def test_get_all_evaluation_tasks(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# no evaluation tasks
task = PostEvaluationTask(temp_dir, params)
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
# directory in path that does NOT match suffix
task.create_dir()
os.makedirs(os.path.join(temp_dir, 'stage.x.1'), mode=0o755)
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
# one task, but is file (weird case)
weirdtaskfile = os.path.join(
temp_dir, 'stage.7.hi.' + EvaluationTaskFactory.SCORING_SUFFIX)
open(weirdtaskfile, 'a').close()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 0)
self.assertEqual(
task.get_email_log(),
'Just a note, found a task with valid name, but '
'it is not a directory ' + weirdtaskfile)
# one task
etask = EvaluationTask(temp_dir, 'foo.evaluation', None, params)
etask.create_dir()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 1)
self.assertTrue(res[0].get_dir_name(), etask.get_dir_name())
# three tasks two with non complete status
etask2 = EvaluationTask(temp_dir,
'bla_dock.extsubmission.evaluation', None,
params)
etask2.create_dir()
open(os.path.join(etask2.get_dir(), D3RTask.ERROR_FILE),
'a').close()
etask3 = EvaluationTask(temp_dir, '12_x.extsubmission.evaluation',
None, params)
etask3.create_dir()
open(os.path.join(etask3.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
res = task.get_all_evaluation_tasks()
self.assertEqual(len(res), 3)
d_name_list = []
for entry in res:
d_name_list.append(entry.get_dir_name())
self.assertTrue(etask.get_dir_name() in d_name_list)
self.assertTrue(etask2.get_dir_name() in d_name_list)
self.assertTrue(etask3.get_dir_name() in d_name_list)
finally:
shutil.rmtree(temp_dir)
def test_get_evaluation_summary(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
task = EvaluationTask(temp_dir, 'foo', None, params)
# test where no RMSD.txt file is found
val = task.get_evaluation_summary()
self.assertEqual(
val, '\nEvaluation of docking\n'
'=====================\nNo ' + task.get_rmsd_txt() +
' file found.\n')
# test with valid RMSD.txt file
task.create_dir()
f = open(task.get_rmsd_txt(), 'w')
f.write('LMCSS\n1fcz 0.465\n')
f.flush()
f.close()
val = task.get_evaluation_summary()
self.assertEqual(
val, '\nEvaluation of docking\n'
'=====================\n'
'LMCSS\n1fcz 0.465\n\n')
# test where reading RMSD.txt throws exception
os.chmod(task.get_rmsd_txt(), 0)
val = task.get_evaluation_summary()
self.assertTrue(
val.startswith('\nEvaluation of docking\n'
'=====================\n'
'Unable to generate evaluation'
' summary ('))
finally:
shutil.rmtree(temp_dir)
def test_get_external_submitter_email_valid(self):
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask('/foo', dtask.get_name(), dtask, params)
plist = [Participant('1name', '1d3rusername', '12345', '*****@*****.**')]
# try single email address
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emails = emailer._get_external_submitter_email(task)
self.assertEqual(emails[0], '*****@*****.**')
self.assertEqual(len(emails), 1)
self.assertEqual(emailer.get_message_log(), None)
# try multiple email address
plist = [
Participant('1name', '1d3rusername', '12345',
'[email protected],[email protected]')
]
# try single email address
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emails = emailer._get_external_submitter_email(task)
self.assertEqual(emails[0], '*****@*****.**')
self.assertEqual(emails[1], '*****@*****.**')
self.assertEqual(len(emails), 2)
self.assertEqual(emailer.get_message_log(), None)
def test_eval_emailer_get_external_submitter_email_none_from_guid(self):
emailer = EvaluationEmailer(None, None)
params = D3RParameters()
task = EvaluationTask('/foo', None, None, params)
self.assertEqual(emailer._get_external_submitter_email(task), None)
self.assertEqual(emailer.get_message_log(),
'\nUnable to extract guid\n')
def test_run_fails_one_evaluation_and_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.postevaluation = 'false'
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
task.run()
self.assertEqual(
task.get_error(), 'Non zero exit code: 1 received. '
'Standard out: Standard error: ')
self.assertEqual(task.get_status(), D3RTask.ERROR_STATUS)
self.assertTrue(
os.path.isfile(os.path.join(task.get_dir(),
D3RTask.ERROR_FILE)))
self.assertTrue('Caught exception trying to '
'send evaluation email' in task.get_email_log())
stdout_file = os.path.join(task.get_dir(),
