cohorts().get()

Returns information about a specific cohort the user has READER or OWNER permission on when given a cohort ID. Authentication is required.

Example:

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

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().get(cohort_id=1).execute()

Request

HTTP request:

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

Parameters

Parameter name	Value	Description
cohort_id	string	Required.

Response

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

{
  "case_count": integer,
  "cases": [string],
  "comments": string,
  "email": string,
  "filters": [
    {
      "name": string,
      "value": string
    }
  ],
  "id": string,
  "last_date_saved": string,
  "name": string,
  "parent_id": [string],
  "permission": string,
  "sample_count": integer,
  "samples": [string],
  "source_notes": string,
  "source_type": string
}

Parameter name	Value	Description
case_count	integer	Total count of unique case barcodes in the cohort.
cases[]	list	List of case barcodes in the cohort.
comments	string	Comments on the cohort.
email	string	Email of user.
filters[]	list	List of filters applied to create cohort, if any.
filters[].name	string	Names of filtering parameters used to create the cohort.
filters[].value	string	Values of filtering parameters used to create the cohort.
id	string	Cohort id.
last_date_saved	string	Last date the cohort was saved.
name	string	Name of the cohort
parent_id[]	list	List of id’s of cohorts that this cohort was derived from, if any.
permission	string	User permissions on cohort: READER or OWNER.
sample_count	integer	Total count of unique sample barcodes in the cohort.
samples[]	list	List of sample barcodes in the cohort.
source_notes	string	Notes on the source of the cohort.
source_type	string	Type of cohort source.

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