Add scripts/datalad.sh

.gitattributes

@@ -8,3 +8,5 @@
 *.h annex.largefiles=nothing
 *.py annex.largefiles=nothing
 *.sh annex.largefiles=nothing
+
+scripts/* annex.largefiles=nothing

.gitignore

@@ -1 +1,2 @@
 .nfs*
+/.tmp/

scripts/datalad.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+source scripts/utils.sh echo -n
+
+function install_datalad {
+	init_venv --name venv --tmp .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"
+}
+
+datalad --version >/dev/null 2>&1 || install_datalad
+exit_on_error_code "Failed to install datalad requirements: pip install"
+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/requirements_datalad.txt

@@ -0,0 +1 @@
+datalad==0.11.8

scripts/utils.sh

@@ -0,0 +1,256 @@
+#!/bin/bash
+
+function exit_on_error_code {
+	local _ERR=$?
+	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}]"
+			;;
+			--tmp) local _TMPDIR="$1"; shift
+			echo "tmp = [${_TMPDIR}]"
+			;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "--name NAME conda env prefix name"
+			>&2 echo "--tmp DIR tmp dir to hold the conda prefix"
+			exit 1
+			;;
+		esac
+	done
+
+	# Configure conda for bash shell
+	eval "$(conda shell.bash hook)"
+
+	if [[ ! -d "${_TMPDIR}/env/${_NAME}/" ]]
+	then
+		conda create --prefix "${_TMPDIR}/env/${_NAME}/" --yes --no-default-packages || \
+		exit_on_error_code "Failed to create ${_NAME} conda env"
+	fi
+
+	conda activate "${_TMPDIR}/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}]"
+			;;
+			--tmp) local _TMPDIR="$1"; shift
+			echo "tmp = [${_TMPDIR}]"
+			;;
+			-h | --help | *)
+			if [[ "${_arg}" != "-h" ]] && [[ "${_arg}" != "--help" ]]
+			then
+				>&2 echo "Unknown option [${_arg}]"
+			fi
+			>&2 echo "Options for $(basename "$0") are:"
+			>&2 echo "--name NAME venv prefix name"
+			>&2 echo "--tmp DIR tmp dir to hold the virtualenv prefix"
+			exit 1
+			;;
+		esac
+	done
+
+	if [[ ! -d "${_TMPDIR}/venv/${_NAME}/" ]]
+	then
+		mkdir -p "${_TMPDIR}/venv/${_NAME}/" && \
+		virtualenv --no-download "${_TMPDIR}/venv/${_NAME}/" || \
+		exit_on_error_code "Failed to create ${_NAME} venv"
+	fi
+
+	source "${_TMPDIR}/venv/${_NAME}/bin/activate" || \
+	exit_on_error_code "Failed to activate ${_NAME} venv"
+	python3 -m pip install --no-index --upgrade pip
+}
+
+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 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