'false' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
stderr_file = os.path.join(task.get_dir(),
'false' + D3RTask.STDERR_SUFFIX)
self.assertTrue(os.path.isfile(stderr_file))
finally:
shutil.rmtree(temp_dir)
def test_generate_external_submission_email_body(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('foo')
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
task.create_dir()
emailer = EvaluationEmailer(None, None)
task.set_evaluation_emailer(emailer)
rmsd = task.get_rmsd_txt()
f = open(rmsd, 'w')
f.write(' LMCSS XXX\n1fcz 0.2 0.4\n')
f.flush()
f.close()
subject, body = emailer\
._generate_external_submission_email_body(task)
self.assertEqual(subject,
'[d3rcelpp] Week 0 evaluation results for foo')
self.assertEqual(
body, 'Dear CELPP Participant,\n\nHere are your '
'docking evaluation results '
'(RMSD, Angstroms) '
'for CELPP week '
'0\n\n\nEvaluation of docking'
'\n=====================\n LMCSS XXX\n'
'1fcz 0.2 0.4\n\n\n\nSincerely,\n\n'
'CELPP Automation')
finally:
shutil.rmtree(temp_dir)
def test_send_external_submission_email_success(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.program = 'foo'
params.version = '1'
dtask = D3RTask('/foo', params)
dtask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
task.create_dir()
f = open(task.get_rmsd_txt(), 'w')
f.write('hi\n')
f.flush()
f.close()
plist = [
Participant('1name', '1d3rusername', '12345', '*****@*****.**')
]
# try single email address
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emailer.set_alternate_smtp_emailer(smtpemailer)
emailer.send_evaluation_email(task)
mockserver.quit.assert_any_call()
self.assertEqual(emailer.get_message_log(),
'\nSent evaluation email to: [email protected]\n')
self.assertEqual(mockserver.sendmail.call_count, 1)
finally:
shutil.rmtree(temp_dir)
def test_get_rmsd_pickle(self):
params = D3RParameters()
task = EvaluationTask('/ha', 'foo', None, params)
self.assertEqual(
task.get_rmsd_pickle(),
os.path.join('/ha', task.get_dir_name(),
EvaluationTask.RMSD_PICKLE))
def test_send_external_submission_email_sendmail_exception(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.program = 'foo'
params.version = '1'
dtask = D3RTask('/foo', params)
dtask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
plist = [
Participant('1name', '1d3rusername', '12345', '*****@*****.**')
]
# try single email address
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock(side_effect=IOError('ha'))
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emailer.set_alternate_smtp_emailer(smtpemailer)
emailer.send_evaluation_email(task)
mockserver.quit.assert_any_call()
self.assertEqual(
emailer.get_message_log(),
'\nCaught exception trying to email '
'participant : Caught exception ha\n')
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'true'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(evaluation.get_error(), None)
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(evaluation.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(evaluation.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_evaluation_is_not_found(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = '/bin/doesnotexist'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(
evaluation.get_error(), 'Caught Exception trying to run ' +
'/bin/doesnotexist --pdbdb /data/pdb ' + '--dockdir ' +
docktask.get_dir() + ' --outdir ' + evaluation.get_dir() +
' : [Errno 2] No such file or directory')
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_evaluation_fails(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'false'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(
evaluation.get_error(),
'Non zero exit code: 1 received. Standard out: ' +
' Standard error: ')
# test file gets created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
stderr = os.path.join(evaluation.get_dir(), 'false.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'false.stdout')
self.assertEqual(os.path.isfile(stdout), True)
finally:
shutil.rmtree(temp_dir)
def get_all_evaluation_tasks(self):
"""Look for all evaluation tasks
"""
task_list = []
prefix_len = len(self._eval_task_prefix_str)
base_dir = self.get_path()
for entry in os.listdir(base_dir):
if not entry.endswith('.' + EvaluationTaskFactory.SCORING_SUFFIX):
continue
full_path = os.path.join(base_dir, entry)
if not os.path.isdir(full_path):
logger.info('Suffix matched, but is not directory: ' +
full_path)
