def read_config_file_arg( argv, default, old_default, cwd=None ):
config_file = None
if '-c' in argv:
pos = argv.index( '-c' )
argv.pop(pos)
config_file = argv.pop( pos )
return find_config_file( default, old_default, config_file, cwd=cwd )
def read_config_file_arg(argv, config_names, cwd=None):
if '-c' in argv:
pos = argv.index('-c')
argv.pop(pos)
return argv.pop(pos)
if cwd:
cwd = [cwd, os.path.join(cwd, 'config')]
return find_config_file(config_names, dirs=cwd)
def get_config(argv, use_argparse=True, cwd=None):
"""
Read sys.argv and parse out repository of migrations and database url.
>>> import os
>>> from six.moves.configparser import SafeConfigParser
>>> from shutil import rmtree
>>> from tempfile import mkdtemp
>>> config_dir = mkdtemp()
>>> os.makedirs(os.path.join(config_dir, 'config'))
>>> def write_ini(path, property, value):
... p = SafeConfigParser()
... p.add_section('app:main')
... p.set('app:main', property, value)
... with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f)
>>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
>>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
>>> config['repo']
'lib/galaxy/webapps/tool_shed/model/migrate'
>>> config['db_url']
'sqlite:///pg/testdb1'
>>> write_ini('galaxy.ini', 'database_file', 'moo.sqlite')
>>> config = get_config(['manage_db.py'], cwd=config_dir)
>>> config['db_url']
'sqlite:///moo.sqlite?isolation_level=IMMEDIATE'
>>> config['repo']
'lib/galaxy/model/migrate'
>>> rmtree(config_dir)
"""
config_file, config_section, database = _read_model_arguments(argv, use_argparse=use_argparse)
database_defaults = DATABASE[database]
if config_file is None:
config_names = database_defaults.get('config_names', DEFAULT_CONFIG_NAMES)
if cwd:
cwd = [cwd, os.path.join(cwd, 'config')]
config_file = find_config_file(config_names, dirs=cwd)
repo = database_defaults['repo']
config_prefix = database_defaults.get('config_prefix', DEFAULT_CONFIG_PREFIX)
config_override = database_defaults.get('config_override', 'GALAXY_CONFIG_')
default_sqlite_file = database_defaults['default_sqlite_file']
if config_section is None:
if not config_file or get_ext(config_file, ignore='sample') == 'yaml':
config_section = database_defaults.get('config_section', None)
else:
# Just use the default found by load_app_properties.
config_section = None
properties = load_app_properties(config_file=config_file, config_prefix=config_override, config_section=config_section)
if ("%sdatabase_connection" % config_prefix) in properties:
db_url = properties["%sdatabase_connection" % config_prefix]
elif ("%sdatabase_file" % config_prefix) in properties:
database_file = properties["%sdatabase_file" % config_prefix]
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % database_file
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % default_sqlite_file
return dict(db_url=db_url, repo=repo, config_file=config_file, database=database)
def optional(config_file=None):
if not config_file:
config_file = find_config_file(['galaxy', 'universe_wsgi'])
if not config_file:
print("galaxy.dependencies.optional: no config file found", file=sys.stderr)
return []
rval = []
conditional = ConditionalDependencies(config_file)
for opt in conditional.conditional_reqs:
if conditional.check(opt.key):
rval.append(str(opt))
return rval
def optional(config_file=None):
if not config_file:
config_file = find_config_file(['galaxy', 'universe_wsgi'], include_samples=True)
if not config_file:
print("galaxy.dependencies.optional: no config file found", file=sys.stderr)
return []
rval = []
conditional = ConditionalDependencies(config_file)
for opt in conditional.conditional_reqs:
if conditional.check(opt.key):
rval.append(str(opt))
return rval
def _resolve_config_file_path(self) -> str:
config_file = self.app_kwds.get("config_file")
if not config_file and os.environ.get(self.props.env_config_file):
config_file = os.path.abspath(os.environ[self.props.env_config_file])
elif self.props.check_galaxy_root:
galaxy_root = self.app_kwds.get("galaxy_root") or os.environ.get("GALAXY_ROOT_DIR")
config_file = find_config(config_file, galaxy_root, app_name=self.props.app_name)
config_file = absolute_config_path(config_file, galaxy_root=galaxy_root)
else:
config_file = find_config_file([self.props.app_name])
if not config_file or not os.path.exists(config_file):
raise FileNotFoundError(f"Can not find a configuration file for {self.props.app_name}")
return config_file
def _app_properties(args):
config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini", args.config_file)
app_properties = load_app_properties(ini_file=config_file)
return app_properties
def _app_properties(args):
config_file = find_config_file("config/galaxy.ini", "universe_wsgi.ini",
args.config_file)
app_properties = load_app_properties(ini_file=config_file)
return app_properties
def get_config(argv, use_argparse=True, cwd=None):
"""
Read sys.argv and parse out repository of migrations and database url.
