def test_create_readme(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1.0'
task = ChallengeDataTask(temp_dir, params)
blast = BlastNFilterTask(temp_dir, params)
blast.create_dir()
sfile = blast.get_blastnfilter_summary_file()
f = open(sfile, 'w')
f.write('hello there\n')
f.flush()
f.close()
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
print line
if re.match('^hello there.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
finally:
shutil.rmtree(temp_dir)
def test_create_readme_version_empty_summary(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1.0'
task = ChallengeDataTask(temp_dir, params)
blast = BlastNFilterTask(temp_dir, params)
blast.create_dir()
sfile = blast.get_blastnfilter_summary_file()
open(sfile, 'a').close()
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
if re.match('^Celpprunner version: 1.0.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
finally:
shutil.rmtree(temp_dir)
def test_create_readme_unable_to_write_file(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = "1.0.0"
task = ChallengeDataTask(temp_dir, params)
try:
task._create_readme(os.path.join(temp_dir, 'doesnotexist'))
self.fail('Expected IOError')
except IOError:
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_create_readme_version_unset_and_no_summary_txt(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task._create_readme(temp_dir)
readme = os.path.join(temp_dir,
ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
f = open(readme, 'r')
found = False
for line in f:
if re.match('^Celpprunner version: Unknown.*$', line):
found = True
break
f.close()
self.assertEqual(found, True)
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)