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 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'