self.append_to_email_log('Just a note, found a task ' +
'with valid name, but it is not '
'a directory ' + full_path)
continue
task = EvaluationTask(base_dir, entry[prefix_len:], None,
self.get_args())
task.update_status_from_filesystem()
if task.get_status() != D3RTask.COMPLETE_STATUS:
logger.info('fyi ' + task.get_name() + ' task ' +
' has a status of ' + task.get_status())
task_list.append(task)
return task_list
def test_is_external_submission(self):
params = D3RParameters()
dtask = D3RTask('/ha', params)
task = EvaluationTask('/ha', 'foo', dtask, params)
dtask.set_name('blah')
self.assertEqual(task.is_external_submission(), False)
dtask.set_name('blah' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
self.assertEqual(task.is_external_submission(), True)
def test_send_evaluation_email_not_external_task(self):
emailer = EvaluationEmailer(None, None)
task = EvaluationTask('/foo',
'blah' + EvaluationTask.EXT_SUBMISSION_SUFFIX,
None, D3RParameters())
emailer.send_evaluation_email(task)
self.assertEqual(emailer.get_message_log(),
'\nNot an external submission\n')
def test_get_external_submitter_email_no_participant_email(self):
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('444' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask('/foo', dtask.get_name(), dtask, params)
plist = [Participant('1name', '1d3rusername', '444', None)]
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
self.assertEqual(emailer._get_external_submitter_email(task), None)
self.assertEqual(emailer.get_message_log(),
'\nEmail not set for participant\n')
def test_send_evaluation_email_no_database(self):
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('444' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask('/foo', dtask.get_name(), dtask, params)
emailer = EvaluationEmailer(None, None)
emailer.send_evaluation_email(task)
self.assertEqual(
emailer.get_message_log(),
'\nParticipant database is None cannot send docking '
'evaluation email!!!\n')
def test_evaluationtask_constructor(self):
params = D3RParameters()
# no dock task found so it cannot run
docktask = D3RTask('/blah', params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
evaluation = EvaluationTask('/blah', 'foo.evaluation', docktask,
params)
self.assertEquals(evaluation.get_name(), 'foo.evaluation')
self.assertEquals(evaluation.get_stage(), 7)
def test_get_evaluationdir_args(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# no evaluation tasks
task = PostEvaluationTask(temp_dir, params)
res = task._get_evaluationdir_args()
self.assertEqual(res, '')
# one task
etask = EvaluationTask(temp_dir, 'foo.evaluation', None, params)
etask.create_dir()
res = task._get_evaluationdir_args()
self.assertEqual(
res, ' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask.get_dir())
# three tasks
etask2 = EvaluationTask(temp_dir,
'bla_dock.extsubmission.evaluation', None,
params)
etask2.create_dir()
open(os.path.join(etask2.get_dir(), D3RTask.ERROR_FILE),
'a').close()
etask3 = EvaluationTask(temp_dir, '12_x.extsubmission.evaluation',
None, params)
etask3.create_dir()
cfile = os.path.join(etask3.get_dir(), D3RTask.COMPLETE_FILE)
open(cfile, 'a').close()
res = task._get_evaluationdir_args()
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask.get_dir() in res)
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask2.get_dir() in res)
self.assertTrue(' ' + PostEvaluationTask.EVALUATIONDIR_ARG + ' ' +
etask3.get_dir() in res)
finally:
shutil.rmtree(temp_dir)
def __init__(self, path, args):
super(PostEvaluationTask, self).__init__(path, args)
self.set_name(PostEvaluationTask.TASK_NAME)
et = EvaluationTask('/foo', '', None, None)
self._eval_task_prefix_str = et.get_dir_name()
self._eval_task_suffix_str = (
'' + EvaluationTask.EXT_SUBMISSION_SUFFIX + '.' +
EvaluationTaskFactory.SCORING_SUFFIX + '$|.' +
EvaluationTaskFactory.SCORING_SUFFIX + '$')
self.set_stage(et.get_stage() + 1)
self._emailer = None
self.set_status(D3RTask.UNKNOWN_STATUS)
def test_run_fails_cause_can_run_is_false(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
# return immediately cause can_run is false
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(evaluation.get_error(),
'foo task has notfound status')
finally:
shutil.rmtree(temp_dir)
def test_permute_chains_and_take_min_rmsd(self):
if not (self.has_oechem) or not (self.has_schrodinger):
sys.stdout.write("Missing essential component. Skipping test.")
