pyAnVIL 0.0.6rc3

AnVIL client library. Combines gen3, terra client APIs with single signon and data harmonization use cases.

pyAnVIL: terra + gen3

A python client integration of gen3 and terra.

For python developers, who have requirements to access both terra and gen3 platforms, pyAnVIL is an integration module that provides SSO (single sign on) using terra as an IDP (identity provider) and manages distribution of dependencies unlike juggling multiple credentials and installs, pyAnVIL provides developer friendly experience.

Installation

Pre-requisites:

• gcloud cli tools installed and configured gcloud.

• Google Id provisioned in both Terra and Gen3:

  • One time Account Linking:
    • Pre-requisite: google account provisioned in both Gen3 and Terra.
    • Log into https://gen3.theanvil.io/
    • Log into https://anvil.terra.bio
    • In Terra, navigate to your profile
      • Under "IDENTITY & EXTERNAL SERVERS", log into NHGRI AnVIL Data Commons Framework Services, the system should present you with a Gen3 Oauth flow.
      • Note the google project used for billing

• Per instance, terra API setup:

  • Use the google account and billing project to setup credentials for the terra api.

      gcloud auth login <google-account>
      gcloud auth application-default set-quota-project <billing-project-id>
    

• Validation

  gcloud auth print-access-token
  >>> ya29.a0AfH6SMBSPFSt252qQNl.......
  
  fissfc config
  >>> ....
  root_url	https://broad-bond-prod.appspot.com/
  

• Setup

  pip install pyAnVIL
  

Use cases

SSO

   from anvil.gen3_auth import Gen3TerraAuth
   from gen3.submission import Gen3Submission

   auth = Gen3TerraAuth()
   gen3_endpoint = "https://gen3.theanvil.io"
   submission_client = Gen3Submission(gen3_endpoint, auth)

sso sequence diagram

API Wrappers

Gen3

   query = '{project(first:0) {code,  subjects {submitter_id}, programs {name}  }}'
   results = submission_client.query(query)
   [p['code'] for p in results['data']['project']]
   >>> ['GTEx', '1000Genomes']

Terra

   from anvil.terra import FAPI
   FAPI.whoami()
   >>> '[e-mail]'

Terra utilities

   from anvil.terra.api import get_projects
   projects = get_projects(namespaces=['anvil-datastorage'], project_pattern='AnVIL_CCDG.*')
   [p['workspace']['name'] for p in projects]
   >>> ['AnVIL_CCDG_WashU_CVD_EOCAD_BioMe_WGS',
        'AnVIL_CCDG_Broad_CVD_EOCAD_TaiChi_WGS',
        'AnVIL_CCDG_Broad_AI_IBD_Brant_DS-IBD_WGS', ...]

Data Dashboard

notebook example

Configuration

The following environment variable can be set in order to configure library functionality

environment	example	default	description
PYANVIL_CACHE_PATH	db.sqlite3	/tmp/pyanvil-cache.sqlite	Configure where you want the pyAnVIL cache to be

Contributing

• set up virtual env

  python3 -m venv venv
  source venv/bin/activate
  python3 -m pip install -r requirements.txt
  python3 -m pip install -r requirements-dev.txt
  

• test gen3 authorization

  python3 -m pytest --user_email <GMAIL ACCOUNT>  --log-level DEBUG  --gen3_endpoint <GEN3_ENDPOINT>  tests/integration/test_gen3_auth.py
  

• continuous integration

  • see service account setup

     # see https://github.com/broadinstitute/firecloud-tools/tree/master/scripts/register_service_account
     docker run --rm -it -v "$HOME"/.config:/.config -v /Users/walsbr/client-apis/pyAnVIL/client_secret.json:/svc.json broadinstitute/firecloud-tools python /scripts/register_service_account/register_service_account.py -j /svc.json -e  [e-mail]
     The service account [e-mail] is now registered with FireCloud. You can share workspaces with this address, or use it to call APIs.
  

Distribution

• PyPi

# refresh from data ingestion tracker spread sheet, update pypi

export TWINE_USERNAME=  #  the username to use for authentication to the repository.
export TWINE_PASSWORD=  # the password to use for authentication to the repository.

rm -r dist/
python3  setup.py data_ingestion_tracker sdist bdist_wheel
twine upload dist/*

• Read The Docs

https://readthedocs.org/projects/pyanvil/