allensdk.internal.api.queries.optimize_config_reader module

class allensdk.internal.api.queries.optimize_config_reader.OptimizeConfigReader

Bases: object

MOD_FILE_TYPE_ID = 292178729

MORPHOLOGY_TYPE_ID = 303941301

NEURONAL_MODEL_PARAMETERS = 329230374

STIMULUS_CONTENT_TYPE = None

build_manifest(self, manifest_path=None)

lims_working_directory(self)

While this is the same directory as the optimize directory, it can be mocked out for testing if the optimize directory is write only.

mod_file_entries(self)

read the NERUON .mod file entries from the lims result corresponding to the NeuronModel :return: well known file entries :rtype: array of dicts

mod_file_paths(self)

Get the paths to the mod files from the lims result. :return: paths to mod files :rtype: array of strings

morphology_file_entries(self)

read the well known file paths from the lims result corresponding to the morphology

Returns:

arrary of dicts:

well known file entries

morphology_path(self)

Get the path to the morphology file from the lims result. :return: path to morphology file :rtype: string

neuronal_model_optimize_dir(self)

read the directory path where output goes from the lims optimization config json

Returns:

string:

directory path

output_directory(self)

read_json(self, path)

read_json_string(self, json_string)

read_lims_file(self, lims_path)

read_lims_message(self, message, lims_path)

stimulus_file_entries(self)

read the well known file path from the lims result corresponding to the stimulus file :return: well_known_file entries :rtype: array of dicts

stimulus_path(self)

Get the path to the stimulus file from the lims result. :return: path to stimulus file :rtype: string

sweep_entries(self)

read the sweep entries from the lims result corresponding to the stimulus :return: stimulus sweep entries :rtype: array of dicts

sweep_numbers(self)

Get the stimulus sweep numbers from the lims result :return: list of sweep numbers :rtype: array of ints

to_manifest(self, manifest_path=None)

update_well_known_file(self, path, well_known_file_type_id=None)

write_file(self, path)