mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Rename lib/galaxy/main.py to scripts/galaxy-main since that makes more
sense and doesn't result in lib/galaxy/ being added to sys.path. Create a symlink at lib/galaxy/main.py for backward compatibility.
This commit is contained in:
Nate Coraor
@@ -1,246 +0,0 @@
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""" Entry point for starting Galaxy without starting as part of a web server.
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Example Usage: Start a job/workflow handler without a web server and with
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a given name using.
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python lib/galaxy/main.py --server-name handler0
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Start as a daemon with (requires daemonized - install with 'pip install daemonize'):
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python lib/galaxy/main.py -d --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --server-name handler0
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In daemon mode logging of Galaxy (as opposed to this script) is configured via
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a loggers section in Galaxy's ini file - this can be overridden with sensible
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defaults logging to a single file with the following:
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python lib/galaxy/main.py -d --server-name handler0 --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --log-file handler0.log
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"""
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import logging
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from logging.config import fileConfig
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import functools
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import os
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import time
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import sys
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try:
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import ConfigParser as configparser
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except ImportError:
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import configparser
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try:
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from daemonize import Daemonize
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except ImportError:
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Daemonize = None
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# Vaguely Python 2.6 compatibile ArgumentParser import
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try:
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from argparse import ArgumentParser
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except ImportError:
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from optparse import OptionParser
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class ArgumentParser(OptionParser):
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def __init__(self, **kwargs):
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self.delegate = OptionParser(**kwargs)
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def add_argument(self, *args, **kwargs):
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if "required" in kwargs:
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del kwargs["required"]
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return self.delegate.add_option(*args, **kwargs)
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def parse_args(self, args=None):
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(options, args) = self.delegate.parse_args(args)
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return options
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REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemonize is unavailable."
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log = logging.getLogger(__name__)
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GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
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GALAXY_LIB_DIR = os.path.join(GALAXY_ROOT_DIR, "lib")
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DEFAULT_INI_APP = "main"
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DEFAULT_INIS = ["config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.ini.sample"]
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DEFAULT_PID = "galaxy.pid"
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DEFAULT_VERBOSE = True
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DESCRIPTION = "Daemonized entry point for Galaxy."
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def load_galaxy_app(
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config_builder,
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config_env=False,
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log=None,
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**kwds
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):
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# Allow specification of log so daemon can reuse properly configured one.
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if log is None:
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log = logging.getLogger(__name__)
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# If called in daemon mode, set the ROOT directory and ensure Galaxy is on
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# sys.path.
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if config_env:
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try:
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os.chdir(GALAXY_ROOT_DIR)
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except Exception:
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log.exception("Failed to chdir")
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raise
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try:
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sys.path.insert(1, GALAXY_LIB_DIR)
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except Exception:
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log.exception("Failed to add Galaxy to sys.path")
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raise
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config_builder.setup_logging()
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from galaxy.util.properties import load_app_properties
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kwds = config_builder.app_kwds()
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kwds = load_app_properties(**kwds)
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from galaxy.app import UniverseApplication
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app = UniverseApplication(
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global_conf={"__file__": config_builder.ini_path},
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**kwds
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)
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app.control_worker.bind_and_start()
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return app
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def app_loop(args, log):
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try:
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config_builder = GalaxyConfigBuilder(args)
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galaxy_app = load_galaxy_app(
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config_builder,
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config_env=True,
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log=log,
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)
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except BaseException:
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log.exception("Failed to initialize Galaxy application")
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raise
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sleep = True
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while sleep:
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try:
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time.sleep(5)
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except KeyboardInterrupt:
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sleep = False
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except SystemExit:
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sleep = False
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except Exception:
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pass
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try:
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galaxy_app.shutdown()
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except Exception:
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log.exception("Failed to shutdown Galaxy application")
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raise
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def absolute_config_path(path, galaxy_root):
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if path and not os.path.isabs(path):
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path = os.path.join(galaxy_root, path)
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return path
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def find_ini(supplied_ini, galaxy_root):
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if supplied_ini:
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return supplied_ini
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# If not explicitly supplied an ini, check server.ini and then
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# just restort to sample if that has not been configured.
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for guess in DEFAULT_INIS:
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ini_path = os.path.join(galaxy_root, guess)
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if os.path.exists(ini_path):
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return ini_path
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return guess
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class GalaxyConfigBuilder(object):
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""" Generate paste-like configuration from supplied command-line arguments.
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"""
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def __init__(self, args=None, **kwds):
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ini_path = kwds.get("ini_path", None) or (args and args.ini_path)
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# If given app_conf_path - use that - else we need to ensure we have an
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# ini path.
