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start.sh: tests, docs, and refinements
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@consideRatio @maresb
consideRatio authored and maresb committed Nov 7, 2021
1 parent 43e0826 commit 1db741b
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227 changes: 118 additions & 109 deletions base-notebook/start.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,8 @@ else
cmd=( "$@" )
fi

# The run-hooks function looks for .sh scripts and executable files
# - .sh scripts will be sourced
# - executable files (+x) will be executed
# The run-hooks function looks for .sh scripts to source and executable files to
# run within a passed directory.
run-hooks () {
if [[ ! -d "${1}" ]] ; then
return
Expand All @@ -41,168 +40,178 @@ run-hooks () {
}



# NOTE: This hook will run as the user the container was started with!
run-hooks /usr/local/bin/start-notebook.d



# If we have started the container as the root user, then we have permission to
# manipulate user identities and storage file permissions before we start the
# server as a non-root user.
# If the container started as the root user, then we have permission to refit
# the jovyan user, and ensure file permissions, grant sudo rights, and such
# things before we run the command passed to start.sh as the desired user
# (NB_USER).
#
# Environment variables of relevance:
# - NB_UID: the user we want to run as, uniquely identified by an id
# - NB_USER: the username and associated home folder we want for our user
# - NB_GID: a group we want our user to belong to, uniquely identified by an id
# - NB_GROUP: the groupname we want for the group
if [ "$(id -u)" == 0 ] ; then

# Optionally ensure the user we want to run as (NB_UID) get filesystem
# ownership of it's home folder and additional folders. This can be relevant
# for attached NFS storage.
#
# Environment variables:
# - NB_USER: the desired username and associated home folder
# - NB_UID: the desired user id
# - NB_GID: a group id we want our user to belong to
# - NB_GROUP: the groupname we want for the group
# - GRANT_SUDO: a boolean ("1" or "yes") to grant the user sudo rights
# - CHOWN_HOME: a boolean ("1" or "yes") to chown the user's home folder
# - CHOWN_EXTRA: a comma separated list of paths to chown
# - CHOWN_HOME_OPTS / CHOWN_EXTRA_OPTS: arguments to the chown command
if [[ "${CHOWN_HOME}" == "1" || "${CHOWN_HOME}" == "yes" ]]; then
echo "Updating ownership of /home/${NB_USER} to ${NB_UID}:${NB_GID} with options '${CHOWN_HOME_OPTS}'"
# shellcheck disable=SC2086
chown $CHOWN_HOME_OPTS "${NB_UID}:${NB_GID}" "/home/${NB_USER}"
fi
if [ -n "${CHOWN_EXTRA}" ]; then
for extra_dir in $(echo "${CHOWN_EXTRA}" | tr ',' ' '); do
echo "Updating ownership of ${extra_dir} to ${NB_UID}:${NB_GID} with options '${CHOWN_EXTRA_OPTS}'"
# shellcheck disable=SC2086
chown ${CHOWN_EXTRA_OPTS} "${NB_UID}:${NB_GID}" "${extra_dir}"
done
fi
# - CHOWN_HOME_OPTS / CHOWN_EXTRA_OPTS: arguments to the chown commands

# Update the jovyan identity to get desired username and its associated home folder.
# Refit the jovyan user to the desired the user (NB_USER)
if id jovyan &> /dev/null ; then
if ! usermod --home "/home/${NB_USER}" --login "${NB_USER}" jovyan 2>&1 | grep "no changes" > /dev/null; then
echo "Updated the jovyan user:"
echo "username: jovyan -> ${NB_USER}"
echo "home dir location: /home/jovyan -> /home/${NB_USER}"
echo "- username: jovyan -> ${NB_USER}"
echo "- home dir: /home/jovyan -> /home/${NB_USER}"
fi
elif ! id -u "${NB_USER}" &> /dev/null; then
echo "ERROR: Neither the jovyan user or '$NB_USER' exists."
echo " This could be the result of stopping and starting, the"
echo " container with a different NB_USER environment variable."
exit 1
fi
# Ensure the desired user (NB_USER) gets its desired user id (NB_UID) and is
# a member of the desired group (NB_GROUP, NB_GID)
if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
echo "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
# Ensure the desired group's existence
if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
groupadd --force --gid "${NB_GID}" --non-unique "${NB_GROUP:-${NB_USER}}"
fi
# Recreate the desired user as we want it
userdel "${NB_USER}"
useradd --home "/home/${NB_USER}" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 --no-log-init "${NB_USER}"
fi
# Update env vars set during image build with the current NB_USER value
export XDG_CACHE_HOME=/home/$NB_USER/.cache

