Python and R code examples (with results) using Google Genomics API and a client_secrets.json file

Python_client_secrets.py

from __future__ import print_function
import httplib2
import os

from apiclient import discovery
import oauth2client
from oauth2client import client
from oauth2client import tools


# If modifying these scopes, delete your previously saved credentials
# at ~/.credentials/cache-account-1.json
SCOPES = 'https://www.googleapis.com/auth/genomics'
CLIENT_SECRET_FILE = 'client_secrets.json'
APPLICATION_NAME = 'Google Genomics Test'


def get_credentials():
    #Gets valid user credentials from storage.

    home_dir = os.path.expanduser('~')
    credential_dir = os.path.join(home_dir, '.credentials')
    if not os.path.exists(credential_dir):
      os.makedirs(credential_dir)
    credential_path = os.path.join(credential_dir,
                                   'cache-account-1.json')

    store = oauth2client.file.Storage(credential_path)
    credentials = store.get()
    if not credentials or credentials.invalid:
      flow = client.flow_from_clientsecrets(CLIENT_SECRET_FILE, SCOPES)
      flow.user_agent = APPLICATION_NAME
      credentials = tools.run_flow(flow, store)
    return credentials

def main():
    credentials = get_credentials()
    http = credentials.authorize(httplib2.Http())
    service = discovery.build('genomics', 'v1', http=http)

    dataset_id = '10473108253681171589'  # This is the 1000 Genomes dataset ID
    sample = 'NA12872'

    request = service.readgroupsets().search(
       body={'datasetIds': [dataset_id], 'name': sample},
       fields='readGroupSets(id)')
    read_group_sets = request.execute().get('readGroupSets', [])

    print(read_group_sets)

if __name__ == '__main__':
    main()

Python_run_result.txt

$ python genomics.py  --noauth_local_webserver
[{u'id': u'CMvnhpKTFhDu5oWzv-LJtIEB'}]

R_code_with_client_secrets.R

library(httr)
library(rjson)

auth_genomics <- function(client_secrets_file="client_secrets.json") {

  clientSecrets <- fromJSON(file=client_secrets_file)
  clientId <- clientSecrets$installed$client_id
  clientSecret <- clientSecrets$installed$client_secret

  # Get oauth token.
  endpoint <- oauth_endpoints("google")
  scope <- "https://www.googleapis.com/auth/genomics"

  app <- oauth_app("google", clientId, clientSecret)
    google_token <- oauth2.0_token(
        endpoint, app,
        scope=scope,
        use_oob=FALSE,
        cache="cache-account-1")
    google_token
}

google_token <- auth_genomics()
google_genomics_endpoint <- "https://genomics.googleapis.com/v1"

dataset_id <- '10473108253681171589'  # This is the 1000 Genomes dataset ID
sampleName <- 'NA12872'

requestBody <- list(datasetIds=list('10473108253681171589'), name=sampleName)
queryParams <- list(fields="readGroupSets(id)")

response <- POST(paste(google_genomics_endpoint,
                         "readgroupsets/search",
                         sep="/"),
                   query=queryParams,
                   body=toJSON(requestBody),
                   config(token=google_token),
add_headers("Content-Type"="application/json"))

content(response)

R_run_result.txt

> content(response)
$readGroupSets
$readGroupSets[[1]]
$readGroupSets[[1]]$id
[1] "CMvnhpKTFhDu5oWzv-LJtIEB"