>>> import os
>>> from configparser import ConfigParser
>>> from shutil import rmtree
>>> from tempfile import mkdtemp
>>> config_dir = mkdtemp()
>>> os.makedirs(os.path.join(config_dir, 'config'))
>>> def write_ini(path, property, value):
... p = ConfigParser()
... p.add_section('app:main')
... p.set('app:main', property, value)
... with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f)
>>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
>>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
>>> config['repo'].endswith('tool_shed/webapp/model/migrate')
True
>>> config['db_url']
'sqlite:///pg/testdb1'
>>> write_ini('galaxy.ini', 'data_dir', '/moo')
>>> config = get_config(['manage_db.py'], cwd=config_dir)
>>> uri_with_env = os.getenv("GALAXY_TEST_DBURI", "sqlite:////moo/universe.sqlite?isolation_level=IMMEDIATE")
>>> config['db_url'] == uri_with_env
True
>>> config['repo'].endswith('galaxy/model/migrate')
True
>>> rmtree(config_dir)
"""
config_file, config_section, database = _read_model_arguments(
argv, use_argparse=use_argparse)
database_defaults = DATABASE[database]
if config_file is None:
config_names = database_defaults.get('config_names',
DEFAULT_CONFIG_NAMES)
if cwd:
cwd = [cwd, os.path.join(cwd, 'config')]
else:
cwd = [DEFAULT_CONFIG_DIR]
config_file = find_config_file(config_names, dirs=cwd)
repo = os.path.join(os.path.dirname(__file__), os.pardir, os.pardir,
os.pardir, database_defaults['repo'])
config_prefix = database_defaults.get('config_prefix',
DEFAULT_CONFIG_PREFIX)
config_override = database_defaults.get('config_override',
'GALAXY_CONFIG_')
default_sqlite_file = database_defaults['default_sqlite_file']
if config_section is None:
if not config_file or get_ext(config_file, ignore='sample') == 'yaml':
config_section = database_defaults.get('config_section', None)
else:
# Just use the default found by load_app_properties.
config_section = None
properties = load_app_properties(config_file=config_file,
config_prefix=config_override,
config_section=config_section)
if (f"{config_prefix}database_connection") in properties:
db_url = properties[f"{config_prefix}database_connection"]
else:
db_url = f"sqlite:///{os.path.join(get_data_dir(properties), default_sqlite_file)}?isolation_level=IMMEDIATE"
install_database_connection = properties.get('install_database_connection')
return dict(db_url=db_url,
repo=repo,
config_file=config_file,
database=database,
install_database_connection=install_database_connection)
def config_file_from_args(args, legacy_config_override=None, app=None):
app = app or getattr(args, "app", "galaxy")
config_file = legacy_config_override or args.config_file or find_config_file(
app)
return config_file
def get_config(argv, use_argparse=True, cwd=None):
"""
Read sys.argv and parse out repository of migrations and database url.
>>> import os
>>> from six.moves.configparser import SafeConfigParser
>>> from shutil import rmtree
>>> from tempfile import mkdtemp
>>> config_dir = mkdtemp()
>>> os.makedirs(os.path.join(config_dir, 'config'))
>>> def write_ini(path, property, value):
... p = SafeConfigParser()
... p.add_section('app:main')
... p.set('app:main', property, value)
... with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f)
>>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
>>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
>>> config['repo']
'lib/galaxy/webapps/tool_shed/model/migrate'
>>> config['db_url']
'sqlite:///pg/testdb1'
>>> write_ini('galaxy.ini', 'database_file', 'moo.sqlite')
>>> config = get_config(['manage_db.py'], cwd=config_dir)
>>> config['db_url']
'sqlite:///moo.sqlite?isolation_level=IMMEDIATE'
>>> config['repo']
'lib/galaxy/model/migrate'
>>> rmtree(config_dir)
"""
config_file, config_section, database = _read_model_arguments(
argv, use_argparse=use_argparse)
database_defaults = DATABASE[database]
if config_file is None:
config_names = database_defaults.get('config_names',
DEFAULT_CONFIG_NAMES)
if cwd:
cwd = [cwd, os.path.join(cwd, 'config')]
config_file = find_config_file(config_names, dirs=cwd)
repo = database_defaults['repo']
config_prefix = database_defaults.get('config_prefix',
DEFAULT_CONFIG_PREFIX)
config_override = database_defaults.get('config_override',
'GALAXY_CONFIG_')
default_sqlite_file = database_defaults['default_sqlite_file']
if config_section is None:
if not config_file or get_ext(config_file, ignore='sample') == 'yaml':
config_section = database_defaults.get('config_section', None)
else:
# Just use the default found by load_app_properties.
config_section = None
properties = load_app_properties(config_file=config_file,
config_prefix=config_override,
config_section=config_section)
if ("%sdatabase_connection" % config_prefix) in properties:
db_url = properties["%sdatabase_connection" % config_prefix]
elif ("%sdatabase_file" % config_prefix) in properties:
database_file = properties["%sdatabase_file" % config_prefix]
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % database_file
else:
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % default_sqlite_file
return dict(db_url=db_url,
repo=repo,
config_file=config_file,
database=database)
def _app_properties(args):
# FIXME: you can use galaxy.util.path.extensions for this
config_file = args.config_file or find_config_file(args.app)
app_properties = load_app_properties(config_file=config_file,
config_section=args.config_section)
return app_properties
def _app_properties(args):
# FIXME: you can use galaxy.util.path.extensions for this
config_file = args.config_file or find_config_file(args.app)
app_properties = load_app_properties(config_file=config_file, config_section=args.config_section)
return app_properties
def config_file_from_args(args, legacy_config_override=None, app=None):
app = app or getattr(args, "app", "galaxy")
config_file = legacy_config_override or args.config_file or find_config_file(app)
return config_file
