Example NTP sandbox clients

readme.md

NTP Sandbox job clients

A job queue for executing computational toxicology jobs is avialable on the NTP Sandbox. Example job clients are provided below. Note that all clients require use of an authentication permission token before using the API.

curl-client.sh

# an example job submission
curl \
    -X POST \
    -H "Authorization: Token abcdefghijklmnopqrstuvwxyz1234567890" \
    -H "Content-Type: application/json" \
    -d '{"jobtype": "success", "name": "Isaac Newton"}' \
    https://sandbox.ntp.niehs.nih.gov/job-runner/api/v1/test/

# an example request to check results of job
curl \
    -X GET \
    -H "Authorization: Token abcdefghijklmnopqrstuvwxyz1234567890" \
    -H "Content-Type: application/json" \
    https://sandbox.ntp.niehs.nih.gov/job-runner/api/v1/test/

python-client.py

import json
import time
import requests


class JobException(Exception):
    pass


def run_job(url, data, api_token, interval=3, timeout=60):
    with requests.Session() as s:
        s.headers.update({
            "Authorization": f"Token {api_token}",
            "Content-Type": "application/json",
            "Accept": "application/json",
        })

        # initial job request
        response = s.post(url, data=json.dumps(data))
        payload = response.json()
        if response.status_code in [400, 403]:
            raise JobException(payload['detail'])

        # handle result if finished
        if payload['is_finished']:
            if payload['has_errors']:
                raise JobException(payload['errors'])
            else:
                return payload['outputs']

        # poll response until job is complete or client-timeout
        wait_time = 0
        url = payload['url']
        while True:
            time.sleep(interval)
            payload = s.get(url).json()

            # handle result if finished
            if payload['is_finished']:
                if payload['has_errors']:
                    raise JobException(payload['errors'])
                else:
                    return payload['outputs']

            wait_time += interval
            if wait_time > timeout:
                raise JobException('Client timeout')


# example use
result = run_job(
    'https://sandbox.ntp.niehs.nih.gov/job-runner/api/v1/casrn-to-smiles/',
    {"casrns": ["1135-66-6", "58918-34-6", "18172-6a-3", "18172-67-3"]},
    'abcdefghijklmnopqrstuvwxyz1234567890',
)

r-client.r

library(stringr)
library(jsonlite)
library(httr)

run_job <- function(qurl, data, api_token, interval = 3, timeout = 60){
  httr::set_config(httr::config(ssl_verifypeer = 0))
  httr::set_config(httr::add_headers(
    "Authorization" = paste("Token", api_token),
    "Content-Type" = "application/json",
    "Accept": "application/json"
  ))

  response <- httr::POST(qurl, body = data,  encode = "json", accept_json())
  if (status_code(response) == 403) {
    stop_for_status(response)
  } else if (status_code(response) == 400) {
    stop_for_status(response)
  }

  job_url <- content(response, "parsed")  %>% .[['url']]

  wait_time <- 0
  while (1) {
    Sys.sleep(interval)
    response2 <- httr::GET(job_url)
    response2l <- content(response2, "parsed")
    if (response2l$is_finished) {
      if (response2l$has_errors) {
        stop(response2l$errors)

      } else {
        return(response2l$outputs)
      }
    }

    wait_time = wait_time + interval
    if (wait_time > timeout) {
      stop("Client timeout")
    }
  }
}

# example use
result <- run_job(
    'https://sandbox.ntp.niehs.nih.gov/job-runner/api/v1/casrn-to-smiles/',
    list(casrns=c("1135-66-6", "58918-34-6", "18172-6a-3", "18172-67-3"))
    'abcdefghijklmnopqrstuvwxyz1234567890',
)