def read_string(self, python_string, description=None, section=None, **kwargs):
'''Read a serialized description from a Python (.pycfg) string.
Parameters
----------
python_string : string
Python string with a serialized description.
Returns
-------
Description
Configuration object.
'''
if description is None:
description = Description()
header = kwargs.get('header', '')
python_string = "%s\n\nallensdk_description = %s" % (
header, python_string)
ns = {}
code = compile(python_string, 'string', 'exec')
exec(code, ns)
data = ns['allensdk_description']
description.unpack(data, section)
return description
def read_string(self,
json_string,
description=None,
section=None,
**kwargs):
'''Parse a complete or partial configuration.
Parameters
----------
json_string : string
Input to parse.
description : Description, optional
Where to put the parsed configuration. If None a new one is created.
section : string, optional
Where to put the parsed configuration within the description.
Returns
-------
Description
The input description with parsed configuration added.
Section is only specified for "bare" objects that are to be added to a section array.
'''
if description is None:
description = Description()
data = JsonComments.read_string(json_string)
description.unpack(data, section)
return description
def read_string(self,
python_string,
description=None,
section=None,
**kwargs):
'''Read a serialized description from a Python (.pycfg) string.
Parameters
----------
python_string : string
Python string with a serialized description.
Returns
-------
Description
Configuration object.
'''
if description == None:
description = Description()
header = kwargs.get('header', '')
python_string = "%s\n\nallensdk_description = %s" % (header,
python_string)
ns = {}
code = compile(python_string, 'string', 'exec')
exec(code, ns)
data = ns['allensdk_description']
description.unpack(data, section)
return description
def read_string(self, json_string, description=None, section=None, **kwargs):
"""Parse a complete or partial configuration.
Parameters
----------
json_string : string
Input to parse.
description : Description, optional
Where to put the parsed configuration. If None a new one is created.
section : string, optional
Where to put the parsed configuration within the description.
Returns
-------
Description
The input description with parsed configuration added.
Section is only specified for "bare" objects that are to be added to a section array.
"""
if description == None:
description = Description()
data = JsonComments.read_string(json_string)
description.unpack(data, section)
return description
def read(self, file_path, description=None, section=None, **kwargs):
'''Parse data needed for a simulation.
Parameters
----------
description : dict
Configuration from parsing previous files.
section : string, optional
What configuration section to read it into if the file does not specify.
'''
if description is None:
description = Description()
self.reader = self.parser_for_extension(file_path)
self.reader.read(file_path, description, section, **kwargs)
return description
def read_model_description(self):
'''parse the model_file field of the application configuration
and read the files.
The model_file field of the application configuration is
first split at commas, since it may list more than one file.
The files may be uris of the form :samp:`file:filename?section=name`,
in which case a bare configuration object is read from filename
into the configuration section with key 'name'.
A simple filename without a section option
is treated as a standard multi-section configuration file.
Returns
-------
description : Description
Configuration object.
'''
reader = DescriptionParser()
description = Description()
Config._log.info("model file: %s" % self.model_file)
# TODO: make space aware w/ regex
for model_file in self.model_file.split(','):
if not model_file.startswith("file:"):
model_file = 'file:' + model_file
file_regex = re.compile(r"^file:([^?]*)(\?(.*)?)?")
m = file_regex.match(model_file)
model_file = m.group(1)
file_url_params = {}
if m.group(3):
file_url_params.update(
((x[0], x[1])
for x in (y.split('=') for y in m.group(3).split('&'))))
if 'section' in file_url_params:
section = file_url_params['section']
else:
section = None
Config._log.info("reading model file %s" % (model_file))
reader.read(model_file, description, section)
return description