def test_get_evaluation_tasks_on_empty_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_participant_database_no_csv_file_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
etf = EvaluationTaskFactory(temp_dir, params)
pdb = etf._get_participant_database()
self.assertEqual(pdb, None)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_with_one_invalid_algo(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
glidedir = os.path.join(
temp_dir, EvaluationTaskFactory.DOCKSTAGE_PREFIX + 'glide')
os.mkdir(glidedir)
open(os.path.join(glidedir, D3RTask.ERROR_FILE), 'a').close()
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_dir_with_webdata_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
os.mkdir(
os.path.join(
temp_dir, EvaluationTaskFactory.DOCKSTAGE_PREFIX +
EvaluationTaskFactory.WEB_DATA_SUFFIX))
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_dir_with_lower_stages_dirs(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dataimport = DataImportTask(temp_dir, params)
blast = BlastNFilterTask(temp_dir, params)
os.mkdir(os.path.join(temp_dir, dataimport.get_dir_name()))
os.mkdir(os.path.join(temp_dir, blast.get_dir_name()))
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_invalid_path(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
path = os.path.join(temp_dir, 'doesnotexist')
stf = EvaluationTaskFactory(path, params)
try:
stf.get_evaluation_tasks()
self.fail('Expected PathNotDirectoryError')
except PathNotDirectoryError:
pass
finally:
shutil.rmtree(temp_dir)
def test_get_participant_database_with_valid_csvfile(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dimport = DataImportTask(temp_dir, params)
dimport.create_dir()
csvfile = dimport.get_participant_list_csv()
f = open(csvfile, 'w')
f.write('name,d3rusername,guid,email\n')
f.write('joe,jj,123,[email protected]\n')
f.flush()
f.close()
etf = EvaluationTaskFactory(temp_dir, params)
pdb = etf._get_participant_database()
p = pdb.get_participant_by_guid('123')
self.assertEqual(p.get_email(), '*****@*****.**')
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_with_two_valid_algo_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
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()
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 2)
self.assertNotEquals(task_list[0].get_name(),
task_list[1].get_name())
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_tasks_on_with_valid_completed_algo_dir(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
glidetask = GlideTask(temp_dir, params)
glidetask.create_dir()
open(os.path.join(glidetask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
etask = EvaluationTask(
temp_dir,
glidetask.get_name() + '.' +
EvaluationTaskFactory.SCORING_SUFFIX, glidetask, params)
etask.create_dir()
open(os.path.join(etask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
stf = EvaluationTaskFactory(temp_dir, params)
task_list = stf.get_evaluation_tasks()
self.assertEquals(len(task_list), 0)
finally:
shutil.rmtree(temp_dir)
def get_task_list_for_stage(theargs, stage_name):
"""Factory method that generates a list of tasks for given stage
Using stage_name get the list of tasks that need to
be run.
:param theargs: parameters set via commandline along with
``theargs.latest_weekly`` which should be set to
to base directory where stages will be run
:param stage_name: Name of stage to run
"""
if stage_name is None:
raise NotImplementedError('stage_name is None')
task_list = []
logger.debug('Getting task list for ' + stage_name)
if stage_name == CREATE_CHALLENGE:
task_list.append(MakeBlastDBTask(theargs.latest_weekly, theargs))
task_list.append(DataImportTask(theargs.latest_weekly, theargs))
task_list.append(BlastNFilterTask(theargs.latest_weekly, theargs))
task_list.append(ChallengeDataTask(theargs.latest_weekly, theargs))
if stage_name == 'makedb':
task_list.append(MakeBlastDBTask(theargs.latest_weekly, theargs))
if stage_name == 'import':
task_list.append(DataImportTask(theargs.latest_weekly, theargs))
if stage_name == 'blast':
task_list.append(BlastNFilterTask(theargs.latest_weekly, theargs))
if stage_name == 'challengedata':
task_list.append(ChallengeDataTask(theargs.latest_weekly, theargs))
if stage_name == 'proteinligprep':
task_list.append(ProteinLigPrepTask(theargs.latest_weekly, theargs))
if stage_name == 'glide':
task_list.append(GlideTask(theargs.latest_weekly, theargs))
if stage_name == 'vina':
task_list.append(AutoDockVinaTask(theargs.latest_weekly, theargs))
if stage_name == CHIMERA_PREP:
task_list.append(
ChimeraProteinLigPrepTask(theargs.latest_weekly, theargs))
if stage_name == 'extsubmission':
extfac = ExternalDataSubmissionFactory(theargs.latest_weekly, theargs)
task_list.extend(extfac.get_external_data_submissions())
if stage_name == 'evaluation':
# use util function call to get all evaluation tasks
# append them to the task_list
eval_task_factory = EvaluationTaskFactory(theargs.latest_weekly,
theargs)
task_list.extend(eval_task_factory.get_evaluation_tasks())
if len(task_list) is 0:
raise NotImplementedError('uh oh no tasks for ' + stage_name +
' stage')
return task_list
def test_evaluationtaskfactory_constructor(self):
params = D3RParameters()
params.hi = True
stf = EvaluationTaskFactory('/foo', params)
self.assertEquals(stf.get_args().hi, True)
self.assertEquals(stf.get_path(), '/foo')