def get_data_metadata(self, gcms, id_label, output_path):
if isinstance(output_path, str):
output_path = Path(output_path)
paramaters_path = output_path.with_suffix('.json')
if paramaters_path.exists():
with paramaters_path.open() as current_param:
metadata = json.load(current_param)
data_metadata = metadata.get('Data')
else:
data_metadata = {}
data_metadata['data_name'] = []
data_metadata['input_data_url'] = []
data_metadata['has_input'] = []
data_metadata['data_name'].append(gcms.sample_name)
data_metadata['input_data_url'].append(str(gcms.file_location))
data_metadata['has_input'].append(id_label +
corems_md5(gcms.file_location))
data_metadata['output_data_name'] = str(output_path.stem)
data_metadata['output_data_url'] = str(output_path)
data_metadata['has_output'] = id_label + corems_md5(output_path)
return data_metadata
def get_calibration_stats(self, gcms, id_label):
calibration_parameters = {}
calibration_parameters[
'calibration_rt_ri_pairs_ref'] = gcms.ri_pairs_ref
calibration_parameters['data_url'] = str(gcms.cal_file_path)
calibration_parameters['has_input'] = id_label + corems_md5(
gcms.cal_file_path)
calibration_parameters['data_name'] = str(gcms.cal_file_path.stem)
calibration_parameters['calibration_method'] = ""
return calibration_parameters
def write_settings(self, output_path, gcms, id_label="corems:"):
import json
output_parameters_dict = {}
blank_parameters = {}
output_parameters_dict['analyzer'] = gcms.analyzer
output_parameters_dict['instrument_label'] = gcms.instrument_label
output_parameters_dict['sample_name'] = gcms.sample_name
output_parameters_dict['sample_id'] = "sample_id"
output_parameters_dict['input_data'] = str(gcms.file_location)
output_parameters_dict['input_data_id'] = id_label + corems_md5(
gcms.file_location)
output_parameters_dict['output_data'] = str(output_path)
output_parameters_dict['output_data_id'] = id_label + uuid.uuid4().hex
output_parameters_dict['corems_version'] = __version__
output_parameters_dict["Stats"] = self.get_data_stats(gcms)
output_parameters_dict["Calibration"] = self.get_calibration_stats(
gcms, id_label)
output_parameters_dict["Blank"] = self.get_blank_stats(gcms)
corems_dict_setting = parameter_to_dict.get_dict_data_gcms(gcms)
output_parameters_dict["CoreMSParameters"] = corems_dict_setting
with open(
output_path.with_suffix('.json'),
'w',
encoding='utf8',
) as outfile:
output = json.dumps(output_parameters_dict,
sort_keys=False,
indent=4,
separators=(',', ': '))
outfile.write(output)