# For non-jovyan username's, populate their home directory with the jovyan's
# home directory as a fallback if they don't have one mounted already.
# Move or symlink the jovyan home directory to the desired users home
# directory if it doesn't already exist, and update the current working
# directory to the new location if needed.
if [[ "${NB_USER}" != "jovyan" ]]; then
if [[ ! -e "/home/${NB_USER}" ]]; then
echo "Attempting to copy /home/jovyan to /home/${NB_USER}..."
mkdir "/home/${NB_USER}"
if cp -a /home/jovyan/. "/home/${NB_USER}/"; then
echo "Done"
echo "Success!"
else
echo "Failed. Attempting to symlink /home/jovyan to /home/${NB_USER}..."
ln -s /home/jovyan "/home/${NB_USER}" && echo "Done"
echo "Failed!"
echo "Attempting to symlink /home/jovyan to /home/${NB_USER}..."
if ln -s /home/jovyan "/home/${NB_USER}"; then
echo "Success!"
else
echo "Failed!"
fi
fi
fi
# Ensure the current working directory is updated
# Ensure the current working directory is updated to the new path
if [[ "${PWD}/" == "/home/jovyan/"* ]]; then
newcwd="/home/${NB_USER}/${PWD:13}"
echo "Changing working directory to ${newcwd}"
cd "${newcwd}"
new_wd="/home/${NB_USER}/${PWD:13}"
echo "Changing working directory to ${new_wd}"
cd "${new_wd}"
fi
fi

# Ensure NB_USER gets the NB_UID user id and is a member of the NB_GID group
if [ "${NB_UID}" != "$(id -u "${NB_USER}")" ] || [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
echo "Update ${NB_USER}'s UID:GID to ${NB_UID}:${NB_GID}"
# Ensure the group's existence
if [ "${NB_GID}" != "$(id -g "${NB_USER}")" ]; then
groupadd --force --gid "$NB_GID" --non-unique "${NB_GROUP:-${NB_USER}}"
fi
# Recreate the user as we want it
userdel "${NB_USER}"
useradd --home "/home/${NB_USER}" --uid "${NB_UID}" --gid "${NB_GID}" --groups 100 --no-log-init "${NB_USER}"
# Optionally ensure the desired user get filesystem ownership of it's home
# folder and/or additional folders
if [[ "${CHOWN_HOME}" == "1" || "${CHOWN_HOME}" == "yes" ]]; then
echo "Ensuring /home/${NB_USER} is owned by ${NB_UID}:${NB_GID} ${CHOWN_HOME_OPTS:+chown options: ${CHOWN_HOME_OPTS}}"
# shellcheck disable=SC2086
chown ${CHOWN_HOME_OPTS} "${NB_UID}:${NB_GID}" "/home/${NB_USER}"
fi

# Conditionally enable passwordless sudo usage for the jovyan user
if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == 'yes' ]]; then
echo "Granting ${NB_USER} passwordless sudo rights!"
echo "${NB_USER} ALL=(ALL) NOPASSWD:ALL" > /etc/sudoers.d/added-by-start-script
if [ -n "${CHOWN_EXTRA}" ]; then
for extra_dir in $(echo "${CHOWN_EXTRA}" | tr ',' ' '); do
echo "Ensuring ${extra_dir} is owned by ${NB_UID}:${NB_GID} ${CHOWN_HOME_OPTS:+(chown options: ${CHOWN_HOME_OPTS})}"
# shellcheck disable=SC2086
chown ${CHOWN_EXTRA_OPTS} "${NB_UID}:${NB_GID}" "${extra_dir}"
done
fi

# Ensure that the initial environment that this container is started with
# is preserved when we run transition from running as root to running as
# NB_USER.
# Update potentially outdated environment variables since image build
export XDG_CACHE_HOME=/home/$NB_USER/.cache

# Notes on how we ensure that the environment that this container is started
# with is preserved (except vars listen in JUPYTER_ENV_VARS_TO_UNSET) when
# we transition from running as root to running as NB_USER.
#
# - We use the sudo command to execute the command as NB_USER. But, what
# - We use `sudo` to execute the command as NB_USER. What then
# happens to the environment will be determined by configuration in
# /etc/sudoers and /etc/sudoers.d/* as well as flags we pass to the sudo
# command. The behavior can be inspected with `sudo -V` run as root.
#
# ref: `man sudo` https://linux.die.net/man/8/sudo
# ref: `man sudoers` https://www.sudo.ws/man/1.8.15/sudoers.man.html
#
# - We use the `--preserve-env` flag to pass through most environment, but
# understand that exceptions are caused by the sudoers configuration:
# `env_delete`, `env_check`, and `secure_path`.
# - We use the `--preserve-env` flag to pass through most environment
# variables, but understand that exceptions are caused by the sudoers
# configuration: `env_delete`, `env_check`, and `secure_path`.
#
# - We use the `--set-home` flag to set the HOME variable appropriatly.
#
# - We reduce the `env_delete` list of default variables to be deleted by
# default which would ignore the `--preserve-env` flag and `env_keep`
# - We reduce the `env_delete` list of default variables to be deleted. It
# has higher priority than the `--preserve-env` flag and `env_keep`
# configuration.
#
# - We manage the PATH variable specifically as `secure_path` is set by
# default in /etc/sudoers and would override the PATH variable. So we
# disable that default.
# - We disable the `secure_path` which is set by default in /etc/sudoers as
# it would override the PATH variable.
echo 'Defaults !secure_path' > /etc/sudoers.d/added-by-start-script
echo 'Defaults env_delete -= "PATH LD_* PYTHON*"' >> /etc/sudoers.d/added-by-start-script
echo 'Defaults !secure_path' >> /etc/sudoers.d/added-by-start-script

