How to use divvy - 5 common examples

log_file = ".".join(job_file.split(".")[:-1]) + ".log"

    # Get computing configuration from config
    if computing_configuration is None:
        try:
            computing_configuration = _CONFIG["preferences"]["computing_configuration"]
        except KeyError:
            msg = "'computing_configuration' was not given"
            msg += " and default could not be get from config."
            hint = " Pass a value or add one to the section"
            hint += " preferences:computing_configuration'"
            hint += " in the ngs_toolkit config file."
            _LOGGER.error(msg + hint)
            raise

    dcc = divvy.ComputingConfiguration()
    if computing_configuration is not None:
        dcc.activate_package(computing_configuration)

    # Generate job script
    d = {"code": code, "logfile": log_file}
    d.update(kwargs)
    dcc.write_script(job_file, d)

    # Submit job
    if not dry_run:
        scmd = dcc["compute"]["submission_command"]
        cmd = scmd.split(" ") + [job_file]

        # simply submit if not limiting submission to the number of already running jobs
        if not limited_number:
            subprocess.call(cmd)

Time in between job submission in seconds.

        Defaults to 5.
    **kwargs : :obj:`dict`
        Additional keyword arguments will be passed to the chosen submission template according to `computing_configuration`.
        Pass for example: jobname="job", cores=2, mem=8000, partition="longq".
    """
    import time
    import subprocess

    import divvy
    from ngs_toolkit import _CONFIG, _LOGGER

    # reduce level of logging from divvy
    # only for divvy <=0.
    if "logging" in divvy.__dict__.keys():
        divvy.logging.getLogger("divvy").setLevel("ERROR")

    def count_jobs_running(check_cmd="squeue", sep="\n"):
        """
        Count running jobs on a cluster by invoquing a command that lists the jobs.
        """
        return subprocess.check_output(check_cmd).split(sep).__len__()

    def submit_job_if_possible(
        cmd, check_cmd="squeue", total_job_lim=800, refresh_time=10, in_between_time=5
    ):
        submit = count_jobs_running(check_cmd) < total_job_lim
        while not submit:
            time.sleep(refresh_time)
            submit = count_jobs_running(check_cmd) < total_job_lim
        subprocess.call(cmd)

Defaults to 5.
    **kwargs : :obj:`dict`
        Additional keyword arguments will be passed to the chosen submission template according to `computing_configuration`.
        Pass for example: jobname="job", cores=2, mem=8000, partition="longq".
    """
    import time
    import subprocess

    import divvy
    from ngs_toolkit import _CONFIG, _LOGGER

    # reduce level of logging from divvy
    # only for divvy <=0.
    if "logging" in divvy.__dict__.keys():
        divvy.logging.getLogger("divvy").setLevel("ERROR")

    def count_jobs_running(check_cmd="squeue", sep="\n"):
        """
        Count running jobs on a cluster by invoquing a command that lists the jobs.
        """
        return subprocess.check_output(check_cmd).split(sep).__len__()

    def submit_job_if_possible(
        cmd, check_cmd="squeue", total_job_lim=800, refresh_time=10, in_between_time=5
    ):
        submit = count_jobs_running(check_cmd) < total_job_lim
        while not submit:
            time.sleep(refresh_time)
            submit = count_jobs_running(check_cmd) < total_job_lim
        subprocess.call(cmd)
        time.sleep(in_between_time)

return path


def _req_input_to_args(req_input):
    """
    Given a list of the required inputs for the build command, create an args
    string

    :param list[str] req_input: input names
    :return str: args string
    """
    return ["--" + x + " " for x in req_input]


subdir_path = _make_sub_dir(args.path, args.genome)
dcc = divvy.ComputingConfiguration()
dcc.activate_package("slurm")
cmd_template = "refgenie build -g {g} -a {a} {req_input_str}"
genome = args.genome
to_remove = ["genome", "path"]

data = vars(args)
for i in to_remove:
    data.pop(i)

for asset in asset_build_packages:
    sub_script = os.path.join(subdir_path, asset + ".sub")
    req_input = asset_build_packages[asset]["required_inputs"]
    if req_input:
        print("{} asset requires additional input in the command ({}), so '{}'"
            " requires manual edit".format(asset, req_input, sub_script))
        req_str = " ".join(_req_input_to_args(req_input))

seconds = int(duration_parts[0][:-1])
                elif len(duration_parts) == 2:
                    seconds = int(duration_parts[0][:-1])*60 + int(duration_parts[1][:-1])

                res.append({
                    "trip_id": tds[0].text,
                    "start_station": tds[1].text,
                    "start_date": tds[2].text,
                    "end_station": tds[3].text,
                    "end_date": tds[4].text,
                    "duration": seconds
                })
        return res

if __name__ == "__main__":
    d = Divvy()
    d.login('iandees', 'password')

    out = csv.DictWriter(open('divvy_rides.csv', 'w'), ['trip_id', 'start_station', 'start_date', 'end_station', 'end_date', 'duration'])

    out.writeheader()
    for ride in d.get_rides():
        out.writerow(ride)