#!/usr/bin/env python
import os
import string
import sys
from argparse import ArgumentParser
try:
import pip
except ImportError:
pip = None # type: ignore[assignment]
CONFIGURE_URL = "https://docs.galaxyproject.org/en/master/admin/"
DESCRIPTION = "Initialize a directory with a minimal Galaxy config."
HELP_CONFIG_DIR = "Directory containing the configuration files for Galaxy."
HELP_DATA_DIR = "Directory containing Galaxy-created data."
HELP_FORCE = "Overwrite existing files if they already exist."
HELP_INSTALL = "Install optional dependencies required by specified configuration (e.g. drmaa, etc...)."
HELP_HOST = (
'Host to bind Galaxy to - defaults to localhost. Specify an IP address or "all" to listen on all interfaces.'
)
HELP_PORT = "Port to bind Galaxy to."
HELP_DB_CONN = "Galaxy database connection URI."
DEFAULT_HOST = "localhost"
DEFAULT_YML = "galaxy.yml"
DEFAULT_DB_CONN = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
SAMPLES_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), "sample"))
GALAXY_CONFIG_TEMPLATE_FILE = os.path.join(SAMPLES_PATH, "galaxy.yml.sample")
STATIC_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "web", "framework", "static"))
CLIENT_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, "client"))
MSG_CONFIG_SUMMARY = """
For help on configuring Galaxy, consult the documentation at: \n {}
Additional sample configuration files for various Galaxy components (jobs,
datatypes, etc.) can be found in:\n {}
Start Galaxy by running the command from directory [{}]:
"""
# The sample is used as the default config file for Galaxy started without a config, and we don't want to duplicate the
# whole thing into galaxy.config for templating, so for now just substitute some lines. In the future we will build
# configs differently.
GALAXY_CONFIG_SUBSTITUTIONS = {
" #config_dir: false": " config_dir: ${config_dir}",
" #data_dir: false": " data_dir: ${data_dir}",
" #database_connection: sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE": " database_connection: ${database_connection}",
}
[docs]def main(argv=None):
dependencies = []
arg_parser = ArgumentParser(description=DESCRIPTION)
arg_parser.add_argument("--config-dir", default=".", help=HELP_CONFIG_DIR)
arg_parser.add_argument("--data-dir", default="./data", help=HELP_DATA_DIR)
arg_parser.add_argument("--host", default=DEFAULT_HOST, help=HELP_HOST)
arg_parser.add_argument("--port", default="8080", help=HELP_PORT)
arg_parser.add_argument("--db-conn", default=DEFAULT_DB_CONN, help=HELP_DB_CONN)
arg_parser.add_argument("--install", action="store_true", help=HELP_INSTALL)
arg_parser.add_argument("--force", action="store_true", default=False, help=HELP_FORCE)
args = arg_parser.parse_args(argv)
config_dir = args.config_dir
relative_config_dir = config_dir
config_dir = os.path.abspath(config_dir)
data_dir = args.data_dir
data_dir = os.path.abspath(data_dir)
mode = _determine_mode(args)
if args.db_conn.startswith("postgresql://"):
dependencies.append("psycopg2-binary")
for directory in (config_dir, data_dir):
if not os.path.exists(directory):
os.makedirs(directory)
print(f"Bootstrapping Galaxy configuration into directory {relative_config_dir}")
_handle_galaxy_yml(args, config_dir, data_dir)
_handle_install(args, dependencies)
_print_config_summary(args, mode, relative_config_dir)
def _print_config_summary(args, mode, relative_config_dir):
_print_galaxy_yml_info(args, mode)
print(MSG_CONFIG_SUMMARY.format(CONFIGURE_URL, SAMPLES_PATH, relative_config_dir))
def _print_galaxy_yml_info(args, mode):
print(" - galaxy.yml created, update to configure Galaxy.")
print(f" * Target web server {mode}")
if args.host == DEFAULT_HOST:
print(" * Binding to host localhost, remote clients will not be able to connect.")
elif _determine_host(args) == "0.0.0.0":
print(" * Binding to all network interfaces.")
else:
print(" * Binding to host [%s].", args.host)
def _determine_mode(args):
return "gunicorn"
def _determine_host(args):
return "0.0.0.0" if args.host == "all" else args.host
def _determine_yml_file(config_dir):
return os.path.join(config_dir, DEFAULT_YML)
def _handle_galaxy_yml(args, config_dir, data_dir):
force = args.force
yml_file = _determine_yml_file(config_dir)
_check_file(yml_file, force)
config_dict = dict(
port=args.port,
host=_determine_host(args),
config_dir=config_dir,
data_dir=data_dir,
client_dir=CLIENT_PATH,
static_path=STATIC_PATH,
database_connection=args.db_conn,
)
galaxy_config_template = []
with open(GALAXY_CONFIG_TEMPLATE_FILE) as fh:
for line in fh:
line = line.rstrip("\n")
for k, v in GALAXY_CONFIG_SUBSTITUTIONS.items():
if line == k:
line = v
galaxy_config_template.append(line)
galaxy_config_template = string.Template("\n".join(galaxy_config_template))
galaxy_config = galaxy_config_template.safe_substitute(**config_dict)
open(yml_file, "w").write(galaxy_config)
def _handle_install(args, dependencies):
if args.install and dependencies:
if pip is None:
raise ImportError("Bootstrapping Galaxy dependencies requires pip.")
pip.main(["install"] + dependencies)
def _check_file(path, force):
if os.path.exists(path) and not force:
print(f"File {path} exists, exiting. Run with --force to replace configuration.", file=sys.stderr)
sys.exit(1)
if __name__ == "__main__":
main()