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
- Basic command-line knowledge
- Python3.x installed on their machine
- Credentials to access data in the S3 bucket (access and secret keys)
Install
Get hca-util from PyPi.
$ pip install hca-utilUsage
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 -o2Use 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> -hSome 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 KeyBy 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