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if not ini_path:
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galaxy_root = kwds.get("galaxy_root", GALAXY_ROOT_DIR)
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ini_path = find_ini(ini_path, galaxy_root)
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ini_path = absolute_config_path(ini_path, galaxy_root=galaxy_root)
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self.ini_path = ini_path
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self.app_name = kwds.get("app") or (args and args.app) or DEFAULT_INI_APP
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self.log_file = (args and args.log_file)
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@classmethod
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def populate_options(cls, arg_parser):
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arg_parser.add_argument("-c", "--ini-path", default=None, help="Galaxy ini config file (defaults to config/galaxy.ini)")
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arg_parser.add_argument("--app", default=DEFAULT_INI_APP, help="app section in ini file (defaults to main)")
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arg_parser.add_argument("-d", "--daemonize", default=False, help="Daemonzie process", action="store_true")
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arg_parser.add_argument("--daemon-log-file", default=None, help="log file for daemon script ")
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arg_parser.add_argument("--log-file", default=None, help="Galaxy log file (overrides log configuration in ini_path if set)")
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arg_parser.add_argument("--pid-file", default=DEFAULT_PID, help="pid file (default is %s)" % DEFAULT_PID)
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arg_parser.add_argument("--server-name", default=None, help="set a galaxy server name")
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def app_kwds(self):
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config = dict(
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ini_file=self.ini_path,
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ini_section="app:%s" % self.app_name,
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)
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return config
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def setup_logging(self):
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# Galaxy will attempt to setup logging if loggers is not present in
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# ini config file - this handles that loggers block however if present
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# (the way paste normally would)
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if not self.ini_path:
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return
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raw_config = configparser.ConfigParser()
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raw_config.read([self.ini_path])
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if raw_config.has_section('loggers'):
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config_file = os.path.abspath(self.ini_path)
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fileConfig(
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config_file,
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dict(__file__=config_file, here=os.path.dirname(config_file))
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)
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def main():
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arg_parser = ArgumentParser(description=DESCRIPTION)
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GalaxyConfigBuilder.populate_options(arg_parser)
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args = arg_parser.parse_args()
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if args.log_file:
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os.environ["GALAXY_CONFIG_LOG_DESTINATION"] = os.path.abspath(args.log_file)
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if args.server_name:
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os.environ["GALAXY_CONFIG_SERVER_NAME"] = args.server_name
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pid_file = args.pid_file
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log.setLevel(logging.DEBUG)
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log.propagate = False
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if args.daemonize:
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if Daemonize is None:
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raise ImportError(REQUIRES_DAEMONIZE_MESSAGE)
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keep_fds = []
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if args.daemon_log_file:
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fh = logging.FileHandler(args.daemon_log_file, "w")
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fh.setLevel(logging.DEBUG)
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log.addHandler(fh)
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keep_fds.append(fh.stream.fileno())
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else:
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fh = logging.StreamHandler(sys.stderr)
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fh.setLevel(logging.DEBUG)
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log.addHandler(fh)
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daemon = Daemonize(
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app="galaxy",
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pid=pid_file,
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action=functools.partial(app_loop, args, log),
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verbose=DEFAULT_VERBOSE,
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logger=log,
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keep_fds=keep_fds,
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)
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daemon.start()
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else:
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app_loop(args, log)
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if __name__ == "__main__":
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main()
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Symlink
+1
@@ -0,0 +1 @@
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../../scripts/galaxy-main
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Executable
+251
@@ -0,0 +1,251 @@
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#!/usr/bin/env python
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""" Entry point for starting Galaxy without starting as part of a web server.
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|
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Example Usage: Start a job/workflow handler without a web server and with
|
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a given name using.
