Start test environment

docker-compose up

CWL compliance tests

The docker image mgrast/awe-submitter-testing has all CWL compliance tests and the awe-submitter installed. Start the container:

docker run -ti --network awe-test_default --name awe-submitter -e SHOCK_SERVER="http://shock:7445" -e AWE_SERVER="http://awe-server:80" --workdir=/go/src/github.com/MG-RAST/AWE -v ${HOME}/gopath/src:/go/src --entrypoint=/bin/ash mgrast/awe-submitter-testing

Optional: Compile the awe-submitter.

cd $AWE ; ./compile-submitter.sh

Submit compliance test #1

cd /common-workflow-language/ ; ./run_test.sh --junit-xml=/output/result.xml --timeout=120 -n1 RUNNER=/go/bin/awe-cwl-submitter-wrapper.sh

Development

The AWE test environment can also be used as a development environment. The approach below allows a developer to replace a container in the docker-compose environment with their own interactive container that has their source code mounted, which makes it easy to compile and test awe code.

AWE server development

Start development container

docker rm -f awe-test_awe-server_1 > /dev/null 2>&1
docker run -ti --name awe-test_awe-server_1 --rm --network awe-test_default --network-alias awe-server -p 81:80 -v ${HOME}/gopath/src:/go/src mgrast/awe-server

(Inside container) Compile:

cd $AWE ; ./compile.sh

(Inside container) Start awe-server:

awe-server --logoutput=console --debuglevel=3 --hosts=awe-mongo --api-port=80 --api-url='http://localhost:81' --title="test AWE server" --max_work_failure=1 --recover --max_client_failure=1000

AWE worker development

Download the statically compiled docker binary if missing. (This is needed by the cwl-runnner to execute CWL workflows.)

DOCKER_VERSION=$(docker --version | grep -o "[0-9]*\.[0-9]*\.[0-9a-z\.-]*")
echo "DOCKER_VERSION: ${DOCKER_VERSION}"
mkdir -p "${HOME}/bin/"
DOCKER_BINARY="${HOME}/bin/docker-${DOCKER_VERSION}"
if [ ! -e ${DOCKER_BINARY} ] ; then
  mkdir -p ${HOME}/tmp/
  cd ${HOME}/tmp/
  curl -fsSLO https://download.docker.com/linux/static/stable/x86_64/docker-${DOCKER_VERSION}.tgz
  tar -xvzf docker-${DOCKER_VERSION}.tgz -C ${HOME}/tmp/ docker/docker
  mv docker/docker ${DOCKER_BINARY}
fi

Start development container

export NAME=awe-test_awe-worker_1
export WORKER_DATADIR=${HOME}/awe_data

docker rm -f ${NAME} > /dev/null 2>&1
docker run -ti --network awe-test_default --name ${NAME} -e NAME=${NAME} -e WORKER_DATADIR=${WORKER_DATADIR} --workdir=/go/src/github.com/MG-RAST/AWE -v ${WORKER_DATADIR}:${WORKER_DATADIR}  -v ${DOCKER_BINARY}:/usr/local/bin/docker -v /var/run/docker.sock:/var/run/docker.sock -v ${HOME}/gopath/src:/go/src -v /tmp:/tmp  mgrast/awe-worker ash

(Inside container) Compile:

cd $AWE ; ./compile-worker.sh

(Inside container) Start awe-worker:

/go/bin/awe-worker  --name ${NAME} --data=${WORKER_DATADIR}/data --logs=${WORKER_DATADIR}/logs --workpath=${WORKER_DATADIR}/work  --serverurl=http://awe-server:80 --group=default --supported_apps=* --auto_clean_dir=false --debuglevel=3