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_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_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_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_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_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_participant_database(self):
pdb = ParticipantDatabase(None)
self.assertEqual(pdb.get_participants(), None)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
pdb = ParticipantDatabase([])
self.assertEqual(len(pdb.get_participants()), 0)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
self.assertEqual(pdb.get_participant_by_guid('bob', exact_match=True),
None)
self.assertEqual(pdb.get_participant_by_guid('guidx'), None)
self.assertEqual(pdb.get_participant_by_guid('xguid'), None)
self.assertEqual(pdb.get_participant_by_guid('GUID'), None)
plist = [
Participant('1name', '1d3rusername', 'guid', '*****@*****.**'),
Participant('2name', '2d3rusername', 'guidy', '*****@*****.**'),
Participant('3name', '3d3rusername', '12345', '*****@*****.**'),
Participant('4name', '4d3rusername', '567890_foo',
'*****@*****.**')
]
pdb = ParticipantDatabase(plist)
self.assertEqual(pdb.get_participant_by_guid(None), None)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
self.assertEqual(pdb.get_participant_by_guid('guidx'), None)
self.assertEqual(pdb.get_participant_by_guid('xguid'), None)
self.assertEqual(pdb.get_participant_by_guid('GUID'), None)
p = pdb.get_participant_by_guid('guid')
self.assertEqual(p.get_name(), '1name')
p = pdb.get_participant_by_guid('guidy')
self.assertEqual(p.get_name(), '2name')
p = pdb.get_participant_by_guid('12345')
self.assertEqual(p.get_name(), '3name')
p = pdb.get_participant_by_guid('12345', exact_match=True)
self.assertEqual(p.get_name(), '3name')
p = pdb.get_participant_by_guid('12345_2')
self.assertEqual(p.get_name(), '3name')
p = pdb.get_participant_by_guid('12345_2', exact_match=False)
self.assertEqual(p.get_name(), '3name')
p = pdb.get_participant_by_guid('12345_mydock', exact_match=False)
self.assertEqual(p.get_name(), '3name')
p = pdb.get_participant_by_guid('12345_my-dock', exact_match=False)
self.assertEqual(p.get_name(), '3name')
# Suffixes can't contain underscores
p = pdb.get_participant_by_guid('12345_my_dock', exact_match=False)
self.assertEqual(p, None)
p = pdb.get_participant_by_guid('12345_2', exact_match=True)
self.assertEqual(p, None)
p = pdb.get_participant_by_guid('12345_2_b')
self.assertEqual(p, None)
# test a longer guid works
p = pdb.get_participant_by_guid('567890_foo')
self.assertEqual(p.get_name(), '4name')
p = pdb.get_participant_by_guid('4567890_foo')
self.assertEqual(p, None)
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.\n")
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)
# Make blastnfilter task
blastnfiltertask = BlastNFilterTask(temp_dir, params)
blastnfiltertask.create_dir()
open(
os.path.join(blastnfiltertask.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.3.'
'blastnfilter/' % test_scale)
os.system('cp -r %s/* %s' %
(source_dir, blastnfiltertask.get_dir()))
# Make challengedata task
challengedatatask = ChallengeDataTask(temp_dir, params)
challengedatatask.create_dir()
open(
os.path.join(challengedatatask.get_dir(),
D3RTask.COMPLETE_FILE), 'a').close()
source_dir = os.path.abspath('tests/celpp/eval_test_data/'
'%s_test_data/stage.4.'
'challengedata/' % test_scale)
os.system('cp -r %s/* %s' %
(source_dir, challengedatatask.get_dir()))
# Make dock task
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()))
print 'docktask.get_dir()', docktask.get_dir()
print 'temp_dir', temp_dir
task = EvaluationTask(temp_dir, '%s.evaluation' % (method),
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)
task.set_evaluation_emailer(emailer)
task.run()
val = task.get_evaluation_summary()
self.assertEqual(
val, '\nEvaluation of docking\n==================='
'==\nTarge'
't_PDBID LMCSS SMCSS '
' h'
'iResApo hiResHolo hiTanimoto '
' '
'LMCSS_ori_distance \n\nSummary Statistics\n'
'\nNumber_of'
'_cases 0 0 '
' 1 '
' 0 0 '
' \nAve'
'rage '
' '
' 6.447 '
' '
' \nMaximum '
' '
' 6.447 '
' '
' \nMinimum '
' '
' 6.447 '
' '
' \nMedian '
' '
' 6.447 '
' '
' \n\nIndividual Results\n'
'\n5t6d '
' '
' 6.44'
'7 (2.176 ) '
' '
' \n\n')
self.assertEqual(task.get_error(), None)
finally:
# pass
shutil.rmtree(temp_dir)
def test_participant_database(self):
pdb = ParticipantDatabase(None)
self.assertEqual(pdb.get_participants(), None)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
pdb = ParticipantDatabase([])
self.assertEqual(len(pdb.get_participants()), 0)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
self.assertEqual(pdb.get_participant_by_guid('guidx'), None)
self.assertEqual(pdb.get_participant_by_guid('xguid'), None)
self.assertEqual(pdb.get_participant_by_guid('GUID'), None)
plist = [
Participant('1name', '1d3rusername', 'guid', '*****@*****.**'),
Participant('2name', '2d3rusername', 'guidy', '*****@*****.**'),
Participant('3name', '3d3rusername', '12345', '*****@*****.**')
]
pdb = ParticipantDatabase(plist)
self.assertEqual(pdb.get_participant_by_guid(None), None)
self.assertEqual(pdb.get_participant_by_guid('bob'), None)
self.assertEqual(pdb.get_participant_by_guid('guidx'), None)
self.assertEqual(pdb.get_participant_by_guid('xguid'), None)
self.assertEqual(pdb.get_participant_by_guid('GUID'), None)
p = pdb.get_participant_by_guid('guid')
self.assertEqual(p.get_name(), '1name')
p = pdb.get_participant_by_guid('guidy')
self.assertEqual(p.get_name(), '2name')
p = pdb.get_participant_by_guid('12345')
self.assertEqual(p.get_name(), '3name')