|
||||
|
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galaxy-main --server-name handler0
|
||||
|
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Start as a daemon with (requires daemonized - install with 'pip install daemonize'):
|
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|
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galaxy-main -d --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --server-name handler0
|
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|
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In daemon mode logging of Galaxy (as opposed to this script) is configured via
|
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a loggers section in Galaxy's ini file - this can be overridden with sensible
|
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defaults logging to a single file with the following:
|
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|
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galaxy-main -d --server-name handler0 --daemon-log-file=handler0-daemon.log --pid-file handler0.pid --log-file handler0.log
|
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"""
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import logging
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from logging.config import fileConfig
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import functools
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import os
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import time
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import sys
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try:
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import ConfigParser as configparser
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except ImportError:
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import configparser
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|
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try:
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from daemonize import Daemonize
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except ImportError:
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Daemonize = None
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|
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# Vaguely Python 2.6 compatibile ArgumentParser import
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try:
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from argparse import ArgumentParser
|
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except ImportError:
|
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from optparse import OptionParser
|
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|
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class ArgumentParser(OptionParser):
|
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|
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def __init__(self, **kwargs):
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self.delegate = OptionParser(**kwargs)
|
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|
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def add_argument(self, *args, **kwargs):
|
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if "required" in kwargs:
|
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del kwargs["required"]
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return self.delegate.add_option(*args, **kwargs)
|
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|
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def parse_args(self, args=None):
|
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(options, args) = self.delegate.parse_args(args)
|
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return options
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REQUIRES_DAEMONIZE_MESSAGE = "Attempted to use Galaxy in daemon mode, but daemonize is unavailable."
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log = logging.getLogger(__name__)
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base_file = os.path.basename(__file__)
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if base_file == 'main.py':
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GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, os.pardir))
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elif base_file == 'galaxy-main':
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GALAXY_ROOT_DIR = os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir))
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GALAXY_LIB_DIR = os.path.join(GALAXY_ROOT_DIR, "lib")
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DEFAULT_INI_APP = "main"
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DEFAULT_INIS = ["config/galaxy.ini", "universe_wsgi.ini", "config/galaxy.ini.sample"]
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|
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DEFAULT_PID = "galaxy.pid"
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DEFAULT_VERBOSE = True
|
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DESCRIPTION = "Daemonized entry point for Galaxy."
|
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|
||||
|
||||
def load_galaxy_app(
|
||||
config_builder,
|
||||
config_env=False,
|
||||
log=None,
|
||||
**kwds
|
||||
):
|
||||
# Allow specification of log so daemon can reuse properly configured one.
|
||||
if log is None:
|
||||
log = logging.getLogger(__name__)
|
||||
|
||||
# If called in daemon mode, set the ROOT directory and ensure Galaxy is on
|
||||
# sys.path.
|
||||
if config_env:
|
||||
try:
|
||||
os.chdir(GALAXY_ROOT_DIR)
|
||||
except Exception:
|
||||
log.exception("Failed to chdir")
|
||||
raise
|
||||
try:
|
||||
sys.path.insert(1, GALAXY_LIB_DIR)
|
||||
except Exception:
|
||||
log.exception("Failed to add Galaxy to sys.path")
|
||||
raise
|
||||
|
||||
config_builder.setup_logging()
|
||||
from galaxy.util.properties import load_app_properties
|
||||
kwds = config_builder.app_kwds()
|
||||
kwds = load_app_properties(**kwds)
|
||||
from galaxy.app import UniverseApplication
|
||||
app = UniverseApplication(
|
||||
global_conf={"__file__": config_builder.ini_path},
|
||||
**kwds
|
||||
)
|
||||
app.control_worker.bind_and_start()
|
||||
return app
|
||||
|
||||
|
||||
def app_loop(args, log):
|
||||
try:
|
||||
config_builder = GalaxyConfigBuilder(args)
|
||||
galaxy_app = load_galaxy_app(
|
||||
config_builder,
|
||||
config_env=True,
|
||||
log=log,
|
||||
)
|
||||
except BaseException:
|
||||
log.exception("Failed to initialize Galaxy application")
|
||||
raise
|
||||
sleep = True
|
||||
while sleep:
|
||||
try:
|
||||
time.sleep(5)
|
||||
except KeyboardInterrupt:
|
||||
sleep = False
|
||||
except SystemExit:
|
||||
sleep = False
|
||||
except Exception:
|
||||
pass
|
||||
try:
|
||||
galaxy_app.shutdown()
|
||||
except Exception:
|
||||
log.exception("Failed to shutdown Galaxy application")
|
||||
raise
|
||||
|
||||
|
||||
def absolute_config_path(path, galaxy_root):
|
||||
if path and not os.path.isabs(path):
|
||||
path = os.path.join(galaxy_root, path)
|
||||
return path
|
||||
|
||||
|
||||
def find_ini(supplied_ini, galaxy_root):
|
||||
if supplied_ini:
|
||||
return supplied_ini
|
||||
|
||||
# If not explicitly supplied an ini, check server.ini and then
|
||||
# just restort to sample if that has not been configured.
|
||||
for guess in DEFAULT_INIS:
|
||||
ini_path = os.path.join(galaxy_root, guess)
|
||||
if os.path.exists(ini_path):
|
||||
return ini_path
|
||||
|
||||
return guess
|
||||
|
||||
|
||||
class GalaxyConfigBuilder(object):
|
||||
""" Generate paste-like configuration from supplied command-line arguments.
