# only include virtualenv if it's set/exists, otherwise this breaks conda-env'd Galaxy
if not __arg_set('virtualenv', uwsgi_kwargs) and (
'VIRTUAL_ENV' in os.environ or os.path.exists('.venv')):
__add_arg(args, 'virtualenv', os.environ.get('VIRTUAL_ENV', '.venv'))
# We always want to append client/src/assets as static-safe.
__add_arg(args, 'static-safe', f'{os.getcwd()}/client/src/assets')
# Do not let uwsgi remap stdin to /dev/null if galaxy is in debug mode
galaxy_kwargs = load_app_properties(config_file=config_file,
config_section='galaxy')
if __arg_set('debug', galaxy_kwargs) and not __arg_set(
'honour-stdin', uwsgi_kwargs):
__add_arg(args, 'honour-stdin', True)
for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
if not __arg_set(arg, uwsgi_kwargs):
__add_arg(args, arg, defaults[arg])
print(' '.join(args))
ACTIONS = {
"get_uwsgi_args": _get_uwsgi_args,
}
if __name__ == '__main__':
main = main_factory(description=DESCRIPTION,
actions=ACTIONS,
default_action="get_uwsgi_args")
main()
last_library = None
log.debug('Beginning library walk')
for library, dataset in _walk_libraries(args, model):
if library != last_library:
log.info('Library: %s', library.name)
filename = object_store.get_filename(dataset)
files_dir = dataset.get_extra_files_path()
if (args.exists and object_store.exists(dataset)) or not args.exists:
output.write('%s\n' % _path(filename, args))
elif args.exists:
log.warning('Missing %s', filename)
if files_dir and os.path.exists(files_dir):
output.write('%s\n' % _path(files_dir, args))
last_library = library
output.close()
ACTIONS = {
"get_library_dataset_paths": _get_library_dataset_paths,
}
if __name__ == '__main__':
main = main_factory(
description=DESCRIPTION,
actions=ACTIONS,
arguments=ARGUMENTS,
default_action="get_library_dataset_paths"
)
main()
'buffer-size': '16384', # https://github.com/galaxyproject/galaxy/issues/1530
'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]),
'static-map': ('/static/style={here}/static/style/blue'.format(here=os.getcwd()),
'/static={here}/static'.format(here=os.getcwd())),
'die-on-term': True,
'enable-threads': True,
'hook-master-start': ('unix_signal:2 gracefully_kill_them_all',
'unix_signal:15 gracefully_kill_them_all'),
'py-call-osafterfork': True,
}
__add_config_file_arg(args, config_file, cliargs.app)
if not __arg_set('module', uwsgi_kwargs):
__add_arg(args, 'module', 'galaxy.webapps.{app}.buildapp:uwsgi_app()'.format(app=cliargs.app))
# only include virtualenv if it's set/exists, otherwise this breaks conda-env'd Galaxy
if not __arg_set('virtualenv', uwsgi_kwargs) and ('VIRTUAL_ENV' in os.environ or os.path.exists('.venv')):
__add_arg(args, 'virtualenv', os.environ.get('VIRTUAL_ENV', '.venv'))
for arg in DEFAULT_ARGS['_all_'] + DEFAULT_ARGS[cliargs.app]:
if not __arg_set(arg, uwsgi_kwargs):
__add_arg(args, arg, defaults[arg])
print(' '.join(args))
ACTIONS = {
"get_uwsgi_args": _get_uwsgi_args,
}
if __name__ == '__main__':
main = main_factory(description=DESCRIPTION, actions=ACTIONS, default_action="get_uwsgi_args")
main()
use_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \
parse_dependency_options(kwargs, root, dependency_resolvers_config_file)
if not use_dependencies:
dependency_manager = NullDependencyManager()
else:
dependency_manager_kwds = {
'default_base_path': tool_dependency_dir,
'conf_file': dependency_resolvers_config_file,
'app_config': kwargs,
}
if use_cached_dependency_manager:
dependency_manager_kwds[
'tool_dependency_cache_dir'] = tool_dependency_cache_dir
dependency_manager = CachedDependencyManager(
**dependency_manager_kwds)
else:
dependency_manager = DependencyManager(**dependency_manager_kwds)
return dependency_manager
ACTIONS = {
"init_if_needed": _init_if_needed,
}
if __name__ == '__main__':
main = main_factory(description=DESCRIPTION, actions=ACTIONS)
main()
kwargs.get('database_connection'),
object_store=object_store)
output = _open_output(args)
last_library = None
log.debug('Beginning library walk')
for library, dataset in _walk_libraries(args, model):
if library != last_library:
log.info('Library: %s', library.name)
filename = object_store.get_filename(dataset)
files_dir = dataset.get_extra_files_path()
if (args.exists and object_store.exists(dataset)) or not args.exists:
output.write('%s\n' % _path(filename, args))
elif args.exists:
log.warning('Missing %s', filename)
if files_dir and os.path.exists(files_dir):
output.write('%s\n' % _path(files_dir, args))
last_library = library
output.close()
ACTIONS = {
"get_library_dataset_paths": _get_library_dataset_paths,
}
if __name__ == '__main__':
main = main_factory(description=DESCRIPTION,
actions=ACTIONS,
arguments=ARGUMENTS,
default_action="get_library_dataset_paths")
main()
