def run(excel_parsed_manifest, sample_status_accepted_values,
sub_race_values, sub_gender_values, sub_ethnicity_values,
sub_sample_blank_values, sub_project_type_values, cast_plate_box_values,
required_field_list):
check_log = clean_logfile(current_dir, logger_filename)
logger = configure_logger(logger_filename)
workbook, carrier_id_sheet, caid_cast_sheet, cast_plate_sheet = get_excel_sheet(excel_parsed_manifest,
logger)
req_carrier_id_headers, unique_carrier_id_headers, req_caid_cast_headers,\
unique_caid_cast_headers, req_cast_plate_sheet, unique_cast_plate_sheet = required_headers(carrier_id_sheet,
caid_cast_sheet, cast_plate_sheet)
carrier_id_empty_record = check_fields(carrier_id_sheet, logger, req_carrier_id_headers, "CARRIER ID")
carrier_id_list, carrier_id_record = index_row_header(carrier_id_sheet, logger, "CARRIER ID")
carrier_unique_field = count_fields(carrier_id_list, unique_carrier_id_headers, logger, "CARRIERS ID")
modified_required_field = get_modified_required_list(required_field_list)
validate_carrier_record = carrier_id_validate(carrier_id_record, logger, sample_status_accepted_values,
sub_race_values, sub_gender_values, sub_ethnicity_values,
"CARRIER ID", modified_required_field)
caid_cast_empty_record = check_fields(caid_cast_sheet, logger, req_caid_cast_headers, "CAID_CAST")
caid_cast_list, caid_cast_record = index_row_header(caid_cast_sheet, logger, "CAID_CAST")
caid_cast_unique_field = count_fields(caid_cast_list, unique_caid_cast_headers, logger, "CAID_CAST")
validate_caid_cast_record = caid_cast_validate(caid_cast_record, logger, sub_sample_blank_values, "CAID_CAST", modified_required_field)
cast_plate_empty_record = check_fields(cast_plate_sheet, logger, req_cast_plate_sheet, "CAST Plate")
cast_plate_list, cast_plate_record = index_row_header(cast_plate_sheet, logger, "CAST Plate")
cat_plate_unique_field = count_fields(cast_plate_list, unique_cast_plate_sheet, logger, "CAST Plate")
solve_date = get_date_field(workbook, cast_plate_sheet, logger, "CAST Plate")
validate_cast_plate_record = cast_plate_validate(cast_plate_record, logger,
sub_project_type_values, cast_plate_box_values, "CAST Plate", modified_required_field)
def run(submission_manifest):
logger = configure_logger(logger_filename)
manifest = get_excel_sheet(submission_manifest, logger)
data_headers, data_row = get_data_headers(manifest, regex)
carrier_table_headers, caid_cast_headers = get_confusing_header(data_headers, carrier_id_table_name_fields,
caid_plate_table_fields)
get_data_index = data_fields_index(manifest, data_row)
carriers_dict, caid_plate_dict, carrier_sample = sample_data(manifest,
data_headers,
get_data_index,
carrier_table_headers,
caid_cast_headers)
pprint.pprint(carriers_dict)
cast_tuple_output, contact_id = cast_plate_parse(manifest)
carrier_id_number = connect_db(logger)
create_carrier_ID, sample_number = generate_carrier_id(carrier_sample, logger, carrier_id_number)
carrier_tuple_output, caid_tuple_output = create_tuple_output(carriers_dict, caid_plate_dict,
create_carrier_ID, sample_number)
excel_output = generate_excel_output(carrier_output_table, carrier_headers, carrier_tuple_output,
caid_cast_output_table, caid_cast_header,
caid_tuple_output, cast_plate_output_table,
cast_plate_header, cast_tuple_output, current_date, contact_id)
def run(excel_workbook, logger_filename):
logger = configure_logger(logger_filename)
check_log = check_validation_log(current_dir)
workbook, carrier_id_sheet, caid_cast_sheet, cast_plate_sheet = get_excel_sheet(excel_workbook, logger)
import_carrier_id_table = connect_to_access(carrier_id_sheet, caid_cast_sheet, cast_plate_sheet)