mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #11329 from mvdbeek/drop_docker_testing_image
Drop docker testing image
This commit is contained in:
Dannon
@@ -1 +0,0 @@
|
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api
|
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@@ -1,3 +0,0 @@
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#!/bin/bash
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|
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./run_tests.sh --dockerize --db postgres --clean_pyc --skip_flakey_fails -api "$@"
|
||||
@@ -1 +0,0 @@
|
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framework
|
||||
@@ -1,3 +0,0 @@
|
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#!/bin/bash
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|
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./run_tests.sh --dockerize --db postgres --clean_pyc --framework "$@"
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@@ -1 +0,0 @@
|
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integration
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@@ -1,3 +0,0 @@
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#!/bin/bash
|
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|
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DOCKER_RUN_EXTRA_ARGS="--privileged" ./run_tests.sh --dockerize --db postgres --clean_pyc --integration "$@"
|
||||
@@ -1 +0,0 @@
|
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main-tools
|
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@@ -1,3 +0,0 @@
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#!/bin/bash
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|
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./run_tests.sh --dockerize --db postgres --clean_pyc -main "$@"
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@@ -1,24 +0,0 @@
|
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FROM toolshed/requirements
|
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LABEL maintainer="John Chilton <jmchilton@gmail.com>"
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|
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RUN apt-get -qq update && \
|
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apt-get install --no-install-recommends -y postgresql-client python-pip libffi-dev python-cffi && \
|
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apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
|
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|
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ENV GALAXY_ROOT=/galaxy \
|
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GALAXY_CONFIG_OVERRIDE_ADMIN_USERS=admin@galaxy.org,test@bx.psu.edu \
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GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DATASET_PURGE=true \
|
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GALAXY_CONFIG_OVERRIDE_ALLOW_LIBRARY_PATH_PASTE=true \
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GALAXY_CONFIG_OVERRIDE_ENABLE_BETA_WORKFLOW_MODULES=true \
|
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GALAXY_CONFIG_OVERRIDE_ALLOW_USER_DELETION=true \
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GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION=postgresql://postgres@postgres/galaxy \
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GALAXY_CONFIG_OVERRIDE_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53 \
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GALAXY_CONFIG_OVERRIDE_JOB_CONFIG_FILE=/galaxy/config/job_conf.xml.sample_basic \
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GALAXY_CONFIG_OVERRIDE_DATATYPES_CONFIG_FILE=/galaxy/test/functional/tools/sample_datatypes_conf.xml \
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GALAXY_CONFIG_OVERRIDE_TOOL_CONFIG_FILE=/galaxy/test/functional/tools/samples_tool_conf.xml \
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GALAXY_CONFIG_FILE=/galaxy/.ci/jenkins/selenium/galaxy.ini \
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GALAXY_VIRTUAL_ENV=/galaxy_env
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|
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ADD run_galaxy.bash /run_galaxy.bash
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EXPOSE 8080
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CMD /run_galaxy.bash
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@@ -1,21 +0,0 @@
|
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version: '2'
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services:
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postgres:
|
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image: postgres
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galaxy:
|
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build: .
|
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image: ubuntu
|
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volumes:
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- "${TARGET_ROOT}:${TARGET_PATH}"
|
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links:
|
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- postgres
|
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ports:
|
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- "${GALAXY_PORT}:8080"
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environment:
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GALAXY_TEST_UID: "${MY_UID}"
|
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selenium:
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image: selenium/standalone-chrome:3.5.2
|
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ports:
|
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- "${SELENIUM_PORT}:4444"
|
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links:
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- galaxy
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@@ -1,17 +0,0 @@
|
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[server:main]
|
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|
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use = egg:Paste#http
|
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port = 8080
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host = 0.0.0.0
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use_threadpool = True
|
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threadpool_kill_thread_limit = 10800
|
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|
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[filter:proxy-prefix]
|
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use = egg:PasteDeploy#prefix
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prefix = /galaxypf
|
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|
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[app:main]
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|
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paste.app_factory = galaxy.web.buildapp:app_factory
|
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|
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filter-with = proxy-prefix
|
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@@ -1,39 +0,0 @@
|
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#!/bin/bash
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|
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set -e
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|
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# Same hacks to setup a Galaxy user as used in test/docker/base/run_test_wrapper.sh
|
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# We want to make sure Galaxy runs as the same user as the external user so the files have the correct permission.
|
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echo "Deleting galaxy user - it may not exist and this is fine."
