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#!/usr/bin/env python
from __future__ import print_function
"""
test_suffix_output_dir.py
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0]))
data_dir = tempdir + "/data"
work_dir = tempdir + "/work"
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, subdivide, merge, suffix, mkdir, pipeline_run, Pipeline, originate
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# imports
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import unittest
import shutil
import json
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Main logic
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
def helper(infiles, outfiles):
"""
Helper function: Writes input output file names and input contents to outfile
"""
# None = []
if outfiles is None:
outfiles = []
# str = [str]
if not isinstance(outfiles, list):
outfiles = [outfiles]
for outfile in outfiles:
with open(outfile, "w") as oo:
# save file name strings before we turn infiles into a list
fn_str = "%s -> %s" % (infiles, outfile)
# None = []
if infiles is None:
infiles = []
# str = [str]
if not isinstance(infiles, list):
infiles = [infiles]
# write header
#if len(infiles):
# for infile in infiles:
# with open(infile) as ii:
# for line in ii:
# line = line.rstrip()
# if line[-1:] == ":":
# oo.write(outfile + ":" + line + "\n")
#else:
# oo.write(outfile + ":\n")
max_white_space = -2
# write content of infiles indented
for infile in infiles:
with open(infile) as ii:
for line in ii:
line = line.rstrip()
if line[-1:] != ":":
oo.write(line + "\n")
max_white_space = max([max_white_space, len(line) - len(line.lstrip())])
# add extra spaces before filenames
oo.write(" " * (max_white_space + 2) + fn_str + "\n")
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
# Tasks
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# task1
#
@mkdir(data_dir, work_dir)
@originate([os.path.join(data_dir, "%s.1" % aa) for aa in "abcd"])
def task1(outfile):
"""
originate
"""
# N.B. originate works with an extra parameter
helper (None, outfile)
#
# task2
#
@mkdir( task1,
suffix(".1"),
".dir",
output_dir = work_dir)
@transform(task1, suffix(".1"), [".1", ".bak"], "extra.tst", 4, r"orig_dir=\1", output_dir = work_dir)
def task2(infile, outfile, extra_str, extra_num, extra_dir):
"""
transform switch directory
"""
if (extra_str, extra_num) != ("extra.tst", 4) or \
extra_dir[:len("orig_dir=" + work_dir)] != "orig_dir=" + work_dir:
raise Exception("transform with output_dir has changed extras: %s, %s %s"
%(extra_str, extra_num, extra_dir))
helper (infile, outfile)
#
# task3
#
@subdivide(task2, suffix(".1"), r"\1.*.2", [r"\1.a.2", r"\1.b.2"], output_dir = data_dir)
def task3(infile, ignore_outfiles, outfiles):
"""
subdivide
"""
helper (infile, outfiles)
#
# task4
#
@transform(task3, suffix(".2"), ".3", output_dir = work_dir)
def task4(infile, outfile):
"""
transform
"""
helper (infile, outfile)
#
# task4
#
@merge(task4, os.path.join(data_dir, "summary.5"))
def task5(infiles, outfile):
"""
merge
"""
helper (infiles, outfile)
expected_active_text = \
"""None -> {tempdir}/data/a.1
{tempdir}/data/a.1 -> {tempdir}/work/a.1
None -> {tempdir}/data/a.1
['{tempdir}/data/a.1'] -> {tempdir}/work/a.bak
['{tempdir}/work/a.1', '{tempdir}/work/a.bak'] -> {tempdir}/data/a.a.2
{tempdir}/data/a.a.2 -> {tempdir}/work/a.a.3
None -> {tempdir}/data/a.1
{tempdir}/data/a.1 -> {tempdir}/work/a.1
None -> {tempdir}/data/a.1
