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| #!/bin/bash | ||
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| ./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc -api "$@" |
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| #!/bin/bash | ||
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| ./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc --framework "$@" |
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| #!/bin/bash | ||
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| ./scripts/common_startup.sh --dev-wheels | ||
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| nosetests test/integration |
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| FROM toolshed/requirements | ||
| MAINTAINER John Chilton, jmchilton@gmail.com | ||
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| RUN apt-get -qq update && \ | ||
| apt-get install --no-install-recommends -y postgresql-client python-pip && \ | ||
| apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* | ||
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| ENV GALAXY_ROOT=/galaxy \ | ||
| GALAXY_CONFIG_OVERRIDE_ADMIN_USERS=admin@galaxy.org \ | ||
| GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DATASET_PURGE=true \ | ||
| GALAXY_CONFIG_OVERRIDE_ALLOW_LIBRARY_PATH_PASTE=true \ | ||
| GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_WORKFLOW_MODULES=true \ | ||
| GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DELETION=true \ | ||
| GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres@postgres/galaxy \ | ||
| GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53 \ | ||
| GALAXY_CONFIG_OVERRIDE_JOB_CONFIG_FILE=/galaxy/config/job_conf.xml.sample_basic \ | ||
| GALAXY_CONFIG_OVERRIDE_DATATYPES_CONFIG_FILE=/galaxy/test/functional/tools/sample_datatypes_conf.xml \ | ||
| GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE=/galaxy/test/functional/tools/samples_tool_conf.xml \ | ||
| GALAXY_CONFIG_FILE=/galaxy/.ci/jenkins/selenium/galaxy.ini \ | ||
| GALAXY_VIRTUAL_ENV=/galaxy_env | ||
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| ADD run_galaxy.bash /run_galaxy.bash | ||
| EXPOSE 8080 | ||
| CMD /run_galaxy.bash |
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| version: '2' | ||
| services: | ||
| postgres: | ||
| image: postgres | ||
| galaxy: | ||
| build: . | ||
| image: ubuntu | ||
| volumes: | ||
| - "${TARGET_ROOT}:${TARGET_PATH}" | ||
| links: | ||
| - postgres | ||
| ports: | ||
| - "${GALAXY_PORT}:8080" | ||
| selenium: | ||
| image: selenium/standalone-chrome:3.0.1-aluminum | ||
| ports: | ||
| - "${SELENIUM_PORT}:4444" | ||
| links: | ||
| - galaxy |
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| [server:main] | ||
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| use = egg:Paste#http | ||
| port = 8080 | ||
| host = 0.0.0.0 | ||
| use_threadpool = True | ||
| threadpool_kill_thread_limit = 10800 | ||
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| [app:main] | ||
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| paste.app_factory = galaxy.web.buildapp:app_factory |
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| #!/bin/bash | ||
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| set -e | ||
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| sleep 30 # TODO: wait on something instead of just sleeping... | ||
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| echo `df` | ||
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| echo "Creating postgres database for Galaxy" | ||
| createdb -w -U postgres -h postgres galaxy | ||
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| echo "Starting and waiting for Galaxy daemon(s)" | ||
| GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait | ||
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| echo "Galaxy daemon ready, monitoring Galaxy logs" | ||
| tail -f "$GALAXY_ROOT/main.log" |
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| #!/bin/bash | ||
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| TEST_DIRECTORY=`dirname $0` | ||
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| DEFAULT_COMPOSE_PROJECT_NAME=`basename $TEST_DIRECTORY` | ||
| COMPOSE_PROJECT_NAME=${COMPOSE_PROJECT_NAME:-$DEFAULT_COMPOSE_PROJECT_NAME} | ||
| # If in Jenkins environment, append ${BUILD_NUMBER} to project so builds don't interfer. | ||
| if [ ! -z "$BUILD_NUMBER" ]; | ||
| then | ||
