def _galaxy_db_exists(env):
"""
Check if galaxy database already exists. Return ``True`` if it does,
``False`` otherwise.
Note that this method does a best-effort attempt at starting the DB server
if one is not already running to do a thorough test. It shuts the server
down upon completion, but only it if also started it.
"""
db_exists = False
started = False
c = _get_galaxy_db_configs(env)
if exists(c['psql_data_dir']) and not _dir_is_empty(c['psql_data_dir']):
sudo("chown --recursive {0}:{0} {1}".format(c['psql_user'], c['psql_data_dir']))
env.logger.debug("Galaxy database directory {0} already exists.".format(c['psql_data_dir']))
# Check if PostgreSQL is already running and try to start the DB if not
if not _postgres_running(env):
with settings(warn_only=True):
env.logger.debug("Trying to start DB server in {0}".format(c['psql_data_dir']))
sudo("{0}".format(c['pg_start_cmd']), user=c['psql_user'])
started = True
# Check if galaxy DB already exists
if 'galaxy' in sudo("{0} -P pager --list | grep {1} || true".format(c['psql_cmd'],
c['galaxy_db_name']), user=c['psql_user']):
env.logger.warning("Galaxy database {0} already exists in {1}! Not creating it."\
.format(c['galaxy_db_name'], c['psql_data_dir']))
db_exists = True
if started:
with settings(warn_only=True):
sudo("{0}".format(c['pg_stop_cmd']), user=c['psql_user'])
return db_exists
def _galaxy_db_exists(env):
"""
Check if galaxy database already exists. Return ``True`` if it does,
``False`` otherwise.
Note that this method does a best-effort attempt at starting the DB server
if one is not already running to do a thorough test. It shuts the server
down upon completion, but only it if also started it.
"""
db_exists = False
started = False
c = _get_galaxy_db_configs(env)
if exists(c['psql_data_dir']) and not _dir_is_empty(c['psql_data_dir']):
sudo("chown --recursive {0}:{0} {1}".format(c['psql_user'], c['psql_data_dir']))
env.logger.debug("Galaxy database directory {0} already exists.".format(c['psql_data_dir']))
# Check if PostgreSQL is already running and try to start the DB if not
if not _postgres_running(env):
with settings(warn_only=True):
env.logger.debug("Trying to start DB server in {0}".format(c['psql_data_dir']))
sudo("{0}".format(c['pg_start_cmd']), user=c['psql_user'])
started = True
# Check if galaxy DB already exists
if 'galaxy' in sudo("{0} -P pager --list | grep {1} || true".format(c['psql_cmd'],
c['galaxy_db_name']), user=c['psql_user']):
env.logger.warning("Galaxy database {0} already exists in {1}! Not creating it."
.format(c['galaxy_db_name'], c['psql_data_dir']))
db_exists = True
if started:
with settings(warn_only=True):
sudo("{0}".format(c['pg_stop_cmd']), user=c['psql_user'])
return db_exists
def _create_galaxy_db(env):
"""
Create a new PostgreSQL database for use by Galaxy
"""
c = _get_galaxy_db_configs(env)
if not env.safe_exists(c['psql_data_dir']):
env.safe_sudo("mkdir -p {0}".format(c['psql_data_dir']))
env.safe_sudo("chown --recursive {0}:{0} {1}".format(
c['psql_user'], c['psql_data_dir']))
# Initialize a new database for Galaxy in ``psql_data_dir``
if _dir_is_empty(c['psql_data_dir']):
env.safe_sudo("{0} -D {1}".format(
os.path.join(c['psql_bin_dir'], 'initdb'), c['psql_data_dir']),
user=c['psql_user'])
# Set port for the database server
env.safe_sed(c['psql_conf_file'],
'#port = 5432',
'port = {0}'.format(c['psql_port']),
use_sudo=True)
env.safe_sudo("chown {0}:{0} {1}".format(c['psql_user'],
c['psql_conf_file']))
# Start PostgreSQL server so a role for Galaxy user can be created
if not _postgres_running(env):
env.safe_sudo(c['pg_start_cmd'], user=c['psql_user'])
started = True
else:
# Restart is required so port setting takes effect
env.safe_sudo("{0} -D {1} -w -l {2} restart".format(c['pg_ctl_cmd']),
c['psql_data_dir'],
c['psql_log'],
user=c['psql_user'])
started = False
# Create a role for env.galaxy_user
env.safe_sudo('{0} -c"CREATE ROLE {1} LOGIN CREATEDB"'.format(
c['psql_cmd'], env.galaxy_user),
user=c['psql_user'])
# Create a Galaxy database
env.safe_sudo('{0} -p {1} {2}'.format(
os.path.join(c['psql_bin_dir'], 'createdb'), c['psql_port'],
c['galaxy_db_name']),
user=env.galaxy_user)
# Create a role for 'galaxyftp' user
env.safe_sudo(
'{0} -c"CREATE ROLE galaxyftp LOGIN PASSWORD \'{1}\'"'.format(
c['psql_cmd'], c['galaxy_ftp_user_pwd']),
user=c['psql_user'])
if started:
with settings(warn_only=True):
env.safe_sudo("{0}".format(c['pg_stop_cmd']), user=c['psql_user'])
exp = "export PATH={0}:$PATH".format(c['psql_bin_dir'])
_add_to_profiles(exp)
def _create_galaxy_db(env):
"""
Create a new PostgreSQL database for use by Galaxy
"""
c = _get_galaxy_db_configs(env)
if not exists(c["psql_data_dir"]):
sudo("mkdir -p {0}".format(c["psql_data_dir"]))
sudo("chown --recursive {0}:{0} {1}".format(c["psql_user"], c["psql_data_dir"]))
# Initialize a new database for Galaxy in ``psql_data_dir``
if _dir_is_empty(c["psql_data_dir"]):
sudo("{0} -D {1}".format(os.path.join(c["psql_bin_dir"], "initdb"), c["psql_data_dir"]), user=c["psql_user"])
# Set port for the database server
sed(c["psql_conf_file"], "#port = 5432", "port = {0}".format(c["psql_port"]), use_sudo=True)
sudo("chown {0}:{0} {1}".format(c["psql_user"], c["psql_conf_file"]))
# Start PostgreSQL server so a role for Galaxy user can be created
if not _postgres_running(env):
sudo(c["pg_start_cmd"], user=c["psql_user"])
started = True
else:
# Restart is required so port setting takes effect
sudo(
"{0} -D {1} -w -l {2} restart".format(c["pg_ctl_cmd"]),
c["psql_data_dir"],
c["psql_log"],
user=c["psql_user"],
)
started = False
# Create a role for env.galaxy_user
sudo('{0} -c"CREATE ROLE {1} LOGIN CREATEDB"'.format(c["psql_cmd"], env.galaxy_user), user=c["psql_user"])
# Create a Galaxy database
sudo(
"{0} -p {1} {2}".format(os.path.join(c["psql_bin_dir"], "createdb"), c["psql_port"], c["galaxy_db_name"]),
user=env.galaxy_user,
)
# Create a role for 'galaxyftp' user
sudo(
"{0} -c\"CREATE ROLE galaxyftp LOGIN PASSWORD '{1}'\"".format(c["psql_cmd"], c["galaxy_ftp_user_pwd"]),
user=c["psql_user"],
)
if started:
with settings(warn_only=True):
sudo("{0}".format(c["pg_stop_cmd"]), user=c["psql_user"])
exp = "export PATH={0}:$PATH".format(c["psql_bin_dir"])
_add_to_profiles(exp)