annotate mtbls-dwnld @ 1:1fd8547867be draft default tip

"planemo upload commit 76293bd47447c171c939b4f3c194fd0cfbd7f69c-dirty"

#!/bin/bash
# vi: fdm=marker

# Constants {{{1
################################################################

PROG_NAME=$(basename $0)
PROG_PATH=$(dirname $0)
ISASLICER="$PROG_PATH/isaslicer.py"
YES=yes
NO=no
ASPERA_PUBLIC_TOKEN=Xz68YfDe
ASCP=ascp
WGET=wget
PLATFORM=
DISTRIBUTION=
[[ -z $(which uname) ]] || PLATFORM=$(uname)
[[ $PLATFORM == Linux && -e /proc/version ]] && DISTRIBUTION=$(sed 's/^.*(\([^ ]*\).*$/\1/' /proc/version)
[[ $DISTRIBUTION == Alpine ]] || WGET_FLAGS="--progress=dot"

# Global variables {{{1
################################################################

ASPERA=
COMPRESSED=
DEBUG=0
FACTOR_VALUE=
HTML=
METADATA_ONLY=
OUTPUT=
PRIVATE=
QUIET=0
TMP_IN_OUTPUT=
TOKEN=

# Print help {{{1
################################################################

function print_help {
	echo "Usage: $PROG_NAME [options] study"
	echo
	echo "Retrieves a study from Metabolights database."
	echo "By default it uses the ftp server, but with -a option you can ask for using aspera server (you will need the aspera client ascp to be installed)."
	echo
	echo "Options:"
	echo "   -a, --aspera                Use aspera server for downloading. You need the ascp client to be installed, it is freely available for linux 64. See http://downloads.asperasoft.com."
	echo "   -c, --compressed            Output in compressed format. If unset, the output will be a directory."
	echo "   -f, --factor-value          Filter study on a factor value. Example: \"-f myfactor=myvalue\". Only available with wget downloader."
	echo "   -g, --debug                 Debug mode."
	echo "   -h, --help                  Print this help message."
	echo "   -H, --html           FILE   Write HTML file that list files contained in output directory. Not compatible with compressed output."
	echo "   -M, --metadata-only         Download only the metadata (ISA-Tab files i_*, m_*, s_* and a_*) files. This option has no effet if aspera is selected (option -a)."
	echo "   -o, --output         NAME   Set the name of the output (both for directory output or compressed file output). By default the name of the output is determined by the download tool."
	echo "   -p, --private               Indicate the study to download is not public. This is meant for aspera download, since the URL will be different for a public or a private study."
	echo "   -q, --quiet                 Does not print any output. Can be specified twice in order to be real quiet."
	echo "   -t, --token          TOKEN  Set the token or password to use. For aspera public download, if you don't specify a token, the default token '$ASPERA_PUBLIC_TOKEN' will be used."
	echo "   -T, --tmp-in-output         If an output is specified and it is a directory (-c option must not be set), then use it for writing intermediate files."
}

# Error {{{1
################################################################

function error {

	local msg=$1

	echo "ERROR: $msg" >&2

	exit 1
}

# Debug {{{1
################################################################

function debug {

	local dbgmsg="$1"

	[[ $DEBUG -ge 1 ]] && echo "[DEBUG] $dbgmsg" >&2
}


# Read args {{{1
################################################################

function read_args {

	local args="$*" # save arguments for debugging purpose
	
	# Read options
	while true ; do
		shift_count=1
		case $1 in
			-a|--aspera)            ASPERA=$YES ;;
			-c|--compressed)        COMPRESSED=$YES ;;
			-f|--factor-value)      FACTOR_VALUE="$2" ; shift_count=2 ;;
			-g|--debug)             DEBUG=$((DEBUG + 1)) ;;
			-h|--help)              print_help ; exit 0 ;;
			-M|--metadata-only)     METADATA_ONLY=$YES ;;
			-H|--html)              HTML="$2" ; shift_count=2 ;;
			-o|--output)            OUTPUT="$2" ; shift_count=2 ;;
			-p|--private)           PRIVATE=$YES ;;
			-q|--quiet)             QUIET=$((QUIET + 1)) ;;
			-t|--token)             TOKEN="$2" ; shift_count=2 ;;
			-T|--tmp-in-output)     TMP_IN_OUTPUT=$YES ;;
			-) error "Illegal option $1." ;;
			--) error "Illegal option $1." ;;
			--*) error "Illegal option $1." ;;
			-?) error "Unknown option $1." ;;
			-[^-]*) split_opt=$(echo $1 | sed 's/^-//' | sed 's/\([a-zA-Z]\)/ -\1/g') ; set -- $1$split_opt "${@:2}" ;;
			*) break
		esac
		shift $shift_count
	done
	shift $((OPTIND - 1))

