def test_get_external_data_submissions_raise_exception(self):
params = D3RParameters()
fac = ExternalDataSubmissionFactory('/foo', params)
tlist = fac.get_external_data_submissions()
self.assertEqual(len(tlist), 0)
class TestCelppRunner(unittest.TestCase):
"""Tests celpprunner command line script
"""
param = D3RParameters()
blast = BlastNFilterTask('/foo', param)
BLAST_DIR_NAME = blast.get_dir_name()
BLAST_NAME = blast.get_name()
data = DataImportTask('/foo', param)
IMPORT_DIR_NAME = data.get_dir_name()
IMPORT_NAME = data.get_name()
makedb = MakeBlastDBTask('/foo', param)
MAKEDB_DIR_NAME = makedb.get_dir_name()
MAKEDB_NAME = makedb.get_name()
glide = GlideTask('/foo', param)
GLIDE_DIR_NAME = glide.get_dir_name()
prot = ProteinLigPrepTask('/foo', param)
PROT_DIR_NAME = prot.get_dir_name()
vina = AutoDockVinaTask('/foo', param)
VINA_DIR_NAME = vina.get_dir_name()
chall = ChallengeDataTask('/foo', param)
CHALL_DIR_NAME = chall.get_dir_name()
CHALL_NAME = chall.get_name()
chimeraprep = ChimeraProteinLigPrepTask('/foo', param)
CHIMERAPREP_DIR_NAME = chimeraprep.get_dir_name()
def setUp(self):
pass
def test_get_lock(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
# get the lock file which should work
lock = celpprunner._get_lock(theargs, 'blast')
expectedLockFile = os.path.join(temp_dir,
'celpprunner.blast.lockpid')
self.assertTrue(os.path.isfile(expectedLockFile))
# try getting lock again which should also work
lock = celpprunner._get_lock(theargs, 'blast')
lock.release()
self.assertFalse(os.path.isfile(expectedLockFile))
finally:
shutil.rmtree(temp_dir)
def test_parse_arguments(self):
theargs = ['--stage', 'blast', 'foo']
result = celpprunner._parse_arguments('hi', theargs)
self.assertEqual(result.stage, 'blast')
self.assertEqual(result.celppdir, 'foo')
self.assertEqual(result.email, None)
self.assertEqual(result.loglevel, celpprunner.DEFAULT_LOG_LEVEL)
self.assertEqual(result.blastnfilter, 'blastnfilter.py')
self.assertEqual(result.proteinligprep, 'proteinligprep.py')
self.assertEqual(result.evaluation, 'evaluate.py')
self.assertEqual(result.makeblastdb, 'makeblastdb')
self.assertEqual(result.genchallenge, 'genchallengedata.py')
self.assertEqual(result.chimeraprep, 'chimera_proteinligprep.py')
self.assertEqual(result.skipimportwait, False)
self.assertEqual(result.importretry, 60)
self.assertEqual(result.importsleep, 600)
self.assertEqual(result.rdkitpython, '')
theargs = [
'foo', '--stage', 'dock,glide', '--email', '[email protected],h@h', '--log',
'ERROR', '--blastnfilter', '/bin/blastnfilter.py',
'--proteinligprep', '/bin/proteinligprep.py', '--postanalysis',
'/bin/postanalysis.py', '--glide', '/bin/glide.py', '--vina',
'/bin/vina.py', '--customweekdir', '--evaluation',
'/bin/evaluation.py', '--makeblastdb', '/bin/makeblastdb',
'--genchallenge', '/bin/gen.py', '--chimeraprep',
'/bin/chimeraprep.py', '--skipimportwait', '--importretry', '10',
'--importsleep', '30', '--rdkitpython', '/usr/bin'
]
result = celpprunner._parse_arguments('hi', theargs)
self.assertEqual(result.stage, 'dock,glide')
self.assertEqual(result.celppdir, 'foo')
self.assertEqual(result.email, '[email protected],h@h')
self.assertEqual(result.loglevel, 'ERROR')
self.assertEqual(result.blastnfilter, '/bin/blastnfilter.py')
self.assertEqual(result.proteinligprep, '/bin/proteinligprep.py')
self.assertEquals(result.postanalysis, '/bin/postanalysis.py')
self.assertEquals(result.glide, '/bin/glide.py')
self.assertEquals(result.evaluation, '/bin/evaluation.py')
self.assertEquals(result.customweekdir, True)
self.assertEqual(result.makeblastdb, '/bin/makeblastdb')
self.assertEqual(result.vina, '/bin/vina.py')
self.assertEqual(result.genchallenge, '/bin/gen.py')
self.assertEqual(result.chimeraprep, '/bin/chimeraprep.py')
self.assertEqual(result.skipimportwait, True)
self.assertEqual(result.importretry, 10)
self.assertEqual(result.importsleep, 30)
