def _create_composite_file_names():
file_names = {}
names = [("tsv_file", ".tsv"), ("yaml_file", ".yaml"), ("json_file", ".json")]
time_stamp = now_utc()
time_stamped_base = "".join(["uni_composite.", time_stamp])
for name, ext in names:
file_names[name] = "".join([time_stamped_base, ext])
return file_names
def test_new_filenames_pass(self):
estimated_time = now_utc()
result_names = ss._new_filenames()
json_base, json_time, json_ext = result_names.json.split('.')
raw_base, raw_time, raw_ext = result_names.raw.split('.')
self.assertEqual(json_time, raw_time)
self.assertAlmostEquals(json_time, estimated_time)
self.assertEqual({json_base, raw_base, 'ss_dis'}, {'ss_dis'})
self.assertEqual(json_ext, 'json')
self.assertEqual(raw_ext, 'txt')
return None
def test_generate_json(self):
time_stamp = now_utc()
json_file_name = (
"{}.{}.{}".format(
'ss_dis',
time_stamp,
'json'
)
)
json_file_path = os.path.join(self.temp_dir, json_file_name)
self.write_fasta(time_stamp)
self.assertFalse(os.path.isfile(json_file_path))
ss.fetch_ss_dis(self.temp_dir)
self.assertTrue(os.path.isfile(json_file_path))
return None
def test_generate_json_and_return_dic(self):
# TODO: Value of expected updated to include '\r' after from __future__ import unicode_literals and from io import os. Validate this data.
expected = {
u'1DBO_A': {
u'disorder': u'',
u'secstr': u'',
u'sequence': u'MKMLNKLAGYLLPIMVLLNVAPCLGQVVASNETLYQVVKEVKPGGLVQIADGTYKDVQLIVSNSGKSGLPITIKALNPGKVFFTGDAKVELRGEHLILEGIWFKDGNRAIQAWKSHGPGLVAIYGSYNRITACVFDCFDEANSAYITTSLTEDGKVPQHCRIDHCSFTDKITFDQVINLNNTARAIKDGSVGGPGMYHRVDHCFFSNPQKPGNAGGGIRIGYYRNDIGRCLVDSNLFMRQDSEAEIITSKSQENVYYGNTYLNCQGTMNFRHGDHQVAINNFYIGNDQRFGYGGMFVWGSRHVIACNYFELSETIKSRGNAALYLNPGAMASEHALAFDMLIANNAFINVNGYAIHFNPLDERRKEYCAANRLKFETPHQLMLKGNLFFKDKPYVYPFFKDDYFIAGKNSWTGNVALGVEKGIPVNISANRSAYKPVKIKDIQPIEGIALDLNALISKGITGKPLSWDEVRPYWLKEMPGTYALTARLSADRAAKFKAVIKRNKEH'
},
u'5C1Z_B': {
u'disorder': u'',
u'secstr': u' EEEEESSSSS EEEE TT BHHHHHHHHHHHHTS GGGEEEEETTEEE TT BHHHHT TT EEEEEE TT EEEETTTT EEEEEEEEEEETTT SS EEESS SHHHHHSTT SBEEE STT BEEEEEEESSS TT EE TTEE TT B TTT B SSEEE STT BEEEHHHHHHHHHHHHHTT EEETTTEEE TT TT S GGGGGG',
u'sequence': u'MIVFVRFNSSHGFPVEVDSDTSIFQLKEVVAKRQGVPADQLRVIFAGKELRNDWTVQNCDLDQQSIVHIVQRPWRKGQEMNATNSFYVYCKGPCQRVQPGKLRVQCSTCRQATLTLTQGPSCWDDVLIPNRMSGECQSPHCPGTSAEFFFKCGAHPTSDKETSVALHLIATNSRNITCITCTDVRSPVLVFQCNSRHVICLDCFHLYCVTRLNDRQFVHDPQLGYSLPCVAGCPNSLIKELHHFRILGEEQYNRYQQYGAEECVLQMGGVLCPRPGCGAGLLPEPDQRKVTCEGGNGLGCGFAFCRECKEAYHEGECSAVFEASGTTTQAYRVDERAAEQARWEAASKETIKKTTKPCPRCHVPVEKNGGCMHMKCPQPQCRLEWCWNCGCEWNRVCMGDHWFDV'
}
}
time_stamp = now_utc()
self.write_fasta(time_stamp)
result = ss.fetch_ss_dis(self.temp_dir)
self.assertEqual(expected, result)
return None
def backup_file(original_file_path):
log_pdb = getLogger('pdb_app_logger')
if not os.path.abspath(original_file_path):
raise RuntimeError("Please pass an absolute file path.")
name_segments = original_file_path.split('.')
if len(name_segments) > 2:
original_fn = ''.join(name_segments[:-1])
extension = ''.join(
['.', name_segments[-1]]
)
elif len(name_segments) == 2:
original_fn = name_segments[0]
extension = ''.join(
['.', name_segments[1]]
)
else:
assert len(name_segments) == 1
original_fn = name_segments[0]
extension = ''
timestamp = now_utc()
new_fn = ''.join([
original_fn,
'.',
timestamp,
extension
])
new_fp = os.path.join(
os.path.basename(original_file_path),
new_fn
)
copy2(original_file_path, new_fp)
assert isfile(new_fp)
assert cmp(original_file_path, new_fp, shallow=False)
log_pdb.info(
"Created a backup of \'{}\' at the following location:\n"
"\t{}".format(original_file_path, new_fp)
)
return None
def _new_filenames():
"""Create text and json filenames with matching timestamps.
Returns:
new_filenames (SS_Names): A named 2-tuple where raw is the
filename of the new text file and json is the name
of the matching (datetime) json file.
"""
timestamp = now_utc()
rfn = "{}.{}.{}".format(
'ss_dis',
timestamp,
'txt'
)
yfn = "{}.{}.{}".format(
'ss_dis',
timestamp,
'json'
)
new_filenames = SS_File_Names(raw=rfn, json=yfn)
return new_filenames