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#!/usr/bin/env python
from __future__ import print_function
NUMBER_OF_RANDOMS = 10000
CHUNK_SIZE = 1000
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]
from ruffus import follows, split, mkdir, files, transform, suffix, posttask, touch_file, merge, Pipeline
import random
import glob
#---------------------------------------------------------------
#
# Create random numbers
#
@follows(mkdir(tempdir))
@files(None, tempdir + "random_numbers.list")
def create_random_numbers(input_file_name, output_file_name):
f = open(output_file_name, "w")
for i in range(NUMBER_OF_RANDOMS):
f.write("%g\n" % (random.random() * 100.0))
f.close()
#---------------------------------------------------------------
#
# Split initial file
#
@follows(create_random_numbers)
@split(tempdir + "random_numbers.list", tempdir + "*.chunks")
def step_4_split_numbers_into_chunks (input_file_name, output_files):
"""
Splits random numbers file into XXX files of CHUNK_SIZE each
"""
#
# clean up files from previous runs
#
for f in glob.glob("*.chunks"):
os.unlink(f)
#
# create new file every CHUNK_SIZE lines and
# copy each line into current file
#
output_file = None
cnt_files = 0
with open(input_file_name) as ii:
for i, line in enumerate(ii):
if i % CHUNK_SIZE == 0:
cnt_files += 1
if output_file:
output_file.close()
output_file = open(tempdir + "%d.chunks" % cnt_files, "w")
output_file.write(line)
if output_file:
output_file.close()
#---------------------------------------------------------------
#
# Calculate sum and sum of squares for each chunk file
#
@transform(step_4_split_numbers_into_chunks, suffix(".chunks"), ".sums")
def step_5_calculate_sum_of_squares (input_file_name, output_file_name):
with open(output_file_name, "w") as oo:
sum_squared, sum = [0.0, 0.0]
cnt_values = 0
with open(input_file_name) as ii:
for line in ii:
cnt_values += 1
val = float(line.rstrip())
sum_squared += val * val
sum += val
oo.write("%s\n%s\n%d\n" % (repr(sum_squared), repr(sum), cnt_values))
def print_hooray_again():
print(" hooray again")
def print_whoppee_again():
print(" whoppee again")
#---------------------------------------------------------------
#
# Calculate sum and sum of squares for each chunk
#
@posttask(lambda: sys.stdout.write(" hooray\n"))
@posttask(print_hooray_again, print_whoppee_again, touch_file(os.path.join(tempdir, "done")))
@merge(step_5_calculate_sum_of_squares, os.path.join(tempdir, "variance.result"))
def step_6_calculate_variance (input_file_names, output_file_name):
"""
Calculate variance naively
"""
output = open(output_file_name, "w")
#
# initialise variables
#
all_sum_squared = 0.0
all_sum = 0.0
all_cnt_values = 0.0
#
# added up all the sum_squared, and sum and cnt_values from all the chunks
#
for input_file_name in input_file_names:
with open(input_file_name) as ii:
sum_squared, sum, cnt_values = list(map(float, ii.readlines()))
all_sum_squared += sum_squared
all_sum += sum
all_cnt_values += cnt_values
all_mean = all_sum / all_cnt_values
variance = (all_sum_squared - all_sum * all_mean)/(all_cnt_values)
#
# print output
#
print(variance, file=output)
output.close()
import unittest, shutil
try:
from StringIO import StringIO
except:
from io import StringIO
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
def tearDown(self):
try:
shutil.rmtree(tempdir)
pass
except:
pass
def atest_ruffus (self):
pipeline_run(multiprocess = 50, verbose = 0, pipeline= "main")
output_file = os.path.join(tempdir, "variance.result")
if not os.path.exists (output_file):
raise Exception("Missing %s" % output_file)
def test_newstyle_ruffus (self):
test_pipeline = Pipeline("test")
test_pipeline.files(create_random_numbers, None, tempdir + "random_numbers.list")\
.follows(mkdir(tempdir))
test_pipeline.split(task_func = step_4_split_numbers_into_chunks,
input = tempdir + "random_numbers.list",
output = tempdir + "*.chunks")\
.follows(create_random_numbers)
test_pipeline.transform(task_func = step_5_calculate_sum_of_squares,
input = step_4_split_numbers_into_chunks,
filter = suffix(".chunks"),
output = ".sums")
test_pipeline.merge(task_func = step_6_calculate_variance, input = step_5_calculate_sum_of_squares, output = os.path.join(tempdir, "variance.result"))\
.posttask(lambda: sys.stdout.write(" hooray\n"))\
.posttask(print_hooray_again, print_whoppee_again, touch_file(os.path.join(tempdir, "done")))
test_pipeline.run(multiprocess = 50, verbose = 0)
output_file = os.path.join(tempdir, "variance.result")
if not os.path.exists (output_file):
raise Exception("Missing %s" % output_file)
if __name__ == '__main__':
unittest.main()
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