	# Read remaining arguments
	[ $# -eq 1 ] || error "You must specify one, and only one, study to retrieve."
	STUDY="$1"

	# Check token
	if [[ -n $ASPERA && -z $TOKEN ]] ; then
		if [[ -z $PRIVATE ]] ; then
			TOKEN=$ASPERA_PUBLIC_TOKEN
		else
			error "You need to specify a token for retrieving private studies with aspera."
		fi
	fi
	[[ -z $PRIVATE || -n $TOKEN ]] || error "You need to set a token for retrieving private studies."

	# Turn off --tmp-to-output if --compressed is set
	[[ $TMP_IN_OUTPUT == $YES && ( $COMPRESSED == $YES || -z $OUTPUT ) ]] && TMP_IN_OUTPUT=$NO

	# Debug
	debug "Arguments are : $args"
	debug "Study to retrieve is : $STUDY"
	debug "ASPERA=$ASPERA"
	debug "COMPRESSED=$COMPRESSED"
	debug "DEBUG=$DEBUG"
	debug "FACTOR_VALUE=$FACTOR_VALUE"
	debug "HTML=$HTML"
	debug "METADATA_ONLY=$METADATA_ONLY"
	debug "OUTPUT=$OUTPUT"
	debug "PRIVATE=$PRIVATE"
	debug "QUIET=$QUIET"
	debug "TMP_IN_OUTPUT=$TMP_IN_OUTPUT"
	debug "TOKEN=$TOKEN"
	[[ -n $ASPERA ]] && debug "Aspera will be used."
	[[ -n $TOKEN ]] && debug "Token/Password is \"$TOKEN\"."
}

# Get download output path {{{1
################################################################

get_download_output_path() {

	local downloader="$1"
	local study_name="$2"
	local output_dir="$3"
	local output_path="$study_name"

	[[ -z $output_dir ]] || output_path="$output_dir/$output_path"
	[[ $downloader == $WGET ]] && output_path+=".zip"

	echo "$output_path"
}

# Download with ascp {{{1
################################################################

download_with_ascp() {

	local study_name="$1"
	local metadata_only="$2"
	local output_dir="$3"
	local dwnld_flags=
	local dwnld_link=

	# Check ascp
	[ -n "$(which ascp)" ] || error "ascp command not found. Please install Aspera client, version 3.7.4 or greater. See http://downloads.asperasoft.com/en/downloads/62."
	debug "$ASCP: $(which $ASCP)"
	debug "QUIET: $QUIET"

	# Silence downloader output
	[[ $QUIET -eq 0 ]] || dwnld_flags=-q

	# Set download flags
	[[ -z $dwnld_flags ]] || dwnld_flags+=" "
	dwnld_flags+="--policy=fair -T -l 1g"

	dwnld_flags+=" -P33001"

	# Set download link
	if [[ -z $PRIVATE ]] ; then

		# Make full path for public study
		study_path=$STUDY
		if [[ -z ${study_path##MTBLS*} ]] ; then
			study_path="/studies/public/$study_path"
		fi
		dwnld_link="[e-mail]:$study_path"

	# Private study
	else
		dwnld_link="[e-mail]:$STUDY"
	fi

	# Export token
	debug "export ASPERA_SCP_PASS=\"$TOKEN\""
	export ASPERA_SCP_PASS="$TOKEN"

	# Run download command
	if [[ -n $output_dir ]] ; then
		mkdir -p "$output_dir"
		curdir=$(pwd)
		cd "$output_dir"
	fi
	if [[ $metadata_only == $YES ]] ; then
		debug "Download command: $ASCP $dwnld_flags -N '?_*.t*' -E '*.*' -E 'p*' $dwnld_link ."
		$ASCP $dwnld_flags -N '?_*.t*' -E '*.*' -E 'p*' $dwnld_link .
		[[ $? == 0 ]] || error "Downloading of study $STUDY has failed. Error code returned is $?."
	else
		debug "Download command: $ASCP $dwnld_flags $dwnld_link ."
		$ASCP $dwnld_flags $dwnld_link .
		[[ $? == 0 ]] || error "Downloading of study $STUDY has failed. Error code returned is $?."
	fi
	[[ -z $output_dir ]] || cd "$curdir"
}

# Download with wget {{{1
################################################################

download_with_wget() {

	local study_name="$1"
	local metadata_only="$2"
	local output_dir="$3"
	local dwnld_flags=

