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|
.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc
.. _new_manual.transform_in_parallel.code:
######################################################################################################
|new_manual.transform_in_parallel.chapter_num|: Python Code for More on ``@transform``-ing data
######################################################################################################
.. seealso::
* :ref:`Manual Table of Contents <new_manual.table_of_contents>`
* :ref:`@transform syntax in detail <decorators.transform>`
* Back to |new_manual.transform_in_parallel.chapter_num|: :ref:`More on @transform-ing data and @originate <new_manual.transform_in_parallel>`
*******************************************
Producing several items / files per job
*******************************************
::
from ruffus import *
#---------------------------------------------------------------
# Create pairs of input files
#
first_task_params = [
['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.b.start'],
]
for input_file_pairs in first_task_params:
for input_file in input_file_pairs:
open(input_file, "w")
#---------------------------------------------------------------
#
# first task
#
@transform(first_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def first_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
#---------------------------------------------------------------
#
# second task
#
@transform(first_task, suffix(".output.1"), ".output2")
def second_task(input_files, output_file):
with open(output_file, "w"): pass
#---------------------------------------------------------------
#
# Run
#
pipeline_run([second_task])
=============================
Resulting Output
=============================
::
>>> pipeline_run([second_task])
Job = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = first_task
Job = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
Job = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
Job = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
Completed Task = second_task
*******************************************
Defining tasks function out of order
*******************************************
.. code-block:: python
:emphasize-lines: 22
from ruffus import *
#---------------------------------------------------------------
# Create pairs of input files
#
first_task_params = [
['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.b.start'],
]
for input_file_pairs in first_task_params:
for input_file in input_file_pairs:
open(input_file, "w")
#---------------------------------------------------------------
#
# second task defined first
#
# task name string wrapped in output_from(...)
@transform(output_from("first_task"), suffix(".output.1"), ".output2")
def second_task(input_files, output_file):
with open(output_file, "w"): pass
#---------------------------------------------------------------
#
# first task
#
@transform(first_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def first_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
#---------------------------------------------------------------
#
# Run
#
pipeline_run([second_task])
=============================
Resulting Output
=============================
.. code-block:: pycon
>>> pipeline_run([second_task])
Job = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = first_task
Job = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
Job = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
Job = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
Completed Task = second_task
.. _new_manual.transform.multiple_dependencies.code:
*******************************************
Multiple dependencies
*******************************************
.. code-block:: python
:emphasize-lines: 58
from ruffus import *
import time
import random
#---------------------------------------------------------------
# Create pairs of input files
#
first_task_params = [
['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.b.start'],
]
second_task_params = [
['job4.a.start', 'job4.b.start'],
['job5.a.start', 'job5.b.start'],
['job6.a.start', 'job6.b.start'],
]
for input_file_pairs in first_task_params + second_task_params:
for input_file in input_file_pairs:
open(input_file, "w")
#---------------------------------------------------------------
#
# first task
#
@transform(first_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def first_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
time.sleep(random.random())
#---------------------------------------------------------------
#
# second task
#
@transform(second_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def second_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
time.sleep(random.random())
#---------------------------------------------------------------
#
# third task
#
# depends on both first_task() and second_task()
@transform([first_task, second_task], suffix(".output.1"), ".output2")
def third_task(input_files, output_file):
with open(output_file, "w"): pass
#---------------------------------------------------------------
#
# Run
#
pipeline_run([third_task], multiprocess = 6)
=============================
Resulting Output
=============================
.. code-block:: pycon
>>> pipeline_run([third_task], multiprocess = 6)
Job = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = second_task
Job = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = first_task
Job = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
Job = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
Job = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
Job = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed
Job = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed
Job = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed
Completed Task = third_task
*******************************************
Multiple dependencies after @follows
*******************************************
.. code-block:: python
:emphasize-lines: 31
from ruffus import *
import time
import random
#---------------------------------------------------------------
# Create pairs of input files
#
first_task_params = [
['job1.a.start', 'job1.b.start'],
['job2.a.start', 'job2.b.start'],
['job3.a.start', 'job3.b.start'],
]
second_task_params = [
['job4.a.start', 'job4.b.start'],
['job5.a.start', 'job5.b.start'],
['job6.a.start', 'job6.b.start'],
]
for input_file_pairs in first_task_params + second_task_params:
for input_file in input_file_pairs:
open(input_file, "w")
#---------------------------------------------------------------
#
# first task
#
@transform(first_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def first_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
time.sleep(random.random())
#---------------------------------------------------------------
#
# second task
#
@follows("first_task")
@transform(second_task_params, suffix(".start"),
[".output.1",
".output.extra.1"],
"some_extra.string.for_example", 14)
def second_task(input_files, output_file_pair,
extra_parameter_str, extra_parameter_num):
for output_file in output_file_pair:
with open(output_file, "w"):
pass
time.sleep(random.random())
#---------------------------------------------------------------
#
# third task
#
# depends on both first_task() and second_task()
@transform([first_task, second_task], suffix(".output.1"), ".output2")
def third_task(input_files, output_file):
with open(output_file, "w"): pass
#---------------------------------------------------------------
#
# Run
#
pipeline_run([third_task], multiprocess = 6)
=======================================================================================
Resulting Output: ``first_task`` completes before ``second_task``
=======================================================================================
.. code-block:: pycon
>>> pipeline_run([third_task], multiprocess = 6)
Job = [[job2.a.start, job2.b.start] -> [job2.a.output.1, job2.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job3.a.start, job3.b.start] -> [job3.a.output.1, job3.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job1.a.start, job1.b.start] -> [job1.a.output.1, job1.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = first_task
Job = [[job4.a.start, job4.b.start] -> [job4.a.output.1, job4.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job6.a.start, job6.b.start] -> [job6.a.output.1, job6.a.output.extra.1], some_extra.string.for_example, 14] completed
Job = [[job5.a.start, job5.b.start] -> [job5.a.output.1, job5.a.output.extra.1], some_extra.string.for_example, 14] completed
Completed Task = second_task
Job = [[job1.a.output.1, job1.a.output.extra.1] -> job1.a.output2] completed
Job = [[job2.a.output.1, job2.a.output.extra.1] -> job2.a.output2] completed
Job = [[job3.a.output.1, job3.a.output.extra.1] -> job3.a.output2] completed
Job = [[job4.a.output.1, job4.a.output.extra.1] -> job4.a.output2] completed
Job = [[job5.a.output.1, job5.a.output.extra.1] -> job5.a.output2] completed
Job = [[job6.a.output.1, job6.a.output.extra.1] -> job6.a.output2] completed
|
