Merge remote-tracking branch 'dataset_template/master' into HEAD

.gitattributes

@@ -1,3 +1,12 @@
 
 * annex.backend=MD5E
-**/.git* annex.largefiles=nothing
+**/.git* annex.largefiles=nothing
+
+* annex.largefiles=(largerthan=1mb)
+*.c annex.largefiles=nothing
+*.cpp annex.largefiles=nothing
+*.h annex.largefiles=nothing
+*.py annex.largefiles=nothing
+*.sh annex.largefiles=nothing
+
+scripts/* annex.largefiles=nothing

.gitignore

@@ -0,0 +1,4 @@
+.nfs*
+*.jugdata/
+/.tmp/
+/logs/

scripts/datalad.sh

@@ -0,0 +1,36 @@
+#!/bin/bash
+
+source scripts/utils.sh echo -n
+
+function activate_gitannex {
+	_conda_env=$(git config --file scripts/config/datalad_config --get datalad.conda.conda-env || echo -n)
+	if [[ ! -z "${_conda_env}" ]]
+	then
+		_modules=$(git config --file scripts/config/datalad_config --get datalad.conda.modules || echo -n)
+		if [[ -z "$(which conda)" ]] && [[ ! -z "${_modules}" ]]
+		then
+			module load ${_modules} 2>/dev/null
+			eval "$(conda shell.bash hook)"
+		fi
+		conda activate ${_conda_env} >/dev/null 2>&1 || eval "$(conda shell.bash hook)"
+		conda activate ${_conda_env}
+		exit_on_error_code "Failed to init git-annex conda env"
+	fi
+}
+
+function install_datalad {
+	init_venv --name venv --prefix .tmp/
+	exit_on_error_code "Failed to init venv"
+
+	datalad --version >/dev/null 2>&1 || python3 -m pip install -r scripts/requirements_datalad.txt
+	exit_on_error_code "Failed to install datalad requirements: pip install"
+}
+
+which git-annex || activate_gitannex
+datalad --version >/dev/null 2>&1 || install_datalad
+exit_on_error_code "Failed to install datalad requirements: pip install"
+
+# Add bin to PATH
+[[ -d "$(realpath bin/)" ]] && export PATH="${PATH}:$(realpath bin)"
+
+datalad "$@"

scripts/get_utils.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+wget -O scripts/utils.sh https://raw.githubusercontent.com/satyaog/datasets_utils/095f79be167b721fbff34e45146dba519c44c305/utils.sh

scripts/jug_exec.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+from jug import is_jug_running
+
+if is_jug_running():
+    from sys import argv
+    from jug.utils import jug_execute
+    jug_execute(argv[1:])
+else:
+    from sys import argv
+    from jug.jug import main
+    try:
+        # Split and reorder jug's argv from script's argv
+        argv[:] = ["jug", "execute"] + argv[1:argv.index("--")] + \
+                  [__file__] + argv[argv.index("--"):]
+    except ValueError:
+        argv[:] = ["jug", "execute", __file__] + argv[1:]
+    main(argv)

scripts/requirements_datalad.txt

@@ -0,0 +1,2 @@
+datalad[core]==0.11.8
+datalad==0.11.8

scripts/stats.sh

@@ -0,0 +1,78 @@
+#!/bin/bash
+set -o errexit -o pipefail -o noclobber
+
+function acquire_lock {
+	if [ -e .tmp/lock_stats ]
+	then
+		[[ "$$" -eq "`cat .tmp/lock_stats`" ]] || return 1
+	else
+		mkdir -p .tmp/
+		echo -n "$$" > .tmp/lock_stats
+		chmod -wx .tmp/lock_stats
+		[[ "$$" -eq "`cat .tmp/lock_stats`" ]] || return 1
+	fi
+}
+
+function delete_lock {
+	rm -f .tmp/lock_stats
+}
+
+function if_empty {
+	if [[ -z "$1" ]]
+	then
+		echo -n "$2"
+	else
+		echo -n "$1"
+	fi
+}
+
+declare -a _dirs
+
+_STDIN=0
+while [[ $# -gt 0 ]]
+do
+	_arg="$1"; shift
+	case "${_arg}" in
+		--stdin) _STDIN=1
+		echo "stdin = [${_STDIN}]"
+		;;
+		--) break ;;
+		-h | --help)
+		>&2 echo "Options for $(basename "$0") are:"
+		>&2 echo "--stdin force read directories from stdin instead of script's arguments"
+		exit 1
+		;;
+		*) _dirs+=("${_arg}") ;;
+	esac
+done
+
+acquire_lock || exit 1
+
+trap delete_lock EXIT
+
+if [[ ${#_dirs[@]} == 0 ]] || [[ ${_STDIN} == 1 ]]
+then
+	readarray -t _dirs
+fi
+
+rm -f files_count.stats
+rm -f disk_usage.stats
+find "${_dirs[@]}" -type d | sort -u | while read d
+do
+	fc=$(find "$d" -maxdepth 1 -type f | wc -l)
+	if [[ "$fc" -ne 0 ]]
+	then
+		printf "%d\t%s\n" "$fc" "$d" >>files_count.stats
+	fi
+
+	du=$(find "$d" -maxdepth 1 -type f | xargs -r du -c | tail -n1 | cut -f1)
+	if [[ ! -z "$du" ]]
+	then
+		printf "%d\t%s\n" "$du" "$d" >>disk_usage.stats
+	fi
+
+	for sd in "$d"/*
+	do
+		echo "$sd"
+	done | xargs chmod a-w
+done

