samples().get_list()

Given a list of sample barcodes (of length 16, eg CCLE-ACC-MESO-1), this endpoint returns the associated case barcode, a list of associated aliquots, and a list of “data_details” blocks describing each of the data files associated with this sample

Example:

curl --data '{"sample_barcodes": ["CCLE-LS1034","CCLE-ACC-MESO-1"]}' https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_ccle_api/v3/ccle/samples

API explorer example:

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

Python API Client Example:

from googleapiclient.discovery import build
import httplib2

def get_unauthorized_service():
        api = 'isb_cgc_ccle_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)
        return build(api, version, discoveryServiceUrl=discovery_url, http=httplib2.Http())

service = get_unauthorized_service()
data = service.samples().get(body={"case_barcodes": ["CCLE-LS1034","CCLE-ACC-MESO-1"]}).execute()

Request

HTTP request:

POST https://api-dot-isb-cgc.appspot.com/_ah/api/isb_cgc_ccle_api/v3/ccle/samples

{

“sample_barcodes”: [

“CCLE-LS1034”, “CCLE-ACC-MESO-1”

]

}

Parameters

Parameter name	Value	Description
widths:50	10	50
analysis_workflow_type	string	Optional.
data_category	string	Optional.
data_format	string	Optional.
data_type	string	Optional.
endpoint_type	string	Optional.
experimental_strategy	string	Optional.
platform	string	Optional.
sample_barcode	string	Required.

Response

If successful, this method returns a response body with the following structure(CCLE does not have any biospecimen data hence it would remain blank):

{
  "aliquots": [string],
  "biospecimen_data": {},
  "case_barcode": string,
  "sample_barcode": string,
  "case_gdc_id": string,
  "data_details": [
    {
      "access": string,
      "analysis_workflow_type": string,
      "data_category": string,
      "data_format": string,
      "data_type": string,
      "disease_code": string,
      "endpoint_type": string,
      "experimental_strategy": string,
      "file_gdc_id": string,
      "file_name": string,
      "file_name_key": string,
      "file_size": string,
      "index_file_name": string,
      "platform": string,
      "program_name": string,
      "project_short_name": string,
      "sample_barcode": string,
      "sample_gdc_id": string,
      "sample_type": string
    }
  ],
  "data_details_count": integer
}

:header: “Parameter name”, “Value”, “Description” :widths: 50, 10, 50

aliquots[]	list	List of barcodes of aliquots taken from this participant.
biospecimen_data	nested object	Biospecimen data about the sample.
case_barcode	string	Barcode of the case.
case_gdc_id	string	Case gdc id.
data_details[]	list	List of information about each file associated with the sample barcode.
data_details[].access	string	An indication of the security protocol necessary to fulfill in order to access the data from the file, e.g. open, controlled.
data_details[].analysis_workflow_type	string	The type of workflow used to generate the data file, e.g. ‘BWA-aln’, ‘STAR 2-Pass’, ‘BWA with Mark Duplicates and Cocleaning’
data_details[].data_category	string	The higher level categorization of the data_type in the file, e.g. ‘Biospecimen’, ‘Clinical’, ‘Raw sequencing data’, ‘Simple nucleotide variation’
data_details[].data_format	string	The format of the data file, e.g. ‘BAM’, ‘BCR XML’, ‘TXT’
data_details[].data_type	string	Data type stored in Google Cloud Storage, e.g. ‘Clinical Supplement’, ‘Biospecimen Supplement’, ‘Aligned reads’, ‘Genotypes’, ‘Diagnostic image’
data_details[].disease_code	string	The disease abbeviation, e.g. ‘ACC’, ‘UVM’, ‘ALL’, ‘WT’
data_details[].endpoint_type	string	The GDC files API the data file information was gottern from, e.g. ‘legacy’, ‘current’
data_details[].experimental_strategy	string	The sequencing, array or other strategy used to generate the data file, e.g. ‘RNA-Seq’, ‘WGS’, ‘Genotyping array’
data_details[].file_gdc_id	string	The GDC assigned id for the file
data_details[].file_name	string	Name of the datafile stored on the GDC system.
data_details[].file_name_key	string	Google Cloud Storage path to file.
data_details[].file_size	string	The size of the file
data_details[].index_file_name	string	For BAM files, the name of its index file
data_details[].platform	string	The sequencing or array platform used, e.g. Illumina HiSeq, Ion Torrent PGM, Affymetrix SNP Array 6.0.
data_details[].program_name	string	The program for which the data was generated, e.g. ‘CCLE’, ‘TARGET’,’TCGA’.
data_details[].project_short_name	string	The id of the project, e.g. ‘CCLE-ACC’, ‘CCLE-UVM’, ‘TARGET-ALL-P1’, ‘ TARGET-WT’, ‘TCGA-ACC’, ‘TCGA-UVM’
data_details[].sample_barcode	string	Sample barcode.
data_details[].sample_gdc_id	string	The GDC assigned id for the sample
data_details[].sample_type	string	The sample type, e.g. ‘01’, ‘10’, ‘11’
data_details_count	integer	Number of files associated with the sample barcode.

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