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 refresh_trials(json):
"""
reload & render HTML for trials
@param json: JSON object specifying review_id, which 'type' of trials to refresh, and whether to generate a new plot
"""
id = json['review_id']
type = json['type']
plot_bool = json['plot']
locked = crud.review_lock_status(id)
sort = json['sort'] if 'sort' in json else 'total_votes'
trials = crud.get_review_trials_fast(
id,
order=sort,
usr=current_user if current_user.is_authenticated else None)
relevant = [
trial['nct_id'] for trial in trials['reg_trials']
if trial['relationship'] == 'relevant'
]
verified = [
trial['nct_id'] for trial in trials['reg_trials']
if trial['relationship'] == 'included'
]
if (type == 'rel' and relevant) or (type == 'incl' and verified):
emit('page_content', {
'section':
'rel_trials' if type == 'rel' else 'incl_trials',
'sort':
sort,
'data':
render_template(
'rel_trials.html' if type == 'rel' else 'incl_trials.html',
reg_trials=trials['reg_trials'],
locked=locked)
},
room=request.sid)
if plot_bool:
formatted = utils.trials_to_plotdata(trials['reg_trials'])
socketio.emit('page_content', {
'section': 'plot',
'data': formatted,
'page': 'reviewdetail',
'review_id': id
},
room=request.sid)
elif type == 'incl' and not verified['ids']:
emit('page_content', {
'section':
'incl_trials',
'sort':
sort,
'data':
render_template('incl_trials.html', reg_trials=[], locked=False)
},
room=request.sid)
def test_get_review_trials_fast(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:
crud.review_trial(id, n, False, 'included', 'testuser_1', 1)
trials = crud.get_review_trials_fast(id)['reg_trials']
retrieved_ncts = [t['nct_id'] for t in trials]
for n in ncts:
self.assertTrue(n in retrieved_ncts)
def get_plot():
""" generate new random TSNE plot for homepage """
ids = crud.get_locked()
test_id = random.choice(ids)
review_data = crud.review_medtadata_db(test_id)
trials = crud.get_review_trials_fast(
test_id, usr=current_user if current_user.is_authenticated else None)
return json.dumps({
'success': True,
'data': {
'section': 'plot',
'data': plot.get_tsne_data(trials['reg_trials']),
'page': 'home',
'review_id': test_id,
'title': review_data['title']
}
}), 200, {
'ContentType': 'application/json'
}
def test_vote(self):
ec = Client()
id = 28934560
nct_id = 'NCT00678431'
article = ec.efetch(db='pubmed', id=id)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
crud.review_trial(id, nct_id, False, 'relevant', 'testuser_2', 2)
link_id = crud.get_link_id(nct_id, id)
crud.vote(link_id, 'up', 1)
trials = crud.get_review_trials_fast(id)['reg_trials']
for i, t in enumerate(trials):
if t['nct_id'] == nct_id:
self.assertEqual(trials[i]['nct_id'], nct_id)
self.assertEqual(trials[i]['upvotes'], 2)
self.assertEqual(set(trials[i]['voters'].split(', ')),
{'testuser_2', 'testuser_1'})
self.assertEqual(trials[i]['downvotes'], 0)
self.assertEqual(trials[i]['verified'], False)
self.assertEqual(trials[i]['relationship'], 'relevant')
def search(json):
"""
conduct a search
@param json: JSON object specifying serch keywords
"""
id = json['review_id']
emit('search_update', {'msg': 'Searching...'}, room=request.sid)
eventlet.sleep(0)
if not id:
emit('page_content', {
'section': 'no_results',
'data': render_template('noresults.html', id=id)
},
room=request.sid)
return
conn = dblib.create_con(VERBOSE=True)
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
# try to retrieve review with matching PMID if id is int
review = ''
found = True
if (utils.RepresentsInt(id)):
review = crud.review_medtadata_db(id)
# try to retrieve review with matching DOI if id is DOI
elif utils.is_doi(id):
cur.execute("SELECT * FROM systematic_reviews WHERE doi = %s;", (id, ))
review = cur.fetchone()
conn.close()
# if not int or DOI, return no results page
else:
conn.close()
emit('search_update',
{'msg': 'Searching for keyword matches in our database'},
room=request.sid)
search_result = request_data.advanced_search(id)
if not search_result:
emit('page_content', {
'section': 'no_results',
'data': render_template('noresults.html', id=id)
},
room=request.sid)
return
emit('page_content', {
'section':
'search_results',
