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'