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#!/usr/bin/env python
from __future__ import print_function
"""
test_split_subdivide_checkpointing.py
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
import sys
# add grandparent to search path for testing
grandparent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", ".."))
sys.path.insert(0, grandparent_dir)
# module name = script name without extension
module_name = os.path.splitext(os.path.basename(__file__))[0]
# funky code to import by file name
parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), ".."))
from ruffus import pipeline_run, pipeline_printout_graph, originate, split, transform, subdivide, formatter, Pipeline
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
from subprocess import *
import unittest
import shutil
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Each time the pipeline is FORCED to rerun,
# More files are created for each task
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
@originate([tempdir + 'start'])
def make_start(outfile):
"""
-> start
"""
open(outfile, 'w').close()
@split(make_start, tempdir + '*.split')
def split_start(infiles, outfiles):
"""
-> XXX.split
where XXX = 0 .. N,
N = previous N + 1
"""
# split always runs exactly one job (unlike @subdivide)
# So it implicitly combines all its inputs before running and generating multiple output
# @originate generates multiple output so the input for @split is a list...
infile = infiles[0]
# clean up previous
for f in outfiles:
os.unlink(f)
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#
# Create more files than the previous invocation
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
n_to_produce = len(outfiles) + 1
for i in range(n_to_produce):
f = '{}{}.split'.format(tempdir, i)
open(f, 'a').close()
@subdivide(split_start, formatter(), tempdir + '{basename[0]}_*.subdivided', tempdir + '{basename[0]}')
def subdivide_start(infile, outfiles, infile_basename):
# cleanup existing
for f in outfiles:
os.unlink(f)
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
#
# Create more files than the previous invocation
#
#!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
n_to_produce = len(outfiles) + 1
for i in range( n_to_produce):
open('{}_{}.subdivided'.format(infile_basename, i), 'a').close()
class Test_ruffus(unittest.TestCase):
def tearDown(self):
# only tear down if not throw exception so we can debug?
try:
shutil.rmtree(tempdir)
except:
pass
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
os.makedirs(tempdir)
#
# check graphviz exists for turning dot files into png, svg etc
#
try:
process = Popen("echo what | dot", stdout=PIPE, stderr=STDOUT, shell = True)
output, unused_err = process.communicate()
retcode = process.poll()
if retcode:
raise CalledProcessError(retcode, "echo what | dot", output=output)
except CalledProcessError as err:
output_str = str(err.output)
if "No such file or directory" in output_str or "not found" in output_str or "Unable to access jarfile" in output_str:
self.graph_viz_present = False
return
self.graph_viz_present = True
def test_ruffus (self):
print(" Run pipeline normally...")
if self.graph_viz_present:
pipeline_printout_graph(tempdir + "flowchart.dot", pipeline= "main")
pipeline_printout_graph(tempdir + "flowchart.png",
target_tasks =[subdivide_start],
forcedtorun_tasks = [split_start],
no_key_legend = True)
pipeline_printout_graph(tempdir + "flowchart.svg", no_key_legend = False, pipeline= "main")
# Unknown format
try:
pipeline_printout_graph(tempdir + "flowchart.unknown", no_key_legend = False, pipeline= "main")
raise Exception("Failed to throw exception for pipeline_printout_graph unknown extension ")
except CalledProcessError as err:
pass
pipeline_printout_graph(tempdir + "flowchart.unknown", "svg", no_key_legend = False, pipeline= "main")
else:
pipeline_printout_graph(tempdir + "flowchart.dot",
target_tasks =[subdivide_start],
forcedtorun_tasks = [split_start],
no_key_legend = True,
pipeline= "main")
def test_newstyle_ruffus (self):
print(" Run pipeline normally...")
test_pipeline = Pipeline("test")
test_pipeline.originate(make_start, [tempdir + 'start'])
test_pipeline.split(split_start, make_start, tempdir + '*.split')
test_pipeline.subdivide(subdivide_start, split_start, formatter(), tempdir + '{basename[0]}_*.subdivided', tempdir + '{basename[0]}')
if self.graph_viz_present:
test_pipeline.printout_graph(tempdir + "flowchart.dot")
test_pipeline.printout_graph(tempdir + "flowchart.png",
target_tasks =[subdivide_start],
forcedtorun_tasks = [split_start],
no_key_legend = True)
test_pipeline.printout_graph(tempdir + "flowchart.svg", no_key_legend = False)
# Unknown format
try:
test_pipeline.printout_graph(tempdir + "flowchart.unknown", no_key_legend = False)
raise Exception("Failed to throw exception for test_pipeline.printout_graph unknown extension ")
except CalledProcessError as err:
pass
test_pipeline.printout_graph(tempdir + "flowchart.unknown", "svg", no_key_legend = False)
else:
test_pipeline.printout_graph(tempdir + "flowchart.dot",
target_tasks =[subdivide_start],
forcedtorun_tasks = [split_start],
no_key_legend = True)
if __name__ == '__main__':
unittest.main()
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