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deluser galaxy | true
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|
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: ${GALAXY_TEST_UID:-"1"}
|
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|
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echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
|
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groupadd -r galaxy -g "$GALAXY_TEST_UID" | true
|
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echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
|
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useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash | true
|
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echo "Setting galaxy user password - the operation may fail."
|
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echo "galaxy:galaxy" | chpasswd | true
|
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|
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virtualenv "$GALAXY_VIRTUAL_ENV"
|
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chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
|
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|
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cd /galaxy
|
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sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh || { echo "common_startup.sh failed"; exit 1; }
|
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|
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echo "Waiting for postgres to become available"
|
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while ! nc -z postgres 5432;
|
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do
|
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sleep 1
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printf "."
|
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done
|
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|
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echo "Creating postgres database for Galaxy"
|
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createdb -w -U postgres -h postgres galaxy
|
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|
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echo "Starting and waiting for Galaxy daemon(s)"
|
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sudo -E -H -u "#${GALAXY_TEST_UID}" GALAXY_RUN_ALL=1 bash "$GALAXY_ROOT/run.sh" --daemon --wait
|
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|
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echo "Galaxy daemon ready, monitoring Galaxy logs"
|
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tail -f "$GALAXY_ROOT/main.log"
|
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@@ -1,124 +0,0 @@
|
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#!/bin/bash
|
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|
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TEST_DIRECTORY=`dirname $0`
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|
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DEFAULT_COMPOSE_PROJECT_NAME=`basename $TEST_DIRECTORY`
|
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COMPOSE_PROJECT_NAME=${COMPOSE_PROJECT_NAME:-$DEFAULT_COMPOSE_PROJECT_NAME}
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# If in Jenkins environment, append ${BUILD_NUMBER} to project so builds don't interfer.
|
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if [ ! -z "$BUILD_NUMBER" ];
|
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then
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COMPOSE_PROJECT_NAME="${COMPOSE_PROJECT_NAME}${BUILD_NUMBER}"
|
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fi
|
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export COMPOSE_PROJECT_NAME
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|
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echo "Running Jenkins test from $TEST_DIRECTORY with compose project name $COMPOSE_PROJECT_NAME"
|
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|
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find lib -iname '*pyc' -exec rm -rf {} \;
|
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find test -iname '*pyc' -exec rm -rf {} \;
|
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|
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./scripts/common_startup.sh --dev-wheels
|
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|
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. .venv/bin/activate
|
||||
|
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pip install docker-compose
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|
||||
# TODO: Let docker-compose pick these at random.
|
||||
export GALAXY_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
|
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export SELENIUM_PORT=`python -c 'from __future__ import print_function; import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()'`
|
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|
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export TARGET_ROOT=`pwd`
|
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export TARGET_PATH=/galaxy
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export MY_UID=$(id -u)
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|
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cd $TEST_DIRECTORY
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|
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echo "Cleaning up previous executions if needed."
|
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docker-compose down | true
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docker-compose build galaxy
|
||||
docker-compose up -d
|
||||
|
||||
function tear_down {
|
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docker-compose down
|
||||
}
|
||||
|
||||
trap tear_down EXIT
|
||||
|
||||
for service_name in postgres galaxy selenium
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||||
do
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echo "Waiting on service ${service_name}"
|
||||
while true
|
||||
do
|
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if docker ps | grep -q "${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}"
|
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break
|
||||
fi
|
||||
printf "."
|
||||
sleep 1;
|
||||
done
|
||||
done
|
||||
|
||||
|
||||
if [ "$1" = "--debug-running-containers" ];
|
||||
then
|
||||
env
|
||||
exit 0
|
||||
fi
|
||||
|
||||
export GALAXY_TEST_EXTERNAL="http://localhost:$GALAXY_PORT/"
|
||||
|
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echo "Waiting on docker-compose managed Galaxy server - $GALAXY_TEST_EXTERNAL."
|
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while ! curl -s "$GALAXY_TEST_EXTERNAL";
|
||||
do
|
||||
for service_name in postgres galaxy selenium
|
||||
do
|
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if ! docker ps | grep -q "${COMPOSE_PROJECT_NAME}_${service_name}"
|
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then
|
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echo "Service ${service_name} stopped before Galaxy came up, exiting and halting containers."
|
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for service_name in postgres galaxy selenium
|
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do
|
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container_id_var="${service_name}_container_id"
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container_id="${!container_id_var}"
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echo "Dumping logs for $service_name container (${container_id})..."
|
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echo "---"
|
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docker logs "${container_id}"
|
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echo "---"
|
||||
done
|
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exit 1
|
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fi
|
||||
done
|
||||
|
||||
printf "."
|
||||
sleep 4;
|
||||
done;
|
||||
|
||||
# Access Selenium on localhost via port $SELENIUM_PORT
|
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export GALAXY_TEST_SELENIUM_REMOTE=1
|
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export GALAXY_TEST_SELENIUM_REMOTE_PORT="${SELENIUM_PORT}"
|
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|
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# Retry all failed Selenium tests a second time to deal
|
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# with transiently failing tests. Failure information for
|
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# first tests is still populated in database/test_errors
|
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# and available at the top of the Jenkins test report.
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export GALAXY_TEST_SELENIUM_RETRIES=1
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|
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# Access Galaxy on localhost via port $GALAXY_PORT
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export GALAXY_TEST_PORT="${GALAXY_PORT}"
|
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|
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# Have Selenium access Galaxy at this URL
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export GALAXY_TEST_EXTERNAL_FROM_SELENIUM="http://galaxy:8080/galaxypf"
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export GALAXY_TEST_EXTERNAL="http://localhost:${GALAXY_TEST_PORT}/galaxypf"
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|
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# Point tests at the Master API Key configured in the Dockerfile.
