def customize_citations(self):
# Obtain the parameters.
show_journal_str = request.params['toggle_journal']
show_authors_str = request.params['toggle_authors']
show_keywords_str = request.params['toggle_keywords']
# Obtain the User object (as opposed to the auth.User object).
cur_user = controller_globals._get_user_from_email(
request.environ.get('repoze.who.identity')['user'].email)
# Make changes to the booleans of the user object.
cur_user.show_journal = {"Show": True, "Hide": False}[show_journal_str]
cur_user.show_authors = {"Show": True, "Hide": False}[show_authors_str]
cur_user.show_keywords = {
"Show": True,
"Hide": False
}[show_keywords_str]
# Add the changes to the database.
Session.commit()
# These messages appear in their designated separate locations,
# i.e. on the top left corner of the div that corresponds to this function.
# This is more appropriate than having a general message on some part of the screen.
c.account_msg = ""
c.account_msg_citation_settings = "Citation Settings changes have been applied."
return render("/accounts/account.mako")
def _clear_this_user_locks(self, all_assignments):
priorities_locked_by_this_user = self._get_all_priorities_locked_by_this_user(all_assignments)
for p in priorities_locked_by_this_user:
p.is_out = 0
p.locked_by = None
Session.add(p)
Session.commit()
def _clear_this_user_locks(self, all_assignments):
priorities_locked_by_this_user = self._get_all_priorities_locked_by_this_user(all_assignments)
for p in priorities_locked_by_this_user:
p.is_out = 0
p.locked_by = None
Session.add(p)
Session.commit()
def customize_citations(self):
# Obtain the parameters.
show_journal_str = request.params['toggle_journal']
show_authors_str = request.params['toggle_authors']
show_keywords_str = request.params['toggle_keywords']
# Obtain the User object (as opposed to the auth.User object).
cur_user = controller_globals._get_user_from_email(request.environ.get('repoze.who.identity')['user'].email)
# Make changes to the booleans of the user object.
cur_user.show_journal = {"Show":True, "Hide":False}[show_journal_str]
cur_user.show_authors = {"Show":True, "Hide":False}[show_authors_str]
cur_user.show_keywords = {"Show":True, "Hide":False}[show_keywords_str]
# Add the changes to the database.
Session.commit()
# These messages appear in their designated separate locations,
# i.e. on the top left corner of the div that corresponds to this function.
# This is more appropriate than having a general message on some part of the screen.
c.account_msg = ""
c.account_msg_citation_settings = "Citation Settings changes have been applied."
return render("/accounts/account.mako")
def create_account_handler(self):
'''
Note that the verification goes on in model/form.py.
'''
# create the new user; post to db via sqlalchemy
new_user = model.User()
new_user.username = request.params['username']
new_user.fullname = " ".join(
[request.params['first_name'], request.params['last_name']])
new_user.experience = request.params['experience']
new_user._set_password(request.params['password'])
new_user.email = request.params['email']
# These are for citation settings,
# initialized to True to make everything in the citation visible by default.
new_user.show_journal = True
new_user.show_authors = True
new_user.show_keywords = True
Session.add(new_user)
Session.commit()
# send out an email
greeting_message = """
Hi, %s.\n
Thanks for signing up at abstrackr (%s). You
should be able to sign up now with username %s (only you know your password).
This is just a welcome email to say hello, and that we've got your email.
Should you ever need to reset your password, we'll send you instructions
to this email. In the meantime, happy screening!
-- The Brown EPC.
""" % (new_user.fullname, url('/', qualified=True), new_user.username)
try:
self.send_email_to_user(new_user, "welcome to abstrackr",
greeting_message)
except:
# this almost certainly means we're on our Windows dev box :)
pass
###
# log this user in programmatically (issue #28)
rememberer = request.environ['repoze.who.plugins']['cookie']
identity = {'repoze.who.userid': new_user.username}
response.headerlist = response.headerlist + \
rememberer.remember(request.environ, identity)
rememberer.remember(request.environ, identity)
# if they were originally trying to join a review prior to
# registering, then join them now. (issue #8).
if 'then_join' in request.params and request.params['then_join'] != '':
redirect(
url(controller="review",
action="join",
review_code=request.params['then_join']))
else:
redirect(url(controller="account", action="login"))
def create_account_handler(self):
'''
Note that the verification goes on in model/form.py.
