Python生物信息学与算法

「工具」loon - 一个懒人适用的远程命令工具箱

2019-11-15  本文已影响0人  王诗翔

相比于 Shell,Python 提供了更好的流程控制,因此,前一段时间我尝试使用 Python 完成了 sync-deploy 命令集的重写(见另一篇文章)。后续新特性的添加都只将在 loon 项目《https://github.com/ShixiangWang/loon》上,sync-deploy 只负责维护异常的修复。

值得一提的是,loon 的使用需要 Python 3的环境以及几个依赖包,所以 sync-deploy 可能更加轻量。


loon is a Python toolkit for operating remote host based on SSH. Idea for developing loon comes from sync-deploy, which is limited by its pure bash code. Therefore, I use Python to implement it and more features will be added to it in the future.

Installation

Install from pypi:

pip install loon

Install from GitHub:

pip install git+https://github.com/ShixiangWang/loon

Usage

Configuration

To access remote host without typing password, you have to generate ssh key with ssh-keygen command if it is not available.

$ ssh-keygen

Follow the commands, for simplicity, just type ENTER to proceed.

Copy your key to remote server, replace user with your username and host with your remote host ip address.

$ ssh-copy-id -i ~/.ssh/id_rsa user@host

Host management

$ loon add -U wsx -H 127.0.0.1 -P 22
=> Added successfully!
# Default port is 22, so don't need to specify it
# And we can create a host alias, otherwise
# it is same as username of remote host
$ loon add -U wsx -H 127.0.0.2 -N host2      
=> Added successfully!
$ loon list
+-----+--------+----------+----+
|Alias|Username|IP address|Port|
+-----+--------+----------+----+
|<wsx>|wsx     |127.0.0.1 |22  |
+-----+--------+----------+----+
|host2|wsx     |127.0.0.2 |22  |
+-----+--------+----------+----+
<active host>
$ loon rename wsx host1
$ loon list
+-------+--------+----------+----+
|Alias  |Username|IP address|Port|
+-------+--------+----------+----+
|<host1>|wsx     |127.0.0.1 |22  |
+-------+--------+----------+----+
|host2  |wsx     |127.0.0.2 |22  |
+-------+--------+----------+----+
<active host>
$ loon switch -N host2
=> Activated.
$ loon list
+-------+--------+----------+----+
|Alias  |Username|IP address|Port|
+-------+--------+----------+----+
|host1  |wsx     |127.0.0.1 |22  |
+-------+--------+----------+----+
|<host2>|wsx     |127.0.0.2 |22  |
+-------+--------+----------+----+
<active host>
$ loon delete -N host2
=> Removing host from available list...
=> Removing active host...
=> Changing active host to host1
$ loon list
+-------+--------+----------+----+
|Alias  |Username|IP address|Port|
+-------+--------+----------+----+
|<host1>|wsx     |127.0.0.1 |22  |
+-------+--------+----------+----+
<active host>

Common tasks

$ loon run 'ls -l ~'
total 168
drwxr-xr-x     2 wsx liulab     25 Apr  7 23:26 bin
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Desktop
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Documents
drwxr-xr-x.    3 wsx liulab     69 Jun 10 16:57 Downloads
drwxr-xr-x     2 wsx liulab      6 Sep 30 10:23 facet
drwxr-xr-x    11 wsx liulab   4096 Sep 22 20:13 metawho
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Music
drwxr-xr-x     3 wsx liulab     60 Apr 30 17:50 Notebooks
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Pictures
drwxr-xr-x     6 wsx liulab    114 Sep 27 17:33 projects
drwxr-xr-x     6 wsx liulab     96 Jun 27 16:50 projects_bk
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Public
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Templates
drwxr-xr-x     5 wsx liulab   4096 Oct  3 12:24 test
drwxr-xr-x  3480 wsx liulab 114688 Oct  3 13:44 tmp
drwxr-xr-x     3 wsx liulab     32 Aug 22 17:13 tools
drwxr-xr-x.    2 wsx liulab      6 Apr  4 10:36 Videos

This will upload scripts to remote host firstly, then run them.

$ loon run -f ../../tests/scripts/t*.py
=> Starting upload...

t1.py                                          100%   50    49.0KB/s   00:00    
t2.py                                          100%   50    77.6KB/s   00:00    

=> Finished uploading in 1s
=> Getting results:
This is t1 script.
This is t2 script.

You can include data directory using --data flag, specify program like bash or python using --prog flag and set remote directory using --dir flag.

Use them like cp command. At default, use scp command to do the job, set --rsync to use rsync command (--rsync is disabled in Windows).

$ loon upload -h
usage: loon upload [-h] [-v] [--rsync] source [source ...] destination

positional arguments:
  source         Source files to upload
  destination    Remote destination directory

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  set loglevel to INFO
  --rsync        Use rsync instead of scp

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  set loglevel to INFO

$ loon download -h
usage: loon download [-h] [-v] [--rsync] source [source ...] destination

positional arguments:
  source         Source files to download
  destination    Local destination directory, note '~' should be quoted in
                 some cases

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  set loglevel to INFO
  --rsync        Use rsync instead of scp

By providing a structed file (CSV, TSV etc) and a sample command with placeholders {index} refer to column index (0 based) of file, batch command can be used to execute a batch of commands. Users can set thread number by -T flag and use --dry flag to dry run the code.

$ loon batch -f src/loon/data/samplefile.csv 'echo hello {0}'
hello TCGA-2A-A8VO-01
hello TCGA-2A-A8VT-01
hello TCGA-2A-A8VV-01
hello TCGA-2A-A8VX-01

$ loon batch -f src/loon/data/samplefile.csv 'echo hello {0}' -T 4
hello TCGA-2A-A8VO-01
hello TCGA-2A-A8VT-01
hello TCGA-2A-A8VV-01
hello TCGA-2A-A8VX-01

$ loon batch -f src/loon/data/samplefile.csv 'echo hello {0}' --dry
=> Running echo hello TCGA-2A-A8VO-01
=> Running echo hello TCGA-2A-A8VT-01
=> Running echo hello TCGA-2A-A8VV-01
=> Running echo hello TCGA-2A-A8VX-01

PBS management and tasks

More details please see -h option of the commands above.

Current usage info

usage: loon [-h] [--version] [--author]
            {add,delete,switch,list,rename,run,upload,download,batch,pbstemp,pbsgen,pbsgen_example,pbssub,pbsdeploy,pbscheck}
            ...

Be an efficient loon.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --author              show info of program's author

subcommands:
  {add,delete,switch,list,rename,run,upload,download,batch,pbstemp,pbsgen,pbsgen_example,pbssub,pbsdeploy,pbscheck}
                        description
    add                 Add a remote host
    delete              Delete a remote host
    switch              Switch active remote host
    list                List all remote hosts
    rename              Rename host alias
    run                 Run commands or scripts on remote
    upload              Upload files to active remote host
    download            Download files from active remote host
    batch               Batch process commands with placeholders
    pbstemp             Generate a PBS template file
    pbsgen              Generate a batch of PBS files
    pbsgen_example      Generate example files for pbsgen command
    pbssub              Submit PBS tasks
    pbsdeploy           Deploy target destination to remote host
    pbscheck            Check status of PBS job on remote host
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