'data':
render_template(
'searchresult.html', reviews=search_result, searchterm=id)
},
room=request.sid)
return
# if there is no match in our DB
if review is None:
found = False
if not current_user.is_authenticated:
conn.close()
emit('page_content', {
'section': 'no_results',
'data': render_template('noresults.html', id=id)
},
room=request.sid)
return
emit('search_update', {
'msg': 'Not found in local database. Searching PubMed for article'
},
room=request.sid)
eventlet.sleep(0)
if utils.is_doi(id):
# try to retrieve PMID if DOI
convert = crud.convert_id(id, 'pmid')
if convert:
id = convert
# return no result if no results
else:
emit('search_update', {'msg': 'Not found in Pubmed :('},
room=request.sid)
emit('page_content', {
'section': 'no_results',
'data': render_template('noresults.html', id=id)
},
room=request.sid)
return
# try to retrieve the review from pubmed
ec = Client(api_key=eutils_key)
article = ec.efetch(db='pubmed', id=id)
found_review = None
for art in article:
if art and str(art.pmid) == id:
found_review = art
break
if found_review:
result = found_review.pmid
if not result:
flash(
'Unable to retrieve metadata for this article. Please try again later'
)
abort(404)
emit('search_update',
{'msg': 'Found article on PubMed. Downloading metadata...'},
room=request.sid)
eventlet.sleep(0)
crud.pubmedarticle_to_db(found_review, 'systematic_reviews')
review = crud.review_medtadata_db(id)
emit('page_content', {
'data': render_template('review_data.html', review=review),
'section': 'review_data'
},
room=request.sid)
eventlet.sleep(0)
emit('search_update', {'msg': 'Saved metadata... triggering bots'},
room=request.sid)
bot.docsim.delay(id, sess_id=request.sid)
eventlet.sleep(0)
if 'cochrane' in review['source'].lower() and 'doi' in review:
cb_bb = bot.cochrane_ongoing_excluded.si(review['doi'],
id,
sess_id=request.sid)
cb_bb.link(bot.basicbot2.si(review_id=id, sess_id=request.sid))
chord(
(bot.cochranebot.s(review['doi'], id, sess_id=request.sid),
bot.check_citations.s(id, sess_id=request.sid)),
cb_bb).delay()
else:
chord((bot.check_citations.s(id, sess_id=request.sid)),
bot.basicbot2.si(review_id=id,
sess_id=request.sid)).delay()
else:
print 'no result'
emit('page_content', {
'section': 'no_results',
'data': render_template('noresults.html', id=id)
},
room=request.sid)
return
# if there IS a match in our DB
if found:
print 'emitting found review'
eventlet.sleep(0)
emit('search_update',
{'msg': 'Found review in our database! Retrieving data..'},
room=request.sid)
eventlet.sleep(0)
print 'emitting review content'
emit('page_content', {
'data':
render_template('review_data.html',
review=review,
starred=crud.is_starred(review['review_id'],
current_user.db_id)
if current_user.is_authenticated else False),
'section':
'review_data',
'related_reviews':
render_template('related_reviews.html',
related_reviews=crud.related_reviews(
review['review_id']))
},
room=request.sid)
eventlet.sleep(0)
trials = crud.get_review_trials_fast(
review[0],
usr=current_user if current_user.is_authenticated else None)
relevant = [
trial['nct_id'] for trial in trials['reg_trials']
if trial['relationship'] == 'relevant'
]
verified = [
trial['nct_id'] for trial in trials['reg_trials']
if trial['relationship'] == 'included'
]
emit('search_update', {'msg': 'Generating cool plots...'},
room=request.sid)
eventlet.sleep(0)
formatted = utils.trials_to_plotdata(trials['reg_trials'])
socketio.emit('page_content', {
'section': 'plot',
'data': formatted,
'page': 'reviewdetail',
'review_id': review[0]
},
room=request.sid)
emit('page_content', {
'section':
'rel_trials',
'data':
render_template('rel_trials.html',
reg_trials=trials['reg_trials'],
locked=review['included_complete'])
},
room=request.sid)
eventlet.sleep(0)
if verified:
emit('page_content', {
'section':
'incl_trials',
'data':
render_template('incl_trials.html',
reg_trials=trials['reg_trials'],
locked=review['included_complete'])
},
room=request.sid)
eventlet.sleep(0)
else:
emit('page_content', {
'section':
'incl_trials',
'data':
render_template(
'incl_trials.html', reg_trials=[], locked=False)
},
room=request.sid)
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')