Human Cell Atlas Data Storage System Command Line Interface
Project description
This repository contains a command line interface (CLI) and Python library for interacting with the Data Coordination Platform (DCP) of the Human Cell Atlas (HCA). Currently it allows interaction with the Staging Service and Data Storage Service (DSS).
Installation
pip install hca.
Usage
The hca package installs a command-line utility hca.
To see the list of commands you can use, type hca --help. Commands are grouped into major categories that
roughly correspond to DCP system components, e.g. DSS, Staging Service. To get detailed help for a particular
command group type, e.g. hca dss --help.
When it is necessary to provide a list of things to a command put them in a single string separated with slashes, e.g.
True/Bob/3806d74a-6ab5-4a6d-ba00-667ea858c7b5/2017-06-30T19:33:38+00:00.
Development
To develop on the CLI, first run pip install -r requirements-dev.txt.
To use the command line interface with a local or test DSS, open <directory_holding_hca_module>/hca/api_spec.json.
Change host to the host you want (if you’re running on a local DSS, this will likely be localhost:5000)
and the first argument of schemes should be the scheme you want (http if running locally,
https otherwise).
Code Generation
Some parts of the CLI are auto-generated from the OpenAPI (Swagger) Specifications (OAS). The Python bindings have to be regenerated to reflect any api changes. To regenerate these, run make bindings. Only package maintainers should run this command and publish new package versions.
Testing
Before you run tests, do an hca login. This will pop up a browser and get you to authenticate with Google. Use an email from one of the whitelisted domains (in DSS_SUBSCRIPTION_AUTHORIZED_DOMAINS_ARRAY from here).
Then make test.
Bugs
Please report bugs, issues, feature requests, etc. on GitHub.
License
Licensed under the terms of the MIT License.
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