['{tempdir}/data/a.1'] -> {tempdir}/work/a.bak
['{tempdir}/work/a.1', '{tempdir}/work/a.bak'] -> {tempdir}/data/a.b.2
{tempdir}/data/a.b.2 -> {tempdir}/work/a.b.3
None -> {tempdir}/data/b.1
{tempdir}/data/b.1 -> {tempdir}/work/b.1
None -> {tempdir}/data/b.1
['{tempdir}/data/b.1'] -> {tempdir}/work/b.bak
['{tempdir}/work/b.1', '{tempdir}/work/b.bak'] -> {tempdir}/data/b.a.2
{tempdir}/data/b.a.2 -> {tempdir}/work/b.a.3
None -> {tempdir}/data/b.1
{tempdir}/data/b.1 -> {tempdir}/work/b.1
None -> {tempdir}/data/b.1
['{tempdir}/data/b.1'] -> {tempdir}/work/b.bak
['{tempdir}/work/b.1', '{tempdir}/work/b.bak'] -> {tempdir}/data/b.b.2
{tempdir}/data/b.b.2 -> {tempdir}/work/b.b.3
None -> {tempdir}/data/c.1
{tempdir}/data/c.1 -> {tempdir}/work/c.1
None -> {tempdir}/data/c.1
['{tempdir}/data/c.1'] -> {tempdir}/work/c.bak
['{tempdir}/work/c.1', '{tempdir}/work/c.bak'] -> {tempdir}/data/c.a.2
{tempdir}/data/c.a.2 -> {tempdir}/work/c.a.3
None -> {tempdir}/data/c.1
{tempdir}/data/c.1 -> {tempdir}/work/c.1
None -> {tempdir}/data/c.1
['{tempdir}/data/c.1'] -> {tempdir}/work/c.bak
['{tempdir}/work/c.1', '{tempdir}/work/c.bak'] -> {tempdir}/data/c.b.2
{tempdir}/data/c.b.2 -> {tempdir}/work/c.b.3
None -> {tempdir}/data/d.1
{tempdir}/data/d.1 -> {tempdir}/work/d.1
None -> {tempdir}/data/d.1
['{tempdir}/data/d.1'] -> {tempdir}/work/d.bak
['{tempdir}/work/d.1', '{tempdir}/work/d.bak'] -> {tempdir}/data/d.a.2
{tempdir}/data/d.a.2 -> {tempdir}/work/d.a.3
None -> {tempdir}/data/d.1
{tempdir}/data/d.1 -> {tempdir}/work/d.1
None -> {tempdir}/data/d.1
['{tempdir}/data/d.1'] -> {tempdir}/work/d.bak
['{tempdir}/work/d.1', '{tempdir}/work/d.bak'] -> {tempdir}/data/d.b.2
{tempdir}/data/d.b.2 -> {tempdir}/work/d.b.3
['{tempdir}/work/a.a.3', '{tempdir}/work/a.b.3', '{tempdir}/work/b.a.3', '{tempdir}/work/b.b.3', '{tempdir}/work/c.a.3', '{tempdir}/work/c.b.3', '{tempdir}/work/d.a.3', '{tempdir}/work/d.b.3'] -> {tempdir}/data/summary.5
""".format(tempdir = tempdir)
class Test_ruffus(unittest.TestCase):
def setUp(self):
try:
shutil.rmtree(tempdir)
except:
pass
for dd in tempdir, work_dir, data_dir:
try:
os.makedirs(dd)
except:
pass
def tearDown(self):
try:
shutil.rmtree(tempdir)
except:
sys.stderr.write("Can't remove %s" % tempdir)
pass
def test_ruffus (self):
pipeline_run(multiprocess = 50, verbose = 0, pipeline= "main")
with open(os.path.join(data_dir, "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" % (expected_active_text, active_text))
def test_newstyle_ruffus (self):
# alternative syntax
test_pipeline = Pipeline("test")
test_pipeline.mkdir(data_dir, work_dir)
test_pipeline.originate(task_func = task1,
output = [os.path.join(data_dir, "%s.1" % aa) for aa in "abcd"])
test_pipeline.mkdir(filter = suffix(".1"),
output = ".dir",
output_dir = work_dir)
test_pipeline.transform(task_func = task2,
input = task1,
filter = suffix(".1"),
output = [".1", ".bak"],
extras = ["extra.tst", 4, r"orig_dir=\1"],
output_dir = work_dir)
test_pipeline.subdivide(task3, task2, suffix(".1"), r"\1.*.2", [r"\1.a.2", r"\1.b.2"], output_dir = data_dir)
test_pipeline.transform(task4, task3, suffix(".2"), ".3", output_dir = work_dir)
test_pipeline.merge(task5, task4, os.path.join(data_dir, "summary.5"))
test_pipeline.run(multiprocess = 50, verbose = 0)
with open(os.path.join(data_dir, "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" % (expected_active_text, active_text))
if __name__ == '__main__':
unittest.main()
|
