def from_xls(self, content, root='objects',**kwargs):
if isinstance(content, six.string_types):
wb = xlrd.open_workbook(file_contents=content)
else:
wb = xlrd.open_workbook(cStringIO.StringIO(content))
if wb.nsheets > 1:
logger.warn('only first page of workbooks supported')
# TODO: if root is specified, then get the sheet by name
sheet = wb.sheet_by_index(0)
if sheet.name.lower() in ['error', 'errors']:
return xlsutils.sheet_rows(sheet)
# because workbooks are treated like sets of csv sheets, now convert
# as if this were a csv sheet
data = csvutils.from_csv_iterate(
xlsutils.sheet_rows(sheet),
list_delimiter=LIST_DELIMITER_XLS,
list_keys=kwargs.get('list_keys', None))
if root:
return { root: data }
else:
return data
def read_xlsx(input_file):
contents = input_file.read()
logger.info('input_file read: %d', len(contents))
# with open('/tmp/test_read1.log','w') as logfile:
#
# wb = xlrd.open_workbook(file_contents=contents, logfile=logfile, verbosity=10)
wb = xlrd.open_workbook(file_contents=contents)
sheets = xlsutils.workbook_sheets(wb)
logger.info('sheets: %r, %d', sheets, wb.nsheets)
plate_matrices = []
errors = {}
sheet_count = 0
for sheet in sheets:
sheet_count += 1
logger.info('read sheet: %d, %r', sheet_count, sheet)
(sheet_plate_matrices,
sheet_errors) = read_rows(xlsutils.sheet_rows(sheet))
logger.info('for sheet: %r, %d matrices read', sheet.name,
len(sheet_plate_matrices))
if sheet_plate_matrices:
plate_matrices += sheet_plate_matrices
logger.info('plate_matrices: %r', len(plate_matrices))
if sheet_errors:
logger.warn('sheet errors: %r: %r', sheet.name, sheet_errors)
errors[sheet.name] = sheet_errors
if not sheet_count:
errors['input_file'] = 'No sheets were read'
elif not plate_matrices:
errors['input_sheets'] = 'No matrices were found'
return (plate_matrices, errors)
def from_xls(self,
content,
root='objects',
list_keys=None,
list_delimiters=None,
**kwargs):
logger.info('deserialize from_xls...')
if isinstance(content, six.string_types):
wb = xlrd.open_workbook(file_contents=content)
else:
wb = xlrd.open_workbook(cStringIO.StringIO(content))
if wb.nsheets > 1:
# TODO: concatentate all sheets?
logger.warn('only first page of workbooks is supported')
logger.info('read first sheet ...')
# TODO: if root is specified, then get the sheet by name
sheet = wb.sheet_by_index(0)
if sheet.name.lower() in ['error', 'errors']:
return xlsutils.sheet_rows(sheet)
list_delimiters = list_delimiters or [
LIST_DELIMITER_XLS,
]
# Workbooks are treated like sets of csv sheets
data = csvutils.input_spreadsheet_reader(
xlsutils.sheet_rows(sheet),
list_delimiters=list_delimiters,
list_keys=list_keys)
# # TODO: use csv_generator
# data = csvutils.input_spreadsheet_reader(
# xlsutils.sheet_rows(sheet),
# list_delimiters=list_delimiters,
# list_keys=list_keys)
if root:
return {root: data}
else:
return data
def from_xls(self, content, root='objects', list_keys=None,
list_delimiters=None, **kwargs):
logger.info('deserialize from_xls...')
if isinstance(content, six.string_types):
wb = xlrd.open_workbook(file_contents=content)
else:
wb = xlrd.open_workbook(cStringIO.StringIO(content))
if wb.nsheets > 1:
# TODO: concatentate all sheets?
logger.warn('only first page of workbooks is supported')
logger.info('read first sheet ...')
# TODO: if root is specified, then get the sheet by name
sheet = wb.sheet_by_index(0)
if sheet.name.lower() in ['error', 'errors']:
return xlsutils.sheet_rows(sheet)
list_delimiters = list_delimiters or [LIST_DELIMITER_XLS,]
# Workbooks are treated like sets of csv sheets
data = csvutils.input_spreadsheet_reader(
xlsutils.sheet_rows(sheet),
list_delimiters=list_delimiters,
list_keys=list_keys)
# # TODO: use csv_generator
# data = csvutils.input_spreadsheet_reader(
# xlsutils.sheet_rows(sheet),
# list_delimiters=list_delimiters,
# list_keys=list_keys)
if root:
return { root: data }
else:
return data
def parse_result_values(parsed_columns, sheets):
'''
Parse the Screen Result input file format into a valid API input format:
- Create a row generator from the result value sheets
'''
logger.info('parse_result_values...')
well_ids = set()
parse_error = ParseError(errors={})
def add_parse_error(sheet_name, validation_error):
sheet_name = str(sheet_name)
if not sheet_name in parse_error.errors:
parse_error.errors[sheet_name] = {}
parse_error.errors[sheet_name].update(validation_error.errors)
for sheet in sheets:
logger.info('parse result values sheet: %r...', sheet.name)
rows = sheet_rows(sheet)
try:
header_row = result_value_field_mapper(rows.next(), parsed_columns)
except ValidationError, e:
logger.exception('error: %r', e)
add_parse_error(sheet.name, e)
continue
logger.info('output result values...')
for i,row in enumerate(rows):
try:
result = parse_result_row(
i,parsed_columns,dict(zip(header_row,row)))
if DEBUG_IMPORTER:
logger.info('parsed row: %d: %r',i, result)
if result['well_id'] in well_ids:
raise ParseError(
key=result['well_id'],
msg='duplicate')
well_ids.add(result['well_id'])
yield result
except ValidationError,e:
logger.exception('parse error: %r', e)
add_parse_error(sheet.name, e)
def parse_result_values(parsed_columns, sheets):
logger.info('parse result values...')
well_ids = set()
parse_error = None
for sheet in sheets:
logger.info('parse result values sheet: %r...', sheet.name)
rows = sheet_rows(sheet)
try:
header_row = result_value_field_mapper(rows.next(), parsed_columns)
except ValidationError, e:
logger.info('error: %r', e)
if not parse_error:
parse_error = ParseError(errors={})
if not sheet.name in parse_error.errors:
parse_error.errors[str(sheet.name)] = {}
parse_error.errors[sheet.name] = e.errors
continue
logger.info('output result values')
for i,row in enumerate(rows):
try:
result = parse_result_row(
i,parsed_columns,dict(zip(header_row,row)))
if result['well_id'] in well_ids:
raise ParseError(
key=result['well_id'],
msg='duplicate')
well_ids.add(result['well_id'])
yield result
except ValidationError,e:
logger.exception('error: %r', e)
if not parse_error:
parse_error = ParseError(errors={})
if not sheet.name in parse_error.errors:
parse_error.errors[sheet.name] = {}
parse_error.errors[sheet.name].update(e.errors)