def test_record_too_large(self):
f = SIO( (tryptophan * ((2000000 // len(tryptophan)) + 1)).replace("$$$$", "1234"))
try:
for x in open_sdf(f):
raise AssertionError("should not be able to read the first record")
except sdf_reader.SDFParseError, err:
self.assertIn("too large", str(err))
self.assertIn("at line 1", str(err))
def test_wrong_format(self):
f = SIO("Spam\n")
try:
for x in open_sdf(f):
raise AssertionError("Bad parse")
except sdf_reader.SDFParseError, err:
self.assertEquals("Could not find a valid SD record" in str(err), True)
self.assertEquals("line 1" in str(err), True, str(err))
def test_bad_format(self):
f = SIO(tryptophan + tryptophan.replace("V2000", "V4000"))
try:
for i, x in enumerate(open_sdf(f)):
if i > 0:
raise AssertionError("bad record count")
except sdf_reader.SDFParseError, err:
self.assertIn("incorrectly formatted record", str(err))
self.assertIn("at line 70", str(err))
def gunzip():
import gzip
from cStringIO import StringIO as SIO
from hashlib import md5
tmp = gzip.GzipFile(mode='rb', fileobj=SIO(data)).read()
md5 = md5(tmp).hexdigest()
if md5 != md5sum:
raise IOError('Corrupted data!')
return tmp
def run_warning(s):
sys.stderr = stderr = SIO()
try:
try:
run(s)
finally:
sys.stderr = real_stderr
except SystemExit, e:
raise AssertionError("unexpected SystemExit: %r and %r" %
(e, stderr.getvalue()))
def test_has_extra_data(self):
f = SIO(tryptophan + tryptophan + "blah")
try:
for i, x in enumerate(open_sdf(f)):
if i > 1:
raise AssertionError("bad record count")
except sdf_reader.SDFParseError, err:
self.assertIn("unexpected content", str(err))
expected_lineno = (tryptophan.count("\n")*2) + 1
expected_lineno_msg = "at line %d" % expected_lineno
self.assertIn(expected_lineno_msg, str(err))
def run_failure(s):
sys.stderr = stderr = SIO()
try:
try:
run(s)
except SystemExit:
pass
else:
raise AssertionError("should have exited: %r" % (s, ))
finally:
sys.stderr = real_stderr
return stderr.getvalue()
def run(s):
args = s.split()
try:
sys.stdin = open(DECODER_SDF)
sys.stdout = stdout = SIO()
sdf2fps.main(args)
finally:
sys.stdout = real_stdout
sys.stdin = real_stdin
result = stdout.getvalue().splitlines()
if result:
assert result[0] == "#FPS1"
return result
def test_my_error_handler(self):
class CaptureErrors(object):
def __init__(self):
self.errors = []
def __call__(self, msg, loc):
self.errors.append( (msg, loc.info()) )
my_error_handler = CaptureErrors()
loc = sdf_reader.FileLocation()
f = SIO(tryptophan + tryptophan.replace("V2000", "V4000") + tryptophan)
titles = [loc.lineno for rec in open_sdf(f, location=loc,
errors=my_error_handler)]
self.assertEquals(titles, [1, 137])
self.assertEquals(my_error_handler.errors, [("incorrectly formatted record",
{"name": None,
"lineno": 70,
"title": "tryptophan.pdb"})])
def test_missing_terminal_newline(self):
f = SIO(tryptophan.rstrip("\n"))
n = sum(1 for x in open_sdf(f))
self.assertEquals(n, 1)