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export GALAXY_CONFIG_MASTER_API_KEY=94a548bea347a35e457a804bf75bec53
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cd ../../..
|
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|
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./run_tests.sh --selenium "$@"
|
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exit_code=$?
|
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|
||||
cd $TEST_DIRECTORY
|
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|
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exit $exit_code
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@@ -1 +0,0 @@
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selenium
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@@ -1,26 +0,0 @@
|
||||
#!/bin/bash
|
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|
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# Enable retries on tests to reduce chances of transient failures.
|
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: ${GALAXY_TEST_SELENIUM_RETRIES:=1}
|
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|
||||
# If in Jenkins environment, use it for artifacts.
|
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if [ -n "$BUILD_NUMBER" ];
|
||||
then
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: ${GALAXY_TEST_ERRORS_DIRECTORY:=${BUILD_NUMBER}-test-errors}
|
||||
: ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=${BUILD_NUMBER}-test-screenshots}
|
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else
|
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: ${GALAXY_TEST_ERRORS_DIRECTORY:=database/test-errors}
|
||||
: ${GALAXY_TEST_SCREENSHOTS_DIRECTORY:=database/test-screenshots}
|
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fi
|
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|
||||
mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
|
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mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
|
||||
|
||||
mkdir -p ~/.jenkins-yarn-cache
|
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YARN_CACHE_FOLDER=~/.jenkins-yarn-cache
|
||||
|
||||
# Start Selenium server in the test Docker container.
|
||||
DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} --shm-size=2g -v $YARN_CACHE_FOLDER:$YARN_CACHE_FOLDER -e YARN_CACHE_FOLDER=$YARN_CACHE_FOLDER -e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY}"
|
||||
export DOCKER_RUN_EXTRA_ARGS
|
||||
|
||||
./run_tests.sh --dockerize --db postgres --clean_pyc --skip_flakey_fails --selenium "$@"
|
||||
@@ -1,3 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
./run_tests.sh --dockerize --db postgres --clean_pyc --toolshed "$@"
|
||||
@@ -162,10 +162,6 @@ Extra options:
|
||||
functional tests).
|
||||
--skip-venv Do not create .venv (passes this flag to
|
||||
common_startup.sh)
|
||||
--dockerize Run tests in a pre-configured Docker container (must be
|
||||
first argument if present).
|
||||
--db <type> For use with --dockerize, run tests using partially
|
||||
migrated 'postgres', 'mysql', or 'sqlite' databases.
|
||||
--external_url External URL to use for Galaxy testing (only certain
|
||||
tests).
|
||||
--external_master_key Master API key used to configure external tests.
|
||||
@@ -270,8 +266,6 @@ exists() {
|
||||
type "$1" >/dev/null 2>/dev/null
|
||||
}
|
||||
|
||||
DOCKER_DEFAULT_IMAGE='galaxy/testing-base:20.05.00'
|
||||
|
||||
test_script="./scripts/functional_tests.py"
|
||||
report_file="run_functional_tests.html"
|
||||
coverage_arg=""
|
||||
@@ -285,61 +279,6 @@ else
|
||||
skip_client_build=""
|
||||
fi
|
||||
|
||||
if [ "$1" = "--dockerize" ];
|
||||
then
|
||||
shift
|
||||
DOCKER_EXTRA_ARGS=${DOCKER_ARGS:-""}
|
||||
DOCKER_RUN_EXTRA_ARGS=${DOCKER_RUN_EXTRA_ARGS:-""}
|
||||
DOCKER_IMAGE=${DOCKER_IMAGE:-${DOCKER_DEFAULT_IMAGE}}
|
||||
db_type="sqlite"
|
||||
while [ $# -gt 0 ]; do
|
||||
case "$1" in
|
||||
--python3)
|
||||
DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} -e GALAXY_VIRTUAL_ENV=/galaxy_venv3"
|
||||
shift 1
|
||||
;;
|
||||
--db)
|
||||
db_type=$2
|
||||
shift 2
|
||||
;;
|
||||
*)
|
||||
break
|
||||
;;
|
||||
esac
|
||||
done
|
||||
# Skip client build process in the Docker container for all tests except Selenium
|
||||
GALAXY_SKIP_CLIENT_BUILD=1
|
||||
case "$*" in
|
||||
*-selenium*)
|
||||
GALAXY_SKIP_CLIENT_BUILD=0
|
||||
;;
|
||||
esac
|
||||
MY_UID=$(id -u)
|
||||
DOCKER_RUN_EXTRA_ARGS="${DOCKER_RUN_EXTRA_ARGS} -e GALAXY_TEST_UID=${MY_UID} -e GALAXY_SKIP_CLIENT_BUILD=${GALAXY_SKIP_CLIENT_BUILD}"
|
||||
echo "Docker version:"
|
||||
docker --version
|
||||
echo "Launching docker container for testing with extra args ${DOCKER_RUN_EXTRA_ARGS}..."