scripts/utils.sh

@@ -0,0 +1,431 @@
+#!/bin/bash
+
+pushd `dirname "${BASH_SOURCE[0]}"` >/dev/null
+_SCRIPT_DIR=`pwd -P`
+popd >/dev/null
+
+function exit_on_error_code {
+	local _ERR=$?
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--err)
+			if [[ ${_ERR} -eq 0 ]]
+			then
+				_ERR=$1
+			fi
+			shift
+			;;
+			-h | --help)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for ${FUNCNAME[0]} are:"
+			>&2 echo "[--err INT] use this exit code if '\$?' is 0 (optional)"
+			>&2 echo "ERROR_MESSAGE error message to print"
+			exit 1
+			;;
+			*) set -- "${_arg}" "$@"; break ;;
+		esac
+	done
+
+	if [[ ${_ERR} -ne 0 ]]
+	then
+		>&2 echo "$(tput setaf 1)ERROR$(tput sgr0): $1: ${_ERR}"
+		exit ${_ERR}
+	fi
+}
+
+function test_enhanced_getopt {
+	! getopt --test > /dev/null
+	if [[ ${PIPESTATUS[0]} -ne 4 ]]
+	then
+		>&2 echo "enhanced getopt is not available in this environment"
+		exit 1
+	fi
+}
+
+function enhanced_getopt {
+	local _NAME=$0
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--options) local _OPTIONS="$1"; shift ;;
+			--longoptions) local _LONGOPTIONS="$1"; shift ;;
+			--name) local _NAME="$1"; shift ;;
+			--) break ;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "--options OPTIONS The short (one-character) options to be recognized"
+			>&2 echo "--longoptions LONGOPTIONS The long (multi-character) options to be recognized"
+			>&2 echo "--name NAME name that will be used by the getopt routines when it reports errors"
+			exit 1
+			;;
+		esac
+	done
+
+	local _PARSED=`getopt --options="${_OPTIONS}" --longoptions="${_LONGOPTIONS}" --name="${_NAME}" -- "$@"`
+	if [[ ${PIPESTATUS[0]} -ne 0 ]]
+	then
+		exit 2
+	fi
+
+	echo "${_PARSED}"
+}
+
+function init_conda_env {
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--name) local _name="$1"; shift
+			echo "name = [${_name}]"
+			;;
+			--prefix) local _prefixroot="$1"; shift
+			echo "prefix = [${_prefixroot}]"
+			;;
+			--tmp) local _prefixroot="$1"; shift
+			>&2 echo "Deprecated --tmp option. Use --prefix instead."
+			echo "tmp = [${_prefixroot}]"
+			;;
+			--) break ;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for ${FUNCNAME[0]} are:"
+			>&2 echo "--name STR conda env prefix name"
+			>&2 echo "--prefix DIR directory to hold the conda prefix"
+			exit 1
+			;;
+		esac
+	done
+
+	local _CONDA_ENV=$CONDA_DEFAULT_ENV
+
+	# Configure conda for bash shell
+	eval "$(conda shell.bash hook)"
+	if [[ ! -z ${_CONDA_ENV} ]]
+	then
+		# Stack previous conda env which gets cleared after
+		# `eval "$(conda shell.bash hook)"`
+		conda activate ${_CONDA_ENV}
+		unset _CONDA_ENV
+	fi
+
+	if [[ ! -d "${_prefixroot}/env/${_name}/" ]]
+	then
+		conda create --prefix "${_prefixroot}/env/${_name}/" --yes --no-default-packages || \
+		exit_on_error_code "Failed to create ${_name} conda env"
+	fi
+
+	conda activate "${_prefixroot}/env/${_name}/" && \
+	exit_on_error_code "Failed to activate ${_name} conda env"
+
+	"$@"
+}
+
+function init_venv {
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--name) local _name="$1"; shift
+			echo "name = [${_name}]"
+			;;
+			--prefix) local _prefixroot="$1"; shift
