arraydata2xls/array2xls/validators.py

import os

from collections import namedtuple

class ValidationError(ValueError):
    pass

Validator = namedtuple('Validator', 'type extension validate id_fields data_fields defaults')
DataFile = namedtuple('DataFile', 'path separator skip validator')

def validate_stx(lines):
    iterator = enumerate(lines)
    _, line = next(iterator)
    if not line.startswith('Report_Format:\t2'):
        raise ValidationError('1 Unsupported File;' + line)
    for i, line in iterator:
        if line.startswith('Probe_Name\t'):
            break
    else:
        raise ValidationError('1 Unsupported File')
    try:
        _, line = next(iterator)
        _, numeric_data = line.split('\t', 1)
    except (ValueError, StopIteration):
        raise ValidationError('No Data Present')
    separator = ',' if numeric_data.count(',') > numeric_data.count('.') else '.'
    return separator, i


def validate_dat(lines):
    iterator = enumerate(lines)
    _, line = next(iterator)
    if not line.startswith('Report_Format:\t2'):
        raise ValidationError('Unsupported File')
    for i, line in iterator:
        if line.startswith('Dot_Number\t'):
            break
    else:
        raise ValidationError('Unsupported File')
    try:
        _, line = next(iterator)
        _, _, _, numeric_data = line.split('\t', 3)
    except (ValueError, StopIteration):
        raise ValidationError('No Data Present')
    separator = ',' if numeric_data.count(',') > numeric_data.count('.') else '.'
    return separator, i


def validate_csv(lines):
    iterator = iter(lines)
    if not next(iterator).startswith(' ID '):
        raise ValidationError('Unsupported File')
    try:
        line = next(iterator)
        _, numeric_data = line.split('\t', 1)
    except (ValueError, StopIteration):
        raise ValidationError('No Data Present')
    separator = ',' if numeric_data.count(',') > numeric_data.count('.') else '.'
    return separator, 0


stx_validator = Validator(
    'Signalyse Statistic Files', '.stx', validate_stx,
    ['Probe_Name'],
    ['Count', 'Net_Signal', 'Net_Signal_SD', 'Net_Integral', 'Net_Integral_SD', 'Proc_Control'],
    ['Net_Signal', 'Net_Signal_SD', 'Net_Integral', 'Net_Integral_SD'])

dat_validator = Validator(
    'Signalyse Data Files', '.dat', validate_dat,
    ['Dot_Number', 'Probe_Name', 'Gene_Name', 'Col', 'Row'],
    ['X[Pix]', 'Y[Pix]', 'DX[Pix]', 'DY[Pix]', 'Spot_Diameter', 'ROI_Width', 'ROI_Heigth', 'Pixels', 'Bkg',
     'Bkg_SD', 'Net_Signal', 'Net_Signal_SD', 'Net_Integral', 'Net_Integral_SD', 'Acc_Number', 'Proc_Control'],
    ['Bkg', 'Net_Signal', 'Net_Integral'] )

csv_validator = Validator(
    'Sensovation Data Files', '.csv', validate_csv,
    [' ID '],
    ['Pos.X', 'Pos.Y', 'Bkg.Mean', 'Spot.Mean', 'Bkg.Median', 'Spot.Median', 'Bkg.StdDev', 'Spot.StdDev',
     'Bkg.Sum', 'Spot.Sum', 'Bkg.Area', 'Spot.Area', 'Spot.Sat. (%)', 'Found', 'Pos.Nom.X', 'Pos.Nom.Y', 'Dia.',
     'Rect.', 'Contour'],
    ['Bkg.Mean', 'Spot.Mean', 'Bkg.Median', 'Spot.Median', 'Bkg.StdDev', 'Spot.StdDev', 'Bkg.Sum', 'Spot.Sum'] )

validation_map = {
    stx_validator.extension: stx_validator,
    dat_validator.extension: dat_validator,
    csv_validator.extension: csv_validator
}


def guess_validator(unvalidated):
    # get the validation method by examining the first file
    _, extension = os.path.splitext(unvalidated[0])
    return validation_map.get(extension, None)

def validate_files(unvalidated, selected_validator):
    # get the validation method by examining the first file
    for file_path in unvalidated:
        try:
            with open(file_path, mode='r', encoding='utf-8') as file_handle:
                separator, skip = selected_validator.validate(file_handle)
                yield DataFile(file_path, separator, skip, selected_validator)
        except (IOError, UnicodeError, ValidationError) as e:
            print(e)