|
||||
name=$(python -c 'import re; import uuid; print(re.sub("-", "", str(uuid.uuid4())))')
|
||||
# Create a cache dir for pip, so it has the right owner
|
||||
DOCKER_PIP_CACHE_DIR="$HOME"/.cache/docker_galaxy_pip
|
||||
mkdir -p "$DOCKER_PIP_CACHE_DIR"
|
||||
_on_exit() {
|
||||
docker kill "$name"
|
||||
}
|
||||
trap _on_exit 0
|
||||
docker $DOCKER_EXTRA_ARGS run $DOCKER_RUN_EXTRA_ARGS \
|
||||
-e "BUILD_NUMBER=$BUILD_NUMBER" \
|
||||
-e "GALAXY_TEST_DATABASE_TYPE=$db_type" \
|
||||
-e "LC_ALL=C" \
|
||||
-e "PIP_CACHE_DIR=/pip_cache_dir" \
|
||||
--rm \
|
||||
--name="$name" \
|
||||
-v "$DOCKER_PIP_CACHE_DIR":/pip_cache_dir \
|
||||
-v "$(pwd)":/galaxy \
|
||||
-v "$(pwd)"/test/docker/base/run_test_wrapper.sh:/usr/local/bin/run_test_wrapper.sh "$DOCKER_IMAGE" "$@"
|
||||
exit $?
|
||||
fi
|
||||
|
||||
# If in Jenkins environment, create xunit-${BUILD_NUMBER}.xml by default.
|
||||
if [ -n "$BUILD_NUMBER" ];
|
||||
then
|
||||
|
||||
@@ -1,40 +0,0 @@
|
||||
## Overview
|
||||
|
||||
Setup Docker environment for use with testing using the following
|
||||
commands.
|
||||
|
||||
% cd test/docker/base
|
||||
% docker build -t galaxy/testing-base .
|
||||
|
||||
Alternatively, this can be fetched from [Dockerhub](https://hub.docker.com/).
|
||||
|
||||
% docker pull galaxy/testing-base
|
||||
|
||||
The resulting docker container is ready to run most of Galaxy tests
|
||||
(functional tests for specific bioinformatics tools may still fail for
|
||||
now until they are migrated out of Galaxy and to the tool shed).
|
||||
|
||||
## Tagging a New Image
|
||||
|
||||
The Galaxy team maintains a password store that contains the password
|
||||
for the Galaxy user on Docker Hub. Docker Hub can be used to trigger a
|
||||
manual build against the dev branch. Once built, it can be pulled,
|
||||
tagged, and tested as follows:
|
||||
|
||||
% docker pull galaxy/testing-base:latest # notice latest digest
|
||||
% docker tag <digest> galaxy/testing-base:<version>
|
||||
% export DOCKER_IMAGE=galaxy/testing-base:<version>
|
||||
% ./run_tests.sh --dockerize --api # or whatever test suite you wish
|
||||
|
||||
Once verified, the tag must be pushed back to Docker Hub with:
|
||||
|
||||
% docker login # Put in galaxy as the username and the secret password
|
||||
% docker push galaxy/testing-base:<version>
|
||||
|
||||
The version should be the next dot release with the current dev Galaxy
|
||||
version as the major and minor release (e.g. 17.01 from Galaxy and .0
|
||||
for the first published image - so 17.01.0, .1 for the second published
|
||||
image - so 17.01.1, etc...).
|
||||
|
||||
A pull request to Galaxy updating the default Docker image to target should
|
||||
be made.
|
||||
@@ -1,137 +0,0 @@
|
||||
FROM ubuntu:18.04
|
||||
LABEL maintainer="John Chilton <jmchilton@gmail.com>"
|
||||
|
||||
ARG CHROME_VERSION="google-chrome-beta"
|
||||
ARG CHROME_DRIVER_VERSION="2.38"
