run.sh

#!/bin/sh
# Wrapper script for docker.
#
# This is used primarily for wrapping the GNU Make workflow.
# Instead of typing "make TARGET", type "./run.sh make TARGET".
# This will run the make workflow within a docker container.
#
# The assumption is that you are working in the src/ontology folder;
# we therefore map the whole repo (../..) to a docker volume.
#
# See README-editors.md for more details.

IMAGE=${IMAGE:-odkfull}
ODK_JAVA_OPTS=${ODK_JAVA_OPTS:--Xmx16G}
ODK_DEBUG=${ODK_DEBUG:-no}

TIMECMD=
if [ x$ODK_DEBUG = xyes ]; then
    # If you wish to change the format string, take care of using
    # non-breaking spaces (U+00A0) instead of normal spaces, to
    # prevent the shell from tokenizing the format string.
    echo "Running ${IMAGE} with ${ODK_JAVA_OPTS} of memory for ROBOT and Java-based pipeline steps."
    TIMECMD="/usr/bin/time -f ### DEBUG STATS ###\nElapsed time: %E\nPeak memory: %M kb"
fi

docker run -v $PWD/../../:/work -w /work/src/ontology -e ROBOT_JAVA_ARGS="$ODK_JAVA_OPTS" -e JAVA_OPTS="$ODK_JAVA_OPTS" --rm -ti obolibrary/$IMAGE $TIMECMD "$@"

case "$@" in
*update_repo*|*release*)
    echo "Please remember to update your ODK image from time to time: https://oboacademy.github.io/obook/howto/odk-update/."
    ;;
esac