def extract_genes(pmid):
log_it_info('extract_genes', 'BEGIN', str(pmid))
try:
check_for_other_users(current_user.name)
words = model.execute(find_genes_in_abstract(pmid), current_user.name)
feature_name_words = words['features'].keys()
alias_name_words = words['aliases'].keys()
message = 'No genes found.'
feature_message = words['feature_message']
alias_message = words['alias_message']
if feature_message != '' and alias_message != '':
message = feature_message + ', ' + alias_message
elif feature_message != '':
message = feature_message
elif alias_message != '':
message = alias_message
log_it_info('extract_genes', 'SUCCESS')
return_value = json.dumps({'message':message, 'highlight_red':list(alias_name_words), 'highlight_blue':list(feature_name_words)})
return return_value
except Exception as e:
flash(e.message, 'error')
log_it_info('extract_genes', 'FAILURE')
logging.error(e.message)
return 'Error.'
def link_ref(pmid):
try:
check_for_other_users(current_user.name)
if request.method == "POST":
tasks = check_form_validity_and_convert_to_tasks(request.form)
model.execute(link_paper(pmid, tasks), current_user.name, commit=True)
#Link successful
summary = model.execute(get_ref_summary(pmid), current_user.name)
flash("Reference for pmid = " + pmid + " has been added into the database and associated with the following data:<br>" + str(summary), 'success')
except Exception as e:
flash(e.message, 'error')
return redirect(request.args.get("next") or url_for("reference"))
def discard_ref(pmid):
try:
check_for_other_users(current_user.name)
if request.method == "POST":
moved = model.execute(move_reftemp_to_refbad(pmid), current_user.name, commit=True)
if not moved:
raise MoveRefException('An error occurred when deleting the reference for pmid=" + pmid + " from the database.')
#Reference deleted
flash("Reference for pmid=" + pmid + " has been removed from the database.", 'success')
except Exception as e:
flash(e.message, 'error')
return redirect(request.args.get("next") or url_for("reference"))
def reference():
refs=[]
num_of_refs=0
try:
check_for_other_users(current_user.name)
refs = model.execute(get_reftemps(), current_user.name)
num_of_refs = len(refs)
except Exception as e:
flash(str(e), 'error')
return render_template('literature_review.html',
ref_list=refs,
ref_count=num_of_refs,
user=current_user.name)
def extract_genes(pmid):
try:
check_for_other_users(current_user.name)
features = model.execute(find_genes_in_abstract(pmid), current_user.name)
names = []
for feature in features:
if feature.gene_name is not None:
names.append(feature.gene_name)
else:
names.append(feature.name)
if len(names) > 0:
return str(", ".join(names))
else:
return 'No genes found.'
except Exception as e:
flash(e.message, 'error')
return 'Test string'
def discard_ref(pmid):
log_it_info('discard_ref', 'BEGIN', str(pmid))
response = ""
try:
check_for_other_users(current_user.name)
#if request.method == "POST":
moved = model.execute(move_reftemp_to_refbad(pmid), current_user.name, commit=True)
if not moved:
raise MoveRefException('An error occurred when deleting the reference for pmid=" + pmid + " from the database.')
#Reference deleted
response = "Reference for pmid=" + pmid + " has been removed from the database."
log_it_info('discard_ref', 'SUCCESS')
except Exception as e:
response = "Error:<br>" + e.message
log_it_info('discard_ref', 'FAILURE')
logging.error(e.message)
return response
def remove_multiple(pmids):
try:
check_for_other_users(current_user.name)
if request.method == "POST":
to_be_removed = pmids.split('_')
to_be_removed.remove('')
for pmid in to_be_removed:
moved = model.execute(move_reftemp_to_refbad(pmid), current_user.name, commit=True)
if not moved:
raise MoveRefException('An error occurred when deleting the reference for pmid=" + pmid + " from the database.')
#Reference deleted
flash("References for pmids= " + str(to_be_removed) + " have been removed from the database.", 'success')
except Exception as e:
flash(e.message, 'error')
return redirect(request.args.get("next") or url_for("reference"))
def reference():
form = ManyReferenceForms(request.form)
refs=[]
num_of_refs=0
try:
check_for_other_users(current_user.name)
refs = model.execute(get_reftemps(), current_user.name)
for ref in refs:
form.create_reference_form(ref.pubmed_id)
num_of_refs = len(refs)
except Exception as e:
flash(str(e), 'error')
return render_template('literature_review.html',
ref_list=refs,
ref_count=num_of_refs,
form=form)
def link_ref(pmid):
log_it_info('link_ref', 'BEGIN', str(pmid))
response = ""
try:
check_for_other_users(current_user.name)
log_it('check_for_other_users', 'SUCCESS')
#if request.method == "POST":
tasks = check_form_validity_and_convert_to_tasks(request.form)
log_it('check_form_validity_and_convert_to_tasks', 'SUCCESS', str(tasks))
model.execute(link_paper(pmid, tasks), current_user.name, commit=True)
log_it('link_paper', 'SUCCESS')
#Link successful
summary = model.execute(get_ref_summary(pmid), current_user.name)
response = summary
log_it_info('link_ref', 'SUCCESS')
except Exception as e:
response = "Error:<br>" + e.message;
log_it_info('link_ref', 'FAILURE')
return response
def login():
form = LoginForm(request.form)
try:
if request.method == "POST" and form.validate():
username = form.username.data.lower()
password = form.password.data
remember = False
check_for_other_users(username)
logged_in = login_lit_review_user(username, password, model, remember)
if not logged_in:
raise LoginException('Login unsuccessful. Reason unknown.')
#Login successful.
flash("Logged in!", 'login')
current_user.login()
return redirect(request.args.get("next") or url_for("index"))
except Exception as e:
flash(e.message, 'error')
return render_template("login.html", form=form)
