def test_run_fails_cause_genchallenge_is_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.genchallenge = '/bin/doesnotexist'
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)
chall.run()
self.assertEqual(chall.get_error(),
'Caught Exception trying to run ' +
'/bin/doesnotexist --candidatedir ' +
blastnfilter.get_dir() + ' --pdbdb ' +
'/foo --outdir ' +
chall.get_dir() +
'/' + chall.get_celpp_challenge_data_dir_name() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_genchallenge_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.genchallenge = 'false'
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)
chall.run()
self.assertEqual(chall.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(chall.get_dir(),
'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(chall.get_dir(),
'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_success_with_ftp_upload(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)
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=[3, 5])
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
chall.set_file_transfer(ftp)
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)
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.version = '1'
# return immediately cause can_run is false
chall = ChallengeDataTask(temp_dir, params)
chall.run()
self.assertEqual(chall.get_error(),
'blastnfilter task has notfound status')
finally:
shutil.rmtree(temp_dir)
def test_can_run(self):
temp_dir = tempfile.mkdtemp()
try:
# no blast task found so it cannot run
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'blastnfilter task has notfound status')
# blastn filter running
blastnfilter = BlastNFilterTask(temp_dir, params)
blastnfilter.create_dir()
open(os.path.join(blastnfilter.get_dir(), D3RTask.START_FILE),
'a').close()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'blastnfilter task has start status')
# blastnfilter failed
error_file = os.path.join(blastnfilter.get_dir(),
D3RTask.ERROR_FILE)
open(error_file, 'a').close()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'blastnfilter task has error status')
# blastnfilter success
os.remove(error_file)
open(os.path.join(blastnfilter.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
task = ChallengeDataTask(temp_dir, params)
self.assertEqual(task.can_run(), True)
self.assertEqual(task.get_error(), None)
# proteinligprep task exists already
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
task.get_dir_name() +
' already exists and status is unknown')
# proteinlibprep already complete
task = ChallengeDataTask(temp_dir, params)
open(os.path.join(task.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(), None)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_genchallenge_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
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)
chall.run()
self.assertEqual(chall.get_error(),
'genchallenge not set')
# test files get created
self.assertEqual(os.path.isdir(chall.get_dir()),
True)
errfile = os.path.join(chall.get_dir(),
D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
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)