bunch = args.bunch
input_dir, output_dir = Utils.init_paths()
annotators = Utils.annators_name(input_dir)
variable_dict, variable_hash_dict, section_dict= Entities.get_annotators_entities(bunch,
annotators,
input_dir,
t_number=False)
merged_variables, owner_file = Merge.merge_entities(variable_dict)
merged_variables = Entities.sorted_entities(merged_variables)
merged_sections, _ = Merge.merge_entities(section_dict)
merged_variables_hash = Merge.merge_hash(variable_hash_dict)
ctakes_dir = input_dir.replace("input", "ctakes_output")
ctakes_variables, ctakes_variables_hash, ctakes_sections = Entities.get_ctakes_entities(bunch,
ctakes_dir,
t_number=False)
merged_variables, merged_variables_hash, merged_sections = Merge.merge_ctakes_annotators(merged_variables,
merged_variables_hash,
merged_sections,
ctakes_variables,
ctakes_variables_hash,
ctakes_sections)
merged_variables = Entities.sorted_entities(merged_variables)
