def options(*args, **kwargs):
"""
Set options for the current session.
Args:
kwargs (dict): List of arbitrary config items to set.
Examples:
>>> # set options to defaults
>>> coda.options()
>>> coda.find_one({'name': 'test'}).path
'/file/on/localhost/server'
>>>
>>> # connect to a database for a different host
>>> coda.options({'host': 'remote'})
>>> coda.find_one({'name': 'test'}).path
'/file/on/remote/server'
"""
global session, __default_config__, __user_config__
with open(__default_config__, 'r') as cfig:
config = composite(cfig)
if os.path.exists(__user_config__):
with open(__user_config__, 'r') as cfig:
config = config + composite(cfig)
if len(kwargs) != 0:
config = config + composite(kwargs)
try:
session = Session(**config._dict)
except TypeError:
raise AssertionError('Something is wrong with your coda configuration'
' -- check your config file for valid parameters.')
return config.json()
def options(**kwargs):
"""
Set options for the current session.
Args:
kwargs (dict): List of arbitrary config items to set.
"""
global session, __default_config__, __user_config__
# read default config
with open(__default_config__, 'r') as cfig:
config = composite.load(cfig)
# read and add user config
if os.path.exists(__user_config__):
with open(__user_config__, 'r') as cfig:
config = config + composite.load(cfig)
if len(kwargs) != 0:
config = config + composite(kwargs)
# update session
try:
session = Session(**config._dict)
except TypeError:
raise exc.SettingsError()
return config.json()
def __init__(self, path, metadata={}):
assert os.path.exists(path), 'Specified file path does not exist!'
assert not os.path.isdir(
path
), 'Specified file is not a file! Use the Collection object for a directory.'
self.path = os.path.realpath(path)
self._metadata = composite(metadata)
return
def __init__(self, files, metadata={}):
if isinstance(files, str):
ft = filetree(files)
self.files = [self.__file_base__(x) for x in ft.filelist()]
if len(self.files) == 0:
raise AssertionError(
'Could not find any files for collection!')
else:
self.files = files
self._metadata = composite(metadata)
return
__config__ = os.path.join(__base__, 'config.json')
__db__ = os.environ.get('PETRI_DATA', '/data/petri')
__data__ = os.path.join(__db__, 'collections')
# instantiate session
# -------------------
default_dict = {
'data_home': __data__,
'resource_home': __resources__,
'host': 'localhost',
'port': 27017,
'write': True,
'genome': 'hg19'
}
defaults = composite(default_dict)
if os.path.exists(__config__):
with open(__config__, 'r') as config_reader:
config = composite(config_reader)
config_reader.close()
defaults = defaults + config
if not os.path.exists(defaults['data_home']):
os.makedirs(defaults['data_home'])
global session
session = Session(**defaults)
# get rest of petri imports
# -------------------------