cohorts().file_manifest()¶
Takes a cohort id as a required parameter and returns a manifest of all files associated with all the samples in that cohort, as well as their metadata, up to a default limit of 50,000 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}/file_manifest
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().file_manifest(cohort_id=1).execute()
Request
HTTP request:
GET https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_api/v3/cohorts/{cohort_id}/file_manifest
Parameters
| Parameter name | Value | Description |
|---|---|---|
| cohort_id | string | Required. |
| genomic_build | string | Optional, The build for which to obtain file entries, default=hg19 |
| offset | string | Optional, The number of file entries to skip before collecting for retrieval (eg. offset 5 = start at 6), default=0 |
| fetch_count | string | Optional, The number of file entries to retrieve, default=50000 |
Response
If successful, this method returns a response body with the following structure:
{
"file_list": [
{
"program": string,
"case_barcode": string,
"case_gdc_uuid": string,
"file_path": string,
"file_gdc_uuid": string,
"disease_code": string,
"project_short_name": string,
"experimental_strategy": string,
"platform": string,
"data_category": string,
"data_type": string,
"data_format": string,
"access": string
}
],
"total_file_count": integer,
"files_retrieved": integer
}
| Parameter name | Value | Description |
|---|---|---|
| file_list[{…}] | list | List of file detail entries of files associated with the cohort. |
| total_file_count | integer | Total number of file entries found for this cohort. |
| files_retrieved | integer | Total number of file entries retrieved in this response. |