+			echo "prefix = [${_prefixroot}]"
+			;;
+			--tmp) local _prefixroot="$1"; shift
+			>&2 echo "Deprecated --tmp option. Use --prefix instead."
+			echo "tmp = [${_prefixroot}]"
+			;;
+			--) break ;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for ${FUNCNAME[0]} are:"
+			>&2 echo "--name STR venv prefix name"
+			>&2 echo "--prefix DIR directory to hold the virtualenv prefix"
+			exit 1
+			;;
+		esac
+	done
+
+	if [[ ! -d "${_prefixroot}/venv/${_name}/" ]]
+	then
+		mkdir -p "${_prefixroot}/venv/${_name}/" && \
+		python3 -m venv "${_prefixroot}/venv/${_name}/" || \
+		exit_on_error_code "Failed to create ${_name} venv"
+	fi
+
+	source "${_prefixroot}/venv/${_name}/bin/activate" || \
+	exit_on_error_code "Failed to activate ${_name} venv"
+	python3 -m pip install --upgrade pip
+
+	"$@"
+}
+
+function print_annex_checksum {
+	local _CHECKSUM=MD5
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			-c | --checksum) local _CHECKSUM="$1"; shift ;;
+			-h | --help)
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "[-c | --checksum CHECKSUM] checksum to print (default: MD5)"
+			exit 1
+			;;
+			--) break ;;
+			*) >&2 echo "Unknown option [${_arg}]"; exit 3 ;;
+		esac
+	done
+
+	for _file in "$@"
+	do
+		local _annex_file=`ls -l -- "${_file}" | grep -o ".git/annex/objects/.*/${_CHECKSUM}.*"`
+		if [[ ! -f "${_annex_file}" ]]
+		then
+			continue
+		fi
+		local _checksum=`echo "${_annex_file}" | xargs basename`
+		local _checksum=${_checksum##*--}
+		echo "${_checksum%%.*}  ${_file}"
+	done
+}
+
+function list {
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			-d | --dataset) local _DATASET="$1"; shift ;;
+			-h | --help)
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "[-d | --dataset PATH] dataset location"
+			git-annex list --help >&2
+			exit 1
+			;;
+			--) break ;;
+			*) >&2 echo "Unknown option [${_arg}]"; exit 3 ;;
+		esac
+	done
+
+	if [[ ! -z "${_DATASET}" ]]
+	then
+		pushd "${_DATASET}" >/dev/null || exit 1
+	fi
+
+	git-annex list "$@" | { grep -o " .*" | grep -Eo "[^ ]+.*" || test $? = 1 ; }
+
+	if [[ ! -z "${_DATASET}" ]]
+	then
+		popd >/dev/null
+	fi
+}
+
+function subdatasets {
+	local _VAR=0
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--var) local _VAR=1 ;;
+			-h | --help)
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "--var also list datasets variants"
+			>&2 echo "then following --"
+			datalad subdatasets --help
+			exit 1
+			;;
+			--) break ;;
+			*) >&2 echo "Unknown option [${_arg}]"; exit 3 ;;
+		esac
+	done
+
+	if [[ ${_VAR} != 0 ]]
+	then
+		datalad subdatasets $@ | grep -o ": .* (dataset)" | grep -o " .* " | grep -o "[^ ]*" | \
+		while read subds
+		do
+			echo ${subds}
+			for _d in "${subds}.var"/*
+			do
+				if [[ -d "$_d" ]]
+				then
+					echo $_d
+				fi
+			done
+		done
+	else
+		datalad subdatasets $@ | grep -o ": .* (dataset)" | grep -o " .* " | grep -o "[^ ]*"
+	fi
+}
+
+function unshare_mount {
+	if [[ ${EUID} -ne 0 ]]
+	then
+		unshare -rm ./"${BASH_SOURCE[0]}" unshare_mount "$@" <&0
+		exit $?
+	fi
+
+	if [[ -z ${_SRC} ]]
+	then
+		local _SRC=${PWD}
+	fi
