond to your subject IDs.

    If you do not specify a study directory, the study directory will 
    default to: ${DEFAULT_STUDY_DIR}.

  Path to gradient coefficients files
  -----------------------------------

  [--gradient-coeffs-dir=<path-to-gradient-coefficients-directory>]

    The specified path will be bound (i.e. mounted) from your system
    to a known location (/export/HCP/gradient_coefficient_files) in the
    container or sandbox. This is where the gradient coefficients
    files must be found within the container or sandbox.

    This gradient coefficients files directory must contain the
    proprietary gradient coefficients files for any scanners used in 
    collecting your image data files.

    If you do not specify a gradient coefficients files directory, it will
    default to: ${DEFAULT_GRADIENT_COEFFS_DIR}.  

    NOTE: The path to the gradient coefficients files is only necessary
    for actual processing of data. If you are running a completion
    check, you can allow this to take its default value even if that
    value is incorrect.  

  Path to FreeSurfer license file
  -------------------------------

  [--freesurfer-license-dir=<path-to-freesurfer-license-directory>]

    The specified path will be bound (i.e. mounted) from your system
    to a known location (/export/freesurfer_license) in the container
    or sandbox. This is where the FreeSurfer license file must be
    found within the container or sandbox.

    If you do not specify a FreeSurfer license directory, it will 
    default to: ${DEFAULT_FREESURFER_LICENSE_DIR}.

  Specification of environment
  ----------------------------

    You must specify whether to enter the Singularity Container 
    (HCPprocessPipelines.simg) or the Singularity Sandbox 
    (HCPprocessPipelinesSandbox/).

    One of the following options must be specified:

      --env=[CONTAINER|SANDBOX]
      --container
      --sandbox

    The value specified for the --env= parameter is not case
    sensitive, but must be either CONTAINER or SANDBOX. For example, 
    --env=ConTAiner, --env=SandBox, and --env=sandbox
    are all valid, but --env=CONTAIN is not valid.

      --container is equivalent to --env=CONTAINER

      --sandbox is equivalent to --env=SANDBOX

EOF
}

abort()
{
	local error_msg
	error_msg="${1}"

	echo ""
	usage
	echo "--------------------------------------------------"
	echo "ERROR: ${error_msg}"
	echo "--------------------------------------------------"
	echo ""
	exit 1
}

get_options()
{
	local arguments=($@)
	
	# initialize global output variables
	g_study_dir="${DEFAULT_STUDY_DIR}"
	g_gradient_coeffs_dir="${DEFAULT_GRADIENT_COEFFS_DIR}"
	g_freesurfer_license_dir="${DEFAULT_FREESURFER_LICENSE_DIR}"
	unset g_env
			
	# parse arguments
	local num_args=${#arguments[@]}
	local argument
	local index=0

	while [ ${index} -lt ${num_args} ]; do
		argument=${arguments[index]}

		case ${argument} in
			--help)
				usage
				exit 1
				;;
			--study-dir=*)
				g_study_dir=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--gradient-coeffs_dir=*)
				g_gradient_coeffs_dir=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--freesurfer-license-dir=*)
				g_freesurfer_license_dir=${argument/*=/""}
				index=$(( index + 1 ))
				;;
			--env=*)
				g_env=${argument/*=/""}
				g_env=$(echo ${g_env} | tr '[:lower:]' '[:upper:]')
				index=$(( index + 1 ))
				;;
			--container)
				g_env="CONTAINER"
				index=$(( index + 1 ))
				;;
			--sandbox)
				g_env="SANDBOX"
				index=$(( index + 1 ))
				;;
			*)
				abort "Unrecognized option: ${argument}"
				;;
		esac

	done

	# check parameters

	if [ -n "${g_study_dir}" ]; then
		echo "INFO: study directory: ${g_study_dir}"
	else
		abort "--study-dir=<study-directory> must be specified"
	fi

	if [ -n "${g_gradient_coeffs_dir}" ]; then
		echo "INFO: gradient coefficients directory: ${g_gradient_coeffs_dir}"
	else
		abort "--gradient-coeffs-dir=<gradient-coeffs-directory> must be specified"
	fi

	if [ -n "${g_freesurfer_license_dir}" ]; then
		echo "INFO: FreeSurfer license directory: ${g_freesurfer_license_dir}"
	else
		abort "--freesurfer-license-dir=<freesurfer-license-directory> must be specified"
	fi
	
	if [ -z "${g_env}" ]; then
		abort "environment (--env=[CONTAINER|SANDBOX], --container, or --sandbox) required"
	fi

	if [ "${g_env}" != "CONTAINER" -a "${g_env}" != "SANDBOX" ]; then 
		abort "environment must be CONTAINER or SANDBOX"
	else
		echo "INFO: Environment: ${g_env}"
	fi
}

main()
{
	local where_study_is_on_my_system
	local where_study_must_be_in_container

	local where_gc_files_are_on_my_system
	local where_gc_files_must_be_in_container

	local where_license_file_is_on_my_system
	local where_license_file_must_be_in_container

	get_options "$@"

	where_study_is_on_my_system="${g_study_dir}"
	where_study_must_be_in_container="/study"
	
	where_gc_files_are_on_my_system="${g_gradient_coeffs_dir}"
	where_gc_files_must_be_in_container="/export/HCP/gradient_coefficient_files"

	where_license_file_is_on_my_system="${g_freesurfer_license_dir}"
	where_license_file_must_be_in_container="/export/freesurfer_license"

	shell_cmd=""
	
	if [ "${g_env}" = "CONTAINER" ]; then

		sudo singularity shell \
			 -B ${where_study_is_on_my_system}:${where_study_must_be_in_container} \
			 -B ${where_gc_files_are_on_my_system}:${where_gc_files_must_be_in_container} \
			 -B ${where_license_file_is_on_my_system}:${where_license_file_must_be_in_container} \
			 HCPprocessPipelines.simg

	elif [ "${g_env}" = "SANDBOX" ]; then

		sudo singularity shell \
			 -B ${where_study_is_on_my_system}:${where_study_must_be_in_container} \
			 -B ${where_gc_files_are_on_my_system}:${where_gc_files_must_be_in_container} \
			 -B ${where_license_file_is_on_my_system}:${where_license_file_must_be_in_container} \
			 HCPprocessPipelinesSandbox

	else

		abort "Unrecognized environment: ${g_env}"
		
	fi
}

# Invoke the main function to get things started
main "$@"