def get(self):
self.check_admin()
info = self.get_info()
portals = Portal.list_portals()
headers = deepcopy(self.study_cols)
headers.insert(0, "portals")
self.render('portals_edit.html', headers=headers, info=info,
portals=portals, submit_url="/admin/portals/studies/")
def test_add_portal(self):
Portal.create("NEWPORTAL", "SOMEDESC")
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.portal_type")
exp = [[1, 'QIITA', 'QIITA portal. Access to all data stored '
'in database.'],
[2, 'EMP', 'EMP portal'],
[4, 'NEWPORTAL', 'SOMEDESC']]
self.assertItemsEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.analysis_portal")
exp = [[1, 1], [2, 1], [3, 1], [4, 1], [5, 1], [6, 1], [7, 2], [8, 2],
[9, 2], [10, 2], [11, 4], [12, 4], [13, 4], [14, 4]]
self.assertItemsEqual(obs, exp)
with self.assertRaises(QiitaDBDuplicateError):
Portal.create("EMP", "DOESNTMATTERFORDESC")
def post(self):
self.check_admin()
portal = self.get_argument('portal')
studies = map(int, self.get_arguments('selected'))
action = self.get_argument('action')
portal = Portal(portal)
try:
with warnings.catch_warnings(record=True) as warns:
if action == "Add":
portal.add_studies(studies)
elif action == "Remove":
portal.remove_studies(studies)
else:
raise HTTPError(400, "Unknown action: %s" % action)
except QiitaDBError as e:
self.write(action.upper() + " ERROR:<br/>" + str(e))
return
msg = '; '.join([str(w.message) for w in warns])
self.write(action + " completed successfully<br/>" + msg)
def get_info(self, portal="QIITA"):
# Add the portals and, optionally, checkbox to the information
studies = [s.id for s in Portal(portal).get_studies()]
if not studies:
return []
study_info = Study.get_info(studies, info_cols=self.study_cols)
info = []
for s in study_info:
# Make sure in correct order
hold = dict(s)
hold['portals'] = ', '.join(sorted(Study(s['study_id'])._portals))
info.append(hold)
return info
def post(self):
self.check_admin()
portal = self.get_argument('portal')
studies = map(int, self.get_arguments('selected'))
action = self.get_argument('action')
try:
portal = Portal(portal)
except Exception:
raise HTTPError(400, reason="Not valid portal: %s" % portal)
try:
with warnings.catch_warnings(record=True) as warns:
if action == "Add":
portal.add_studies(studies)
elif action == "Remove":
portal.remove_studies(studies)
else:
raise HTTPError(400, reason="Unknown action: %s" % action)
except QiitaDBError as e:
self.write(action.upper() + " ERROR:<br/>" + str(e))
return
msg = '; '.join([str(w.message) for w in warns])
self.write(action + " completed successfully<br/>" + msg)
def test_remove_portal(self):
Portal.create("NEWPORTAL", "SOMEDESC")
# Select some samples on a default analysis
qiita_config.portal = "NEWPORTAL"
a = Analysis(User("*****@*****.**").default_analysis)
a.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
Portal.delete("NEWPORTAL")
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.portal_type")
exp = [[1, 'QIITA', 'QIITA portal. Access to all data stored '
'in database.'],
[2, 'EMP', 'EMP portal']]
self.assertItemsEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.analysis_portal")
exp = [[1, 1], [2, 1], [3, 1], [4, 1], [5, 1], [6, 1], [7, 2], [8, 2],
[9, 2], [10, 2]]
self.assertItemsEqual(obs, exp)
with self.assertRaises(QiitaDBLookupError):
Portal.delete("NOEXISTPORTAL")
with self.assertRaises(QiitaDBError):
Portal.delete("QIITA")
Portal.create("NEWPORTAL2", "SOMEDESC")
# Add analysis to this new portal and make sure error raised
qiita_config.portal = "NEWPORTAL2"
Analysis.create(User("*****@*****.**"), "newportal analysis", "desc")
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL2")
# Add study to this new portal and make sure error raised
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"emp_person_id": StudyPerson(2),
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)
}
Portal.create("NEWPORTAL3", "SOMEDESC")
qiita_config.portal = "NEWPORTAL3"
Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], info)
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL3")
def test_list_portals(self):
obs = Portal.list_portals()
exp = ['EMP']
self.assertEqual(obs, exp)
def setUp(self):
self.study = Study(1)
self.analysis = Analysis(1)
self.qiita_portal = Portal('QIITA')
self.emp_portal = Portal('EMP')
class TestPortal(TestCase):
portal = qiita_config.portal
def setUp(self):
self.study = Study(1)
self.analysis = Analysis(1)
self.qiita_portal = Portal('QIITA')
self.emp_portal = Portal('EMP')
def tearDown(self):
qiita_config.portal = self.portal
def test_list_portals(self):
obs = Portal.list_portals()
exp = ['EMP']
self.assertEqual(obs, exp)
def test_add_portal(self):
Portal.create("NEWPORTAL", "SOMEDESC")
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.portal_type")
exp = [[1, 'QIITA', 'QIITA portal. Access to all data stored '
'in database.'],
[2, 'EMP', 'EMP portal'],
[4, 'NEWPORTAL', 'SOMEDESC']]
