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#!/usr/bin/env python
from __future__ import print_function
import shutil
import unittest
import json
from ruffus import transform, follows, originate, pipeline_run, Pipeline, \
suffix, regex, mkdir, active_if, collate, merge
import sys
"""
test_active_if.py
"""
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
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Main logic
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
def helper(infiles, outfiles):
if not isinstance(infiles, (tuple, list)):
infiles = [infiles]
if not isinstance(outfiles, list):
outfiles = [outfiles]
output_text = ""
preamble_len = 0
for infile in infiles:
if infile:
with open(infile) as ii:
for line in ii:
output_text += line
preamble_len = max(preamble_len, len(
line) - len(line.lstrip()))
preamble = " " * (preamble_len + 4) if len(output_text) else ""
for outfile in outfiles:
file_output_text = preamble + \
json.dumps(infile) + " -> " + json.dumps(outfile) + "\n"
with open(outfile, "w") as oo:
oo.write(output_text + file_output_text)
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
# 88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
pipeline_active_if = True
#
# task1
#
@follows(mkdir("test_active_if"))
@originate(['test_active_if/a.1', 'test_active_if/b.1'], "an extra_parameter")
def task1(outfile, extra):
"""
First task
"""
# N.B. originate works with an extra parameter
helper(None, outfile)
#
# task2
#
@transform(task1, suffix(".1"), ".2")
def task2(infile, outfile):
"""
Second task
"""
helper(infile, outfile)
#
# task3
#
@active_if(lambda: pipeline_active_if)
@transform(task1, suffix(".1"), ".3")
def task3(infile, outfile):
"""
Third task
"""
helper(infile, outfile)
#
# task4
#
@collate([task2, task3], regex(r"(.+)\.[23]"), r"\1.4")
def task4(infiles, outfile):
"""
Fourth task
"""
helper(infiles, outfile)
#
# task4
#
@merge(task4, "test_active_if/summary.5")
def task5(infiles, outfile):
"""
Fifth task
"""
helper(infiles, outfile)
expected_active_text = """null -> "test_active_if/a.1"
"test_active_if/a.1" -> "test_active_if/a.2"
null -> "test_active_if/a.1"
"test_active_if/a.1" -> "test_active_if/a.3"
"test_active_if/a.3" -> "test_active_if/a.4"
null -> "test_active_if/b.1"
"test_active_if/b.1" -> "test_active_if/b.2"
null -> "test_active_if/b.1"
"test_active_if/b.1" -> "test_active_if/b.3"
"test_active_if/b.3" -> "test_active_if/b.4"
"test_active_if/b.4" -> "test_active_if/summary.5"
"""
expected_inactive_text = """null -> "test_active_if/a.1"
"test_active_if/a.1" -> "test_active_if/a.2"
"test_active_if/a.2" -> "test_active_if/a.4"
null -> "test_active_if/b.1"
"test_active_if/b.1" -> "test_active_if/b.2"
"test_active_if/b.2" -> "test_active_if/b.4"
"test_active_if/b.4" -> "test_active_if/summary.5"
"""
# alternative syntax
test_pipeline = Pipeline("test")
test_pipeline.originate(task1, ['test_active_if/a.1', 'test_active_if/b.1'], "an extra_parameter")\
.follows(mkdir("test_active_if"))
test_pipeline.transform(task2, task1, suffix(".1"), ".2")
test_pipeline.transform(task3, task1, suffix(
".1"), ".3").active_if(lambda: pipeline_active_if)
test_pipeline.collate(task4, [task2, task3], regex(r"(.+)\.[23]"), r"\1.4")
test_pipeline.merge(task5, task4, "test_active_if/summary.5")
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
os.makedirs(tempdir)
def tearDown(self):
try:
shutil.rmtree(tempdir)
pass
except:
pass
def test_active_if_true(self):
global pipeline_active_if
pipeline_active_if = True
pipeline_run(multiprocess=50, verbose=0, pipeline="main")
with open("test_active_if/summary.5") as ii:
active_text = ii.read()
if active_text != expected_active_text:
raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" %
(active_text, expected_active_text))
def test_active_if_false(self):
global pipeline_active_if
pipeline_active_if = False
pipeline_run(multiprocess=50, verbose=0, pipeline="main")
with open("test_active_if/summary.5") as ii:
inactive_text = ii.read()
if inactive_text != expected_inactive_text:
raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" %
(inactive_text, expected_inactive_text))
shutil.rmtree("test_active_if")
def test_newstyle_active_if_true(self):
global pipeline_active_if
pipeline_active_if = True
test_pipeline.run(multiprocess=50, verbose=0)
with open("test_active_if/summary.5") as ii:
active_text = ii.read()
if active_text != expected_active_text:
raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" %
(active_text, expected_active_text))
def test_newstyle_active_if_false(self):
global pipeline_active_if
pipeline_active_if = False
test_pipeline.run(multiprocess=50, verbose=0)
with open("test_active_if/summary.5") as ii:
inactive_text = ii.read()
if inactive_text != expected_inactive_text:
raise Exception("Error:\n\tExpected\n%s\nInstead\n%s\n" %
(inactive_text, expected_inactive_text))
shutil.rmtree("test_active_if")
if __name__ == '__main__':
unittest.main()
|
