def test_convert_id(self):
ec = Client()
id = 28795402
article = ec.efetch(db='pubmed', id=id)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
self.assertEqual(crud.convert_id(id, 'doi'), '10.1002/ijc.30922')
self.assertEqual(crud.convert_id('10.1002/ijc.30922', 'pmid'), id)
article = ec.efetch(db='pubmed', id=24829965)
for i, a in enumerate(article):
crud.pubmedarticle_to_db(a, 'systematic_reviews')
self.assertEqual(crud.convert_id(24829965, 'doi'), None)
def vote():
"""
vote for a specified trial
@return: success message & updated list of voters for specified trial
"""
if not current_user.is_authenticated:
return "Sorry! This action is only available to logged-in users", 400, {
'ContentType': 'application/json'
}
current_userid = current_user.db_id
data = request.json
if utils.is_doi(data['review']):
# try to retrieve PMID if potenially DOI
data['review'] = crud.convert_id(data['review'], 'pmid')
conn = dblib.create_con(VERBOSE=True)
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
# check if user has already voted for this trial
link_id = crud.get_link_id(data['id'], data['review'])
cur.execute("SELECT * FROM votes WHERE link_id = %s AND user_id = %s;",
(link_id, current_userid))
current = cur.fetchone()
if data['up'] and (not current or
(current and current['vote_type'] == 'down')):
crud.vote(link_id, 'up', current_userid)
if data['down'] and (not current or
(current and current['vote_type'] == 'up')):
crud.vote(link_id, 'down', current_userid)
if current and (data['up'] is False and data['down'] is False) or (
data['up'] is False
and data['down'] == 0) or (data['down'] is False
and data['up'] == 0):
cur.execute("DELETE FROM votes WHERE vote_id = %s;",
(current['vote_id'], ))
conn.commit()
conn.close()
return json.dumps({
'success': True,
'voters': update_voters(data['review'], data['id'])
}), 200, {
'ContentType': 'application/json'
}
def rel_incl():
"""
Move the trial specified in the JSON data from 'relevant' to 'included'
@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
if utils.is_doi(data['review']):
# try to retrieve PMID if potenially DOI
data['review'] = crud.convert_id(data['review'], 'pmid')
link_id = crud.get_link_id(data['nct_id'], data['review'])
crud.change_relationship(link_id, 'included')
return json.dumps({
'success': True,
'message': 'Trial moved successfully'
}), 200, {
'ContentType': 'application/json'
}
def submit_trial():
"""
submit a relevant or included trial for the current article
@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
conn = dblib.create_con(VERBOSE=True)
cur = conn.cursor(cursor_factory=psycopg2.extras.DictCursor)
if data['nct_id'] and data['review']:
# check if the trial exists already
cur.execute("SELECT * FROM tregistry_entries WHERE nct_id =%s;",
(data['nct_id'], ))
trial_reg_data = cur.fetchone()
# if not exists
conn.close()
if not trial_reg_data:
missing = crud.add_missing_trial(data['nct_id'])
if not missing:
conn.close()
return json.dumps({
'success': False,
'message': 'Unable to retrieve trial'
}), 200, {
'ContentType': 'application/json'
}
if utils.is_doi(data['review']):
data['review'] = crud.convert_id(data['review'], 'review_id')
result = crud.check_existing_review_trial(data['review'],
data['nct_id'])
if not result:
crud.review_trial(data['review'], data['nct_id'], False,
data['relationship'], current_user.nickname,
current_user.db_id)
return json.dumps({
'success': True,
'message': 'Added trial successfully',
'data': str(data)
}), 200, {
'ContentType': 'application/json'
}
elif data['relationship'] == result['relationship']:
return json.dumps({
'success': False,
'message': 'Trial already exists',
'move': False
}), 200, {
'ContentType': 'application/json'
}
elif data['relationship'] == 'relevant' and result[
'relationship'] == 'included':
return json.dumps({
'success': False,
'message': 'Trial is already listed as included',
'move': True
}), 200, {
'ContentType': 'application/json'
}
else:
return json.dumps({
'success': False,
'message': 'Trial already in list of relevant trials',
'move': True
}), 200, {
'ContentType': 'application/json'
}
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)