allensdk.internal.api.queries.biophysical_module_reader module

class allensdk.internal.api.queries.biophysical_module_reader.BiophysicalModuleReader[source]

Bases: object

MOD_FILE_TYPE_ID = 292178729
MORPHOLOGY_TYPE_ID = 303941301
STIMULUS_CONTENT_TYPE = None
fit_parameters_file_entries(self)[source]

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(self)[source]

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

lims_working_directory(self)[source]

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(self)[source]

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)[source]

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

model_type(self)[source]

TODO: comment

morphology_file_entries(self)[source]

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)[source]

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

neuronal_model_run_dir(self)[source]

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

Returns:
string:

directory path

read_json(self, path)[source]
read_json_string(self, json_string)[source]
read_lims_file(self, lims_path)[source]
read_lims_message(self, message, lims_path)[source]
set_workflow_state(self, state)[source]
stimulus_file_entries(self)[source]

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)[source]

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

sweep_entries(self)[source]

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

sweep_numbers(self)[source]

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

sweep_numbers_by_type(self)[source]
to_manifest(self, manifest_path=None)[source]
update_well_known_file(self, path, well_known_file_type_id=None)[source]
write_file(self, path)[source]