# Optionally grant passwordless sudo rights for the desired user
if [[ "$GRANT_SUDO" == "1" || "$GRANT_SUDO" == 'yes' ]]; then
echo "Granting $NB_USER passwordless sudo rights!"
echo "$NB_USER ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers.d/added-by-start-script
fi

# NOTE: This hook is run as the root user!
run-hooks /usr/local/bin/before-notebook.d

echo "Running as ${NB_USER}:" "${cmd[@]}"
exec sudo --preserve-env --set-home --user "${NB_USER}" "${cmd[@]}"



# The container didn't start as the root user.
# The container didn't start as the root user, so we will have to act as the
# user we started as.
else
if [[ "${NB_UID}" == "$(id -u jovyan 2>/dev/null)" && "${NB_GID}" == "$(id -g jovyan 2>/dev/null)" ]]; then
# User is not attempting to override user/group via environment
# variables, but they could still have overridden the uid/gid that
# container runs as. Check that the user has an entry in the passwd
# file and if not add an entry.
STATUS=0 && whoami &> /dev/null || STATUS=$? && true
if [[ "${STATUS}" != "0" ]]; then
if [[ -w /etc/passwd ]]; then
echo "Adding passwd file entry for $(id -u)"
sed -e "s/^jovyan:/nayvoj:/" /etc/passwd > /tmp/passwd
echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /tmp/passwd
cat /tmp/passwd > /etc/passwd
rm /tmp/passwd
else
echo "WARNING: Container must be run with group 'root' to update passwd file"
fi
fi
# Warn about misconfiguration of: desired username, user id, or group id
if [[ -n "${NB_USER}" && "${NB_USER}" != "$(id -un)" ]]; then
echo "WARNING: container must be started as root to change the desired user's name with NB_USER!"
fi
if [[ -n "${NB_UID}" && "${NB_UID}" != "$(id -u)" ]]; then
echo "WARNING: container must be started as root to change the desired user's id with NB_UID!"
fi
if [[ -n "${NB_GID}" && "${NB_GID}" != "$(id -g)" ]]; then
echo "WARNING: container must be started as root to change the desired user's group id with NB_GID!"
fi

# Warn if the user isn't going to be able to write files to ${HOME}.
if [[ ! -w /home/jovyan ]]; then
echo "WARNING: Container must be run with group 'users' to update files"
fi
else
# Warn if looks like user want to override uid/gid but hasn't
# run the container as root.
if [[ -n "${NB_UID}" && "${NB_UID}" != "$(id -u)" ]]; then
echo "Container must be run as root to set NB_UID to ${NB_UID}"
fi
if [[ -n "${NB_GID}" && "${NB_GID}" != "$(id -g)" ]]; then
echo "Container must be run as root to set NB_GID to ${NB_GID}"
# Warn about misconfiguration of: granting sudo rights
if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == 'yes' ]]; then
echo "WARNING: container must be started as root to grant sudo permissions!"
fi

# Attempt to ensure the user uid we currently run as has a named entry in
# the /etc/passwd file, as it avoids software crashing on hard assumptions
# on such entry. Writing to the /etc/passwd was allowed for the root group
# from the Dockerfile during build.
#
# ref: https://github.com/jupyter/docker-stacks/issues/552
if ! whoami &> /dev/null; then
if [[ -w /etc/passwd ]]; then
sed --in-place "s/^jovyan:/nayvoj:/" /etc/passwd
echo "Renamed old jovyan user to nayvoy (1000:100)"

echo "jovyan:x:$(id -u):$(id -g):,,,:/home/jovyan:/bin/bash" >> /etc/passwd
echo "Added new jovyan user ($(id -u):$(id -g))"
else
echo "WARNING: container must be started with group 'root' (0) to add a user entry in /etc/passwd!"
fi
fi

# Warn about a probable misconfiguration of sudo
if [[ "${GRANT_SUDO}" == "1" || "${GRANT_SUDO}" == 'yes' ]]; then
echo "WARNING: container must be started up as root to grant sudo permissions."
# Warn if the user isn't able to write files to ${HOME}
if [[ ! -w /home/jovyan ]]; then
echo "WARNING: container must be started with group 'users' (100) to be allowed to write to /home/jovyan!"
fi

# NOTE: This hook is run as the user we started the container as!
run-hooks /usr/local/bin/before-notebook.d
echo "Executing the command:" "${cmd[@]}"
exec "${cmd[@]}"
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