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--src) local _SRC="$1"; shift
+			echo "src = [${_SRC}]"
+			;;
+			--dir) local _DIR="$1"; shift
+			echo "dir = [${_DIR}]"
+			;;
+			--cd) local _CD=1
+			echo "cd = [${_CD}]"
+			;;
+	                --) break ;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "[--dir DIR] mount location"
+			>&2 echo "[--src DIR] source dir (optional)"
+			exit 1
+			;;
+		esac
+	done
+
+	mkdir -p ${_SRC}
+	mkdir -p ${_DIR}
+
+	local _SRC=$(cd "${_SRC}" && pwd -P)
+	local _DIR=$(cd "${_DIR}" && pwd -P)
+
+	mount -o bind ${_SRC} ${_DIR}
+	exit_on_error_code "Could not mount directory"
+
+	if [[ ! ${_CD} -eq 0 ]]
+	then
+		cd ${_DIR}
+	fi
+
+	unshare -U ${SHELL} -s "$@" <&0
+}
+
+function jug_exec {
+	if [[ -z ${_jug_exec} ]]
+	then
+		local _jug_exec=${_SCRIPT_DIR}/jug_exec.py
+	fi
+	local _jug_argv=()
+	while [[ $# -gt 0 ]]
+	do
+		local _arg="$1"; shift
+		case "${_arg}" in
+			--script | -s) local _jug_exec="$1"; shift ;;
+			-h | --help)
+			>&2 echo "Options for ${FUNCNAME[0]} are:"
+			>&2 echo "[--script | -s JUG_EXEC] path to the jug wrapper script (default: '${_jug_exec}')"
+			${_jug_exec} --help
+			exit
+			;;
+			--) break ;;
+			*) _jug_argv+=("${_arg}") ;;
+		esac
+	done
+	# Remove trailing '/' in argv before sending to jug
+	jug execute "${_jug_argv[@]%/}" ${_jug_exec} -- "${@%/}"
+}
+
+# function unshare_mount {
+# 	if [[ ${EUID} -ne 0 ]]
+# 	then
+# 		unshare -rm ./"${BASH_SOURCE[0]}" unshare_mount "$@" <&0
+# 		exit $?
+# 	fi
+#
+# 	if [[ -z ${_SRC} ]]
+# 	then
+# 		local _SRC=${PWD}
+# 	fi
+# 	if [[ -z ${_DIR} ]]
+# 	then
+# 		local _DIR=${_PWD}
+# 	fi
+# 	while [[ $# -gt 0 ]]
+# 	do
+# 		local _arg="$1"; shift
+# 		case "${_arg}" in
+# 			--src) local _SRC="$1"; shift
+# 			echo "src = [${_SRC}]"
+# 			;;
+# 			--upper) local _UPPER="$1"; shift
+# 			echo "upper = [${_UPPER}]"
+# 			;;
+# 			--dir) local _DIR="$1"; shift
+# 			echo "dir = [${_DIR}]"
+# 			;;
+# 			--wd) local _WD="$1"; shift
+# 			echo "wd = [${_WD}]"
+# 			;;
+# 			--cd) local _CD=1
+# 			echo "cd = [${_CD}]"
+# 			;;
+# 	                --) break ;;
+# 			-h | --help | *)
+# 			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+# 			then
+# 				>&2 echo "Unknown option [${_arg}]"
+# 			fi
+# 			>&2 echo "Options for $(basename "$0") are:"
+# 			>&2 echo "[--upper DIR] upper mount overlay"
+# 			>&2 echo "[--wd DIR] overlay working directory"
+# 			>&2 echo "[--src DIR] lower mount overlay (optional)"
+# 			>&2 echo "[--dir DIR] mount location (optional)"
+# 			exit 1
+# 			;;
+# 		esac
+# 	done
+#
+# 	mkdir -p ${_SRC}
+# 	mkdir -p ${_UPPER}
+# 	mkdir -p ${_WD}
+# 	mkdir -p ${_DIR}
+#
+# 	local _SRC=$(cd "${_SRC}" && pwd -P) || echo "${_SRC}"
+# 	local _UPPER=$(cd "${_UPPER}" && pwd -P)
+# 	local _WD=$(cd "${_WD}" && pwd -P)
+# 	local _DIR=$(cd "${_DIR}" && pwd -P)
+#
+# 	mount -t overlay overlay -o lowerdir="${_SRC}",upperdir="${_UPPER}",workdir="${_WD}" "${_DIR}"
+# 	exit_on_error_code "Could not mount overlay"
+#
+# 	if [[ ! ${_CD} -eq 0 ]]
+# 	then
+# 		cd ${_DIR}
+# 	fi
+#
+# 	unshare -U ${SHELL} -s "$@" <&0
+# }
+
+if [[ ! -z "$@" ]]
+then
+	"$@"
+fi