def test_cell_values_with_long_name(self):
cell_str = 'B_subtilis_WT_JH642_Colony_1, B_subtilis_WT_JH642_Colony_2, B_subtilis_WT_JH642_Colony_3'
expected_values = [
'B_subtilis_WT_JH642_Colony_1', 'B_subtilis_WT_JH642_Colony_2',
'B_subtilis_WT_JH642_Colony_3'
]
self.assertListEqual(expected_values, tu.extract_name_value(cell_str))
def _process_control_with_captions(self, cell, control_tables):
controls = []
for table_caption in table_utils.extract_name_value(cell.get_text()):
canonicalize_caption = ''.join(table_caption.lower().split())
if canonicalize_caption in control_tables:
for control in control_tables[canonicalize_caption]:
controls.append(control)
return controls
def _process_reagent_media(self, cell, header_cell):
reagents_media = []
text = cell.get_text()
name_dict, timepoint_dict = cell_parser.PARSER.process_reagent_header(
header_cell, self._timepoint_units, unit_type='timepoints')
# Determine if cells is numerical or name value
if table_utils.is_valued_cells(text):
try:
for value, unit in table_utils.transform_cell(
text, self._fluid_units, cell_type='fluid'):
if timepoint_dict:
numerical_dict = {
'name': name_dict,
'value': value,
'unit': unit,
'timepoint': timepoint_dict
}
else:
numerical_dict = {
'name': name_dict,
'value': value,
'unit': unit
}
reagents_media.append(numerical_dict)
except TableException as err:
message = err.get_message()
self._validation_errors.append(message)
elif table_utils.is_number(text):
err = '%s is missing a unit' % text
message = 'Measurement table has invalid reagent/media value: %s' % err
self._validation_errors.append(message)
return []
else:
for name in table_utils.extract_name_value(text):
if timepoint_dict:
named_dict = {
'name': name_dict,
'value': name,
'timepoint': timepoint_dict
}
else:
named_dict = {'name': name_dict, 'value': name}
reagents_media.append(named_dict)
return reagents_media
def parse_content_item(self, cell, fluid_units={}, timepoint_units={}):
list_of_contents = []
tokens = self._cell_tokenizer.tokenize(cell.get_text(),
keep_skip=False)
if len(tokens) < 1:
raise TableException('Invalid value: %s does not contain a name' %
cell.get_text())
cell_type = self._get_token_type(self._cell_parser.parse(tokens))
label, value, unit, timepoint_value, timepoint_unit = (None, None,
None, None,
None)
if cell_type == 'NAME_VALUE_UNIT_TIMEPOINT':
label, value, unit, timepoint_value, timepoint_unit = self._get_name_values_unit_timepoint(
tokens)
content = {}
content['name'] = self.process_name_with_uri(
label, cell.get_text_with_url())
content['value'] = value
content['unit'] = self.process_content_item_unit(
unit, fluid_units, timepoint_units)
content['timepoints'] = self.process_timepoint(
timepoint_value, timepoint_unit, timepoint_units)
list_of_contents.append(content)
elif cell_type == 'NAME_VALUE_UNIT':
label, value, unit = self._get_name_values_unit(tokens)
content = {}
content['name'] = self.process_name_with_uri(
label, cell.get_text_with_url())
content['value'] = value
content['unit'] = self.process_content_item_unit(
unit, fluid_units, timepoint_units)
list_of_contents.append(content)
elif cell_type == 'NAME':
labels = table_utils.extract_name_value(cell.get_text())
for label in labels:
content = {}
content['name'] = self.process_name_with_uri(
label, cell.get_text_with_url())
list_of_contents.append(content)
else:
raise TableException('Unable to parse %s' % cell.get_text())
return list_of_contents
def _process_file_type(self, cell):
file_type = cell.get_text()
return [value for value in table_utils.extract_name_value(file_type)]
def test_cell_with_unicode_characters(self):
cell_str = '\x0bApp'
self.assertTrue('App', tu.extract_name_value(cell_str))
def test_cell_with_trailing_whitespace(self):
cell_str = 'Yeast1_, Yeast2_, Yeast3_ '
exp_res = ['Yeast1_', 'Yeast2_', 'Yeast3_']
for name in tu.extract_name_value(cell_str):
self.assertTrue(name in exp_res)
def test_cell_values_with_named_and_numerical_spacing(self):
cell_str = 'B. subtilis 168 PmtlA-comKS'
for name in tu.extract_name_value(cell_str):
self.assertEquals(cell_str, name)
def test_cell_values_with_named_spacing(self):
cell_str = 'Yeast_Extract_Peptone_Adenine_Dextrose (a.k.a. YPAD Media)'
for name in tu.extract_name_value(cell_str):
self.assertEquals(cell_str, name)
def test_cell_values_with_one_name(self):
cell_str = 'CSV'
expected_values = ['CSV']
self.assertListEqual(expected_values, tu.extract_name_value(cell_str))
def test_cell_values_without_underscore(self):
cell_str = 'CSV, FCS'
expected_values = ['CSV', 'FCS']
self.assertListEqual(expected_values, tu.extract_name_value(cell_str))
def test_cell_values_with_name_containing_underscore_numbers(self):
cell_str = 'AND_00, NAND_00'
expected_values = ['AND_00', 'NAND_00']
self.assertListEqual(expected_values, tu.extract_name_value(cell_str))