def test_read_csv_gse_as_key_invalid_format1(self, L):
m = mock.mock_open(read_data=os.linesep.join(
['GSE1,GSM1', 'GSE1,H**o sapiens,GSM2', 'GSE2,H**o sapiens,GSM3']))
m.return_value.__iter__ = lambda self: StringIO.StringIO(self.read())
m.return_value.__next__ = lambda self: self.readline()
with mock.patch('rsempipeline.parsers.isamp_parser.open', m):
res = isamp_parser.read_csv_gse_as_key('infile.csv')
self.assertEqual(res, {'GSE1': ['GSM2'], 'GSE2': ['GSM3']})
L.check(('rsempipeline.parsers.isamp_parser', 'ERROR',
"Ignored invalid row (1): ['GSE1', 'GSM1']"))
def test_read_csv_gse_as_key_invalid_format3(self, L):
m = mock.mock_open(read_data=os.linesep.join(
[
'GSE1,H**o sapiens,GSM',
]))
m.return_value.__iter__ = lambda self: StringIO.StringIO(self.read())
m.return_value.__next__ = lambda self: self.readline()
with mock.patch('rsempipeline.parsers.isamp_parser.open', m):
res = isamp_parser.read_csv_gse_as_key('infile.csv')
self.assertEqual(res, {})
L.check(('rsempipeline.parsers.isamp_parser', 'ERROR',
"Ignored invalid row (1): ['GSE1', 'H**o sapiens', 'GSM']"))
def test_read_csv_gse_as_key(self):
m = mock.mock_open(read_data=os.linesep.join([
'GSE1,H**o sapiens,GSM1', 'GSE1,H**o sapiens,GSM2',
'GSE2,H**o sapiens,GSM3'
]))
# use StringIO.StringIO because inf will be read by csv.reader, it must
# return an iternator, refer to test_soft_parser.test_parse for the
# other scenario
m.return_value.__iter__ = lambda self: StringIO.StringIO(self.read())
m.return_value.__next__ = lambda self: self.readline()
with mock.patch('rsempipeline.parsers.isamp_parser.open', m):
res = isamp_parser.read_csv_gse_as_key('infile.csv')
self.assertEqual(res, {'GSE1': ['GSM1', 'GSM2'], 'GSE2': ['GSM3']})
def test_read_csv_gse_as_key(self):
m = mock.mock_open(read_data=os.linesep.join(
[
'GSE1,H**o sapiens,GSM1',
'GSE1,H**o sapiens,GSM2',
'GSE2,H**o sapiens,GSM3'
]))
# use StringIO.StringIO because inf will be read by csv.reader, it must
# return an iternator, refer to test_soft_parser.test_parse for the
# other scenario
m.return_value.__iter__ = lambda self: StringIO.StringIO(self.read())
m.return_value.__next__ = lambda self: self.readline()
with mock.patch('rsempipeline.parsers.isamp_parser.open', m):
res = isamp_parser.read_csv_gse_as_key('infile.csv')
self.assertEqual(res, {
'GSE1': ['GSM1', 'GSM2'],
'GSE2': ['GSM3']
})
