Kernel API

The Kernel API allows you to automate repeated tasks programmatically.

To get started, have your Organization Owner generate an API key on the Organization Settings page.

External/Customer facing API

Routes for:

• All dataset IDs + metadata in a study
• Run a pipeline, given a dataset ID and pipeline name
• Status for most recent pipeline run and signed urls if present, given dataset ID and pipeline name

headers={"Authorization": f"{api_key}"}

Common ways to use Kernel API

To find yourstudy_id:

Navigate to the study in portal and notice the URL looks like:

https://portal.kernel.com/organizations/2d1fee1c-c2bc-4833-b560-afc673140f42/studies/b249e4b9-9108-4ce4-a7ce-41cc3bbd2bf2/datasets

The bold part b249e4b9-9108-4ce4-a7ce-41cc3bbd2bf2 is your study_id to use in the following routes.

List all dataset IDs and metadata in a study:

list_datasets(study_id : str)--> Dict[str, List[dict]]

/api/vi/study/{study_id}/datasets

• Parameters:
  • study_id (str) - study id
• Returns:
  • All dataset IDs and metadata in a study
• Return Type:
  • Dict[str, List[dict]]

{
    "datasets": [
        {
            "id": "00000000000000000000000000000000",
            "meta": {}, # possible keys include "description", "name", "experiment"
            "participant": {
                "id": "00000000000000000000000000000000"
                "participant_id": "00000000000000000000000000000000"
                "created_at": 0.0, # seconds since epoch
                "active": True, # participant active status
                "pending": False, # participant pending status
                "status": "active" # participant status in the study,
            },
            "created_date": 0.0, # seconds since epoch
            "started_at": 0.0, # seconds since epoch
            "stopped_at": 0.0, # seconds since epoch
        } 
     ]
 }

Examples

>>> response = requests.get("https://api.kernel.com/api/v1/study/000000000000000/datasets")
>>> assert response.status_code == 200
>>> datasets = response.json()["datasets"]
>>> dataset_ids = [dataset["id"] for dataset in datasets]

Available pipelines:

# Available pipelines are:
   "analysis_eeg"
   "analysis_nirs_epoched"
   "analysis_nirs_glm"
   "analysis_task"
   "qc_eeg"
   "qc_nirs_basic"
   "qc_nirs"
   "qc_syncbox"
   "reconstruction"
   "pipeline_snirf_gated"
   "snirf_hb_moments"
   "snirf_moments"

Get the status of the most recent pipeline run for a dataset and asset URLs if available:

pipeline_status(study_id : str, dataset_id: str, pipeline_name: str)

/api/vi/study/{study_id}/dataset/{dataset_id}/pipeline/{pipeline_name]/status

• Parameters:     
  • study_id (str) - study id
  • dataset_id (str) - dataset id
  • pipeline_name (str) - pipeline name
• Returns: 
  • Status of the most recent pipeline run and asset URLs if available 
• Return Type:
  • dict

{
       "job_id": "00000000000000000000000000000000",
       "status": "SUCCEEDED",
       "signed_urls": {
           "urls": {
               "filename1": "https://someurl"
           }, "sizes": {
               "filename1": 123.1
           },
           "batch_job_id": "00000000000000000000000000000000"
           "execution_id": "00000000000000000000000000000000"
       }
}

Examples

>>> response = requests.get("https://api.kernel.com/api/v1/study/000000000000000/dataset/000000000000000/pipeline/name/status")
>>> assert response.status_code == 200
>>> status = response.json()
>>> assert status["status"] == "SUCCEEDED"

Run a pipeline for a dataset:

run_pipeline(study_id : str, dataset_id: str, pipeline_name: str) --> Dict[str, Any]

/api/vi/study/{study_id}/dataset/{dataset_id}/pipeline/{pipeline_name}

• Parameters:     
  • study_id (str) - study id
  • dataset_id (str) - dataset id
  • pipeline_name (str) - pipeline name
• Returns: 
  • Job ID if the pipeline run 
• Return Type:
  • Dict

Response json structure:
{
       "job_id": "00000000000000000000000000000000"
}

Examples

>>> response = requests.post("https://api.kernel.com/api/v1/study/00000000000000/dataset/00000000000000/pipeline/name")
>>> assert response.status_code == 200
>>> job_id = response.json()["job_id"]

.