def read_workbook(wb):
'''
Parse the Screen Result load file into valid API input format
'''
try:
logger.info('read screen result file sheets...')
sheets = workbook_sheets(wb)
sheet = sheets.next()
logger.info('read Screen Info sheet: %r', sheet.name)
meta_cols = sheet_cols(sheet)
meta_raw = dict(zip(meta_cols.next(),meta_cols.next()))
meta = { META_MAP.get(key, key):val for key,val in meta_raw.items() }
logger.info('meta: %r', meta)
sheet = sheets.next()
logger.info('read Data Columns sheet: %r...', sheet.name)
columns = parse_columns(data_column_generator(sheet_cols(sheet)))
result_values = parse_result_values(columns,sheets)
return OrderedDict((
('meta', meta),
('fields', columns),
('objects', result_values),
))
except ValidationError,e:
logger.exception('parse error: %r', e)
raise
def parse_columns(columns_sheet):
logger.info('parsing columns sheet: %r', columns_sheet.name)
columns = data_column_generator(sheet_cols(columns_sheet))
parsed_cols = OrderedDict()
errors = {}
for i,column in enumerate(columns):
parsed_col = {
'is_derived': False,
'is_follow_up_data': False,
'ordinal': i
}
logger.debug('parsing column: %r', column['data_worksheet_column'])
parsed_cols[column['data_worksheet_column']] = parsed_col
for key,val in column.items():
if key == 'is_follow_up_data':
parsed_col[key] = ( val and val.lower() == 'follow up')
elif key == 'data_type':
val = default_converter(val)
# handle validation errors in the api
if val not in DATA_TYPES:
key = '%s:%s' % (column['data_worksheet_column'],'data_type')
errors[key] = 'val: %r must be one of %r' % (val,DATA_TYPES)
parsed_col[key] = val
elif key == 'assay_readout_type':
parsed_col[key] = default_converter(val)
else:
if key == 'how_derived':
parsed_col['is_derived'] = (
val is not None and val.strip() is not '' )
parsed_col[key] = val
if parsed_col.get('decimal_places', None):
try:
key = '%s:%s' % (column['data_worksheet_column'],'data_type')
column['decimal_places'] = parse_val(
column['decimal_places'],key,'integer')
except ValidationError, e:
errors.update(e.errors)
logger.debug('parsed_col: %r', parsed_col)
