def test_send_postevaluation_email_success(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
weekyear = os.path.join(temp_dir, '2017', 'dataset.week.12')
os.makedirs(weekyear, mode=0o755)
task = PostEvaluationTask(weekyear, params)
task.create_dir()
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
pee = PostEvaluationEmailer(['*****@*****.**'], smtpemailer)
task.set_evaluation_emailer(pee)
f = open(task.get_summary_txt(), 'w')
f.write('hello')
f.flush()
f.close()
pee.send_postevaluation_email(task)
mockserver.quit.assert_any_call()
self.assertEqual(pee.get_message_log(),
'\nSent post evaluation email to: [email protected]\n')
self.assertEqual(mockserver.sendmail.call_count, 1)
finally:
shutil.rmtree(temp_dir)
def test_send_postevaluation_email_exception(self):
temp_dir = tempfile.mkdtemp()
try:
params = D3RParameters()
weekyear = os.path.join(temp_dir, '2017', 'dataset.week.12')
os.makedirs(weekyear, mode=0o755)
task = PostEvaluationTask(weekyear, params)
task.create_dir()
csvfile = os.path.join(task.get_dir(), 'foo.csv')
open(csvfile, 'a').close()
smtpemailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock(side_effect=IOError('ha'))
mockserver.quit = Mock()
smtpemailer.set_alternate_smtp_server(mockserver)
pee = PostEvaluationEmailer(['*****@*****.**'], smtpemailer)
task.set_evaluation_emailer(pee)
f = open(task.get_summary_txt(), 'w')
f.write('hello')
f.flush()
f.close()
pee.send_postevaluation_email(task)
mockserver.quit.assert_any_call()
self.assertEqual(
pee.get_message_log(), '\nCaught exception trying to email :'
' [email protected] : Caught exception ha\n')
self.assertEqual(mockserver.sendmail.call_count, 1)
finally:
shutil.rmtree(temp_dir)
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_sending_real_email_but_to_invalid_port_and_host(self):
emailer = SmtpEmailer(port=1231231231232)
try:
emailer.send_email('*****@*****.**', ['*****@*****.**'], 'subby2',
'hi\n')
self.fail('Expected EmailSendError')
except EmailSendError:
pass
def test_smtp_emailer_generate_from_address_using_login_and_host(self):
emailer = SmtpEmailer()
val = emailer._generate_from_address_using_login_and_host()
self.assertEqual(val,
pwd.getpwuid(os.getuid())[0] + '@' + platform.node())
val = emailer._generate_from_address_using_login_and_host(hostname='')
self.assertEqual(val, pwd.getpwuid(os.getuid())[0] + '@localhost')
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_get_server_with_altserver_set_and_login_needed(self):
emailer = SmtpEmailer(user='******', password='******')
mockserver = D3RParameters()
mockserver.login = Mock()
emailer.set_alternate_smtp_server(mockserver)
emailer._get_server()
mockserver.login.assert_called_once_with('bob', 'smith')
def test_send_valid_email_to_fake_server(self):
emailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock()
mockserver.quit = Mock()
emailer.set_alternate_smtp_server(mockserver)
emailer.send_email(['*****@*****.**'], 'subby2', 'hi\n')
mockserver.quit.assert_any_call()
self.assertEqual(mockserver.sendmail.call_count, 1)
def test_send_invalid_email_to_fake_server_that_throws_exception(self):
emailer = SmtpEmailer()
mockserver = D3RParameters()
mockserver.sendmail = Mock(side_effect=IOError('some error'))
mockserver.quit = Mock()
emailer.set_alternate_smtp_server(mockserver)
try:
emailer.send_email(['*****@*****.**'], 'subby2', 'hi\n')
except EmailSendError:
pass
mockserver.quit.assert_any_call()
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_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_append_attachments(self):
temp_dir = tempfile.mkdtemp()
try:
emailer = SmtpEmailer()
# try no attachments
msg_root = MIMEMultipart("alternative")
res = emailer._append_attachments(msg_root, None)
self.assertEqual(msg_root, res)
# try 1 text attachment
txtfile = os.path.join(temp_dir, 'my.txt')
f = open(txtfile, 'w')
f.write('hello')
f.flush()
f.close()
msg_root = MIMEMultipart("alternative")
a = Attachment(txtfile, 'renamed.txt')
res = emailer._append_attachments(msg_root, [a])
res.as_string().index('Content-Type: text/plain; '
'charset="us-ascii"')
res.as_string().index('Content-Disposition: attachment; '
'filename="renamed.txt"')
res.as_string().index('hello')
# try 1 image attachment
img = os.path.join(temp_dir, 'yo.ppm')
f = open(img, 'w')
f.write('P6\n1 1\n255\n')
f.write('%c' % 255)
f.flush()
f.close()
msg_root = MIMEMultipart("alternative")
b = Attachment(img, None)
res = emailer._append_attachments(msg_root, [b])
res.as_string().index('Content-Type: image/x-portable-pixmap')
res.as_string().index('Content-Disposition: attachment; '
'filename="yo.ppm"')
# try 1 gzip attachment
mygz = os.path.join(temp_dir, 'foo.gz')
f = gzip.open(mygz, 'wb')
f.write('some compressed data')
f.flush()
f.close()
c = Attachment(mygz, 'well.gz')
res = emailer._append_attachments(msg_root, [c])
res.as_string().index('Content-Type: application/octet-stream')
res.as_string().index('Content-Disposition: attachment; '
'filename="well.gz"')
# try 3 attachments above together
msg_root = MIMEMultipart("alternative")
res = emailer._append_attachments(msg_root, [a, b, c])
res.as_string().index('Content-Type: text/plain; '
'charset="us-ascii"')
res.as_string().index('Content-Disposition: attachment; '
'filename="renamed.txt"')
res.as_string().index('hello')
res.as_string().index('Content-Type: image/x-portable-pixmap')
res.as_string().index('Content-Disposition: attachment; '
'filename="yo.ppm"')
res.as_string().index('Content-Type: application/octet-stream')
res.as_string().index('Content-Disposition: attachment; '
'filename="well.gz"')
finally:
shutil.rmtree(temp_dir)
def test_get_server_with_altserver_set(self):
emailer = SmtpEmailer()
fake = D3RParameters()
fake.hi = 'fake'
emailer.set_alternate_smtp_server(fake)
self.assertEqual(emailer._get_server().hi, fake.hi)
def _get_smtp_emailer(self):
"""Gets `SmtpEmailer` object or alternate
"""
if self._alt_smtp_emailer is not None:
return self._alt_smtp_emailer
return SmtpEmailer(smtp_host=self._smtp, port=self._smtpport)
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)