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#!/usr/bin/env python
from __future__ import print_function
"""
test_files_decorator.py
test @files which take single files forwards arguments as single files rather
than as lists
"""
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]
import ruffus
from ruffus import transform, follows, pipeline_run, Pipeline, regex, mkdir, files
#from ruffus.file_name_parameters import
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import json
# use simplejson in place of json for python < 2.6
#try:
#except ImportError:
# import simplejson
# json = simplejson
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
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):
infile_names = [infiles]
elif infiles is None:
infile_names = []
else:
infile_names = infiles
if isinstance(outfiles, str):
outfile_names = [outfiles]
else:
outfile_names = outfiles
output_text = list()
for f in infile_names:
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 outfile_names:
with open(f, "w") as oo:
oo.write(output_text)
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
@follows(mkdir(tempdir))
#
# task1
#
@files(None, tempdir + 'a.1')
def task1(infiles, outfiles, *extra_params):
"""
First task
"""
test_job_io(infiles, outfiles, extra_params)
#
# task2
#
@transform(task1, regex(r".*"), tempdir + 'b.1')
def task2(infiles, outfiles, *extra_params):
"""
Second task
"""
test_job_io(infiles, outfiles, extra_params)
assert(infiles == tempdir + "a.1")
#
# task3
#
@files(task2, tempdir + 'c.1')
def task3(infiles, outfiles, *extra_params):
"""
Second task
"""
test_job_io(infiles, outfiles, extra_params)
assert(infiles == tempdir + "b.1")
#
# task4
#
@follows(task3)
@files([[None, tempdir + 'd.1'], [None, tempdir + 'e.1']])
def task4(infiles, outfiles, *extra_params):
"""
Second task
"""
test_job_io(infiles, outfiles, extra_params)
#
# task5
#
@files(task4, tempdir + "f.1")
def task5(infiles, outfiles, *extra_params):
"""
Second task
"""
test_job_io(infiles, outfiles, extra_params)
assert(infiles == [tempdir + "d.1", tempdir + "e.1"])
import unittest
class Test_task(unittest.TestCase):
def tearDown (self):
"""
"""
import glob
for f in glob.glob(tempdir + "*"):
os.unlink(f)
os.rmdir(tempdir)
def test_task (self):
pipeline_run(multiprocess = 10, verbose = 0, pipeline= "main")
def test_newstyle_task (self):
"""
Same as above but construct a new pipeline on the fly without decorators
"""
test_pipeline = Pipeline("test")
test_pipeline.files(task1, None, tempdir + 'a.1')\
.follows(mkdir(tempdir))
test_pipeline.transform(task_func = task2,
input = task1,
filter = regex(r".*"),
output = tempdir + 'b.1')
test_pipeline.files(task3, task2, tempdir + 'c.1')
test_pipeline.files(task4, [[None, tempdir + 'd.1'], [None, tempdir + 'e.1']])\
.follows(task3)
test_pipeline.files(task5, task4, tempdir + "f.1")
test_pipeline.run(multiprocess = 10, verbose = 0)
if __name__ == '__main__':
unittest.main()
|
