CLI tool to allow submitters to upload to and download from the EBI S3 buckets.
Project description
hca-util
This tool is intended to allow HCA wranglers and contributors to upload and download data to/from the HCA S3 bucket.
https://github.com/ebi-ait/hca-util
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 and configure
-
Get the tool from PyPi
$ pip install hca-util -
Run the
hca-utiltool$ hca-util Type ? to list commands hca> -
Run
configcommand specifying your credentialshca> config ACCESS_KEY SECRET_KEY
Step 2 opens an interactive prompt.
Step 3 adds a new hca-util profile to your local AWS configuration which the tool uses.
Use the tool to upload and download data
The following commands are currently possible.
command description
======= ===========
config ACCESS_KEY SECRET_KEY Configure your machine with credentials
create [project_name] [-udx] Create an upload directory for project (authorised user only)
If specified, project name needs to be between 1-36 alphanumeric characters with no space
If specified, allowed permissions include 'u', 'ud', 'ux' and 'udx'; otherwise default 'ux'
u - upload, d - download, x - delete
list List contents of bucket (authorised user only)
list DIR_NAME List contents of directory
select DIR_NAME Set active directory for upload and download
dir Show selected directory
upload F1 [f2] [f3] ... Multi-files upload to selected directory
upload . Upload all files from current user directory
delete F1 [f2] [f3] ... Delete specified file(s) from selected directory
delete . Delete all files from selected directory
delete Delete selected directory (authorised user only)
download F1 [f2] [f3] ... Download specified file(s) from selected directory to local machine
download . Download all files from selected directory to local machine
exit (or quit) Exit the tool. Shorthand: x, q, or Ctrl-D
Type ? or help to list commands.
Type help <command> to display help info about a command.
Note only authorised users (for e.g. wranglers, devs) with their elevated access can create directory and list all directories.
For Developers
Run
python -m hca_util.__main__
Run tests
python -m tests.test_hca_util
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