def test_remote_fna_kwargs(self):
url = ('http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmax=1'
'00&retmode=text&tool=skbio&db=nucleotide&id=459567&rettype=fas'
'ta&retstart=0&[email protected]')
with open_files([url], stream=True) as fhs:
for f in fhs:
self.assertEqual(f.read(), FASTA)
def test_remote_fna_kwargs(self):
url = ('http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?retmax=1'
'00&retmode=text&tool=skbio&db=nucleotide&id=459567&rettype=fas'
'ta&retstart=0&[email protected]')
with open_files([url], stream=True) as fhs:
for f in fhs:
self.assertEqual(f.read(), FASTA)
def test_files_closed(self):
"""File gets closed in decorator"""
f = tempfile.NamedTemporaryFile('r')
f2 = tempfile.NamedTemporaryFile('r')
filepath = f.name
filepath2 = f2.name
with open_files([filepath, filepath2]) as fhs:
pass
for fh in fhs:
self.assertTrue(fh.closed)
def test_files_closed(self):
"""File gets closed in decorator"""
f = tempfile.NamedTemporaryFile('r')
f2 = tempfile.NamedTemporaryFile('r')
filepath = f.name
filepath2 = f2.name
with open_files([filepath, filepath2]) as fhs:
pass
for fh in fhs:
self.assertTrue(fh.closed)
def test_files_closed_harder(self):
"""File gets closed in decorator, even if exceptions happen."""
f = tempfile.NamedTemporaryFile('r')
f2 = tempfile.NamedTemporaryFile('r')
filepath = f.name
filepath2 = f2.name
try:
with open_files([filepath, filepath2]) as fhs:
raise TypeError
except TypeError:
for fh in fhs:
self.assertTrue(fh.closed)
else:
# If we're here, no exceptions have been raised inside the
# try clause, so the context manager swallowed them. No
# good.
raise Exception("`open_file` didn't propagate exceptions")
def test_files_closed_harder(self):
"""File gets closed in decorator, even if exceptions happen."""
f = tempfile.NamedTemporaryFile('r')
f2 = tempfile.NamedTemporaryFile('r')
filepath = f.name
filepath2 = f2.name
try:
with open_files([filepath, filepath2]) as fhs:
raise TypeError
except TypeError:
for fh in fhs:
self.assertTrue(fh.closed)
else:
# If we're here, no exceptions have been raised inside the
# try clause, so the context manager swallowed them. No
# good.
raise Exception("`open_file` didn't propagate exceptions")
def test_BytesIO(self):
"""BytesIO (useful e.g. for testing) slips through."""
f = BytesIO(b"File contents")
with open_files([f]) as fhs:
self.assertTrue(fhs[0] is f)
def test_remote_failing_fna(self):
with self.assertRaises(HTTPError) as e:
with open_files(['http://google.com/foo-seqs.fna']) as fhs:
for f in fhs:
f.read()
self.assertEquals(str(e.exception), '404 Client Error: Not Found')
def test_BytesIO(self):
"""BytesIO (useful e.g. for testing) slips through."""
f = BytesIO(b"File contents")
with open_files([f]) as fhs:
self.assertTrue(fhs[0] is f)
def test_remote_failing_fna(self):
with self.assertRaises(HTTPError) as e:
with open_files(['http://google.com/foo-seqs.fna']) as fhs:
for f in fhs:
f.read()
self.assertEqual(str(e.exception), '404 Client Error: Not Found')