|
||||
|
||||
# TODO: merge with first ENV statement.
|
||||
ENV DEBIAN_FRONTEND=noninteractive \
|
||||
DEBCONF_NONINTERACTIVE_SEEN=true \
|
||||
MYSQL_MAJOR=5.7 \
|
||||
POSTGRES_MAJOR=9.5 \
|
||||
GALAXY_ROOT=/galaxy \
|
||||
GALAXY_VIRTUAL_ENV=/galaxy_venv \
|
||||
LC_ALL=C.UTF-8
|
||||
|
||||
# Pre-install a bunch of packages to speed up ansible steps.
|
||||
RUN apt-get update -y && apt-get install -y software-properties-common apt-transport-https curl && \
|
||||
apt-add-repository -y ppa:ansible/ansible && \
|
||||
curl -s https://dl-ssl.google.com/linux/linux_signing_key.pub | apt-key add - && \
|
||||
echo "deb http://dl.google.com/linux/chrome/deb/ stable main" >> /etc/apt/sources.list.d/google-chrome.list && \
|
||||
apt-get update -y && \
|
||||
apt-get install -y --no-install-recommends postgresql postgresql-client ansible wget \
|
||||
python3-dev \
|
||||
git-core \
|
||||
rsync swig sysstat unzip \
|
||||
openssl \
|
||||
bzip2 \
|
||||
ca-certificates \
|
||||
openjdk-8-jre-headless \
|
||||
tzdata \
|
||||
sudo \
|
||||
locales \
|
||||
xvfb \
|
||||
${CHROME_VERSION:-google-chrome-stable} \
|
||||
libnss3 libgconf-2-4 && \
|
||||
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
|
||||
|
||||
|
||||
RUN mkdir -p /tmp/ansible && \
|
||||
mkdir -p /opt/galaxy/db && \
|
||||
chown -R postgres:postgres /opt/galaxy/db
|
||||
|
||||
ADD ansible_vars.yml /tmp/ansible/ansible_vars.yml
|
||||
ADD provision.yml /tmp/ansible/provision.yml
|
||||
|
||||
RUN mkdir /etc/galaxy && cd /tmp/ansible && mkdir roles && \
|
||||
mkdir roles/galaxyprojectdotorg.galaxy-os && \
|
||||
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-os/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-os && \
|
||||
mkdir roles/galaxyprojectdotorg.cloudman-database && \
|
||||
wget --quiet -O- https://github.com/galaxyproject/ansible-cloudman-database/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.cloudman-database && \
|
||||
mkdir roles/galaxyprojectdotorg.galaxy && \
|
||||
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy && \
|
||||
mkdir roles/galaxyprojectdotorg.galaxy-extras && \
|
||||
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-extras/archive/dynamic_uwsgi_config.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-extras && \
|
||||
mkdir roles/galaxyprojectdotorg.galaxy-toolshed && \
|
||||
wget --quiet -O- https://github.com/galaxyproject/ansible-galaxy-toolshed/archive/master.tar.gz | tar -xzf- --strip-components=1 -C roles/galaxyprojectdotorg.galaxy-toolshed && \
|
||||
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=image -c local -e "@ansible_vars.yml" && \
|
||||
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=database -c local -e "@ansible_vars.yml" && \
|
||||
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=galaxy -c local -e "@ansible_vars.yml" && \
|
||||
ANSIBLE_FORCE_COLOR=1 PYTHONUNBUFFERED=1 ansible-playbook /tmp/ansible/provision.yml --tags=toolshed -c local -e "@ansible_vars.yml" && \
|
||||
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
|
||||
|
||||
RUN cd $GALAXY_ROOT && \
|
||||
virtualenv -p /usr/bin/python3 $GALAXY_VIRTUAL_ENV && \
|
||||
./scripts/common_startup.sh --dev-wheels && \
|
||||
$GALAXY_VIRTUAL_ENV/bin/pip install psycopg2-binary && \
|
||||
rm -rf ~/.cache/pip
|
||||
|
||||
#========================================
|
||||
# Add Selenium user with passwordless sudo
|
||||
#========================================
|
||||
RUN useradd seluser \
|
||||
--shell /bin/bash \
|
||||
--create-home \
|
||||
&& usermod -a -G sudo seluser \
|
||||
&& echo 'ALL ALL = (ALL) NOPASSWD: ALL' >> /etc/sudoers \
|
||||
&& echo 'seluser:secret' | chpasswd
|
||||
|
||||
USER seluser
|
||||
|
||||
#==========
|
||||
# Selenium
|
||||
#==========
|
||||
RUN sudo mkdir -p /opt/selenium \
|
||||
&& sudo chown seluser:seluser /opt/selenium \
|
||||
&& wget --no-verbose https://selenium-release.storage.googleapis.com/3.6/selenium-server-standalone-3.6.0.jar \
|
||||
-O /opt/selenium/selenium-server-standalone.jar
|
||||
|
||||
USER root
|
||||
|
||||
#==============================
|
||||
# Scripts to run Selenium Node
|
||||
#==============================
|
||||
COPY selenium/entry_point.sh selenium/functions.sh selenium/wrap_chrome_binary selenium/generate_config /opt/bin/
|
||||
|
||||
RUN /opt/bin/wrap_chrome_binary
|
||||
|
||||
USER seluser
|
||||
|
||||
