def create()

in src/main/scripts/model/global_config.py [0:0]

• 40 lines of code
• 10 McCabe index (conditional complexity)

    def create(self, config_json, additional_options, flag_xenome=False, cores_per_sample=4, genome_load=None):
        if not self.workflow:
            print("Workflow name is required")
            sys.exit(2)
        if not self.toolset:
            print("Toolset is required")
            sys.exit(2)
        if not self.template:
            print("Template file is required")
            sys.exit(2)
        if not config_json:
            print("Configuration json file is required")
            sys.exit(2)
        if not cores_per_sample:
            cores_per_sample = 4
        main_dir = os.path.dirname(os.path.realpath(__import__("__main__").__file__))
        config_path = "{}/config_templates/global_config/{}".format(main_dir, config_json)
        if not os.path.exists(config_path):
            raise RuntimeError('Required config json file %s not found' % config_path)
        flag_xenome = "yes" if flag_xenome == "True" or flag_xenome == "true" else "no"
        args_to_json = {"workflow": self.workflow,
                        "species": self.species,
                        "read_type": self.read_type,
                        "toolset": self.toolset,
                        "flag_xenome": flag_xenome,
                        "numthreads": cores_per_sample,
                        "genome_load": genome_load}

        with open(config_path) as file:
            data = json.load(file)
            self.java_path = data['java']
            data.update(args_to_json)
            if additional_options:
                data.update(additional_options)

        env = Environment(loader=FileSystemLoader("{}/config_templates/templates".format(main_dir)), trim_blocks=True,
                          lstrip_blocks=True)
        global_template = env.get_template(self.template)

        with open("global_template_{}.txt".format(self.workflow), "w") as f:
            f.write(global_template.render(data))
            f.close()
        return "{}/global_template_{}.txt".format(os.getcwd(), self.workflow)