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_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_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_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# return immediately cause can_run is false
task = ChimeraProteinLigPrepTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(),
'challengedata task has notfound status')
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_can_run(self):
temp_dir = tempfile.mkdtemp()
try:
# no blastnfilter task found so it cannot run
params = D3RParameters()
task = ChimeraProteinLigPrepTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'challengedata task has notfound status')
# blastnfilter running
chall = ChallengeDataTask(temp_dir, params)
chall.create_dir()
open(os.path.join(chall.get_dir(), D3RTask.START_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'challengedata task has start status')
# blastnfilter failed
error_file = os.path.join(chall.get_dir(), D3RTask.ERROR_FILE)
open(error_file, 'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
self.assertEqual(task.can_run(), False)
self.assertEqual(task.get_error(),
'challengedata task has error status')
# blastnfilter success
os.remove(error_file)
open(os.path.join(chall.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
task = ChimeraProteinLigPrepTask(temp_dir, params)
self.assertEqual(task.can_run(), True)
self.assertEqual(task.get_error(), None)
# chimeraproteinligprep task exists already
task = ChimeraProteinLigPrepTask(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')
# chimeraproteinligprep already complete
task = ChimeraProteinLigPrepTask(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)