self.assertEqual(result.rdkitpython, '/usr/bin')
def test_run_tasks_passing_none_and_empty_list(self):
self.assertEquals(celpprunner.run_tasks(None), 3)
task_list = []
self.assertEquals(celpprunner.run_tasks(task_list), 2)
def test_run_one_successful_task(self):
success_task = DummyTask(D3RParameters(), 'foo', None, True, None,
None)
success_task.set_name('dummy')
task_list = []
task_list.append(success_task)
self.assertEquals(celpprunner.run_tasks(task_list), 0)
def test_run_one_fail_task_with_error_message(self):
task = DummyTask(D3RParameters(), 'foo', 'someerror', True, None, None)
task.set_name('dummy')
task_list = []
task_list.append(task)
self.assertEquals(celpprunner.run_tasks(task_list), 1)
self.assertEquals(task.get_error(), 'someerror')
def test_run_one_fail_task_with_exception_and_no_message(self):
task = DummyTask(D3RParameters(), 'foo', None, True, None,
Exception('hi'))
task.set_name('dummy')
task_list = []
task_list.append(task)
self.assertEquals(celpprunner.run_tasks(task_list), 1)
self.assertEquals(task.get_error(),
'Caught Exception running task: hi')
def test_run_two_tasks_success(self):
task_list = []
task = DummyTask(D3RParameters(), 'foo', None, True, None, None)
task.set_name('dummy')
task_list.append(task)
task_list.append(task)
self.assertEquals(celpprunner.run_tasks(task_list), 0)
self.assertEquals(task._run_count, 2)
def test_run_two_tasks_second_task_has_error(self):
task_list = []
task = DummyTask(D3RParameters(), 'foo', None, True, None, None)
task.set_name('dummy')
task_list.append(task)
task_two = DummyTask(D3RParameters(), 'foo', None, True, None,
Exception('hi'))
task_two.set_name('dummy')
task_list.append(task_two)
self.assertEquals(celpprunner.run_tasks(task_list), 1)
self.assertEquals(task._run_count, 1)
self.assertEquals(task_two._run_count, 1)
self.assertEquals(task_two.get_error(),
'Caught Exception running task: hi')
def test_run_two_tasks_first_task_has_error(self):
task_list = []
task = DummyTask(D3RParameters(), 'foo', None, True, None,
Exception('hi'))
task.set_name('dummy')
task_list.append(task)
task_two = DummyTask(D3RParameters(), 'foo', None, True, None, None)
task_two.set_name('dummy')
task_list.append(task_two)
self.assertEquals(celpprunner.run_tasks(task_list), 1)
self.assertEquals(task.get_error(),
'Caught Exception running task: hi')
self.assertEquals(task._run_count, 1)
self.assertEquals(task_two._run_count, 1)
def test_get_task_list_for_stage_with_invalid_stage_name(self):
try:
celpprunner.get_task_list_for_stage(D3RParameters(), None)
self.fail('Expected exception')
except NotImplementedError as e:
self.assertEquals(e.message, 'stage_name is None')
try:
celpprunner.get_task_list_for_stage(D3RParameters(), '')
self.fail('Expected exception')
except NotImplementedError as e:
self.assertEquals(e.message, 'uh oh no tasks for stage')
try:
celpprunner.get_task_list_for_stage(D3RParameters(), 'foo')
self.fail('Expected exception')
except NotImplementedError as e:
self.assertEquals(e.message, 'uh oh no tasks for foo stage')
def test_get_task_list_for_stage_with_valid_stages(self):
params = D3RParameters()
params.latest_weekly = 'foo'
task_list = celpprunner.get_task_list_for_stage(params, 'blast')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.BLAST_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(
params, 'proteinligprep')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.PROT_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(params, 'import')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.IMPORT_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(params, 'glide')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.GLIDE_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(params, 'vina')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.VINA_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(
