entrypoint-aws-batch

#!/bin/bash
set -euo pipefail

# Show what we're running for the benefit of the logs.
set -x

# Download the working dir.
case "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" in
    s3://*.zip)
        aws s3 cp --no-progress "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" "$PWD.zip"
        unzip "$PWD.zip"
        ;;
    s3://*)
        # Note that this doesn't preserve file permissions/modes.
        aws s3 sync --no-progress "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" .
        ;;
    *)
        echo "entrypoint-aws-batch: No handler for NEXTSTRAIN_AWS_BATCH_WORKDIR_URL <$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL>" >&2
        exit 1
        ;;
esac

# Run the passed command, with the effect of "set -e" temporarily disabled,
# saving the exit status for later.
"$@" && exited=0 || exited=$?

# Upload the new workdir state with results.
#
# XXX TODO: In the future this may want to be separate from the initial workdir
# state instead of overwriting it.  That would let us hash the local workdir
# before uploading and re-use previously uploaded initial workdirs.
#   -trs, 13 Sept 2018
case "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" in
    s3://*.zip)
        succeed-when-nothing-to-update() {
            local zipstatus="$1"
            if [[ $zipstatus -eq 12 ]]; then
                return 0
            else
                return "$zipstatus"
            fi
        }
        zip -u "$PWD.zip" -r . --exclude ".snakemake/*"     || succeed-when-nothing-to-update $?
        zip -u "$PWD.zip" -r . --include ".snakemake/log/*" || succeed-when-nothing-to-update $?
        aws s3 cp --no-progress "$PWD.zip" "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL"
        ;;
    s3://*)
        aws s3 sync --no-progress . "$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL" --exclude ".snakemake/*" --include ".snakemake/log/*"
        ;;
    *)
        echo "entrypoint-aws-batch: No handler for NEXTSTRAIN_AWS_BATCH_WORKDIR_URL <$NEXTSTRAIN_AWS_BATCH_WORKDIR_URL>" >&2
        exit 1
        ;;
esac

# Exit with the same status as the passed command.
exit "$exited"