Source code for toil.test.mesos.helloWorld

# Copyright (C) 2015-2021 Regents of the University of California
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
A simple user script for Toil

from configargparse import ArgumentParser

from toil.common import Toil
from toil.job import Job

childMessage = "The child job is now running!"
parentMessage = "The parent job is now running!"

[docs] def hello_world(job): job.fileStore.logToMaster(parentMessage) with open('foo_bam.txt', 'w') as handle: handle.write('\nThis is a triumph...\n') # Assign FileStoreID to a given file foo_bam = job.fileStore.writeGlobalFile('foo_bam.txt') # Spawn child job.addChildJobFn(hello_world_child, foo_bam, memory=100, cores=0.5, disk="3G")
[docs] def hello_world_child(job, hw): path = job.fileStore.readGlobalFile(hw) job.fileStore.logToMaster(childMessage) # NOTE: path and the udpated file are stored to /tmp # If we want to SAVE our changes to this tmp file, we must write it out. with open(path) as r: with open('bar_bam.txt', 'w') as handle: for line in r.readlines(): handle.write(line) # Assign FileStoreID to a given file # can also use: job.updateGlobalFile() given the FileStoreID instantiation. job.fileStore.writeGlobalFile('bar_bam.txt')
[docs] def main(): # Boilerplate -- startToil requires options parser = ArgumentParser() Job.Runner.addToilOptions(parser) options = parser.parse_args() # Create object that contains our FileStoreIDs # Launch first toil Job i = Job.wrapJobFn(hello_world, memory=100, cores=0.5, disk="3G") with Toil(options) as toil: toil.start(i)
if __name__ == '__main__': main()