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#!/usr/bin/env python
from __future__ import print_function
"""
test_pausing.py
test time.sleep keeping input files and output file times correct
"""
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 *
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import re
import operator
import sys,os
from collections import defaultdict
import random
import json
# use simplejson in place of json for python < 2.6
#try:
# import json
#except ImportError:
# import simplejson
# json = simplejson
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Functions
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import time
def test_job_io(infiles, outfiles, extra_params):
"""
cat input files content to output files
after writing out job parameters
"""
# dump parameters
params = (infiles, outfiles) + extra_params
if isinstance(infiles, str):
infiles = [infiles]
elif infiles is None:
infiles = []
if isinstance(outfiles, str):
outfiles = [outfiles]
output_text = list()
for f in infiles:
with open(f) as ii:
output_text.append(ii.read())
output_text = "".join(sorted(output_text))
output_text += json.dumps(infiles) + " -> " + json.dumps(outfiles) + "\n"
for f in outfiles:
with open(f, "w") as ff:
ff.write(output_text)
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# 1 -> 2 -> 3 ->
# -> 4 ->
# 5 -> 6
#
def do_write(file_name, what):
with open(file_name, "a") as oo:
oo.write(what)
test_file = tempdir + "task.done"
#
# task1
#
@files(None, [tempdir + d for d in ('a.1', 'b.1', 'c.1')])
@follows(mkdir(tempdir))
@posttask(lambda: do_write(test_file, "Task 1 Done\n"))
def task1(infiles, outfiles, *extra_params):
"""
First task
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
#
# task2
#
@posttask(lambda: do_write(test_file, "Task 2 Done\n"))
@follows(task1)
@transform(tempdir + "*.1", suffix(".1"), ".2")
def task2(infiles, outfiles, *extra_params):
"""
Second task
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
#
# task3
#
@transform(task2, regex('(.*).2'), inputs([r"\1.2", tempdir + "a.1"]), r'\1.3')
@posttask(lambda: do_write(test_file, "Task 3 Done\n"))
def task3(infiles, outfiles, *extra_params):
"""
Third task
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
#
# task4
#
@transform(tempdir + "*.1", suffix(".1"), ".4")
@follows(task1)
@posttask(lambda: do_write(test_file, "Task 4 Done\n"))
def task4(infiles, outfiles, *extra_params):
"""
Fourth task
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
#
# task5
#
@files(None, tempdir + 'a.5')
@follows(mkdir(tempdir))
@posttask(lambda: do_write(test_file, "Task 5 Done\n"))
def task5(infiles, outfiles, *extra_params):
"""
Fifth task is extra slow
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
#
# task6
#
#@files([[[tempdir + d for d in 'a.3', 'b.3', 'c.3', 'a.4', 'b.4', 'c.4', 'a.5'], tempdir + 'final.6']])
@merge([task3, task4, task5], tempdir + "final.6")
@follows(task3, task4, task5, )
@posttask(lambda: do_write(test_file, "Task 6 Done\n"))
def task6(infiles, outfiles, *extra_params):
"""
final task
"""
with open(tempdir + "jobs.start", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
test_job_io(infiles, outfiles, extra_params)
with open(tempdir + "jobs.finish", "a") as oo:
oo.write('job = %s\n' % json.dumps([infiles, outfiles]))
def check_job_order_correct(filename):
"""
1 -> 2 -> 3 ->
-> 4 ->
5 -> 6
"""
precedence_rules = [[1, 2],
[2, 3],
[1, 4],
[5, 6],
[3, 6],
[4, 6]]
index_re = re.compile(r'.*\.([0-9])["\]\n]*$')
job_indices = defaultdict(list)
with open(filename) as ii:
for linenum, l in enumerate(ii):
m = index_re.search(l)
if not m:
raise "Non-matching line in [%s]" % filename
job_indices[int(m.group(1))].append(linenum)
for job_index in job_indices:
job_indices[job_index].sort()
for before, after in precedence_rules:
if job_indices[before][-1] >= job_indices[after][0]:
raise "Precedence violated for job %d [line %d] and job %d [line %d] of [%s]"
def check_final_output_correct():
"""
check if the final output in final.6 is as expected
"""
expected_output = \
""" ["DIR/a.1"] -> ["DIR/a.2"]
["DIR/a.1"] -> ["DIR/a.4"]
["DIR/a.2", "DIR/a.1"] -> ["DIR/a.3"]
["DIR/a.3", "DIR/b.3", "DIR/c.3", "DIR/a.4", "DIR/b.4", "DIR/c.4", "DIR/a.5"] -> ["DIR/final.6"]
["DIR/b.1"] -> ["DIR/b.2"]
["DIR/b.1"] -> ["DIR/b.4"]
["DIR/b.2", "DIR/a.1"] -> ["DIR/b.3"]
["DIR/c.1"] -> ["DIR/c.2"]
["DIR/c.1"] -> ["DIR/c.4"]
["DIR/c.2", "DIR/a.1"] -> ["DIR/c.3"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.1", "DIR/b.1", "DIR/c.1"]
[] -> ["DIR/a.5"]"""
expected_output = expected_output.replace(" ", "").replace("DIR/", tempdir).split("\n")
with open(tempdir + "final.6", "r") as ii:
final_6_contents = sorted([l.rstrip() for l in ii.readlines()])
if final_6_contents != expected_output:
for i, (l1, l2) in enumerate(zip(final_6_contents, expected_output)):
if l1 != l2:
sys.stderr.write("%d\n >%s<\n >%s<\n" % (i, l1, l2))
raise Exception ("Final.6 output is not as expected\n")
import unittest, shutil, os
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)
except:
pass
def test_ruffus (self):
pipeline_run(multiprocess = 50, verbose = 0, pipeline= "main")
check_final_output_correct()
check_job_order_correct(tempdir + "jobs.start")
check_job_order_correct(tempdir + "jobs.finish")
def test_newstyle_ruffus (self):
test_pipeline = Pipeline("test")
test_pipeline.files(task1,
None,
[tempdir + d for d in ('a.1', 'b.1', 'c.1')])\
.follows(mkdir(tempdir))\
.posttask(lambda: do_write(test_file, "Task 1 Done\n"))
test_pipeline.transform(task2, tempdir + "*.1", suffix(".1"), ".2")\
.posttask(lambda: do_write(test_file, "Task 2 Done\n"))\
.follows(task1)
test_pipeline.transform(task3, task2, regex('(.*).2'), inputs([r"\1.2", tempdir + "a.1"]), r'\1.3')\
.posttask(lambda: do_write(test_file, "Task 3 Done\n"))
test_pipeline.transform(task_func = task4,
input = tempdir + "*.1",
filter = suffix(".1"),
output = ".4")\
.follows(task1)\
.posttask(lambda: do_write(test_file, "Task 4 Done\n"))
test_pipeline.files(task5, None, tempdir + 'a.5')\
.follows(mkdir(tempdir))\
.posttask(lambda: do_write(test_file, "Task 5 Done\n"))
test_pipeline.merge(task_func = task6,
input = [task3, task4, task5],
output = tempdir + "final.6")\
.follows(task3, task4, task5, )\
.posttask(lambda: do_write(test_file, "Task 6 Done\n"))
test_pipeline.run(multiprocess = 50, verbose = 0)
check_final_output_correct()
check_job_order_correct(tempdir + "jobs.start")
check_job_order_correct(tempdir + "jobs.finish")
if __name__ == '__main__':
unittest.main()
|
