loon 0.4.2

A Python toolkit for operating remote host based on SSH

loon - A Python toolkit for operating remote host

Description

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

• Add a remote host

$ 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!

• List all remote hosts

$ loon list
+-----+--------+----------+----+
|Alias|Username|IP address|Port|
+-----+--------+----------+----+
|<wsx>|wsx     |127.0.0.1 |22  |
+-----+--------+----------+----+
|host2|wsx     |127.0.0.2 |22  |
+-----+--------+----------+----+
<active host>

• Rename alias

$ 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>

• Switch active remote 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>

• Delete a 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

• Run commands

$ 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

• Run local scripts

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.

• If input contains both files and directories, all files in directory will not be executed. This is a way to include child scripts which does not need to be executed.
• If input is only a directory, all scripts (not including scripts in subdirectories) under it will be executed. This is the way to maintain an independent project.

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

• Upload and download files

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). Note there are some differences between scp and rsync, especially processing directory.

$ 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

• Batch process commands

By providing a structed stdin/file (CSV, TSV etc) and a sample command with placeholders {index} refer to column index (0 based) or column name 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

You can also read the input from pipe.

$ echo "yes,no" | loon batch 'echo {0} is not {1}'
yes is not no

$ cat src/loon/data/samplefile.csv | loon batch 'echo sample {0} has a longer name {1}'
sample TCGA-2A-A8VO-01 has a longer name TCGA-2A-A8VO-01-01
sample TCGA-2A-A8VT-01 has a longer name TCGA-2A-A8VT-01-01
sample TCGA-2A-A8VV-01 has a longer name TCGA-2A-A8VV-01-01
sample TCGA-2A-A8VX-01 has a longer name TCGA-2A-A8VX-01-01

You can also handle header and refer to column names with index or name!

$ cat tests/header.txt | loon batch 'echo hello {0}' 
hello user
hello wsx
hello zd

$ cat tests/header.txt | loon batch 'echo hello {0}' --header
hello wsx
hello zd
$ cat tests/header.txt | loon batch 'echo hello {0}, your score is {1}' --header
hello wsx, your score is 100
hello zd, your score is 100

$ cat tests/header.txt | loon 'echo hello {user}, your score is {score}' --header
hello wsx, your score is 100
hello zd, your score is 100
$ cat tests/header2.txt | loon 'echo hello {user name}, your score is {score}' --header
hello wsx, your score is 100
hello zd, your score is 100

• Generate a batch of (script) files

gen command is similar to the pbsgen command below, but removes the .pbs file extension, so users have to add the file extension in the first column of the SAMPLEFILE if necessary.

The example files can be generated using pbsgen_example.

usage: loon gen [-h] [-v] [-t TEMPLATE] [-s SAMPLEFILE] [-m MAPFILE]
                       [-o OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -v, --verbose         set loglevel to INFO
  -t TEMPLATE, --template TEMPLATE
                        A template file containing placeholders
  -s SAMPLEFILE, --samplefile SAMPLEFILE
                        A csv file containing unique filenames (the first
                        column) and replacing labels
  -m MAPFILE, --mapfile MAPFILE
                        A csv file containing placeholders and column index
                        (0-based) indicating replacing labels in samplefile
  -o OUTPUT, --output OUTPUT
                        Output directory

PBS management and tasks

• 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 - Upload a target directory and submit containing PBS files (have .pbs extension)
• pbscheck - Check status of PBS job on remote host

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

Current usage info

usage: loon [-h] [-V] [--author]
                   {add,delete,switch,list,rename,run,upload,download,gen,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,gen,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
    gen                 Generate a batch of (script) files
    batch               Batch process commands with placeholders
    pbstemp             Generate a PBS template file
    pbsgen              Generate a batch of PBS files (with .pbs extension)
    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

Note

This project has been set up using PyScaffold 3.2.2. For details and usage information on PyScaffold see https://pyscaffold.org/.