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_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_can_run(self):
temp_dir = tempfile.mkdtemp()
try:
# no proteinligprep task found so it cannot run
params = D3RParameters()
vina = AutoDockVinaTask(temp_dir, params)
self.assertEqual(vina.can_run(), False)
self.assertEqual(vina.get_error(),
'chimeraprep task has notfound status')
# proteinligprep filter running
proteinligprep = ChimeraProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
open(os.path.join(proteinligprep.get_dir(), D3RTask.START_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
self.assertEqual(vina.can_run(), False)
self.assertEqual(vina.get_error(),
'chimeraprep task has start status')
# proteinligprep failed
error_file = os.path.join(proteinligprep.get_dir(),
D3RTask.ERROR_FILE)
open(error_file, 'a').close()
vina = AutoDockVinaTask(temp_dir, params)
self.assertEqual(vina.can_run(), False)
self.assertEqual(vina.get_error(),
'chimeraprep task has error status')
# proteinligprep success
os.remove(error_file)
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
self.assertEqual(vina.can_run(), True)
self.assertEqual(vina.get_error(), None)
# vina task exists already
vina = AutoDockVinaTask(temp_dir, params)
vina.create_dir()
self.assertEqual(vina.can_run(), False)
self.assertEqual(
vina.get_error(),
vina.get_dir_name() + ' already exists and status is unknown')
# vina already complete
vina = AutoDockVinaTask(temp_dir, params)
open(os.path.join(vina.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
self.assertEqual(vina.can_run(), False)
self.assertEqual(vina.get_error(), None)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.vina = 'true'
proteinligprep = ChimeraProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
vina.run()
self.assertEqual(vina.get_error(), None)
# test files get created
errfile = os.path.join(vina.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(vina.get_dir(), D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(vina.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(vina.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_vina_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.vina = 'false'
proteinligprep = ChimeraProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
vina.run()
self.assertEqual(
vina.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(vina.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(vina.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(vina.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
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)
def test_run_fails_cause_vina_is_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.vina = '/bin/doesnotexist'
proteinligprep = ChimeraProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
vina.run()
self.assertEqual(
vina.get_error(), 'Caught Exception trying to run ' +
'/bin/doesnotexist --structuredir ' +
proteinligprep.get_dir() + ' --outdir ' + vina.get_dir() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(vina.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_get_uploadable_files(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = ChimeraProteinLigPrepTask(temp_dir, params)
# try with no dir
self.assertEqual(task.get_uploadable_files(), [])
# try with empty dir
task.create_dir()
self.assertEqual(task.get_uploadable_files(), [])
# try with final log
final_log = os.path.join(task.get_dir(),
ChimeraProteinLigPrepTask.FINAL_LOG)
open(final_log, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 1)
flist.index(final_log)
# add error out files and try with second pbdid folder
# with ligand.mae
errfile = os.path.join(task.get_dir(),
'chimera_proteinligprep.py.stderr')
open(errfile, 'a').close()
outfile = os.path.join(task.get_dir(),
'chimera_proteinligprep.py.stdout')
open(outfile, 'a').close()
flist = task.get_uploadable_files()
self.assertEqual(len(flist), 3)
flist.index(errfile)
flist.index(outfile)
flist.index(final_log)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_vina_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
proteinligprep = ChimeraProteinLigPrepTask(temp_dir, params)
proteinligprep.create_dir()
open(os.path.join(proteinligprep.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
vina = AutoDockVinaTask(temp_dir, params)
vina.run()
self.assertEqual(vina.get_error(), 'vina not set')
# test files get created
self.assertEqual(os.path.isdir(vina.get_dir()), True)
errfile = os.path.join(vina.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def run(self):
"""Runs AutoDockVinaTask after verifying chimeraproteinligprep was good
Method requires can_run() to be called before hand with
successful outcome
Otherwise method invokes D3RTask.start then this method
creates a directory and invokes blastnfilter script. Upon
completion results are analyzed and success or error status
is set appropriately and D3RTask.end is invoked
"""
super(AutoDockVinaTask, self).run()
if self._can_run is False:
logger.debug(self.get_dir_name() +
' cannot run cause _can_run flag '
'is False')
return
try:
logger.debug('vina set to ' + self.get_args().vina)
except AttributeError:
self.set_error('vina not set')
self.end()
return
ligprep = ChimeraProteinLigPrepTask(self._path, self._args)
#
# vinadocking.py --structuredir <path to stage.3.chimeraprep> \
# --outdir <path to stage.4.vina>
#
cmd_to_run = (self.get_args().vina + ' --structuredir ' +
ligprep.get_dir() + ' --outdir ' + self.get_dir())
vina_name = os.path.basename(self.get_args().vina)
self.run_external_command(vina_name, cmd_to_run, True)
# assess the result
self.end()