	# Check wget
	[ -n "$(which wget)" ] || error "wget command not found."
	debug "$WGET: $(which $WGET)"

	# Set download link
	file="$study_name"
	[[ $metadata_only == $YES ]] && file=metadata
	dwnld_link="https://www.ebi.ac.uk/metabolights/$study_name/files/$file"
	[[ -n $TOKEN ]] && dwnld_link+="?token=$TOKEN"

	# Set download output
	output_path="$study_name.zip"
	if [[ -n $output_dir ]] ; then
		mkdir -p "$output_dir"
		output_path="$output_dir/$output_path"
	fi
	dwnld_flags="-O $output_path"

	# Silence downloader output
	wget_log_file=$(mktemp -t $PROG_NAME.XXXXXX)
	[[ $QUIET -eq 0 ]] || dwnld_flags+=" -q -o $wget_log_file"

	# Run download command
	debug "Download command: $WGET $WGET_FLAGS $dwnld_flags $dwnld_link"
	$WGET $WGET_FLAGS $dwnld_flags $dwnld_link
	[[ $? == 0 ]] || error "Downloading of study $STUDY has failed. wget log file: $(cat $wget_log_file)"
	rm -f $wget_log_file
}

# Download {{{1
################################################################

download() {

	local downloader="$1"
	local study_name="$2"
	local metadata_only="$3"
	local output_dir="$4"

	if [[ $downloader == $WGET ]] ; then
		download_with_wget "$2" "$3" "$output_dir"
	else
		download_with_ascp "$2" "$3" "$output_dir"
	fi
}

# Check download {{{1
################################################################

check_download() {

	local download_path="$1"

	[[ -d $download_path || -f $download_path ]] || error "The downloading of $tmp_output failed. The output file doesn't exist."
	[[ ! -f $download_path || -s $download_path ]] || error "The downloading of $tmp_output failed. The output file is empty."
}

# Unzip study {{{1
################################################################

unzip_study() {

	local tmp_output="$1"
	local output="$2"
	local unzip_flags=

	# Silence unzip program
	[[ $QUIET -eq 0 ]] || unzip_flags=-qq

	debug "Unzipping file \"$tmp_output\"."
	[[ -z $output ]] || debug "Unzipping into \"$output\"."

	[[ -n $(which unzip) ]] || error "unzip command not found. Please install zip package."

	zip=$tmp_output
	debug "Zipped file is \"$zip\"."
	if [[ -z $output ]] ; then
		output=${zip%.*}
		[[ -d "$output" ]] && rm -r "$output"
	fi
	debug "Output directory will be \"$output\"."
	zip_abs_path=$(realpath "$zip")
	curdir=$(pwd)
	debug "Current directory is \"$curdir\"."
	mkdir -p "$output"
	cd "$output"
	unzip $unzip_flags "$zip_abs_path" >&2 || error "Unable to unzip archive $zip_abs_path."
	cd "$curdir"

	echo "$output"
}

# As zip {{{1
################################################################

as_zip() {

	local path="$1"

	if [[ -d $path ]] ; then

		zip_file="$path.zip"
		zip "$zip_file" $path/*
		rm -r "$path"
		path="$zip_file"
	fi

	echo "$path"
}

# As folder {{{1
################################################################

as_folder() {

	local path="$1"
	local output="$2"

	debug "as_folder($path, $output)"
	if [[ -f $path && ${path##*.} == 'zip' ]] ; then
		folder=$(unzip_study "$path" "$output")
		rm "$path"
		path="$folder"
	elif [[ -d $path && -n $output && $path != $output ]] ; then
		mkdir -p "$output"
		mv "$path"/* "$output"/.
		rm -r "$path"
		path="$output"
	fi

	echo "$path"
}

# Make folder or zip {{{1
################################################################

make_folder_or_zip() {

	local path="$1"
	local compressed="$2"
	local output="$3"

	debug "make_folder_or_zip($path, $compressed, $output)"
	[[ -e $path ]] || error "No file or folder at path \"$path\"."

	# Compress folder
	if [[ $compressed == $YES ]] ; then
		path=$(as_zip "$path")
	else
		path=$(as_folder "$path" "$output")
	fi

	echo "$path"
}

# Write HTML file {{{1
################################################################

function write_html_file {

	local HTML=$1
	local tmp_output=$2

	cat >$HTML <<EOF
<html>
	<header>
		<title>Metabolights study</title>
	</header>
	<body>
		<a href="i_Investigation.txt">Investigation file</a><br/>
EOF

	echo "<br/>" >>$HTML
	echo "          Study files:<br/>" >>$HTML
	for f in $tmp_output/s_* ; do
		filename=$(basename "$f")
		echo "          <a href=\"$filename\">$filename</a><br/>" >>$HTML
	done