'''
# create the new user; post to db via sqlalchemy
new_user = model.User()
new_user.username = request.params['username']
new_user.fullname = " ".join([request.params['first_name'], request.params['last_name']])
new_user.experience = request.params['experience']
new_user._set_password(request.params['password'])
new_user.email = request.params['email']
# These are for citation settings,
# initialized to True to make everything in the citation visible by default.
new_user.show_journal = True
new_user.show_authors = True
new_user.show_keywords = True
Session.add(new_user)
Session.commit()
# send out an email
greeting_message = """
Hi, %s.\n
Thanks for signing up at abstrackr (%s). You
should be able to sign up now with username %s (only you know your password).
This is just a welcome email to say hello, and that we've got your email.
Should you ever need to reset your password, we'll send you instructions
to this email. In the meantime, happy screening!
-- The Brown EPC.
""" % (new_user.fullname, url('/', qualified=True), new_user.username)
try:
self.send_email_to_user(new_user, "welcome to abstrackr", greeting_message)
except:
# this almost certainly means we're on our Windows dev box :)
pass
###
# log this user in programmatically (issue #28)
rememberer = request.environ['repoze.who.plugins']['cookie']
identity = {'repoze.who.userid': new_user.username}
response.headerlist = response.headerlist + \
rememberer.remember(request.environ, identity)
rememberer.remember(request.environ, identity)
# if they were originally trying to join a review prior to
# registering, then join them now. (issue #8).
if 'then_join' in request.params and request.params['then_join'] != '':
redirect(url(controller="review", action="join", review_code=request.params['then_join']))
else:
redirect(url(controller="account", action="login"))
def import_csv_with_labels(project_id, csv_file_location):
project = Session.query(model.Project).filter_by(id=project_id).first()
with open(csv_file_location) as csv_file:
csv_reader = csv.reader(csv_file, delimiter=',', quotechar='"')
users, assignments = parse_csv_header(next(csv_reader), project)
for row in csv_reader:
parse_csv_row(row, users, assignments, project)
Session.commit()
def change_password(self):
current_user = request.environ.get('repoze.who.identity')['user']
if request.params["password"] == request.params["password_confirm"]:
current_user._set_password(request.params['password'])
Session.commit()
c.account_msg = "ok, your password has been changed."
else:
c.account_msg = "whoops -- the passwords didn't match! try again."
c.account_msg_citation_settings = ""
return render("/accounts/account.mako")
def change_password(self):
current_user = request.environ.get('repoze.who.identity')['user']
if request.params["password"] == request.params["password_confirm"]:
current_user._set_password(request.params['password'])
Session.commit()
c.account_msg = "ok, your password has been changed."
else:
c.account_msg = "whoops -- the passwords didn't match! try again."
c.account_msg_citation_settings = ""
return render("/accounts/account.mako")
def gen_token_to_reset_pwd(self, user):
# generate a random token for the user to reset their password; stick
# it in the database
make_token = lambda N: ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(N))
reset_pwd_q = Session.query(model.ResetPassword)
existing_tokens = [entry.token for entry in reset_pwd_q.all()]
token_length=10
cur_token = make_token(token_length)
while cur_token in existing_tokens:
cur_token = make_code(token_length)
reset = model.ResetPassword()
reset.token = cur_token
reset.user_email = user.email
Session.add(reset)
Session.commit()
return cur_token
def gen_token_to_reset_pwd(self, user):
# generate a random token for the user to reset their password; stick
# it in the database
make_token = lambda N: ''.join(random.choice(string.ascii_uppercase + string.digits) for x in range(N))
reset_pwd_q = Session.query(model.ResetPassword)
existing_tokens = [entry.token for entry in reset_pwd_q.all()]
token_length=10
cur_token = make_token(token_length)
while cur_token in existing_tokens:
cur_token = make_code(token_length)
reset = model.ResetPassword()
reset.token = cur_token
reset.user_email = user.email
Session.add(reset)
Session.commit()
return cur_token
def confirm_password_reset(self, id):
token = str(id)
reset_pwd_q = Session.query(model.ResetPassword)
