def test_handles_comment_headerlines_appropriately(self):
t = TableResource()
is_valid, err = t.validate_type(
os.path.join(TESTDIR, 'test_general_table.with_comment.tsv'),
'tsv')
self.assertTrue(is_valid)
self.assertIsNone(err)
def test_fails_at_empty_table(self):
'''
If the file is literally empty, check that it fails
'''
t = TableResource()
is_valid, err = t.validate_type(os.path.join(TESTDIR,
'test_empty.tsv'))
self.assertFalse(is_valid)
self.assertEqual(err, PARSE_ERROR)
def test_reads_basic_table(self):
'''
Is able to parse and report validation on a well-formatted
general table.
'''
t = TableResource()
is_valid, err = t.validate_type(
os.path.join(TESTDIR, 'test_general_table.tsv'))
self.assertTrue(is_valid)
self.assertIsNone(err)
def test_reader_type(self):
'''
Is able to return the correct parser for the file extension
Note that none of the paths below actually have to exist.
The method is just examining the file extension.
'''
t = TableResource()
reader = t.get_reader('test_general_table.tsv')
self.assertEqual(reader, pd.read_table)
reader = t.get_reader('test_integer_matrix.csv')
self.assertEqual(reader, pd.read_csv)
reader = t.get_reader('test_integer_matrix.CSV')
self.assertEqual(reader, pd.read_csv)
reader = t.get_reader('example_bed.bed')
self.assertEqual(reader, pd.read_table)
reader = t.get_reader('something.xls')
self.assertEqual(reader, pd.read_excel)
reader = t.get_reader('junk.abc')
self.assertIsNone(reader)
reader = t.get_reader('junk.odc')
self.assertIsNone(reader)
def test_fails_malformatted_basic_table(self):
t = TableResource()
is_valid, err = t.validate_type(
os.path.join(TESTDIR, 'test_malformatted_table.tsv'))
self.assertFalse(is_valid)
self.assertEqual(err, PARSE_ERROR)
def test_reports_unknown_parser(self):
t = TableResource()
is_valid, err = t.validate_type(os.path.join(TESTDIR, 'something.abc'))
self.assertFalse(is_valid)
self.assertEqual(err, PARSER_NOT_FOUND_ERROR)