| COMPOSE_PROJECT_NAME="${COMPOSE_PROJECT_NAME}${BUILD_NUMBER}" | ||
| fi | ||
| export COMPOSE_PROJECT_NAME | ||
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| echo "Running Jenkins test from $TEST_DIRECTORY with compose project name $COMPOSE_PROJECT_NAME" | ||
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| find lib -iname '*pyc' -exec rm -rf {} \; | ||
| find test -iname '*pyc' -exec rm -rf {} \; | ||
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| ./scripts/common_startup.sh --dev-wheels | ||
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| . .venv/bin/activate | ||
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| pip install docker-compose | ||
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| # TODO: Let docker-compose pick these at random. | ||
| export GALAXY_PORT=`python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'` | ||
| export SELENIUM_PORT=`python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'` | ||
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| export TARGET_ROOT=`pwd` | ||
| export TARGET_PATH=/galaxy | ||
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| cd $TEST_DIRECTORY | ||
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| echo "Cleaning up previous executions if needed." | ||
| docker-compose down | true | ||
| docker-compose build galaxy | ||
| docker-compose up -d | ||
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| for service_name in postgres galaxy selenium | ||
| do | ||
| echo "Waiting on service ${service_name}" | ||
| while true | ||
| do | ||
| if docker ps | grep -q "${COMPOSE_PROJECT_NAME}_${service_name}" | ||
| then | ||
| container_id=`docker ps | grep "${COMPOSE_PROJECT_NAME}_${service_name}" | cut -d " " -f 1` | ||
| eval "${service_name}_container_id=${container_id}" | ||
| echo "Service ${service_name} ready - with container ID ${container_id}" | ||
| break | ||
| fi | ||
| printf "." | ||
| sleep 1; | ||
| done | ||
| done | ||
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| if [ "$1" = "--debug-running-containers" ]; | ||
| then | ||
| env | ||
| exit 0 | ||
| fi | ||
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| export GALAXY_TEST_EXTERNAL="http://localhost:$GALAXY_PORT/" | ||
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| echo "Waiting on docker-compose managed Galaxy server - $GALAXY_TEST_EXTERNAL." | ||
| while ! curl -s "$GALAXY_TEST_EXTERNAL"; | ||
| do | ||
| for service_name in postgres galaxy selenium | ||
| do | ||
| if ! docker ps | grep -q "${COMPOSE_PROJECT_NAME}_${service_name}" | ||
| then | ||
| echo "Service ${service_name} stopped before Galaxy came up, exiting and halting containers." | ||
| for service_name in postgres galaxy selenium | ||
| do | ||
| container_id_var="${service_name}_container_id" | ||
| container_id="${!container_id_var}" | ||
| echo "Dumping logs for $service_name container (${container_id})..." | ||
| echo "---" | ||
| docker logs "${container_id}" | ||
| echo "---" | ||
| done | ||
| docker-compose down | true | ||
| exit 1 | ||
| fi | ||
| done | ||
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| printf "." | ||
| sleep 4; | ||
| done; | ||
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| # Access Selenium on localhost via port $SELENIUM_PORT | ||
| export GALAXY_TEST_SELENIUM_REMOTE=1 | ||
| export GALAXY_TEST_SELENIUM_REMOTE_PORT="${SELENIUM_PORT}" | ||
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| # Access Galaxy on localhost via port $GALAXY_PORT | ||
| export GALAXY_TEST_PORT="${GALAXY_PORT}" | ||
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| # Have Selenium access Galaxy at this URL | ||
| export GALAXY_TEST_EXTERNAL_FROM_SELENIUM="http://galaxy:8080" | ||
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| cd ../../.. | ||
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| ./run_tests.sh --selenium "$@" | ||
| exit_code=$? | ||
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| cd $TEST_DIRECTORY | ||
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| docker-compose down | ||
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| exit $exit_code |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,3 @@ | ||
| #!/bin/bash | ||
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| ./run_tests.sh --dockerize --db postgres --external_tmp --clean_pyc --toolshed "$@" |
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