RUN CD_VERSION=$(if [ ${CHROME_DRIVER_VERSION:-latest} = "latest" ]; then echo $(wget -qO- https://chromedriver.storage.googleapis.com/LATEST_RELEASE); else echo $CHROME_DRIVER_VERSION; fi) \
|
||||
&& echo "Using chromedriver version: "$CD_VERSION \
|
||||
&& wget --no-verbose -O /tmp/chromedriver_linux64.zip https://chromedriver.storage.googleapis.com/$CD_VERSION/chromedriver_linux64.zip \
|
||||
&& rm -rf /opt/selenium/chromedriver \
|
||||
&& unzip /tmp/chromedriver_linux64.zip -d /opt/selenium \
|
||||
&& rm /tmp/chromedriver_linux64.zip \
|
||||
&& mv /opt/selenium/chromedriver /opt/selenium/chromedriver-$CD_VERSION \
|
||||
&& chmod 755 /opt/selenium/chromedriver-$CD_VERSION \
|
||||
&& sudo ln -fs /opt/selenium/chromedriver-$CD_VERSION /usr/bin/chromedriver
|
||||
|
||||
RUN /opt/bin/generate_config > /opt/selenium/config.json
|
||||
|
||||
#============================
|
||||
# Some configuration options
|
||||
#============================
|
||||
ENV SCREEN_WIDTH=1360 \
|
||||
SCREEN_HEIGHT=1020 \
|
||||
SCREEN_DEPTH=24 \
|
||||
DISPLAY=:99.0 \
|
||||
NODE_MAX_INSTANCES=1 \
|
||||
NODE_MAX_SESSION=1 \
|
||||
NODE_PORT=5555 \
|
||||
NODE_REGISTER_CYCLE=5000 \
|
||||
NODE_POLLING=5000 \
|
||||
NODE_UNREGISTER_IF_STILL_DOWN_AFTER=60000 \
|
||||
NODE_DOWN_POLLING_LIMIT=2 \
|
||||
NODE_APPLICATION_NAME="" \
|
||||
DBUS_SESSION_BUS_ADDRESS=/dev/null
|
||||
|
||||
USER root
|
||||
|
||||
ADD run_test_wrapper.sh /usr/local/bin/run_test_wrapper.sh
|
||||
|
||||
EXPOSE 9009
|
||||
EXPOSE 8080
|
||||
EXPOSE 80
|
||||
|
||||
ENTRYPOINT ["/bin/bash", "/usr/local/bin/run_test_wrapper.sh"]
|
||||
@@ -1,50 +0,0 @@
|
||||
---
|
||||
add_system_users: no
|
||||
galaxyFS_base_dir: /opt/galaxy
|
||||
# TODO: use GALAXY_ROOT via cmd line instead
|
||||
galaxy_server_dir: "/galaxy"
|
||||
galaxy_venv_dir: "/galaxy_venv"
|
||||
galaxy_vcs: git
|
||||
galaxy_git_repo: https://github.com/galaxyproject/galaxy.git
|
||||
galaxy_changeset_id: dev
|
||||
galaxy_download_url: https://codeload.github.com/galaxyproject/galaxy/tar.gz/dev
|
||||
galaxy_manage_clone: no
|
||||
galaxy_manage_download: yes
|
||||
galaxy_root: "{{ galaxy_server_dir}}"
|
||||
galaxy_db_dir: "{{ galaxyFS_base_dir }}/db"
|
||||
galaxy_db_port: 5930
|
||||
galaxy_db_log: /tmp/pSQL.log
|
||||
psql_galaxyftp_password: ignoredthis
|
||||
galaxy_config_file: "{{ galaxy_server_dir }}/config/galaxy.ini"
|
||||
configure_docker: no
|
||||
postgresql_bin_dir: /usr/lib/postgresql/10/bin
|
||||
galaxy_manage_database: no
|
||||
# avoid some packages unneeded packages install by ansible-galaxy-os
|
||||
install_maintainance_packages: false
|
||||
galaxy_user_name: "root"
|
||||
galaxy_extras_install_packages: true
|
||||
galaxy_job_conf_path: "/etc/galaxy/job_conf.xml"
|
||||
galaxy_build_client: no
|
||||
galaxy_virtualenv_python: python3
|
||||
|
||||
galaxy_web_processes: 1
|
||||
galaxy_handler_processes: 2
|
||||
galaxy_log_dir: "/root"
|
||||
|
||||
galaxy_extras_config_nginx: false
|
||||
galaxy_extras_config_proftpd: false
|
||||
galaxy_extras_config_slurm: true
|
||||
galaxy_extras_config_supervisor: false
|
||||
galaxy_extras_config_galaxy_root: false
|
||||
galaxy_extras_config_galaxy_job_metrics: false
|
||||
galaxy_extras_config_uwsgi: false
|
||||
|
||||
manage_shed_db: yes
|
||||
galaxy_toolshed_manage_static_setup: yes
|
||||
galaxy_toolshed_manage_database: no
|
||||
galaxy_toolshed_server_dir: "/galaxy"
|
||||
galaxy_toolshed_venv_dir: "{{ galaxy_venv_dir }}"
|
||||
|
||||
galaxy_toolshed_config_file: "{{ galaxy_toolshed_server_dir }}/config/tool_shed.ini"
|
||||
galaxy_toolshed_config_templates:
|
||||
- {dest: '{{ galaxy_toolshed_config_file }}', src: tool_shed.ini.j2}
|
||||
@@ -1,16 +0,0 @@
|
||||
- hosts: localhost
|
||||
connection: local
|
||||
roles:
|
||||
- role: galaxyprojectdotorg.galaxy-os
|
||||
become: true
|
||||
tags: image
|
||||
- role: galaxyprojectdotorg.cloudman-database
|
||||
become: true
|
||||
become_user: postgres
|
||||
tags: database
|
||||
- role: galaxyprojectdotorg.galaxy
|
||||
become: true
|
||||
tags: galaxy
|
||||
- role: galaxyprojectdotorg.galaxy-toolshed
|
||||
become: true
|
||||
tags: toolshed
|
||||
@@ -1,98 +0,0 @@
|
||||
#!/bin/bash
|
||||
set -e
|
||||
|
||||
if [ -n "$USE_SELENIUM" ]; then
|
||||
# Start Selenium.
|
||||
sudo -E -H -u seluser /opt/bin/entry_point.sh &
|
||||
fi
|
||||
|
||||
echo "Deleting galaxy user - it may not exist and this is fine."
