def test_odd_quotes(self):
"""Test that an odd # of single quotes generates an error."""
content = "((h_ ,'p)h p,g()[],:_)hpg;"
tok = NewickTokenizer(StringIO(content))
self.assertRaises(Exception, tok.tokens)
content = "((h_ ,'p')h p,'g()[]',:_')hpg;"
tok = NewickTokenizer(StringIO(content))
self.assertRaises(Exception, tok.tokens)
def _do_test(self, content, expected):
"""Part of the testing harness.
Writes `content`, the parses and compares to `expected`.
"""
self.assertEqual(list(NewickTokenizer(StringIO(content))), expected)
self.assertEqual(list(NewickTokenizer(newick=content)), expected)
fp = path_map.next_unique_scratch_filepath('tok_test')
try:
write_to_filepath(content, fp)
self.assertEqual(list(NewickTokenizer(filepath=fp)), expected)
finally:
try:
os.unlink(fp)
except: # pragma: no cover
pass
def _do_test(self, content, expected):
"""Part of the testing harness.
Writes `content`, the parses and compares to `expected`.
"""
nt = NewickTokenizer(stream=StringIO(content))
e = [deepcopy(i) for i in NewickEventFactory(tokenizer=nt)]
self.assertEqual(e, expected)
new_e = []
def append_to_new_e(event):
new_e.append(deepcopy(event))
NewickEventFactory(newick=content, event_handler=append_to_new_e)
self.assertEqual(new_e, expected)
def test_open_closed(self):
"""Tests that () generates an error."""
nt = NewickTokenizer(newick='(a,(),(d,e));')
self.assertRaises(ValueError, nt.tokens)
def test_label(self):
"""Test that unquoted labels with newline character generate errors."""
nt = NewickTokenizer(newick="(a\n'b',(b,c),(d,e));")
self.assertRaises(ValueError, nt.tokens)
def test_unexpected_comma(self):
"""Test consecutive commas generate errors."""
nt = NewickTokenizer(newick='(a,(b,c),,(d,e));')
self.assertRaises(ValueError, nt.tokens)
def test_comma_bef_semicolon(self):
"""Test that terminating ; is not preceded by ,."""
nt = NewickTokenizer(newick='(a,(b,c),(d,e)),;')
self.assertRaises(ValueError, nt.tokens)
def test_unclosed_comment(self):
"""Tests that unclosed [] comments generate errors."""
nt = NewickTokenizer(newick='(a,(b,c),[(d,e));')
self.assertRaises(ValueError, nt.tokens)
def test_sans_comma(self):
"""Tests error with a comma is omitted."""
nt = NewickTokenizer(newick='(a,(b,c)(d,e));')
self.assertRaises(ValueError, nt.tokens)
def test_peek_none(self):
"""Tests behavior of peek when there are no more tokens."""
nt = NewickTokenizer(newick='(a,(b,c));')
nt.tokens()
self.assertIsNone(nt._peek())
def test_extra_closed(self):
"""Tests Newick with extra close parens generate errors."""
nt = NewickTokenizer(newick='(a,(b,c)));')
self.assertRaises(ValueError, nt.tokens)
def test_unclosed(self):
"""Tests Newick open parens are closed."""
nt = NewickTokenizer(newick='(a,(b,c)')
self.assertRaises(ValueError, nt.tokens)
def test_extra_suffix(self):
"""Tests Newick must end with ) or ;."""
nt = NewickTokenizer(newick='(a,(b,c));suffix')
self.assertRaises(ValueError, nt.tokens)