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Merge pull request #736 from pneerincx/fix/envsync
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Improved hpc-environment-permissions.bash
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@marieke-bijlsma
marieke-bijlsma authored Feb 27, 2023
2 parents a71d4f5 + 0738d54 commit ee037c9
Showing 1 changed file with 39 additions and 38 deletions.
77 changes: 39 additions & 38 deletions roles/envsync/templates/hpc-environment-permissions.bash
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Original file line number Diff line number Diff line change
Expand Up @@ -42,36 +42,36 @@ REAL_USER="$(logname 2>/dev/null || echo 'no login name')"
# Retain ownership and change group + perms if necessary on the originals.
#
function verifyAndFixOriginals() {
local _ROOT_OF_HPC_ENV_ORIGINAL="$1"

declare -a local _HPC_ENV_FOLDERS=("${_ROOT_OF_HPC_ENV_ORIGINAL}/modules/"
local _ROOT_OF_HPC_ENV_ORIGINAL="${1}"
declare -a _HPC_ENV_FOLDERS=("${_ROOT_OF_HPC_ENV_ORIGINAL}/modules/"
"${_ROOT_OF_HPC_ENV_ORIGINAL}/software/"
"${_ROOT_OF_HPC_ENV_ORIGINAL}/data/"
"${_ROOT_OF_HPC_ENV_ORIGINAL}/sources/"
"${_ROOT_OF_HPC_ENV_ORIGINAL}/.tmp/")

for (( i = 0 ; i < ${#_HPC_ENV_FOLDERS[@]:-0} ; i++ ))
for (( i = 0 ; i < ${#_HPC_ENV_FOLDERS[@]} ; i++ ))
do
find "${_HPC_ENV_FOLDERS[${i}]}" \! -group "${SYS_GROUP}" -exec chgrp "${SYS_GROUP}" '{}' \;
verifyPermissions "${_HPC_ENV_FOLDERS[${i}]}" '0775' '0664' 'ug+rwX,o+rX,o-w' '2775'
if [[ -e "${_HPC_ENV_FOLDERS[${i}]}" ]]; then
find "${_HPC_ENV_FOLDERS[${i}]}" \! -group "${SYS_GROUP}" -a \! -type l -exec chgrp "${SYS_GROUP}" '{}' \;
verifyPermissions "${_HPC_ENV_FOLDERS[${i}]}" '0775' '0664' 'ug+rwX,o+rX,o-w' '2775'
fi
done
}

#
# Change ownership, group and perms if necessary on the copies.
#
function verifyAndFixCopies() {
local _ROOT_OF_HPC_ENV_COPY="$1"

declare -a local _HPC_ENV_FOLDERS=("${_ROOT_OF_HPC_ENV_COPY}/modules/"
"${_ROOT_OF_HPC_ENV_COPY}/software/"
"${_ROOT_OF_HPC_ENV_COPY}/data/")

for (( i = 0 ; i < ${#_HPC_ENV_FOLDERS[@]:-0} ; i++ ))
local _ROOT_OF_HPC_ENV_COPY="${1}"
declare -a _HPC_ENV_FOLDERS=("${_ROOT_OF_HPC_ENV_COPY}/modules/"
"${_ROOT_OF_HPC_ENV_COPY}/software/"
"${_ROOT_OF_HPC_ENV_COPY}/data/")
for (( i = 0 ; i < ${#_HPC_ENV_FOLDERS[@]} ; i++ ))
do
find "${_HPC_ENV_FOLDERS[${i}]}" \! -user "${SYS_USER}" -exec chown "${SYS_USER}" '{}' \;
find "${_HPC_ENV_FOLDERS[${i}]}" \! -group "${SYS_GROUP}" -exec chgrp "${SYS_GROUP}" '{}' \;
verifyPermissions "${_HPC_ENV_FOLDERS[${i}]}" '0755' '0644' 'u+rwX,go+rX,go-w' '2755'
if [[ -e "${_HPC_ENV_FOLDERS[${i}]}" ]]; then
find "${_HPC_ENV_FOLDERS[${i}]}" \! -user "${SYS_USER}" -a \! -type l -exec chown "${SYS_USER}" '{}' \;
find "${_HPC_ENV_FOLDERS[${i}]}" \! -group "${SYS_GROUP}" -a \! -type l -exec chgrp "${SYS_GROUP}" '{}' \;
verifyPermissions "${_HPC_ENV_FOLDERS[${i}]}" '0755' '0644' 'u+rwX,go+rX,go-w' '2755'
fi
done
}

Expand All @@ -81,14 +81,14 @@ function verifyAndFixCopies() {
# unless there really was something to change. Mostly used for "group" folders.
#
function verifyPermissions() {
local _FOLDER="$1"
local _FIND_FILE_PERMS_EXECUTABLE="$2"
local _FIND_FILE_PERMS_REGULAR="$3"
local _CHMOD_FILE_PERMS="$4"
local _FOLDER_PERMS="$5"
local _FOLDER="${1}"
local _FIND_FILE_PERMS_EXECUTABLE="${2}"
local _FIND_FILE_PERMS_REGULAR="${3}"
local _CHMOD_FILE_PERMS="${4}"
local _FOLDER_PERMS="${5}"
echo "INFO: Verify and fix permissions with file perms ${_CHMOD_FILE_PERMS} and folder perms ${_FOLDER_PERMS} for for folder ${_FOLDER}... "
find "${_FOLDER}" -type f -a \! \( -perm ${_FIND_FILE_PERMS_EXECUTABLE} -o -perm ${_FIND_FILE_PERMS_REGULAR} \) -exec chmod "${_CHMOD_FILE_PERMS}" '{}' \;
find "${_FOLDER}" -type d -a \! -perm ${_FOLDER_PERMS} -exec chmod "${_FOLDER_PERMS}" '{}' \;
find "${_FOLDER}" -type f -a \! \( -perm "${_FIND_FILE_PERMS_EXECUTABLE}" -o -perm "${_FIND_FILE_PERMS_REGULAR}" \) -exec chmod "${_CHMOD_FILE_PERMS}" '{}' \;
find "${_FOLDER}" -type d -a \! -perm "${_FOLDER_PERMS}" -exec chmod "${_FOLDER_PERMS}" '{}' \;
}

