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
|
.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.pipeline_printout.code:
############################################################################################################################################################################################################
|new_manual.pipeline_printout.chapter_num|: Python Code for Understanding how your pipeline works with :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>`
############################################################################################################################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` syntax
* Back to |new_manual.pipeline_printout.chapter_num|: :ref:`Understanding how your pipeline works <new_manual.pipeline_printout>`
******************************************
Display the initial state of the pipeline
******************************************
::
from ruffus import *
import sys
#---------------------------------------------------------------
# create initial files
#
@originate([ ['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', '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
pipeline_printout(sys.stdout, [second_task], verbose = 1)
pipeline_printout(sys.stdout, [second_task], verbose = 3)
************************************
Normal Output
************************************
::
>>> pipeline_printout(sys.stdout, [second_task], verbose = 1)
________________________________________
Tasks which will be run:
Task = create_initial_file_pairs
Task = first_task
Task = second_task
************************************
High Verbosity Output
************************************
::
>>> pipeline_printout(sys.stdout, [second_task], verbose = 4)
________________________________________
Tasks which will be run:
Task = create_initial_file_pairs
Job = [None
-> job1.a.start
-> job1.b.start]
Job needs update: Missing files [job1.a.start, job1.b.start]
Job = [None
-> job2.a.start
-> job2.b.start]
Job needs update: Missing files [job2.a.start, job2.b.start]
Job = [None
-> job3.a.start
-> job3.b.start]
Job needs update: Missing files [job3.a.start, job3.b.start]
Task = first_task
Job = [[job1.a.start, job1.b.start]
-> job1.a.output.1]
Job needs update: Missing files [job1.a.start, job1.b.start, job1.a.output.1]
Job = [[job2.a.start, job2.b.start]
-> job2.a.output.1]
Job needs update: Missing files [job2.a.start, job2.b.start, job2.a.output.1]
Job = [[job3.a.start, job3.b.start]
-> job3.a.output.1]
Job needs update: Missing files [job3.a.start, job3.b.start, job3.a.output.1]
Task = second_task
Job = [job1.a.output.1
-> job1.a.output.2]
Job needs update: Missing files [job1.a.output.1, job1.a.output.2]
Job = [job2.a.output.1
-> job2.a.output.2]
Job needs update: Missing files [job2.a.output.1, job2.a.output.2]
Job = [job3.a.output.1
-> job3.a.output.2]
Job needs update: Missing files [job3.a.output.1, job3.a.output.2]
________________________________________
******************************************
Display the partially up-to-date pipeline
******************************************
Run the pipeline, modify ``job1.stage`` so that the second task is no longer up-to-date
and printout the pipeline stage again::
>>> pipeline_run([second_task], verbose=3)
Task enters queue = create_initial_file_pairs
Job = [None -> [job1.a.start, job1.b.start]]
Job = [None -> [job2.a.start, job2.b.start]]
Job = [None -> [job3.a.start, job3.b.start]]
Job = [None -> [job1.a.start, job1.b.start]] completed
Job = [None -> [job2.a.start, job2.b.start]] completed
Job = [None -> [job3.a.start, job3.b.start]] completed
Completed Task = create_initial_file_pairs
Task enters queue = first_task
Job = [[job1.a.start, job1.b.start] -> job1.a.output.1]
Job = [[job2.a.start, job2.b.start] -> job2.a.output.1]
Job = [[job3.a.start, job3.b.start] -> job3.a.output.1]
Job = [[job1.a.start, job1.b.start] -> job1.a.output.1] completed
Job = [[job2.a.start, job2.b.start] -> job2.a.output.1] completed
Job = [[job3.a.start, job3.b.start] -> job3.a.output.1] completed
Completed Task = first_task
Task enters queue = second_task
Job = [job1.a.output.1 -> job1.a.output.2]
Job = [job2.a.output.1 -> job2.a.output.2]
Job = [job3.a.output.1 -> job3.a.output.2]
Job = [job1.a.output.1 -> job1.a.output.2] completed
Job = [job2.a.output.1 -> job2.a.output.2] completed
Job = [job3.a.output.1 -> job3.a.output.2] completed
Completed Task = second_task
# modify job1.stage1
>>> open("job1.a.output.1", "w").close()
At a verbosity of 6, even jobs which are up-to-date will be displayed::
>>> pipeline_printout(sys.stdout, [second_task], verbose = 6)
________________________________________
Tasks which are up-to-date:
Task = create_initial_file_pairs
Job = [None
-> job1.a.start
-> job1.b.start]
Job = [None
-> job2.a.start
-> job2.b.start]
Job = [None
-> job3.a.start
-> job3.b.start]
Task = first_task
Job = [[job1.a.start, job1.b.start]
-> job1.a.output.1]
Job = [[job2.a.start, job2.b.start]
-> job2.a.output.1]
Job = [[job3.a.start, job3.b.start]
-> job3.a.output.1]
________________________________________
________________________________________
Tasks which will be run:
Task = second_task
Job = [job1.a.output.1
-> job1.a.output.2]
Job needs update:
Input files:
* 22 Jul 2014 15:29:19.33: job1.a.output.1
Output files:
* 22 Jul 2014 15:29:07.53: job1.a.output.2
Job = [job2.a.output.1
-> job2.a.output.2]
Job = [job3.a.output.1
-> job3.a.output.2]
________________________________________
We can now see that the there is only one job in "second_task" which needs to be re-run
because 'job1.stage1' has been modified after 'job1.stage2'
|