return
test_scale = 'github'
method_list = ['autodockvina']
try:
temp_dir = tempfile.mkdtemp()
for method in method_list:
params = D3RParameters()
params.evaluation = 'evaluate.py'
params.pdbdb = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/mini_pdb/' %
(test_scale))
docktask = D3RTask(temp_dir, params)
docktask.set_name(method)
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.6.%s/' %
(test_scale, method))
os.system('cp -r %s/* %s' % (source_dir, docktask.get_dir()))
task = EvaluationTask(temp_dir, '%s.evaluation' % (method),
docktask, params)
task.run()
val = task.get_evaluation_summary()
self.assertEqual(
val, '\nEvaluation of docking\n============='
'========\nTarget_PDBID LMCSS '
' SMCSS hiResApo hiResHolo hiTani'
'moto \nNumber_of_cases 0 0'
' 1 0 0 '
'\nAverage '
' 6.452 \nMi'
'nimum 6'
'.452 \nMaximum '
' 6.452 '
' \n5t6d '
' 6.452 '
' \n\n')
self.assertEqual(task.get_error(), None)
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_with_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.evaluation = 'true'
params.pdbdb = '/data/pdb'
docktask = D3RTask(temp_dir, params)
docktask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, docktask.get_name(),
docktask, params)
plist = [
Participant('1name', '1d3rusername', '12345',
'[email protected],[email protected]')
]
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
emailer.set_alternate_smtp_emailer(smtpemailer)
evaluation.set_evaluation_emailer(emailer)
evaluation.run()
self.assertEqual(evaluation.get_error(), None)
# test files get created
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), False)
compfile = os.path.join(evaluation.get_dir(),
D3RTask.COMPLETE_FILE)
self.assertEqual(os.path.isfile(compfile), True)
stderr = os.path.join(evaluation.get_dir(), 'true.stderr')
self.assertEqual(os.path.isfile(stderr), True)
stdout = os.path.join(evaluation.get_dir(), 'true.stdout')
self.assertEqual(os.path.isfile(stdout), True)
res = evaluation.get_email_log().endswith('\nSent evaluation '
'email to: [email protected],'
' [email protected]\n')
self.assertTrue(res)
finally:
shutil.rmtree(temp_dir)
def test_run_fails_cause_evaluation_not_set(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
docktask = D3RTask(temp_dir, params)
docktask.set_name('foo')
docktask.set_stage(EvaluationTaskFactory.DOCKSTAGE)
docktask.create_dir()
open(os.path.join(docktask.get_dir(), D3RTask.COMPLETE_FILE),
'a').close()
evaluation = EvaluationTask(temp_dir, 'foo.evaluation', docktask,
params)
evaluation.run()
self.assertEqual(evaluation.get_error(), 'evaluation not set')
# test files get created
self.assertEqual(os.path.isdir(evaluation.get_dir()), True)
errfile = os.path.join(evaluation.get_dir(), D3RTask.ERROR_FILE)
self.assertEqual(os.path.isfile(errfile), True)
finally:
shutil.rmtree(temp_dir)
def test_send_external_submission_email_no_submitter_email(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.program = 'foo'
params.version = '1'
dtask = D3RTask('/foo', params)
dtask.set_name('12345' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
plist = [
Participant('1name', '1d3rusername', '1234', '*****@*****.**')
]
# try single email address
emailer = EvaluationEmailer(ParticipantDatabase(plist), None)
smtpemailer = SmtpEmailer()
emailer.set_alternate_smtp_emailer(smtpemailer)
emailer.send_evaluation_email(task)
self.assertEqual(emailer.get_message_log(),
'\nNo participant found with guid: 12345\n')
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_one_evaluation_and_no_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
params.postevaluation = 'echo'
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
ctask = ChallengeDataTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
