hca-util 0.1.3

CLI tool for file transfer (upload and download) to/from AWS S3.

hca-util

CLI tool for file transfer (upload and download) to/from AWS S3.

https://github.com/ebi-ait/hca-util

Users

Prerequisites

Users need to have

1. Basic command-line knowledge
2. Python3.x installed on their machine
3. Credentials to access data in the S3 bucket (access and secret keys)

Install

Get hca-util from PyPi.

$ pip install hca-util

Usage

Display help

$ hca-util -h
usage: hca-util [-h] [--profile PROFILE]
                   {config,create,select,dir,clear,list,upload,download,delete}

In the above, optional arguments are between [] and choices between {}.

The basic usage is as follows:

$ hca-util cmd ARG1 ARG2 -o1 -o2

Use the tool by specifying a command (cmd - see list below) to run, any mandatory (positional) arguments (e.g. ARG1 and ARG2 - see positional args for each command), and any optional arguments (e.g. -o1 and o2 - see options for each command).

List of commands

help for a specific command:

$ hca-util <command> -h

Some commands or options/flags are restricted to authorised users (for e.g. wranglers, admin) only.

config command

Configure AWS credentials

$ hca-util config ACCESS_KEY SECRET_KEY

positional arguments:
  ACCESS_KEY         AWS Access Key ID
  SECRET_KEY         AWS Secret Access Key

By default, this tool looks for and uses the profile name hca-util, if it exists, or it can be set by the config command.

Running a command with the --profile argument uses the specified profile instead of the default hca-util profile.

create command

Create an upload directory (authorised user only)

$ hca-util create [-n name] [-p {u,ud,ux,udx}]

optional arguments:
  -n name            optional project name for new directory
  -p {u,ud,ux,udx}   allowed actions (permissions) on new directory. u for
                     upload, x for delete and d for download. Default is ux

select command

Select active directory

$ hca-util select DIR

positional arguments:
  DIR                directory uuid

dir command

Display active (selected) directory

$ hca-util dir

clear command

Clear current selection

$ hca-util clear [-a]

optional arguments:
  -a          clear all - selection and known dirs

list command

List contents of selected directory

$ hca-util list [-b]

optional arguments:
  -b                 list all directories in bucket **(authorised user only)**

upload command

Upload files to selected directory

$ hca-util upload (-a | -f file [file ...]) [-o]

optional arguments:
  -a                  upload all files from current user directory
  -f file [file ...]  upload specified file(s)
  -o                  overwrite files with same names

download command

Download files from selected directory

$ hca-util download (-a | -f file [file ...])

optional arguments:
  -a                  download all files from selected directory
  -f file [file ...]  download specified file(s) only

delete command

Delete files from selected directory

$ hca-util delete (-a | -f file [file ...] | -d)

optional arguments:
  -a                  delete all files from selected directory
  -f file [file ...]  delete specified file(s) only
  -d                  delete directory and contents **(authorised user only)**

Developers

Run

python -m hca_util.__main__

Run tests

python -m tests.test_hca_util