Source code for allensdk.model.biophys_sim.config

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import re
import logging
from pkg_resources import resource_filename  # @UnresolvedImport
from allensdk.config.app.application_config import ApplicationConfig
from allensdk.config.model.description_parser import DescriptionParser
from allensdk.config.model.description import Description


[docs]class Config(ApplicationConfig): _log = logging.getLogger(__name__) _DEFAULT_LOG_CONFIG = resource_filename(__name__, 'logging.conf') #: A structure that defines the available configuration parameters. #: The default value and help strings may be seen by viewing the source. _DEFAULTS = { 'workdir': {'default': 'workdir', 'help': 'writable directory where intermediate and output files are written.'}, 'data_dir': {'default': '', 'help': 'writable directory where intermediate and output files are written.'}, 'model_file': {'default': 'config.json', 'help': 'file where the model parameters are set.'}, 'main': {'default': 'simulation#run', 'help': 'module#function that runs the actual simulation'} } def __init__(self): super(Config, self).__init__(Config._DEFAULTS, name='biophys', halp='tools for biophysically detailed modeling at the Allen Institute.', default_log_config=Config._DEFAULT_LOG_CONFIG)
[docs] def load(self, config_path, disable_existing_logs=False): '''Parse the application configuration then immediately load the model configuration files. Parameters ---------- disable_existing_logs : boolean, optional If false (default) leave existing logs after configuration. ''' super(Config, self).load([config_path], disable_existing_logs) description = self.read_model_description() return description
[docs] 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