auto_process_ngs.apps

Utilities for generating and executing command lines to run various command line applications.

Provides the following classes with static methods which will return a Command instance for running a specific command line application:

  • general

For example, to create a Command object representing the command line for a simple mirroring rsync job:

>>> rsync = general.rsync('source','target',mirror=True)
>>> rsync
rsync -av --delete-after source target
>>> rsync.command_line
['rsync', '-av', '--delete-after', 'source', 'target']

The resulting command line string or list can be fed to another function or class, or it can be executed directly via the subprocess module using the ‘run_subprocess’ method of the Command object, e.g:

>>> rsync.run_subprocess()
class auto_process_ngs.apps.general

General command line applications (e.g. rsync, make)

Provides static methods to create Command instances for a class of ‘general’ command line applications:

  • rsync

  • make

  • ssh_command

  • scp

static make(makefile=None, working_dir=None, nprocessors=None)

Generate Command instance for ‘make’ command

Creates a Command instance to run ‘make’.

Parameters:

  • makefile – optional, name of input Makefile (-f)

  • working_dir – optional, specify the working directory to change to (-C)

  • nprocessors – optional, specify number of processors to use (-j)

Returns:

Command object.

static rsync(source, target, dry_run=False, mirror=False, chmod=None, prune_empty_dirs=False, escape_spaces=True, extra_options=None)

Generate Command instance for ‘rsync’ command

Create a Command instance to run the ‘rsync’ command line, to recursively copy/sync one directory (the ‘source’) into another (the ‘target’).

The target can be a local directory or on a remote system (in which case it should be qualified with a user and hostname i.e. ‘user@hostname:target’).

Parameters:

  • source – the directory being copied/sync’ed

  • target – the directory the source will be copied into

  • dry_run – run rsync using –dry-run option i.e. no files will be copied/sync’ed, just reported

  • mirror – if True then run rsync in ‘mirror’ mode i.e. with –delete-after option (to remove files from the target that have also been removed from the source)

  • chmod – optional, mode specification to be applied to the copied files e.g. chmod=’u+rwX,g+rwX,o-w

  • prune_empty_dirs – optional, don’t include empty target directories i.e. -m option

  • escape_spaces – optional, if True then add ‘’ in front of spaces in file name paths to escape them (default)

  • extra_options – optional, a list of additional rsync options to be added to the command (e.g. –include and –exclude filter patterns)

Returns:

Command object.

static scp(user, server, source, target, recursive=False)

Generate Command instance for ‘scp’

Creates a Command instance to run ‘scp’ to copy to another system.

Parameters:

  • user – name of the remote user

  • server – name of the server

  • source – source file on local system

  • target – target destination on remote system

  • recursive – optional, if True then copy source recursively (i.e. specify the ‘-r’ option)

Returns:

Command object.

static ssh_command(user, server, cmd)

Generate Command instance for ‘ssh’ to execute a remote command

Creates a Command instance to run ‘ssh … COMMAND’.

Parameters:

  • user – name of the remote user

  • server – name of the server

  • cmd – command to execute on the server via ssh

Returns:

Command object.