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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__), ".."))
import ruffus
from ruffus import pipeline_run, pipeline_printout, Pipeline, formatter, originate, subdivide, split
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
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)
def check_file_exists_or_not_as_expected(self, expected_files, not_expected_files):
"""
Check if files exist / not exist
"""
for ee in expected_files:
if not os.path.exists(tempdir + ee):
raise Exception("Expected file %s" % (tempdir + ee))
for ne in not_expected_files:
if os.path.exists(tempdir + ne):
raise Exception("Unexpected file %s" % (tempdir + ne ))
def test_newstyle_ruffus (self):
test_pipeline = Pipeline("test")
test_pipeline.originate(task_func = make_start, output = [tempdir + 'start'])
test_pipeline.split(task_func = split_start, input = make_start, output = tempdir + '*.split')
test_pipeline.subdivide(task_func = subdivide_start, input = split_start, filter = formatter(), output = tempdir + '{basename[0]}_*.subdivided', extras = [tempdir + '{basename[0]}'])
expected_files_after_1_runs = ["start", "0.split", "0_0.subdivided"]
expected_files_after_2_runs = ["1.split", "0_1.subdivided", "1_0.subdivided"]
expected_files_after_3_runs = ["2.split", "0_2.subdivided", "1_1.subdivided", "2_0.subdivided"]
expected_files_after_4_runs = ["3.split", "0_3.subdivided", "1_2.subdivided", "2_1.subdivided", "3_0.subdivided"]
print(" Run pipeline normally...")
test_pipeline.run(multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs,
expected_files_after_2_runs)
print(" Check that running again does nothing. (All up to date).")
test_pipeline.run(multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs,
expected_files_after_2_runs)
print(" Running again with forced tasks to generate more files...")
test_pipeline.run(forcedtorun_tasks = ["test::make_start"], multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs,
expected_files_after_3_runs)
print(" Check that running again does nothing. (All up to date).")
test_pipeline.run(multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs,
expected_files_after_3_runs)
print(" Running again with forced tasks to generate even more files...")
test_pipeline.run(forcedtorun_tasks = make_start, multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs
+ expected_files_after_3_runs,
expected_files_after_4_runs)
print(" Check that running again does nothing. (All up to date).")
test_pipeline.run(multiprocess = 10, verbose=0)
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs
+ expected_files_after_3_runs,
expected_files_after_4_runs)
def test_ruffus (self):
expected_files_after_1_runs = ["start", "0.split", "0_0.subdivided"]
expected_files_after_2_runs = ["1.split", "0_1.subdivided", "1_0.subdivided"]
expected_files_after_3_runs = ["2.split", "0_2.subdivided", "1_1.subdivided", "2_0.subdivided"]
expected_files_after_4_runs = ["3.split", "0_3.subdivided", "1_2.subdivided", "2_1.subdivided", "3_0.subdivided"]
print(" Run pipeline normally...")
pipeline_run(multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs,
expected_files_after_2_runs)
print(" Check that running again does nothing. (All up to date).")
pipeline_run(multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs,
expected_files_after_2_runs)
print(" Running again with forced tasks to generate more files...")
pipeline_run(forcedtorun_tasks = [make_start], multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs,
expected_files_after_3_runs)
print(" Check that running again does nothing. (All up to date).")
pipeline_run(multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs,
expected_files_after_3_runs)
print(" Running again with forced tasks to generate even more files...")
pipeline_run(forcedtorun_tasks = [make_start], multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs
+ expected_files_after_3_runs,
expected_files_after_4_runs)
print(" Check that running again does nothing. (All up to date).")
pipeline_run(multiprocess = 10, verbose=0, pipeline= "main")
self.check_file_exists_or_not_as_expected(expected_files_after_1_runs
+ expected_files_after_2_runs
+ expected_files_after_3_runs,
expected_files_after_4_runs)
if __name__ == '__main__':
unittest.main()
|
