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
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
|
#!/usr/bin/env python
from __future__ import print_function
from ruffus.ruffus_utility import RUFFUS_HISTORY_FILE, CHECKSUM_FILE_TIMESTAMPS
from ruffus.ruffus_exceptions import RethrownJobError
from ruffus import pipeline_run, pipeline_printout, suffix, transform, split, merge, \
dbdict, follows, mkdir, originate, Pipeline
import re
import shutil
import sys
"""
test_verbosity.py
"""
import unittest
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 = list(map(__import__, [ruffus_name]))[0]
try:
from StringIO import StringIO
except:
from io import StringIO
# ---------------------------------------------------------------
# create initial files
#
@mkdir(tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven')
@originate([[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job1.a.start', tempdir + 'job1.b.start'],
[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job2.a.start',
tempdir + 'job2.b.start'],
[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job3.a.start', tempdir + 'job3.b.start']])
def create_initial_file_pairs(output_files):
# create both files as necessary
for output_file in output_files:
with open(output_file, "w") as oo:
pass
# ---------------------------------------------------------------
# first task
@transform(create_initial_file_pairs, suffix(".start"), ".output.1")
def first_task(input_files, output_file):
with open(output_file, "w"):
pass
# ---------------------------------------------------------------
# second task
@transform(first_task, suffix(".output.1"), ".output.2")
def second_task(input_files, output_file):
with open(output_file, "w"):
pass
test_pipeline = Pipeline("test")
test_pipeline.originate(output=[[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job1.a.start', tempdir + 'job1.b.start'],
[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job2.a.start',
tempdir + 'job2.b.start'],
[tempdir + 'data/scratch/lg/what/one/two/three/four/five/six/seven/job3.a.start', tempdir + 'job3.b.start']],
task_func=create_initial_file_pairs)
test_pipeline.transform(task_func=first_task, input=create_initial_file_pairs,
filter=suffix(".start"), output=".output.1")
test_pipeline.transform(input=first_task, filter=suffix(
".output.1"), output=".output.2", task_func=second_task)
decorator_syntax = 0
oop_syntax = 1
class Test_verbosity(unittest.TestCase):
# ___________________________________________________________________________
#
# test_printout_abbreviated_path1
# ___________________________________________________________________________
def test_printout_abbreviated_path1(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=1)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=1, wrap_width=500, pipeline="main")
ret = s.getvalue()
self.assertTrue(
"[[.../job1.a.start, test_verbosity/job1.b.start]" in ret)
# ___________________________________________________________________________
#
# test_printout_abbreviated_path2
# ___________________________________________________________________________
def test_printout_abbreviated_path2(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=2, wrap_width=500)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=2, wrap_width=500, pipeline="main")
ret = s.getvalue()
self.assertTrue(
"[[.../seven/job1.a.start, test_verbosity/job1.b.start]" in ret)
# ___________________________________________________________________________
#
# test_printout_abbreviated_path3
# ___________________________________________________________________________
def test_printout_abbreviated_path3(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=3, wrap_width=500)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=3, wrap_width=500, pipeline="main")
ret = s.getvalue()
self.assertTrue(
"[[.../six/seven/job1.a.start, test_verbosity/job1.b.start]" in ret)
# ___________________________________________________________________________
#
# test_printout_abbreviated_path9
# ___________________________________________________________________________
def test_printout_abbreviated_path9(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=9, wrap_width=500)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=9, wrap_width=500, pipeline="main")
ret = s.getvalue()
self.assertTrue(
"[[.../what/one/two/three/four/five/six/seven/job1.a.start, test_verbosity/job1.b.start]" in ret)
# ___________________________________________________________________________
#
# test_printout_abbreviated_path0
# ___________________________________________________________________________
def test_printout_abbreviated_path0(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=0, wrap_width=500)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=0, wrap_width=500, pipeline="main")
ret = s.getvalue()
path_str = os.path.abspath(
'%sdata/scratch/lg/what/one/two/three/four/five/six/seven/job2.a.start' % tempdir)
path_str = '[[%s' % path_str
# ___________________________________________________________________________
#
# test_printout_abbreviated_path_minus_60
# ___________________________________________________________________________
def test_printout_abbreviated_path_minus_60(self):
"""Input file exists, output doesn't exist"""
for syntax in decorator_syntax, oop_syntax:
s = StringIO()
if syntax == oop_syntax:
test_pipeline.printout(
s, [second_task], verbose=5, verbose_abbreviated_path=-60, wrap_width=500)
else:
pipeline_printout(
s, [second_task], verbose=5, verbose_abbreviated_path=-60, wrap_width=500, pipeline="main")
ret = s.getvalue()
self.assertTrue(
'[<???> ve/six/seven/job1.a.start, test_verbosity/job1.b.start]' in ret)
#
# 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()
|
