handle_request_raw_viollier

#!/bin/bash

configfile=viollier.conf

usage() { echo "Usage: $0 [ -f ] [-c <configfile>]" 1>&2; exit $1; }

# Helper
fail() {
	printf '\e[31;1mArgh: %s\e[0m\n'	"$1"	1>&2
	[[ -n "$2" ]] && echo "$2" 1>&2
	exit 1
}

oops() {
	printf '\e[33;1mOops:%s\e[0m\n'	"$1"	 1>&2
}

title() {
	printf '\e[34;1m======================\n%s\n======================\e[0m\n\n'	"$1"
}

message() {
	printf '\e[37;1m%s\t%s\e[0m\n' "$1" "$2"
}

status() {
	printf '\e[36;1m%s\e[0m\n'	"$1"
}

force=0
while getopts "c:fh" o; do
	case "${o}" in
		c)	configfile=${OPTARG}
			if [[ ! -r ${configfile} ]]; then
				echo "Cannot read ${configfile}" 1>&2
				usage 1
			fi
			;;
		f)	force=1 ;;
		h)	usage 0	;;
		*)	usage 1	;;
	esac
done
shift $((OPTIND-1))


. ${configfile}

: ${fileserver:?}
# ${srvport}
: ${expname:?}
: ${basedir:=$(pwd)}
: ${download:?}
: ${sampleset:?}


target_base='raw_othercenters'
req_file='fastq_requests.tsv'
msg_file='request_results.txt'

[[ "${1}" == '-h' || "${1}" == '--help' ]] && usage 0


if [[ $( < ~/.netrc ) =~ machine[[:space:]]+${fileserver}[[:space:]]?login[[:space:]]+([^[:space:]]+) ]]; then
	username="${BASH_REMATCH[1]}"
elif [[ $( < ~/.ssh/config ) =~ Host[[:space:]]+${fileserver}[[:space:]]+ ]]; then
	username=
else
	fail "cannot find login for machine ${fileserver} in ~/.netrc nor ~/.ssh/config" 
fi


cd ${basedir}

# download new request file and compare with old one
if lftp -c "set xfer:clobber on; get1 sftp://${username:+${username}@}${fileserver}${srvport:+:${srvport}}/${expname}/${target_base}/${req_file} -o ${download}/${target_base}/"; then
	if (( force )); then
		status "Forcing update"
	# check content
	elif [[ -e "${download}/${target_base}/${req_file}.old" ]] && diff -q "${download}/${target_base}/${req_file}"{,.old}; then
		# same: nothing to do
		status "No new uploads in ${req_file}"
		grep -P '^(\([[:alpha:]]+|[[:space:]]+|summary)' ${download}/${target_base}/${msg_file}
		exit 0
	fi
else
	# error
	fail "Cannot download request file sftp://${username:+${username}@}${fileserver}${srvport:+:${srvport}}/${expname}/${target_base}/${req_file}" "Please check that ${configfile} is correctly setup"	
fi

# create result file
tee ${download}/${target_base}/${msg_file} <<MSG
starting on $(date --rfc-3339=seconds)
new ${req_file}, date $(date --rfc-3339=seconds -r "${download}/${target_base}/${req_file}")

validating input:
MSG

# validate input
validated_file='fastq_requests_validated.tsv'
if python ./validate_request_raw_viollier.py --req_file ${download}/${target_base}/${req_file} --out_file ${download}/${target_base}/${validated_file} --db_config ${basedir}/${dbconfigfile} 2>&1; then
	printf '\e[36;1mValidation successful\e[0m\n' 1>&2
	echo -e "successfully validated input\n"
else
	# error
	printf '\e[31;1mValidation failed!\e[0m'     1>&2
	echo -e "error while trying to validate the request, see above\n"
fi | tee -a ${download}/${target_base}/${msg_file}

tee ${download}/${target_base}/${msg_file} <<MSG2

attempting upload:
MSG2

# attempt upload
subdir=$(date '+%Y-%m-%d' -r "${download}/${target_base}/${req_file}")
if ./upload_viollier_raw -q -c "${configfile}" -s "${subdir}" "${download}/${target_base}/${validated_file}" 2>&1; then 
	# upload success
	printf '\e[36;1mSuccess\e[0m\n' 1>&2
	echo -e "successfully uploaded to ${subdir}\n"
	mv -v "${download}/${target_base}/${req_file}"{,.old}
	mv -v "${download}/${target_base}/${validated_file}"{,.old}
else
	# error
	printf '\e[31;1mArgh:\e[0m'	1>&2
	echo -e "error while trying to upload, see above\n"
fi | tee -a ${download}/${target_base}/${msg_file}

(echo  $'\nsummary of troubles'; grep -oP '(?<=[\(])(zero yield|[[:alpha:]]+)' ${download}/${target_base}/${msg_file}|sort|uniq -c || echo $'\tno troubles found' ) | tee -a ${download}/${target_base}/${msg_file}

exec lftp -c "set xfer:clobber on; put ${download}/${target_base}/${msg_file} -o sftp://${username:+${username}@}${fileserver}${srvport:+:${srvport}}/${expname}/${target_base}/"