run_test_wrapper.sh

#!/bin/bash
set -e

if [ ! -z "$USE_SELENIUM" ];
then
    # Start Selenium.
    sudo -H -E -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"}

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_venv

: ${GALAXY_TEST_DATABASE_TYPE:-"postgres"}
if [ "$GALAXY_TEST_DATABASE_TYPE" = "postgres" ];
then
    echo "Starting postgres and then sleeping for 3 seconds"
    su -c '/usr/lib/postgresql/9.5/bin/pg_ctl -o "-F" start -D /opt/galaxy/db' postgres
    sleep 3
    GALAXY_TEST_INSTALL_DB_MERGED="true"
    GALAXY_TEST_DBURI="postgres://root@localhost:5930/galaxy?client_encoding=utf8"
    TOOL_SHED_TEST_DBURI="postgres://root@localhost:5930/toolshed?client_encoding=utf8"
    export GALAXY_CONFIG_OVERRIDE_DATABASE_ENCODING="SQL_ASCII"
elif [ "$GALAXY_TEST_DATABASE_TYPE" = "mysql" ];
then
    sh /opt/galaxy/start_mysql.sh
    GALAXY_TEST_INSTALL_DB_MERGED="true"
    GALAXY_TEST_DBURI="mysql://galaxy:galaxy@localhost/galaxy?unix_socket=/var/run/mysqld/mysqld.sock"
    TOOL_SHED_TEST_DBURI="mysql://galaxy:galaxy@localhost/toolshed?unix_socket=/var/run/mysqld/mysqld.sock"
elif [ "$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"
    exit 1
fi
export GALAXY_TEST_DBURI
export TOOL_SHED_TEST_DBURI
export GALAXY_TEST_INSTALL_DB_MERGED

cd /galaxy

: ${GALAXY_VIRTUAL_ENV:=.venv}

HOME=/galaxy
echo "Running common startup for updated dependencies (if any)"
sudo -E -u "#${GALAXY_TEST_UID}" ./scripts/common_startup.sh --dev-wheels || { echo "common_startup.sh failed"; exit 1; }

echo "Upgrading test database..."
sudo -E -u "#${GALAXY_TEST_UID}" GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI" sh manage_db.sh upgrade
echo "Upgrading tool shed database... $TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION"
sudo -E -u "#${GALAXY_TEST_UID}" TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI" sh manage_db.sh upgrade tool_shed

# Ensure Selenium is running before starting tests.
if [ ! -z "$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 "$GALAXY_NO_TESTS" ];
then
    sudo -E -u "#${GALAXY_TEST_UID}" sh run_tests.sh --skip-common-startup $@
else
    GALAXY_CONFIG_OVERRIDE_DATABASE_CONNECTION="$GALAXY_TEST_DBURI"
    TOOL_SHED_CONFIG_OVERRIDE_DATABASE_CONNECTION="$TOOL_SHED_TEST_DBURI"
    GALAXY_CONFIG_MASTER_API_KEY=${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=${GALAXY_CONFIG_FILE:-config/galaxy.ini.sample}
    if [ ! -f "$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=${GALAXY_CONFIG_JOB_CONFIG_FILE:-config/job_conf.xml.sample}
    GALAXY_CONFIG_FILE_PATH=${GALAXY_CONFIG_FILE_PATH:-/tmp/gx1}
    GALAXY_CONFIG_NEW_FILE_PATH=${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