hca 3.1.0

Human Cell Atlas Data Storage System Command Line Interface

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 Upload 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 upload --help.

Development

To develop on the CLI, first run pip install -r requirements-dev.txt. You can install your locally modified copy of the hca package by running make install in the repository root directory.

To use the command line interface with a local or test DSS, first run hca (or scripts/hca if you want to use the package in place from the repository root directory). This will create the file ~/.config/hca/config.json, which you can modify to update the value of DSSClient.swagger_url to point to the URL of the Swagger definition served by your DSS deployment. You can also layer a minimal config file on top of the default config.json using the HCA_CONFIG_FILE environment variable, for example:

export SWAGGER_URL="https://dss.staging.data.humancellatlas.org/v1/swagger.json"
jq -n .DSSClient.swagger_url=env.SWAGGER_URL > ~/.config/hca/config.staging.json
export HCA_CONFIG_FILE=~/.config/hca/config.staging.json

To use the Python interface with a local or test DSS, set the host attribute of the API client:

client = hca.dss.DSSClient()
client.host = "https://dss.example.com/v1"
res = client.post_search(...)

Testing

Before you run tests, first run hca dss 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.