params, 'challengedata')
self.assertEquals(len(task_list), 1)
self.assertEquals(task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.CHALL_DIR_NAME))
task_list = celpprunner.get_task_list_for_stage(params, 'chimeraprep')
self.assertEquals(len(task_list), 1)
self.assertEquals(
task_list[0].get_dir(),
os.path.join('foo', TestCelppRunner.CHIMERAPREP_DIR_NAME))
def test_get_task_list_for_stage_createchallenge(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.latest_weekly = temp_dir
task_list = celpprunner.get_task_list_for_stage(
params, celpprunner.CREATE_CHALLENGE)
self.assertEqual(len(task_list), 4)
self.assertEqual(task_list[0].get_name(),
TestCelppRunner.MAKEDB_NAME)
self.assertEqual(task_list[1].get_name(),
TestCelppRunner.IMPORT_NAME)
self.assertEqual(task_list[2].get_name(),
TestCelppRunner.BLAST_NAME)
self.assertEqual(task_list[3].get_name(),
TestCelppRunner.CHALL_NAME)
finally:
shutil.rmtree(temp_dir)
def test_get_task_list_for_stage_for_scoring_stage_with_nonefound(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.latest_weekly = temp_dir
try:
celpprunner.get_task_list_for_stage(params, 'evaluation')
except NotImplementedError as e:
self.assertEqual(e.message,
'uh oh no tasks for evaluation stage')
finally:
shutil.rmtree(temp_dir)
def test_get_task_list_for_stage_for_scoring_stage_with_onefound(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.latest_weekly = temp_dir
glidedir = os.path.join(
temp_dir, EvaluationTaskFactory.DOCKSTAGE_PREFIX + 'glide')
os.mkdir(glidedir)
open(os.path.join(glidedir, D3RTask.COMPLETE_FILE), 'a').close()
task_list = celpprunner.get_task_list_for_stage(
params, 'evaluation')
self.assertEqual(len(task_list), 1)
self.assertEqual(task_list[0].get_name(), 'glide.evaluation')
finally:
shutil.rmtree(temp_dir)
def test_get_task_list_for_stage_for_scoring_stage_with_twofound(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.latest_weekly = temp_dir
glidedir = os.path.join(
temp_dir, EvaluationTaskFactory.DOCKSTAGE_PREFIX + 'glide')
os.mkdir(glidedir)
open(os.path.join(glidedir, D3RTask.COMPLETE_FILE), 'a').close()
freddir = os.path.join(
temp_dir, EvaluationTaskFactory.DOCKSTAGE_PREFIX + 'fred')
os.mkdir(freddir)
open(os.path.join(freddir, D3RTask.COMPLETE_FILE), 'a').close()
task_list = celpprunner.get_task_list_for_stage(
params, 'evaluation')
self.assertEqual(len(task_list), 2)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_no_weekly_datasetfound(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_invalid_stage(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.stage = 'foo'
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
try:
celpprunner.run_stages(theargs)
except NotImplementedError as e:
self.assertEquals(e.message, 'uh oh no tasks for foo stage')
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_stage_data_import_missing(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.stage = 'blast'
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
makedb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.MAKEDB_DIR_NAME)
os.makedirs(makedb_dir)
open(os.path.join(makedb_dir, 'complete'), 'a').close()
self.assertEquals(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast'
theargs.pdbdb = '/pdbdb'
makedb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.MAKEDB_DIR_NAME)
os.makedirs(makedb_dir)
open(os.path.join(makedb_dir, 'complete'), 'a').close()
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, 'complete'), 'a').close()
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_has_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast'
os.mkdir(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME))
open(
os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME,
'error'), 'a').close()
os.mkdir(os.path.join(temp_dir, '2015'))
os.mkdir(os.path.join(temp_dir, '2015', 'dataset.week.1'))
