예제 #1
0
파일: cli.py 프로젝트: pb-cdunn/pbsmrtpipe
def _args_run_pipeline_id(args):

    registered_tasks_d, registered_files_d, chunk_operators, pipelines = __dynamically_load_all()

    if args.pipeline_id not in pipelines:
        raise ValueError("Unable to find pipeline id '{i}'".format(i=args.pipeline_id))

    pipeline = pipelines[args.pipeline_id]

    if args.debug:
        slog.debug(args)

    ep_d = _cli_entry_point_args_to_dict(args.entry_points)

    force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
    preset_xmls = [os.path.abspath(os.path.expandvars(p)) for p in args.preset_xml]
    preset_jsons = [os.path.abspath(os.path.expandvars(p)) for p in args.preset_json]
    return D.run_pipeline(pipelines, registered_files_d,
                          registered_tasks_d,
                          chunk_operators,
                          pipeline,
                          ep_d, args.output_dir, preset_jsons, preset_xmls,
                          args.preset_rc_xml, args.service_uri,
                          force_distribute=force_distribute,
                          force_chunk_mode=force_chunk)
예제 #2
0
def _args_run_pipeline(args):

    if args.debug:
        slog.debug(args)

    ep_d = _cli_entry_point_args_to_dict(args.entry_points)

    registered_tasks_d, registered_files_d, chunk_operators, pipelines_d = __dynamically_load_all(
    )

    force_distribute, force_chunk = resolve_dist_chunk_overrides(args)

    # Validate all preset files exist
    preset_xmls = [
        os.path.abspath(os.path.expandvars(p)) for p in args.preset_xml
    ]
    return D.run_pipeline(pipelines_d,
                          registered_files_d,
                          registered_tasks_d,
                          chunk_operators,
                          args.pipeline_template_xml,
                          ep_d,
                          args.output_dir,
                          preset_xmls,
                          args.preset_rc_xml,
                          args.service_uri,
                          force_distribute=force_distribute,
                          force_chunk_mode=force_chunk,
                          debug_mode=args.debug)
예제 #3
0
def _args_run_pipeline_id(args):

    registered_tasks_d, registered_files_d, chunk_operators, pipelines = __dynamically_load_all(
    )

    if args.pipeline_id not in pipelines:
        raise ValueError(
            "Unable to find pipeline id '{i}'".format(i=args.pipeline_id))

    pipeline = pipelines[args.pipeline_id]

    if args.debug:
        slog.debug(args)

    ep_d = _cli_entry_point_args_to_dict(args.entry_points)

    force_distribute, force_chunk = resolve_dist_chunk_overrides(args)
    preset_xmls = [
        os.path.abspath(os.path.expandvars(p)) for p in args.preset_xml
    ]
    return D.run_pipeline(pipelines,
                          registered_files_d,
                          registered_tasks_d,
                          chunk_operators,
                          pipeline,
                          ep_d,
                          args.output_dir,
                          preset_xmls,
                          args.preset_rc_xml,
                          args.service_uri,
                          force_distribute=force_distribute,
                          force_chunk_mode=force_chunk)
예제 #4
0
파일: cli.py 프로젝트: yqin22/pbsmrtpipe
def _args_run_pipeline(args):

    if args.debug:
        slog.debug(args)

    ep_d = _cli_entry_point_args_to_dict(args.entry_points)

    registered_tasks_d, registered_files_d, chunk_operators, pipelines_d = __dynamically_load_all()

    force_distribute, force_chunk = resolve_dist_chunk_overrides(args)

    return D.run_pipeline(pipelines_d, registered_files_d, registered_tasks_d, chunk_operators,
                          args.pipeline_template_xml,
                          ep_d, args.output_dir, args.preset_xml, args.preset_rc_xml, args.service_uri,
                          force_distribute=force_distribute, force_chunk_mode=force_chunk, debug_mode=args.debug)
예제 #5
0
파일: cli.py 프로젝트: pb-cdunn/pbsmrtpipe
def _args_run_pipeline(args):

    if args.debug:
        slog.debug(args)

    ep_d = _cli_entry_point_args_to_dict(args.entry_points)

    registered_tasks_d, registered_files_d, chunk_operators, pipelines_d = __dynamically_load_all()

    force_distribute, force_chunk = resolve_dist_chunk_overrides(args)

    # Validate all preset files exist
    preset_xmls = [os.path.abspath(os.path.expandvars(p)) for p in args.preset_xml]
    preset_jsons = [os.path.abspath(os.path.expandvars(p)) for p in args.preset_json]
    return D.run_pipeline(pipelines_d, registered_files_d, registered_tasks_d, chunk_operators,
                          args.pipeline_template_xml,
                          ep_d, args.output_dir, preset_jsons, preset_xmls, args.preset_rc_xml, args.service_uri,
                          force_distribute=force_distribute, force_chunk_mode=force_chunk, debug_mode=args.debug)