# we pull all in case they've tried to reset their pwd a few times
# by the way, these should time-expire...
matches = reset_pwd_q.filter(model.ResetPassword.token == token).all()
if len(matches) == 0:
return """
Hrmm... It looks like you're trying to reset your password, but I can't match the provided token.
Please go back to the email that was sent to you and make sure you've copied the URL correctly.
"""
user = controller_globals._get_user_from_email(matches[0].user_email)
for match in matches:
Session.delete(match)
user._set_password(token)
Session.commit()
return '''
ok! your password has been set to %s (you can change it once you've logged in).\n
<a href="%s">log in here</a>.''' % (token, url('/', qualified=True))
def confirm_password_reset(self, id):
token = str(id)
reset_pwd_q = Session.query(model.ResetPassword)
# we pull all in case they've tried to reset their pwd a few times
# by the way, these should time-expire...
matches = reset_pwd_q.filter(model.ResetPassword.token == token).all()
if len(matches) == 0:
return """
Hrmm... It looks like you're trying to reset your password, but I can't match the provided token.
Please go back to the email that was sent to you and make sure you've copied the URL correctly.
"""
user = controller_globals._get_user_from_email(matches[0].user_email)
for match in matches:
Session.delete(match)
user._set_password(token)
Session.commit()
return '''
ok! your password has been set to %s (you can change it once you've logged in).\n
<a href="%s">log in here</a>.''' % (token, url('/', qualified=True))
def _create_reviews(p_id, iter_size, which_iter):
lock_file_path = join(dirname(abspath(__file__)), '_delete_lock.lck')
if not isfile(lock_file_path):
Session.query(
model.Citation).filter(model.Citation.project_id != p_id).delete()
Session.query(
model.Label).filter(model.Label.project_id != p_id).delete()
Session.commit()
open(lock_file_path, 'w+').close()
u_id = 2629
k_init = 400
c_count = len(
Session.query(model.Citation).filter_by(project_id=p_id).all())
k_inc = 100
for itercount in range(iter_size * which_iter,
iter_size * which_iter + iter_size):
### THIS is the code for one run of the experiment
## labeled citation counter
labeled_citation_counter = 0
labels = Session.query(model.Label).filter_by(project_id=p_id).all()
user = Session.query(model.User).filter_by(id=u_id).first()
citations = Session.query(
model.Citation).filter_by(project_id=p_id).all()
print len(citations)
c_count = len(citations)
r_sample = defaultdict(list)
sample_indexes = sample(range(c_count), k_init)
C_r = []
for ii in sample_indexes:
C_r.append(citations[ii])
for cc in C_r:
for ll in Session.query(model.Label).filter_by(
project_id=p_id).filter_by(study_id=cc.id).all():
r_sample[ll.study_id].append(ll)
new_review = model.Project()
new_review.leaders.append(user)
new_review.initial_round_size = 0
new_review.tag_privacy = True
Session.add(new_review)
Session.flush()
state_dict = defaultdict(int)
citation_dict = {}
for c in citations:
citation = model.Citation()
citation.project_id = new_review.id
citation.title = c.title
citation.abstract = c.abstract
citation.keywords = c.keywords
citation.refman = c.refman
model.Session.add(citation)
Session.flush()
citation_dict[citation.id] = c.id
if c.id in r_sample:
labeled_citation_counter += 1
state_dict[citation.id] = 1
for t in r_sample[c.id]:
label = model.Label()
label.project_id = new_review.id
label.study_id = citation.id
label.label = t.label
model.Session.add(label)
print new_review.id
Session.commit()
## i is a counter for the current increment
i = 0
while True:
## we want to change the increment size if there are a certain number of citations is labeled
#if labeled_citation_counter > 15000:
