def test_change_to_private_multiple_ids(self):
# adding the accession to yml file
with open(GEO_ACCESSIONS_PATH, "a") as my_file:
my_file.write("\n - %s%s" % (self.geo_ids[0], os.linesep))
my_file.write("\n - %s%s" % (self.geo_ids[1], os.linesep))
sql_stmt = """INSERT INTO experiments (accession, status, is_deleted)
VALUES ('%s', 'AE2 Export Complete', 0),
('%s', 'AE2 Export Complete', 0);""" % tuple(
self.ae_ids)
execute_insert(sql_stmt, ae_autosubs_db)
geo.retrieve_study_id_by_acc = mock.Mock(return_value=[{'ID': 12345}])
geo.ConanPage = mock.Mock()
geo.retrieve_plantain_connection = mock.Mock(
return_value=(mock.Mock(), mock.Mock()))
geo.change_to_private(self.email_body_multiple_series,
settings.CONAN_LOGIN_EMAIL)
geo.wait_execution = mock.Mock()
# self.assertTrue(geo.ConanPage.unload_experiment.called)
self.assertTrue(geo.retrieve_plantain_connection.called)
self.assertEqual(retrieve_experiment_status(self.ae_ids[0]),
'Checking failed')
self.assertEqual(retrieve_experiment_status(self.ae_ids[1]),
'Checking failed')
f = open(GEO_ACCESSIONS_PATH, 'r')
txt = f.read()
f.close()
self.assertNotIn(self.geo_ids[0], txt)
self.assertNotIn(self.geo_ids[1], txt)
def wait_for_ae_export(accession):
status = retrieve_experiment_status(accession)
while status != 'AE2 Export Complete':
print status
time.sleep(30)
status = retrieve_experiment_status(accession)
if status in [
'Export failed', 'Checking failed', 'Abandoned',
'** CHECKER CRASH **', 'MAGE-TAB export failed',
'Validation failed'
]:
with LOCK:
REPORT[accession] += 'Failure: Experiment Reset Failed'
print colored.red('Failure: Experiment Reset Failed')
return False
return True
def wait_for_ae_export(accession, exp_dir):
status = retrieve_experiment_status(accession)
while status != 'AE2 Export Complete':
# print status
time.sleep(30)
status = retrieve_experiment_status(accession)
if status in [
'Export failed', 'Checking failed', 'Abandoned',
'** CHECKER CRASH **', 'MAGE-TAB export failed',
'Validation failed'
]:
checker_score = retrieve_checker_score(accession)
if checker_score == 34:
print 'Checker score 34. Exporting'
os.subprocess.call('source %s; reset_experiment.pl -e %s\n' %
(BASH_PATH, exp_dir),
shell=True,
env=dict(ENV=BASH_PATH))
time.sleep(120)
wait_for_ae_export(accession, exp_dir)
else:
print colored.red('Failure: Experiment Reset Failed')
# exit(1)
print colored.green('Export Complete')
def change_to_private(email_body, email_address):
ids = geo_email_parse(email_body)
for geo_id, ae_id in ids.items():
check_url = 'http://ves-hx-69.ebi.ac.uk:8983/solr/analytics/select?q=experimentAccession%3A' + ae_id + '&rows=0&wt=json&indent=true'
# print check_url
r = requests.get(check_url)
# print colored.blue(r.content)
if r.json()['response']['numFound'] > 0:
ATLAS_EXPERIMENTS.append(ae_id)
print 'geo id: ', geo_id, ' AE id: ', ae_id
status = retrieve_experiment_status(ae_id)
remove_geo_accession(geo_id)
if status is None:
print 'Not Imported'
continue
update_experiment_status(ae_id)
if status not in ([
'Checking failed', 'GEO import failed', 'Validation failed',
None
]):
exp = retrieve_study_id_by_acc(ae_id)
if exp and len(exp) > 0:
print colored.green('%s found and unloading starting' % ae_id)
plantain, plantain_ssh = retrieve_plantain_connection()
plantain.send(
'dos2unix /ebi/microarray/home/arrayexpress/ae2_production/data/EXPERIMENT/GEOD/%s*.txt\n'
% ae_id)
wait_execution(plantain)
# conan = ConanPage(url=settings.CONAN_URL)
# conan.login(login_email=email_address)
# conan.unload_experiment(ae_id)
submit_conan_task(accession=ae_id,
pipeline_name=CONAN_PIPELINES.unload)
print '%s unload submitted to Conan' % ae_id
else:
print colored.blue(
'%s not in AE database. It might has been unloaded before.'
% ae_id)
else:
print colored.yellow('%s status is: %s. No need to unload' %
(ae_id, status))
if ATLAS_EXPERIMENTS:
print 'sending email for ', ATLAS_EXPERIMENTS
body = """Dear %s,
The following GEO experiments are turned into private as requested by GEO, and they are found in Atlas.
=======================================================================================================
%s
This email was sent automatically from the AE Automation Tool.
Thank You!
AE Automation Tool.""" % (settings.ATLAS_CONTACT['name'],
'\n'.join(ATLAS_EXPERIMENTS))
send_email(from_email=settings.AUTOMATION_EMAIL,
to_emails=[settings.ATLAS_CONTACT['email']],
subject='GEO to Private Notification',
body=body)
print colored.green('EMAIL SENT')