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
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
|
#!/usr/bin/env python
from __future__ import print_function
"""
test_mkdir.py
test product, combine, permute, combine_with_replacement
"""
import os
tempdir = os.path.relpath(os.path.abspath(os.path.splitext(__file__)[0]))
import os
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]
from ruffus import pipeline_run, pipeline_printout, transform, split, mkdir, formatter, Pipeline
from ruffus.ruffus_utility import RUFFUS_HISTORY_FILE, CHECKSUM_FILE_TIMESTAMPS
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
#
# imports
#
#88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
import unittest
import shutil
try:
from StringIO import StringIO
except:
from io import StringIO
import time
#sub-1s resolution in system?
#___________________________________________________________________________
#
# generate_initial_files1
#___________________________________________________________________________
@split(1, [tempdir + "/" + prefix + "_name.tmp1" for prefix in "abcd"])
def generate_initial_files1(in_name, out_names):
for on in out_names:
with open(on, 'w') as outfile:
pass
#___________________________________________________________________________
#
# test_product_task
#___________________________________________________________________________
@mkdir(tempdir + "/test1")
@mkdir(tempdir + "/test2")
@mkdir(generate_initial_files1, formatter(),
["{path[0]}/{basename[0]}.dir", 3, "{path[0]}/{basename[0]}.dir2"])
@transform( generate_initial_files1,
formatter(),
"{path[0]}/{basename[0]}.dir/{basename[0]}.tmp2")
def test_transform( infiles, outfile):
with open(outfile, "w") as p: pass
@mkdir(tempdir + "/test3")
@mkdir(generate_initial_files1, formatter(),
"{path[0]}/{basename[0]}.dir2")
def test_transform2():
print(" Loose cannon!", file=sys.stderr)
def cleanup_tmpdir():
os.system('rm -f %s %s' % (os.path.join(tempdir, '*'), RUFFUS_HISTORY_FILE))
class Testmkdir(unittest.TestCase):
def setUp(self):
try:
os.mkdir(tempdir)
except OSError:
pass
#___________________________________________________________________________
#
# test mkdir() pipeline_printout and pipeline_run
#___________________________________________________________________________
def test_mkdir_printout(self):
"""Input file exists, output doesn't exist"""
cleanup_tmpdir()
s = StringIO()
pipeline_printout(s, [test_transform, test_transform2], verbose=5, wrap_width = 10000, pipeline= "main")
#self.assertIn('Job needs update: Missing files '
# '[tmp_test_mkdir/a_name.tmp1, '
# 'tmp_test_mkdir/e_name.tmp1, '
# 'tmp_test_mkdir/h_name.tmp1, '
# 'tmp_test_mkdir/a_name.e_name.h_name.tmp2]', s.getvalue())
def test_mkdir_run(self):
"""Run mkdir"""
# output is up to date, but function body changed (e.g., source different)
cleanup_tmpdir()
pipeline_run([test_transform, test_transform2], verbose=0, multiprocess = 2, pipeline= "main")
def test_newstyle_mkdir_run(self):
test_pipeline = Pipeline("test")
test_pipeline.split(task_func = generate_initial_files1,
input = 1,
output = [tempdir + "/" + prefix + "_name.tmp1" for prefix in "abcd"])
test_pipeline.transform( task_func = test_transform,
input = generate_initial_files1,
filter = formatter(),
output = "{path[0]}/{basename[0]}.dir/{basename[0]}.tmp2")\
.mkdir(tempdir + "/test1")\
.mkdir(tempdir + "/test2")\
.mkdir(generate_initial_files1, formatter(),
["{path[0]}/{basename[0]}.dir", 3, "{path[0]}/{basename[0]}.dir2"])
test_pipeline.mkdir(test_transform2, tempdir + "/test3")\
.mkdir(generate_initial_files1, formatter(),
"{path[0]}/{basename[0]}.dir2")
cleanup_tmpdir()
pipeline_run([test_transform, test_transform2], verbose=0, multiprocess = 2, pipeline= "main")
#___________________________________________________________________________
#
# cleanup
#___________________________________________________________________________
def tearDown(self):
shutil.rmtree(tempdir)
#
# Necessary to protect the "entry point" of the program under windows.
# see: http://docs.python.org/library/multiprocessing.html#multiprocessing-programming
#
if __name__ == '__main__':
unittest.main()
|
