def test_create_challenge_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
cyear = os.path.join(temp_dir, '2016')
cweek = os.path.join(cyear, 'dataset.week.5')
os.mkdir(cyear)
os.mkdir(cweek)
task = ChallengeDataTask(cweek, params)
task.create_dir()
cdir = os.path.join(task.get_dir(),
task.get_celpp_challenge_data_dir_name())
task._create_challenge_dir()
self.assertEqual(os.path.isdir(cdir), True)
task._create_challenge_dir()
self.assertEqual(os.path.isdir(cdir), True)
finally:
shutil.rmtree(temp_dir)
def test_copy_over_tsv_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
ctsv = dimport.get_crystalph_tsv()
f = open(ctsv, 'w')
f.write('crystal')
f.flush()
f.close()
nonpoly = dimport.get_nonpolymer_tsv()
f = open(nonpoly, 'w')
f.write('nonpoly')
f.flush()
f.close()
seq = dimport.get_sequence_tsv()
f = open(seq, 'w')
f.write('seq')
f.flush()
f.close()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
challenge_dir = task._create_challenge_dir()
self.assertEqual(os.path.isdir(challenge_dir), True)
task._copy_over_tsv_files(challenge_dir)
cop_ctsv = os.path.join(challenge_dir,
DataImportTask.CRYSTALPH_TSV)
self.assertEqual(os.path.isfile(cop_ctsv), True)
f = open(cop_ctsv)
self.assertEqual(f.readline(), 'crystal')
f.close()
cop_nonpoly = os.path.join(challenge_dir,
DataImportTask.NONPOLYMER_TSV)
self.assertEqual(os.path.isfile(cop_nonpoly), True)
f = open(cop_nonpoly)
self.assertEqual(f.readline(), 'nonpoly')
f.close()
cop_seq = os.path.join(challenge_dir,
DataImportTask.SEQUENCE_TSV)
self.assertEqual(os.path.isfile(cop_seq), True)
f = open(cop_seq)
self.assertEqual(f.readline(), 'seq')
f.close()
finally:
shutil.rmtree(temp_dir)
def test_copy_over_tsv_files_no_dataimport(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
challenge_dir = task._create_challenge_dir()
self.assertEqual(os.path.isdir(challenge_dir), True)
task._copy_over_tsv_files(challenge_dir)
finally:
shutil.rmtree(temp_dir)
def test_create_challenge_dir_unable_to_make_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
cyear = os.path.join(temp_dir, '2016')
cweek = os.path.join(cyear, 'dataset.week.5')
os.mkdir(cyear)
os.mkdir(cweek)
task = ChallengeDataTask(cweek, params)
task.create_dir()
cdir = os.path.join(task.get_dir(),
task.get_celpp_challenge_data_dir_name())
open(cdir, 'a').close()
try:
task._create_challenge_dir()
self.fail('Expected OSError')
except OSError:
pass
finally:
shutil.rmtree(temp_dir)
def test_tar_challenge_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
open(dimport.get_sequence_tsv(), 'a').close()
open(dimport.get_nonpolymer_tsv(), 'a').close()
open(dimport.get_crystalph_tsv(), 'a').close()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
chall_dir = task._create_challenge_dir()
final_log = os.path.join(chall_dir, 'final.log')
open(final_log, 'a').close()
task._create_readme(chall_dir)
task._copy_over_tsv_files(chall_dir)
# make a fake candidate
file_list = self.make_fake_candidate_dir(chall_dir, '5hib',
'2eb2', 'CSX')
self.assertEqual(os.path.isdir(chall_dir), True)
name = task.get_celpp_challenge_data_dir_name()
tfile = task._tar_challenge_dir(name)
self.assertEqual(os.path.isfile(tfile), True)
foodir = os.path.join(temp_dir, 'foo')
tar = tarfile.open(tfile, 'r:*')
tar.extractall(path=foodir)
tar.close()
cdir = os.path.join(foodir, name)
readme = os.path.join(cdir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
final_log = os.path.join(foodir, 'final.log')
self.assertEqual(os.path.isfile(final_log), False)
for fname in file_list:
chk = os.path.join(cdir, fname)
self.assertEqual(os.path.isfile(chk), True, chk)
finally:
shutil.rmtree(temp_dir)
def test_tar_challenge_dir_nothing_but_readme(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
chall_dir = task._create_challenge_dir()
task._create_readme(chall_dir)
self.assertEqual(os.path.isdir(chall_dir), True)
name = task.get_celpp_challenge_data_dir_name()
tfile = task._tar_challenge_dir(name)
self.assertEqual(os.path.isfile(tfile), True)
foodir = os.path.join(temp_dir, 'foo')
tar = tarfile.open(tfile, 'r:*')
tar.extractall(path=foodir)
tar.close()
cdir = os.path.join(foodir, name)
readme = os.path.join(cdir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
finally:
shutil.rmtree(temp_dir)