gistfile1.txt

### Editing this command? Also update https://ci.commonwl.org/job/cwl-spec-pr/configure
venv() {
        if ! test -d $1 ; then
                virtualenv $1
        fi
        . $1/bin/activate
}
venv venv
(. venv/bin/activate && pip install -U setuptools wheel pip)
(. venv/bin/activate && pip install --ignore-installed --verbose -U cwltest cwltool)


shutdownGalaxy() {
    bash scripts/end_cwl_conformance.bash
}
trap "shutdownGalaxy" EXIT

START_DIR=$(pwd)
GALAXY_SKIP_CLIENT_BUILD=1 sh scripts/common_startup.sh
(. .venv/bin/activate && pip install psycopg2)

bash scripts/run_for_cwl_conformance.bash
### Editing this command? Also update https://ci.commonwl.org/job/cwl-spec-pr/configure
(. venv/bin/activate && cd common-workflow-language && ./run_test.sh \
  --junit-xml=${START_DIR}/result.xml \
  RUNNER=${START_DIR}/scripts/cwl-runner) || /bin/true
set -e
shutdownGalaxy || /bin/true

gistfile2.txt

#!/bin/bash
export LC_ALL=en_US.UTF-8
cloneorpull() {
        if test -d $1 ; then
                (cd $1 && git pull)
        else
                git clone $2
        fi
}
venv() {
        if ! test -d $1 ; then
                virtualenv $1
        fi
        . $1/bin/activate
}
if [[ "${implementation}" == *arvados* ]]
then
	cloneorpull arvados https://github.com/curoverse/arvados.git
	docker volume ls -qf dangling=true | grep -v metadata.db | xargs -r docker volume rm || true
    docker pull arvados/arvbox-demo:latest
	export PATH=$PATH:$PWD/tools/arvbox/bin
	export ARVBOX_CONTAINER=cwltest
    arvados/sdk/cwl/test_with_arvbox.sh --config localdemo --leave-running --junit-xml=/tmp/junit.xml \
    	RUNNER=/tmp/cwltest/arv-cwl-containers
    CODE=$?
	docker exec $ARVBOX_CONTAINER cat /tmp/junit.xml > junit.xml
	arvbox reset -f
	docker volume ls -qf dangling=true | grep -v metadata.db | xargs -r docker volume rm || true
	docker rmi $(docker images -a --no-trunc | grep "^arvados/arvbox-demo" | grep -v "latest" | sed 's/  */ /g' \
    	| cut -d' ' -f3) || true
	exit $CODE
elif [[ "${implementation}" == *cwltool* ]]
then
    cloneorpull cwltool https://github.com/common-workflow-language/cwltool.git
    venv cwltool-venv
    (. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install -U setuptools wheel pip)
	(. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install ./cwltool/)
	(. cwltool-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install "cwltest>=1.0.20180518074130")
	(. cwltool-venv/bin/activate && cd common-workflow-language && \
    	./run_test.sh --junit-xml=result.xml RUNNER=cwltool DRAFT=$version EXTRA=--enable-dev -j2)
elif [[ "${implementation}" == *rabix* ]]
then
	cloneorpull bunny https://github.com/rabix/bunny.git
    venv cwltest-venv
    (. cwltest-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install -U setuptools wheel pip)
    (. cwltest-venv/bin/activate && PIP_DOWNLOAD_CACHE=/var/lib/jenkins/pypi-cache/ pip install "cwltest>=1.0.20180518074130")
    cd bunny
    mvn clean package -P cwl
    tar xzf rabix-cli/target/rabix-cli-*-release.tar.gz
    set +e
    LC_ALL=C
    LANG=C
    (. ../cwltest-venv/bin/activate && export DOCKER_HOST="unix:///var/run/docker.sock" \
    	&& cd ../common-workflow-language && ./run_test.sh --junit-xml=result.xml \
        RUNNER=../bunny/rabix-cli-*/rabix DRAFT=$version -j$(($(nproc) / 2)))
    set -e
elif [[ "${implementation}" == *cromwell* ]]
then
	CWLDIR=$PWD
    if [ -d "${CWLDIR}/v1.0" ];
	then
		docker run --mount type=bind,source=${CWLDIR},destination=/cwl debian:latest rm -Rf /cwl/v1.0
	fi
    cloneorpull cromwell https://github.com/broadinstitute/cromwell.git
	venv cromwell_venv
	(. cromwell_venv/bin/activate && pip install -U setuptools wheel pip)
	(. cromwell_venv/bin/activate && pip install -U "cwltest>=1.0.20180518074130" cwltool)
    cd cromwell
	sbt clean assembly
	CROMWELL_JAR=$(find "$(pwd)/server/target/scala-2.12" -name "cromwell-*.jar")
    CENTAUR_CWL_JAR=$(find "$(pwd)/centaurCwlRunner/target/scala-2.12" -name "centaur-cwl-runner-*.jar")
	shutdownCromwell() {
    if [ -z "${CROMWELL_PID}" ]; then
        if [ -d "${CWLDIR}/v1.0" ]; then
			docker run --mount type=bind,source=${CWLDIR},destination=/cwl debian:latest rm -Rf /cwl/v1.0
		fi
        if [ -z "${CROMWELL_PID}" ]; then
        	kill -9 ${CROMWELL_PID}
        fi
    fi
	}
	trap "shutdownCromwell" EXIT
	
	START_DIR=$(pwd)
	cd ../common-workflow-language/v1.0/v1.0
	java \
      -Xmx2g \
      -Dsystem.new-workflow-poll-rate=1 \
      -Dbackend.providers.Local.config.script-epilogue="sleep 5 && sync" \
      -Dsystem.job-shell=/bin/sh \
      -jar ${CROMWELL_JAR} server &
	CROMWELL_PID=$$
	
	sleep 10
	
	cd ${START_DIR}
    cat > ${START_DIR}/centaur-cwl-runner << EOF
#!/bin/sh
exec java -Xmx1g -jar ${CENTAUR_CWL_JAR} \$@
EOF
	chmod a+x ${START_DIR}/centaur-cwl-runner
	(. ../cromwell_venv/bin/activate && cd ../common-workflow-language && \
    	./run_test.sh --junit-xml=${START_DIR}/result.xml -j$(($(nproc) /2 ))\
    	RUNNER=${START_DIR}/centaur-cwl-runner) || /bin/true
	set -e
    shutdownCromwell
fi