sort_viollier

#!/bin/bash

configfile=server.conf

usage() { echo "Usage: $0 [-c <configfile>] [-r <recent>] [ -4 <protocolsyaml> ] [ <directories [...]> ]" 1>&2; exit $1; }

protocolsyaml=

while getopts "c:r:4:h" o; do
	case "${o}" in
		c)	configfile=${OPTARG}
			if [[ ! -r ${configfile} ]]; then
				echo "Cannot read ${configfile}" 1>&2
				usage 2
			fi
			;;
		r)	recent=${OPTARG}
			if [[ ! ${recent} =~ ^20[[:digit:]]{2}([01][[:digit:]]([0-3][[:digit:]])?)?$ ]]; then
				echo "Wrong format ${recent}" 1>&2
				usage 2
			fi
			;;
		4)	protocolsyaml=${OPTARG}
			if [[ ! -r ${protocolsyaml} ]]; then
				echo "Cannot read ${protocolsyaml}" 1>&2
				usage 2
			fi
			;;
		h)	usage 0	;;
		*)	usage 2	;;
	esac
done
shift $((OPTIND-1))

duplicates=1

. ${configfile}

: ${lab:?}
: ${basedir:=$(pwd)}
: ${download:?}
: ${sampleset:?}



if (( ${#@} < 1)); then
	scan=( ${basedir}/${download}/*/ )
else
	scan=( "${@}" )
fi

rx_folder='^(20[[:digit:]]{2}[01][[:digit:]][0-3][[:digit:]])_([[:alnum:]]+)$'  # e.g.: 20210528_061936
#            ^-[1]: date                                      ^-[2]: time

# appended batches: make shared header (cf. sort_samples_jobinfo)
# and also setup combined error status (GRANDTOTAL_ALLOK)
cat > ${basedir}/${sampleset}/movedatafiles.sh <<SH_HEAD
link='--link'

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

warn() {
	printf '\e[33;1mArgh: %s\e[0m\n'	"\$1"	1>&2
	[[ -n "\$2" ]] && echo "\$2" 1>&2
}

GRANDTOTAL_ALLOK=1
ALLOK=1
X() {
	ALLOK=0
}

# sanity checks
[[ -d '${sampleset}' ]] || fail 'No sampleset directory:' '${sampleset}'
SH_HEAD

success=1
b=0
for d in "${scan[@]}"; do
	# progress bar
	(( v = b * 128 / ${#scan[@]} ))
	bar1="$(for ((i=0;i< (v>>3);++i)) do echo -n $'\u2588'; done)"
	if (( (v&7) > 0 )); then
		bar2="$(echo -ne "\u$(printf '%04x' $((0x2590 - (v&7) )) )")"
	else
		bar2=''
	fi
	bar3="$(for ((i=0;i< ( (128-v)>>3);++i)) do echo -n $'\u22C5' ; done)" # normally: \u00b7
	cat >> ${basedir}/${sampleset}/movedatafiles.sh <<SH_BAR
echo -ne '\\r[${bar1}${bar2}${bar3}] ${b}/${#scan[@]}\\r'
SH_BAR
	(( ++b ))
	# findable ?
	if [[ ! -d "${d}" ]]; then
		echo "No ${d}" 1>&2
		success=0
		continue
	fi
	# skip older
	if [[ -n "${recent}" && "$(basename ${d})" < "${recent}" ]]; then
		continue
	fi
	# folder ?
	if [[ $(basename ${d}) =~ ${rx_folder} ]]; then
		# check for left-over (windows') partial download files
		if [[ -n "$(find "${d}" -type f -name '*.filepart' | tee /dev/stderr)" ]]; then
			echo -e "\e[33;1mIncompletely downloaded files in $(basename ${d})\e[0m skipping..."
			touch status/syncviollier_failed
			continue
		fi
		# Remove irrelevant samples from sample sheet
		if [[ "$(< ${d}/SampleSheetUsed.csv)" =~ [[:space:]]Error ]]; then
			echo -e "Filtering out 'Error<n>' samples"
			mv ${d}/SampleSheetUsed.csv{,.err}
			grep -vP '^Error' ${d}/SampleSheetUsed.csv.err > ${d}/SampleSheetUsed.csv
		fi
		# Search for patchmap if available
		patch=
		if [[ -e "${d%%/}.patchmap.tsv" ]]; then
			echo "Patchmap found for $(basename ${d})"
			patchmap="--patchmap=${d%%/}.patchmap.tsv"
		fi
		./sort_samples_jobinfo --summary --sourcedir=${d} ${patchmap} --outdir=${basedir}/${sampleset} ${mode:+--mode=${mode}} --force --forcelanes --batch ${lab} --append --staging ${protocolsyaml:+--protocols=${protocolsyaml}}
		# between appended batches: combine error status into overall status  & reset local error status
		cat >> ${basedir}/${sampleset}/movedatafiles.sh <<MERGE_ALLOK
(( GRANDTOTAL_ALLOK &= ALLOK ))
ALLOK=1
MERGE_ALLOK
	else
		# ignore mal formed folders
		echo "Can't parse $(basename ${d})"
	fi
done

# coda: (cf. sort_samples_jobinfo)
# progress bar & based on combined exit status
bar1="$(for ((i=0;i< (128>>3);++i)) do echo -n $'\u2588'; done)"
cat >> ${basedir}/${sampleset}/movedatafiles.sh <<SH_FOOT
echo -e '\\r[${bar1}] done.'

if (( ! GRANDTOTAL_ALLOK )); then
	echo Some errors
	exit 1
fi;

echo All Ok
exit 0
SH_FOOT

if (( success )); then
	echo "All ok"
	exit 0
else
	echo "Some problems"
	exit 1
fi