For a research analysis, I'm writing a small bash script that serves as a frontend to Singularity. The reason is that I want to save in this script which options are needed for singularity. For example, I want the working directory to appear at a fixed path in the container, regardless of the actual working directory path.
Singularity has the --contain option for this, but this requires me to manually define a temporary directory for the container. I use mktemp for that. After the end of the script, I use trap to
delete that directory. However, I fear that there might be a corner case where trap "rm -rf '$tmpdir' might delete the wrong directory.
The script, called cexec, executes an arbitrary command inside the container. For example ./cexec R starts R inside the container.
Is there a corner case in the following script where the script deletes a directory that it didn't create?
#!/bin/bash
# Execute a command in the container
set -ue
thisdir="$(dirname "$BASH_SOURCE")"
container="rserver_200211_commitd117c677.sif" # get such a file by using `singularity pull ...`
# Create a temporary directory
tmpdir="$(mktemp -d -t cexec-XXXXXXXX)"
# We delete this directory afterwards, so its important that $tmpdir
# really has the path to an empty, temporary dir, and nothing else!
# (for example empty string or home dir)
if [[ ! "$tmpdir" || ! -d "$tmpdir" ]]; then
echo "Error: Could not create temp dir $tmpdir"
exit 1
fi
# check if temp dir is empty
tmpcontent="$(ls -A "$tmpdir")"
if [ ! -z "$tmpcontent" ]; then
echo "Error: Temp dir '$tmpdir' is not empty"
exit 1
fi
# Delete the temporary directory after the end of the script
trap "rm -rf '$tmpdir'" EXIT
singularity exec \
-B "$tmpdir:/tmp" \
--contain \
-H "$thisdir:/data" \
"$container" \
"$@"