	echo "<br/>" >>$HTML
	echo "          Assay files:<br/>" >>$HTML
	for f in $tmp_output/a_* ; do
		filename=$(basename "$f")
		echo "          <a href=\"$filename\">$filename</a><br/>" >>$HTML
	done

	echo "<br/>" >>$HTML
	echo "          Data files:<br/>" >>$HTML
	for f in $tmp_output/m_* ; do
		filename=$(basename "$f")
		echo "          <a href=\"$filename\">$filename</a><br/>" >>$HTML
	done

	cat >>$HTML <<EOF
	</body>
</html>
EOF
}

# Get data files {{{1
################################################################

get_data_files() {

	local json_file="$1"

	python3 <<EOF
# @@@BEGIN_PYTHON@@@
import json
import sys
with open('$json_file') as f:
    data_list = json.load(f)
    for elem in data_list:
	    print("\n".join(elem['data_files']))
# @@@END_PYTHON@@@
EOF
}

# MAIN {{{1
################################################################

read_args "$@"

study_name=$(basename $STUDY)
downloader=$WGET
output_dir=
[[ $ASPERA == $YES ]] && downloader=$ASCP
[[ $TMP_IN_OUTPUT != $YES ]] || output_dir="$OUTPUT"

# Download only part of the study using factor value
if [[ -n $FACTOR_VALUE ]] ; then

	# Get factor name and value
	factor_name=${FACTOR_VALUE%%=*}
	factor_value=${FACTOR_VALUE#*=}

	# Download only metadata
	download "$downloader" "$study_name" "$YES" # XXX Download output must be written into $OUTPUT if TMP_IN_OUTPUT is set
	dwnld_output=$(get_download_output_path "$downloader" "$study_name")
	dwnld_output=$(as_folder "$dwnld_output")

	# Get data files to download
	data_files=$(mktemp -t $PROG_NAME.XXXXXX) # XXX must be created into $OUTPUT if TMP_IN_OUTPUT is set
	[[ -x "$ISASLICER" ]] || error "Cannot find or run isaslicer.py script."
	debug "Run ISA slicer: \"$ISASLICER\" 'isa-tab-get-data-list' \"$abs_dwnld_output\" \"$data_files\" --json-query \"{ \\\"$factor_name\\\": \\\"$factor_value\\\" }\""
	abs_dwnld_output=$(realpath "$dwnld_output")
	"$ISASLICER" --log-level DEBUG 'isa-tab-get-data-list' "$abs_dwnld_output" "$data_files" --json-query "{ \"$factor_name\": \"$factor_value\" }" 2>&1 || error "Call to isaslicer failed."

	# Download data files
	wget_log_file=$(mktemp -t $PROG_NAME.XXXXXX)
	get_data_files "$data_files" | sort | uniq | while read file ; do
		if [[ -n $file ]] ; then
			dwnld_flags=
			[[ $QUIET -eq 0 ]] || dwnld_flags+=" -q -o $wget_log_file"
			dwnld_link="https://www.ebi.ac.uk/metabolights/$study_name/files/$file"
			debug "Download command: $WGET $WGET_FLAGS $dwnld_flags $dwnld_link"
			$WGET $WGET_FLAGS $dwnld_flags -O "$dwnld_output/$file" "$dwnld_link" # XXX Download output must be written into $OUTPUT if TMP_IN_OUTPUT is set
			[[ $? == 0 ]] || error "Downlad of study file \"$file\" has failed. wget log file: $(cat $wget_log_file)"
		fi
	done
	rm -f $wget_log_file

	# Remove data files list
	rm "$data_files"

# Download whole study
else

	# Download whole study
	download "$downloader" "$study_name" "$METADATA_ONLY" "$output_dir" # XXX Download output must be written into $OUTPUT if TMP_IN_OUTPUT is set

	# Get output path
	dwnld_output=$(get_download_output_path "$downloader" "$study_name" "$output_dir") # XXX Correct output path when TMP_IN_OUTPUT is set
fi

# Check output
check_download "$dwnld_output"

# Output in right format (zipped or folder)
dwnld_output=$(make_folder_or_zip "$dwnld_output" "$COMPRESSED" "$output_dir") # XXX zip must be written into $OUTPUT and unzipped into $OUTPUT if TMP_IN_OUTPUT is set

# Output HTML
[[ -z $HTML || ! -d $dwnld_output ]] || write_html_file "$HTML" "$dwnld_output"

# Rename output
[[ -z $OUTPUT || $TMP_IN_OUTPUT == $YES ]] || mv "$dwnld_output" "$OUTPUT"