cohorts().cloud_storage_file_paths()

Takes a cohort id as a required parameter and returns cloud storage paths to files associated with all the samples in that cohort, up to a default limit of 10,000 files. Authentication is required. User must have READER or OWNER permissions on the cohort.

Example:

python isb_curl.py https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_api/v3/cohorts/{COHORT ID}/cloud_storage_file_paths

API explorer example:

Click here to see this endpoint in Google’s API explorer.

Python API Client Example:

from googleapiclient.discovery import build
from oauth2client.client import OAuth2WebServerFlow
from oauth2client import tools
from oauth2client.file import Storage
import httplib2
import os

CLIENT_ID = '907668440978-0ol0griu70qkeb6k3gnn2vipfa5mgl60.apps.googleusercontent.com'
CLIENT_SECRET = 'To_WJH7-1V-TofhNGcEqmEYi'
EMAIL_SCOPE = 'https://www.googleapis.com/auth/userinfo.email'
DEFAULT_STORAGE_FILE = os.path.join(os.path.expanduser('~'), '.isb_credentials')

def get_credentials():
        oauth_flow_args = ['--noauth_local_webserver']
        storage = Storage(DEFAULT_STORAGE_FILE)
        credentials = storage.get()
        if not credentials or credentials.invalid:
                flow = OAuth2WebServerFlow(CLIENT_ID, CLIENT_SECRET, EMAIL_SCOPE)
                flow.auth_uri = flow.auth_uri.rstrip('/') + '?approval_prompt=force'
                credentials = tools.run_flow(flow, storage, tools.argparser.parse_args(oauth_flow_args))
        return credentials

def get_authorized_service():
        api = 'isb_cgc_api'
        version = 'v3'
        site = 'https://api-dot-isb-cgc.appspot.com'
        discovery_url = '%s/_ah/api/discovery/v1/apis/%s/%s/rest' % (site, api, version)
        credentials = get_credentials()
        http = credentials.authorize(httplib2.Http())
        if credentials.access_token_expired or credentials.invalid:
                credentials.refresh(http)
        authorized_service = build(api, version, discoveryServiceUrl=discovery_url, http=http)
        return authorized_service

service = get_authorized_service()
data = service.cohorts().cloud_storage_file_paths(cohort_id=1).execute()

Request

HTTP request:

GET https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_api/v3/cohorts/{cohort_id}/cloud_storage_file_paths

Parameters

Parameter name	Value	Description
analysis_workflow_type	string	Optional.
cohort_id	string	Required.
data_category	string	Optional.
data_format	string	Optional.
data_type	string	Optional.
experimental_strategy	string	Optional.
genomic_build	string	Optional.
limit	string	Optional.
platform	string	Optional.

Response

If successful, this method returns a response body with the following structure:

{
  "cloud_storage_file_paths": [string],
  "count": integer
}

Parameter name	Value	Description
cloud_storage_file_paths[]	list	List of Google Cloud Storage paths of files associated with the cohort.
count	integer	Number of Google Cloud Storage paths returned for the cohort.

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Have feedback or corrections? You can file an issue here or email us at feedback@isb-cgc.org.