Utilities for the Terra notebook environment.
Project description
terra-notebook-utils
Utilities for the Terra notebook environment.
-
Fetch a DRS url from a Terra data table:
drs_url = table.fetch_drs_url("data table name", "file name") -
Download a DRS object to your workspace VM file system:
drs.download(drs_url, "file name") -
Copy a DRS object to your workspace bucket:
drs.copy(drs_url, "my_key", bucket=[bucket name])
Credentials
When running in a Terra notebook environment, no user action is required to obtain credentials. For applications outside of the Terra notebook
environment, users should obtain "application default credentials" using the command gcloud auth application-default login.
Testing
The account used to run the test suite should be authorized to access TopMED data through Gen3.
Credentials can be made available by logging in with the command gcloud auth application-default login.
Tests
To run tests,
- log in with your Google credentials using
gcloud auth application-default login, - install requirements with
pip install -r requirements-dev.txt, - run
make testin the package root.
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