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#!/usr/bin/env python
#
# pyFlow - a lightweight parallel task engine
#
# Copyright (c) 2012-2017 Illumina, Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in
# the documentation and/or other materials provided with the
# distribution.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
# FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
# COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
# INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
# BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
# CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
# LIABILITY, OR TORT INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY
# WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#
#
import os.path
import sys
# add module path by hand
#
scriptDir=os.path.abspath(os.path.dirname(__file__))
sys.path.append(scriptDir+"/../../src")
from pyflow import WorkflowRunner
#
# very simple task scripts called by the demo:
#
testJobDir=os.path.join(scriptDir,"testtasks")
sleepjob=os.path.join(testJobDir,"sleeper.bash") # sleeps
yelljob=os.path.join(testJobDir,"yeller.bash") # generates some i/o
runjob=os.path.join(testJobDir,"runner.bash") # runs at 100% cpu
# all pyflow workflows are written into classes derived from pyflow.WorkflowRunner:
#
# this workflow is a simple example of a workflow we can either run directly,
# or run as a task within another workflow:
#
class SubWorkflow(WorkflowRunner) :
# a workflow is defined by overloading the WorkflowRunner.workflow() method:
#
def workflow(self) :
# this workflow executes a simple dependency diamond:
self.addTask("task1",yelljob+" 1")
self.addTask("task2a",yelljob+" 1",dependencies="task1")
self.addTask("task2b",yelljob+" 1",dependencies="task1")
self.addTask("task3",yelljob+" 1",dependencies=("task2a","task2b"))
#
# This workflow will use SubWorkflow as a task:
#
class SimpleWorkflow(WorkflowRunner) :
# a workflow is defined by overloading the WorkflowRunner.workflow() method:
#
def workflow(self) :
# it's fine to repeat task names in two workflows, even if you're sub-tasking one from the other
self.addTask("task1",yelljob+" 1")
self.addTask("task2",runjob+" 3")
# instantiate a new workflow and run it as soon as task1 and task2 complete
wflow=SubWorkflow()
self.addWorkflowTask("subwf_task3",wflow,dependencies=("task1","task2"))
# this job will not run until the workflow-task completes. This means that all of the
# tasks that SubWorkflow launches will need to complete successfully beforehand:
#
self.addTask("task4",sleepjob+" 1",dependencies="subwf_task3")
# Instantiate our workflow
#
wflow = SimpleWorkflow()
# Run the worklow:
#
retval=wflow.run(mode="local",nCores=8)
# If we want to run the SubWorkflow as a regular workflow, that can be done as well:
#
#wflow2 = SubWorkflow()
#retval2=wflow2.run()
sys.exit(retval)
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