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At the moment, FlowETL (because of the parent image and airflow) will allow you to configure many things using env vars. Obviously we'd rather use secrets in many cases. This should be supported.
Worth considering that this snippet:
shopt -s nullglob
FILES=/run/secrets/*
for f in $FILES; do
echo "Loading secret $f."
export $(basename $f)=$(cat $f)
done
will read all secrets as env vars named for the secret, which might simplify matters.
Alternatively, https://github.com/jezdez/envdir is built for exactly this purpose.