|
||||
deluser galaxy || true
|
||||
|
||||
: "${GALAXY_TEST_UID:=1}"
|
||||
: "${GALAXY_VIRTUAL_ENV:=/galaxy_venv}"
|
||||
|
||||
echo "Creating galaxy group with gid $GALAXY_TEST_UID - it may already exist and this is fine."
|
||||
groupadd -r galaxy -g "$GALAXY_TEST_UID" || true
|
||||
echo "Creating galaxy user with uid $GALAXY_TEST_UID - it may already exist and this is fine."
|
||||
useradd -u $GALAXY_TEST_UID -r -g galaxy -d /home/galaxy -c "Galaxy User" galaxy -s /bin/bash || true
|
||||
echo "Setting galaxy user password - the operation may fail."
|
||||
echo "galaxy:galaxy" | chpasswd || true
|
||||
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" "$GALAXY_VIRTUAL_ENV"
|
||||
|
||||
: "${GALAXY_TEST_DATABASE_TYPE:=postgres}"
|
||||
if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ]; then
|
||||
echo "Starting postgres and then sleeping for 3 seconds"
|
||||
su -c '/usr/lib/postgresql/10/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
|
||||
sleep 3
|
||||
GALAXY_TEST_INSTALL_DB_MERGED="true"
|
||||
GALAXY_TEST_DBURI="postgresql://root@localhost:5930/galaxy?client_encoding=utf8"
|
||||
TOOL_SHED_TEST_DBURI="postgresql://root@localhost:5930/toolshed?client_encoding=utf8"
|
||||
export GALAXY_CONFIG_OVERRIDE_DATABASE_ENCODING="UTF-8"
|
||||
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "sqlite" ]; then
|
||||
GALAXY_TEST_INSTALL_DB_MERGED="true"
|
||||
GALAXY_TEST_DBURI="sqlite:////opt/galaxy/galaxy.sqlite"
|
||||
TOOL_SHED_TEST_DBURI="sqlite:////opt/galaxy/toolshed.sqlite"
|
||||
chown -R "$GALAXY_TEST_UID:$GALAXY_TEST_UID" /opt/galaxy
|
||||
else
|
||||
echo "Unknown database type '$GALAXY_TEST_DATABASE_TYPE'"
|
||||
exit 1
|
||||
fi
|
||||
export GALAXY_TEST_DBURI
|
||||
export TOOL_SHED_TEST_DBURI
|
||||
export GALAXY_TEST_INSTALL_DB_MERGED
|
||||
|
||||
cd /galaxy
|
||||
|
||||
echo "Running common startup for updated dependencies (if any)"
|
||||
sudo -E -H -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }
|
||||
|
||||
# Ensure Selenium is running before starting tests.
|
||||
if [ -n "$USE_SELENIUM" ]; then
|
||||
while ! curl -s "http://localhost:4444";
|
||||
do
|
||||
printf "."
|
||||
sleep 4;
|
||||
done;
|
||||
GALAXY_TEST_SELENIUM_REMOTE=1
|
||||
GALAXY_TEST_SELENIUM_REMOTE_HOST=localhost
|
||||
GALAXY_TEST_SELENIUM_REMOTE_PORT=4444
|
||||
|
||||
export GALAXY_TEST_SELENIUM_REMOTE
|
||||
export GALAXY_TEST_SELENIUM_REMOTE_HOST
|
||||
export GALAXY_TEST_SELENIUM_REMOTE_PORT
|
||||
fi
|
||||
|
||||
if [ -z "$GALAXY_NO_TESTS" ]; then
|
||||
sudo -E -H -u "#${GALAXY_TEST_UID}" ./run_tests.sh --skip-common-startup $@
|
||||
else
|
||||
GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI"
|
||||
TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI"
|
||||
: "${GALAXY_CONFIG_MASTER_API_KEY:=testmasterapikey}"