self.assertEqual(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_challenge_and_proteinligprep_no_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'challengedata,proteinligprep'
blastdb_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.BLAST_DIR_NAME)
os.makedirs(blastdb_dir)
open(os.path.join(blastdb_dir, 'complete'), 'a').close()
theargs.proteinligprep = 'echo'
theargs.genchallenge = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_blast_and_proteinligprep_blast_has_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'blast,proteinligprep'
os.mkdir(os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME))
open(
os.path.join(temp_dir, TestCelppRunner.MAKEDB_DIR_NAME,
'complete'), 'a').close()
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, D3RTask.ERROR_FILE), 'a').close()
theargs.blastnfilter = 'echo'
theargs.proteinligprep = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 1)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_makedb_blast_chall_proteinligprep_glide_no_error(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'makedb,blast,challengedata,proteinligprep,glide'
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, D3RTask.COMPLETE_FILE),
'a').close()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
theargs.pdbsequrl = 'file://' + fakegz
theargs.makeblastdb = 'echo'
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
theargs.proteinligprep = 'echo'
theargs.glide = 'echo'
theargs.genchallenge = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_makedb_through_glide(self):
"""This should test the following stages will run
makedb,import,blast,challengedata,proteinligprep,glide,vina
"""
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.celppdir = os.path.join(temp_dir)
theargs.stage = 'makedb,import,blast,challengedata,proteinligprep,' \
'chimeraprep,glide,vina'
d_import_dir = os.path.join(temp_dir, '2015', 'dataset.week.1',
TestCelppRunner.IMPORT_DIR_NAME)
os.makedirs(d_import_dir)
open(os.path.join(d_import_dir, D3RTask.COMPLETE_FILE),
'a').close()
fakegz = os.path.join(temp_dir, 'fake.gz')
f = gzip.open(fakegz, 'wb')
f.write('hello\n')
f.flush()
f.close()
theargs.pdbsequrl = 'file://' + fakegz
theargs.pdbfileurl = 'file://' + fakegz
theargs.compinchi = 'file://' + fakegz
theargs.version = '1.0.0'
theargs.makeblastdb = 'echo'
theargs.blastnfilter = 'echo'
theargs.postanalysis = 'true'
theargs.proteinligprep = 'echo'
theargs.glide = 'echo'
theargs.vina = 'echo'
theargs.genchallenge = 'echo'
theargs.chimeraprep = 'echo'
self.assertEqual(celpprunner.run_stages(theargs), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_task_list_for_stage_extsubmission(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.pdbdb = '/pdbdb'
theargs.latest_weekly = temp_dir
theargs.stage = 'extsubmission'
try:
celpprunner.get_task_list_for_stage(theargs, 'extsubmission')
self.fail('expected NotImplementedError')
except NotImplementedError:
pass
finally:
shutil.rmtree(temp_dir)
def test_run_stages_createweekdir_set(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = os.path.join(temp_dir)
theargs.createweekdir = True
theargs.stage = ''
d = date.today()
celp_week = util.get_celpp_week_of_year_from_date(d)
try:
self.assertEquals(celpprunner.run_stages(theargs), 0)
self.fail('Expected NotImplementedError')
except NotImplementedError:
pass
expected_dir = os.path.join(temp_dir, str(celp_week[1]),
'dataset.week.' + str(celp_week[0]))
self.assertEquals(os.path.isdir(expected_dir), True)
finally:
shutil.rmtree(temp_dir)
def test_run_stages_customweekdir_set(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.celppdir = temp_dir
theargs.customweekdir = True
theargs.createweekdir = True
theargs.stage = ''
try:
self.assertEquals(celpprunner.run_stages(theargs), 0)
self.fail('Expected NotImplementedError')
except NotImplementedError:
pass
finally:
shutil.rmtree(temp_dir)
def tearDown(self):
pass