def test_complete_studies(self):
ec = Client()
id = 28795402
ncts = [
'NCT00031265', 'NCT02199847', 'NCT00902980', 'NCT01266824',
'NCT03418909'
]
article = ec.efetch(db='pubmed', id=id)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
for n in ncts[:3]:
crud.review_trial(id, n, False, 'included', 'testuser_1', 1)
for n in ncts[3:]:
crud.review_trial(id, n, False, 'relevant', 'testuser_1', 1)
crud.complete_studies(id, True)
metadata = crud.review_medtadata_db(id)
self.assertEqual(metadata['included_complete'], True)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] in ncts[:3]:
self.assertEqual(trials[i]['verified'], True)
self.assertEqual(trials[i]['relationship'], 'included')
if t['nct_id'] in ncts[3:]:
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'relevant')
crud.complete_studies(id, False)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] in ncts[:3]:
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'included')
def test_review_lock_status(self):
ec = Client()
ids = [28616955, 28800192, 28797191]
for id in ids:
self.assertIsNone(crud.review_medtadata_db(id))
article = ec.efetch(db='pubmed', id=ids)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
self.assertEqual(crud.review_lock_status(ids[i]), False)
crud.complete_studies(ids[i], True)
self.assertEqual(crud.review_lock_status(ids[i]), True)
crud.complete_studies(ids[i], False)
self.assertEqual(crud.review_lock_status(ids[i]), False)
def included_complete():
"""
mark the current review as having a complete list of included trials
@return: success/failure message
"""
if not current_user.is_authenticated:
return "Sorry! This action is only available to logged-in users", 400, {
'ContentType': 'application/json'
}
data = request.json
review = data['review_id']
complete = data['value']
crud.complete_studies(review, complete)
return json.dumps({
'success': True,
'message': 'Thanks for verifying!'
}), 200, {
'ContentType': 'application/json'
}
def test_add_trial_to_locked(self):
ec = Client()
ids = [28616955, 28800192, 28797191]
nct_ids = ['NCT00195624', 'NCT00200889', 'NCT00207688']
test_nct = 'NCT00695409'
for id in ids:
self.assertIsNone(crud.review_medtadata_db(id))
article = ec.efetch(db='pubmed', id=ids)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
crud.review_trial(ids[i], nct_ids[i], False, 'included',
'testuser_1', 1, 'up')
crud.complete_studies(ids[i], True)
crud.review_trial(ids[i], test_nct, False, 'included',
'testuser_1', 1, 'up')
self.assertIsNone(
crud.check_existing_review_trial(ids[i], test_nct))
crud.complete_studies(ids[i], False)
crud.review_trial(ids[i], test_nct, False, 'included',
'testuser_1', 1, 'up')
self.assertIsNotNone(
crud.check_existing_review_trial(ids[i], test_nct))
def test_get_locked(self):
ec = Client()
ids = [28569363, 29202845, 28933578]
for id in ids:
self.assertIsNone(crud.review_medtadata_db(id))
article = ec.efetch(db='pubmed', id=ids)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
self.assertIsNone(crud.get_locked())
crud.complete_studies(ids[0], True)
self.assertEqual(crud.get_locked(), [ids[0]])
crud.complete_studies(ids[1], True)
self.assertEqual(crud.get_locked(), [ids[0], ids[1]])
crud.complete_studies(ids[2], True)
self.assertEqual(crud.get_locked(), [ids[0], ids[1], ids[2]])
crud.complete_studies(ids[1], False)
self.assertEqual(crud.get_locked(), [ids[0], ids[2]])
def test_review_trial(self):
ec = Client()
id = 28616955
nct_ids = ['NCT00195624', 'NCT00200889', 'NCT00207688']
article = ec.efetch(db='pubmed', id=id)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
self.assertEqual(len(crud.get_review_trials_fast(id)['reg_trials']), 0)
# trial is inserted with correct values
crud.review_trial(id, nct_ids[0], False, 'relevant', 'testuser_1', 1)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[0]:
self.assertEqual(trials[i]['nct_id'], nct_ids[0])
self.assertEqual(trials[i]['upvotes'], 1)
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['voters'], 'testuser_1')
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'relevant')
# when the trial is added again by another user, it should recieve an upvote
crud.review_trial(id, nct_ids[0], False, 'relevant', 'testuser_2', 2)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[0]:
self.assertEqual(trials[i]['nct_id'], nct_ids[0])
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'testuser_1', 'testuser_2'})
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'relevant')
# adding an existing trial from the relevant column as included will move it
crud.review_trial(id, nct_ids[0], False, 'included', 'testuser_2', 2)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[0]:
self.assertEqual(trials[i]['nct_id'], nct_ids[0])
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'testuser_1', 'testuser_2'})
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'included')
# test included trial
crud.review_trial(id, nct_ids[1], False, 'included', 'testuser_2', 2)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[1]:
self.assertEqual(trials[i]['nct_id'], nct_ids[1])
self.assertEqual(trials[i]['upvotes'], 1)
self.assertEqual(trials[i]['voters'], 'testuser_2')
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'included')
# trying to insert a relevant trial when it's already included will give a vote but not move the trial
crud.review_trial(id, nct_ids[1], False, 'relevant', 'testuser_1', 1)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[1]:
self.assertEqual(trials[i]['nct_id'], nct_ids[1])
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'testuser_1', 'testuser_2'})
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'included')
# except for user_id 17 which can move included to relevant
crud.review_trial(id,
nct_ids[1],
False,
'relevant',
'cochranebot',
17,
vote_type='down')
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[1]:
self.assertEqual(trials[i]['nct_id'], nct_ids[1])
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'cochranebot', 'testuser_1', 'testuser_2'})
self.assertEqual(trials[i]['downvotes'], 1)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'relevant')
# if the review is locked and the trial is included, allow a vote
crud.review_trial(id, nct_ids[2], False, 'included', 'testuser_1', 1)
crud.complete_studies(id, True)
crud.review_trial(id, nct_ids[2], False, 'included', 'testuser_2', 2)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_ids[2]:
self.assertEqual(trials[i]['nct_id'], nct_ids[2])
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'testuser_1', 'testuser_2'})
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], True)
self.assertEqual(trials[i]['relationship'], 'included')