|
||||
# This is a path baked inside of Docker it seems, so we should support both ini and
|
||||
# YAML for some time.
|
||||
: "${GALAXY_CONFIG_FILE:=config/galaxy.ini.sample}"
|
||||
if [ ! -f "$GALAXY_CONFIG_FILE" ]; then
|
||||
GALAXY_CONFIG_FILE=config/galaxy.yml.sample
|
||||
fi
|
||||
TOOL_SHED_CONFIG_FILE=${GALAXY_CONFIG_FILE:-config/tool_shed.ini.sample}
|
||||
if [ ! -f "$TOOL_SHED_CONFIG_FILE" ]; then
|
||||
TOOL_SHED_CONFIG_FILE=config/tool_shed.yml.sample
|
||||
fi
|
||||
GALAXY_CONFIG_CHECK_MIGRATE_TOOLS=false
|
||||
: "${GALAXY_CONFIG_JOB_CONFIG_FILE:=config/job_conf.xml.sample}"
|
||||
: "${GALAXY_CONFIG_FILE_PATH:=/tmp/gx1}"
|
||||
: "${GALAXY_CONFIG_NEW_FILE_PATH:=/tmp/gxtmp}"
|
||||
|
||||
export GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION
|
||||
export TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION
|
||||
export GALAXY_CONFIG_MASTER_API_KEY
|
||||
export GALAXY_CONFIG_FILE
|
||||
export TOOL_SHED_CONFIG_FILE
|
||||
export GALAXY_CONFIG_CHECK_MIGRATE_TOOLS
|
||||
export GALAXY_CONFIG_JOB_CONFIG_FILE
|
||||
export GALAXY_CONFIG_FILE_PATH
|
||||
export GALAXY_CONFIG_NEW_FILE_PATH
|
||||
|
||||
sh run.sh $@
|
||||
fi
|
||||
@@ -1,2 +0,0 @@
|
||||
The files in this directory are from https://github.com/SeleniumHQ/docker-selenium and as such
|
||||
fall under the Apache Version 2.0 license as described here https://github.com/SeleniumHQ/docker-selenium/blob/master/LICENSE.md.
|
||||
@@ -1 +0,0 @@
|
||||
LICENSE
|
||||
@@ -1,28 +0,0 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
# IMPORTANT: Change this file only in directory Standalone!
|
||||
|
||||
source /opt/bin/functions.sh
|
||||
|
||||
export GEOMETRY="$SCREEN_WIDTH""x""$SCREEN_HEIGHT""x""$SCREEN_DEPTH"
|
||||
|
||||
function shutdown {
|
||||
kill -s SIGTERM $NODE_PID
|
||||
wait $NODE_PID
|
||||
}
|
||||
|
||||
if [ ! -z "$SE_OPTS" ]; then
|
||||
echo "appending selenium options: ${SE_OPTS}"
|
||||
fi
|
||||
|
||||
SERVERNUM=$(get_server_num)
|
||||
|
||||
rm -f /tmp/.X*lock
|
||||
|
||||
xvfb-run -n $SERVERNUM --server-args="-screen 0 $GEOMETRY -ac +extension RANDR" \
|
||||
java ${JAVA_OPTS} -jar /opt/selenium/selenium-server-standalone.jar \
|
||||
${SE_OPTS} &
|
||||
NODE_PID=$!
|
||||
|
||||
trap shutdown SIGTERM SIGINT
|
||||
wait $NODE_PID
|
||||
@@ -1,6 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
# https://github.com/SeleniumHQ/docker-selenium/issues/184
|
||||
function get_server_num() {
|
||||
echo $(echo $DISPLAY | sed -r -e 's/([^:]+)?:([0-9]+)(\.[0-9]+)?/\2/')
|
||||
}
|
||||
@@ -1,25 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
CHROME_VERSION=$(/usr/bin/google-chrome -version | awk '{ print $3 }')
|
||||
|
||||
cat <<_EOF
|
||||
{
|
||||
"capabilities": [
|
||||
{
|
||||
"version": "$CHROME_VERSION",
|
||||
"browserName": "chrome",
|
||||
"maxInstances": $NODE_MAX_INSTANCES,
|
||||
"seleniumProtocol": "WebDriver",
|
||||
"applicationName": "$NODE_APPLICATION_NAME"
|
||||
}
|
||||
],
|
||||
"proxy": "org.openqa.grid.selenium.proxy.DefaultRemoteProxy",
|
||||
"maxSession": $NODE_MAX_SESSION,
|
||||
"port": $NODE_PORT,
|
||||
"register": true,
|
||||
"registerCycle": $NODE_REGISTER_CYCLE,
|
||||
"nodePolling": $NODE_POLLING,
|
||||
"unregisterIfStillDownAfter": $NODE_UNREGISTER_IF_STILL_DOWN_AFTER,
|
||||
"downPollingLimit": $NODE_DOWN_POLLING_LIMIT
|
||||
}
|
||||
_EOF
|
||||
@@ -1,13 +0,0 @@
|
||||
#!/bin/bash
|
||||
|
||||
WRAPPER_PATH=$(readlink -f /usr/bin/google-chrome)
|
||||
BASE_PATH="$WRAPPER_PATH-base"
|
||||
mv "$WRAPPER_PATH" "$BASE_PATH"
|
||||
|
||||
cat > "$WRAPPER_PATH" <<_EOF
|
||||
#!/bin/bash
|
||||
|
||||
# Note: exec -a below is a bashism.
|
||||
exec -a "\$0" "$BASE_PATH" --no-sandbox "\$@"
|
||||
_EOF
|
||||
chmod +x "$WRAPPER_PATH"
|
||||
Reference in New Issue
Block a user