#
Expand All @@ -104,7 +104,7 @@ fi
#
# Check (and fix if necessary) our original shared HPC environment.
#
if [ -e ${ORIGINAL_HPC_ENV_PREFIX} ] && [ -d ${ORIGINAL_HPC_ENV_PREFIX} ]; then
if [[ -e "${ORIGINAL_HPC_ENV_PREFIX}" ]] && [[ -d "${ORIGINAL_HPC_ENV_PREFIX}" ]]; then
echo "INFO: Found original environment @ ${ORIGINAL_HPC_ENV_PREFIX}: will verify and fix permissions... "
verifyAndFixOriginals "${ORIGINAL_HPC_ENV_PREFIX}"
echo 'INFO: Done!'
Expand All @@ -115,40 +115,41 @@ fi
#
# Find all rsynced copies of our shared HPC environment.
#
declare -a COPIED_HPC_ENV_PREFIXES
for (( i = 0 ; i < ${#COPIED_HPC_ENV_MOUNT_POINT_PARENTS[@]:-0} ; i++ ))
declare -a COPIED_HPC_ENV_PREFIXES=()
for (( i = 0 ; i < ${#COPIED_HPC_ENV_MOUNT_POINT_PARENTS[@]} ; i++ ))
do
#
# Check for presence of folders for logical file system (LFS) names
# and if present whether they contain a copy of ${ORIGINAL_HPC_ENV_PREFIX}.
#
declare -a LFS_MOUNT_POINTS="$(find ${COPIED_HPC_ENV_MOUNT_POINT_PARENTS[${i}]} -mindepth 1 -maxdepth 1 -type d)"
for (( j = 0 ; j < ${#LFS_MOUNT_POINTS[@]:-0} ; j++ ))
declare -a LFS_MOUNT_POINTS
readarray -t LFS_MOUNT_POINTS< <(find "${COPIED_HPC_ENV_MOUNT_POINT_PARENTS[${i}]}" -mindepth 1 -maxdepth 1 -type d)
for (( j = 0 ; j < ${#LFS_MOUNT_POINTS[@]} ; j++ ))
do
[ -z ${LFS_MOUNT_POINTS[${j}]} ] && continue
[[ -z "${LFS_MOUNT_POINTS[${j}]}" ]] && continue
COPIED_HPC_ENV_PREFIX="${LFS_MOUNT_POINTS[${j}]}${ORIGINAL_HPC_ENV_PREFIX}"
if [ -e "${COPIED_HPC_ENV_PREFIX}" ] && \
[ -r "${COPIED_HPC_ENV_PREFIX}" ] && \
[ -w "${COPIED_HPC_ENV_PREFIX}" ] && \
[ -d "${COPIED_HPC_ENV_PREFIX}" ]; then
if [ "${#COPIED_HPC_ENV_PREFIXES[@]:-0}" -eq 0 ]; then
if [[ -e "${COPIED_HPC_ENV_PREFIX}" ]] && \
[[ -r "${COPIED_HPC_ENV_PREFIX}" ]] && \
[[ -w "${COPIED_HPC_ENV_PREFIX}" ]] && \
[[ -d "${COPIED_HPC_ENV_PREFIX}" ]]; then
if [[ "${#COPIED_HPC_ENV_PREFIXES[@]}" -eq 0 ]]; then
COPIED_HPC_ENV_PREFIXES=("${COPIED_HPC_ENV_PREFIX}")
else
COPIED_HPC_ENV_PREFIXES=("${COPIED_HPC_ENV_PREFIXES[@]:-}" "${COPIED_HPC_ENV_PREFIX}")
fi
else
echo "WARN: ${COPIED_HPC_ENV_PREFIX} not available (symlink dead or mount missing)."
echo "INFO: No ${ORIGINAL_HPC_ENV_PREFIX} copy found on ${LFS_MOUNT_POINTS[${j}]}."
fi
done
done

#
# Check (and fix if necessary) all rsynced copies of our shared HPC environment.
#
if [ "${#COPIED_HPC_ENV_PREFIXES[@]:-0}" -eq 0 ]; then
if [[ "${#COPIED_HPC_ENV_PREFIXES[@]}" -eq 0 ]]; then
echo "WARN: Found no environment copies and will not verify and fix permissions for environment copies."
else
for THIS_HPC_ENV_PREFIX in ${COPIED_HPC_ENV_PREFIXES[@]:-}; do
for THIS_HPC_ENV_PREFIX in "${COPIED_HPC_ENV_PREFIXES[@]:-}"; do
echo "INFO: Will verify and fix permissions for environment copy @ ${THIS_HPC_ENV_PREFIX} ... "
verifyAndFixCopies "${THIS_HPC_ENV_PREFIX}"
echo 'INFO: Done!'
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