dbio-cli 1.0.0

Installation

pip install dbio.

Usage

Documentation on readthedocs.io:

• CLI documentation

• Python API documentation

To see the list of commands you can use, type dbio --help.

Development

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

To use the command line interface with a local or test DSS, first run dbio (or scripts/dbio if you want to use the package in-place from the repository root directory). This will create the file ~/.config/dbio/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. Lastly, the CLI enforces HTTPS connection to the DSS API. If you are connecting to a local DSS, make this change in dbio/util/__init__.py in the SwaggerClient object:

scheme = "http"

To use the Python interface with a local or test DSS, pass the URL of the Swagger definition to the DSSClient constructor via the swagger_url parameter:

client = DSSClient(swagger_url="https://dss.example.com/v1/swagger.json")

You can also layer a minimal config file on top of the default config.json using the DBIO_CONFIG_FILE environment variable, for example:

export SWAGGER_URL="https://dss.dev.ucsc-cgp-redwood.org/v1/swagger.json"
jq -n .DSSClient.swagger_url=env.SWAGGER_URL > ~/.config/dbio/config.staging.json
export DBIO_CONFIG_FILE=~/.config/dbio/config.staging.json

Testing

Before you run tests, first run dbio dss login. This will open a browser where you can log in to authenticate with Google. Use an email address from one of the whitelisted domains (in DSS_SUBSCRIPTION_AUTHORIZED_DOMAINS_ARRAY from here).

Then make test.

Primary CI testing is through Travis CI on the Gitlab toilspark instance.

Security Policy

Please email reports about any security related issues you find to team-redwood@ucsc.edu. Use a descriptive subject line for your report email. In addition, please include the following information along with your report:

• Your name and affiliation (if any).

• A description of the technical details of the vulnerabilities, to help us reproduce your findings.

• An explanation of who can exploit this vulnerability, and what they gain when doing so (an attack scenario).

• Whether this vulnerability is public or known to third parties. If so, please provide details.

License

Licensed under the terms of the MIT License.