投递任务命令

命令结构

Usage: bioctl submission [OPTIONS] COMMAND [ARGS]...

Commands:
  submit <workflow_name>     投递工作流
    Options:
        -w, --workspace          （*）指定投递的工作流所在Workspace
        -f, --file               （*）Inputs/outputs File Path
        -m, --datamodel           Datamodel 名称
        --data-model-rows         data-model具体row的id，不输入就是所有id
        --call-caching            是否callcache，默认为true
        -d，--description         投递描述
        
  list   
    Options:
        -w, --workspace   （*）指定投递所在Workspace
        --workflow         指定投递的Workflowm名精确查找
        -p, --page         分页页数，默认为1  
        -s, --size         分页大小，默认为10
        --search-word      submission name/description中模糊匹配
        --status           查询指定状态的投递
        --ids              指定submission id展示特定submission完整信息，包括名称、创建时间、挂载目录
        
  query <submission_id>    查询投递状态，不指定run和task时会返回Run列表
    Options:
        -w, --workspace          （*）指定投递所在Workspace
        -r, --run-id string       查询submission下特定run的状态
        -t, --task-name string    查询submission下特定task的状态

  stop   <submission_id>    终止投递如option指定run运行，则只终止单个运行
    Options:
        -w, --workspace           （*）指定投递所在Workspace
        -r, --run-id string        终止特定run-id的运行

  delete <submission_id>    删除投递历史
    Options:
        -w, --workspace          （*）指定投递所在Workspace
        
  log <submission_id>  查看投递日志,不指定run和task时会列出所有run日志的tos地址
     Options: 
        -w, --workspace        （*）指定投递所在Workspace  
        -r, --run-id string     投递中的具体运行的日志，不指定task时会打印run的日志
        -t, --task-name string  投递中的具体运行的task日志，指定时会打印log，output和error日志的内容
        
  output <submission_id> 查看投递所有输出
     Options: 
        -w, --workspace        （*）指定投递所在Workspace    
        -r, --run-id string     指定投递的具体运行id

命令示例

投递工作流

bioctl submission submit myworkflow -f workflows/myworkflow/myworkflow.inputs.json -m sample -w demo

以下为输入输出文件的json格式

#input/Output json格式
{
  "inputs": {
    "CryoSTARAnalysis.dataset_rel_path": "tutorial_data_1ake/uniform_snr0-0001_ctf",
    "CryoSTARAnalysis.dataset_zip_file": "s3://bioos-dev-wch4ejbdeig44addonemg/tutorial_data_1ake.zip",
    "CryoSTARAnalysis.docker_image": "bioos-dev-cn-beijing.cr.volces.com/infcprelease/lab.drug.cryostar_deploy:1.0.0.3",
    "CryoSTARAnalysis.reconstructAtomic": true,
    "CryoSTARAnalysis.ref_pdb_rel_path": "tutorial_data_1ake/pdbs/1akeA_50.pdb",
    "CryoSTARAnalysis.starfile_rel_path": "tutorial_data_1ake/uniform_snr0-0001_ctf/simulation.star",
    "CryoSTARAnalysis.train_batch_per_gpu": 16,
    "CryoSTARAnalysis.trainer_device": "NVIDIA-A30",
    "CryoSTARAnalysis.trainer_devices_num": 2,
    "CryoSTARAnalysis.trainer_memory": "468G"
  }
}

终止投递

##终止某个投递
bioctl submission stop <submission_id> -w <workspace_name>
##终止某个工作流运行
bioctl submission stop <submission_id> --run_id <run_id> -w <workspace_name>

查询运行状态

bioctl submission query <submission_id> -w <workspace_name>

查询展示如下，每个run对应一个数据实体

+----------+--------------------------+--------------------------------------+------------+
| RunID                                |       StartTime        | Status  |
+----------+--------------------------+--------------------------------------+------------+
| 87546541-f41d-4745-9d1e-4b9b0f27b033     | 2020-10-21T06:34:10.859Z |  Running    |
| cc195aee-41c7-44b0-89e5-4e94ba47f56b     | 2020-10-21T05:52:28.360Z |  Succeeded  |
| 7209675e-4277-4d68-8848-725abca6b143     | 2020-10-21T05:52:08.340Z |  Succeeded  |
| 05ed1979-39d4-41db-8535-446919088a2b     | 2020-10-21T03:50:01.010Z |  Succeeded  |
| b2394c34-9086-441f-af49-02735b5710ed     | 2020-10-21T03:45:40.783Z |  Succeeded  |
+----------+--------------------------+--------------------------------------+------------+

查询运行输出文件

bioctl submission output <submission_id>

输出类似, 如果是字符则显示字符串，如果是文件则提供文件地址

Run rcmnn5sleig4968oearvg: {"CramToBamFlow.outputBai":"s3://bioos-workspaceid/analysis/scmnn5sleig4968oearv0/CramToBamFlow/c2f3e9a6-e640-4809-8d06-9609c774726b/call-CramToBamTask/execution/NA12878.bai","CramToBamFlow.outputBam":"s3://bioos-wcmjk08teig440co6bnr0/analysis/scmnn5sleig4968oearv0/CramToBamFlow/c2f3e9a6-e640-4809-8d06-9609c774726b/call-CramToBamTask/execution/NA12878.bam"}
Run rcmnn5sleig4968oeas00: {"CramToBamFlow.outputBai":"s3://bioos-workspaceid/analysis/scmnn5sleig4968oearv0/CramToBamFlow/d705f98c-0523-4325-9233-8c0fca8ce82b/call-CramToBamTask/execution/my_sample_data.bai","CramToBamFlow.outputBam":"s3://bioos-wcmjk08teig440co6bnr0/analysis/scmnn5sleig4968oearv0/CramToBamFlow/d705f98c-0523-4325-9233-8c0fca8ce82b/call-CramToBamTask/execution/my_sample_data.bam"}