1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
|
#!/usr/bin/env python
from __future__ import print_function
import unittest
import shutil
import sys
"""
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])) + "/"
# 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
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() + ";")
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()
|
