Пример #1
0
    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"))
Пример #2
0
 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()
Пример #3
0
 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()
Пример #4
0
    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"))
Пример #5
0
    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
Пример #6
0
    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
Пример #7
0
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
Пример #8
0
 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()
Пример #9
0
found = 0
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
Пример #10
0
 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()