allensdk.internal.api.queries.biophysical_module_reader module

class allensdk.internal.api.queries.biophysical_module_reader.BiophysicalModuleReader

Bases: object

MOD_FILE_TYPE_ID = 292178729

MORPHOLOGY_TYPE_ID = 303941301

STIMULUS_CONTENT_TYPE = None

fit_parameters_file_entries()

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

fit_parameters_path()

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

lims_working_directory()

While this is the same directory as the neuronal_model_run directory, it can be mocked out for testing if the other directory is read only.

mod_file_entries()

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()

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

model_type()

TODO: comment

morphology_file_entries()

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

Returns:

arrary of dicts:

well known file entries

morphology_path()

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

neuronal_model_run_dir()

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

Parameters:

Returns:

string:

directory path

read_json(path)

read_json_string(json_string)

read_lims_file(lims_path)

read_lims_message(message, lims_path)

set_workflow_state(state)

stimulus_file_entries()

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()

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

sweep_entries()

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

sweep_numbers()

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

sweep_numbers_by_type()

to_manifest(manifest_path=None)

update_well_known_file(path, well_known_file_type_id=None)

write_file(path)