sra_ascp

#!/bin/bash

## Upload files to NCBI SRA using aspera ascp CLI
## @sbamin

# usage
show_help() {
cat << EOF

Wrapper to transfer data via aspera ascp command line interface to NCBI SRA

Required parameters: 
    If aspera command line client is not installed, visit https://downloads.asperasoft.com to install aspera cli.

Usage: ${0##*/} -p <Absolute path to file to be uploaded: One at a time> -s subasp@upload.ncbi.nlm.nih.gov:uploads/foo@example.com_xXXYz12X/SUB0000000/

Required arguments:
	-p Absolute path to file to be uploaded: One at a time
	-s remote server path, including path to directory under which data will be stored

Optional arguments:
	-k path to aspera SRA ssh key (default: ~/.ssh/ncbi_ascp.openssh)
	-l limit upload bandwidth (default: 100m)

EOF
}

if [[ $# -lt 1 ]];then show_help;exit 1;fi

while getopts "p:k:l:s:h" opt; do
    case "$opt" in
        h) show_help;exit 0;;
        p) FILEPATH=$OPTARG;;
		k) ASCP_SSH_KEY=$OPTARG;;
		l) UP_BANDWIDTH=$OPTARG;;
		s) REMOTEPATH=$OPTARG;;
       '?') show_help >&2 exit 1 ;;
    esac
done

## Defaults ##
FILEPATH=${FILEPATH:-"NA"}
ASCP_SSH_KEY=${ASCP_SSH_KEY:-"$HOME/.ssh/ncbi_ascp.openssh"}
UP_BANDWIDTH=${UP_BANDWIDTH:-"100m"}
REMOTEPATH=${REMOTEPATH:-"subasp@upload.ncbi.nlm.nih.gov:uploads/foo@example.com_xXXYz12X/SUB0000000/"}

if ! command -v ascp; then
	echo -e "Missing aspera ascp cli" >&2
	exit 1
fi

if [[ ! -f "$ASCP_SSH_KEY" ]]; then
	echo -e "\nMissing SRA aspera ssh key at ${ASCP_SSH_KEY}\nProvide path to SRA aspera ssh key at -k" >&2
	exit 1
fi

## make log dir
ASCPLOG="${HOME}"/logs/ascp
mkdir -p "${ASCPLOG}"
ASCPLOGFILE="${ASCPLOG}"/sra_cgp_ascp.log

if [[ ! -f "${FILEPATH}" ]]; then
	echo -e "\nWARN: Skipping upload as can not locate file to be uploaded at ${FILEPATH} or -p argument is empty\n" >&2
	
	## update log file with SKIP_FNF (file not found) and exit code of 1
	TSTAMP=$(date +%d%b%y_%H%M%S%Z)

	if command -v slacktee; then
		printf "SKIP_FNF\t%s\t%s\t1\n" "$FILEPATH" "$TSTAMP" | slacktee -t "SKIP_FNF" -i "warning" | tee -a "${ASCPLOGFILE}"
	else
		printf "SKIP_FNF\t%s\t%s\t1\n" "$FILEPATH" "$TSTAMP" | tee -a "${ASCPLOGFILE}"
	fi

	## let slack ping before exiting
	sleep 2
else
	## update log file
	TSTAMP=$(date +%d%b%y_%H%M%S%Z)
	printf "ACTIVE\t%s\t%s\tNA\n" "$FILEPATH" "$TSTAMP" | tee -a "${ASCPLOGFILE}"
	sleep 2

	## Add -q to run in quiet mode
	ascp -i "$ASCP_SSH_KEY" -QT -l"${UP_BANDWIDTH}" -k1 -d "${FILEPATH}" "${REMOTEPATH}"
	exitstat=$?

	## update log file
	if [[ "$exitstat" == 0 ]]; then
		TSTAMP=$(date +%d%b%y_%H%M%S%Z)
		printf "OK\t%s\t%s\t%s\n" "$FILEPATH" "$TSTAMP" "$exitstat" | tee -a "${ASCPLOGFILE}"
		sleep 2
	else
		TSTAMP=$(date +%d%b%y_%H%M%S%Z)

		if command -v slacktee; then
			printf "ERROR\t%s\t%s\t%s\n" "$FILEPATH" "$TSTAMP" "$exitstat" | slacktee -t "ERROR" -i "stop" | tee -a "${ASCPLOGFILE}"
		else
			printf "ERROR\t%s\t%s\t%s\n" "$FILEPATH" "$TSTAMP" "$exitstat" | tee -a "${ASCPLOGFILE}"
		fi

		sleep 2
	fi
fi

## END ##