def test_get_uploadable_files(self):
temp_dir = tempfile.mkdtemp()
try:
# test where directory doesn't even exist
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.get_uploadable_files(), [])
# test on empty dir
task.create_dir()
self.assertEqual(task.get_uploadable_files(), [])
# test with tarfile
tarfile = task.get_celpp_challenge_data_tar_file()
open(tarfile, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 1)
flist.index(tarfile)
# test with additional stderr/stdout files
errfile = os.path.join(task.get_dir(),
'genchallengedata.py.stderr')
open(errfile, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 2)
flist.index(errfile)
outfile = os.path.join(task.get_dir(),
'genchallengedata.py.stdout')
open(outfile, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 3)
flist.index(outfile)
flist.index(errfile)
flist.index(tarfile)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_no_ftp(self):
temp_dir = tempfile.mkdtemp()
try:
script = self.create_gen_challenge_script(temp_dir)
params = D3RParameters()
params.genchallenge = script
params.pdbdb = '/foo'
params.version = '1'
blastnfilter = BlastNFilterTask(temp_dir, params)
blastnfilter.create_dir()
open(os.path.join(blastnfilter.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
chall = ChallengeDataTask(temp_dir, params)
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()
chall.run()
self.assertEqual(chall.get_error(), None)
# verify test files get created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(chall.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(chall.get_dir(),
'genchallenge.py.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(chall.get_dir(),
'genchallenge.py.stdout')
self.assertEqual(os.path.isfile(stdout), True)
# verify challenge directory is created and
# filled with valid files
chall_dir = os.path.join(chall.get_dir(),
chall.get_celpp_challenge_data_dir_name())
self.assertEqual(os.path.isdir(chall_dir), True)
readme = os.path.join(chall_dir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
crystal = os.path.join(chall_dir, DataImportTask.CRYSTALPH_TSV)
self.assertEqual(os.path.isfile(crystal), True)
seq = os.path.join(chall_dir, DataImportTask.SEQUENCE_TSV)
self.assertEqual(os.path.isfile(seq), True)
nonpoly = os.path.join(chall_dir, DataImportTask.NONPOLYMER_TSV)
self.assertEqual(os.path.isfile(nonpoly), True)
fivehibdir = os.path.join(chall_dir, '5hib')
fivehibtxt = os.path.join(fivehibdir, '5hib.txt')
self.assertEqual(os.path.isfile(fivehibtxt), True)
fivehibfas = os.path.join(fivehibdir, '5hib.fasta')
self.assertEqual(os.path.isfile(fivehibfas), True)
fivehicdir = os.path.join(chall_dir, '5hic')
fivehictxt = os.path.join(fivehicdir, '5hic.txt')
self.assertEqual(os.path.isfile(fivehictxt), True)
fivehicfas = os.path.join(fivehicdir, '5hic.fasta')
self.assertEqual(os.path.isfile(fivehicfas), True)
# verify tarball is created
tfile = chall.get_celpp_challenge_data_tar_file()
self.assertEqual(os.path.isfile(tfile), True)
foodir = os.path.join(temp_dir, 'foo')
os.mkdir(foodir)
tar = tarfile.open(tfile, 'r:*')
tar.extractall(path=foodir)
tar.close()
name = chall.get_celpp_challenge_data_dir_name()
cdir = os.path.join(foodir, name)
readme = os.path.join(cdir, ChallengeDataTask.README_TXT_FILE)
self.assertEqual(os.path.isfile(readme), True)
final = os.path.join(foodir, name, 'final.log')
self.assertEqual(os.path.isfile(final), False)
e_con = os.path.join(foodir, name, 'error_container')
self.assertEqual(os.path.isdir(e_con), False)
finally:
shutil.rmtree(temp_dir)