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)
>>> uri_with_env = os.getenv("GALAXY_TEST_DBURI", "sqlite:///moo.sqlite?isolation_level=IMMEDIATE")
>>> config['db_url'] == uri_with_env
True
>>> 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 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 __add_config_file_arg(args, config_file, app):
ext = None
if config_file:
ext = get_ext(config_file)
if ext in ('yaml', 'json'):
__add_arg(args, ext, config_file)
elif ext == 'ini':
config = nice_config_parser(config_file)
has_logging = config.has_section('loggers')
if config.has_section('app:main'):
# uWSGI does not have any way to set the app name when loading with paste.deploy:loadapp(), so hardcoding
# the name to `main` is fine
__add_arg(args, 'ini-paste' if not has_logging else 'ini-paste-logged', config_file)
return # do not add --module
else:
__add_arg(args, ext, config_file)
if has_logging:
__add_arg(args, 'paste-logger', True)
def __add_config_file_arg(args, config_file, app):
ext = None
if config_file:
ext = get_ext(config_file)
if ext in ('yaml', 'json'):
__add_arg(args, ext, config_file)
elif ext == 'ini':
config = nice_config_parser(config_file)
has_logging = config.has_section('loggers')
if config.has_section('app:main'):
# uWSGI does not have any way to set the app name when loading with paste.deploy:loadapp(), so hardcoding
# the name to `main` is fine
__add_arg(args, 'ini-paste' if not has_logging else 'ini-paste-logged', config_file)
return # do not add --module
else:
__add_arg(args, ext, config_file)
if has_logging:
__add_arg(args, 'paste-logger', True)
def get_config(argv, cwd=None):
"""
Read sys.argv and parse out repository of migrations and database url.
>>> import os
>>> from 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)
"""
if argv and (argv[-1] in DATABASE):
database = argv.pop() # database name tool_shed, galaxy, or install.
else:
database = 'galaxy'
database_defaults = DATABASE[database]
config_names = database_defaults.get('config_names', DEFAULT_CONFIG_NAMES)
config_file = read_config_file_arg(argv, config_names, cwd=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 not config_file or get_ext(config_file, ignore='sample') == 'yaml':
config_section = database_defaults.get('config_section', None)
else:
# An .ini file - just let load_app_properties find app:main.
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)
