auto_process_ngs.cli.fetch_data

auto_process_ngs.cli.fetch_data.copy_dir_contents(src, dst, replace_spaces=True, flatten=False, overwrite=False)

Copy the contents of one directory into another

Parameters:

  • src (str) – path of source directory

  • dst (str) – path of destination directory

  • replace_spaces (bool) – if True (default) then replace spaces in source names with underscores in the destination names

  • flatten (bool) – if True then don’t replicate the source directory structure (default is to retain the directory structure)

  • overwrite (bool) – if True then replace (i.e. overwrite) existing destination files if an imported file has the same name (default is to skip existing files)

auto_process_ngs.cli.fetch_data.copy_file(src, dst, replace_spaces=True, overwrite=False)

Copy a file

Parameters:

  • src (str) – path of source file

  • dst (str) – path of destination (can be an existing directory or a new file)

  • replace_spaces (bool) – if True (default) then replace spaces in source name with underscores in the destination name

  • overwrite (bool) – if True then replace (i.e. overwrite) existing destination file if the imported file has the same name (default is to skip existing file)

auto_process_ngs.cli.fetch_data.main()

Implements the ‘fetch_data.py’ CLI utility

auto_process_ngs.cli.fetch_data.run_command(cmd, runner, working_dir=None)

Run a command

Given a Command instance, execute that comamnd using the specified job runner.

Parameters:

  • cmd (Command) – the command line to be executed

  • runner (JobRunner) – the job runner to use

  • working_dir (str) – path to the working directory (or None to default to CWD)

Returns:

exit code from the job.

Return type:

Integer

auto_process_ngs.cli.fetch_data.run_rsync(src, dst, runner, working_dir)

Run ‘rsync’ command to copy files and directories

Parameters:

  • src (str) – path of source directory

  • dst (str) – path of destination directory

  • runner (JobRunner) – the job runner to use

  • working_dir (str) – path to the working directory (or None to default to CWD)