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#!/usr/bin/env python
from __future__ import print_function
"""
test_transform_with_no_re_matches.py
test messages with no regular expression matches
"""
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__), ".."))
ruffus_name = os.path.basename(parent_dir)
ruffus = __import__ (ruffus_name)
for attr in "follows", "transform", "merge", "add_inputs", "inputs", "mkdir", "regex", "pipeline_run", "Pipeline":
globals()[attr] = getattr (ruffus, attr)
print("\tRuffus Version = ", ruffus.__version__)
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import shutil
def touch (outfile):
with open(outfile, "w"):
pass
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
@follows(mkdir(tempdir))
@ruffus.files([[None, tempdir+ "a.1"], [None, tempdir+ "b.1"]])
def task1(i, o):
touch(o)
@follows(mkdir(tempdir))
@ruffus.files([[None, tempdir+ "c.1"], [None, tempdir+ "d.1"]])
def task2(i, o):
touch(o)
#@transform(input = task1, filter = regex(r"(.*)"), add_inputs = (task2, "test_transform_inputs.*y"), output = r"\1.output")
@transform(input = task1, filter = regex(r"(.*)"), add_inputs = add_inputs(task2, "test_transform_inputs.*y"), output = r"\1.output")
#@transform(input = task1, filter = regex(r"(.*)"), replace_inputs = [task2, "test_transform_inputs.*y"], output = r"\1.output")
#@transform(input = task1, filter = regex(r"(.*)"), replace_inputs = inputs([task2, "test_transform_inputs.*y"]), output = r"\1.output")
def task3_add_inputs(i, o):
names = ",".join(sorted(i))
with open(o, "w") as oo:
oo.write(names)
@merge((task3_add_inputs), tempdir + "final.output")
def task4(i, o):
with open(o, "w") as o_file:
for f in sorted(i):
with open(f) as ii:
o_file.write(f +":" + ii.read() + ";")
import unittest
class Test_task(unittest.TestCase):
def tearDown (self):
"""
"""
try:
shutil.rmtree(tempdir)
except:
pass
def test_task (self):
pipeline_run(multiprocess = 10, verbose = 0, pipeline= "main")
correct_output = "{tempdir}a.1.output:{tempdir}a.1,{tempdir}c.1,{tempdir}d.1,test_transform_inputs.py;{tempdir}b.1.output:{tempdir}b.1,{tempdir}c.1,{tempdir}d.1,test_transform_inputs.py;".format(tempdir = tempdir)
with open(tempdir + "final.output") as real_output:
real_output_str = real_output.read()
self.assertEqual(correct_output, real_output_str)
def test_newstyle_task (self):
test_pipeline = Pipeline("test")
test_pipeline.files(task1, [[None, tempdir+ "a.1"], [None, tempdir+ "b.1"]])\
.follows(mkdir(tempdir))
test_pipeline.files(task2, [[None, tempdir+ "c.1"], [None, tempdir+ "d.1"]])\
.follows(mkdir(tempdir))
test_pipeline.transform(task_func = task3_add_inputs,
input = task1,
filter = regex(r"(.*)"),
add_inputs = add_inputs(task2, "test_transform_inputs.*y"),
output = r"\1.output")
test_pipeline.merge( task_func = task4,
input = task3_add_inputs,
output = tempdir + "final.output")
test_pipeline.run(multiprocess = 10, verbose = 0)
correct_output = "{tempdir}a.1.output:{tempdir}a.1,{tempdir}c.1,{tempdir}d.1,test_transform_inputs.py;{tempdir}b.1.output:{tempdir}b.1,{tempdir}c.1,{tempdir}d.1,test_transform_inputs.py;".format(tempdir = tempdir)
with open(tempdir + "final.output") as real_output:
real_output_str = real_output.read()
self.assertEqual(correct_output, real_output_str)
if __name__ == '__main__':
unittest.main()
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