|
||||
"""
|
||||
|
||||
def __init__(self, args=None, **kwds):
|
||||
ini_path = kwds.get("ini_path", None) or (args and args.ini_path)
|
||||
# If given app_conf_path - use that - else we need to ensure we have an
|
||||
# ini path.
|
||||
if not ini_path:
|
||||
galaxy_root = kwds.get("galaxy_root", GALAXY_ROOT_DIR)
|
||||
ini_path = find_ini(ini_path, galaxy_root)
|
||||
ini_path = absolute_config_path(ini_path, galaxy_root=galaxy_root)
|
||||
self.ini_path = ini_path
|
||||
self.app_name = kwds.get("app") or (args and args.app) or DEFAULT_INI_APP
|
||||
self.log_file = (args and args.log_file)
|
||||
|
||||
@classmethod
|
||||
def populate_options(cls, arg_parser):
|
||||
arg_parser.add_argument("-c", "--ini-path", default=None, help="Galaxy ini config file (defaults to config/galaxy.ini)")
|
||||
arg_parser.add_argument("--app", default=DEFAULT_INI_APP, help="app section in ini file (defaults to main)")
|
||||
arg_parser.add_argument("-d", "--daemonize", default=False, help="Daemonzie process", action="store_true")
|
||||
arg_parser.add_argument("--daemon-log-file", default=None, help="log file for daemon script ")
|
||||
arg_parser.add_argument("--log-file", default=None, help="Galaxy log file (overrides log configuration in ini_path if set)")
|
||||
arg_parser.add_argument("--pid-file", default=DEFAULT_PID, help="pid file (default is %s)" % DEFAULT_PID)
|
||||
arg_parser.add_argument("--server-name", default=None, help="set a galaxy server name")
|
||||
|
||||
def app_kwds(self):
|
||||
config = dict(
|
||||
ini_file=self.ini_path,
|
||||
ini_section="app:%s" % self.app_name,
|
||||
)
|
||||
return config
|
||||
|
||||
def setup_logging(self):
|
||||
# Galaxy will attempt to setup logging if loggers is not present in
|
||||
# ini config file - this handles that loggers block however if present
|
||||
# (the way paste normally would)
|
||||
if not self.ini_path:
|
||||
return
|
||||
raw_config = configparser.ConfigParser()
|
||||
raw_config.read([self.ini_path])
|
||||
if raw_config.has_section('loggers'):
|
||||
config_file = os.path.abspath(self.ini_path)
|
||||
fileConfig(
|
||||
config_file,
|
||||
dict(__file__=config_file, here=os.path.dirname(config_file))
|
||||
)
|
||||
|
||||
|
||||
def main():
|
||||
arg_parser = ArgumentParser(description=DESCRIPTION)
|
||||
GalaxyConfigBuilder.populate_options(arg_parser)
|
||||
args = arg_parser.parse_args()
|
||||
if args.log_file:
|
||||
os.environ["GALAXY_CONFIG_LOG_DESTINATION"] = os.path.abspath(args.log_file)
|
||||
if args.server_name:
|
||||
os.environ["GALAXY_CONFIG_SERVER_NAME"] = args.server_name
|
||||
pid_file = args.pid_file
|
||||
|
||||
log.setLevel(logging.DEBUG)
|
||||
log.propagate = False
|
||||
if args.daemonize:
|
||||
if Daemonize is None:
|
||||
raise ImportError(REQUIRES_DAEMONIZE_MESSAGE)
|
||||
|
||||
keep_fds = []
|
||||
if args.daemon_log_file:
|
||||
fh = logging.FileHandler(args.daemon_log_file, "w")
|
||||
fh.setLevel(logging.DEBUG)
|
||||
log.addHandler(fh)
|
||||
keep_fds.append(fh.stream.fileno())
|
||||
else:
|
||||
fh = logging.StreamHandler(sys.stderr)
|
||||
fh.setLevel(logging.DEBUG)
|
||||
log.addHandler(fh)
|
||||
|
||||
daemon = Daemonize(
|
||||
app="galaxy",
|
||||
pid=pid_file,
|
||||
action=functools.partial(app_loop, args, log),
|
||||
verbose=DEFAULT_VERBOSE,
|
||||
logger=log,
|
||||
keep_fds=keep_fds,
|
||||
)
|
||||
daemon.start()
|
||||
else:
|
||||
app_loop(args, log)
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
main()
|
||||
Reference in New Issue
Block a user