def test_extract_gz(self):
with TemporaryDirectory() as tempd:
extract_gz(Test_File.TAR_GZ_FILE, tempd)
self.assertEqual(
sha256(Path(os_path.join(
tempd, 'data.tar')).read_bytes()).hexdigest(),
'd3eb1c4b3604e6863fb4c4da930b4df74217fcf95c78439bc721ea83ce280f19'
)
def test_generate_cache(self):
r"""Test of genrating all rpCache files from input_cache.
Method: Generate a full rpCache. Then, for each file, compare its size
with it is supposed to be.
"""
self.skipTest("Tool long, not in standard tests")
rpCache.generate_cache(self.outdir)
for file, size in self.files:
outfile = extract_gz(file, self.outdir)
self.assertTrue(Main._check_file_size(outfile, size))
os_rm(outfile)
def setUp(self):
self.logger = create_logger(__name__, 'ERROR')
# Create persistent temp folder
# to deflate compressed data file so that
# it remains reachable outside of this method.
# Has to remove manually it in tearDown() method
self.temp_d = mkdtemp()
self.e_coli_model_path = extract_gz(
self.e_coli_model_path_gz,
self.temp_d
)
def test_compress_gz_with_outFile(self):
infile_t = '100l_file.txt'
infile = os_path.join('data', infile_t)
outfile_temp = NamedTemporaryFile().name
outfile = compress_gz(infile, outfile_temp)
# Check if the original file still exists
self.assertTrue(os_path.isfile(infile))
# Check if outfile is well named
self.assertEqual(outfile, outfile_temp)
# Check if extracted file is equal to original one
with TemporaryDirectory() as tempd:
self.assertTrue(cmp(infile, extract_gz(outfile, tempd)))
remove(outfile)
def test_compress_gz_delete(self):
infile_t = '100l_file.txt'
infile = os_path.join('data', infile_t)
infile_temp = NamedTemporaryFile().name
copyfile(infile, infile_temp)
outfile = compress_gz(infile_temp, delete=True)
# Check if the original file does not exist anymore
self.assertTrue(not os_path.isfile(infile_temp))
# Check if outfile is well named
self.assertEqual(outfile, infile_temp + '.gz')
# Check if extracted file is equal to original one
with TemporaryDirectory() as tempd:
self.assertTrue(cmp(infile, extract_gz(outfile, tempd)))
remove(outfile)
def gunzip_to_csv(filename: str, indir: str) -> str:
"""
Uncompress gzip file into indir.
Parameters
----------
filename : str
Path of file to deflate.
indir : str
Path where install.
"""
new_f = os_path.join(indir, os_path.basename(filename) + '.gz')
copyfile(filename, new_f)
filename = extract_gz(new_f, indir)
rename(filename, filename + '.csv')
filename += '.csv'
return filename
