bioqueue.py 文件源码

def get_steps(protocol_id):
    """
    Get steps of a protocol
    :param protocol_id: int, protocol id
    :return: list, list of unresolved steps
    """
    step_list = []

    steps = Protocol.objects.filter(parent=protocol_id).order_by('step_order')
    html_parser = HTMLParser()
    workspace_path = settings['env']['workspace']
    for index, step in enumerate(steps):
        # priority for self-compiled tool
        software_path = os.path.join(os.path.join(os.path.join(workspace_path, str(step.user_id)), 'bin'),
                                     str(step.software))
        if os.path.exists(software_path) and os.path.isfile(software_path):
            step.software = software_path
        step_list.append({
            'id': index,
            'parameter': html_parser.unescape(str(step.software).rstrip() + " " + str(step.parameter)),
            'specify_output': step.specify_output,
            'hash': step.hash,
        })
    return step_list