self.assertItemsEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.analysis_portal")
exp = [[1, 1], [2, 1], [3, 1], [4, 1], [5, 1], [6, 1], [7, 2], [8, 2],
[9, 2], [10, 2], [11, 4], [12, 4], [13, 4], [14, 4]]
self.assertItemsEqual(obs, exp)
with self.assertRaises(QiitaDBDuplicateError):
Portal.create("EMP", "DOESNTMATTERFORDESC")
def test_remove_portal(self):
Portal.create("NEWPORTAL", "SOMEDESC")
# Select some samples on a default analysis
qiita_config.portal = "NEWPORTAL"
a = Analysis(User("*****@*****.**").default_analysis)
a.add_samples({1: ['1.SKB8.640193', '1.SKD5.640186']})
Portal.delete("NEWPORTAL")
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.portal_type")
exp = [[1, 'QIITA', 'QIITA portal. Access to all data stored '
'in database.'],
[2, 'EMP', 'EMP portal']]
self.assertItemsEqual(obs, exp)
obs = self.conn_handler.execute_fetchall(
"SELECT * FROM qiita.analysis_portal")
exp = [[1, 1], [2, 1], [3, 1], [4, 1], [5, 1], [6, 1], [7, 2], [8, 2],
[9, 2], [10, 2]]
self.assertItemsEqual(obs, exp)
with self.assertRaises(QiitaDBLookupError):
Portal.delete("NOEXISTPORTAL")
with self.assertRaises(QiitaDBError):
Portal.delete("QIITA")
Portal.create("NEWPORTAL2", "SOMEDESC")
# Add analysis to this new portal and make sure error raised
qiita_config.portal = "NEWPORTAL2"
Analysis.create(User("*****@*****.**"), "newportal analysis", "desc")
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL2")
# Add study to this new portal and make sure error raised
info = {
"timeseries_type_id": 1,
"metadata_complete": True,
"mixs_compliant": True,
"number_samples_collected": 25,
"number_samples_promised": 28,
"study_alias": "FCM",
"study_description": "Microbiome of people who eat nothing but "
"fried chicken",
"study_abstract": "Exploring how a high fat diet changes the "
"gut microbiome",
"emp_person_id": StudyPerson(2),
"principal_investigator_id": StudyPerson(3),
"lab_person_id": StudyPerson(1)
}
Portal.create("NEWPORTAL3", "SOMEDESC")
qiita_config.portal = "NEWPORTAL3"
Study.create(User('*****@*****.**'), "Fried chicken microbiome",
[1], info)
qiita_config.portal = "QIITA"
with self.assertRaises(QiitaDBError):
Portal.delete("NEWPORTAL3")
def test_check_studies(self):
with self.assertRaises(QiitaDBError):
self.qiita_portal._check_studies([2000000000000, 122222222222222])
def test_check_analyses(self):
with self.assertRaises(QiitaDBError):
self.qiita_portal._check_analyses([2000000000000, 122222222222222])
with self.assertRaises(QiitaDBError):
self.qiita_portal._check_analyses([8, 9])
def test_get_studies_by_portal(self):
obs = self.emp_portal.get_studies()
self.assertEqual(obs, set())
obs = self.qiita_portal.get_studies()
self.assertEqual(obs, {1})
def test_add_study_portals(self):
self.emp_portal.add_studies([self.study.id])
obs = self.study._portals
self.assertEqual(obs, ['EMP', 'QIITA'])
obs = npt.assert_warns(
QiitaDBWarning, self.emp_portal.add_studies, [self.study.id])
def test_remove_study_portals(self):
with self.assertRaises(ValueError):
self.qiita_portal.remove_studies([self.study.id])
self.emp_portal.add_studies([1])
# Set up the analysis in EMP portal
self.emp_portal.add_analyses([self.analysis.id])
obs = self.analysis._portals
self.assertItemsEqual(obs, ['QIITA', 'EMP'])
# Test study removal failure
with self.assertRaises(QiitaDBError):
self.emp_portal.remove_studies([self.study.id])
obs = self.study._portals
self.assertItemsEqual(obs, ['QIITA', 'EMP'])
# Test study removal
self.emp_portal.remove_analyses([self.analysis.id])
self.emp_portal.remove_studies([self.study.id])
obs = self.study._portals
self.assertEqual(obs, ['QIITA'])
obs = npt.assert_warns(
QiitaDBWarning, self.emp_portal.remove_studies, [self.study.id])
def test_get_analyses_by_portal(self):
obs = self.emp_portal.get_analyses()
self.assertEqual(obs, {7, 8, 9, 10})
obs = self.qiita_portal.get_analyses()
self.assertEqual(obs, {1, 2, 3, 4, 5, 6})
def test_add_analysis_portals(self):
obs = self.analysis._portals
self.assertEqual(obs, ['QIITA'])
with self.assertRaises(QiitaDBError):
self.emp_portal.add_analyses([self.analysis.id])
obs = self.analysis._portals
self.assertEqual(obs, ['QIITA'])
self.emp_portal.add_studies([1])
self.emp_portal.add_analyses([self.analysis.id])
obs = self.analysis._portals
self.assertEqual(obs, ['EMP', 'QIITA'])
obs = npt.assert_warns(
QiitaDBWarning, self.emp_portal.add_analyses, [self.analysis.id])
def test_remove_analysis_portals(self):
with self.assertRaises(ValueError):
self.qiita_portal.remove_analyses([self.analysis.id])
# set up the analysis in EMP portal
self.emp_portal.add_studies([1])
self.emp_portal.add_analyses([self.analysis.id])
obs = self.analysis._portals
self.assertItemsEqual(obs, ['QIITA', 'EMP'])
# Test removal
self.emp_portal.remove_analyses([self.analysis.id])
obs = self.analysis._portals
self.assertEqual(obs, ['QIITA'])
obs = npt.assert_warns(
QiitaDBWarning, self.emp_portal.remove_analyses,
[self.analysis.id])
