def test_get_task_list_for_stage_postevaluation(self):
temp_dir = tempfile.mkdtemp()
try:
theargs = D3RParameters()
theargs.latest_weekly = temp_dir
theargs.stage = celpprunner.POST_EVAL
t_list = celpprunner.get_task_list_for_stage(theargs,
theargs.stage)
self.assertEqual(len(t_list), 1)
self.assertEqual(t_list[0].get_name(), 'postevaluation')
# try this time with email set
theargs.email = '[email protected],[email protected]'
t_list = celpprunner.get_task_list_for_stage(theargs,
theargs.stage)
self.assertEqual(len(t_list), 1)
self.assertEqual(t_list[0].get_name(), 'postevaluation')
# try this time with both set
theargs.email = '[email protected],[email protected]'
theargs.summaryemail = '[email protected],[email protected]'
t_list = celpprunner.get_task_list_for_stage(theargs,
theargs.stage)
self.assertEqual(len(t_list), 1)
self.assertEqual(t_list[0].get_name(), 'postevaluation')
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_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_get_task_list_for_stage_for_scoring_stage_with_twofound(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
blasttask = BlastNFilterTask(temp_dir, params)
blasttask.create_dir()
open(os.path.join(blasttask.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
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_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_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_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_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')
