def to_manifest(self, manifest_path=None):
b = ManifestBuilder()
b.add_path('BASEDIR', os.path.realpath(os.curdir))
b.add_path('WORKDIR', os.path.realpath(os.curdir))
b.add_path('MORPHOLOGY', self.morphology_path(), typename='file')
b.add_path('CODE_DIR', 'templates')
b.add_path('MODFILE_DIR', 'modfiles')
for modfile in self.mod_file_entries():
b.add_path('MOD_FILE_%s' %
(os.path.splitext(modfile['filename'])[0]),
os.path.join(modfile['storage_directory'],
modfile['filename']),
typename='file',
format='MODFILE')
b.add_path('neuronal_model_run_data', self.lims_path, typename='file')
b.add_path('stimulus_path',
self.stimulus_path(),
typename='file',
format='NWB')
b.add_path('manifest',
os.path.join(os.path.realpath(os.curdir), manifest_path),
typename='file')
neuronal_model_run_id = self.lims_data['id']
nwb_file_name, extension = \
os.path.splitext(os.path.basename(self.stimulus_path()))
b.add_path('output_path',
'%d_virtual_experiment%s' %
(neuronal_model_run_id, extension),
typename='file',
parent_key='WORKDIR',
format='NWB')
b.add_path('fit_parameters', self.fit_parameters_path())
b.add_section(
'biophys', {
"biophys": [{
"model_file": [manifest_path,
self.fit_parameters_path()],
"model_type":
self.model_type()
}]
})
b.add_section(
'stimulus_conf', {
"runs": [{
"neuronal_model_run_id": neuronal_model_run_id,
"sweeps": self.sweep_numbers(),
"sweeps_by_type": self.sweep_numbers_by_type()
}]
})
b.add_section(
'hoc_conf',
{"neuron": [{
"hoc": ["stdgui.hoc", "import3d.hoc", "cell.hoc"]
}]})
m = Manifest(config=b.path_info)
if manifest_path != None:
b.write_json_file(manifest_path, overwrite=True)
return m
def build_manifest(self, manifest_path=None):
b = ManifestBuilder()
b.add_path('BASEDIR', os.path.realpath(os.curdir))
b.add_path('WORKDIR', self.output_directory())
b.add_path('MORPHOLOGY', self.morphology_path(), typename='file')
b.add_path('MODFILE_DIR', 'modfiles')
for modfile in self.mod_file_entries():
b.add_path('MOD_FILE_%s' %
(os.path.splitext(modfile['filename'])[0]),
os.path.join(modfile['storage_directory'],
modfile['filename']),
typename='file',
format='MODFILE')
b.add_path('stimulus_path',
self.stimulus_path(),
typename='file',
format='NWB')
b.add_path('manifest',
os.path.join(os.path.realpath(os.curdir), manifest_path),
typename='file')
b.add_path('output',
os.path.basename(self.stimulus_path()),
typename='file',
parent_key='WORKDIR',
format='NWB')
b.add_path('neuronal_model_data', self.lims_path, typename='file')
b.add_path('upfile',
'upbase.dat',
typename='file',
parent_key='WORKDIR')
b.add_path('downfile',
'downbase.dat',
typename='file',
parent_key='WORKDIR')
b.add_path('passive_fit_data',
'passive_fit_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('stage_1_jobs',
'stage_1_jobs.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_1_file',
'fit_1_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_2_file',
'fit_2_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_3_file',
'fit_3_data.json',
typename='file',
parent_key='WORKDIR')
b.add_path('fit_type_path',
typename='file',
spec='%s',
parent_key='WORKDIR')
b.add_path('target_path',
typename='file',
spec='target.json',
parent_key='WORKDIR')
b.add_path('fit_config_json',
typename='file',
spec='%s/config.json',
parent_key='WORKDIR')
b.add_path('final_hof_fit',
typename='file',
spec='%s/s%d/final_hof_fit.txt',
parent_key='WORKDIR')
b.add_path('final_hof',
typename='file',
spec='%s/s%d/final_hof.txt',
parent_key='WORKDIR')
b.add_path('output_fit_file', typename='file', spec='fit_%s_%s.json')
b.add_section('biophys',
{"biophys": [{
"model_file": [manifest_path]
}]})
b.add_section(
'stimulus_conf', {
"runs": [{
"sweeps": self.sweep_numbers(),
"specimen_id": self.lims_data['specimen_id']
}]
})
b.add_section(
'hoc_conf',
{"neuron": [{
"hoc": ["stdgui.hoc", "import3d.hoc", "cell.hoc"]
}]})
return b
