tlapp/dev-scripts/submit-job at master · BerkeleyBiostats/tlapp · GitHub

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#!/usr/bin/env python

import json
import os
import sys
import requests
import click
import pyotp


def post_job(
    backend,
    job_script_filename,
    inputs_filename,
    username,
    password,
    ip,
    baseurl,
    longbowurl,
    token,
):
    with open(job_script_filename) as f:
        job_code = f.read()

    job_data = {"backend": backend}

    with open(inputs_filename) as f:
        job_data["inputs"] = json.loads(f.read())

    job_data["code"] = job_code

    if backend == "ghap":
        job_data["ghap_credentials"] = {
            "username": username,
            "password": password,
            "ip": ip,
        }
    if backend == "savio":
        job_data["savio_credentials"] = {
            "username": username,
            "password": password,
        }

    if baseurl:
        job_data["base_url"] = baseurl

    endpoint = os.path.join(longbowurl, "submit_job_token/")
    response = requests.post(
        endpoint, data=json.dumps(job_data), headers={"Authorization": token}
    )

    print(response)
    print(response.text)


@click.command()
@click.argument("job_directory")
@click.option("--username")
@click.option("--password")
@click.option("--pin")
@click.option("--secret")
@click.option("--ip")
@click.option("--baseurl")
@click.option("--longbowurl", default="http://localhost:5721/")
@click.option("--token", default="admintoken")
@click.option("--backend", default="ghap")
def cli(
    job_directory,
    username,
    password,
    pin,
    secret,
    ip,
    baseurl,
    longbowurl,
    token,
    backend,
):
    inputs_directory = os.path.join(job_directory, "inputs")
    inputs_filename = os.path.join(job_directory, "inputs.json")
    job_script_filename = os.path.join(job_directory, "code.Rmd")

    if pin and secret:
        totp = pyotp.TOTP(secret)
        password = pin + totp.now()

    if os.path.exists(inputs_directory):
        for root, dirs, files in os.walk(inputs_directory):
            for filename in files:
                inputs_filename = os.path.join(root, filename)
                post_job(
                    backend,
                    job_script_filename,
                    inputs_filename,
                    username,
                    password,
                    ip,
                    baseurl,
                    longbowurl,
                    token,
                )
    else:
        post_job(
            backend,
            job_script_filename,
            inputs_filename,
            username,
            password,
            ip,
            baseurl,
            longbowurl,
            token,
        )


if __name__ == "__main__":
    cli()