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#!/usr/bin/env python
from __future__ import print_function
import json
from collections import defaultdict
import shutil
import unittest
from ruffus import pipeline_run, Pipeline, follows, posttask, split, collate, mkdir, regex
import sys
"""
test_collate.py
test branching dependencies
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0])) + "/"
# 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]
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
try:
from StringIO import StringIO
except:
from io import StringIO
# use simplejson in place of json for python < 2.6
# try:
# import json
# except ImportError:
# import simplejson
# json = simplejson
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Main logic
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
species_list = defaultdict(list)
species_list["mammals"].append("cow")
species_list["mammals"].append("horse")
species_list["mammals"].append("sheep")
species_list["reptiles"].append("snake")
species_list["reptiles"].append("lizard")
species_list["reptiles"].append("crocodile")
species_list["fish"].append("pufferfish")
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# task1
#
def do_write(file_name, what):
with open(file_name, "a") as oo:
oo.write(what)
test_file = tempdir + "task.done"
@follows(mkdir(tempdir, tempdir + "test"))
@posttask(lambda: do_write(tempdir + "task.done", "Task 1 Done\n"))
@split(None, tempdir + '*.animal')
def prepare_files(no_inputs, outputs):
# cleanup previous
for f in outputs:
os.unlink(f)
for grouping in species_list:
for species_name in species_list[grouping]:
filename = tempdir + "%s.%s.animal" % (species_name, grouping)
with open(filename, "w") as oo:
oo.write(species_name + "\n")
#
# task2
#
@collate(prepare_files, regex(r'(.*/).*\.(.*)\.animal'), r'\1\2.results')
@posttask(lambda: do_write(tempdir + "task.done", "Task 2 Done\n"))
def summarise_by_grouping(infiles, outfile):
"""
Summarise by each species group, e.g. mammals, reptiles, fish
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfile]))
with open(outfile, "w") as oo:
for i in infiles:
with open(i) as ii:
oo.write(ii.read())
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfile]))
def check_species_correct():
"""
#cow.mammals.animal
#horse.mammals.animal
#sheep.mammals.animal
# -> mammals.results
#
#snake.reptiles.animal
#lizard.reptiles.animal
#crocodile.reptiles.animal
# -> reptiles.results
#
#pufferfish.fish.animal
# -> fish.results
"""
for grouping in species_list:
with open(tempdir + grouping + ".results") as oo:
assert(oo.read() == "".join(
s + "\n" for s in sorted(species_list[grouping])))
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
def tearDown(self):
try:
shutil.rmtree(tempdir)
except:
pass
def test_ruffus(self):
pipeline_run(multiprocess=10, verbose=0, pipeline="main")
check_species_correct()
def test_newstyle_ruffus(self):
test_pipeline = Pipeline("test")
test_pipeline.split(task_func=prepare_files,
input=None,
output=tempdir + '*.animal')\
.follows(mkdir(tempdir, tempdir + "test"))\
.posttask(lambda: do_write(tempdir + "task.done", "Task 1 Done\n"))
test_pipeline.collate(task_func=summarise_by_grouping,
input=prepare_files,
filter=regex(r'(.*/).*\.(.*)\.animal'),
output=r'\1\2.results')\
.posttask(lambda: do_write(tempdir + "task.done", "Task 2 Done\n"))
test_pipeline.run(multiprocess=10, verbose=0)
check_species_correct()
if __name__ == '__main__':
unittest.main()
|
