docker-player-entrypoint.sh

#!/bin/bash

# Exit on error
set -e

# The controller-container entrypoint.
# The environment variable FRAGMENTOR_PLAY defines
# what the container image will do (and a working directory).
# It is expected to be one of the plays.
# i.e. 'standardise' for the site-standardise.yaml play.
#
# The user can also add arbitrary arguments to the play
# using FRAGMENTOR_PLAY_EXTRA_ARGS.

: "${FRAGMENTOR_PLAY?Need to set FRAGMENTOR_PLAY}"
: "${FRAGMENTOR_NAMESPACE?Need to set FRAGMENTOR_NAMESPACE}"

echo "+> FRAGMENTOR_PLAY is ${FRAGMENTOR_PLAY}"
echo "+> FRAGMENTOR_NAMESPACE is ${FRAGMENTOR_NAMESPACE}"

# You also need AWS access keys (for bucket access)
: "${AWS_ACCESS_KEY_ID?Need to set AWS_ACCESS_KEY_ID}"
: "${AWS_SECRET_ACCESS_KEY?Need to set AWS_SECRET_ACCESS_KEY}"

# A playbook parameter file '$HOME/parameters.yaml' is expected to be mapped
# into the container. Ths file contains user-specific parameters for
# the play that is to be run.

PARAMETER_FILE=${HOME}/parameters.yaml
echo "+> PARAMETER_FILE is ${PARAMETER_FILE}"
if [ ! -f "${PARAMETER_FILE}" ]; then
    echo "+> PARAMETER_FILE does not exist"
    exit 1
fi

# A Nextflow configuration file ('$HOME/nextflow.config')
# is expected to be mapped
# into the container...

NF_CONFIG_FILE=${HOME}/.nextflow/config
echo "+> NF_CONFIG_FILE is ${NF_CONFIG_FILE}"
if [ ! -f "${NF_CONFIG_FILE}" ]; then
    echo "+> NF_CONFIG_FILE does not exist"
    exit 1
fi

# A Kubernetes configuration file '$HOME/.kube/config' is expected to be mapped
# into the container, which we then copy so we can write to it...

KUBECONFIG_FILE=${HOME}/.kube/config
echo "+> KUBECONFIG_FILE is ${KUBECONFIG_FILE}"
if [ ! -f "${KUBECONFIG_FILE}" ]; then
    echo "+> KUBECONFIG_FILE does not exist"
    exit 1
fi

echo "+> KUBECONFIG is ${KUBECONFIG}"
echo "+> Copying ${KUBECONFIG_FILE} to ${KUBECONFIG}..."
cp "${KUBECONFIG_FILE}" "${KUBECONFIG}"

echo "+> kubectl version..."
kubectl version

# Now set default kubernetes namespace (i.e. the fragmentor)
echo "+> kubectl config set-context..."
kubectl config set-context --current --namespace="${FRAGMENTOR_NAMESPACE}"

# All set - run the playbook (ignoring but capturing any failure)...

echo "+> psql version..."
psql --version

echo "+> pip list..."
pip list

echo "+> Ansible version..."
ansible --version

# Display an 'extra arguments'
echo "+> FRAGMENTOR_PLAY_EXTRA_ARGS='${FRAGMENTOR_PLAY_EXTRA_ARGS}'"
# Has the 'skip tags' environment variable been?
echo "+> FRAGMENTOR_PLAY_SKIP_TAGS='${FRAGMENTOR_PLAY_SKIP_TAGS}'"
if [ -n "${FRAGMENTOR_PLAY_SKIP_TAGS}" ]; then
  FRAGMENTOR_PLAY_SKIP_TAGS="--skip-tags ${FRAGMENTOR_PLAY_SKIP_TAGS}"
fi

PLAYBOOK="site-${FRAGMENTOR_PLAY}.yaml"
echo "+> Playing ${PLAYBOOK}..."
pushd ansible || exit 1
EXIT_CODE=0
ansible-playbook ${FRAGMENTOR_PLAY_SKIP_TAGS} ${FRAGMENTOR_PLAY_EXTRA_ARGS} "${PLAYBOOK}" \
  -e @${PARAMETER_FILE} \
  -e ansible_python_interpreter=/usr/local/bin/python \
  || EXIT_CODE=$?
echo "+> Played"

if [ "${EXIT_CODE}" -ne "0" ]; then

    # An error - display the Nextflow log file if there is one.
    # We do this even if Nextflow turns out not to be the source of the problem
    # because it's easier than figuring out what failed in the playbook.
    #
    # The logfile will be in the working directory for the play,
    # set by each play's nextflow command with the '-log' option.
    NEXTFLOW_LOG="/work/${FRAGMENTOR_PLAY}/nextflow.log"
    if [ -f "${NEXTFLOW_LOG}" ]; then
        echo "+> Found a Nextflow logfile."
        echo "+> ${NEXTFLOW_LOG} BEGIN..."
        echo "+>"
        cat "${NEXTFLOW_LOG}"
        echo "+>"
        echo "+> ...${NEXTFLOW_LOG} END"
    else
        echo "+> No ${NEXTFLOW_LOG} file to display."
    fi

    # Finish with a bold error statement...
    echo ""
    echo "   *********"
    echo "   * ERROR *"
    echo "   *********"
    echo ""
    echo "+> Play ended with exit code ${EXIT_CODE}"
    echo "+> Inspect the Play's output (above) to see what went wrong."

else
    echo "+> SUCCESS"
fi

# Keep the Pod alive for a period of time?
# Usually for debug.
KEEP_ALIVE_SECONDS=${KEEP_ALIVE_SECONDS:-0}
if [ "${KEEP_ALIVE_SECONDS}" -ne "0" ]; then
    echo "+> KEEP_ALIVE_SECONDS is ${KEEP_ALIVE_SECONDS}"
    echo "+> Sleeping (${KEEP_ALIVE_SECONDS})..."
    sleep "${KEEP_ALIVE_SECONDS}"
    echo "+> Slept"
fi