covid-util

CLI tool for uploading and downloading files from the EMBL-EBI hosted Embassy cloud infrastructure

PyPi: https://pypi.org/project/covid-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 covid-util from PyPi.

$ pip install covid-util

Usage

Display help

$ covid-util -h
usage: covid-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:

$ covid-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:

$ covid-util <command> -h

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

config command

Configure AWS credentials

$ covid-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 _covid-util_embassy, 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 covid-util profile.

create command

Create an upload area (authorised users only)

$ covid-util create NAME [-p {u,ud,ux,udx}]


positional arguments:
  NAME               name for the new area

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

select command

Select or show the active upload area

$ covid-util select AREA

positional arguments:
  AREA                area uuid. If not present then selected area is shown

list command

List contents of selected area

$ covid-util list [-b]

optional arguments:
  -b                 list all areas in bucket **(authorised users only)**

upload command

Upload files to the selected area

$ covid-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 the selected area

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

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

delete command

Delete files from the selected area

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

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