Source code for allensdk.model.biophysical.run_simulate

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from . import runner as single_cell
import logging
import os
import sys
import traceback
import subprocess
import logging.config as lc
from ..biophys_sim.config import Config
from pkg_resources import resource_filename  # @UnresolvedImport


[docs]class RunSimulate(object): _log = logging.getLogger('allensdk.model.biophysical.run_simulate') def __init__(self, input_json, output_json): self.input_json = input_json self.output_json = output_json self.app_config = None self.manifest = None
[docs] def load_manifest(self): self.app_config = Config().load(self.input_json) self.manifest = self.app_config.manifest fix_sections = ['passive', 'axon_morph,', 'conditions', 'fitting'] self.app_config.fix_unary_sections(fix_sections)
[docs] def nrnivmodl(self): RunSimulate._log.debug("nrnivmodl") subprocess.call(['nrnivmodl', './modfiles'])
[docs] def simulate(self): from allensdk.internal.api.queries.biophysical_module_reader \ import BiophysicalModuleReader self.load_manifest() try: stimulus_path = self.manifest.get_path('stimulus_path') RunSimulate._log.info("stimulus path: %s" % (stimulus_path)) except: raise Exception( 'Could not read input stimulus path from input config.') try: out_path = self.manifest.get_path('output_path') RunSimulate._log.info("result NWB file: %s" % (out_path)) except: raise Exception('Could not read output path from input config.') try: morphology_path = self.manifest.get_path('MORPHOLOGY') RunSimulate._log.info("morphology path: %s" % (morphology_path)) except: raise Exception( 'Could not read morphology path from input config.') single_cell.run(self.app_config) lims_upload_config = BiophysicalModuleReader() lims_upload_config.read_json( self.manifest.get_path('neuronal_model_run_data')) lims_upload_config.update_well_known_file(out_path) lims_upload_config.set_workflow_state('passed') lims_upload_config.write_file(self.output_json)
[docs]def main(command, lims_strategy_json, lims_response_json): ''' Entry point for module. :param command: select behavior, nrnivmodl or simulate :type command: string :param lims_strategy_json: path to json file output from lims. :type lims_strategy_json: string :param lims_response_json: path to json file returned to lims. :type lims_response_json: string ''' rs = RunSimulate(lims_strategy_json, lims_response_json) RunSimulate._log.debug("command: %s" % (command)) RunSimulate._log.debug("lims strategy json: %s" % (lims_strategy_json)) RunSimulate._log.debug("lims upload json: %s" % (lims_response_json)) log_config = resource_filename('allensdk.model.biophysical.run_simulate', 'logging.conf') lc.fileConfig(log_config) os.environ['LOG_CFG'] = log_config if 'nrnivmodl' == command: rs.nrnivmodl() else: rs.simulate()
if __name__ == '__main__': command, input_json, output_json = sys.argv[-3:] try: main(command, input_json, output_json) RunSimulate._log.debug("success") except Exception as e: RunSimulate._log.error(traceback.format_exc()) exit(1)