def test_run_succeeds(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = 'true'
params.pdbdb = '/foo'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
# test files get created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(task.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(task.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_chimeraprep_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = 'false'
params.pdbdb = '/foo'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(task.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(task.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_chimeraprep_is_not_found_rdkitpython_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.chimeraprep = '/bin/doesnotexist'
params.pdbdb = '/foo'
params.rdkitpython = '/data/miniconda2/bin'
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
challdir = os.path.join(chall.get_dir(),
chall.get_celpp_challenge_data_dir_name())
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'Caught Exception trying to run ' +
'/bin/doesnotexist --candidatedir ' + challdir +
' --rdkitpython \'/data/miniconda2/bin\' ' + '--pdbdb ' +
'/foo --outdir ' + task.get_dir() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_uploader_successful(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
yeardir = os.path.join(temp_dir, '2017')
os.mkdir(yeardir)
weekdir = os.path.join(yeardir, 'dataset.week.1')
os.mkdir(weekdir)
chall = ChallengeDataTask(weekdir, params)
chall.create_dir()
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=[3, 5])
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
ftp.connect()
chall.set_file_transfer(ftp)
tarball = os.path.join(chall.get_dir(), 'celppweek1_2017.tar.gz')
f = open(tarball, 'w')
f.write('hi')
f.flush()
f.close()
latest_file = os.path.join(chall.get_dir(),
ChallengeDataTask.LATEST_TXT)
chall._upload_challenge_file(tarball)
f = open(latest_file, 'r')
line = f.readline()
self.assertEqual(line, 'celppweek1_2017.tar.gz')
f.close()
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_upload_challenge_file_uploader_upload_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
yeardir = os.path.join(temp_dir, '2016')
os.mkdir(yeardir)
weekdir = os.path.join(yeardir, 'dataset.week.50')
os.mkdir(weekdir)
chall = ChallengeDataTask(weekdir, params)
chall.create_dir()
mockftp = D3RParameters()
mockftp.put = Mock(side_effect=IOError('hi'))
ftp = FtpFileTransfer(None)
ftp.set_remote_challenge_dir('/challenge')
ftp.set_connection(mockftp)
ftp.connect()
chall.set_file_transfer(ftp)
tarball = os.path.join(chall.get_dir(), 'celppweek50_2016.tar.gz')
f = open(tarball, 'w')
f.write('hi')
f.flush()
f.close()
try:
chall._upload_challenge_file(tarball)
self.fail('Expected exception')
except Exception as e:
self.assertEqual(str(e),
'Unable to upload ' + tarball +
' to /challenge/celppweek50_2016.tar.gz : ' +
'hi')
ftp.disconnect()
finally:
shutil.rmtree(temp_dir)
def test_get_celpp_challenge_data_dir_name_not_standard_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChallengeDataTask(temp_dir, params)
task.create_dir()
self.assertEqual(task.get_celpp_challenge_data_dir_name(),
'celpp_week0_0')
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_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_get_celpp_challenge_data_dir_name(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()
self.assertEqual(task.get_celpp_challenge_data_dir_name(),
'celpp_week5_2016')
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_chimeraprep_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), 'chimeraprep not set')
# test files get created
self.assertEqual(os.path.isdir(task.get_dir()), True)
errfile = os.path.join(task.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
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_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_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_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)
def test_permute_chains_and_take_min_rmsd(self):
if not (self.has_oechem) or not (self.has_schrodinger):
sys.stdout.write("Missing essential component. Skipping test.\n")
return
test_scale = 'github'
method_list = ['autodockvina']
try:
temp_dir = tempfile.mkdtemp()
for method in method_list:
params = D3RParameters()
params.evaluation = 'evaluate.py'
params.pdbdb = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/mini_pdb/' %
test_scale)
# Make blastnfilter task
blastnfiltertask = BlastNFilterTask(temp_dir, params)
blastnfiltertask.create_dir()
open(
os.path.join(blastnfiltertask.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.3.'
'blastnfilter/' % test_scale)
os.system('cp -r %s/* %s' %
(source_dir, blastnfiltertask.get_dir()))
# Make challengedata task
challengedatatask = ChallengeDataTask(temp_dir, params)
challengedatatask.create_dir()
open(
os.path.join(challengedatatask.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.4.'
'challengedata/' % test_scale)
os.system('cp -r %s/* %s' %
(source_dir, challengedatatask.get_dir()))
# Make dock task
docktask = D3RTask(temp_dir, params)
docktask.set_name(method)
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.6.%s/' %
(test_scale, method))
os.system('cp -r %s/* %s' % (source_dir, docktask.get_dir()))
print 'docktask.get_dir()', docktask.get_dir()
print 'temp_dir', temp_dir
task = EvaluationTask(temp_dir, '%s.evaluation' % (method),
docktask, params)
plist = [
Participant('1name', '1d3rusername', '12345',
'[email protected],[email protected]')
]
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emailer.set_alternate_smtp_emailer(smtpemailer)
task.set_evaluation_emailer(emailer)
task.run()
val = task.get_evaluation_summary()
self.assertEqual(
val, '\nEvaluation of docking\n==================='
'==\nTarge'
't_PDBID LMCSS SMCSS '
' h'
'iResApo hiResHolo hiTanimoto '
' '
'LMCSS_ori_distance \n\nSummary Statistics\n'
'\nNumber_of'
'_cases 0 0 '
' 1 '
' 0 0 '
' \nAve'
'rage '
' '
' 6.447 '
' '
' \nMaximum '
' '
' 6.447 '
' '
' \nMinimum '
' '
' 6.447 '
' '
' \nMedian '
' '
' 6.447 '
' '
' \n\nIndividual Results\n'
'\n5t6d '
' '
' 6.44'
'7 (2.176 ) '
' '
' \n\n')
self.assertEqual(task.get_error(), None)
finally:
# pass
shutil.rmtree(temp_dir)