# k_inc = 2000
#elif labeled_citation_counter > 5000:
# k_inc = 1000
#else:
# k_inc = 500
r_sample = defaultdict(list)
print "EXPERIMENT NO: " + str(itercount)
make_predictions(new_review.id)
######################## here's where I record the results
preds_for_review = Session.query(model.Prediction).filter(
model.Prediction.project_id == new_review.id).all()
path_to_preds_out = os.path.join(
"_exports",
"predictions_%d_%d_of_%d.csv" % (p_id, i, itercount))
with open(path_to_preds_out, 'w+') as fout:
csv_out = csv.writer(fout)
preds_file_headers = [
"citation_id", "refman", "title",
"predicted p of being relevant",
"'hard' screening prediction*", "state"
]
csv_out.writerow(preds_file_headers)
sorted_preds = sorted(preds_for_review,
key=lambda x: x.predicted_probability,
reverse=True)
for pred in sorted_preds:
citation = Session.query(model.Citation).filter(
model.Citation.id == pred.study_id).first()
#citation = self._get_citation_from_id(pred.study_id)
citation_title = citation.title.encode('ascii', 'ignore')
row_str = [
citation.id, citation.refman, citation_title,
pred.predicted_probability, pred.prediction,
state_dict[citation.id]
]
csv_out.writerow(row_str)
######################### ---------------------------
i += 1
if labeled_citation_counter >= c_count:
break
P_a = []
for pa in Session.query(model.Prediction).filter_by(
project_id=new_review.id).order_by(
model.Prediction.predicted_probability.desc()).all():
if state_dict[pa.study_id] == 0:
P_a.append(pa)
if len(P_a) == k_inc:
break
if len(P_a) == 0:
print "~~~NO PREDS!!!"
ccc = [
label
for label in Session.query(model.Citation.id).filter_by(
project_id=new_review.id).filter(
~model.Citation.labels.any()).limit(k_inc)
]
print len(ccc)
for cc in ccc:
labeled_citation_counter += 1
state_dict[cc.id] = 1
for ll in Session.query(model.Label).filter_by(
study_id=citation_dict[cc.id]).all():
label = model.Label()
label.project_id = new_review.id
label.study_id = cc.id
label.label = ll.label
model.Session.add(label)
else:
for pp in P_a:
labeled_citation_counter += 1
state_dict[pp.study_id] = 2
for ll in Session.query(
model.Label).filter_by(project_id=p_id).filter_by(
study_id=citation_dict[pp.study_id]).all():
label = model.Label()
label.project_id = new_review.id
label.study_id = pp.study_id
label.label = ll.label
model.Session.add(label)
Session.commit()
print len(
Session.query(
model.Label).filter_by(project_id=new_review.id).all())
return
def _set_assignment_done_status(self, all_assignments):
for a in all_assignments:
b_assignment_done = controller_globals._check_assignment_done(a)
a.done = b_assignment_done
Session.add(a)
Session.commit()
def _set_assignment_done_status(self, all_assignments):
for a in all_assignments:
b_assignment_done = controller_globals._check_assignment_done(a)
a.done = b_assignment_done
Session.add(a)
Session.commit()
not_found = 0
with open(FILE_PATH, 'r') as f:
reader = csv.DictReader(f, delimiter='\t')
for row in reader:
#print(row['id'], row['title'], row['abstract'])
citation = citations_q.filter_by(title=row['title'], project_id=PROJECT_ID).first()
if not citation:
print('could not find title matching with %s' % row['title'])
not_found += 1
else:
found += 1
citation.refman = row['id']
Session.add(citation)
Session.commit()
print("found %s" % found)
print("not found %s" % not_found)
##############################################################################################
### This was for getting PMID's from the titles
#citations_q = Session.query(model.Citation)
#citations = citations_q.filter(model.Citation.pmid == 0).all()
#
#print(len(citations))
#
#for c in citations:
# id = c.id
# title = c.title