bgc_data_processing.providers.nmdc

Specific parameters to load NMDC-provided data.

loader = DataSource(provider_name='NMDC', data_format='csv', dirin=Path(PROVIDERS_CONFIG['NMDC']['PATH']), data_category=PROVIDERS_CONFIG['NMDC']['CATEGORY'], excluded_files=PROVIDERS_CONFIG['NMDC']['EXCLUDE'], files_pattern=FileNamePattern('NMDC_1990-2019_all.csv'), variable_ensemble=SourceVariableSet(provider=VARS['provider'].not_in_file(), expocode=VARS['expocode'].in_file_as('SDN_CRUISE'), date=VARS['date'].in_file_as('Time'), year=VARS['year'].not_in_file(), month=VARS['month'].not_in_file(), day=VARS['day'].not_in_file(), hour=VARS['hour'].not_in_file(), longitude=VARS['longitude'].in_file_as('Longitude'), latitude=VARS['latitude'].in_file_as('Latitude'), depth=VARS['depth'].in_file_as('depth').remove_when_nan().correct_with(lambda : -x), temperature=VARS['temperature'].not_in_file(), salinity=VARS['salinity'].not_in_file(), oxygen=VARS['oxygen'].in_file_as('DOW').correct_with(units.convert_doxy_ml_by_l_to_mmol_by_m3), phosphate=VARS['phosphate'].in_file_as(('Phosphate', 'Phosphate_SEADATANET_QC', [1])).remove_when_all_nan(), nitrate=VARS['nitrate'].in_file_as(('Nitrate', 'Nitrate_SEADATANET_QC', [1])).remove_when_all_nan(), silicate=VARS['silicate'].in_file_as(('Silicate', 'Silicate_SEADATANET_QC', [1])).remove_when_all_nan(), chlorophyll=VARS['chlorophyll'].in_file_as(('ChlA', 'ChlA_SEADATANET_QC', [1])).remove_when_all_nan()), read_params={'low_memory': False, 'skiprows': [1]}) module-attribute