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# Copyright 1999 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
from __future__ import print_function
import os.path
import shutil
import sys
import tempfile
import unittest
from Bio import bgzf
from Bio import File
from Bio._py3k import StringIO
data = """This
is
a multi-line
file"""
class UndoHandleTests(unittest.TestCase):
def test_one(self):
h = File.UndoHandle(StringIO(data))
self.assertEqual(h.readline(), "This\n")
self.assertEqual(h.peekline(), "is\n")
self.assertEqual(h.readline(), "is\n")
# TODO - Meaning of saveline lacking \n?
h.saveline("saved\n")
self.assertEqual(h.peekline(), "saved\n")
h.saveline("another\n")
self.assertEqual(h.readline(), "another\n")
self.assertEqual(h.readline(), "saved\n")
# Test readlines after saveline
h.saveline("saved again\n")
lines = h.readlines()
self.assertEqual(len(lines), 3)
self.assertEqual(lines[0], "saved again\n")
self.assertEqual(lines[1], "a multi-line\n")
self.assertEqual(lines[2], "file") # no trailing \n
# should be empty now
self.assertEqual(h.readline(), "")
h.saveline("save after empty\n")
self.assertEqual(h.readline(), "save after empty\n")
self.assertEqual(h.readline(), "")
def test_read(self):
"""Test read method"""
h = File.UndoHandle(StringIO("some text"))
h.saveline("more text")
self.assertEqual(h.read(), 'more textsome text')
def test_undohandle_read_block(self):
for block in [1, 2, 10]:
s = StringIO(data)
h = File.UndoHandle(s)
h.peekline()
new = ""
while True:
tmp = h.read(block)
if not tmp:
break
new += tmp
self.assertEqual(data, new)
h.close()
class RandomAccess(unittest.TestCase):
def test_plain(self):
with File._open_for_random_access("Quality/example.fastq") as handle:
self.assertTrue("r" in handle.mode)
self.assertTrue("b" in handle.mode)
def test_bgzf(self):
with File._open_for_random_access("Quality/example.fastq.bgz") as handle:
self.assertIsInstance(handle, bgzf.BgzfReader)
def test_gzip(self):
self.assertRaises(ValueError,
File._open_for_random_access,
"Quality/example.fastq.gz")
class AsHandleTestCase(unittest.TestCase):
def setUp(self):
# Create a directory to work in
self.temp_dir = tempfile.mkdtemp(prefix='biopython-test')
def tearDown(self):
shutil.rmtree(self.temp_dir)
def _path(self, *args):
return os.path.join(self.temp_dir, *args)
def test_handle(self):
"Test as_handle with a file-like object argument"
p = self._path('test_file.fasta')
with open(p, 'wb') as fp:
with File.as_handle(fp) as handle:
self.assertEqual(fp, handle, "as_handle should "
"return argument when given a "
"file-like object")
self.assertFalse(handle.closed)
self.assertFalse(handle.closed,
"Exiting as_handle given a file-like object "
"should not close the file")
def test_string_path(self):
"Test as_handle with a string path argument"
p = self._path('test_file.fasta')
mode = 'wb'
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(p, handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
@unittest.skipIf(
sys.version_info < (3, 6),
'Passing Path objects to File.as_handle requires Python >= 3.6',
)
def test_path_object(self):
"Test as_handle with a pathlib.Path object"
from pathlib import Path
p = Path(self._path('test_file.fasta'))
mode = 'wb'
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(str(p.absolute()), handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
@unittest.skipIf(
sys.version_info < (3, 6),
'Passing path-like objects to File.as_handle requires Python >= 3.6',
)
def test_custom_path_like_object(self):
"Test as_handle with a custom path-like object"
class CustomPathLike:
def __init__(self, path):
self.path = path
def __fspath__(self):
return self.path
p = CustomPathLike(self._path('test_file.fasta'))
mode = 'wb'
with File.as_handle(p, mode=mode) as handle:
self.assertEqual(p.path, handle.name)
self.assertEqual(mode, handle.mode)
self.assertFalse(handle.closed)
self.assertTrue(handle.closed)
def test_stringio(self):
s = StringIO()
with File.as_handle(s) as handle:
self.assertIs(s, handle)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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