self.assertEqual(task.get_status(), D3RTask.COMPLETE_STATUS)
cfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertTrue(os.path.isfile(cfile))
stdout_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
f = open(stdout_file, 'r')
data = f.read()
f.close()
ctaskdir = os.path.join(ctask.get_dir(),
ctask.get_celpp_challenge_data_dir_name())
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(' --challengedir ' + ctaskdir in data)
self.assertTrue('--stageprefix stage.7. --evaluationsuffix ' +
'.extsubmission.evaluation$|.evaluation$' in data)
stderr_file = os.path.join(task.get_dir(),
'echo' + D3RTask.STDERR_SUFFIX)
self.assertTrue(os.path.isfile(stderr_file))
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 test_get_external_submitter_email_participant_not_found(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()
fac = ParticipantDatabaseFromCSVFactory(csvfile)
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('444' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask(temp_dir, dtask.get_name(), dtask, params)
emailer = EvaluationEmailer(fac.get_participant_database(), None)
self.assertEqual(emailer._get_external_submitter_email(task), None)
self.assertEqual(emailer.get_message_log(),
'\nNo participant found with guid: 444\n')
finally:
shutil.rmtree(temp_dir)
def test_run_succeeds_one_evaluation_with_emailer(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
foo_script = os.path.join(temp_dir, 'foo.py')
f = open(foo_script, 'w')
f.write('#! /usr/bin/env python\n')
f.write('import sys\nimport os\n')
f.write('outdir = sys.argv[1]\n')
f.write('sys.stdout.write(" ".join(sys.argv))\n')
f.write('f = open(os.path.join(outdir, "summary.txt"),"w")\n')
f.write('f.write("summary")\n')
f.write('f.flush()\nf.close()\n')
f.write('f = open(os.path.join(outdir, "yo.csv"), "a")\n')
f.write('f.write("hi")\nf.flush()\nf.close()\n')
f.write('sys.exit(0)\n')
f.flush()
f.close()
os.chmod(foo_script, stat.S_IRWXU)
params.postevaluation = foo_script
etask = EvaluationTask(
temp_dir, 'foo_dock.' + EvaluationTaskFactory.SCORING_SUFFIX,
None, params)
etask.create_dir()
task = PostEvaluationTask(temp_dir, params)
# setup emailer
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
pee = PostEvaluationEmailer(['*****@*****.**'], smtpemailer)
task.set_evaluation_emailer(pee)
ctask = ChallengeDataTask(temp_dir, params)
task.run()
self.assertEqual(task.get_error(), None)
self.assertEqual(task.get_status(), D3RTask.COMPLETE_STATUS)
cfile = os.path.join(task.get_dir(), D3RTask.COMPLETE_FILE)
self.assertTrue(os.path.isfile(cfile))
stdout_file = os.path.join(task.get_dir(),
'foo.py' + D3RTask.STDOUT_SUFFIX)
self.assertTrue(os.path.isfile(stdout_file))
f = open(stdout_file, 'r')
data = f.read()
f.close()
ctaskdir = os.path.join(ctask.get_dir(),
ctask.get_celpp_challenge_data_dir_name())
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(' --challengedir ' + ctaskdir in data)
self.assertTrue('--stageprefix stage.7. --evaluationsuffix ' +
'.extsubmission.evaluation$|.evaluation$' in data)
stderr_file = os.path.join(task.get_dir(),
'foo.py' + D3RTask.STDERR_SUFFIX)
f = open(stdout_file, 'r')
data = f.read()
f.close()
self.assertTrue(' --evaluationdir ' + etask.get_dir() in data)
self.assertTrue(os.path.isfile(stderr_file))
self.assertEqual(task.get_error(), None)
self.assertTrue('Sent post evaluation email to: '
'*****@*****.**' in task.get_email_log())
finally:
shutil.rmtree(temp_dir)
def test_get_guid_for_task(self):
params = D3RParameters()
dtask = D3RTask('/foo', params)
dtask.set_name('123' + EvaluationTask.EXT_SUBMISSION_SUFFIX)
task = EvaluationTask('/foo', dtask.get_name(), dtask, params)
self.assertEqual(task.get_guid_for_task(), '123')